From 320c220422ee17d965b3beaa3e1797f3b07334b8 Mon Sep 17 00:00:00 2001 From: tokebe <43009413+tokebe@users.noreply.github.com> Date: Tue, 7 May 2024 13:37:48 -0400 Subject: [PATCH] feat: single-queue subquerying, per-subquery cache This commit also contains a lot of refactoring and renaming, not keeping things particularly pretty given the planned migration to python down the line. --- CHANGELOG.md | 293 --- package.json | 19 +- packages/api-response-transform/package.json | 17 +- packages/api-response-transform/src/index.ts | 21 +- .../api-response-transform/src/jq_utils.ts | 3 +- .../src/transformers/biothings_transformer.ts | 4 +- .../src/transformers/transformer.ts | 23 +- .../src/transformers/trapi_transformer.ts | 4 +- packages/api-response-transform/src/types.ts | 55 +- packages/api-response-transform/tsconfig.json | 32 +- packages/biolink-model/package.json | 9 +- .../biolink-model/src/loader/url_loader.ts | 2 +- packages/biomedical_id_resolver/package.json | 6 +- packages/biomedical_id_resolver/src/attrs.ts | 2 +- .../src/query/builder/biothings_builder.ts | 2 +- .../biomedical_id_resolver/src/query/index.ts | 2 +- .../src/query/scheduler.ts | 2 +- .../src/resolve/base_resolver.ts | 2 +- .../src/resolve/biolink_based_resolver.ts | 2 +- .../src/resolve/default_resolver.ts | 2 +- packages/biomedical_id_resolver/src/sri.ts | 2 +- packages/call-apis/package.json | 22 +- packages/call-apis/src/dispatch_thread.ts | 62 + packages/call-apis/src/dispatcher.ts | 331 +-- packages/call-apis/src/index.old.no | 185 ++ packages/call-apis/src/index.ts | 239 +-- packages/call-apis/src/queries/subquery.ts | 86 +- .../call-apis/src/queries/subquery_factory.ts | 12 +- .../src/queries/template_subquery.ts | 41 +- .../call-apis/src/queries/trapi_subquery.ts | 45 +- packages/call-apis/src/query_pool.ts | 253 ++- packages/call-apis/src/query_queue.ts | 32 +- packages/call-apis/src/rate_limiter.ts | 4 +- packages/call-apis/src/types.ts | 122 +- packages/call-apis/tsconfig.json | 14 +- packages/graph/package.json | 43 + packages/graph/src/api_edge.ts | 38 + .../src/graph => graph/src}/graph.ts | 16 +- packages/graph/src/index.ts | 17 + .../src/graph => graph/src}/kg_edge.ts | 5 +- .../src/graph => graph/src}/kg_node.ts | 2 +- .../graph => graph/src}/knowledge_graph.ts | 54 +- .../src/query_edge.ts | 38 +- .../src/query_graph.ts | 200 +- .../src/query_node.ts | 88 +- .../src/record.ts | 161 +- packages/graph/tsconfig.json | 43 + packages/node-expansion/package.json | 2 +- packages/query_graph_handler/package.json | 25 +- .../src/batch_edge_query.ts | 135 +- .../query_graph_handler/src/cache_handler.ts | 38 +- .../query_graph_handler/src/edge_manager.ts | 125 +- .../src/exceptions/bte_error.ts | 16 - .../exceptions/invalid_query_graph_error.ts | 16 - packages/query_graph_handler/src/index.ts | 44 +- .../query_graph_handler/src/qedge2apiedge.ts | 44 +- .../src/results_assembly/pfocr.ts | 4 +- .../src/results_assembly/query_results.ts | 10 +- .../src/results_assembly/score.ts | 4 +- packages/query_graph_handler/src/types.ts | 2 +- .../query_graph_handler/src/update_nodes.ts | 9 +- packages/query_graph_handler/tsconfig.json | 12 +- packages/server/data/predicates.json | 2 +- packages/server/data/smartapi_specs.json | 2 +- packages/server/docs/smartapi.yaml | 2 +- packages/server/package.json | 23 +- packages/server/src/config/api_list.ts | 2 +- packages/server/src/config/index.ts | 2 +- .../server/src/config/smartapi_exclusions.ts | 2 +- .../server/src/controllers/association.ts | 4 +- .../src/controllers/async/asyncquery.ts | 10 +- .../src/controllers/async/asyncquery_queue.ts | 8 +- .../src/controllers/cron/clear_edge_cache.ts | 4 +- .../controllers/cron/update_local_smartapi.ts | 2 +- .../src/controllers/meta_knowledge_graph.ts | 4 +- .../server/src/controllers/opentelemetry.ts | 4 +- .../src/controllers/threading/taskHandler.ts | 16 +- .../controllers/threading/threadHandler.ts | 59 +- packages/server/src/middlewares/error.ts | 6 +- packages/server/src/middlewares/logging.ts | 2 +- packages/server/src/routes/bullboard.ts | 4 +- packages/server/src/routes/frontpage.ts | 19 - packages/server/src/routes/index.ts | 4 +- packages/server/src/routes/performance.ts | 2 +- .../server/src/routes/v1/asyncquery_status.ts | 6 +- .../server/src/routes/v1/asyncquery_v1.ts | 4 +- .../src/routes/v1/asyncquery_v1_by_api.ts | 4 +- .../src/routes/v1/asyncquery_v1_by_team.ts | 4 +- packages/server/src/routes/v1/query_v1.ts | 6 +- .../server/src/routes/v1/query_v1_by_api.ts | 4 +- .../server/src/routes/v1/query_v1_by_team.ts | 4 +- packages/server/src/server.ts | 4 +- packages/server/src/types.ts | 4 +- packages/server/src/utils/common.ts | 2 +- .../server/src/utils/errors/status_error.ts | 2 +- packages/server/tsconfig.json | 6 +- packages/smartapi-kg/bundle.js | 2 +- packages/smartapi-kg/package.json | 11 +- .../smartapi-kg/src/data/smartapi_specs.json | 2 +- packages/smartapi-kg/src/filter.ts | 2 +- packages/smartapi-kg/src/index.ts | 2 +- .../src/load/all_specs_sync_loader.ts | 2 +- .../src/load/api_list_specs_sync_loader.ts | 2 +- .../smartapi-kg/src/load/base_async_loader.ts | 2 +- .../src/load/single_spec_sync_loader.ts | 2 +- .../src/load/sync_loader_factory.ts | 2 +- .../async_operations_builder_with_reasoner.ts | 6 +- .../base_operations_builder.ts | 2 +- .../sync_operations_builder_with_reasoner.ts | 6 +- packages/smartapi-kg/src/parser/endpoint.ts | 2 +- packages/smartapi-kg/src/parser/index.ts | 2 +- .../smartapi-kg/src/parser/query_operation.ts | 120 +- packages/smartapi-kg/src/parser/types.ts | 22 +- packages/types/package.json | 14 +- packages/types/src/exceptions.ts | 31 + packages/types/src/global.ts | 5 +- packages/types/src/index.ts | 2 + packages/types/src/misc.ts | 23 + packages/types/src/tasks.ts | 2 +- packages/types/src/x_bte.ts | 4 + packages/types/tsconfig.json | 8 +- packages/utils/package.json | 16 +- .../src/biolink.ts | 6 +- packages/utils/src/cache.ts | 242 +++ packages/utils/src/index.ts | 2 + packages/utils/src/log_entry.ts | 40 +- packages/utils/src/misc.ts | 13 +- packages/utils/src/redis-client.ts | 2 +- packages/utils/src/telemetry.ts | 6 +- packages/utils/tsconfig.json | 16 +- packages/web-app/.eslintrc.cjs | 14 - packages/web-app/.vscode/extensions.json | 3 - packages/web-app/README.md | 52 - packages/web-app/index.html | 13 - packages/web-app/package.json | 68 - packages/web-app/postcss.config.js | 7 - packages/web-app/public/bte.svg | 115 - packages/web-app/src/App.vue | 42 - .../src/assets/img/biothings-explorer-128.png | Bin 6553 -> 0 bytes .../src/assets/img/biothings-explorer-16.png | Bin 785 -> 0 bytes .../src/assets/img/biothings-explorer-2.png | Bin 105476 -> 0 bytes .../src/assets/img/biothings-explorer-2.svg | 417 ---- .../src/assets/img/biothings-explorer-256.png | Bin 6595 -> 0 bytes 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++--------------- pnpm-workspace.yaml | 1 - tsconfig.build.json | 19 +- tsconfig.json | 3 +- 183 files changed, 2444 insertions(+), 6942 deletions(-) delete mode 100644 CHANGELOG.md create mode 100644 packages/call-apis/src/dispatch_thread.ts create mode 100644 packages/call-apis/src/index.old.no create mode 100644 packages/graph/package.json create mode 100644 packages/graph/src/api_edge.ts rename packages/{query_graph_handler/src/graph => graph/src}/graph.ts (92%) create mode 100644 packages/graph/src/index.ts rename packages/{query_graph_handler/src/graph => graph/src}/kg_edge.ts (94%) rename packages/{query_graph_handler/src/graph => graph/src}/kg_node.ts (96%) rename packages/{query_graph_handler/src/graph => graph/src}/knowledge_graph.ts (80%) rename packages/{query_graph_handler => graph}/src/query_edge.ts (95%) rename packages/{query_graph_handler => graph}/src/query_graph.ts (66%) rename packages/{query_graph_handler => graph}/src/query_node.ts (78%) rename packages/{api-response-transform => graph}/src/record.ts (80%) create mode 100644 packages/graph/tsconfig.json delete mode 100644 packages/query_graph_handler/src/exceptions/bte_error.ts delete mode 100644 packages/query_graph_handler/src/exceptions/invalid_query_graph_error.ts delete mode 100644 packages/server/src/routes/frontpage.ts create mode 100644 packages/types/src/exceptions.ts create mode 100644 packages/types/src/x_bte.ts rename packages/{query_graph_handler => utils}/src/biolink.ts (94%) create mode 100644 packages/utils/src/cache.ts delete mode 100644 packages/web-app/.eslintrc.cjs delete mode 100644 packages/web-app/.vscode/extensions.json delete mode 100644 packages/web-app/README.md delete mode 100644 packages/web-app/index.html delete mode 100644 packages/web-app/package.json delete mode 100644 packages/web-app/postcss.config.js delete mode 100644 packages/web-app/public/bte.svg delete mode 100644 packages/web-app/src/App.vue delete mode 100644 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documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. - -### [2.8.1](https://github.com/biothings/biothings_explorer/compare/v2.8.0...v2.8.1) (2021-06-05) - - -### Features - -* :sparks: update to consume trapi v1.1 apis ([5b2f465](https://github.com/biothings/biothings_explorer/commits/5b2f465483b7e817a0d75721ea16e6655b4bd215)) -* transform graph data from v1.1 to legacy format, uncomment code ([b1d2413](https://github.com/biothings/biothings_explorer/commits/b1d24135c7831041a17eda277bfb6264959d957a)) - - -### Bug Fixes - -* add details to meta graph error ([1d36a18](https://github.com/biothings/biothings_explorer/commits/1d36a18694e4ca291afda8d25ddc878e33bf1b16)) - -## [2.8.0](https://github.com/biothings/biothings_explorer/compare/v2.7.0...v2.8.0) (2021-05-25) - - -### Features - -* :sparkles: added meta_knowledge_graph endpoints by team and ip ([8882df4](https://github.com/biothings/biothings_explorer/commits/8882df487e7348918e437fa6f971fadd7b24cb3f)) - - -### Bug Fixes - -* :bug: fix meta_kg endpoint for a given API ([85ff733](https://github.com/biothings/biothings_explorer/commits/85ff733bbaefec91c55d36b9bf62bc4bc16259de)) - -## [2.7.0](https://github.com/biothings/biothings_explorer/compare/v2.6.0...v2.7.0) (2021-05-16) - - -### Features - -* :sparkles: add handler logics for creating v1 metakg ([c1c5011](https://github.com/biothings/biothings_explorer/commits/c1c50116dcec2c131c36c8c3ec52502f49e65d2d)) -* :sparkles: add metakg routes to index ([7c7b8e1](https://github.com/biothings/biothings_explorer/commits/7c7b8e1fed0f195c8ab5854b8a49d0cf9b71ae96)) -* :sparkles: create route for metakg ([cd379bc](https://github.com/biothings/biothings_explorer/commits/cd379bc8f16c491090c2982f5c0fb5fbbc4dda3d)) - -## [2.6.0](https://github.com/biothings/biothings_explorer/compare/v2.5.0...v2.6.0) (2021-05-11) - - -### Features - -* :sparkles: upgrade handler to support trapi 1.1.0 ([3cec3f2](https://github.com/biothings/biothings_explorer/commits/3cec3f2868864cd4a6501ba441ac4927b8034250)) -* trapi v1.1.0 support, update handler ([3109a8a](https://github.com/biothings/biothings_explorer/commits/3109a8a14071198ae038c5001f0d1bd76c566ad2)) - - -### Bug Fixes - -* :bug: change from NCBIGENE to NCBIGene ([88d6035](https://github.com/biothings/biothings_explorer/commits/88d6035d9c9e76451be5514409f3a416da062c55)) - -## [2.5.0](https://github.com/biothings/biothings_explorer/compare/v2.4.0...v2.5.0) (2021-04-23) - - -### Bug Fixes - -* :bug: fix issue when output ids contain special characters ([898483a](https://github.com/biothings/biothings_explorer/commits/898483a89d678e7fc4c95dd43ab607e3bbc4ae46)) - -## [2.4.0](https://github.com/biothings/biothings_explorer/compare/v2.3.0...v2.4.0) (2021-04-23) - - -### Features - -* :sparkles: allow user to set MAX_QUERIES_PER_MIN as env ([8686092](https://github.com/biothings/biothings_explorer/commits/8686092a8cbeedacbc38f8670a7be6470eeafc9d)) -* :sparkles: set rate limit to max 3 queries per min ([aeea89c](https://github.com/biothings/biothings_explorer/commits/aeea89c867eace66ba485b1c8b146af2a4328912)) - - -### Bug Fixes - -* :bug: fix unable to resolve biocarta id issue ([551e4b1](https://github.com/biothings/biothings_explorer/commits/551e4b1f938eb08054f303ec6d2460f558e32d08)) -* :fire: temporarily disable text mining co-occurrence kp ([d214a4d](https://github.com/biothings/biothings_explorer/commits/d214a4dbec36a60d6df7d150f89835a6ea32bac8)) -* :sparkles: re-enable clinical risk kp ([4464dfc](https://github.com/biothings/biothings_explorer/commits/4464dfcffcb470ee7478cd16b2d93d712367ebd7)) - -## [2.3.0](https://github.com/biothings/biothings_explorer/compare/v2.2.0...v2.3.0) (2021-04-20) - - -### Features - -* :sparkles: set a hard limit of 3s for all TRAPI APIs ([db96e0b](https://github.com/biothings/biothings_explorer/commits/db96e0bc48dda0a345fac6500fcb8851516dc7ac)) - - -### Bug Fixes - -* :bug: disable Automat CTD due to poor perform ([3753b2c](https://github.com/biothings/biothings_explorer/commits/3753b2cfe69b6c9ef2e82254fe688a039e4e73e3)) -* :bug: fix wrong output type ([714f9ab](https://github.com/biothings/biothings_explorer/commits/714f9abf81bd5735b2a011d9513a8b9347443adb)) - -## [2.2.0](https://github.com/biothings/biothings_explorer/compare/v2.1.0...v2.2.0) (2021-04-02) - -## [2.1.0](https://github.com/biothings/biothings_explorer/compare/v2.0.1...v2.1.0) (2021-04-02) - - -### Features - -* :sparkles: add /test/query endpoint to support user specified smartapi spec ([c75e44d](https://github.com/biothings/biothings_explorer/commits/c75e44db6b79ccd2ef7b3f6f5cfd2cc448fd2814)) -* :sparkles: add additional node attributes to knowledge graph ([4fb93e3](https://github.com/biothings/biothings_explorer/commits/4fb93e37c8a16bc2ae9381747ba56a4e13aa33ed)) -* :sparkles: add cron job to periodically pull from /predicates endpoint ([94461b1](https://github.com/biothings/biothings_explorer/commits/94461b1a7c96b9b7ea66b4f5eb41f55b1a87dcb9)) -* :sparkles: add num_of_participants property for pathway ([3d9f820](https://github.com/biothings/biothings_explorer/commits/3d9f8209134a5625f2940500a65bf0fd277cb457)) -* :sparkles: have bte only use a specified number of APIs ([7fa1732](https://github.com/biothings/biothings_explorer/commits/7fa17323faa8e457a60a6df4dea508cc0489a061)) -* :sparkles: support restricting /predicates to only api names provide ([9260ec9](https://github.com/biothings/biothings_explorer/commits/9260ec969b4244f878f8a0a6c360b04a7dfde8dd)) -* :sparkles: update local predicates file and smartapi specs ([425093e](https://github.com/biothings/biothings_explorer/commits/425093ee3e96af0b969620805bf796ffe592a6fc)) - - -### Bug Fixes - -* :bug: add support for resolving protein ids ([500161a](https://github.com/biothings/biothings_explorer/commits/500161ac8357cb89739da58189f73afd1f91cb58)) -* :bug: fix api_response_transform bug ([4d911d6](https://github.com/biothings/biothings_explorer/commits/4d911d6aa91120775b3d2b70c71fbd1a8e2feefb)) -* :bug: fix cache related bug causing query failure ([3bd87ae](https://github.com/biothings/biothings_explorer/commits/3bd87aec0283b12dfe1676e9fc7e2b57dd51c41e)) -* :bug: fix id resolver failure issue ([eecbe4f](https://github.com/biothings/biothings_explorer/commits/eecbe4f163d535a3a0f589d98fbdc0d76d8dd86d)) -* :bug: fix missing biolink prefix issue ([153b601](https://github.com/biothings/biothings_explorer/commits/153b6011641263bd1d420defa0c881b62b0741a2)) -* :bug: fix typo ([5b32009](https://github.com/biothings/biothings_explorer/commits/5b320097664afb438f6b9e2fc11b7dc232069b3e)) -* :bug: fix wrong edge id in query results ([4bb1aa7](https://github.com/biothings/biothings_explorer/commits/4bb1aa7e3e98da8cd713f89236840f91439d00cb)) - -### [2.0.1](https://github.com/biothings/biothings_explorer/compare/v2.0.0...v2.0.1) (2021-03-12) - - -### Bug Fixes - -* :bug: fix wrong uniprot issuue ([92fac04](https://github.com/biothings/biothings_explorer/commits/92fac04398329d3dec5d579ed5dcf1d397d515ee)) - -## [2.0.0](https://github.com/biothings/biothings_explorer/compare/v1.12.0...v2.0.0) (2021-03-09) - - -### Features - -* :sparkles: have /query and /v1/query the same behavior ([2db1ff8](https://github.com/biothings/biothings_explorer/commits/2db1ff8bd40de94b8d99935e58a711f42441cdf7)) -* :sparkles: use redis to enable cacheing query results ([dd42583](https://github.com/biothings/biothings_explorer/commits/dd42583b4a458d29a57007872779f33e6034b27b)) - - -### Bug Fixes - -* :bug: check semantic type match input type before creating bte edge ([2731602](https://github.com/biothings/biothings_explorer/commits/2731602e8f033b71f033a7e98ff7d269fd4c6d34)) -* :bug: fix wrong logic to determine if redis cache is enabled ([fdf71ab](https://github.com/biothings/biothings_explorer/commits/fdf71ab29b35de00f24428763c7514ad2b4c874a)) -* :bug: fix wrongly generated cache hash id ([49a9734](https://github.com/biothings/biothings_explorer/commits/49a97348ad3d34b3becc358be01d45cef3c62e33)) -* :bug: remove non-edge data from knowledge graph edge attributes ([500a66b](https://github.com/biothings/biothings_explorer/commits/500a66bd948ca9cb59a64c04f5114fdfb5b90ceb)) -* :bug: stringify all values of dbIDs ([0919e7d](https://github.com/biothings/biothings_explorer/commits/0919e7d45f5aa8c4dbe93bc62121d96b6e650a63)) - -## [1.12.0](https://github.com/biothings/biothings_explorer/compare/v1.11.0...v1.12.0) (2021-02-19) - - -### Features - -* :sparkles: adapt to new output from id resolver module ([1b7d1b8](https://github.com/biothings/biothings_explorer/commits/1b7d1b8519b2990b0f7b6b42e1115aa97e22015e)) - - -### Bug Fixes - -* :bug: add missing next parameter ([d943307](https://github.com/biothings/biothings_explorer/commits/d9433077038a72392f3e93f6a75f8d64e96d76be)) -* :bug: fix /performance endpoint not working issue ([6f59473](https://github.com/biothings/biothings_explorer/commits/6f59473c3155e3b19727cc26aab6babe6b8ea821)) -* :bug: fix wrong generate curie logic ([8c0e585](https://github.com/biothings/biothings_explorer/commits/8c0e585a8706d5cd0dfcdeb35ef29f0b043bb1cc)) - -### [1.11.1](https://github.com/biothings/biothings_explorer/compare/v1.11.0...v1.11.1) (2021-02-19) - -## [1.11.0](https://github.com/biothings/biothings_explorer/compare/v1.10.0...v1.11.0) (2021-02-09) - - -### Features - -* :sparkles: run cron job in expressjs event loop ([d2d44bc](https://github.com/biothings/biothings_explorer/commits/d2d44bc584583947d6cfad796e13cf7e55ff0588)) -* :sparkles: set cron job to pull smartapi spec from API every 10 mins ([8f8dbe1](https://github.com/biothings/biothings_explorer/commits/8f8dbe1c1ede0e492ac75157be6c0aa501b14382)) -* :sparkles: update metakg endpoint to read from local copy of SmartAPI specs ([c5f40d0](https://github.com/biothings/biothings_explorer/commits/c5f40d0dfb9966812acfd46356c394cb82fb9b20)) - -## [1.10.0](https://github.com/biothings/biothings_explorer/compare/v1.9.2...v1.10.0) (2021-02-02) - - -### Features - -* :sparkles: add debug and log for qedge2bteedge module ([abc9265](https://github.com/biothings/biothings_explorer/commits/abc92651f9869a566d0e092dcaec1ecf10361060)) -* :sparkles: add debug message for nodeUpdateHandler module ([6cf9b5d](https://github.com/biothings/biothings_explorer/commits/6cf9b5dc9b75f0845acd49236f9021bb852679c2)) -* :sparkles: look for symmetric predicate if qEdge is reversed ([a167345](https://github.com/biothings/biothings_explorer/commits/a1673454c396b196c1d6970a65fe67468802e057)) -* :sparkles: support edge reversal ([862560d](https://github.com/biothings/biothings_explorer/commits/862560daa9da0005dd85fdd5612e72ce5364e0f4)) - - -### Bug Fixes - -* :bug: check if user provided predicate is undefined ([56eb1fe](https://github.com/biothings/biothings_explorer/commits/56eb1feed819ea4c682c7700602796a663f85ff0)) -* :bug: modify query predicate to fit biolink json file ([fc91a31](https://github.com/biothings/biothings_explorer/commits/fc91a318c7e218bcf2e37351e3f1921ab970a0cc)) -* :bug: synchronize the predicate in kg with the qg ([658aa43](https://github.com/biothings/biothings_explorer/commits/658aa434b0efa035cbd79053cbe76a36be132b21)) -* :bug: terminate the query if one of the critical intermediate step return empty results ([15ee30a](https://github.com/biothings/biothings_explorer/commits/15ee30aef234ebe20ca45372fe5d349ee88a2ed0)) -* :bug: use predicate from api if no predicate supplied in qg ([a073f99](https://github.com/biothings/biothings_explorer/commits/a073f9959c8a3c2f7fdda8fe0c83768d125e943f)) - -### [1.9.2](https://github.com/biothings/biothings_explorer/compare/v1.9.1...v1.9.2) (2021-02-01) - - -### Bug Fixes - -* :bug: fix issue regarding missing type information for node attributes ([7cf6119](https://github.com/biothings/biothings_explorer/commits/7cf61195a7e0dac0f6615e2e7f97defbba365e57)) - -### [1.9.1](https://github.com/biothings/biothings_explorer/compare/v1.9.0...v1.9.1) (2021-01-27) - - -### Bug Fixes - -* :bug: fix CHANGELOG bug ([f72c660](https://github.com/biothings/biothings_explorer/commits/f72c660e7afd6fdeec8f4092478b1683b9bdfcb2)) -* :bug: fix wrong url in CHANGELOG and autogenerate tools ([f927d5e](https://github.com/biothings/biothings_explorer/commits/f927d5ea3a73b24951c9a195d5522d7965e00e19)) - -## [1.9.0](https://github.com/biothings/biothings_explorer/compare/v1.4.0...v1.9.0) (2021-01-26) - - -### Features - -* :sparkles: disable id resolution module for text mining KPs ([f3f5067](https://github.com/biothings/biothings_explorer/commits/f3f506759c54386fc8394d27b3240a7327b2317b)) -* :sparkles: include call apis error message in log ([4ff93b0](https://github.com/biothings/biothings_explorer/commits/4ff93b0362b31c06927e489bfd8a442b015d4bd3)) - - -### Bug Fixes - -* :bug: Fix issue related to publication extraction ([cfe3c3c](https://github.com/biothings/biothings_explorer/commits/cfe3c3c0366eef8962dccd8b810b0ec6abf5b067)) - -## [1.8.0](https://github.com/biothings/biothings_explorer/compare/v1.4.0...v1.8.0) (2021-01-26) - - - -### Features - -* :sparkles: include call apis error message in log ([4ff93b0](https://github.com/biothings/biothings_explorer/commits/4ff93b0362b31c06927e489bfd8a442b015d4bd3)) - - -### Bug Fixes - -* :bug: Fix issue related to publication extraction ([cfe3c3c](https://github.com/biothings/biothings_explorer/commits/cfe3c3c0366eef8962dccd8b810b0ec6abf5b067)) - -## [1.7.0](https://github.com/biothings/biothings_explorer/compare/v1.4.0...v1.7.0) (2021-01-26) - - -### Features - -* :sparkles: include call apis error message in log ([4ff93b0](https://github.com/biothings/biothings_explorer/commits/4ff93b0362b31c06927e489bfd8a442b015d4bd3)) - - -### Bug Fixes - -* :bug: Fix issue related to publication extraction ([cfe3c3c](https://github.com/biothings/biothings_explorer/commits/cfe3c3c0366eef8962dccd8b810b0ec6abf5b067)) - -## [1.6.0](https://github.com/biothings/biothings_explorer/compare/v1.4.0...v1.6.0) (2021-01-26) - - -### Features - -* :sparkles: include call apis error message in log ([4ff93b0](https://github.com/biothings/biothings_explorer/commits/4ff93b0362b31c06927e489bfd8a442b015d4bd3)) - - -### Bug Fixes - -* :bug: Fix issue related to publication extraction ([cfe3c3c](https://github.com/biothings/biothings_explorer/commits/cfe3c3c0366eef8962dccd8b810b0ec6abf5b067)) - -## [1.5.0](https://github.com/biothings/biothings_explorer/compare/v1.4.0...v1.5.0) (2021-01-26) - - -### Features - -* :sparkles: include call apis error message in log ([4ff93b0](https://github.com/biothings/biothings_explorer/commits/4ff93b0362b31c06927e489bfd8a442b015d4bd3)) - -## [1.4.0](https://github.com/biothings/biothings_explorer/compare/v1.3.0...v1.4.0) (2021-01-26) - - -### Features - -* :sparkles: Enable logging for call-apis module ([406a62b](https://github.com/biothings/biothings_explorer/commits/406a62b64e3cd0e1d961782f27e39485b90ded25)) - -## [1.3.0](https://github.com/biothings/biothings_explorer/compare/v1.1.1...v1.3.0) (2021-01-26) - - -### Features - -* :sparkles: Enable BTE TRAPI to query SmartAPI on real time ([be00d80](https://github.com/biothings/biothings_explorer/commits/be00d804af9a93d1f84f4cbb968160c62fd3fbd2)) - - -### Bug Fixes - -* :bug: change log level to warning if no smartapi edge found ([082759f](https://github.com/biothings/biothings_explorer/commits/082759f0c5abc51e3a3b8f2700a82f2c4a86e60c)) -* :bug: Display correct log message based on whether smartapi edges are found or not ([54cf072](https://github.com/biothings/biothings_explorer/commits/54cf0722076201bfeb617749986e478e552597b0)) -* added jenkinsfile ([b35c484](https://github.com/biothings/biothings_explorer/commits/b35c48408872c4686120715daa3f7f4e146a72cc)) -* update the image name ([77c74f7](https://github.com/biothings/biothings_explorer/commits/77c74f72e0d8505b26b7b95eb8ddb03bb19a9fbe)) - -## [1.2.0](https://github.com/biothings/biothings_explorer/compare/v1.1.1...v1.2.0) (2021-01-26) - - -### Features - -* :sparkles: Enable BTE TRAPI to query SmartAPI on real time ([be00d80](https://github.com/biothings/biothings_explorer/commits/be00d804af9a93d1f84f4cbb968160c62fd3fbd2)) - - -### Bug Fixes - -* added jenkinsfile ([b35c484](https://github.com/biothings/biothings_explorer/commits/b35c48408872c4686120715daa3f7f4e146a72cc)) -* update the image name ([77c74f7](https://github.com/biothings/biothings_explorer/commits/77c74f72e0d8505b26b7b95eb8ddb03bb19a9fbe)) - -### [1.1.1](https://github.com/biothings/biothings_explorer/compare/v3.6.11...v1.1.1) (2021-01-25) - - -### Bug Fixes - -* :bug: change teamName to team_name for api input ([95e71ce](https://github.com/biothings/biothings_explorer/commits/95e71cef9f66c34a995dad8a57ffd249dde31971)) diff --git a/package.json b/package.json index 678f694..017fadb 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { - "name": "@biothings-explorer/bte-trapi", + "name": "@retriever/main", "version": "3.0.0", - "description": "BioThings Explorer's TRAPI Knowledgebase Query API", + "description": "Retriever, a centralized subgraph-retrieval module", "main": "packages/server/built/server.js", "scripts": { "setup": "pnpm run clone && pnpm i", @@ -26,7 +26,7 @@ "start": "./scripts/start_server.sh", "stop": "./scripts/stop_server.sh", "watch": "nodemon -e js,mjs,json,ts --watch './packages/**/src/*' './packages/**/data/*' --exec 'pnpm run build && node .'", - "debug": "DEBUG=biomedical-id-resolver,bte* pnpm run watch" + "debug": "DEBUG=biomedical-id-resolver,retriever* pnpm run watch" }, "engines": { "node": ">=18.0.0", @@ -34,21 +34,23 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/biothings_explorer.git" + "url": "git+https://github.com/BioPack-team/retriever.git" }, "keywords": [ - "bte", + "BioPack", + "retriever", "biothings", + "biopack", "single", "hop", "query" ], - "author": "BioThings Team", + "author": "BioPack Team", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/biothings_explorer/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/biothings_explorer#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "devDependencies": { "@types/node": "^20.8.7", "@typescript-eslint/eslint-plugin": "^6.8.0", @@ -75,6 +77,7 @@ "typescript": "5.2.2" }, "dependencies": { + "@retriever/call-apis": "workspace:./packages/call-apis", "@bull-board/express": "^5.9.1", "@sentry/node": "^7.74.1", "@sentry/profiling-node": "^1.2.1", diff --git a/packages/api-response-transform/package.json b/packages/api-response-transform/package.json index 6ef2796..7aa966f 100644 --- a/packages/api-response-transform/package.json +++ b/packages/api-response-transform/package.json @@ -1,5 +1,5 @@ { - "name": "@biothings-explorer/api-response-transform", + "name": "@retriever/api-response-transform", "version": "1.12.0", "description": "a NodeJS library to transform API responses into biolink model", "main": "built/index.js", @@ -18,20 +18,22 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/api-respone-transform.js.git" + "url": "git+https://github.com/BioPack-team/retriever" }, "keywords": [ + "BioPack", + "retriever", "transform", "biolink", "api", "json" ], - "author": "BioThings Team", + "author": "BioPack Team", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/api-respone-transform.js/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/api-respone-transform.js#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "devDependencies": { "@babel/core": "^7.23.2", "@babel/preset-env": "^7.23.2", @@ -58,7 +60,10 @@ "typescript": "^5.2.2" }, "dependencies": { - "@biothings-explorer/utils": "workspace:../utils", + "@retriever/utils": "workspace:../utils", + "@retriever/types": "workspace:../types", + "@retriever/graph": "workspace:../graph", + "@retriever/smartapi-kg": "workspace:../smartapi-kg", "@commitlint/cli": "^17.8.1", "@commitlint/config-conventional": "^11.0.0", "async": "^3.2.4", diff --git a/packages/api-response-transform/src/index.ts b/packages/api-response-transform/src/index.ts index 68b99fd..b101001 100644 --- a/packages/api-response-transform/src/index.ts +++ b/packages/api-response-transform/src/index.ts @@ -7,18 +7,17 @@ import BaseTransformer from "./transformers/transformer"; import TRAPITransformer from "./transformers/trapi_transformer"; import EBIProteinTransformer from "./transformers/ebi_protein_transformer"; import JQTransformer from "./transformers/jq_transformer"; -import { BTEQueryObject } from "./types"; -import { Record } from "./record"; +import { RetrieverQueryObject } from "./types"; +import { Record } from "@retriever/graph"; import Debug from "debug"; -const debug = Debug("bte:api-response-transform:index"); -export * from "./record"; +const debug = Debug("retriever:api-response-transform:index"); export * from "./types"; export default class Transformer { - private data: BTEQueryObject; + private data: RetrieverQueryObject; private tf: BaseTransformer; config: any; - constructor(data: BTEQueryObject, config: any) { + constructor(data: RetrieverQueryObject, config: any) { this.data = data; this.config = config; this.route(); @@ -46,12 +45,18 @@ export default class Transformer { } else if (api.startsWith("SEMMED")) { this.tf = new SemmedTransformer(this.data, this.config); } else if (api === "Monarch API") { - this.tf = new JQTransformer(this.data, { ...this.config, type: "monarch" }); + this.tf = new JQTransformer(this.data, { + ...this.config, + type: "monarch", + }); } else if (api === "EBI Proteins API") { // this.tf = new EBIProteinTransformer(this.data, this.config) this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" }); } else if (tags.includes("biothings")) { - this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" }); + this.tf = new JQTransformer(this.data, { + ...this.config, + type: "biothings", + }); } else if (tags.includes("ctd")) { this.tf = new JQTransformer(this.data, { ...this.config, type: "ctd" }); } else if (tags.includes("opentarget")) { diff --git a/packages/api-response-transform/src/jq_utils.ts b/packages/api-response-transform/src/jq_utils.ts index aadcbf2..40b18b0 100644 --- a/packages/api-response-transform/src/jq_utils.ts +++ b/packages/api-response-transform/src/jq_utils.ts @@ -1,7 +1,6 @@ -import { JQVariable, BTEKGOperationObject } from "./types"; +import { JQVariable } from "./types"; import Path from "path"; import fs from "fs"; -import { toArray } from "./utils"; const functions = fs.readFileSync( Path.resolve(`${__dirname}/../data/jq/utils.jq`), diff --git a/packages/api-response-transform/src/transformers/biothings_transformer.ts b/packages/api-response-transform/src/transformers/biothings_transformer.ts index 8676dbc..e19313c 100644 --- a/packages/api-response-transform/src/transformers/biothings_transformer.ts +++ b/packages/api-response-transform/src/transformers/biothings_transformer.ts @@ -5,10 +5,10 @@ export default class BioThingsTransformer extends BaseTransformer { async pairCurieWithAPIResponse() { if (this.edge.query_operation.method === "post") { let res = {}; - const mapper = item => { + const mapper = (item: { query: string | string[]; }) => { // for input not found, BioThings API returns an entry with a key "notfound" equal to true if (!("notfound" in item)) { - let input = generateCurie(this.edge.association.input_id, item.query); + let input = generateCurie(this.edge.association.input_id as string, item.query); if (input in res) { res[input].push(item); } else { diff --git a/packages/api-response-transform/src/transformers/transformer.ts b/packages/api-response-transform/src/transformers/transformer.ts index 02f1df3..1f9b273 100644 --- a/packages/api-response-transform/src/transformers/transformer.ts +++ b/packages/api-response-transform/src/transformers/transformer.ts @@ -1,20 +1,19 @@ import { transform } from "../json_transform/index"; import { JSONDoc } from "../json_transform/types"; import { generateCurie, toArray } from "../utils"; -import { BTEKGOperationObject, BTEQueryObject } from "../types"; -import { Record } from "../record"; -import { FrozenRecord } from "../record"; -import * as _ from "lodash"; +import { RetrieverQueryObject } from "../types"; +import _ from "lodash"; import Debug from "debug"; import async from "async"; -const debug = Debug("bte:api-response-transform:transformer"); +import { Record, APIEdge } from "@retriever/graph"; +const debug = Debug("retriever:api-response-transform:transformer"); export default class BaseTransformer { - protected edge: BTEKGOperationObject; - protected data: BTEQueryObject; + protected edge: APIEdge; + protected data: RetrieverQueryObject; public config: any; - constructor(data: BTEQueryObject, config: any) { + constructor(data: RetrieverQueryObject, config: any) { this.data = data; this.edge = data.edge; this.config = config; @@ -25,7 +24,7 @@ export default class BaseTransformer { */ async pairCurieWithAPIResponse() { const input = generateCurie( - this.edge.association.input_id, + this.edge.association.input_id as string, this.edge.input.hasOwnProperty("queryInputs") ? this.edge.input["queryInputs"] : (this.edge.input as string), @@ -228,7 +227,7 @@ export default class BaseTransformer { _removeNonEdgeData(mappedResponse: any) { delete mappedResponse["@type"]; - delete mappedResponse[this.edge.association.output_id]; + delete mappedResponse[this.edge.association.output_id as string]; delete mappedResponse["input_name"]; delete mappedResponse["output_name"]; return mappedResponse; @@ -298,7 +297,7 @@ export default class BaseTransformer { ); await async.eachSeries( Object.entries(predicateResponse), - async ([predicate, mappedResponses]) => { + async ([_predicate, mappedResponses]) => { if ( Array.isArray(mappedResponses) && mappedResponses.length > 0 @@ -330,7 +329,7 @@ export default class BaseTransformer { * @param {Object} mappedResponse - JSON response representing an output. */ extractObjectIDs(mappedResponse: object) { - const output_id_type = this.edge.association.output_id; + const output_id_type = this.edge.association.output_id as string; if (!(output_id_type in mappedResponse)) { return []; } diff --git a/packages/api-response-transform/src/transformers/trapi_transformer.ts b/packages/api-response-transform/src/transformers/trapi_transformer.ts index 0eb5dee..1a27ce2 100644 --- a/packages/api-response-transform/src/transformers/trapi_transformer.ts +++ b/packages/api-response-transform/src/transformers/trapi_transformer.ts @@ -1,7 +1,7 @@ import BaseTransformer from "./transformer"; -import { Record } from "../record"; +import { Record } from "@retriever/graph"; import { JSONDoc } from "../json_transform/types"; -import { removeBioLinkPrefix } from "@biothings-explorer/utils"; +import { removeBioLinkPrefix } from "@retriever/utils"; export default class TRAPITransformer extends BaseTransformer { _getUniqueEdges() { diff --git a/packages/api-response-transform/src/types.ts b/packages/api-response-transform/src/types.ts index 6c24101..19355cc 100644 --- a/packages/api-response-transform/src/types.ts +++ b/packages/api-response-transform/src/types.ts @@ -1,65 +1,24 @@ +import { APIEdge } from "@retriever/graph"; import { JSONDoc } from "./json_transform/types"; +import { XBTEKGSOperationObject } from "@retriever/smartapi-kg"; -interface KGAssociationObject { - input_id?: string; - input_type: string; - output_id?: string; - output_type: string; - predicate: string; - source?: string; - api_name?: string; -} - -interface XBTEParametersObject { - [key: string]: string | number; -} - -interface TransformerObject { +export interface TransformerObject { wrap?: string; pair?: string; } -interface TransformerSet { +export interface TransformerSet { [transformerPattern: string]: TransformerObject; } -interface QueryOperationInterface { - path: string; - method: string; - server: string; - tags: string[]; - path_params: string[]; - params: XBTEParametersObject; - request_body: object; - supportBatch: boolean; - inputSeparator: string; - transformer: TransformerSet; -} - -interface SmartAPIKGOperationObject { - association: KGAssociationObject; - query_operation?: QueryOperationInterface; - response_mapping?: any; - id?: string; - tags?: string[]; -} - -interface TemplatedInput { +export interface TemplatedInput { queryInputs: string | string[]; [additionalAttributes: string]: string | string[]; } -export interface BTEKGOperationObject extends SmartAPIKGOperationObject { - input: string | string[] | TemplatedInput; - reasoner_edge?: any; - filter?: string; - original_input?: object; - input_resolved_identifiers?: object; -} - -export interface BTEQueryObject { +export interface RetrieverQueryObject { response: JSONDoc | JSONDoc[] | { hits: JSONDoc[] }; - edge: BTEKGOperationObject; + edge: APIEdge; } export interface JQVariable { diff --git a/packages/api-response-transform/tsconfig.json b/packages/api-response-transform/tsconfig.json index 304a67a..b899ef8 100644 --- a/packages/api-response-transform/tsconfig.json +++ b/packages/api-response-transform/tsconfig.json @@ -5,14 +5,40 @@ "outDir": "./built", "rootDir": "./src", "paths": { - "@biothings-explorer/utils": ["../utils"] + "@retriever/utils": [ + "../utils" + ], + "@retriever/types": [ + "../types" + ], + "@retriever/graph": [ + "../graph" + ], + "@retriever/smartapi_kg": [ + "../smartapi-kg" + ] } }, - "include": ["./src/**/*"], - "exclude": ["node_modules", "__tests__/"], + "include": [ + "./src/**/*" + ], + "exclude": [ + "node_modules", + "__tests__/" + ], "references": [ { "path": "../utils" + }, + { + "path": "../types" + }, + { + "path": "../graph" + }, + { + "path": "../smartapi-kg" } + ] } diff --git a/packages/biolink-model/package.json b/packages/biolink-model/package.json index e1c3ae2..ef82b9a 100644 --- a/packages/biolink-model/package.json +++ b/packages/biolink-model/package.json @@ -17,10 +17,11 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/biolink-model.js.git" + "url": "git+https://github.com/BioPack-team/retriever" }, "keywords": [ - "biothings-explorer", + "BioPack", + "retriever", "biolink", "biomedical", "ontology" @@ -28,9 +29,9 @@ "author": "jiwen xin", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/biolink-model.js/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/biolink-model.js#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "devDependencies": { "@types/debug": "^4.1.10", "@types/jest": "^26.0.24", diff --git a/packages/biolink-model/src/loader/url_loader.ts b/packages/biolink-model/src/loader/url_loader.ts index d5e623c..d5dfab0 100644 --- a/packages/biolink-model/src/loader/url_loader.ts +++ b/packages/biolink-model/src/loader/url_loader.ts @@ -7,7 +7,7 @@ export default class URLLoader extends Loader { async load(input) { let res; try { - const userAgent = `BTE/${process.env.NODE_ENV === 'production' ? 'prod' : 'dev'} Node/${process.version} ${ + const userAgent = `Retriever/${process.env.NODE_ENV === 'production' ? 'prod' : 'dev'} Node/${process.version} ${ process.platform }`; res = await axios.get(input, { diff --git a/packages/biomedical_id_resolver/package.json b/packages/biomedical_id_resolver/package.json index 7c5b2d0..9d30264 100644 --- a/packages/biomedical_id_resolver/package.json +++ b/packages/biomedical_id_resolver/package.json @@ -18,7 +18,7 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/biomedical_id_resolver.js.git" + "url": "git+https://github.com/BioPack-team/retriever" }, "keywords": [ "id", @@ -28,9 +28,9 @@ "author": "jiwen xin", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/biomedical_id_resolver.js/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/biomedical_id_resolver.js#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "devDependencies": { "@types/debug": "^4.1.10", "@types/jest": "^26.0.24", diff --git a/packages/biomedical_id_resolver/src/attrs.ts b/packages/biomedical_id_resolver/src/attrs.ts index 822318a..a13f62e 100644 --- a/packages/biomedical_id_resolver/src/attrs.ts +++ b/packages/biomedical_id_resolver/src/attrs.ts @@ -20,7 +20,7 @@ import { import { BioLink } from 'biolink-model'; import Debug from 'debug'; -const debug = Debug('biomedical-id-resolver:AddAttributes'); +const debug = Debug('retriever:biomedical-id-resolver:AddAttributes'); function groupCuriesByPrefix(curies: string[]): ObjectWithStringKeyAndArrayValues { const grped: ObjectWithStringKeyAndArrayValues = {}; diff --git a/packages/biomedical_id_resolver/src/query/builder/biothings_builder.ts b/packages/biomedical_id_resolver/src/query/builder/biothings_builder.ts index 904ac4c..da157a8 100644 --- a/packages/biomedical_id_resolver/src/query/builder/biothings_builder.ts +++ b/packages/biomedical_id_resolver/src/query/builder/biothings_builder.ts @@ -21,7 +21,7 @@ import { ResolvableBioEntity } from '../../bioentity/valid_bioentity'; import { IrresolvableBioEntity } from '../../bioentity/irresolvable_bioentity'; import { QueryBuilder } from './base_builder'; import Debug from 'debug'; -const debug = Debug('biomedical-id-resolver:QueryBuilder'); +const debug = Debug('retriever:biomedical-id-resolver:QueryBuilder'); export class BioThingsQueryBuilder extends QueryBuilder { static queryTemplate: string = 'q={inputs}&scopes={scopes}&fields={fields}&dotfield=true&species=human'; diff --git a/packages/biomedical_id_resolver/src/query/index.ts b/packages/biomedical_id_resolver/src/query/index.ts index c7b636b..ae5c42d 100644 --- a/packages/biomedical_id_resolver/src/query/index.ts +++ b/packages/biomedical_id_resolver/src/query/index.ts @@ -1,7 +1,7 @@ import { Scheduler } from './scheduler'; import { DBIdsObject, IndividualResolverOutput } from '../common/types'; import Debug from 'debug'; -const debug = Debug('biomedical-id-resolver:Query'); +const debug = Debug('retriever:biomedical-id-resolver:Query'); const query = async (resolvable: DBIdsObject): Promise => { const scheduler = new Scheduler(resolvable); diff --git a/packages/biomedical_id_resolver/src/query/scheduler.ts b/packages/biomedical_id_resolver/src/query/scheduler.ts index 7d3c0da..954257a 100644 --- a/packages/biomedical_id_resolver/src/query/scheduler.ts +++ b/packages/biomedical_id_resolver/src/query/scheduler.ts @@ -4,7 +4,7 @@ import { BioThingsQueryBuilder } from './builder/biothings_builder'; import { DBIdsObject, Buckets } from '../common/types'; import { MAX_CONCURRENT_QUERIES } from '../config'; import Debug from 'debug'; -const debug = Debug('biomedical-id-resolver:Scheduler'); +const debug = Debug('retriever:biomedical-id-resolver:Scheduler'); export class Scheduler { private validInput: DBIdsObject; diff --git a/packages/biomedical_id_resolver/src/resolve/base_resolver.ts b/packages/biomedical_id_resolver/src/resolve/base_resolver.ts index a5c8f84..7fb5084 100644 --- a/packages/biomedical_id_resolver/src/resolve/base_resolver.ts +++ b/packages/biomedical_id_resolver/src/resolve/base_resolver.ts @@ -1,7 +1,7 @@ import { IResolver, ResolverOutput, DBIdsObject } from '../common/types'; import { IrresolvableBioEntity } from '../bioentity/irresolvable_bioentity'; import Debug from 'debug'; -const debug = Debug('biomedical-id-resolver:resolver'); +const debug = Debug('retriever:biomedical-id-resolver:resolver'); export default abstract class BaseResolver implements IResolver { protected annotateUnresolvedInputs(unresolvedInputs: DBIdsObject, currentResult: ResolverOutput): ResolverOutput { diff --git a/packages/biomedical_id_resolver/src/resolve/biolink_based_resolver.ts b/packages/biomedical_id_resolver/src/resolve/biolink_based_resolver.ts index f952331..b7868bd 100644 --- a/packages/biomedical_id_resolver/src/resolve/biolink_based_resolver.ts +++ b/packages/biomedical_id_resolver/src/resolve/biolink_based_resolver.ts @@ -4,7 +4,7 @@ import query from '../query/index'; import { ResolverOutput, IndividualResolverOutput, DBIdsObject } from '../common/types'; import BioLinkHandlerInstance from '../biolink'; import Debug from 'debug'; -const debug = Debug('biomedical-id-resolver:resolver'); +const debug = Debug('retriever:biomedical-id-resolver:resolver'); export default class BioLinkBasedResolver extends BaseResolver { private _biolink: typeof BioLinkHandlerInstance; diff --git a/packages/biomedical_id_resolver/src/resolve/default_resolver.ts b/packages/biomedical_id_resolver/src/resolve/default_resolver.ts index cd0faee..3edcfab 100644 --- a/packages/biomedical_id_resolver/src/resolve/default_resolver.ts +++ b/packages/biomedical_id_resolver/src/resolve/default_resolver.ts @@ -3,7 +3,7 @@ import { ResolverOutput, IndividualResolverOutput } from '../common/types'; import query from '../query/index'; import DefaultValidator from '../validate/default_validator'; import Debug from 'debug'; -const debug = Debug('biomedical-id-resolver:resolver'); +const debug = Debug('retriever:biomedical-id-resolver:resolver'); export default class DefaultResolver extends BaseResolver { private organizeResolvedOutputs(resolved: IndividualResolverOutput[]): ResolverOutput { diff --git a/packages/biomedical_id_resolver/src/sri.ts b/packages/biomedical_id_resolver/src/sri.ts index 043f23a..2f86ab0 100644 --- a/packages/biomedical_id_resolver/src/sri.ts +++ b/packages/biomedical_id_resolver/src/sri.ts @@ -5,7 +5,7 @@ import { SRIResolverOutput, ResolverInput, SRIBioEntity, SRIResponseEntity, SRIR import Debug from 'debug'; import _ from 'lodash'; import SRINodeNormFailure from './exceptions/sri_resolver_failiure'; -const debug = Debug('bte:biomedical-id-resolver:SRI'); +const debug = Debug('retriever:biomedical-id-resolver:SRI'); /** sets up request retry policy (weird typescript b/c old axios version) */ // @ts-ignore diff --git a/packages/call-apis/package.json b/packages/call-apis/package.json index 5b1f316..e191884 100644 --- a/packages/call-apis/package.json +++ b/packages/call-apis/package.json @@ -1,7 +1,7 @@ { - "name": "@biothings-explorer/call-apis", + "name": "@retriever/call-apis", "version": "1.24.0", - "description": "A nodejs module to make api calls for biothings explorer", + "description": "A nodejs module to make api calls for retriever", "main": "built/index.js", "types": "built/index.d.ts", "scripts": { @@ -18,9 +18,11 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/call-apis.js.git" + "url": "git+https://github.com/BioPack-team/retriever" }, "keywords": [ + "BioPack", + "retriever", "api", "biothings", "explorer" @@ -28,14 +30,17 @@ "author": "jiwen xin", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/call-apis.js/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/call-apis.js#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "dependencies": { - "@biothings-explorer/api-response-transform": "workspace:../api-response-transform", - "@biothings-explorer/smartapi-kg": "workspace:../smartapi-kg", - "@biothings-explorer/utils": "workspace:../utils", + "@retriever/api-response-transform": "workspace:../api-response-transform", + "@retriever/graph": "workspace:../graph", + "@retriever/smartapi-kg": "workspace:../smartapi-kg", + "@retriever/types": "workspace:../types", + "@retriever/utils": "workspace:../utils", "@sentry/node": "^7.74.1", + "async": "^3.2.4", "axios": "^0.21.4", "axios-retry": "^3.8.1", "biomedical_id_resolver": "workspace:../biomedical_id_resolver", @@ -47,6 +52,7 @@ "devDependencies": { "@commitlint/cli": "^11.0.0", "@commitlint/config-conventional": "^11.0.0", + "@types/async": "^3.2.22", "@types/debug": "^4.1.10", "@types/jest": "^29.5.6", "@types/lodash": "^4.14.200", diff --git a/packages/call-apis/src/dispatch_thread.ts b/packages/call-apis/src/dispatch_thread.ts new file mode 100644 index 0000000..80a9586 --- /dev/null +++ b/packages/call-apis/src/dispatch_thread.ts @@ -0,0 +1,62 @@ +// import { +// NodeNormalizerResultObj, +// Record, +// } from "@retriever/api-response-transform"; +// import { LogEntry } from "@retriever/utils"; +// import SubqueryDispatcher from "./dispatcher"; +// import { JSONDoc, QueryHandlerOptions, UnavailableAPITracker } from "./types"; +// import Subquery from "./queries/subquery"; +// import Debug from "debug"; +// import { +// ResolvableBioEntity, +// ResolverOutput, +// SRIResolverOutput, +// generateInvalidBioentities, +// getAttributes, +// resolveSRI, +// } from "biomedical_id_resolver"; +// const debug = Debug("retriever:call-apis:query"); +// import ESSerializer from 'esserializer'; +// import TemplateSubquery from "./queries/template_subquery"; +// import TrapiSubquery from "./queries/trapi_subquery"; +// import { QEdge } from "@retriever/graph"; +// +// ESSerializer.registerClasses([ +// Subquery, +// TemplateSubquery, +// TrapiSubquery, +// QEdge, +// ]); +// +// const subqueryDispatcher = new SubqueryDispatcher(); +// +// +// +// export default async function query({ +// query, +// resolveOutputIDs = true, +// options, +// }: { +// query: string; +// resolveOutputIDs: boolean; +// options: QueryHandlerOptions; +// }) { +// // let startTime = performance.now(); +// +// const { records, logs } = await subqueryDispatcher.execute(ESSerializer.deserialize(query), options); +// +// // let finishTime = performance.now(); +// // const timeElapsed = Math.round( +// // finishTime - startTime > 1000 +// // ? (finishTime - startTime) / 1000 +// // : finishTime - startTime, +// // ); +// // // const timeUnits = finishTime - startTime > 1000 ? "s" : "ms"; +// debug("query completes."); +// +// debug("Start to use id resolver module to annotate output ids."); +// const annotatedRecords = await annotate(records, resolveOutputIDs); +// debug("id annotation completes"); +// +// return { records: Record.packRecords(annotatedRecords), logs }; +// } diff --git a/packages/call-apis/src/dispatcher.ts b/packages/call-apis/src/dispatcher.ts index 97338e5..b29ff16 100644 --- a/packages/call-apis/src/dispatcher.ts +++ b/packages/call-apis/src/dispatcher.ts @@ -1,163 +1,242 @@ -import { Record } from "@biothings-explorer/api-response-transform"; +import { Record } from "@retriever/graph"; import APIQueryPool from "./query_pool"; import APIQueryQueue from "./query_queue"; -import { QueryHandlerOptions, UnavailableAPITracker } from "./types"; -import { - LogEntry, - StampedLog, - Telemetry, - RedisClient, -} from "@biothings-explorer/utils"; +import { QueryHandlerOptions } from "@retriever/types"; +import { SerializableLog } from "@retriever/utils"; import Debug from "debug"; import Subquery from "./queries/subquery"; -const debug = Debug("bte:call-apis:query"); +import { cacheContent } from "@retriever/utils"; +import { + ResolvableBioEntity, + ResolverOutput, + SRIBioEntity, + SRIResolverOutput, + generateInvalidBioentities, + getAttributes, + resolveSRI, +} from "biomedical_id_resolver"; +const debug = Debug("retriever:call-apis:dispatch"); + +export interface CuriesBySemanticType { + [semanticType: string]: string[]; +} export default class SubqueryDispatcher { - redisClient: RedisClient; - options: QueryHandlerOptions; queue: APIQueryQueue; pool: APIQueryPool; - records: Record[]; currentlyDispatched: number; complete: (value: unknown) => void; - unavailableAPIs: UnavailableAPITracker; - maxRecords: number; - globalMaxRecords: number; - totalRecords: number; - done: boolean; - logs: StampedLog[]; - qEdgeID: string; - constructor( - queries: Subquery[], - redisClient: RedisClient, - unavailableAPIs: UnavailableAPITracker, - options: QueryHandlerOptions = {}, - ) { - this.qEdgeID = queries[0].APIEdge.reasoner_edge?.id; - this.redisClient = redisClient; - this.unavailableAPIs = unavailableAPIs; - this.options = options; - this.queue = new APIQueryQueue(queries, redisClient); - this.pool = new APIQueryPool(options); - this.records = []; + subscribers: { + [subqueryHash: string]: ( + hash: string, + records: Record[], + logs: SerializableLog[], + apiUnavailable: boolean, + ) => void; + }; + awaitingFollowUp: { + [subqueryHash: string]: { + originalHash: string; + records: Record[]; + logs: SerializableLog[]; + apiUnavailable: boolean; + }; + }; + constructor() { + this.queue = new APIQueryQueue(); + this.pool = new APIQueryPool(); this.currentlyDispatched = 0; - this.maxRecords = parseInt(process.env.MAX_RECORDS_PER_EDGE) || 50000; - this.globalMaxRecords = parseInt(process.env.MAX_RECORDS_TOTAL) || 100000; - this.totalRecords = 0; - this.done = false; - this.logs = []; + this.subscribers = {}; + this.awaitingFollowUp = {}; } - async execute(): Promise<{ records: Record[]; logs: StampedLog[] }> { - const promise: Promise<{ records: Record[]; logs: StampedLog[] }> = - new Promise(resolve => { - this.complete = ({ - records, - logs, - }: { - records: Record[]; - logs: StampedLog[]; - }) => resolve({ records, logs }); - }); - for (let i = 0; i < this.pool.size; i++) { + async execute( + query: Subquery, + options: QueryHandlerOptions, + ): Promise<{ + hash: string; + records: Record[]; + logs: SerializableLog[]; + apiUnavailable: boolean; + }> { + this.queue.add(query, options); + const promise: Promise<{ + hash: string; + records: Record[]; + logs: SerializableLog[]; + apiUnavailable: boolean; + }> = new Promise(resolve => { + this.subscribers[query.hash] = (hash, records, logs, apiUnavailable) => + // Need original hash given by executor, as query hash changes when page-scrolling + resolve({ hash, records, logs, apiUnavailable }); + }); + + if (this.currentlyDispatched < this.pool.size) { await this.queryPool(); } + return promise; } async queryPool(): Promise { - const query = await this.queue.getNext(); - if (!query) return; + const next = await this.queue.getNext(); + if (!next) return; + const { query, options } = next; this.currentlyDispatched += 1; void this.pool.query( query, - this.unavailableAPIs, - async (logs, records, followUp) => { - await this.onQueryComplete(logs, records, followUp); + options, + async ({ logs, records, fromCache, followUp, apiUnavailable }) => { + await this.onQueryComplete( + query.hash, + logs, + options, + records, + fromCache, + apiUnavailable, + followUp, + ); }, ); } - - checkMaxRecords(): boolean { - return ( - (this.maxRecords > 0 && this.totalRecords >= this.maxRecords) || - (this.globalMaxRecords > 0 && - global.queryInformation?.totalRecords > this.globalMaxRecords) - ); - } - - wrapup() { - this.done = true; - this.pool.stop = true; - } - async onQueryComplete( - logs: StampedLog[], + hash: string, + logs: SerializableLog[], + options: QueryHandlerOptions, records?: Record[], - followUp?: Subquery[], + fromCache?: boolean, + apiUnavailable?: boolean, + followUp?: Subquery, ): Promise { - if (this.done) return; - if (logs) this.logs.push(...logs); - if (records) { - this.records.push(...records); + if (!records) { + records = []; + } + this.currentlyDispatched -= 1; + let originalHash = hash; + + // Check if this query is a follow-up to a previous query + // If so, collect the previous for response or new storage + const previous = this.awaitingFollowUp[hash]; + if (previous) { + records.push(...previous.records); + logs.push(...previous.logs); + originalHash = previous.originalHash; + delete this.awaitingFollowUp[hash]; + } - const globalRecords = global.queryInformation?.totalRecords; - if (global.queryInformation) { - global.queryInformation.totalRecords = globalRecords - ? globalRecords + records.length - : records.length; + // If there's a follow-up query, store results for when it's done + if (followUp) { + this.awaitingFollowUp[followUp.hash] = { + originalHash: originalHash, + records, + logs, + apiUnavailable, + }; + this.queue.add(followUp, options); + } + + if (!followUp) { + // Update subscriber and remove it + const callback = this.subscribers[originalHash]; + delete this.subscribers[originalHash]; + + if (!fromCache) { + debug("Start to use id resolver module to annotate output ids."); + records = await this.annotate(records, options.resolveOutputIDs); + debug("id annotation completes"); + } + + callback(originalHash, records, logs, apiUnavailable); + + // Cache for future use + if (!fromCache && (options.caching ?? true) && records.length > 0) { + await this.cacheQuery(originalHash, records); } } - if (followUp) this.queue.add(followUp); - this.currentlyDispatched -= 1; - if ( - this.checkMaxRecords() || - (this.queue.isEmpty && this.currentlyDispatched <= 0) - ) { - if (this.checkMaxRecords()) { - const stoppedOnGlobalMax = - this.globalMaxRecords > 0 && - global.queryInformation?.totalRecords >= this.globalMaxRecords; - let message = [ - `Qedge ${this.qEdgeID}`, - `obtained ${this.records.length} records,`, - this.records.length === this.maxRecords ? "hitting" : "exceeding", - `maximum of ${this.maxRecords}`, - `Truncating records to ${this.maxRecords} and skipping remaining`, - `${this.queue.length + this.currentlyDispatched}`, - `queries for this edge.`, - `Your query may be too general?`, - ]; - if (stoppedOnGlobalMax) { - message = message.slice(0, 2); - message.push( - ...[ - `totalling ${global.queryInformation.totalRecords} for this query.`, - `This exceeds the per-query maximum of ${this.globalMaxRecords}.`, - `For stability purposes, this query is terminated.`, - `Please consider refining your query further.`, - ], - ); - debug(message.join(" ")); - this.logs.push( - new LogEntry("WARNING", null, message.join(" ")).getLog(), - ); - this.complete({ logs: this.logs }); - Telemetry.captureException( - new Error( - `Stopped on globalMaxRecords (exceeded ${this.globalMaxRecords})`, - ), - ); + + if (this.currentlyDispatched < this.pool.size) { + await this.queryPool(); + } + } + + groupCuriesBySemanticType(records: Record[]): CuriesBySemanticType { + const curies: { [semanticType: string]: Set | string[] } = {}; + records.map(record => { + if (record && record.association) { + // INPUTS + const inputType = record.association.input_type; + if (!(inputType in curies)) { + curies[inputType] = new Set(); + } + (curies[inputType] as Set).add(record.subject.original); + // OUTPUTS + const outputType = record.association.output_type; + if (!(outputType in curies)) { + curies[outputType] = new Set(); } + (curies[outputType] as Set).add(record.object.original); } - this.wrapup(); - this.complete({ - records: this.records.slice(0, this.maxRecords), - logs: this.logs, - }); - return; + }); + Object.entries(curies).forEach(([semanticType, curiesOfType]) => { + // remove undefined curies + const goodCuries = [...curiesOfType].filter(id => id !== undefined); + curies[semanticType] = goodCuries; + }); + return curies as CuriesBySemanticType; + } + /** + * Add equivalent ids to all entities using biomedical-id-resolver service + */ + async annotate( + records: Record[], + resolveOutputIDs = true, + ): Promise { + const groupedCuries = this.groupCuriesBySemanticType(records); + let res: SRIResolverOutput | ResolverOutput; + let attributes: unknown; + if (resolveOutputIDs === false) { + res = generateInvalidBioentities(groupedCuries); + } else { + res = await resolveSRI(groupedCuries); + attributes = await getAttributes(groupedCuries); } - await this.queryPool(); + records.map(record => { + if (record && record !== undefined) { + record.object.normalizedInfo = res[ + record.object.original + ] as SRIBioEntity; + record.subject.normalizedInfo = res[ + record.subject.original + ] as SRIBioEntity; + } + // add attributes + if ( + attributes && + record && + Object.hasOwnProperty.call(attributes, record.subject.original) + ) { + if (record instanceof ResolvableBioEntity) { + record.subject.normalizedInfo.attributes = + attributes[record.subject.original]; + } + } + if ( + attributes && + record && + Object.hasOwnProperty.call(attributes, record.object.original) + ) { + if (record instanceof ResolvableBioEntity) { + record.object.normalizedInfo.attributes = + attributes[record.object.original]; + } + } + }); + return records; + } + async cacheQuery(hash: string, records: Record[]): Promise { + debug(`Caching ${records.length} records for subquery ${hash}`); + const recordPack = Record.packRecords(records); + await cacheContent(hash, recordPack); } } diff --git a/packages/call-apis/src/index.old.no b/packages/call-apis/src/index.old.no new file mode 100644 index 0000000..d521d16 --- /dev/null +++ b/packages/call-apis/src/index.old.no @@ -0,0 +1,185 @@ +import { LogEntry, StampedLog, RedisClient } from "@retriever/utils"; +import { APIEdge, QueryHandlerOptions, UnavailableAPITracker } from "./types"; +import SubqueryDispatcher from "./dispatcher"; +import Debug from "debug"; +const debug = Debug("retriever:call-apis:query"); +import { + NodeNormalizerResultObj, + Record, +} from "@retriever/api-response-transform"; +import { + ResolverOutput, + SRIResolverOutput, + generateInvalidBioentities, + getAttributes, + resolveSRI, + ResolvableBioEntity, +} from "biomedical_id_resolver"; +import TrapiSubquery from "./queries/trapi_subquery"; +import subqueryFactory from "./queries/subquery_factory"; + +export * from "./types"; + +export interface CuriesBySemanticType { + [semanticType: string]: string[]; +} + +export default class APIQueryDispatcher { + APIEdges: APIEdge[]; + logs: StampedLog[]; + options: QueryHandlerOptions; + redisClient: RedisClient; + constructor( + APIEdges: APIEdge[], + options: QueryHandlerOptions = {}, + redisClient?: RedisClient, + ) { + this.APIEdges = APIEdges; + this.logs = []; + this.options = options; + this.redisClient = redisClient; + } + + _constructQueries(APIEdges: APIEdge[]) { + return APIEdges.map(edge => { + const subQuery = subqueryFactory(edge); + if (subQuery instanceof TrapiSubquery) { + subQuery.addSubmitter?.(this.options.submitter); + } + return subQuery; + }); + } + + _groupCuriesBySemanticType(records: Record[]): CuriesBySemanticType { + const curies: { [semanticType: string]: Set | string[] } = {}; + records.map(record => { + if (record && record.association) { + // INPUTS + const inputType = record.association.input_type; + if (!(inputType in curies)) { + curies[inputType] = new Set(); + } + (curies[inputType] as Set).add(record.subject.original); + // OUTPUTS + const outputType = record.association.output_type; + if (!(outputType in curies)) { + curies[outputType] = new Set(); + } + (curies[outputType] as Set).add(record.object.original); + } + }); + Object.entries(curies).forEach(([semanticType, curiesOfType]) => { + // remove undefined curies + const goodCuries = [...curiesOfType].filter(id => id !== undefined); + curies[semanticType] = goodCuries; + }); + return curies as CuriesBySemanticType; + } + /** + * Add equivalent ids to all entities using biomedical-id-resolver service + */ + async _annotate( + records: Record[], + resolveOutputIDs = true, + ): Promise { + const groupedCuries = this._groupCuriesBySemanticType(records); + let res: SRIResolverOutput | ResolverOutput; + let attributes: unknown; + if (resolveOutputIDs === false) { + res = generateInvalidBioentities(groupedCuries); + } else { + res = await resolveSRI(groupedCuries); + attributes = await getAttributes(groupedCuries); + } + records.map(record => { + if (record && record !== undefined) { + record.object.normalizedInfo = res[ + record.object.original + ] as NodeNormalizerResultObj; + record.subject.normalizedInfo = res[ + record.subject.original + ] as NodeNormalizerResultObj; + } + // add attributes + if ( + attributes && + record && + Object.hasOwnProperty.call(attributes, record.subject.original) + ) { + if (record instanceof ResolvableBioEntity) { + record.subject.normalizedInfo.attributes = + attributes[record.subject.original]; + } + } + if ( + attributes && + record && + Object.hasOwnProperty.call(attributes, record.object.original) + ) { + if (record instanceof ResolvableBioEntity) { + record.object.normalizedInfo.attributes = + attributes[record.object.original]; + } + } + }); + return records; + } + + async query( + resolveOutputIDs = true, + unavailableAPIs: UnavailableAPITracker = {}, + ): Promise { + // Used for temporarily storing a message to log via both debug and TRAPI logs + let message: string; + message = `Resolving ID feature is turned ${resolveOutputIDs ? "on" : "off" + }`; + debug(message); + this.logs.push(new LogEntry("DEBUG", null, message).getLog()); + message = [ + `call-apis: ${this.APIEdges.length}`, + `planned queries for edge`, + `${this.APIEdges[0].reasoner_edge?.id}`, + ].join(" "); + debug(message); + this.logs.push(new LogEntry("DEBUG", null, message).getLog()); + const queries = this._constructQueries(this.APIEdges); + const startTime = performance.now(); + const subQueryDispatcher = new SubqueryDispatcher( + queries, + this.redisClient, + unavailableAPIs, + this.options, + ); + const { records, logs } = await subQueryDispatcher.execute(); + this.logs.push(...logs); + // Occurs when globalMaxRecords hit, requiring query termination + if (!records) return undefined; + + const finishTime = performance.now(); + const timeElapsed = Math.round( + finishTime - startTime > 1000 + ? (finishTime - startTime) / 1000 + : finishTime - startTime, + ); + const timeUnits = finishTime - startTime > 1000 ? "s" : "ms"; + + debug("query completes."); + message = `Total number of records returned for this qEdge is ${records.length}`; + debug(message); + this.logs.push(new LogEntry("DEBUG", null, message).getLog()); + + debug("Start to use id resolver module to annotate output ids."); + const annotatedRecords = await this._annotate(records, resolveOutputIDs); + debug("id annotation completes"); + debug(`qEdge queries complete in ${timeElapsed}${timeUnits}`); + this.logs.push( + new LogEntry( + "DEBUG", + null, + `call-apis: qEdge queries complete in ${timeElapsed}${timeUnits}`, + ).getLog(), + ); + + return annotatedRecords; // TODO: additional stuff like annotation + } +} diff --git a/packages/call-apis/src/index.ts b/packages/call-apis/src/index.ts index 6ea1cb4..94314e7 100644 --- a/packages/call-apis/src/index.ts +++ b/packages/call-apis/src/index.ts @@ -1,185 +1,90 @@ -import { LogEntry, StampedLog, RedisClient } from "@biothings-explorer/utils"; -import { APIEdge, QueryHandlerOptions, UnavailableAPITracker } from "./types"; +import { Record, RecordPackage } from "@retriever/graph"; +import { SerializableLog } from "@retriever/utils"; +import { QueryHandlerOptions } from "@retriever/types"; +import Subquery from "./queries/subquery"; +import subqueryFactory from "./queries/subquery_factory"; +import { APIEdge } from "@retriever/graph"; import SubqueryDispatcher from "./dispatcher"; import Debug from "debug"; -const debug = Debug("bte:call-apis:query"); -import { - NodeNormalizerResultObj, - Record, -} from "@biothings-explorer/api-response-transform"; -import { - ResolverOutput, - SRIResolverOutput, - generateInvalidBioentities, - getAttributes, - resolveSRI, - ResolvableBioEntity, -} from "biomedical_id_resolver"; -import TrapiSubquery from "./queries/trapi_subquery"; -import subqueryFactory from "./queries/subquery_factory"; +import async from "async"; +const debug = Debug("retriever:call-apis:relay"); + +const subqueryDispatcher = new SubqueryDispatcher(); -export * from "./types"; +export { default as Subquery } from "./queries/subquery"; -export interface CuriesBySemanticType { - [semanticType: string]: string[]; +export interface SubqueryResults { + hash: string; + records: RecordPackage; + logs: SerializableLog[]; + apiUnavailable: boolean; } -export default class APIQueryDispatcher { - APIEdges: APIEdge[]; - logs: StampedLog[]; - options: QueryHandlerOptions; - redisClient: RedisClient; - constructor( - APIEdges: APIEdge[], - options: QueryHandlerOptions = {}, - redisClient?: RedisClient, - ) { - this.APIEdges = APIEdges; - this.logs = []; - this.options = options; - this.redisClient = redisClient; - } +export interface SubqueryCallback { + (results: SubqueryResults): void; +} - _constructQueries(APIEdges: APIEdge[]) { - return APIEdges.map(edge => { - const subQuery = subqueryFactory(edge); - if (subQuery instanceof TrapiSubquery) { - subQuery.addSubmitter?.(this.options.submitter); - } - return subQuery; - }); +export default class SubqueryRelay { + subscriberMap: { + [subqueryHash: string]: SubqueryCallback[]; + }; + constructor() { + this.subscriberMap = {}; } - _groupCuriesBySemanticType(records: Record[]): CuriesBySemanticType { - const curies: { [semanticType: string]: Set | string[] } = {}; - records.map(record => { - if (record && record.association) { - // INPUTS - const inputType = record.association.input_type; - if (!(inputType in curies)) { - curies[inputType] = new Set(); - } - (curies[inputType] as Set).add(record.subject.original); - // OUTPUTS - const outputType = record.association.output_type; - if (!(outputType in curies)) { - curies[outputType] = new Set(); - } - (curies[outputType] as Set).add(record.object.original); - } - }); - Object.entries(curies).forEach(([semanticType, curiesOfType]) => { - // remove undefined curies - const goodCuries = [...curiesOfType].filter(id => id !== undefined); - curies[semanticType] = goodCuries; - }); - return curies as CuriesBySemanticType; - } - /** - * Add equivalent ids to all entities using biomedical-id-resolver service - */ - async _annotate( - records: Record[], - resolveOutputIDs = true, - ): Promise { - const groupedCuries = this._groupCuriesBySemanticType(records); - let res: SRIResolverOutput | ResolverOutput; - let attributes: unknown; - if (resolveOutputIDs === false) { - res = generateInvalidBioentities(groupedCuries); - } else { - res = await resolveSRI(groupedCuries); - attributes = await getAttributes(groupedCuries); - } - records.map(record => { - if (record && record !== undefined) { - record.object.normalizedInfo = res[ - record.object.original - ] as NodeNormalizerResultObj; - record.subject.normalizedInfo = res[ - record.subject.original - ] as NodeNormalizerResultObj; - } - // add attributes - if ( - attributes && - record && - Object.hasOwnProperty.call(attributes, record.subject.original) - ) { - if (record instanceof ResolvableBioEntity) { - record.subject.normalizedInfo.attributes = - attributes[record.subject.original]; - } + async subscribe( + queries: Subquery[], + options: QueryHandlerOptions, + callback: SubqueryCallback, + ) { + debug(`Subquery relay received ${queries.length} subqueries.`); + // Add all subqueries simultaneously + await async.each(queries, async query => { + const qHash = query.hash; // Avoid calculating hash repeatedly + let newHash = false; + if (!this.subscriberMap[qHash]) { + this.subscriberMap[qHash] = []; + newHash = true; } - if ( - attributes && - record && - Object.hasOwnProperty.call(attributes, record.object.original) - ) { - if (record instanceof ResolvableBioEntity) { - record.object.normalizedInfo.attributes = - attributes[record.object.original]; - } + this.subscriberMap[qHash].push(callback); + if (!newHash) { + debug( + `Subquery ${qHash} already in queue, subscribing (${Object.keys(this.subscriberMap[qHash]).length} subscribed)`, + ); + // waiting for another execution + return; } - }); - return records; - } - async query( - resolveOutputIDs = true, - unavailableAPIs: UnavailableAPITracker = {}, - ): Promise { - // Used for temporarily storing a message to log via both debug and TRAPI logs - let message: string; - message = `Resolving ID feature is turned ${resolveOutputIDs ? "on" : "off" - }`; - debug(message); - this.logs.push(new LogEntry("DEBUG", null, message).getLog()); - message = [ - `call-apis: ${this.APIEdges.length}`, - `planned queries for edge`, - `${this.APIEdges[0].reasoner_edge?.id}`, - ].join(" "); - debug(message); - this.logs.push(new LogEntry("DEBUG", null, message).getLog()); - const queries = this._constructQueries(this.APIEdges); - const startTime = performance.now(); - const subQueryDispatcher = new SubqueryDispatcher( - queries, - this.redisClient, - unavailableAPIs, - this.options, - ); - const { records, logs } = await subQueryDispatcher.execute(); - this.logs.push(...logs); - // Occurs when globalMaxRecords hit, requiring query termination - if (!records) return undefined; + debug(`New subquery ${qHash} added to queue.`); - const finishTime = performance.now(); - const timeElapsed = Math.round( - finishTime - startTime > 1000 - ? (finishTime - startTime) / 1000 - : finishTime - startTime, - ); - const timeUnits = finishTime - startTime > 1000 ? "s" : "ms"; + const { hash, records, logs, apiUnavailable } = + await subqueryDispatcher.execute(query, options); - debug("query completes."); - message = `Total number of records returned for this qEdge is ${records.length}`; - debug(message); - this.logs.push(new LogEntry("DEBUG", null, message).getLog()); + debug( + `Subquery ${qHash} completes, returning records to ${Object.keys(this.subscriberMap[qHash]).length} subscribers`, + ); - debug("Start to use id resolver module to annotate output ids."); - const annotatedRecords = await this._annotate(records, resolveOutputIDs); - debug("id annotation completes"); - debug(`qEdge queries complete in ${timeElapsed}${timeUnits}`); - this.logs.push( - new LogEntry( - "DEBUG", - null, - `call-apis: qEdge queries complete in ${timeElapsed}${timeUnits}`, - ).getLog(), - ); + const packedRecords = Record.packRecords(records); - return annotatedRecords; // TODO: additional stuff like annotation + for (const subscribedCallback of this.subscriberMap[qHash]) { + subscribedCallback({ + hash, + records: packedRecords, + logs, + apiUnavailable, + }); + } + delete this.subscriberMap[qHash]; + }); } } + +export function constructQueries( + APIEdges: APIEdge[], + options: QueryHandlerOptions, +) { + return APIEdges.map(edge => { + const subQuery = subqueryFactory(edge, options); + return subQuery; + }); +} diff --git a/packages/call-apis/src/queries/subquery.ts b/packages/call-apis/src/queries/subquery.ts index 668fcba..5cedaf0 100644 --- a/packages/call-apis/src/queries/subquery.ts +++ b/packages/call-apis/src/queries/subquery.ts @@ -1,17 +1,36 @@ import { AxiosRequestConfig, Method } from "axios"; import stringify from "json-stable-stringify"; import crypto from "crypto"; +import { QueryParams, BiothingsResponse } from "../types"; import { - QueryParams, APIEdge, BatchAPIEdge, NonBatchAPIEdge, - BiothingsResponse, + QEdge, + QEdgeInfo, TemplatedInput, -} from "../types"; +} from "@retriever/graph"; +import { APIDefinition, QueryHandlerOptions } from "@retriever/types"; + +const SUBQUERY_DEFAULT_TIMEOUT = parseInt( + process.env.SUBQUERY_DEFAULT_TIMEOUT ?? "50000", +); + +export interface FrozenAPIEdge extends Omit { + reasoner_edge: QEdgeInfo; +} + +export interface FrozenSubquery { + type: string; + start: number; + hasNext: boolean; + delayUntil: Date; + APIEdge: FrozenAPIEdge; + options: QueryHandlerOptions; +} /** - * Build API queries serving as input for Axios library based on BTE Edge info + * Build API queries serving as input for Axios library based on Retriever Edge info */ export default class Subquery { start: number; @@ -19,14 +38,16 @@ export default class Subquery { APIEdge: APIEdge; delayUntil: Date; config: AxiosRequestConfig; + options: QueryHandlerOptions; /** * Constructor for Query Builder - * @param {object} APIEdge - BTE Edge object with input field provided + * @param {object} APIEdge - Retriever Edge object with input field provided */ - constructor(APIEdge: APIEdge) { + constructor(APIEdge: APIEdge, options: QueryHandlerOptions) { this.start = 0; this.hasNext = false; this.APIEdge = APIEdge; + this.options = options; } get url(): string { @@ -56,8 +77,8 @@ export default class Subquery { const params: QueryParams = {}; Object.keys(this.APIEdge.query_operation.params).map(param => { if ( - Array.isArray(this.APIEdge.query_operation.path_params) && - this.APIEdge.query_operation.path_params.includes(param) + Array.isArray(this.APIEdge.query_operation.pathParams) && + this.APIEdge.query_operation.pathParams.includes(param) ) { return; } @@ -77,10 +98,10 @@ export default class Subquery { */ get requestBody(): unknown { if ( - this.APIEdge.query_operation.request_body !== undefined && - "body" in this.APIEdge.query_operation.request_body + this.APIEdge.query_operation.requestBody !== undefined && + "body" in this.APIEdge.query_operation.requestBody ) { - const body = this.APIEdge.query_operation.request_body.body; + const body = this.APIEdge.query_operation.requestBody.body; const data = Object.keys(body).reduce( (accumulator, key) => accumulator + @@ -101,6 +122,15 @@ export default class Subquery { .digest("hex"); } + get timeout(): number { + const apiID = this.APIEdge.association.smartapi.id; + const timeout = + this.options.apiList?.include.find( + (api: APIDefinition) => api.id === apiID, + )?.timeout ?? SUBQUERY_DEFAULT_TIMEOUT; + return timeout; + } + /** * Construct the request config for Axios reqeust. */ @@ -110,6 +140,7 @@ export default class Subquery { params: this.params, data: this.requestBody, method: this.APIEdge.query_operation.method as Method, + timeout: this.timeout, }; this.config = config; return config; @@ -152,4 +183,37 @@ export default class Subquery { } return this.constructAxiosRequestConfig(); } + + freeze(): FrozenSubquery { + return { + type: "base", + start: this.start, + hasNext: this.hasNext, + delayUntil: this.delayUntil, + options: this.options, + APIEdge: { + ...this.APIEdge, + reasoner_edge: this.APIEdge.reasoner_edge.freeze(), + }, + }; + } + + static async unfreeze(frozenSubquery: FrozenSubquery): Promise { + const { default: template } = await import("./template_subquery"); + const { default: trapi } = await import("./trapi_subquery"); + const mapping = { + base: Subquery, + template, + trapi, + }; + const apiEdge: APIEdge = { + ...frozenSubquery.APIEdge, + reasoner_edge: new QEdge(frozenSubquery.APIEdge.reasoner_edge), + }; + const subquery = new mapping[frozenSubquery.type](apiEdge, frozenSubquery.options); + subquery.start = frozenSubquery.start; + subquery.hasNext = frozenSubquery.hasNext; + subquery.delayUntil = frozenSubquery.delayUntil; + return subquery; + } } diff --git a/packages/call-apis/src/queries/subquery_factory.ts b/packages/call-apis/src/queries/subquery_factory.ts index 6e4d8b7..427d69d 100644 --- a/packages/call-apis/src/queries/subquery_factory.ts +++ b/packages/call-apis/src/queries/subquery_factory.ts @@ -1,22 +1,24 @@ import Debug from "debug"; -const debug = Debug("bte:call-apis:query"); -import type { APIEdge } from "../types"; +const debug = Debug("retriever:call-apis:query"); import TrapiSubquery from "./trapi_subquery"; import TemplateSubquery from "./template_subquery"; import Subquery from "./subquery"; +import { APIEdge } from "@retriever/graph"; +import { QueryHandlerOptions } from "@retriever/types"; function subqueryFactory( APIEdge: APIEdge, + options: QueryHandlerOptions, ): Subquery { if ("tags" in APIEdge && APIEdge.tags.includes("bte-trapi")) { debug(`using trapi builder now`); - return new TrapiSubquery(APIEdge); + return new TrapiSubquery(APIEdge, options); } else if (APIEdge.query_operation.useTemplating) { debug("using template builder"); - return new TemplateSubquery(APIEdge); + return new TemplateSubquery(APIEdge, options); } debug("using default builder"); - return new Subquery(APIEdge); + return new Subquery(APIEdge, options); } export default subqueryFactory; diff --git a/packages/call-apis/src/queries/template_subquery.ts b/packages/call-apis/src/queries/template_subquery.ts index 7dfaa6b..3c3d856 100644 --- a/packages/call-apis/src/queries/template_subquery.ts +++ b/packages/call-apis/src/queries/template_subquery.ts @@ -1,11 +1,12 @@ /** - * Build API queries serving as input for Axios library based on BTE Edge info + * Build API queries serving as input for Axios library based on Retriever Edge info */ import nunjucks from "nunjucks"; import nunjucksConfig from "./nunjucks_config"; -import { BiothingsResponse, QueryParams, TemplatedInput } from "../types"; +import { BiothingsResponse, QueryParams } from "../types"; +import { TemplatedInput } from "@retriever/graph"; import { AxiosRequestConfig } from "axios"; -import Subquery from "./subquery"; +import Subquery, { FrozenSubquery } from "./subquery"; const env = nunjucks.configure({ autoescape: false }); nunjucksConfig(env); @@ -16,8 +17,8 @@ export default class TemplateSubquery extends Subquery { server = server.substring(0, server.length - 1); } let path = this.APIEdge.query_operation.path; - if (Array.isArray(this.APIEdge.query_operation.path_params)) { - this.APIEdge.query_operation.path_params.map(param => { + if (Array.isArray(this.APIEdge.query_operation.pathParams)) { + this.APIEdge.query_operation.pathParams.map(param => { const val = String(this.APIEdge.query_operation.params[param]); path = nunjucks.renderString( path.replace("{" + param + "}", val), @@ -48,8 +49,8 @@ export default class TemplateSubquery extends Subquery { } Object.keys(this.APIEdge.query_operation.params).map(param => { if ( - Array.isArray(this.APIEdge.query_operation.path_params) && - this.APIEdge.query_operation.path_params.includes(param) + Array.isArray(this.APIEdge.query_operation.pathParams) && + this.APIEdge.query_operation.pathParams.includes(param) ) { return; } @@ -70,20 +71,25 @@ export default class TemplateSubquery extends Subquery { */ get requestBody(): unknown { if ( - this.APIEdge.query_operation.request_body !== undefined && - "body" in this.APIEdge.query_operation.request_body + this.APIEdge.query_operation.requestBody !== undefined && + "body" in this.APIEdge.query_operation.requestBody ) { - const body = this.APIEdge.query_operation.request_body.body; + const body = this.APIEdge.query_operation.requestBody.body; let data: unknown; if (this.APIEdge.query_operation.requestBodyType === "object") { - data = JSON.parse(nunjucks.renderString(body, this.input as TemplatedInput)); + data = JSON.parse( + nunjucks.renderString(body, this.input as TemplatedInput), + ); } else { data = Object.keys(body).reduce((accumulator, key) => { return ( accumulator + key + "=" + - nunjucks.renderString(body[key].toString(), this.input as TemplatedInput) + + nunjucks.renderString( + body[key].toString(), + this.input as TemplatedInput, + ) + "&" ); }, ""); @@ -142,4 +148,15 @@ export default class TemplateSubquery extends Subquery { this.config = config; return config; } + + freeze(): FrozenSubquery { + return { + type: "template", + start: this.start, + hasNext: this.hasNext, + delayUntil: this.delayUntil, + APIEdge: this.APIEdge, + options: this.options, + }; + } } diff --git a/packages/call-apis/src/queries/trapi_subquery.ts b/packages/call-apis/src/queries/trapi_subquery.ts index 3c82e28..06510cc 100644 --- a/packages/call-apis/src/queries/trapi_subquery.ts +++ b/packages/call-apis/src/queries/trapi_subquery.ts @@ -1,10 +1,10 @@ -import type { APIEdge, TrapiResponse } from "../types"; +import { APIEdge } from "@retriever/graph"; import { AxiosRequestConfig, Method } from "axios"; -import { TrapiRequest } from "../types"; -import Subquery from "./subquery"; +import Subquery, { FrozenSubquery } from "./subquery"; +import { TrapiQuery, TrapiResponse } from "packages/types/src"; /** - * Build API queries serving as input for Axios library based on BTE Edge info + * Build API queries serving as input for Axios library based on Retriever Edge info */ export default class TrapiSubquery extends Subquery { start: number; @@ -18,8 +18,8 @@ export default class TrapiSubquery extends Subquery { server = server.substring(0, server.length - 1); } let path = this.APIEdge.query_operation.path; - if (Array.isArray(this.APIEdge.query_operation.path_params)) { - this.APIEdge.query_operation.path_params.map(param => { + if (Array.isArray(this.APIEdge.query_operation.pathParams)) { + this.APIEdge.query_operation.pathParams.map(param => { const val = String(this.APIEdge.query_operation.params[param]); path = path .replace("{" + param + "}", val) @@ -35,15 +35,12 @@ export default class TrapiSubquery extends Subquery { return (this.APIEdge.input as string[]).sort(); } - addSubmitter(submitter: string): void { - this.originalSubmitter = submitter; - } /** * Construct TRAPI request body */ - get requestBody(): TrapiRequest { - const queryGraph: TrapiRequest = { + get requestBody(): TrapiQuery { + const queryBody: TrapiQuery = { message: { query_graph: { nodes: { @@ -64,12 +61,12 @@ export default class TrapiSubquery extends Subquery { }, }, }, - submitter: "infores:bte", + submitter: "infores:retriever", }; const qualifierConstraints = this.APIEdge.reasoner_edge?.getQualifierConstraints?.(); if (qualifierConstraints) { - queryGraph.message.query_graph.edges.e01.qualifier_constraints = + queryBody.message.query_graph.edges.e01.qualifier_constraints = qualifierConstraints; } const xmaturityMap = { @@ -79,10 +76,10 @@ export default class TrapiSubquery extends Subquery { dev: "dev", }; if (process.env.INSTANCE_ENV) - queryGraph.submitter += `; bte-${xmaturityMap[process.env.INSTANCE_ENV]}`; - if (this.originalSubmitter) - queryGraph.submitter += `; subquery for client "${this.originalSubmitter}"`; - return queryGraph; + queryBody.submitter += `; retriever-${xmaturityMap[process.env.INSTANCE_ENV]}`; + if (this.options.submitter) + queryBody.submitter += `; subquery for client "${this.options.submitter}"`; + return queryBody; } /** @@ -96,12 +93,13 @@ export default class TrapiSubquery extends Subquery { headers: { "Content-Type": "application/json", }, + timeout: this.timeout, }; this.config = config; return config; } - needPagination(_apiResponse: TrapiResponse): number { + needsPagination(_apiResponse: TrapiResponse): number { this.hasNext = false; return 0; } @@ -110,4 +108,15 @@ export default class TrapiSubquery extends Subquery { const config = this.constructAxiosRequestConfig(); return config; } + + freeze(): FrozenSubquery { + return { + type: "trapi", + start: this.start, + hasNext: this.hasNext, + delayUntil: this.delayUntil, + APIEdge: this.APIEdge, + options: this.options, + }; + } } diff --git a/packages/call-apis/src/query_pool.ts b/packages/call-apis/src/query_pool.ts index f89010f..2e7d123 100644 --- a/packages/call-apis/src/query_pool.ts +++ b/packages/call-apis/src/query_pool.ts @@ -1,26 +1,33 @@ -import Transformer, { - BTEQueryObject, - Record, -} from "@biothings-explorer/api-response-transform"; -import { - APIDefinition, - QueryHandlerOptions, - UnavailableAPITracker, -} from "./types"; +import Transformer, { RetrieverQueryObject } from "@retriever/api-response-transform"; +import { QEdge, Record, RecordPackage } from "@retriever/graph"; import os from "os"; import axios, { AxiosRequestConfig, AxiosResponse } from "axios"; import Debug from "debug"; -const debug = Debug("bte:call-apis:query"); -import { Telemetry, LogEntry, StampedLog } from "@biothings-explorer/utils"; +const debug = Debug("retriever:call-apis:query-pool"); +import { + Telemetry, + LogEntry, + SerializableLog, + TrapiLog, +} from "@retriever/utils"; import axiosRetry from "axios-retry"; import Subquery from "./queries/subquery"; +import _ from "lodash"; +import { + APIDefinition, + QueryHandlerOptions, + UnavailableAPITracker, +} from "@retriever/types"; +import { cacheLookup } from "@retriever/utils"; const SUBQUERY_DEFAULT_TIMEOUT = parseInt( process.env.SUBQUERY_DEFAULT_TIMEOUT ?? "50000", ); +/* Information about a given query, mostly for logging */ export interface QueryInfo { qEdgeID: string; + hash: string; url: string; api_name: string; subject: string; @@ -29,34 +36,33 @@ export interface QueryInfo { ids: number; } +/* Headers, like you'd expect, instead of Axios's Any */ export interface headers { - [header: string]: string; + [name: string]: string; } export default class APIQueryPool { size: number; usage: number; - options: QueryHandlerOptions; stop: boolean; - constructor(options: QueryHandlerOptions) { - this.stop = false; - this.options = options; - this.size = os.cpus().length * 2; + unavailableAPIs: UnavailableAPITracker; + constructor() { + this.size = os.cpus().length * 8; this.usage = 0; + this.unavailableAPIs = {}; } - _getTimeout(apiID: string): number { + _getTimeout(apiID: string, options: QueryHandlerOptions): number { const timeout = - this.options.apiList?.include.find( - (api: APIDefinition) => api.id === apiID, - )?.timeout ?? SUBQUERY_DEFAULT_TIMEOUT; + options.apiList?.include.find((api: APIDefinition) => api.id === apiID) + ?.timeout ?? SUBQUERY_DEFAULT_TIMEOUT; return timeout; } getQueryConfig( query: Subquery, - unavailableAPIs: UnavailableAPITracker, - logs: StampedLog[], + options: QueryHandlerOptions, + logs: TrapiLog[], ): { queryConfig: AxiosRequestConfig; nInputs: number; @@ -69,13 +75,6 @@ export default class APIQueryPool { edgeOperation: string; try { queryConfig = query.getConfig(); - // Skip if query API has been marked unavailable - if (unavailableAPIs[query.APIEdge.query_operation.server]?.skip) { - unavailableAPIs[ - query.APIEdge.query_operation.server - ].skippedQueries += 1; - return undefined; - } if (Array.isArray(query.APIEdge.input)) { nInputs = query.APIEdge.input.length; // TemplatedInput @@ -90,6 +89,7 @@ export default class APIQueryPool { // Put together additional shorthands queryInfo = { qEdgeID: query.APIEdge.reasoner_edge?.id, + hash: query.hash, url: queryConfig.url, api_name: query.APIEdge.association.api_name, subject: query.APIEdge.association.input_type, @@ -104,6 +104,7 @@ export default class APIQueryPool { ].join(" > "); queryConfig.timeout = this._getTimeout( query.APIEdge.association.smartapi.id, + options, ); return { @@ -123,7 +124,7 @@ export default class APIQueryPool { ).toString()} while configuring query. Query dump: ${JSON.stringify( query, )}`, - ).getLog(), + ).getSerializeable(), ); return undefined; } @@ -131,45 +132,101 @@ export default class APIQueryPool { async query( query: Subquery, - unavailableAPIs: UnavailableAPITracker, - finish: ( - logs?: StampedLog[], - records?: Record[], - followUp?: Subquery[], - ) => Promise, + options: QueryHandlerOptions, + finish: ({ + logs, + records, + fromCache, + followUp, + apiUnavailable, + }: { + logs?: SerializableLog[]; + records?: Record[]; + fromCache?: boolean; + followUp?: Subquery; + apiUnavailable?: boolean; + }) => Promise, ) { - // Check if pool has been stopped due to limit hit (save some computation) - if (this.stop) { - await finish(); - return; - } - const logs: StampedLog[] = []; - const followUp: Subquery[] = []; + const hash = query.hash; + const logs: SerializableLog[] = []; + let followUp: Subquery; + let apiUnavailable: boolean; const dryrun_only = process.env.DRYRUN === "true"; const span = Telemetry.startSpan({ description: "apiCall" }); span?.setData("apiName", query.APIEdge.association.api_name); - const queryConfigAttempt = this.getQueryConfig( - query, - unavailableAPIs, - logs, - ); + const queryConfigAttempt = this.getQueryConfig(query, options, logs); if (!queryConfigAttempt) { span?.finish(); - await finish(logs); + await finish({ + logs, + }); return; } const { queryConfig, nInputs, queryInfo, edgeOperation } = queryConfigAttempt; - debug(queryConfig); + // Skip if query API has been marked unavailable + if (this.unavailableAPIs[query.APIEdge.query_operation.server]?.skip) { + this.unavailableAPIs[ + query.APIEdge.query_operation.server + ].skippedQueries += 1; + apiUnavailable = true; + const message = [ + `Subquery ${query.APIEdge.query_operation.server}`, + `(${nInputs} ID${nInputs > 1 ? "s" : ""}):`, + `skipped as it has been temporarily marked unavailable.`, + ].join(" "); + debug(message); + logs.push( + new LogEntry("WARNING", null, message, { + type: "query", + error: true, + ...queryInfo + }).getSerializeable(), + ); + await finish({ logs, apiUnavailable }); + return; + } + + if (options.caching ?? true) { + const records = await this.cacheLookup(hash, query.APIEdge.reasoner_edge); + if (records) { + span?.setData("queryBody", queryConfig.data); + const log_msg = [ + `Successful cache retrieval for subquery`, + query.APIEdge.query_operation.server, + `(${nInputs} ID${nInputs > 1 ? "s" : ""}):`, + `${edgeOperation} (retrieved ${records.length}`, + `record${records.length === 1 ? "" : "s"}).`, + ].join(" "); + debug(log_msg); + logs.push( + new LogEntry("DEBUG", null, log_msg, { + type: "cacheHit", + hits: records.length, + ...queryInfo, + }).getSerializeable(), + ); + + span?.finish(); + await finish({ + records, + logs, + fromCache: true, + }); + return; + } + } + + debug(JSON.stringify({ hash, ...queryConfig })); try { const userAgent = [ - `BTE/${process.env.NODE_ENV === "production" ? "prod" : "dev"}`, + `Retriever/${process.env.NODE_ENV === "production" ? "prod" : "dev"}`, `Node/${process.version}`, `${process.platform}`, ].join(" "); @@ -193,24 +250,12 @@ export default class APIQueryPool { }, }); - // Check if pool has been stopped due to limit hit (save some computation) - if (this.stop) { - await finish(); - return; - } - const queryResponse = dryrun_only ? { data: [] } : await axios(queryConfig); - // Check if pool has been stopped due to limit hit (save some computation) - if (this.stop) { - await finish(); - return; - } - const finishTime = performance.now(); - debug("query success, transforming hits->records..."); + debug("Subquery success, transforming hits->records..."); const timeElapsed = Math.round( finishTime - startTime > 1000 ? (finishTime - startTime) / 1000 @@ -227,29 +272,24 @@ export default class APIQueryPool { unTransformedHits.response, ); if (queryNeedsPagination) { - const log = `Query requires pagination, will re-query to window ${queryNeedsPagination}-${ - queryNeedsPagination + 1000 - }: ${query.APIEdge.query_operation.server} (${nInputs} ID${ - nInputs > 1 ? "s" : "" - })`; + const log = `Subquery requires pagination, will re-query to window ${queryNeedsPagination}-${queryNeedsPagination + 1000 + }: ${query.APIEdge.query_operation.server} (${nInputs} ID${nInputs > 1 ? "s" : "" + })`; debug(log); if (queryNeedsPagination >= 9000) { - const log = `Biothings query reaches 10,000 max: ${ - query.APIEdge.query_operation.server - } (${nInputs} ID${nInputs > 1 ? "s" : ""})`; + const log = `Biothings subquery reaches 10,000 max: ${query.APIEdge.query_operation.server + } (${nInputs} ID${nInputs > 1 ? "s" : ""})`; debug(log); - logs.push(new LogEntry("WARNING", null, log).getLog()); + logs.push(new LogEntry("WARNING", null, log).getSerializeable()); } - followUp.push(query); + followUp = query; } const transformSpan = Telemetry.startSpan({ description: "transformRecords", }); - // have to go through unknown for now to avoid conversion warnings - // TODO eventually fix this when we pull out more types const transformer = new Transformer( - unTransformedHits as unknown as BTEQueryObject, - this.options, + unTransformedHits as RetrieverQueryObject, + options, ); const transformedRecords = (await transformer.transform()).filter( record => { @@ -258,12 +298,12 @@ export default class APIQueryPool { ); transformSpan.finish(); - if (global.queryInformation?.queryGraph) { - const globalRecords = global.queryInformation.totalRecords; - global.queryInformation.totalRecords = globalRecords - ? globalRecords + transformedRecords.length - : transformedRecords.length; - } + // if (global.queryInformation?.queryGraph) { + // const globalRecords = global.queryInformation.totalRecords; + // global.queryInformation.totalRecords = globalRecords + // ? globalRecords + transformedRecords.length + // : transformedRecords.length; + // } const log_msg = [ `Successful ${queryConfig.method.toUpperCase()}`, query.APIEdge.query_operation.server, @@ -279,32 +319,40 @@ export default class APIQueryPool { type: "query", hits: transformedRecords.length, ...queryInfo, - }).getLog(), + }).getSerializeable(), ); // end span span?.finish(); - await finish(logs, transformedRecords, followUp); + await finish({ + logs, + records: transformedRecords, + followUp, + }); } catch (error) { - // TODO add method for followup to explicitely have a delay? if ( axios.isAxiosError(error) && (error.response?.status >= 502 || error.code === "ECONNABORTED") ) { + // Assume API is unavailable, stop trying to reach it for 30 seconds const errorMessage = [ `${query.APIEdge.query_operation.server}`, `appears to be unavailable. Queries to it will be skipped.`, ].join(" "); debug(errorMessage); - unavailableAPIs[query.APIEdge.query_operation.server] = { + this.unavailableAPIs[query.APIEdge.query_operation.server] = { skip: true, skippedQueries: 0, }; + apiUnavailable = true; + setTimeout(() => { + delete this.unavailableAPIs[query.APIEdge.query_operation.server]; + }, 30000); } else if (axios.isAxiosError(error) && error.response?.status === 429) { debug( [ `${query.APIEdge.query_operation.server}`, - `has rate-limited BTE.`, + `has rate-limited Retriever.`, `Queries to it will be skipped until the provided time.`, ].join(" "), ); @@ -315,12 +363,12 @@ export default class APIQueryPool { : new Date(Date.now() + parseInt(retryAfter) * 1000) : new Date(Date.now() + 10000); // default wait for 10 seconds - followUp.push(query); + followUp = query; } debug( [ - `Failed to make to following query:`, + `Failed to make to following subquery:`, `${JSON.stringify(query.config)}.`, `The error is ${(error as Error).toString()}`, `with ${(error as Error).stack}`, @@ -331,7 +379,7 @@ export default class APIQueryPool { "ERROR", null, [ - `call-apis: Failed ${queryConfig.method.toUpperCase()}`, + `Failed ${queryConfig.method.toUpperCase()}`, `${query.APIEdge.query_operation.server}`, `(${nInputs} ID${nInputs > 1 ? "s" : ""}):`, `${edgeOperation}: (${(error as Error).toString()})`, @@ -341,7 +389,7 @@ export default class APIQueryPool { error: (error as Error).toString(), ...queryInfo, }, - ).getLog(), + ).getSerializeable(), ); if (axios.isAxiosError(error)) { debug( @@ -356,13 +404,26 @@ export default class APIQueryPool { `Error response for above failure: ${JSON.stringify( error.response?.data, )}`, - ).getLog(), + ).getSerializeable(), ); } Telemetry.captureException(error as Error); span?.finish(); - await finish(logs, undefined, followUp); + await finish({ + logs, + followUp, + apiUnavailable, + }); } } + + async cacheLookup(hash: string, qEdge: QEdge): Promise { + debug(`Checking for cached records for subquery ${hash}...`); + const recordPackage = await cacheLookup(hash); + const records = recordPackage + ? Record.unpackRecords(recordPackage as RecordPackage, qEdge) + : null; + return records; + } } diff --git a/packages/call-apis/src/query_queue.ts b/packages/call-apis/src/query_queue.ts index ed64140..de23945 100644 --- a/packages/call-apis/src/query_queue.ts +++ b/packages/call-apis/src/query_queue.ts @@ -1,14 +1,20 @@ import RateCounter from "./rate_limiter"; -import { RedisClient } from "@biothings-explorer/utils"; +import { redisClient } from "@retriever/utils"; import Debug from "debug"; import Subquery from "./queries/subquery"; -const debug = Debug("bte:call-apis:query"); +import { QueryHandlerOptions } from "@retriever/types"; +const debug = Debug("retriever:call-apis:query"); + +export interface SubqueryBundle { + query: Subquery; + options: QueryHandlerOptions; +} export default class APIQueryQueue { - queue: Subquery[]; + queue: SubqueryBundle[]; rateCounter: RateCounter; - constructor(queries: Subquery[], redisClient?: RedisClient) { - this.queue = [...queries]; + constructor() { + this.queue = []; this.rateCounter = new RateCounter(redisClient); } @@ -20,14 +26,14 @@ export default class APIQueryQueue { return this.queue.length === 0; } - add(query: Subquery | Subquery[]) { - if (!Array.isArray(query)) query = [query]; - this.queue.unshift(...query); + add(query: Subquery, options: QueryHandlerOptions) { + this.queue.unshift({ query, options }); } - async getNext(): Promise { - const query = this.queue.pop(); - if (!query) return; + async getNext(): Promise<{ query: Subquery; options: QueryHandlerOptions }> { + const next = this.queue.pop(); + if (!next) return; + const { query, options } = next; const queryDelayed = query.delayUntil && query.delayUntil >= new Date(); if ((await this.rateCounter.atLimit(query)) || queryDelayed) { debug( @@ -36,13 +42,13 @@ export default class APIQueryQueue { `rate-limited or delayed, will-retry after rest of sub-query queue`, ].join(" "), ); - this.queue.unshift(query); + this.queue.unshift({ query, options }); return new Promise(resolve => { setImmediate(async () => { resolve(await this.getNext()); }); }); } - return query; + return { query, options }; } } diff --git a/packages/call-apis/src/rate_limiter.ts b/packages/call-apis/src/rate_limiter.ts index 5505a62..b215ee0 100644 --- a/packages/call-apis/src/rate_limiter.ts +++ b/packages/call-apis/src/rate_limiter.ts @@ -1,7 +1,7 @@ -import { RedisClient } from "@biothings-explorer/utils"; +import { RedisClient } from "@retriever/utils"; import Debug from "debug"; import Subquery from "./queries/subquery"; -const debug = Debug("bte:call-apis:query"); +const debug = Debug("retriever:call-apis:query"); // Default rate limit of 100 queries per second, which shouldn't ever be reached // But just in case, this should keep multiple instances from overloading anyone diff --git a/packages/call-apis/src/types.ts b/packages/call-apis/src/types.ts index 1452bba..eef0555 100644 --- a/packages/call-apis/src/types.ts +++ b/packages/call-apis/src/types.ts @@ -1,11 +1,11 @@ -import { SmartAPIKGOperationObject } from "@biothings-explorer/smartapi-kg"; -import { SmartAPISpec } from "@biothings-explorer/smartapi-kg"; -import { Record } from "@biothings-explorer/api-response-transform"; -import { StampedLog } from "@biothings-explorer/utils"; +import { SmartAPIKGOperationObject } from "@retriever/smartapi-kg"; +import { SmartAPISpec } from "@retriever/smartapi-kg"; +import { StampedLog } from "@retriever/utils"; import { SRIBioEntity } from "biomedical_id_resolver"; +import { Record, QEdge } from "@retriever/graph"; /* TODO: most of these are temporarily pulled from other packages - * Instead, they should be pulled out into a new package ('@biothings-explorer/types' or similar). + * Instead, they should be pulled out into a new package ('@retriever/types' or similar). * This would allow for greater flexibility in package structure/type importing */ @@ -87,12 +87,12 @@ export interface TrapiAttribute { value_url?: string | null; attributes?: TrapiAttribute; [additionalProperties: string]: - | string - | string[] - | null - | TrapiAttribute - | number - | number[]; + | string + | string[] + | null + | TrapiAttribute + | number + | number[]; } export interface TrapiQualifier { @@ -191,107 +191,7 @@ export interface JSONDoc { [key2: number]: any; } -export interface TemplatedInput { - queryInputs: string | string[]; - [additionalProperties: string]: string | string[]; -} - -export interface SRIResolvedSet { - [originalCurie: string]: SRIBioEntity; -} export interface ExpandedCuries { [originalCurie: string]: string[]; } - -export interface QNode { - id: string; - categories: string[]; - equivalentIDs?: SRIResolvedSet; - expandedCategories: string[]; - equivalentIDsUpdated: boolean; - curie: string[]; - is_set: boolean; - expanded_curie: ExpandedCuries; - entity_count: number; - held_curie: string[]; - held_expanded: ExpandedCuries; - constraints: any; // TODO type - connected_to: Set; -} - -export interface QEdge { - id: string; - predicate: string[]; - subject: QNode; - object: QNode; - expanded_predicates: string[]; - qualifier_constraints: TrapiQualifierConstraint[]; - reverse: boolean; - executed: boolean; - logs: StampedLog[]; - records: Record[]; - filter?: any; - getQualifierConstraints: () => TrapiQualifierConstraint[]; -} - -export interface APIEdge extends SmartAPIKGOperationObject { - reasoner_edge: QEdge; - input: string | string[] | TemplatedInput; - input_resolved_identifiers: { - [curie: string]: unknown; - }; - original_input: { - [equivalentCurie: string]: string; - }; -} - -export interface NonBatchAPIEdge extends APIEdge { - input: string; -} - -export interface BatchAPIEdge extends APIEdge { - input: string[]; -} - -export interface TemplateNonBatchAPIEdge extends APIEdge { - input: TemplatedInput; -} - -export interface TemplateBatchAPIEdge extends APIEdge { - input: TemplatedInput; -} - -export type APIDefinition = { - // Must have one of id or infores - id?: string; // SmartAPI ID, takes priority over infores - name: string; // Must match name on SmartAPI registry - infores?: string; // infores of API - primarySource?: boolean; - timeout?: number; -} & ({ id: string } | { infores: string }); - -export interface APIList { - include: APIDefinition[]; - // takes priority over include, taking into account id/infores prioritization - exclude: APIDefinition[]; -} - -export interface QueryHandlerOptions { - provenanceUsesServiceProvider?: boolean; - smartAPIID?: string; - teamName?: string; - enableIDResolution?: boolean; - // TODO: type instances of `any` - apiList?: APIList; - schema?: any; // might be hard to type -- it's the entire TRAPI schema IIRC - dryrun?: boolean; - resolveOutputIDs?: boolean; - submitter?: string; - caching?: boolean; // from request url query values - EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?: string[]; -} - -export interface UnavailableAPITracker { - [server: string]: { skip: boolean; skippedQueries: number }; -} diff --git a/packages/call-apis/tsconfig.json b/packages/call-apis/tsconfig.json index 0010778..0f63670 100644 --- a/packages/call-apis/tsconfig.json +++ b/packages/call-apis/tsconfig.json @@ -5,10 +5,12 @@ "rootDir": "./src", "outDir": "./built", "paths": { - "@biothings-explorer/smartapi-kg": ["../smartapi-kg"], - "@biothings-explorer/api-response-transform": ["../api-response-transform"], + "@retriever/smartapi-kg": ["../smartapi-kg"], + "@retriever/api-response-transform": ["../api-response-transform"], "biomedical_id_resolver": ["../biomedical_id_resolver"], - "@biothings-explorer/utils": ["../utils"] + "@retriever/utils": ["../utils"], + "@retriever/types": ["../types"], + "@retriever/graph": ["../graph"] } }, "include": ["./src/**/*"], @@ -25,6 +27,12 @@ }, { "path": "../utils" + }, + { + "path": "../types" + }, + { + "path": "../graph" } ] } diff --git a/packages/graph/package.json b/packages/graph/package.json new file mode 100644 index 0000000..81c30c7 --- /dev/null +++ b/packages/graph/package.json @@ -0,0 +1,43 @@ +{ + "$schema": "https://json.schemastore.org/package.json", + "name": "@retriever/graph", + "version": "1.0.0", + "description": "A collection of common graph handlers used by Retriever", + "main": "./built/index.js", + "types": "./built/index.d.ts", + "scripts": { + "prepare": "npm run build", + "build": "tsc -b", + "clean": "rimraf ./built './**/tsconfig.tsbuildinfo'", + "build:clean": "pnpm run clean && pnpm run build", + "format": "prettier --check 'src/**/*.js'", + "format:fix": "prettier --write 'src/**/*.js'", + "lint": "eslint . --ext .js", + "lint:fix": "pnpm lint --fix", + "test": "jest", + "test-cov": "jest --coverage" + }, + "keywords": [ + "BioPack", + "retriever", + "biothings", + "single", + "hop", + "query" + ], + "author": "BioPack Team", + "license": "ISC", + "bugs": { + "url": "https://github.com/BioPack-team/retriever/issues" + }, + "homepage": "https://github.com/BioPack-team/retriever#readme", + "dependencies": { + "@retriever/smartapi-kg": "workspace:../smartapi-kg", + "@retriever/utils": "workspace:../utils", + "@retriever/types": "workspace:../types", + "@retriever/biomedical_id_resolver": "workspace:../biomedical_id_resolver" + }, + "devDependencies": { + "@types/jest": "^29.5.12" + } +} diff --git a/packages/graph/src/api_edge.ts b/packages/graph/src/api_edge.ts new file mode 100644 index 0000000..6e4bc0b --- /dev/null +++ b/packages/graph/src/api_edge.ts @@ -0,0 +1,38 @@ +import { SmartAPIKGOperationObject } from "@retriever/smartapi-kg"; +import QEdge from "./query_edge"; +import { SRIBioEntity } from "@retriever/biomedical_id_resolver"; + +export interface MetaXEdge extends SmartAPIKGOperationObject { + reasoner_edge: QEdge; +} + +export interface TemplatedInput { + queryInputs: string | string[]; + [additionalAttributes: string]: string | string[]; +} + +export interface APIEdge extends MetaXEdge { + input: string | string[] | TemplatedInput; + input_resolved_identifiers: { + [curie: string]: SRIBioEntity; + }; + original_input: { + [equivalentCurie: string]: string; + }; +} + +export interface NonBatchAPIEdge extends APIEdge { + input: string; +} + +export interface BatchAPIEdge extends APIEdge { + input: string[]; +} + +export interface TemplateNonBatchAPIEdge extends APIEdge { + input: TemplatedInput; +} + +export interface TemplateBatchAPIEdge extends APIEdge { + input: TemplatedInput; +} diff --git a/packages/query_graph_handler/src/graph/graph.ts b/packages/graph/src/graph.ts similarity index 92% rename from packages/query_graph_handler/src/graph/graph.ts rename to packages/graph/src/graph.ts index 018a096..e6efe52 100644 --- a/packages/query_graph_handler/src/graph/graph.ts +++ b/packages/graph/src/graph.ts @@ -1,13 +1,11 @@ -import kg_edge from './kg_edge'; -import kg_node from './kg_node'; import Debug from 'debug'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +import { LogEntry, StampedLog } from '@retriever/utils'; import KGNode from './kg_node'; import KGEdge from './kg_edge'; -import { Record } from '../../../api-response-transform/built'; -import { TrapiAuxiliaryGraph, TrapiResult } from '../types'; +import { Record } from './record'; +import { TrapiAuxiliaryGraph, TrapiResult } from '@retriever/types'; import KnowledgeGraph from './knowledge_graph'; -const debug = Debug('bte:biothings-explorer-trapi:Graph'); +const debug = Debug('retriever:Graph'); export interface BTEGraphUpdate { nodes: { @@ -52,7 +50,7 @@ export default class BTEGraph { const recordHash = record.recordHash; if (!(outputBTENodeID in this.nodes)) { - this.nodes[outputBTENodeID] = new kg_node(outputBTENodeID, { + this.nodes[outputBTENodeID] = new KGNode(outputBTENodeID, { primaryCurie: outputPrimaryCurie, qNodeID: outputQNodeID, curies: record.object.equivalentCuries, @@ -69,7 +67,7 @@ export default class BTEGraph { } if (!(inputBTENodeID in this.nodes)) { - this.nodes[inputBTENodeID] = new kg_node(inputBTENodeID, { + this.nodes[inputBTENodeID] = new KGNode(inputBTENodeID, { primaryCurie: inputPrimaryCurie, qNodeID: inputQNodeID, curies: record.subject.equivalentCuries, @@ -90,7 +88,7 @@ export default class BTEGraph { this.nodes[inputBTENodeID].addTargetNode(outputBTENodeID); this.nodes[inputBTENodeID].addTargetQNodeID(outputQNodeID); if (!(recordHash in this.edges)) { - this.edges[recordHash] = new kg_edge(recordHash, { + this.edges[recordHash] = new KGEdge(recordHash, { predicate: record.predicate, subject: inputPrimaryCurie, object: outputPrimaryCurie, diff --git a/packages/graph/src/index.ts b/packages/graph/src/index.ts new file mode 100644 index 0000000..8f498de --- /dev/null +++ b/packages/graph/src/index.ts @@ -0,0 +1,17 @@ +export * from "./graph"; +export * from "./knowledge_graph"; +export * from "./kg_edge"; +export * from "./kg_node"; +export * from "./query_graph"; +export * from "./query_edge"; +export * from "./query_node"; +export * from "./api_edge"; +export * from "./record"; + +export { default as BTEGraph } from "./graph"; +export { default as KnowledgeGraph } from "./knowledge_graph"; +export { default as KGEdge } from "./kg_edge"; +export { default as KGNode } from "./kg_node"; +export { default as QueryGraph } from "./query_graph"; +export { default as QEdge } from "./query_edge"; +export { default as QNode } from "./query_node"; diff --git a/packages/query_graph_handler/src/graph/kg_edge.ts b/packages/graph/src/kg_edge.ts similarity index 94% rename from packages/query_graph_handler/src/graph/kg_edge.ts rename to packages/graph/src/kg_edge.ts index d6422ab..fd8305e 100644 --- a/packages/query_graph_handler/src/graph/kg_edge.ts +++ b/packages/graph/src/kg_edge.ts @@ -1,5 +1,4 @@ -import { ProvenanceChainItem } from '@biothings-explorer/api-response-transform'; -import { TrapiAttribute } from '../types'; +import { TrapiAttribute, TrapiSource } from '@retriever/types'; export interface KGEdgeInfo { object: string; @@ -68,7 +67,7 @@ export default class KGEdge { }); } - addSource(source: ProvenanceChainItem | ProvenanceChainItem[]): void { + addSource(source: TrapiSource | TrapiSource[]): void { if (typeof source === 'undefined') { return; } diff --git a/packages/query_graph_handler/src/graph/kg_node.ts b/packages/graph/src/kg_node.ts similarity index 96% rename from packages/query_graph_handler/src/graph/kg_node.ts rename to packages/graph/src/kg_node.ts index cf16dfe..c140167 100644 --- a/packages/query_graph_handler/src/graph/kg_node.ts +++ b/packages/graph/src/kg_node.ts @@ -1,4 +1,4 @@ -import { TrapiAttribute } from '../types'; +import { TrapiAttribute } from '@retriever/types'; export interface KGNodeInfo { label: string; diff --git a/packages/query_graph_handler/src/graph/knowledge_graph.ts b/packages/graph/src/knowledge_graph.ts similarity index 80% rename from packages/query_graph_handler/src/graph/knowledge_graph.ts rename to packages/graph/src/knowledge_graph.ts index 0ac539c..3083a9e 100644 --- a/packages/query_graph_handler/src/graph/knowledge_graph.ts +++ b/packages/graph/src/knowledge_graph.ts @@ -1,5 +1,5 @@ -import { toArray } from '../utils'; -import Debug from 'debug'; +import { toArray } from "@retriever/utils"; +import Debug from "debug"; import { TrapiAttribute, TrapiKnowledgeGraph, @@ -9,13 +9,13 @@ import { TrapiKGNodes, TrapiQualifier, TrapiSource, -} from '../types'; -import KGNode from './kg_node'; -import KGEdge from './kg_edge'; -import { BTEGraphUpdate } from './graph'; -import { APIDefinition } from '@biothings-explorer/types'; + APIDefinition, +} from "@retriever/types"; +import KGNode from "./kg_node"; +import KGEdge from "./kg_edge"; +import { BTEGraphUpdate } from "./graph"; -const debug = Debug('bte:biothings-explorer-trapi:KnowledgeGraph'); +const debug = Debug("retriever:KnowledgeGraph"); export default class KnowledgeGraph { nodes: { @@ -50,11 +50,11 @@ export default class KnowledgeGraph { name: Array.isArray(kgNode.label) ? kgNode.label[0] : kgNode.label, attributes: [ { - attribute_type_id: 'biolink:xref', + attribute_type_id: "biolink:xref", value: kgNode.curies, }, { - attribute_type_id: 'biolink:synonym', + attribute_type_id: "biolink:synonym", value: kgNode.names.length ? kgNode.names : toArray(kgNode.label), }, // Currently unused @@ -91,12 +91,14 @@ export default class KnowledgeGraph { } _createQualifiers(kgEdge: KGEdge): TrapiQualifier[] { - const qualifiers = Object.entries(kgEdge.qualifiers || {}).map(([qualifierType, qualifier]) => { - return { - qualifier_type_id: qualifierType, - qualifier_value: qualifier, - }; - }); + const qualifiers = Object.entries(kgEdge.qualifiers || {}).map( + ([qualifierType, qualifier]) => { + return { + qualifier_type_id: qualifierType, + qualifier_value: qualifier, + }; + }, + ); return qualifiers.length ? qualifiers : undefined; } @@ -107,14 +109,14 @@ export default class KnowledgeGraph { // publications if (Array.from(kgEdge.publications).length) { attributes.push({ - attribute_type_id: 'biolink:publications', + attribute_type_id: "biolink:publications", value: Array.from(kgEdge.publications), - value_type_id: 'linkml:Uriorcurie', + value_type_id: "linkml:Uriorcurie", }); } Object.entries(kgEdge.attributes).forEach(([key, value]) => { - if (key == 'edge-attributes') return; + if (key == "edge-attributes") return; // if (key == 'edge-attributes') return; attributes.push({ attribute_type_id: key, @@ -124,7 +126,7 @@ export default class KnowledgeGraph { }); //handle TRAPI APIs (Situation A of https://github.com/biothings/BioThings_Explorer_TRAPI/issues/208) and APIs that define 'edge-atributes' in x-bte - kgEdge.attributes['edge-attributes']?.forEach((attribute) => { + kgEdge.attributes["edge-attributes"]?.forEach(attribute => { attributes.push(attribute); }); return attributes; @@ -136,7 +138,9 @@ export default class KnowledgeGraph { Object.entries(roles).forEach(([, sourceObj]) => { const trapiSource: TrapiSource = { ...sourceObj, - upstream_resource_ids: sourceObj.upstream_resource_ids ? [...sourceObj.upstream_resource_ids] : undefined, + upstream_resource_ids: sourceObj.upstream_resource_ids + ? [...sourceObj.upstream_resource_ids] + : undefined, }; sources.push(trapiSource); }); @@ -156,10 +160,12 @@ export default class KnowledgeGraph { } update(bteGraph: BTEGraphUpdate): void { - Object.keys(bteGraph.nodes).map((node) => { - this.nodes[bteGraph.nodes[node].primaryCurie] = this._createNode(bteGraph.nodes[node]); + Object.keys(bteGraph.nodes).map(node => { + this.nodes[bteGraph.nodes[node].primaryCurie] = this._createNode( + bteGraph.nodes[node], + ); }); - Object.keys(bteGraph.edges).map((edge) => { + Object.keys(bteGraph.edges).map(edge => { this.edges[edge] = this._createEdge(bteGraph.edges[edge]); }); this.kg = { diff --git a/packages/query_graph_handler/src/query_edge.ts b/packages/graph/src/query_edge.ts similarity index 95% rename from packages/query_graph_handler/src/query_edge.ts rename to packages/graph/src/query_edge.ts index e380b51..6ac411c 100644 --- a/packages/query_graph_handler/src/query_edge.ts +++ b/packages/graph/src/query_edge.ts @@ -1,29 +1,27 @@ -import helper from './helper'; import Debug from 'debug'; -import * as utils from './utils'; -import biolink from './biolink'; -import { Record, RecordNode, FrozenRecord } from '@biothings-explorer/api-response-transform'; +import * as utils from '@retriever/utils'; +import { Record, RecordNode, FrozenRecord } from './record'; import QNode from './query_node'; import { QNodeInfo } from './query_node'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; -import { TrapiAttributeConstraint, TrapiQualifierConstraint } from './types'; +import { StampedLog } from '@retriever/utils'; +import { TrapiAttributeConstraint, TrapiQualifierConstraint } from '@retriever/types'; -const debug = Debug('bte:biothings-explorer-trapi:QEdge'); +const debug = Debug('retriever:QEdge'); -interface ExpandedQualifier { +export interface ExpandedQualifier { qualifier_type_id: string; qualifier_value: string[]; } -interface ExpandedQEdgeQualifierConstraint { +export interface ExpandedQEdgeQualifierConstraint { qualifier_set: ExpandedQualifier[]; } -interface CompactQualifiers { +export interface CompactQualifiers { [qualfier_type_id: string]: string | string[]; } -interface QEdgeInfo { +export interface QEdgeInfo { id: string; object: QNodeInfo | QNode; subject: QNodeInfo | QNode; @@ -36,11 +34,11 @@ interface QEdgeInfo { predicates?: string[]; } -interface AliasesByPrimary { +export interface AliasesByPrimary { [primaryClient: string]: string[]; } -interface AliasesByPrimaryByType { +export interface AliasesByPrimaryByType { [semanticType: string]: AliasesByPrimary; } @@ -125,11 +123,11 @@ export default class QEdge { (this.getInputCurie() || []).sort() + qualifiersSorted; - return helper._generateHash(toBeHashed); + return utils.hash(toBeHashed); } expandPredicates(predicates: string[]): string[] { - return Array.from(new Set(predicates.reduce((acc, cur) => [...acc, ...biolink.getDescendantPredicates(cur)], []))); + return Array.from(new Set(predicates.reduce((acc, cur) => [...acc, ...utils.biolink.getDescendantPredicates(cur)], []))); } getPredicate(): string[] { @@ -141,7 +139,7 @@ export default class QEdge { debug(`Expanded edges: ${expandedPredicates}`); return expandedPredicates .map((predicate) => { - return this.isReversed() === true ? biolink.reverse(predicate) : predicate; + return this.isReversed() === true ? utils.biolink.reverse(predicate) : predicate; }) .filter((item) => !(typeof item === 'undefined')); } @@ -154,7 +152,7 @@ export default class QEdge { ? Array.isArray(qualifier_value) ? Array.from( qualifier_value.reduce((set: Set, predicate: string) => { - biolink + utils.biolink .getDescendantPredicates(utils.removeBioLinkPrefix(predicate)) .forEach((item) => set.add(`biolink:${utils.removeBioLinkPrefix(item)}`)); return set; @@ -162,13 +160,13 @@ export default class QEdge { ) : Array.from( new Set( - biolink + utils.biolink .getDescendantPredicates(utils.removeBioLinkPrefix(qualifier_value)) .map((item) => `biolink:${utils.removeBioLinkPrefix(item)}`), ), ) : Array.from( - new Set(biolink.getDescendantQualifiers(utils.removeBioLinkPrefix(qualifier_value as string))), + new Set(utils.biolink.getDescendantQualifiers(utils.removeBioLinkPrefix(qualifier_value as string))), ); return { @@ -575,6 +573,6 @@ export default class QEdge { } getReversedPredicate(predicate: string): string { - return predicate ? biolink.reverse(predicate) : undefined; + return predicate ? utils.biolink.reverse(predicate) : undefined; } } diff --git a/packages/query_graph_handler/src/query_graph.ts b/packages/graph/src/query_graph.ts similarity index 66% rename from packages/query_graph_handler/src/query_graph.ts rename to packages/graph/src/query_graph.ts index 7a6f9d8..b9e060c 100644 --- a/packages/query_graph_handler/src/query_graph.ts +++ b/packages/graph/src/query_graph.ts @@ -1,15 +1,16 @@ -import QEdge from './query_edge'; -import InvalidQueryGraphError from './exceptions/invalid_query_graph_error'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; -import Debug from 'debug'; -import QNode from './query_node'; -import biolink from './biolink'; -import { resolveSRI } from 'biomedical_id_resolver'; -import _ from 'lodash'; -import * as utils from './utils'; -import { TrapiQueryGraph } from './types'; +import QEdge from "./query_edge"; +import { + InvalidQueryGraphError, + TrapiQueryGraph, +} from "@retriever/types"; +import { LogEntry, StampedLog, biolink } from "@retriever/utils"; +import Debug from "debug"; +import QNode from "./query_node"; +import { resolveSRI } from "@retriever/biomedical_id_resolver"; +import _ from "lodash"; +import * as utils from "@retriever/utils"; -const debug = Debug('bte:biothings-explorer-trapi:query_graph'); +const debug = Debug("retriever:query_graph"); export default class QueryGraph { queryGraph: TrapiQueryGraph; @@ -25,34 +26,45 @@ export default class QueryGraph { _validateEmptyNodes(queryGraph: TrapiQueryGraph): void { if (Object.keys(queryGraph.nodes).length === 0) { - throw new InvalidQueryGraphError('Your Query Graph has no nodes defined.'); + throw new InvalidQueryGraphError( + "Your Query Graph has no nodes defined.", + ); } } _validateOneNodeID(queryGraph: TrapiQueryGraph): void { for (const nodeID in queryGraph.nodes) { - if (queryGraph.nodes[nodeID] && queryGraph.nodes[nodeID]?.ids?.length > 0) { + if ( + queryGraph.nodes[nodeID] && + queryGraph.nodes[nodeID]?.ids?.length > 0 + ) { return; } } throw new InvalidQueryGraphError( - 'body/message.query_graph.nodes should contain at least one node with at least one non-null id', + "body/message.query_graph.nodes should contain at least one node with at least one non-null id", ); } _validateEmptyEdges(queryGraph: TrapiQueryGraph): void { if (Object.keys(queryGraph.edges).length === 0) { - throw new InvalidQueryGraphError('Your Query Graph has no edges defined.'); + throw new InvalidQueryGraphError( + "Your Query Graph has no edges defined.", + ); } } _validateNodeEdgeCorrespondence(queryGraph: TrapiQueryGraph): void { for (const qEdgeID in queryGraph.edges) { if (!(this.queryGraph.edges[qEdgeID].subject in queryGraph.nodes)) { - throw new InvalidQueryGraphError(`The subject of edge ${qEdgeID} is not defined in the query graph.`); + throw new InvalidQueryGraphError( + `The subject of edge ${qEdgeID} is not defined in the query graph.`, + ); } if (!(this.queryGraph.edges[qEdgeID].object in queryGraph.nodes)) { - throw new InvalidQueryGraphError(`The object of edge ${qEdgeID} is not defined in the query graph.`); + throw new InvalidQueryGraphError( + `The object of edge ${qEdgeID} is not defined in the query graph.`, + ); } } } @@ -60,7 +72,9 @@ export default class QueryGraph { _validateBatchSize(queryGraph: TrapiQueryGraph): void { Object.entries(queryGraph.nodes).forEach(([nodeID, node]) => { if (node.ids && node.ids.length > 150) { - throw new InvalidQueryGraphError(`Query node ${nodeID} exceeds batch size limit.`); + throw new InvalidQueryGraphError( + `Query node ${nodeID} exceeds batch size limit.`, + ); } }); } @@ -70,8 +84,11 @@ export default class QueryGraph { for (const edgeID in queryGraph.edges) { const subject = queryGraph.edges[edgeID].subject; const object = queryGraph.edges[edgeID].object; - if (edgeSet.has(`${subject}-${object}`) || edgeSet.has(`${object}-${subject}`)) { - throw new InvalidQueryGraphError('Multiple edges between two nodes.'); + if ( + edgeSet.has(`${subject}-${object}`) || + edgeSet.has(`${object}-${subject}`) + ) { + throw new InvalidQueryGraphError("Multiple edges between two nodes."); } edgeSet.add(`${subject}-${object}`); } @@ -94,14 +111,18 @@ export default class QueryGraph { for (const firstNode in nodes) { if (nodes[firstNode].visited === true) continue; - const stack: { curNode: string; parent: string | number }[] = [{ curNode: firstNode, parent: -1 }]; + const stack: { curNode: string; parent: string | number }[] = [ + { curNode: firstNode, parent: -1 }, + ]; nodes[firstNode].visited = true; while (stack.length !== 0) { const { curNode, parent } = stack.pop(); for (const conNode of nodes[curNode].connections) { if (conNode == parent) continue; if (nodes[conNode].visited === true) { - throw new InvalidQueryGraphError('The query graph contains a cycle.'); + throw new InvalidQueryGraphError( + "The query graph contains a cycle.", + ); } stack.push({ curNode: conNode, parent: curNode }); nodes[conNode].visited = true; @@ -129,9 +150,11 @@ export default class QueryGraph { if (badProperties.size !== 0) { this.logs.push( new LogEntry( - 'WARNING', + "WARNING", null, - `Ignoring unrecognized properties (${[...badProperties].join(',')}) on nodes (${[...badNodes].join(',')}).`, + `Ignoring unrecognized properties (${[...badProperties].join( + ",", + )}) on nodes (${[...badNodes].join(",")}).`, ).getLog(), ); } @@ -156,9 +179,11 @@ export default class QueryGraph { if (badProperties.size !== 0) { this.logs.push( new LogEntry( - 'WARNING', + "WARNING", null, - `Ignoring unrecognized properties (${[...badProperties].join(',')}) on edges (${[...badEdges].join(',')}).`, + `Ignoring unrecognized properties (${[...badProperties].join( + ",", + )}) on edges (${[...badEdges].join(",")}).`, ).getLog(), ); } @@ -196,7 +221,9 @@ export default class QueryGraph { } private async _findNodeCategories(curies: string[]): Promise { - const noMatchMessage = `No category match found for ${JSON.stringify(curies)}.`; + const noMatchMessage = `No category match found for ${JSON.stringify( + curies, + )}.`; if (curies.length == 1) { let matchedCategories: string[]; const resolved = await resolveSRI({ @@ -205,10 +232,10 @@ export default class QueryGraph { debug(`Query node missing categories...Looking for match...`); if (resolved[curies[0]] && resolved[curies[0]].primaryTypes) { matchedCategories = resolved[curies[0]].primaryTypes; - return matchedCategories.filter((c) => c).map((c) => `biolink:${c}`); + return matchedCategories.filter(c => c).map(c => `biolink:${c}`); } else { debug(noMatchMessage); - this.logs.push(new LogEntry('ERROR', null, noMatchMessage).getLog()); + this.logs.push(new LogEntry("ERROR", null, noMatchMessage).getLog()); return []; } } else { @@ -219,17 +246,23 @@ export default class QueryGraph { // get array of all unique categories for all curies const allCategories = [ ...Object.values(await resolveSRI({ unknown: curies })) - .map((resolvedCurie) => resolvedCurie.semanticTypes) - .filter((semanticTypes) => semanticTypes.some((item) => item !== null)) - .map((semanticTypes) => semanticTypes.map((t) => utils.removeBioLinkPrefix(t))) - .reduce((set: Set, arr: string[]): Set => new Set([...set, ...arr]), new Set()), + .map(resolvedCurie => resolvedCurie.semanticTypes) + .filter(semanticTypes => semanticTypes.some(item => item !== null)) + .map(semanticTypes => + semanticTypes.map(t => utils.removeBioLinkPrefix(t)), + ) + .reduce( + (set: Set, arr: string[]): Set => + new Set([...set, ...arr]), + new Set(), + ), ]; if (allCategories.length) { finalCategories.push(allCategories[0]); } else { debug(noMatchMessage); - this.logs.push(new LogEntry('ERROR', null, noMatchMessage).getLog()); + this.logs.push(new LogEntry("ERROR", null, noMatchMessage).getLog()); return []; } @@ -237,7 +270,7 @@ export default class QueryGraph { const keepSet: Set = new Set(); const rmSet: Set = new Set(); // check against each currently selected category - finalCategories.forEach((selected) => { + finalCategories.forEach(selected => { if (tree[selected].is_mixin) { rmSet.add(selected); } @@ -250,7 +283,10 @@ export default class QueryGraph { let parent = category; while (parent) { - if (selected === parent || tree[selected].children.includes(parent)) { + if ( + selected === parent || + tree[selected].children.includes(parent) + ) { rmSet.add(selected); return keepSet.add(category); } @@ -259,7 +295,10 @@ export default class QueryGraph { parent = selected; while (parent) { - if (category === parent || tree[category].children.includes(parent)) { + if ( + category === parent || + tree[category].children.includes(parent) + ) { rmSet.add(category); return keepSet.add(selected); } @@ -268,7 +307,7 @@ export default class QueryGraph { // add both if neither is ancestor of the other keepSet.add(category).add(selected); }); - finalCategories = [...keepSet].filter((cat) => !rmSet.has(cat)); + finalCategories = [...keepSet].filter(cat => !rmSet.has(cat)); // in event no categories are kept (due to mixin shenanigans/etc) if (!finalCategories.length && i < allCategories.length - 1) { finalCategories = [allCategories[i + 1]]; @@ -276,13 +315,13 @@ export default class QueryGraph { }); if (!finalCategories.length) { debug(noMatchMessage); - this.logs.push(new LogEntry('ERROR', null, noMatchMessage).getLog()); + this.logs.push(new LogEntry("ERROR", null, noMatchMessage).getLog()); } - return [...finalCategories].map((cat) => 'biolink:' + cat); + return [...finalCategories].map(cat => "biolink:" + cat); } catch (error) { const errorMessage = `Unable to retrieve categories due to error ${error}`; debug(errorMessage); - this.logs.push(new LogEntry('ERROR', null, errorMessage).getLog()); + this.logs.push(new LogEntry("ERROR", null, errorMessage).getLog()); return []; } } @@ -293,16 +332,21 @@ export default class QueryGraph { for (const qNodeID in this.queryGraph.nodes) { //if node has ID but no categories if ( - (!this.queryGraph.nodes[qNodeID].categories && this.queryGraph.nodes[qNodeID].ids) || + (!this.queryGraph.nodes[qNodeID].categories && + this.queryGraph.nodes[qNodeID].ids) || (this.queryGraph.nodes[qNodeID].categories && // this.queryGraph.nodes[qNodeID].categories.length == 0 && this.queryGraph.nodes[qNodeID].ids) ) { let userAssignedCategories = this.queryGraph.nodes[qNodeID].categories; - let categories = await this._findNodeCategories(this.queryGraph.nodes[qNodeID].ids); + let categories = await this._findNodeCategories( + this.queryGraph.nodes[qNodeID].ids, + ); if (userAssignedCategories) { userAssignedCategories = [...userAssignedCategories]; // new Array for accurate logging after node updated - categories = categories.filter((category) => !userAssignedCategories.includes(category)); + categories = categories.filter( + category => !userAssignedCategories.includes(category), + ); } if (categories.length) { if (!this.queryGraph.nodes[qNodeID].categories) { @@ -310,55 +354,75 @@ export default class QueryGraph { } else { this.queryGraph.nodes[qNodeID].categories.push(...categories); } - debug(`Node categories found. Assigning value: ${JSON.stringify(this.queryGraph.nodes[qNodeID])}`); + debug( + `Node categories found. Assigning value: ${JSON.stringify( + this.queryGraph.nodes[qNodeID], + )}`, + ); this.logs.push( new LogEntry( - 'INFO', + "INFO", null, [ `Node ${qNodeID} `, - `with id${this.queryGraph.nodes[qNodeID].ids.length > 1 ? 's' : ''} `, - `[${this.queryGraph.nodes[qNodeID].ids.join(', ')}] `, + `with id${ + this.queryGraph.nodes[qNodeID].ids.length > 1 ? "s" : "" + } `, + `[${this.queryGraph.nodes[qNodeID].ids.join(", ")}] `, `${ userAssignedCategories && userAssignedCategories.length - ? `and categor${userAssignedCategories.length === 1 ? 'y' : 'ies'} [${userAssignedCategories.join( - ', ', - )}] augmented with` + ? `and categor${ + userAssignedCategories.length === 1 ? "y" : "ies" + } [${userAssignedCategories.join(", ")}] augmented with` : `assigned` } `, - `categor${categories.length > 1 ? 'ies' : 'y'} `, - `[${categories.join(', ')}] inferred from `, - `id${this.queryGraph.nodes[qNodeID].ids.length > 1 ? 's' : ''}.`, - ].join(''), + `categor${categories.length > 1 ? "ies" : "y"} `, + `[${categories.join(", ")}] inferred from `, + `id${ + this.queryGraph.nodes[qNodeID].ids.length > 1 ? "s" : "" + }.`, + ].join(""), ).getLog(), ); } - nodes[qNodeID] = new QNode({ id: qNodeID, ...this.queryGraph.nodes[qNodeID] }); + nodes[qNodeID] = new QNode({ + id: qNodeID, + ...this.queryGraph.nodes[qNodeID], + }); } else { debug(`Creating node...`); - nodes[qNodeID] = new QNode({ id: qNodeID, ...this.queryGraph.nodes[qNodeID] }); + nodes[qNodeID] = new QNode({ + id: qNodeID, + ...this.queryGraph.nodes[qNodeID], + }); } if (nodes[qNodeID].categories !== undefined) { if ( - nodes[qNodeID].categories.includes('biolink:Disease') || - nodes[qNodeID].categories.includes('biolink:PhenotypicFeature') + nodes[qNodeID].categories.includes("biolink:Disease") || + nodes[qNodeID].categories.includes("biolink:PhenotypicFeature") ) { nodes[qNodeID].categories = nodes[qNodeID].categories.filter( - (e) => e !== 'biolink:Disease' && e !== 'biolink:PhenotypicFeature', + e => e !== "biolink:Disease" && e !== "biolink:PhenotypicFeature", ); - nodes[qNodeID].categories.push('biolink:DiseaseOrPhenotypicFeature'); + nodes[qNodeID].categories.push("biolink:DiseaseOrPhenotypicFeature"); } if ( - nodes[qNodeID].categories.includes('biolink:Protein') && - !nodes[qNodeID].categories.includes('biolink:Gene') + nodes[qNodeID].categories.includes("biolink:Protein") && + !nodes[qNodeID].categories.includes("biolink:Gene") ) { - nodes[qNodeID].categories.push('biolink:Gene'); + nodes[qNodeID].categories.push("biolink:Gene"); } } } this.logs.push( - new LogEntry('DEBUG', null, `BTE identified ${Object.keys(nodes).length} qNodes from your query graph`).getLog(), + new LogEntry( + "DEBUG", + null, + `Retriever identified ${ + Object.keys(nodes).length + } qNodes from your query graph`, + ).getLog(), ); return nodes; } @@ -390,9 +454,11 @@ export default class QueryGraph { this.edges = edges; this.logs.push( new LogEntry( - 'DEBUG', + "DEBUG", null, - `BTE identified ${Object.keys(this.edges).length} qEdges from your query graph`, + `Retriever identified ${ + Object.keys(this.edges).length + } qEdges from your query graph`, ).getLog(), ); return Object.values(this.edges); diff --git a/packages/query_graph_handler/src/query_node.ts b/packages/graph/src/query_node.ts similarity index 78% rename from packages/query_graph_handler/src/query_node.ts rename to packages/graph/src/query_node.ts index 9816002..4415570 100644 --- a/packages/query_graph_handler/src/query_node.ts +++ b/packages/graph/src/query_node.ts @@ -1,11 +1,10 @@ /* eslint-disable @typescript-eslint/no-var-requires */ -import _ from 'lodash'; -import * as utils from './utils'; -import biolink from './biolink'; -import Debug from 'debug'; -import InvalidQueryGraphError from './exceptions/invalid_query_graph_error'; -import { SRIBioEntity } from 'biomedical_id_resolver'; -const debug = Debug('bte:biothings-explorer-trapi:QNode'); +import _ from "lodash"; +import * as utils from "@retriever/utils"; +import Debug from "debug"; +import { ExpandedCuries, InvalidQueryGraphError, SRIResolvedSet } from "@retriever/types"; +import { SRIBioEntity } from "@retriever/biomedical_id_resolver"; +const debug = Debug("retriever:QNode"); export interface QNodeInfo { id: string; @@ -20,13 +19,6 @@ export interface QNodeInfo { equivalentIDs?: SRIResolvedSet; } -export interface SRIResolvedSet { - [originalCurie: string]: SRIBioEntity; -} - -export interface ExpandedCuries { - [originalCurie: string]: string[]; -} export default class QNode { id: string; @@ -45,7 +37,7 @@ export default class QNode { constructor(info: QNodeInfo) { this.id = info.id; - this.categories = info.categories || ['NamedThing']; + this.categories = info.categories || ["NamedThing"]; this.expandedCategories = this.categories; this.equivalentIDsUpdated = false; // mainIDs @@ -53,17 +45,22 @@ export default class QNode { //is_set this.is_set = info.is_set; //mainID : its equivalent ids - this.expanded_curie = info.expanded_curie !== undefined ? info.expanded_curie : {}; + this.expanded_curie = + info.expanded_curie !== undefined ? info.expanded_curie : {}; this.entity_count = info.ids ? info.ids.length : 0; - debug(`(1) Node "${this.id}" has (${this.entity_count}) entities at start.`); + debug( + `(1) Node "${this.id}" has (${this.entity_count}) entities at start.`, + ); //when choosing a lower entity count a node with higher count // might be told to store its curies temporarily this.held_curie = info.held_curie !== undefined ? info.held_curie : []; - this.held_expanded = info.held_expanded !== undefined ? info.held_expanded : {}; + this.held_expanded = + info.held_expanded !== undefined ? info.held_expanded : {}; //node constraints this.constraints = info.constraints; //list of edge ids that are connected to this node - this.connected_to = info.connected_to !== undefined ? new Set(info.connected_to) : new Set(); + this.connected_to = + info.connected_to !== undefined ? new Set(info.connected_to) : new Set(); //object-ify array of initial curies if (info.expanded_curie === undefined) this.expandCurie(); this.validateConstraints(); @@ -91,12 +88,14 @@ export default class QNode { } validateConstraints(): void { - const required = ['id', 'operator', 'value']; + const required = ["id", "operator", "value"]; if (this.constraints && this.constraints.length) { this.constraints.forEach((constraint: unknown) => { const constraint_keys = Object.keys(constraint); if (_.intersection(constraint_keys, required).length < 3) { - throw new InvalidQueryGraphError(`Invalid constraint specification must include (${required})`); + throw new InvalidQueryGraphError( + `Invalid constraint specification must include (${required})`, + ); } }); } @@ -104,12 +103,16 @@ export default class QNode { expandCurie(): void { if (this.curie && this.curie.length) { - this.curie.forEach((id) => { + this.curie.forEach(id => { if (!Object.hasOwnProperty.call(id, this.expanded_curie)) { this.expanded_curie[id] = [id]; } }); - debug(`(1) Node "${this.id}" expanded initial curie. ${JSON.stringify(this.expanded_curie)}`); + debug( + `(1) Node "${this.id}" expanded initial curie. ${JSON.stringify( + this.expanded_curie, + )}`, + ); } } @@ -147,11 +150,17 @@ export default class QNode { this.held_expanded = {}; } if (!this.curie.length) { - debug(`Node "${this.id}" saving (${Object.keys(curies).length}) curies...`); + debug( + `Node "${this.id}" saving (${Object.keys(curies).length}) curies...`, + ); this.curie = Object.keys(curies); this.expanded_curie = curies; } else { - debug(`Node "${this.id}" intersecting (${this.curie.length})/(${Object.keys(curies).length}) curies...`); + debug( + `Node "${this.id}" intersecting (${this.curie.length})/(${ + Object.keys(curies).length + }) curies...`, + ); // let intersection = this.intersectCuries(this.curie, curies); // this.curie = intersection; // debug(`Node "${this.id}" kept (${intersection.length}) curies...`); @@ -164,11 +173,11 @@ export default class QNode { // curies {originalID : ['aliasID']} //combine all curies into single list for easy intersection const combined: Set = new Set(); - Object.values(curies).forEach((expanded) => { + Object.values(curies).forEach(expanded => { if (!Array.isArray(expanded)) { combined.add(expanded); } else { - expanded.forEach((curie) => { + expanded.forEach(curie => { combined.add(curie); }); } @@ -176,7 +185,6 @@ export default class QNode { return [...combined]; } - intersectWithExpandedCuries(newCuries: ExpandedCuries): void { const keep: { [mainID: string]: string[] } = {}; @@ -242,10 +250,12 @@ export default class QNode { if (this.hasEquivalentIDs() === false) { const categories = utils.toArray(this.categories); let expanded_categories = []; - categories.map((category) => { + categories.map(category => { expanded_categories = [ ...expanded_categories, - ...(biolink.getDescendantClasses(utils.removeBioLinkPrefix(category)) || []), + ...(utils.biolink.getDescendantClasses( + utils.removeBioLinkPrefix(category), + ) || []), ]; }); this.expandedCategories = utils.getUnique(expanded_categories); @@ -258,14 +268,22 @@ export default class QNode { // .reduce((arr, category) => [...arr, ...biolink.getAncestorClasses(category)], []) // .filter((category) => !utils.toArray(this.category).includes(`biolink:${category}`)), // ); - let categories = utils.toArray(this.categories).map((category) => utils.removeBioLinkPrefix(category)); - Object.values(this.equivalentIDs).map((entity) => { + let categories = utils + .toArray(this.categories) + .map(category => utils.removeBioLinkPrefix(category)); + Object.values(this.equivalentIDs).map(entity => { categories = [...categories, ...entity.primaryTypes]; }); this.expandedCategories = utils.getUnique( utils .getUnique(categories) - .reduce((arr, category) => [...arr, ...(biolink.getDescendantClasses(category) || [])], []), + .reduce( + (arr, category) => [ + ...arr, + ...(utils.biolink.getDescendantClasses(category) || []), + ], + [], + ), ); // .filter(category => !ancestors.has(category)); } @@ -275,7 +293,7 @@ export default class QNode { } getPrimaryIDs(): string[] { - return this.getEntities().map((entity) => entity.primaryID); + return this.getEntities().map(entity => entity.primaryID); } setEquivalentIDs(equivalentIDs: SRIResolvedSet): void { @@ -297,7 +315,7 @@ export default class QNode { } hasEquivalentIDs(): boolean { - return !(typeof this.equivalentIDs === 'undefined'); + return !(typeof this.equivalentIDs === "undefined"); } getEntityCount(): number { diff --git a/packages/api-response-transform/src/record.ts b/packages/graph/src/record.ts similarity index 80% rename from packages/api-response-transform/src/record.ts rename to packages/graph/src/record.ts index e1a7b2f..c77343b 100644 --- a/packages/api-response-transform/src/record.ts +++ b/packages/graph/src/record.ts @@ -1,3 +1,5 @@ +import { SRIBioEntity } from "@retriever/biomedical_id_resolver"; +import { KGAssociationObject } from "@retriever/smartapi-kg"; import crypto from "crypto"; import _ from "lodash"; @@ -7,7 +9,7 @@ function hash(string: string) { export class RecordNode { original: string; - normalizedInfo: NodeNormalizerResultObj; + normalizedInfo: SRIBioEntity; _qNode: QNode; _apiLabel: string; @@ -25,7 +27,7 @@ export class RecordNode { makeFakeInfo( node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode, - ): NodeNormalizerResultObj { + ): SRIBioEntity { return { primaryID: node.curie, equivalentIDs: node.equivalentCuries ?? [], @@ -134,7 +136,7 @@ export class RecordNode { } export class Record { - association: Association; + association: KGAssociationObject; qEdge: QEdge; config: any; subject: RecordNode; @@ -146,11 +148,11 @@ export class Record { constructor( record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord, config?: any, - apiEdge?: Association, + association?: KGAssociationObject, qEdge?: QEdge, reverse?: boolean, ) { - this.association = apiEdge ? apiEdge : this.makeAPIEdge(record); + this.association = association ? association : this.makeAssociation(record); this.qEdge = qEdge ? qEdge : this.makeFakeQEdge(record); this.config = config ? config : { EDGE_ATTRIBUTES_USED_IN_RECORD_HASH: [] }; this.reverseToExecution = reverse || false; @@ -170,18 +172,18 @@ export class Record { reverse() { const frozen = { ...this.freezeVerbose() }; - const reversedAPIEdge: Association = { ...frozen.association }; - reversedAPIEdge.input_id = frozen.association.output_id; - reversedAPIEdge.input_type = frozen.association.output_type; - reversedAPIEdge.output_id = frozen.association.input_id; - reversedAPIEdge.output_type = frozen.association.input_type; + const reversedAssociation: KGAssociationObject = { ...frozen.association }; + reversedAssociation.input_id = frozen.association.output_id; + reversedAssociation.input_type = frozen.association.output_type; + reversedAssociation.output_id = frozen.association.input_id; + reversedAssociation.output_type = frozen.association.input_type; const predicate = this.qEdge.getReversedPredicate( frozen.association.predicate, ); - reversedAPIEdge.predicate = predicate; - if (reversedAPIEdge.qualifiers) { + reversedAssociation.predicate = predicate; + if (reversedAssociation.qualifiers) { const reversedQualifiers = Object.fromEntries( - Object.entries(reversedAPIEdge.qualifiers).map( + Object.entries(reversedAssociation.qualifiers).map( ([qualifierType, qualifier]) => { let newQualifierType: string = qualifierType; let newQualifier: string | string[] = qualifier; @@ -210,11 +212,11 @@ export class Record { ), ); - reversedAPIEdge.qualifiers = reversedQualifiers; + reversedAssociation.qualifiers = reversedQualifiers; frozen.qualifiers = reversedQualifiers; } // frozen.predicate = 'biolink:' + predicate; - frozen.association = reversedAPIEdge; + frozen.association = reversedAssociation; const temp = frozen.subject; frozen.subject = frozen.object; frozen.object = temp; @@ -271,27 +273,29 @@ export class Record { getHashedEdgeRepresentation(): string { return hash( record.subject.semanticType + - record.predicate + - record.object.semanticType + - (record.subject.equivalentCuries || record.object.equivalentCuries), + record.predicate + + record.object.semanticType + + (record.subject.equivalentCuries || record.object.equivalentCuries), ); }, }; } - makeAPIEdge( + makeAssociation( record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord, - ): Association { + ): KGAssociationObject { return { + input_type: record.subject.semanticType, + output_type: record.object.semanticType, predicate: record.predicate?.replace("biolink:", ""), qualifiers: record.qualifiers ? Object.fromEntries( - Object.entries(record.qualifiers).map( - ([qualifierType, qualifier]: [string, string]) => { - return [qualifierType.replace("biolink:", ""), qualifier]; - }, - ), - ) + Object.entries(record.qualifiers).map( + ([qualifierType, qualifier]: [string, string]) => { + return [qualifierType.replace("biolink:", ""), qualifier]; + }, + ), + ) : undefined, api_name: record.api, source: record.metaEdgeSource, @@ -316,32 +320,32 @@ export class Record { } public static packRecords(records: Record[]): RecordPackage { - // save string space by storing apiEdge and recordNode .normalizedInfo's separately (eliminates duplicates) + // save string space by storing association and recordNode .normalizedInfo's separately (eliminates duplicates) const frozenRecords = []; - const apiEdgeHashes = []; - const apiEdges = []; + const associationHashes = []; + const associations = []; records.forEach((record: Record, i: number) => { const frozenRecord = record.freezeMinimal(); - const apiEdgeHash = hash(JSON.stringify(record.association)); + const associationHash = hash(JSON.stringify(record.association)); - let apiEdgeHashIndex = apiEdgeHashes.findIndex( - hash => hash === apiEdgeHash, + let associationHashIndex = associationHashes.findIndex( + hash => hash === associationHash, ); - if (apiEdgeHashIndex === -1) { - apiEdgeHashes.push(apiEdgeHash); - apiEdges.push(record.association); - apiEdgeHashIndex = apiEdgeHashes.length - 1; + if (associationHashIndex === -1) { + associationHashes.push(associationHash); + associations.push(record.association); + associationHashIndex = associationHashes.length - 1; } frozenRecords.push({ ...frozenRecord, - apiEdge: apiEdgeHashIndex, + association: associationHashIndex, }); }); - return [apiEdges, ...frozenRecords]; + return [associations, ...frozenRecords]; } public static unpackRecords( @@ -349,10 +353,10 @@ export class Record { qEdge: QEdge, config?: any, ): Record[] { - const [apiEdges, ...frozenRecords] = recordPack; + const [associations, ...frozenRecords] = recordPack; return frozenRecords.map((record: any): Record => { - const apiEdge = apiEdges[record.apiEdge]; - return new Record(record, config, apiEdge, qEdge); + const association = associations[record.association]; + return new Record(record, config, association, qEdge); }); } @@ -402,14 +406,14 @@ export class Record { _getFlattenedEdgeAttributes(attributes: EdgeAttribute[]): EdgeAttribute[] { return attributes ? attributes.reduce((arr: EdgeAttribute[], attribute: EdgeAttribute) => { - attribute.attributes - ? arr.push( - attribute, - ...this._getFlattenedEdgeAttributes(attribute.attributes), - ) - : arr.push(attribute); - return arr; - }, []) + attribute.attributes + ? arr.push( + attribute, + ...this._getFlattenedEdgeAttributes(attribute.attributes), + ) + : arr.push(attribute); + return arr; + }, []) : []; } @@ -520,8 +524,8 @@ export class Record { } returnValue.push({ resource_id: this.config.provenanceUsesServiceProvider - ? "infores:service-provider-trapi" - : "infores:biothings-explorer", + ? "infores:retriever-non-trapi" + : "infores:retriever", resource_role: "aggregator_knowledge_source", upstream_resource_ids: [this.apiInforesCurie], }); @@ -536,31 +540,31 @@ export class Record { export interface FrozenRecord { subject: FrozenNode; object: FrozenNode; - predicate?: string; // not required if given apiEdge, qEdge + predicate?: string; // not required if given association, qEdge qualifiers?: BulkQualifiers; - publications?: string[]; // not required if given apiEdge, qEdge + publications?: string[]; // not required if given association, qEdge recordHash?: string; // always supplied by Record, not required from user - api?: string; // not required if given apiEdge, qEdge - apiInforesCurie?: string; // not required if given apiEdge, qEdge - metaEdgeSource?: string; // not required if given apiEdge, qEdge + api?: string; // not required if given association, qEdge + apiInforesCurie?: string; // not required if given association, qEdge + metaEdgeSource?: string; // not required if given association, qEdge mappedResponse?: MappedResponse; } export interface VerboseFrozenRecord { subject: VerboseFrozenNode; object: VerboseFrozenNode; - association: Association; - predicate?: string; // not required if given apiEdge, qEdge + association: KGAssociationObject; + predicate?: string; // not required if given association, qEdge qualifiers: BulkQualifiers; - publications?: string[]; // not required if given apiEdge, qEdge + publications?: string[]; // not required if given association, qEdge recordHash?: string; // always supplied by Record, not required from user - api?: string; // not required if given apiEdge, qEdge - apiInforesCurie?: string; // not required if given apiEdge, qEdge - metaEdgeSource?: string; // not required if given apiEdge, qEdge + api?: string; // not required if given association, qEdge + apiInforesCurie?: string; // not required if given association, qEdge + metaEdgeSource?: string; // not required if given association, qEdge mappedResponse?: MappedResponse; } -// removes all computed values on assumption that apiEdge and qEdge are saved elsewhere +// removes all computed values on assumption that association and qEdge are saved elsewhere export interface MinimalFrozenRecord { subject: VerboseFrozenNode | MinimalFrozenNode; object: VerboseFrozenNode | MinimalFrozenNode; @@ -585,7 +589,7 @@ export interface FrozenNode { export interface VerboseFrozenNode { original: string; - normalizedInfo?: NodeNormalizerResultObj; // always supplied by Record, not required from user + normalizedInfo?: SRIBioEntity; // always supplied by Record, not required from user qNodeID: string; isSet: boolean; curie: string; @@ -601,12 +605,12 @@ export interface VerboseFrozenNode { export interface MinimalFrozenNode { original: string; - normalizedInfo?: NodeNormalizerResultObj; // always supplied by Record, not required from user + normalizedInfo?: SRIBioEntity; // always supplied by Record, not required from user apiLabel?: string; [additionalProperties: string]: any; // cleanest way to handler undefined properties } -export type RecordPackage = [apiEdges: any[], ...frozenRecords: FrozenRecord[]]; +export type RecordPackage = [associations: any[], ...frozenRecords: FrozenRecord[]]; export interface MappedResponse { trapi_sources?: ProvenanceChainItem[]; @@ -614,20 +618,6 @@ export interface MappedResponse { [mappedItems: string]: any; } -export interface Association { - input_id?: string; - input_type?: string; - output_id?: string; - output_type?: string; - predicate: string; - source?: string; - api_name?: string; - "x-translator"?: any; - qualifiers?: BulkQualifiers; - apiIsPrimaryKnowledgeSource?: boolean; - [additionalProperties: string]: any; -} - export interface QEdge { getInputNode(): QNode; getOutputNode(): QNode; @@ -656,17 +646,6 @@ export interface Identifier { label?: string; } -export interface NodeNormalizerResultObj { - primaryID: string; - equivalentIDs: string[]; - label: string; - labelAliases: string[]; - primaryTypes: string[]; - semanticTypes: string[]; - attributes: { - [attributeID: string]: any; - }; -} export interface BulkQualifiers { [qualifierTypeID: string]: string | string[]; // qualifierValue diff --git a/packages/graph/tsconfig.json b/packages/graph/tsconfig.json new file mode 100644 index 0000000..0c397e8 --- /dev/null +++ b/packages/graph/tsconfig.json @@ -0,0 +1,43 @@ +{ + "$schema": "http://json.schemastore.org/tsconfig", + "extends": "../../tsconfig.base.json", + "compilerOptions": { + "rootDir": "./src", + "outDir": "./built", + "paths": { + "@retriever/smartapi-kg": [ + "../smartapi-kg" + ], + "@retriever/utils": [ + "../utils" + ], + "@retriever/types": [ + "../types" + ], + "@retriever/biomedical_id_resolver": [ + "../biomedical_id_resolver" + ] + } + }, + "include": [ + "./src/**/*" + ], + "exclude": [ + "**/node_modules/**", + "**/__test__/**" + ], + "references": [ + { + "path": "../smartapi-kg" + }, + { + "path": "../utils" + }, + { + "path": "../types" + }, + { + "path": "../biomedical_id_resolver" + } + ] +} diff --git a/packages/node-expansion/package.json b/packages/node-expansion/package.json index 639e58c..eb857b4 100644 --- a/packages/node-expansion/package.json +++ b/packages/node-expansion/package.json @@ -1,5 +1,5 @@ { - "name": "@biothings-explorer/node-expansion", + "name": "@retriever/node-expansion", "version": "1.0.1", "description": "Module for expanding terms to children.", "main": "built/index.js", diff --git a/packages/query_graph_handler/package.json b/packages/query_graph_handler/package.json index 6426eca..9d146d7 100644 --- a/packages/query_graph_handler/package.json +++ b/packages/query_graph_handler/package.json @@ -1,5 +1,5 @@ { - "name": "@biothings-explorer/query_graph_handler", + "name": "@retriever/query_graph_handler", "version": "1.18.0", "description": "A nodejs module to query TRAPI Query Graph", "main": "built/index.js", @@ -18,19 +18,21 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/bte_trapi_query_graph_handler.git" + "url": "git+https://github.com/BioPack-team/retriever" }, "keywords": [ + "BioPack", + "retriever", "id", "conversion", "biomedical" ], - "author": "BioThings Team", + "author": "BioPack Team", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/bte_trapi_query_graph_handler/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/bte_trapi_query_graph_handler#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "devDependencies": { "@types/async": "^3.2.22", "@types/debug": "^4.1.10", @@ -53,12 +55,13 @@ "typescript": "^5.2.2" }, "dependencies": { - "@biothings-explorer/api-response-transform": "workspace:../api-response-transform", - "@biothings-explorer/call-apis": "workspace:../call-apis", - "@biothings-explorer/node-expansion": "workspace:../node-expansion", - "@biothings-explorer/smartapi-kg": "workspace:../smartapi-kg", - "@biothings-explorer/utils": "workspace:../utils", - "@biothings-explorer/types": "workspace:../types", + "@retriever/api-response-transform": "workspace:../api-response-transform", + "@retriever/call-apis": "workspace:../call-apis", + "@retriever/node-expansion": "workspace:../node-expansion", + "@retriever/smartapi-kg": "workspace:../smartapi-kg", + "@retriever/utils": "workspace:../utils", + "@retriever/types": "workspace:../types", + "@retriever/graph": "workspace:../graph", "biolink-model": "workspace:../biolink-model", "biomedical_id_resolver": "workspace:../biomedical_id_resolver", "@sentry/node": "^7.74.1", diff --git a/packages/query_graph_handler/src/batch_edge_query.ts b/packages/query_graph_handler/src/batch_edge_query.ts index f3dab51..f02b35f 100644 --- a/packages/query_graph_handler/src/batch_edge_query.ts +++ b/packages/query_graph_handler/src/batch_edge_query.ts @@ -1,17 +1,17 @@ -import call_api from '@biothings-explorer/call-apis'; -import { redisClient } from '@biothings-explorer/utils'; -import QEdge2APIEdgeHandler, { APIEdge } from './qedge2apiedge'; +import { constructQueries } from '@retriever/call-apis'; +import { LogEntry, SerializableLog } from '@retriever/utils'; +import QEdge2APIEdgeHandler from './qedge2apiedge'; +import { APIEdge, RecordPackage } from '@retriever/graph'; import NodesUpdateHandler from './update_nodes'; import Debug from 'debug'; -const debug = Debug('bte:biothings-explorer-trapi:batch_edge_query'); +const debug = Debug('retriever:batch_edge_query'); import CacheHandler from './cache_handler'; import { threadId } from 'worker_threads'; -import MetaKG from '@biothings-explorer/smartapi-kg'; -import { StampedLog } from '@biothings-explorer/utils'; -import { QueryHandlerOptions } from '@biothings-explorer/types'; -import QEdge from './query_edge'; +import MetaKG from '@retriever/smartapi-kg'; +import { StampedLog } from '@retriever/utils'; +import { QueryHandlerOptions, ThreadMessage } from '@retriever/types'; +import { Record, QEdge } from '@retriever/graph'; import { UnavailableAPITracker } from './types'; -import { Record } from '@biothings-explorer/api-response-transform'; export interface BatchEdgeQueryOptions extends QueryHandlerOptions { recordHashEdgeAttributes: string[]; @@ -25,7 +25,7 @@ export default class BatchEdgeQueryHandler { options: QueryHandlerOptions; resolveOutputIDs: boolean; qEdges: QEdge | QEdge[]; - constructor(metaKG: MetaKG, resolveOutputIDs = true, options?: BatchEdgeQueryOptions) { + constructor(metaKG: MetaKG, options?: BatchEdgeQueryOptions) { this.metaKG = metaKG; this.logs = []; this.caching = options && options.caching; @@ -33,7 +33,6 @@ export default class BatchEdgeQueryHandler { if (options && options.recordHashEdgeAttributes) { this.options.EDGE_ATTRIBUTES_USED_IN_RECORD_HASH = options.recordHashEdgeAttributes; } - this.resolveOutputIDs = resolveOutputIDs; } /** @@ -61,11 +60,62 @@ export default class BatchEdgeQueryHandler { /** * @private */ - async _queryAPIEdges(APIEdges: APIEdge[], unavailableAPIs: UnavailableAPITracker = {}): Promise { - const executor = new call_api(APIEdges, this.options, redisClient); - const records: Record[] = await executor.query(this.resolveOutputIDs, unavailableAPIs); - this.logs = [...this.logs, ...executor.logs]; - return records; + _queryAPIEdges(APIEdges: APIEdge[], unavailableAPIs: UnavailableAPITracker = {}): Promise { + // Skip queueing queries to unavailable APIs + const queries = constructQueries(APIEdges, this.options).filter((query) => { + if (unavailableAPIs[query.APIEdge.query_operation.server]?.skip === true) { + unavailableAPIs[query.APIEdge.query_operation.server].skippedQueries += 1; + return false; + } + return true; + }); + + const queriesByHash = Object.fromEntries(queries.map((query) => [query.hash, query])); + + const qEdge = APIEdges[0].reasoner_edge; + const message = `${queries.length} planned queries for edge ${qEdge.id}`; + debug(message); + this.logs.push(new LogEntry('INFO', null, message).getLog()); + let finishedCount = 0; + const completedLogs = this.logs; + const completedRecords: Record[] = []; + return new Promise((resolve) => { + function listener(msg: ThreadMessage) { + if (msg.type !== 'subQueryResult') return; + const { hash, records, logs, apiUnavailable } = msg.value as { + hash: string; + records: RecordPackage; + logs: SerializableLog[]; + apiUnavailable: boolean; + }; + completedLogs.push(...LogEntry.deserialize(logs)); + completedRecords.push(...Record.unpackRecords(records, qEdge)); + + // Update any APIs that were unavailable for this segment + const server = queriesByHash[hash].APIEdge.query_operation.server; + if (apiUnavailable) { + if (!unavailableAPIs[server]) { + unavailableAPIs[server] = { skip: true, skippedQueries: 0 }; + } + unavailableAPIs[server].skippedQueries += 1; + } + + finishedCount += 1; + if (finishedCount >= queries.length) { + debug(`Total number of records returned for qEdge ${qEdge.id} is ${completedRecords.length}`); + resolve(completedRecords); + global.workerSide.off('message', listener); // Clean up + } + } + global.workerSide.on('message', listener); + global.workerSide.postMessage({ + type: 'subqueryRequest', + value: { + queries: queries.map((query) => query.freeze()), + options: this.options, + }, + }); + }); } /** @@ -100,7 +150,7 @@ export default class BatchEdgeQueryHandler { const equivalentAlreadyIncluded = qEdge .getInputNode() .getEquivalentIDs() - [curie].equivalentIDs.some((equivalentCurie) => reducedCuries.includes(equivalentCurie)); + [curie].equivalentIDs.some((equivalentCurie) => reducedCuries.includes(equivalentCurie)); if (!equivalentAlreadyIncluded) { reducedCuries.push(curie); } else { @@ -112,7 +162,8 @@ export default class BatchEdgeQueryHandler { strippedCuries.push(...nodeStrippedCuries); if (nodeStrippedCuries.length > 0) { debug( - `stripped (${nodeStrippedCuries.length}) duplicate equivalent curies from ${node.id + `stripped (${nodeStrippedCuries.length}) duplicate equivalent curies from ${ + node.id }: ${nodeStrippedCuries.join(',')}`, ); } @@ -133,40 +184,26 @@ export default class BatchEdgeQueryHandler { await this._rmEquivalentDuplicates(qEdges); debug('Node Update Success'); - const cacheHandler = new CacheHandler(this.caching, this.metaKG, this.options); - const { cachedRecords, nonCachedQEdges } = await cacheHandler.categorizeEdges(qEdges); - this.logs = [...this.logs, ...cacheHandler.logs]; + // const cacheHandler = new CacheHandler(this.caching, this.metaKG, this.options); + // const { cachedRecords, nonCachedQEdges } = await cacheHandler.categorizeEdges(qEdges); + // this.logs = [...this.logs, ...cacheHandler.logs]; let queryRecords: Record[]; - if (nonCachedQEdges.length === 0) { - queryRecords = []; - if (global.parentPort) { - global.parentPort.postMessage({ threadId, type: "cacheDone", value: true }); - } - } else { - debug('Start to convert qEdges into APIEdges....'); - const edgeConverter = new QEdge2APIEdgeHandler(nonCachedQEdges, this.metaKG); - const APIEdges = await edgeConverter.convert(nonCachedQEdges); - debug(`qEdges are successfully converted into ${APIEdges.length} APIEdges....`); - this.logs = [...this.logs, ...edgeConverter.logs]; - if (APIEdges.length === 0 && cachedRecords.length === 0) { - return []; - } - const expanded_APIEdges = this._expandAPIEdges(APIEdges); - debug('Start to query APIEdges....'); - queryRecords = await this._queryAPIEdges(expanded_APIEdges, unavailableAPIs); - if (queryRecords === undefined) return; - debug('APIEdges are successfully queried....'); - queryRecords = await this._postQueryFilter(queryRecords); - debug(`Total number of records is (${queryRecords.length})`); - const cacheTask = cacheHandler.cacheEdges(queryRecords); - if (!(process.env.USE_THREADING === 'false')) { - global.cachingTasks?.push(cacheTask); - } else { - await cacheTask; - } + debug('Start to convert qEdges into APIEdges....'); + const edgeConverter = new QEdge2APIEdgeHandler(qEdges, this.metaKG); + const APIEdges = await edgeConverter.convert(qEdges); + debug(`qEdges are successfully converted into ${APIEdges.length} APIEdges....`); + this.logs = [...this.logs, ...edgeConverter.logs]; + if (APIEdges.length === 0) { + return []; } - queryRecords = [...queryRecords, ...cachedRecords]; + const expanded_APIEdges = this._expandAPIEdges(APIEdges); + debug('Start to query APIEdges....'); + queryRecords = await this._queryAPIEdges(expanded_APIEdges, unavailableAPIs); + if (queryRecords === undefined) return; + debug('APIEdges are successfully queried....'); + queryRecords = await this._postQueryFilter(queryRecords); + debug(`Total number of records is (${queryRecords.length})`); debug('Start to update nodes...'); nodeUpdate.update(queryRecords); debug('Update nodes completed!'); diff --git a/packages/query_graph_handler/src/cache_handler.ts b/packages/query_graph_handler/src/cache_handler.ts index d29454c..8303940 100644 --- a/packages/query_graph_handler/src/cache_handler.ts +++ b/packages/query_graph_handler/src/cache_handler.ts @@ -1,17 +1,17 @@ -import { redisClient } from '@biothings-explorer/utils'; +import { redisClient } from '@retriever/utils'; import Debug from 'debug'; -const debug = Debug('bte:biothings-explorer-trapi:cache_handler'); -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +const debug = Debug('retriever:cache_handler'); +import { LogEntry, StampedLog } from '@retriever/utils'; import async from 'async'; import helper from './helper'; import lz4 from 'lz4'; import chunker from 'stream-chunker'; import { Readable, Transform } from 'stream'; -import { Record, RecordPackage } from '@biothings-explorer/api-response-transform'; import { threadId } from 'worker_threads'; import MetaKG from '../../smartapi-kg/built'; -import QEdge from './query_edge'; -import { QueryHandlerOptions } from '@biothings-explorer/types'; +import { QEdge } from '@retriever/graph'; +import { QueryHandlerOptions } from '@retriever/types'; +import { Record, RecordPackage } from '@retriever/graph'; export interface RecordPacksByQedgeMetaKGHash { [QEdgeHash: string]: RecordPackage; @@ -113,7 +113,7 @@ export default class CacheHandler { } async categorizeEdges(qEdges: QEdge[]): Promise<{ cachedRecords: Record[]; nonCachedQEdges: QEdge[] }> { - if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS === "true") { + if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS === 'true') { return { cachedRecords: [], nonCachedQEdges: qEdges, @@ -210,14 +210,14 @@ export default class CacheHandler { } async cacheEdges(queryRecords: Record[]): Promise { - if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS === "true") { - if (global.parentPort) { - global.parentPort.postMessage({ threadId, type: "cacheDone", value: true }); + if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS === 'true') { + if (global.workerSide) { + global.workerSide.postMessage({ threadId, type: 'cacheDone', value: true }); } return; } - if (global.parentPort) { - global.parentPort.postMessage({ threadId, type: "cacheInProgress", value: 1 }); + if (global.workerSide) { + global.workerSide.postMessage({ threadId, type: 'cacheInProgress', value: 1 }); } debug('Start to cache query records.'); try { @@ -228,8 +228,8 @@ export default class CacheHandler { await async.eachSeries(qEdgeHashes, async (hash) => { // lock to prevent caching to/reading from actively caching edge const redisID = 'bte:edgeCache:' + hash; - if (global.parentPort) { - global.parentPort.postMessage({ threadId, type: "addCacheKey", value: redisID }); + if (global.workerSide) { + global.workerSide.postMessage({ threadId, type: 'addCacheKey', value: redisID }); } await redisClient.client.usingLock([`redisLock:${redisID}`, 'redisLock:EdgeCaching'], 600000, async () => { try { @@ -257,7 +257,7 @@ export default class CacheHandler { resolve(); }); }); - if (process.env.QEDGE_CACHE_TIME_S !== "0") { + if (process.env.QEDGE_CACHE_TIME_S !== '0') { await redisClient.client.expireTimeout(redisID, process.env.QEDGE_CACHE_TIME_S || 1800); } } catch (error) { @@ -266,8 +266,8 @@ export default class CacheHandler { `Failed to cache qEdge ${hash} records due to error ${error}. This does not stop other edges from caching nor terminate the query.`, ); } finally { - if (global.parentPort) { - global.parentPort.postMessage({ threadId, type: "completeCacheKey", value: redisID }); + if (global.workerSide) { + global.workerSide.postMessage({ threadId, type: 'completeCacheKey', value: redisID }); } } }); @@ -283,8 +283,8 @@ export default class CacheHandler { } catch (error) { debug(`Caching failed due to ${error}. This does not terminate the query.`); } finally { - if (global.parentPort) { - global.parentPort.postMessage({ threadId, type: "cacheDone", value: 1 }); + if (global.workerSide) { + global.workerSide.postMessage({ threadId, type: 'cacheDone', value: 1 }); } } } diff --git a/packages/query_graph_handler/src/edge_manager.ts b/packages/query_graph_handler/src/edge_manager.ts index 543a6ea..fb178ef 100644 --- a/packages/query_graph_handler/src/edge_manager.ts +++ b/packages/query_graph_handler/src/edge_manager.ts @@ -1,20 +1,22 @@ import _ from 'lodash'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; -import BTEError from './exceptions/bte_error'; +import { LogEntry, StampedLog } from '@retriever/utils'; +import { RetrieverError } from '@retriever/types'; import Debug from 'debug'; -const debug = Debug('bte:biothings-explorer-trapi:edge-manager'); +const debug = Debug('retriever:edge-manager'); import * as config from './config'; import BatchEdgeQueryHandler, { BatchEdgeQueryOptions } from './batch_edge_query'; -import { Telemetry } from '@biothings-explorer/utils'; -import QEdge from './query_edge'; -import MetaKG from '@biothings-explorer/smartapi-kg'; -import { QueryHandlerOptions } from '@biothings-explorer/types'; -import { Record } from '@biothings-explorer/api-response-transform'; +import { Telemetry } from '@retriever/utils'; +import { Record, QEdge } from '@retriever/graph'; +import MetaKG from '@retriever/smartapi-kg'; +import { QueryHandlerOptions } from '@retriever/types'; import { UnavailableAPITracker } from './types'; import { RecordsByQEdgeID } from './results_assembly/query_results'; import path from 'path'; import { promises as fs } from 'fs'; +const MAX_RECORDS_PER_EDGE = parseInt(process.env.MAX_RECORDS_PER_EDGE ?? '100000'); +const MAX_RECORDS_PER_QUERY = parseInt(process.env.MAX_RECORDS_PER_EDGE ?? '200000'); + export default class QueryEdgeManager { private _qEdges: QEdge[]; private _metaKG: MetaKG; @@ -108,7 +110,7 @@ export default class QueryEdgeManager { } debug( `(5) Sending next edge '${nextQEdge.getID()}' ` + - `WITH entity count...(${nextQEdge.subject.entity_count || nextQEdge.object.entity_count})`, + `WITH entity count...(${nextQEdge.subject.entity_count || nextQEdge.object.entity_count})`, ); return this.preSendOffCheck(nextQEdge); } @@ -117,9 +119,9 @@ export default class QueryEdgeManager { this._qEdges.forEach((qEdge) => { debug( `'${qEdge.getID()}'` + - ` : (${qEdge.subject.entity_count || 0}) ` + - `${qEdge.reverse ? '<--' : '-->'}` + - ` (${qEdge.object.entity_count || 0})`, + ` : (${qEdge.subject.entity_count || 0}) ` + + `${qEdge.reverse ? '<--' : '-->'}` + + ` (${qEdge.object.entity_count || 0})`, ); }); } @@ -127,8 +129,9 @@ export default class QueryEdgeManager { _logSkippedQueries(unavailableAPIs: UnavailableAPITracker): void { Object.entries(unavailableAPIs).forEach(([api, { skippedQueries }]) => { if (skippedQueries > 0) { - const skipMessage = `${skippedQueries} additional quer${skippedQueries > 1 ? 'ies' : 'y'} to ${api} ${skippedQueries > 1 ? 'were' : 'was' - } skipped as the API was unavailable.`; + const skipMessage = `${skippedQueries} additional quer${skippedQueries > 1 ? 'ies' : 'y'} to ${api} ${ + skippedQueries > 1 ? 'were' : 'was' + } skipped as the API was unavailable.`; debug(skipMessage); this.logs.push(new LogEntry('WARNING', null, skipMessage).getLog()); } @@ -148,7 +151,7 @@ export default class QueryEdgeManager { (obj_count > max && sub_count == 0) || (obj_count > max && sub_count > max) ) { - throw new BTEError(`Max number of entities exceeded (${max}) in '${nextQEdge.getID()}'`); + throw new RetrieverError(`Max number of entities exceeded (${max}) in '${nextQEdge.getID()}'`); } } @@ -194,7 +197,7 @@ export default class QueryEdgeManager { const objectCuries = qEdge.object.curie; debug( `'${qEdge.getID()}' Reversed[${qEdge.reverse}] (${JSON.stringify(subjectCuries.length || 0)})` + - `--(${JSON.stringify(objectCuries.length || 0)}) entities / (${records.length}) records.`, + `--(${JSON.stringify(objectCuries.length || 0)}) entities / (${records.length}) records.`, ); // debug(`IDS SUB ${JSON.stringify(sub_count)}`) // debug(`IDS OBJ ${JSON.stringify(obj_count)}`) @@ -301,45 +304,6 @@ export default class QueryEdgeManager { currentQEdge.storeRecords(filteredRecords); } - /** - * Unused - */ - // updateNeighborsEdgeRecords(currentQEdge) { - // //update and filter only immediate neighbors - // debug(`Updating neighbors...`); - // const currentQEdgeID = currentQEdge.getID(); - // //get neighbors of this edges subject that are not this edge - // let left_connections = currentQEdge.subject.getConnections(); - // left_connections = left_connections.filter((qEdgeID) => qEdgeID !== currentQEdgeID); - // //get neighbors of this edges object that are not this edge - // let right_connections = currentQEdge.object.getConnections(); - // right_connections = right_connections.filter((qEdgeID) => qEdgeID !== currentQEdgeID); - // debug(`(${left_connections})<--edge neighbors-->(${right_connections})`); - // if (left_connections.length) { - // //find edge by id - // left_connections.forEach((qEdgeID) => { - // const edge = this._qEdges.find((edge) => edge.getID() == qEdgeID); - // if (edge && edge.records.length) { - // debug(`Updating "${edge.getID()}" neighbor edge of ${currentQEdgeID}`); - // debug(`Updating neighbor (X)<----()`); - // this.updateEdgeRecords(edge); - // } - // }); - // } - // - // if (right_connections.length) { - // //find edge by id - // right_connections.forEach((neighbor_id) => { - // const edge = this._qEdges.find((edge) => edge.getID() == neighbor_id); - // if (edge && edge.records.length) { - // debug(`Updating "${edge.getID()}" neighbor edge of ${currentQEdgeID}`); - // debug(`Updating neighbor ()---->(X)`); - // this.updateEdgeRecords(edge); - // } - // }); - // } - // } - updateAllOtherEdges(currentQEdge: QEdge): void { //update and filter all other edges debug(`Updating all other edges...`); @@ -354,11 +318,9 @@ export default class QueryEdgeManager { } _createBatchQueryHandler(qEdge: QEdge, metaKG: MetaKG): BatchEdgeQueryHandler { - const handler = new BatchEdgeQueryHandler(metaKG, this.options.resolveOutputIDs, { - caching: this.options.caching, - submitter: this.options.submitter, + const handler = new BatchEdgeQueryHandler(metaKG, { + ...this.options, recordHashEdgeAttributes: config.EDGE_ATTRIBUTES_USED_IN_RECORD_HASH, - provenanceUsesServiceProvider: this.options.provenanceUsesServiceProvider, } as BatchEdgeQueryOptions); handler.setEdges(qEdge); return handler; @@ -396,13 +358,14 @@ export default class QueryEdgeManager { new LogEntry( 'INFO', null, - `Executing ${currentQEdge.getID()}${currentQEdge.isReversed() ? ' (reversed)' : ''}: ${currentQEdge.subject.id + `Executing ${currentQEdge.getID()}${currentQEdge.isReversed() ? ' (reversed)' : ''}: ${ + currentQEdge.subject.id } ${currentQEdge.isReversed() ? '<--' : '-->'} ${currentQEdge.object.id}`, ).getLog(), ); debug(`(5) Executing current edge >> "${currentQEdge.getID()}"`); //execute current edge query - const queryRecords = await queryBatchHandler.query(queryBatchHandler.qEdges, unavailableAPIs); + let queryRecords = await queryBatchHandler.query(queryBatchHandler.qEdges, unavailableAPIs); this.logs = [...this.logs, ...queryBatchHandler.logs]; if (queryRecords === undefined) return; // create an edge execution summary @@ -412,6 +375,7 @@ export default class QueryEdgeManager { const cached = this.logs.filter( ({ data }) => data?.qEdgeID === currentQEdge.id && data?.type === 'cacheHit', ).length; + total += cached; this.logs .filter(({ data }) => data?.qEdgeID === currentQEdge.id && data?.type === 'query') .forEach(({ data }) => { @@ -422,7 +386,7 @@ export default class QueryEdgeManager { new LogEntry( 'INFO', null, - `${currentQEdge.id} execution: ${total} queries (${success} success/${fail} fail) and (${cached}) cached qEdges return (${queryRecords.length}) records`, + `${currentQEdge.id} execution: ${total} queries (${success} success/${fail} fail/${cached} cached) return (${queryRecords.length}) records`, {}, ).getLog(), ); @@ -439,6 +403,43 @@ export default class QueryEdgeManager { span.finish(); return; } + + // Check if record count threatens stability + const totalRecords = + this._qEdges.reduce((total, qEdge) => { + return total + qEdge.records.length; + }, 0) + queryRecords.length; + let maxRecordsMessage = [ + `Qedge ${currentQEdge.id}`, + `obtained ${queryRecords.length} records,`, + queryRecords.length === MAX_RECORDS_PER_EDGE ? 'meeting' : 'exceeding', + `maximum of ${MAX_RECORDS_PER_QUERY}`, + `Truncating records for this edge to ${MAX_RECORDS_PER_EDGE}.`, + `Your query may be too general?`, + ]; + if (totalRecords > MAX_RECORDS_PER_QUERY) { + maxRecordsMessage = maxRecordsMessage.slice(0, 2); + maxRecordsMessage.push( + ...[ + `totalling ${totalRecords} for this query.`, + `This exceeds the per-query maximum of ${MAX_RECORDS_PER_QUERY}.`, + `For stability purposes, this query is terminated.`, + `Please consider further refining your query.`, + ], + ); + debug(maxRecordsMessage.join(' ')); + this.logs.push(new LogEntry('WARNING', null, maxRecordsMessage.join(' ')).getLog()); + Telemetry.captureException(new Error(`Stopped on globalMaxRecords (exceeded ${MAX_RECORDS_PER_QUERY})`)); + return; + } + + if (queryRecords.length > MAX_RECORDS_PER_EDGE) { + debug(maxRecordsMessage.join(' ')); + this.logs.push(new LogEntry('WARNING', null, maxRecordsMessage.join(' ')).getLog()); + + queryRecords = queryRecords.slice(0, MAX_RECORDS_PER_EDGE); + } + // storing records will trigger a node entity count update currentQEdge.storeRecords(queryRecords); diff --git a/packages/query_graph_handler/src/exceptions/bte_error.ts b/packages/query_graph_handler/src/exceptions/bte_error.ts deleted file mode 100644 index 986234b..0000000 --- a/packages/query_graph_handler/src/exceptions/bte_error.ts +++ /dev/null @@ -1,16 +0,0 @@ -export default class BTEError extends Error { - statusCode: string; - constructor(message = 'Query aborted', name = 'QueryAborted', code = '501', ...params: any) { - super(...params); - - if (Error.captureStackTrace) { - Error.captureStackTrace(this, BTEError); - } - - this.name = name; - this.message = message; - this.statusCode = code; - } -} - -module.exports = BTEError; diff --git a/packages/query_graph_handler/src/exceptions/invalid_query_graph_error.ts b/packages/query_graph_handler/src/exceptions/invalid_query_graph_error.ts deleted file mode 100644 index 9974b54..0000000 --- a/packages/query_graph_handler/src/exceptions/invalid_query_graph_error.ts +++ /dev/null @@ -1,16 +0,0 @@ -export default class InvalidQueryGraphError extends Error { - statusCode: number; - constructor(message = 'Your Input Query Graph is invalid.', ...params: string[]) { - super(...params); - - Object.setPrototypeOf(this, InvalidQueryGraphError.prototype); - - if (Error.captureStackTrace) { - Error.captureStackTrace(this, InvalidQueryGraphError); - } - - this.name = 'InvalidQueryGraphError'; - this.message = message; - this.statusCode = 400; - } -} diff --git a/packages/query_graph_handler/src/index.ts b/packages/query_graph_handler/src/index.ts index fb9da3b..c98f606 100644 --- a/packages/query_graph_handler/src/index.ts +++ b/packages/query_graph_handler/src/index.ts @@ -1,21 +1,16 @@ -import MetaKG from '@biothings-explorer/smartapi-kg'; +import MetaKG, { SmartAPISpec } from '@retriever/smartapi-kg'; import path from 'path'; -import QueryGraph from './query_graph'; -import KnowledgeGraph from './graph/knowledge_graph'; import TrapiResultsAssembler from './results_assembly/query_results'; -import InvalidQueryGraphError from './exceptions/invalid_query_graph_error'; +import { InvalidQueryGraphError } from '@retriever/types'; import Debug from 'debug'; -const debug = Debug('bte:biothings-explorer-trapi:main'); -import Graph from './graph/graph'; +const debug = Debug('retriever:main'); import EdgeManager from './edge_manager'; import _ from 'lodash'; import QEdge2APIEdgeHandler from './qedge2apiedge'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +import { LogEntry, StampedLog } from '@retriever/utils'; import { promises as fs } from 'fs'; -import { getDescendants } from '@biothings-explorer/node-expansion'; +import { getDescendants } from '@retriever/node-expansion'; import { resolveSRI, SRINodeNormFailure } from 'biomedical_id_resolver'; -import KGNode from './graph/kg_node'; -import KGEdge from './graph/kg_edge'; import { TrapiAuxGraphCollection, TrapiAuxiliaryGraph, @@ -24,16 +19,12 @@ import { TrapiResponse, TrapiResult, } from './types'; -import { QueryHandlerOptions } from '@biothings-explorer/types'; -import BTEGraph from './graph/graph'; -import QEdge from './query_edge'; -import { Telemetry } from '@biothings-explorer/utils'; +import { QueryHandlerOptions } from '@retriever/types'; +import { BTEGraph, QEdge, QNode, KGNode, KGEdge, KnowledgeGraph, QueryGraph } from "@retriever/graph"; +import { Telemetry } from '@retriever/utils'; // Exports for external availability export * from './types'; -export { default as QEdge } from './query_edge'; -export { default as QNode } from './query_node'; -export { default as InvalidQueryGraphError } from './exceptions/invalid_query_graph_error'; export * from './qedge2apiedge'; export default class TRAPIQueryHandler { @@ -76,8 +67,7 @@ export default class TRAPIQueryHandler { const inforesIds: string[] = []; const unregisteredAPIs: string[] = []; - // TODO typing for smartapiRegistration - JSON.parse(smartapiRegistry).hits.forEach((smartapiRegistration) => { + JSON.parse(smartapiRegistry).hits.forEach((smartapiRegistration: SmartAPISpec) => { smartapiIds.push(smartapiRegistration._id); inforesIds.push(smartapiRegistration.info?.['x-translator']?.infores); }); @@ -97,7 +87,7 @@ export default class TRAPIQueryHandler { const metaKG = new MetaKG(this.path, this.predicatePath); debug( `Query options are: ${JSON.stringify({ - ...this.options, + ..._.omit(this.options, "apiList"), schema: this.options.schema ? this.options.schema.info.version : 'not included', })}`, ); @@ -175,8 +165,8 @@ export default class TRAPIQueryHandler { { resource_id: source, resource_role: 'primary_knowledge_source' }, { resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', + ? 'infores:retriever-non-trapi' + : 'infores:retriever', resource_role: 'aggregator_knowledge_source', }, ]); @@ -222,8 +212,8 @@ export default class TRAPIQueryHandler { boundEdge.addSource([ { resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', + ? 'infores:retriever-non-trapi' + : 'infores:retriever', resource_role: 'primary_knowledge_source', }, ]); @@ -390,7 +380,7 @@ export default class TRAPIQueryHandler { _initializeResponse(): void { this.knowledgeGraph = new KnowledgeGraph(this.options?.apiList?.include); this.trapiResultsAssembler = new TrapiResultsAssembler(this.options); - this.bteGraph = new Graph(); + this.bteGraph = new BTEGraph(); this.bteGraph.subscribe(this.knowledgeGraph); } @@ -572,8 +562,8 @@ export default class TRAPIQueryHandler { new LogEntry( 'INFO', null, - `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${ - cached ? ` (${cached} cached qEdges)` : '' + `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) subqueries${ + cached ? ` (${cached} cached subqueries)` : '' } returned results from(${sources.length}) unique API${sources.length === 1 ? 's' : ''}`, ).getLog(), new LogEntry('INFO', null, `APIs: ${sources.join(', ')} `).getLog(), diff --git a/packages/query_graph_handler/src/qedge2apiedge.ts b/packages/query_graph_handler/src/qedge2apiedge.ts index 29e592d..170d17c 100644 --- a/packages/query_graph_handler/src/qedge2apiedge.ts +++ b/packages/query_graph_handler/src/qedge2apiedge.ts @@ -1,48 +1,14 @@ import _ from 'lodash'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +import { LogEntry, StampedLog } from '@retriever/utils'; import * as config from './config'; const CURIE_WITH_PREFIXES = ['MONDO', 'DOID', 'UBERON', 'EFO', 'HP', 'CHEBI', 'CL', 'MGI', 'NCIT']; import Debug from 'debug'; -import QEdge from './query_edge'; -import MetaKG from '@biothings-explorer/smartapi-kg'; -import { SmartAPIKGOperationObject } from '@biothings-explorer/smartapi-kg'; +import { APIEdge, BatchAPIEdge, MetaXEdge, NonBatchAPIEdge, QEdge, TemplateBatchAPIEdge, TemplateNonBatchAPIEdge } from '@retriever/graph'; +import MetaKG from '@retriever/smartapi-kg'; +import { SmartAPIKGOperationObject } from '@retriever/smartapi-kg'; import { SRIBioEntity } from 'biomedical_id_resolver'; -const debug = Debug('bte:biothings-explorer-trapi:qedge2btedge'); +const debug = Debug('retriever:qedge2btedge'); -export interface MetaXEdge extends SmartAPIKGOperationObject { - reasoner_edge: QEdge; -} - -export interface TemplatedInput { - queryInputs: string | string[]; - [additionalAttributes: string]: string | string[]; -} - -export interface APIEdge extends MetaXEdge { - input: string | string[] | TemplatedInput; - input_resolved_identifiers: { - [curie: string]: SRIBioEntity; - }; - original_input: { - [equivalentCurie: string]: string; - }; -} - -export interface NonBatchAPIEdge extends APIEdge { - input: string; -} - -export interface BatchAPIEdge extends APIEdge { - input: string[]; -} - -export interface TemplateNonBatchAPIEdge extends APIEdge { - input: TemplatedInput; -} - -export interface TemplateBatchAPIEdge extends APIEdge { - input: TemplatedInput; -} export default class QEdge2APIEdgeHandler { qEdges: QEdge[]; diff --git a/packages/query_graph_handler/src/results_assembly/pfocr.ts b/packages/query_graph_handler/src/results_assembly/pfocr.ts index 1afd52b..f4dfd2e 100644 --- a/packages/query_graph_handler/src/results_assembly/pfocr.ts +++ b/packages/query_graph_handler/src/results_assembly/pfocr.ts @@ -1,9 +1,9 @@ import axios from 'axios'; import Debug from 'debug'; -const debug = Debug('bte:biothings-explorer-trapi:pfocr'); +const debug = Debug('retriever:pfocr'); import { intersection } from '../utils'; import _ from 'lodash'; -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +import { LogEntry, StampedLog } from '@retriever/utils'; import { TrapiResult } from '../types'; // the minimum acceptable intersection size between the CURIEs diff --git a/packages/query_graph_handler/src/results_assembly/query_results.ts b/packages/query_graph_handler/src/results_assembly/query_results.ts index 026556f..a52f77c 100644 --- a/packages/query_graph_handler/src/results_assembly/query_results.ts +++ b/packages/query_graph_handler/src/results_assembly/query_results.ts @@ -1,10 +1,10 @@ -import { LogEntry, StampedLog } from '@biothings-explorer/utils'; +import { LogEntry, StampedLog } from '@retriever/utils'; import { TrapiResult } from '../types'; import Debug from 'debug'; import { zip } from 'lodash'; -const debug = Debug('bte:biothings-explorer-trapi:QueryResult'); +const debug = Debug('retriever:QueryResult'); import { getScores, calculateScore, ScoreCombos } from './score'; -import { Record } from '@biothings-explorer/api-response-transform'; +import { Record } from '@retriever/graph'; import { enrichTrapiResultsWithPfocrFigures } from './pfocr'; import * as config from '../config'; @@ -432,8 +432,8 @@ export default class TrapiResultsAssembler { analyses: [ { resource_id: this.options.provenanceUsesServiceProvider - ? `infores:service-provider-trapi` - : `infores:biothings-explorer`, + ? `infores:retriever-non-trapi` + : `infores:retriever`, edge_bindings: {}, score: score, }, diff --git a/packages/query_graph_handler/src/results_assembly/score.ts b/packages/query_graph_handler/src/results_assembly/score.ts index 5b55c4c..2ef0dd4 100644 --- a/packages/query_graph_handler/src/results_assembly/score.ts +++ b/packages/query_graph_handler/src/results_assembly/score.ts @@ -1,12 +1,12 @@ import Debug from 'debug'; import axios from 'axios'; -const debug = Debug('bte:biothings-explorer-trapi:score'); +const debug = Debug('retriever:score'); import os from 'os'; import async from 'async'; import _ from 'lodash'; import { ConsolidatedSolutionRecord, RecordsByQEdgeID } from './query_results'; -import { Telemetry } from '@biothings-explorer/utils'; +import { Telemetry } from '@retriever/utils'; const tuning_param = 2.0; diff --git a/packages/query_graph_handler/src/types.ts b/packages/query_graph_handler/src/types.ts index 77ac472..4eda85e 100644 --- a/packages/query_graph_handler/src/types.ts +++ b/packages/query_graph_handler/src/types.ts @@ -1,4 +1,4 @@ -import { TrapiLog } from '@biothings-explorer/utils'; +import { TrapiLog } from '@retriever/utils'; export interface TrapiQNode { ids?: string[]; diff --git a/packages/query_graph_handler/src/update_nodes.ts b/packages/query_graph_handler/src/update_nodes.ts index e6df65a..ce3bb98 100644 --- a/packages/query_graph_handler/src/update_nodes.ts +++ b/packages/query_graph_handler/src/update_nodes.ts @@ -1,10 +1,9 @@ import { resolveSRI } from 'biomedical_id_resolver'; import Debug from 'debug'; import { ResolverInput, SRIResolverOutput } from 'biomedical_id_resolver'; -import { Record } from '@biothings-explorer/api-response-transform'; -import QEdge from './query_edge'; -import { NodeNormalizerResultObj } from '../../api-response-transform/built'; -const debug = Debug('bte:biothings-explorer-trapi:nodeUpdateHandler'); +import { Record, QEdge } from '@retriever/graph'; +import { SRIBioEntity } from 'biomedical_id_resolver'; +const debug = Debug('retriever:nodeUpdateHandler'); export interface CuriesByCategory { [category: string]: string[]; @@ -64,7 +63,7 @@ export default class NodesUpdateHandler { return; } - _createEquivalentIDsObject(record: Record): { [curie: string]: NodeNormalizerResultObj } { + _createEquivalentIDsObject(record: Record): { [curie: string]: SRIBioEntity } { if (record.object.normalizedInfo !== undefined) { return { [record.object.curie]: record.object.normalizedInfo, diff --git a/packages/query_graph_handler/tsconfig.json b/packages/query_graph_handler/tsconfig.json index b712fdc..521ebb0 100644 --- a/packages/query_graph_handler/tsconfig.json +++ b/packages/query_graph_handler/tsconfig.json @@ -5,12 +5,13 @@ "outDir": "./built", "rootDir": "./src", "paths": { - "@biothings-explorer/call-apis": ["../call-apis"], + "@retriever/call-apis": ["../call-apis"], "biolink-model": ["../biolink-model"], "biomedical_id_resolver": ["../biomedical_id_resolver"], - "@biothings-explorer/smartapi-kg": ["../smartapi-kg"], - "@biothings-explorer/utils": ["../utils"], - "@biothings-explorer/types": ["../types"] + "@retriever/smartapi-kg": ["../smartapi-kg"], + "@retriever/utils": ["../utils"], + "@retriever/types": ["../types"], + "@retriever/graph": ["../graph"] } }, "include": ["./src/**/*", "./src/biolink.json", "./src/smartapi_specs.json", "./src/predicates.json"], @@ -33,6 +34,9 @@ }, { "path": "../types" + }, + { + "path": "../graph" } ] } diff --git a/packages/server/data/predicates.json b/packages/server/data/predicates.json index 1591965..edd2d12 100644 --- a/packages/server/data/predicates.json +++ b/packages/server/data/predicates.json @@ -1 +1 @@ -[{"association":{"api_name":"OpenPredict API","smartapi":{"id":"e9f69b81e755e163fdf6c41a2b5e07c0","meta":{"date_created":"2021-01-29T00:00:15.735608+00:00","last_updated":"2024-03-14T07:01:19.637825+00:00","url":"https://openpredict.semanticscience.org/openapi.json","username":"vemonet"}},"x-translator":{"component":"KP","team":["Clinical Data Provider"],"infores":"infores:openpredict"},"x-trapi":{}},"tags":["reasoner","trapi","models","openpredict","translator"],"query_operation":{"path":"/query","server":"https://openpredict.transltr.io","method":"post"},"predicates_path":"/meta_knowledge_graph","predicates":{"biolink:Disease":{"biolink:Drug":[{"predicate":"biolink:treats"}],"biolink:Disease":[{"predicate":"biolink:similar_to"}]}},"nodes":{"biolink:Disease":{"id_prefixes":["OMIM"]},"biolink:Drug":{"id_prefixes":["DRUGBANK"]}}},{"association":{"api_name":"Connections Hypothesis Provider API","smartapi":{"id":"23f770568b92b7a82063989b3ddd9706","meta":{"date_created":"2023-05-19T16:49:31.063624+00:00","last_updated":"2024-03-14T07:01:03.027368+00:00","url":"https://raw.githubusercontent.com/di2ag/chp_metadata/master/smartapi-1.4.yaml","username":"GregHydeDartmouth"}},"x-translator":{"component":"KP","team":["Connections Hypothesis 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The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"subject.umls:C0055723","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). 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All responses are in JSON format and can be retrieved as either JSON or JSON-LD linked data format.","termsOfService":"https://www.pharmgkb.org/page/policies","title":"PharmGKB REST API","version":"1.0","x-translator":{"biolink-version":"3.5.0","component":"KP","infores":"infores:pharmgkb","team":["Service Provider"]}},"paths":{"/data/connection":{"get":{"parameters":[{"description":"the subject ID (PA# or numeric ID)","example":"PA154426155","in":"query","name":"object1Id","schema":{"type":"string"}},{"description":"the subject name (can be RSID for Variants)","in":"query","name":"object1Name","schema":{"type":"string"}},{"description":"the subject PharmGKB type","in":"query","name":"object1Type","schema":{"type":"string"}},{"description":"the object ID (PA# or numeric ID)","in":"query","name":"object2Id","schema":{"type":"string"}},{"description":"the object name (can be RSID for Variants)","in":"query","name":"object2Name","schema":{"type":"string"}},{"description":"the object 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Learn more about [MyGene.info](https://docs.mygene.info/en/latest/index.html)","termsOfService":"http://mygene.info/terms/","title":"MyGene.info API","version":"3.0","x-translator":{"biolink-version":"3.5.0","component":"KP","infores":"infores:mygene-info","team":["Service Provider"]}},"paths":{"/gene/{id}":{"get":{"description":"By default, this will return the complete gene annotation object in JSON format. See [here](https://docs.mygene.info/en/latest/doc/annotation_service.html#returned-object) for an example and [here](https://docs.mygene.info/en/latest/doc/data.html#gene-object) for more details. If the input gene ID is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the gene object. Multiple attributes should be separated by commas. If an attribute is not available for a specific gene object, it will be ignored. Note that the attribute names are case-sensitive.\n\nJust like the gene query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"description":"Entrez (\"1017\") or Ensembl gene id (\"ENSG00000123374\"). A retired Entrez Gene id works too if it is replaced by a new one, e.g., 245794. 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help desk","url":"https://monarchinitiative.org/help","x-role":"responsible developer"},"description":"The [Monarch Application Programming Interface (API)](https://api-v3.monarchinitiative.org/v3/docs#/) is a RESTful API that wraps functionality required by the [Monarch Initiative website](https://monarchinitiative.org/), including the retrieval of disease, gene, and phenotype associations, phenotypic profile comparisons, and other graph operations.","termsOfService":"https://monarchinitiative.org/terms","title":"Monarch API","version":"0.1.0","x-translator":{"biolink-version":"3.5.3","component":"KP","infores":"infores:monarchinitiative","team":["Service Provider","Standards Reference Implementation Team"]}},"paths":{"/v3/api/association":{"get":{"description":"Retrieves all associations for a given entity, or between two entities.","operationId":"_get_associations_v3_api_association_get","parameters":[{"in":"query","name":"category","required":false,"schema":{"items":{"$ref":"#/components/schemas/AssociationCategory"},"title":"Category","type":"array"}},{"in":"query","name":"subject","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject"}},{"in":"query","name":"subject_category","required":false,"schema":{"items":{"$ref":"#/components/schemas/EntityCategory"},"title":"Subject Category","type":"array"}},{"in":"query","name":"subject_namespace","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject Namespace"}},{"in":"query","name":"subject_taxon","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject 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\n Node: Entity details for the specified id","operationId":"_get_entity_v3_api_entity__id__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to retrieve","type":"string"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/Node"},{"type":"string"}],"title":"Response Get Entity V3 Api Entity Id Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Get Entity","tags":["entity"]}},"/v3/api/entity/{id}/{category}":{"get":{"description":"Retrieves association table data for a given entity and association type\n\nArgs:
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\n category (str): Category of association to retrieve association table data for, ex: biolink:DiseaseToPhenotypicFeatureAssociation
\n Path (str, optional): Path string to limit results to a subset. Defaults to None.
\n pagination (PaginationParams, optional): Pagination parameters. Defaults to Depends().
\n\nReturns:
\n AssociationResults: Association table data for the specified entity and association type","operationId":"_association_table_v3_api_entity__id___category__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to retrieve association table data for","type":"string"}},{"in":"path","name":"category","required":true,"schema":{"allOf":[{"$ref":"#/components/schemas/AssociationCategory"}],"title":"Type of association to retrieve association table data for"}},{"in":"query","name":"query","required":false,"schema":{"title":"query string to limit results to a subset","type":"string"}},{"in":"query","name":"sort","required":false,"schema":{"items":{"type":"string"},"title":"Sort results by a list of field + direction statements","type":"array"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}},{"in":"query","name":"download","required":false,"schema":{"default":false,"title":"Download the results as a file","type":"boolean"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/AssociationTableResults"},{"type":"string"}],"title":"Response Association Table V3 Api Entity Id Category Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Association Table","tags":["entity"]}},"/v3/api/histopheno/{id}":{"get":{"description":"Retrieves the entity with the specified id","operationId":"_get_histopheno_v3_api_histopheno__id__get","parameters":[{"in":"path","name":"id","required":true,"schema":{"title":"ID of the entity to get histopheno data for","type":"string"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}}],"responses":{"200":{"content":{"application/json":{"schema":{"anyOf":[{"$ref":"#/components/schemas/HistoPheno"},{"type":"string"}],"title":"Response Get Histopheno V3 Api Histopheno Id Get"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Get Histopheno","tags":["histopheno"]}},"/v3/api/search":{"get":{"description":"Search for entities by label, with optional filters\n\nArgs:\n q (str, optional): Query string. Defaults to \"*:*\".\n category (str, optional): Filter by biolink model category. Defaults to None.\n in_taxon_label (str, optional): Filter by taxon label. Defaults to None.\n offset (int, optional): Offset for pagination. Defaults to 0.\n limit (int, optional): Limit results. Defaults to 20.\n\nReturns:\n EntityResults","operationId":"search_v3_api_search_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"title":"Q","type":"string"}},{"in":"query","name":"category","required":false,"schema":{"anyOf":[{"items":{"$ref":"#/components/schemas/EntityCategory"},"type":"array"}],"title":"Category"}},{"in":"query","name":"in_taxon_label","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"In Taxon Label"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Search","tags":["search"]}},"/v3/api/autocomplete":{"get":{"description":"Autocomplete for entities by label\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["search"]}},"/v3/api/mappings":{"get":{"operationId":"mappings_v3_api_mappings_get","parameters":[{"in":"query","name":"entity_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Entity Id"}},{"in":"query","name":"subject_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject Id"}},{"in":"query","name":"predicate_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Predicate Id"}},{"in":"query","name":"object_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Object Id"}},{"in":"query","name":"mapping_justification","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Mapping Justification"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Mappings","tags":["search"]}},"/v3/api/semsim/autocomplete":{"get":{"description":"Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations.\nNote: This API endpoint is experimental and may evolve or disappear over time.\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_semsim_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["semsim"]}},"/v3/api/semsim/compare/{subjects}/{objects}":{"get":{"description":"Get pairwise similarity between two sets of terms\n\nArgs:
\n subjects (str, optional): List of subjects for comparison. Defaults to \"\".
\n objects (str, optional): List of objects for comparison. Defaults to \"\".
\n\nReturns:
\n TermSetPairwiseSimilarity: Pairwise similarity between subjects and objects","operationId":"_compare_v3_api_semsim_compare__subjects___objects__get","parameters":[{"in":"path","name":"subjects","required":true,"schema":{"title":"List of subjects for comparison","type":"string"}},{"in":"path","name":"objects","required":true,"schema":{"title":"List of objects for comparison","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Compare","tags":["semsim"]}},"/v3/api/semsim/compare":{"post":{"description":"Pairwise similarity between two sets of terms
\n
\n Example:
\n

\n{\n  \"subjects\": [\"MP:0010771\",\"MP:0002169\",\"MP:0005391\",\"MP:0005389\",\"MP:0005367\"],\n  \"objects\": [\"HP:0004325\",\"HP:0000093\",\"MP:0006144\"]\n}\n
","operationId":"_post_compare_v3_api_semsim_compare_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimCompareRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Compare","tags":["semsim"]}},"/v3/api/semsim/search/{termset}/{group}":{"get":{"description":"Search for terms in a termset\n\nArgs:
\n termset (str, optional): Comma separated list of term IDs to find matches for.
\n group (str, optional): Group of entities to search within (e.g. Human Genes)
\n limit (int, optional): Limit the number of results. Defaults to 10.\n\nReturns:
\n List[str]: List of matching terms","operationId":"_search_v3_api_semsim_search__termset___group__get","parameters":[{"in":"path","name":"termset","required":true,"schema":{"title":"Termset to search","type":"string"}},{"in":"path","name":"group","required":true,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimSearchGroup"}],"title":"Group of entities to search within (e.g. Human Genes)"}},{"in":"query","name":"limit","required":false,"schema":{"default":10,"maximum":50,"minimum":1,"title":"Limit","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Search","tags":["semsim"]}},"/v3/api/semsim/search":{"post":{"description":"Search for terms in a termset
\n
\n Example:
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There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API","tags":["query"]}},"/team/{team_name}/query":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name","tags":["query"]}},"/asyncquery":{"post":{"parameters":[{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/smartapi/{smartapi_id}/asyncquery":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"ITRB Production server","url":"https://bte.transltr.io/v1","x-maturity":"production"},{"description":"ITRB Test server","url":"https://bte.test.transltr.io/v1","x-maturity":"testing"},{"description":"ITRB CI server","url":"https://bte.ci.transltr.io/v1","x-maturity":"staging"},{"description":"Non-ITRB dev (internal 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TRAPI","version":"1.0.0","x-translator":{"biolink-version":"3.1.1","component":"ARS","infores":"infores:ars","team":["Link Brokers"]},"x-trapi":{"asyncquery":false,"operations":["lookup"],"version":"1.4.0"}},"paths":{"/ars/api/submit":{"post":{"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","predicates":["biolink:risk_affected_by"],"subject":"n0"}},"nodes":{"n0":{"categories":["biolink:Disease"],"ids":["MONDO:0021117"]},"n1":{"categories":["biolink:NamedThing"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"201":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"The initial json response back from submitting the query."}},"summary":"Initiate a TRAPI-format query to ARS and wait to receive a Response","tags":["Submit"]}},"/ars/api/agents":{"get":{"responses":{"200":{"description":"Returns a list of all available agents with the following properties: name, uri, description, contact. registered, updated"}},"summary":"list all the available agents","tags":["Agents"]}},"/ars/api/actors":{"get":{"responses":{"200":{"description":"Returns a list of all available actors with the following properties: name, channel, agent, urlRemote, path, active"}},"summary":"list all the available actors","tags":["Actors"]}},"/ars/api/messages/{UUID}":{"get":{"parameters":[{"description":"pk string value received from the initial query response","example":"7a0713fb-550b-462e-bde7-18a9de4ccfad","in":"path","name":"UUID","required":true,"schema":{"type":"string"}},{"description":"tracing children responses","example":"y","in":"query","name":"trace","schema":{"type":"string"}}],"responses":{"200":{"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation"}},"summary":"This endpoint will show the response json from all individual ARAs","tags":["Messages"]}},"/ars/api/filter/{UUID}":{"get":{"parameters":[{"description":"pk string value to perform the filtering on","example":"df1869b5-1be2-49a7-9b5a-88166edfbb78","in":"path","name":"UUID","required":true,"schema":{"type":"string"}},{"description":"hop level filter","example":3,"in":"query","name":"hop","required":false,"schema":{"type":"integer"}},{"allowReserved":true,"description":"score filter i.e. [20,80]","explode":false,"in":"query","name":"score","required":false,"schema":{"type":"string"},"style":"form"},{"allowReserved":true,"description":"specific node category filter i.e. ['ChemicalEntity','BiologicalEntity']","explode":false,"in":"query","name":"node_type","required":false,"schema":{"type":"string"},"style":"form"},{"allowReserved":true,"description":"specific node curie filter i.e. 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}}","scopes":"_id"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/part_of"},"source":"infores:go","supportBatch":true,"testExamples":[{"oneOutput":"GO:0000137","qInput":"GO:0000136"}],"useTemplating":true}],"subclass_of":[{"inputs":[{"id":"GO","semantic":"CellularComponent"}],"outputs":[{"id":"GO","semantic":"CellularComponent"}],"parameters":{"fields":"parents"},"predicate":"subclass_of","requestBody":{"body":{"q":"{{ queryInputs | replPrefix('GO') }}","scopes":"_id"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/subclass_of"},"source":"infores:go","supportBatch":true,"testExamples":[{"oneOutput":"GO:0000153","qInput":"GO:0000835"}],"useTemplating":true}]},"x-bte-response-mapping":{"has_part":{"GO":"_id"},"has_subclass":{"GO":"children"},"part_of":{"GO":"part_of.go"},"subclass_of":{"GO":"parents"}}},"info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible developers"},"description":"Documentation of the BioThings API for [Gene Ontology Cellular Component sub-ontology](https://geneontology.org/docs/ontology-documentation/) data.","termsOfService":"https://biothings.io/about","title":"BioThings GO Cellular Component API","version":"2020.07","x-translator":{"biolink-version":"3.5.0","component":"KP","infores":"infores:biothings-go-cc","team":["Service Provider"]}},"paths":{"/geneset/{id}":{"get":{"description":"By default, this will return the complete ontology term record in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the association. Multiple attributes should be separated by commas. If an attribute is not available for a specific ontology term, it will be ignored. Note that the attribute names are case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"GO:0043034","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["ontology"]}},"/geneset":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving multiple ontology terms). Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple ontology term ids separated by commas. Note that currently we only take ids up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["GO:0043034","GO:1990111"]},"schema":{"properties":{"ids":{"description":"Accepts multiple ontology term ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["ontology"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"go:\"GO:0043034\"","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). Fortunately, you can also make batch queries via POST requests when you need to.\n\nThe \"query” field in the returned object indicates the matching query term. If a query term has no match, it will return with a “notfound” field with the value “true”.","parameters":[{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"q","required":false,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"Optional, specify one or more fields (separated by commas) to search. Default: _id\n\nThe request body can also be used to provide this information.","in":"query","name":"scopes","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"}],"requestBody":{"content":{"application/json":{"example":{"q":["GO:0043034","GO:1990111"],"scopes":["go"]},"schema":{"properties":{"q":{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"},"scopes":{"description":"Specify one or more fields (separated by commas) to search. 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Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"name":"ids","description":"Accepts multiple association ids separated by commas. Note that currently we only take ids up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["C0015063-CAUSES-C0544884","C0543800-CAUSES-C0392525"]},"schema":{"type":"object","properties":{"ids":{"description":"Accepts multiple association ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","type":"array","items":{"type":"string"}}}}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["association"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query/ngd":{"get":{"parameters":[{"name":"umls","description":"Query string.","in":"query","required":true,"example":["C0003762,C0262587"],"schema":{"type":"array","items":{"type":"string"}}}],"responses":{"200":{"description":"Success"}},"tags":["ngd"]},"post":{"parameters":[{"name":"umls","description":"Query string.","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}}],"requestBody":{"content":{"application/json":{"example":{"umls":[["C0003762","C0262587"]]},"schema":{"type":"object","properties":{"umls":{"type":"array","items":{"type":"array","items":{"type":"string"}}}}}}}},"responses":{"200":{"description":"Success"}},"tags":["ngd"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"name":"q","description":"Required, passing user query. The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","in":"query","required":true,"example":"subject.umls:C0055723","schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). 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The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/smartapi/{smartapi_id}/asyncquery":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}},{"description":"When specified, the TRAPI logs returned will be of this level of importance or higher. This setting will override the log_level setting in the job's TRAPI query.\nIf it's not specified, BTE will use the log_level setting in the job's TRAPI query or return all logs (the default). ","in":"query","name":"log_level","required":false,"schema":{"enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}},"/asyncquery_response/{job_id}":{"get":{"operationId":"asyncquery_response","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}},{"description":"When specified, the TRAPI logs returned will be of this level of importance or higher. This setting will override the log_level setting in the job's TRAPI query.\nIf it's not specified, BTE will use the log_level setting in the job's TRAPI query or return all logs (the default). ","in":"query","name":"log_level","required":false,"schema":{"enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/AsyncQueryStatusResponse"},{"$ref":"#/components/schemas/Response"}]}}},"description":"Response format depends on status of the job (pending/in-progress vs finished)"},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"If the previously submitted asyncquery is still pending/in-progress, this endpoint will return the same response as the asyncquery_status endpoint (status, logs). But if the asyncquery job is finished, the complete TRAPI response to the query will be returned","tags":["asyncquery_response"]}}},"servers":[{"description":"ITRB Production server","url":"https://bte.transltr.io/v1","x-maturity":"production"},{"description":"ITRB Test server","url":"https://bte.test.transltr.io/v1","x-maturity":"testing"}],"tags":[{"name":"1.4.0"},{"name":"meta_knowledge_graph"},{"name":"query"},{"name":"asyncquery"},{"name":"asyncquery_status"},{"name":"translator"},{"name":"trapi"},{"name":"biothings"}]},{"_id":"cecdb8aed0bbd2334784c89c75e8f805","_meta":{"date_created":"2024-04-11T00:14:31.871614+00:00","last_updated":"2024-04-30T07:02:52.072944+00:00","url":"https://raw.githubusercontent.com/suihuanglab/improving-agent/1.4-legacy/app/improving-agent.yaml","username":"brettasmi"},"info":{"contact":{"email":"brett.smith@isbscience.org","x-role":"responsible developer"},"description":"imProving Agent - An NIH NCATS Translator Autonomous Reasoning Agent","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"https://spoke.rbvi.ucsf.edu/license.html","title":"imProving Agent for TRAPI 1.4","version":"1.4.0","x-translator":{"biolink-version":"3.5.4","component":"ARA","externalDocs":{"description":"Code repository and example notebook","url":"https://github.com/suihuanglab/improving-agent"},"infores":"infores:improving-agent","team":["imProving Agent"]},"x-trapi":{"asyncquery":false,"batch_size_limit":20,"operations":["lookup"],"rate_limit":20,"test_data_location":{"default":{"url":"https://github.com/suihuanglab/improving-agent/tree/main/test-data"}},"version":"1.4.0"}},"paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:1681\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Gene\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n }\n}","schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query and wait to receive a Response","tags":["query"]}},"/asyncquery":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n \"message\": {\n \"query_graph\": {\n \"nodes\": {\n \"n00\": {\n \"ids\": [\"DOID:1681\"],\n \"categories\": [\"biolink:Disease\"]\n },\n \"n01\": {\n \"categories\": [\"biolink:Gene\"]\n }\n },\n \"edges\": {\n \"e00\": {\n \"subject\": \"n00\",\n \"object\": \"n01\"\n }\n }\n }\n }\n}","schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query with a callback to receive the response","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","example":"rXEOAosN3L","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"ITRB Prod server","url":"https://ia.transltr.io/api/v1.4/","x-maturity":"production"},{"description":"ITRB Test server","url":"https://ia.test.transltr.io/api/v1.4/","x-maturity":"testing"}],"tags":[{"description":"Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Initiate a query with a callback to receive the response","name":"asyncquery"},{"description":"Retrieve the current status of a previously submitted asyncquery given its job_id","name":"asyncquery_status"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]},{"_id":"36f82f05705c317bac17ddae3a0ea2f0","_ignored":["paths.pathitem.post.summary.raw"],"_meta":{"date_created":"2022-03-30T20:09:40.195442+00:00","last_updated":"2024-04-30T07:02:49.458913+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/service-provider-trapi.yaml","username":"colleenXu"},"info":{"contact":{"email":"cwu@scripps.edu","name":"Chunlei Wu","x-id":"https://github.com/newgene","x-role":"responsible developer"},"description":"Separate registration for the BTE's Service-Provider-specific endpoints. This allows others use BTE as a TRAPI service/interface to query all of the non-TRAPI APIs that Service Provider ingests through x-bte annotation. ","termsOfService":"https://biothings.io/about","title":"Service Provider TRAPI","version":"3.0.0","x-translator":{"biolink-version":"3.5.3","component":"KP","infores":"infores:retriever-non-trapi","team":["Service Provider"]},"x-trapi":{"asyncquery":true,"batch_size_limit":150,"operations":["lookup"],"rate_limit":15,"test_data_location":{"default":{"url":["https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-service-provider.json","https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/qualifier-sri-test-service.json","https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-multiomics.json","https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-text-mining.json"]}},"version":"1.4.0"}},"paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for Service Provider's SmartAPI KP APIs (that have x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for Service Provider's SmartAPI KP APIs (that have x-bte annotation)","tags":["meta_knowledge_graph"]}},"/query":{"post":{"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query Service Provider's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service","tags":["query"]}},"/asyncquery":{"post":{"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying Service Provider's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}}},"servers":[{"description":"ITRB Production server","url":"https://bte.transltr.io/v1/team/Service%20Provider","x-maturity":"production"},{"description":"ITRB Test server","url":"https://bte.test.transltr.io/v1/team/Service%20Provider","x-maturity":"testing"}],"tags":[{"name":"1.4.0"},{"name":"meta_knowledge_graph"},{"name":"query"},{"name":"asyncquery"},{"name":"asyncquery_status"},{"name":"translator"},{"name":"trapi"},{"name":"biothings"}]},{"_id":"b99c6dd64abcefe87dcd0a51c249ee6d","_ignored":["paths.pathitem.get.description.raw"],"_meta":{"date_created":"2022-07-27T02:18:15.391589+00:00","last_updated":"2024-04-30T07:01:17.592932+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/bioplanet/bioplanet-pathway-gene.yaml","username":"colleenXu"},"components":{"x-bte-kgs-operations":{"gene-pathway":[{"agent_type":"manual_agent","inputs":[{"id":"NCBIGene","semantic":"Gene"}],"knowledge_level":"knowledge_assertion","outputs":[{"id":"ncats.bioplanet","semantic":"Pathway"}],"parameters":{"fields":"object.PATHWAY_ID, object.PATHWAY_NAME","size":1000},"predicate":"participates_in","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"subject.GENE_ID"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/pathway"},"source":"infores:bioplanet","supportBatch":true,"testExamples":[{"oneOutput":"ncats.bioplanet:bioplanet_789","qInput":"NCBIGene:1463"}],"useTemplating":true}],"pathway-gene":[{"agent_type":"manual_agent","inputs":[{"id":"ncats.bioplanet","semantic":"Pathway"}],"knowledge_level":"knowledge_assertion","outputs":[{"id":"NCBIGene","semantic":"Gene"}],"parameters":{"fields":"subject.GENE_ID, object.PATHWAY_NAME","size":1000},"predicate":"has_participant","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"object.PATHWAY_ID"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene"},"source":"infores:bioplanet","supportBatch":true,"testExamples":[{"oneOutput":"NCBIGene:9672","qInput":"ncats.bioplanet:bioplanet_869"}],"useTemplating":true}]},"x-bte-response-mapping":{"gene":{"NCBIGene":"subject.GENE_ID","input_name":"object.PATHWAY_NAME"},"pathway":{"ncats.bioplanet":"object.PATHWAY_ID","output_name":"object.PATHWAY_NAME"}}},"info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible developers"},"description":"Documentation of the BioThings API for \n[BioPlanet](https://tripod.nih.gov/bioplanet/#) pathway-gene data.","termsOfService":"https://biothings.io/about","title":"BioThings BioPlanet Pathway-Gene API","version":"1.0","x-translator":{"biolink-version":"3.5.0","component":"KP","infores":"infores:biothings-bioplanet-pathway-gene","team":["Service Provider"]}},"paths":{"/association/{id}":{"get":{"description":"By default, this will return the complete association in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the association. Multiple attributes should be separated by commas. If an attribute is not available for a specific association, it will be ignored. Note that the attribute names are case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"bioplanet_465-23118","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["association"]}},"/association":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving multiple associations). Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple association ids separated by commas. Note that currently we only take ids up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["bioplanet_464-10437","bioplanet_465-23118"]},"schema":{"properties":{"ids":{"description":"Accepts multiple association ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["association"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. 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help desk","url":"https://monarchinitiative.org/help","x-role":"responsible developer"},"description":"The [Monarch Application Programming Interface (API)](https://api-v3.monarchinitiative.org/v3/docs#/) is a RESTful API that wraps functionality required by the [Monarch Initiative website](https://monarchinitiative.org/), including the retrieval of disease, gene, and phenotype associations, phenotypic profile comparisons, and other graph operations.","termsOfService":"https://monarchinitiative.org/terms","title":"Monarch API","version":"0.1.0","x-translator":{"biolink-version":"3.5.3","component":"KP","infores":"infores:monarchinitiative","team":["Service Provider","Standards Reference Implementation Team"]}},"paths":{"/v3/api/association":{"get":{"description":"Retrieves all associations for a given entity, or between two entities.","operationId":"_get_associations_v3_api_association_get","parameters":[{"in":"query","name":"category","required":false,"schema":{"items":{"$ref":"#/components/schemas/AssociationCategory"},"title":"Category","type":"array"}},{"in":"query","name":"subject","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject"}},{"in":"query","name":"subject_category","required":false,"schema":{"items":{"$ref":"#/components/schemas/EntityCategory"},"title":"Subject Category","type":"array"}},{"in":"query","name":"subject_namespace","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject Namespace"}},{"in":"query","name":"subject_taxon","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject 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\n Path (str, optional): Path string to limit results to a subset. Defaults to None.
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\n\nReturns:
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Defaults to \"*:*\".\n category (str, optional): Filter by biolink model category. Defaults to None.\n in_taxon_label (str, optional): Filter by taxon label. Defaults to None.\n offset (int, optional): Offset for pagination. Defaults to 0.\n limit (int, optional): Limit results. Defaults to 20.\n\nReturns:\n EntityResults","operationId":"search_v3_api_search_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"title":"Q","type":"string"}},{"in":"query","name":"category","required":false,"schema":{"anyOf":[{"items":{"$ref":"#/components/schemas/EntityCategory"},"type":"array"}],"title":"Category"}},{"in":"query","name":"in_taxon_label","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"In Taxon Label"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Search","tags":["search"]}},"/v3/api/autocomplete":{"get":{"description":"Autocomplete for entities by label\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["search"]}},"/v3/api/mappings":{"get":{"operationId":"mappings_v3_api_mappings_get","parameters":[{"in":"query","name":"entity_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Entity Id"}},{"in":"query","name":"subject_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Subject Id"}},{"in":"query","name":"predicate_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Predicate Id"}},{"in":"query","name":"object_id","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Object Id"}},{"in":"query","name":"mapping_justification","required":false,"schema":{"anyOf":[{"items":{"type":"string"},"type":"array"}],"title":"Mapping Justification"}},{"in":"query","name":"format","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/OutputFormat"}],"default":"json","title":"Output format for the response"}},{"in":"query","name":"limit","required":false,"schema":{"default":20,"title":"Limit","type":"integer"}},{"in":"query","name":"offset","required":false,"schema":{"default":0,"title":"Offset","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Mappings","tags":["search"]}},"/v3/api/semsim/autocomplete":{"get":{"description":"Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations.\nNote: This API endpoint is experimental and may evolve or disappear over time.\n\nArgs:\n q (str): Query string to autocomplete against\n\nReturns:\n SearchResults","operationId":"autocomplete_v3_api_semsim_autocomplete_get","parameters":[{"in":"query","name":"q","required":false,"schema":{"default":"*:*","title":"Query string to autocomplete against","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SearchResults"}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Autocomplete","tags":["semsim"]}},"/v3/api/semsim/compare/{subjects}/{objects}":{"get":{"description":"Get pairwise similarity between two sets of terms\n\nArgs:
\n subjects (str, optional): List of subjects for comparison. Defaults to \"\".
\n objects (str, optional): List of objects for comparison. Defaults to \"\".
\n\nReturns:
\n TermSetPairwiseSimilarity: Pairwise similarity between subjects and objects","operationId":"_compare_v3_api_semsim_compare__subjects___objects__get","parameters":[{"in":"path","name":"subjects","required":true,"schema":{"title":"List of subjects for comparison","type":"string"}},{"in":"path","name":"objects","required":true,"schema":{"title":"List of objects for comparison","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Compare","tags":["semsim"]}},"/v3/api/semsim/compare":{"post":{"description":"Pairwise similarity between two sets of terms
\n
\n Example:
\n
\n{\n  \"subjects\": [\"MP:0010771\",\"MP:0002169\",\"MP:0005391\",\"MP:0005389\",\"MP:0005367\"],\n  \"objects\": [\"HP:0004325\",\"HP:0000093\",\"MP:0006144\"]\n}\n
","operationId":"_post_compare_v3_api_semsim_compare_post","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemsimCompareRequest"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Post Compare","tags":["semsim"]}},"/v3/api/semsim/search/{termset}/{group}":{"get":{"description":"Search for terms in a termset\n\nArgs:
\n termset (str, optional): Comma separated list of term IDs to find matches for.
\n group (str, optional): Group of entities to search within (e.g. Human Genes)
\n limit (int, optional): Limit the number of results. Defaults to 10.\n\nReturns:
\n List[str]: List of matching terms","operationId":"_search_v3_api_semsim_search__termset___group__get","parameters":[{"in":"path","name":"termset","required":true,"schema":{"title":"Termset to search","type":"string"}},{"in":"path","name":"group","required":true,"schema":{"allOf":[{"$ref":"#/components/schemas/SemsimSearchGroup"}],"title":"Group of entities to search within (e.g. Human Genes)"}},{"in":"query","name":"limit","required":false,"schema":{"default":10,"maximum":50,"minimum":1,"title":"Limit","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{}}},"description":"Successful Response"},"404":{"description":"Not Found"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":" Search","tags":["semsim"]}},"/v3/api/semsim/search":{"post":{"description":"Search for terms in a termset
\n
\n Example:
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ID","tags":["data"]}},"/data/vip/{id}":{"get":{"parameters":[{"description":"The annotation's ID","in":"path","name":"id","required":true,"schema":{"type":"number"}},{"description":"How much data to retrieve on the object","in":"query","name":"view","schema":{"enum":["min","base","max"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/VipOverviewDisplay"}}},"description":"success"}},"summary":"Retrieve a VIP annotation using the ID","tags":["data"]}},"/data/ontologyTerm":{"get":{"parameters":[{"description":"the ontology resource to get terms for","in":"query","name":"resource","required":true,"schema":{"enum":["biomarkerStatus","alleleFunction","cpicLevelOfEvidence","cpicStatus","geneTestLevel","guidelineStrength","levelsOfEvidence"],"type":"string"}},{"description":"How much data to retrieve on the 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Annotations","tags":["data"]}},"/report/guideline/{id}/annotations":{"post":{"description":"This endpoint is meant to query `GuidelineAnnotation` model objects that have extended\nannotations. The front-end may show these options as allele names but the backend stores and\nqueries by allele function so that is what must be queried on. Those functions can be found in\nthe `guidelineGenes` property of the `DosingGuideline` object.\n\n**IMPORTANT NOTE**: This data is PharmGKB annotation of CPIC guideline information. Our annotations may contain typos or errors or may be out of date. If you're interested in using this data please get it directly from [the CPIC website](https://cpicpgx.org/).","parameters":[{"description":"The accession ID of a Guideline Annotation with annotations","in":"path","name":"id","required":true,"schema":{"default":"PA166104948","type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"CYP2C19":{"items":{"description":"Allele function values, must be 2 per gene","type":"string"},"type":"array"}},"type":"object"}}},"description":"The functional phenotype to query for. 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This can have more than 1 gene specified, if needed.","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/GuidelineAnnotationGroup"}}},"description":"success"}},"summary":"Query the annotations for a guideline by allele function","tags":["report"],"x-codegen-request-body-name":"body"}},"/report/variantFrequency":{"get":{"parameters":[{"description":"a variant fingerprint to query (e.g. RSID)","in":"query","name":"fp","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/FrequencyResult"}}},"description":"success"}},"summary":"Get all variant frequency data for a given variant fingerprint","tags":["report"]}},"/report/stats":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/StatsResult"}}},"description":"success"}},"summary":"Get all the statistics for object counts in 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query with a callback to receive the response","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","example":"rXEOAosN3L","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. 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You can also pass \"all\" to get a list of\n all API metadata (using \"from\" and \"size\" for pagination).","in":"path","name":"api_id","required":true,"schema":{"type":"string"}},{"description":"include \"_meta\" and \"_id\" fields in the response if passed \"1\" or \"true\". Default is \"false\".","in":"query","name":"meta","schema":{"type":"string"}},{"description":"return raw metadata document if passed \"1\" or \"true\". Default is \"false\".","in":"query","name":"raw","schema":{"type":"string"}},{"description":"You can use this parameter to filter the fields returned from the raw metadata document. Only effective when \"raw=1\" is passed. E.g. \"info.contact.name,servers\". Nested fields are supported via dot notation, and multiple fields can be passed as a comma-separated string.","in":"query","name":"fields","schema":{"type":"string"}},{"description":"Output format for the return API metadata. The value can be \"json\" or \"yaml\". 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Learn more about [MyChem.info](https://docs.mychem.info/en/latest/index.html)","termsOfService":"http://MyChem.info/terms","title":"MyChem.info API","version":"1.0","x-translator":{"infores":"infores:mychem-info","component":"KP","team":["Service Provider"],"biolink-version":"4.1.6"}},"servers":[{"description":"Encrypted Production server","url":"https://mychem.info/v1","x-maturity":"production"}],"tags":[{"name":"chemical"},{"name":"drug"},{"name":"annotation"},{"name":"query"},{"name":"translator"},{"name":"biothings"}],"paths":{"/chem/{id}":{"get":{"description":"By default, this will return the complete chemical annotation object in JSON format. See [here](https://docs.mychem.info/en/latest/doc/chem_annotation_service.html#returned-object) for an example and [here](https://docs.mychem.info/en/latest/doc/data.html#chemical-object) for more details. If the input chemical ID is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the object. Multiple attributes should be separated by commas. If an attribute is not available for a specific object, it will be ignored. 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Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"name":"ids","description":"Accepts multiple chemical ids separated by comma, e.g., \"ids=SDUQYLNIPVEERB-QPPQHZFASA-N,SESFRYSPDFLNCH-UHFFFAOYSA-N,SHGAZHPCJJPHSC-ZVCIMWCZSA-N\". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["USNINKBPBVKHHZ-CYUUQNCZSA-L","CHEMBL266510"]},"schema":{"type":"object","properties":{"ids":{"description":"Accepts multiple chemical ids. 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The detailed query syntax for parameter is explained [here](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","in":"query","required":true,"example":"CHEMBL266510","schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our chemical query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving chemical annotation for multiple chemicals). Fortunately, you can also make batch queries via POST requests when you need to.\n\nThe \"query\" field in the returned object indicates the matching query term. If a query term has no match, it will return with a \"notfound\" field with the value \"true\".","parameters":[{"name":"q","description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}},{"name":"scopes","description":"Optional, specify one or more fields (separated by commas) to search, e.g., \"scopes=chebi\". The available \"fields\" can be passed to \"scopes\" parameter are listed [here](https://docs.mychem.info/en/latest/doc/data.html#available-fields). Default: _id\n\nThe request body can also be used to provide this information.","in":"query","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"}],"requestBody":{"content":{"application/json":{"example":{"q":["CHEMBL266510","CHEMBL1200833"],"scopes":["chembl.molecule_chembl_id"]},"schema":{"type":"object","properties":{"q":{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.","type":"array","items":{"type":"string"}},"scopes":{"description":"Specify one or more fields (separated by commas) to search, e.g., \"scopes=chebi\". 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E.g. \"facets=chembl.molecule_properties.full_mwt\". See [examples of faceted queries here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries).","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}},"fetch_all":{"name":"fetch_all","description":"Optional, a boolean, which when TRUE, allows fast retrieval of all unsorted query hits. The return object contains a _scroll_id field, which when passed as a parameter to the query endpoint (see the scroll_id parameter), returns the next 1000 query results. Setting fetch_all = TRUE causes the results to be inherently unsorted, therefore the sort parameter is ignored. For more information, see [examples using fetch_all here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries). Default: FALSE.","in":"query","required":false,"schema":{"type":"boolean","default":false}},"fields":{"name":"fields","description":"Optional, can be a comma-separated list to limit the fields returned from the object. If \"fields=all\", all available fields will be returned. Look [here](https://docs.mychem.info/en/latest/doc/data.html#available-fields) for a list of available fields. \n\nNote that it supports dot notation as well, e.g., you can pass \"chebi.name\". Default: \"fields=all\". The parameter \"filter\" is an alias for this parameter.","in":"query","required":false,"schema":{"type":"string","default":"all"}},"from":{"name":"from","description":"Optional, the number of matching hits to skip, starting from 0. Default: 0. ","in":"query","required":false,"schema":{"type":"integer","default":0}},"scroll_id":{"name":"scroll_id","description":"Optional, a string containing the _scroll_id returned from a query request with fetch_all = TRUE. 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Learn more about [MyDisease.info](https://docs.mydisease.info/en/latest/index.html)","termsOfService":"https://mydisease.info/terms","title":"MyDisease.info API","version":"1.0","x-translator":{"biolink-version":"3.5.0","component":"KP","infores":"infores:mydisease-info","team":["Service Provider"]}},"paths":{"/disease/{id}":{"get":{"description":"By default, this will return the complete disease annotation object in JSON format. See [here](https://docs.mydisease.info/en/latest/doc/data.html#disease-object) for more details. If the input disease ID is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the disease object. Multiple attributes should be separated by commas. If an attribute is not available for a specific disease object, it will be ignored. Note that the attribute names are case-sensitive.\n\nJust like the disease query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"description":"Retrieve disease data based on ID","example":"MONDO:0000490","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["disease"]}},"/disease":{"post":{"description":"Although making simple GET requests above to our disease query service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving disease annotations for multiple diseases). 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Default: _id","type":"array","items":{"type":"string"}}}}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."},"400":{"description":"A response indicating an improperly formatted query"}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/pubchem_treats_mondo"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_treats_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_studiedToTreat_mondo"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_studiedToTreat_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_preclinicalTreats_mondo"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_preclinicalTreats_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_clinicalTrialTreats_mondo"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_clinicalTrialTreats_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_treats_icd11"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_treats_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_studiedToTreat_icd11"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_studiedToTreat_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_preclinicalTreats_icd11"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_preclinicalTreats_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_clinicalTrialTreats_icd11"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_clinicalTrialTreats_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_treats_mondo"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_treats_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_studiedToTreat_mondo"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_studiedToTreat_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_preclinicalTreats_mondo"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_preclinicalTreats_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_clinicalTrialTreats_mondo"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_clinicalTrialTreats_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_treats_icd11"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_treats_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_studiedToTreat_icd11"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_studiedToTreat_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_preclinicalTreats_icd11"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_preclinicalTreats_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_clinicalTrialTreats_icd11"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_clinicalTrialTreats_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/uniprotkb_target_for_mondo"},{"$ref":"#/components/x-bte-kgs-operations/uniprotkb_target_for_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/uniprotkb_target_for_icd11"},{"$ref":"#/components/x-bte-kgs-operations/uniprotkb_target_for_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_target_id_target_for_mondo"},{"$ref":"#/components/x-bte-kgs-operations/ttd_target_id_target_for_mondo-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_target_id_target_for_icd11"},{"$ref":"#/components/x-bte-kgs-operations/ttd_target_id_target_for_icd11-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_interacts_with_uniprotkb"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_interacts_with_uniprotkb-rev"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_interacts_with_ttd_target_id"},{"$ref":"#/components/x-bte-kgs-operations/pubchem_interacts_with_ttd_target_id-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_uniprotkb"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_uniprotkb-rev"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_ttd_target_id"},{"$ref":"#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_ttd_target_id-rev"}]}}},"components":{"parameters":{"callback":{"name":"callback","description":"Optional, you can pass a \"callback\" parameter to make a JSONP call.","in":"query","required":false,"schema":{"type":"string"}},"dotfield":{"name":"dotfield","description":"Optional, can be used to control the format of the returned object. If \"dotfield\" is true, the returned data object is returned flattened (no nested objects) using dotfield notation for key names. Default: false.","in":"query","required":false,"schema":{"type":"boolean","default":false}},"facet_size":{"name":"facet_size","description":"Optional, an integer (1 <= facet_size <= 1000) that specifies how many buckets to return in a [faceted query](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries).","in":"query","required":false,"schema":{"type":"integer","default":10}},"facets":{"name":"facets","description":"Optional, a single field or comma-separated fields to return facets, can only be used on non-free text fields. E.g. “facets=chembl.molecule_properties.full_mwt”. See [examples of faceted queries for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries).","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}},"fetch_all":{"name":"fetch_all","description":"Optional, a boolean, which when TRUE, allows fast retrieval of all unsorted query hits. The return object contains a _scroll_id field, which when passed as a parameter to the query endpoint (see the scroll_id parameter), returns the next 1000 query results. Setting fetch_all = TRUE causes the results to be inherently unsorted, therefore the sort parameter is ignored. For more information, see [examples using fetch_all for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries). Default: FALSE.","in":"query","required":false,"schema":{"type":"boolean","default":false}},"fields":{"name":"fields","description":"Optional, can be a comma-separated list to limit the fields returned from the object. If \"fields=all\", all available fields will be returned.\n\nNote that it supports dot notation as well, e.g., you can pass \"chebi.name\". Default: \"fields=all\". The parameter \"filter\" is an alias for this parameter.","in":"query","required":false,"schema":{"type":"string","default":"all"}},"from":{"name":"from","description":"Optional, the number of matching hits to skip, starting from 0. Default: 0.","in":"query","required":false,"schema":{"type":"integer","default":0}},"scroll_id":{"name":"scroll_id","description":"Optional, a string containing the _scroll_id returned from a query request with fetch_all = TRUE. Supplying a valid scroll_id will return the next 1000 unordered results. If the next results are not obtained within 1 minute of the previous set of results, the scroll_id becomes stale, and a new one must be obtained with another query request with fetch_all = TRUE. All other parameters are ignored when the scroll_id parameter is supplied. For more information see [examples using scroll_id for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries).","in":"query","required":false,"schema":{"type":"string"}},"size":{"name":"size","description":"Optional, the maximum number of matching hits to return (with a cap of 1000 at the moment). Default: 10. The combination of \"size\" and \"from\" parameters can be used to get paging for a large query.","in":"query","required":false,"schema":{"type":"integer","default":10}},"sort":{"name":"sort","description":"Optional, the comma-separated fields to sort on. Prefix with \"-\" for descending order, otherwise in ascending order. Default: sort by matching scores in descending order.","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}},"aggs":{"name":"aggs","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}},"allow_null":{"name":"allow_null","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}},"always_list":{"name":"always_list","in":"query","required":false,"schema":{"type":"array","items":{"type":"string"}}},"format":{"name":"format","description":"controls output format of server response, currently supports: \"json\", \"jsonld\", \"html\". Type: string. Default: json.","in":"query","required":false,"schema":{"type":"string","default":"json"}},"prefix":{"name":"prefix","in":"query","required":false,"schema":{"type":"string"}},"search":{"name":"search","in":"query","required":false,"schema":{"type":"string"}}},"x-bte-kgs-operations":{"pubchem_treats_mondo":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"PUBCHEM.COMPOUND","semantic":"SmallMolecule"}],"requestBody":{"body":{"q":"{{ queryInputs | rmPrefix() }}","scopes":"subject.pubchem_compound"}},"outputs":[{"id":"MONDO","semantic":"Disease"}],"parameters":{"fields":"object.mondo, object.name, subject.name","size":1000,"filter":"_exists_:subject.pubchem_compound AND _exists_:object.mondo AND association.predicate:\"biolink:treats\" AND (association.clinical_trial.status:approved OR association.clinical_trial.status:\"phase 4\" OR association.clinical_trial.status:\"approved (orphan drug)\" OR association.clinical_trial.status:\"NDA 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The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.","operationId":"get_meta_knowledge_graph_meta_knowledge_graph_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Successful Response"}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["trapi"]}},"/sri_testing_data":{"get":{"description":"Returns a list of edges that are representative examples of the knowledge graph.","operationId":"get_sri_testing_data_sri_testing_data_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SRITestData"}}},"description":"Successful Response"}},"summary":"Test data for usage by the SRI Testing Harness.","tags":["trapi"]}},"/query":{"post":{"description":"Accepts a TRAPI Query and returns a TRAPI Response. 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"}},"/{node_type}/{curie}":{"get":{"description":"Returns `node` matching `curie`.","operationId":"node__node_type___curie__get","parameters":[{"in":"path","name":"node_type","required":true,"schema":{"title":"Node Type","type":"string"}},{"in":"path","name":"curie","required":true,"schema":{"title":"Curie","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{},"title":"Response Node Node Type Curie Get","type":"array"}}},"description":"Successful Response"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Find `node` by `curie`"}},"/simple_spec":{"get":{"description":"Returns a list of available predicates when choosing a single source or target curie. Calling this endpoint with no query parameters will return all possible hops for all types.","operationId":"simple_spec_simple_spec_get","parameters":[{"in":"query","name":"source","required":false,"schema":{"title":"Source","type":"string"}},{"in":"query","name":"target","required":false,"schema":{"title":"Target","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/SimpleSpecElement"},"title":"Response Simple Spec Simple Spec Get","type":"array"}}},"description":"Successful Response"},"422":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/HTTPValidationError"}}},"description":"Validation Error"}},"summary":"Get one-hop connection schema"}}},"servers":[{"description":"Default server","url":"https://automat.ci.transltr.io/binding-db","x-location":"ITRB","x-maturity":"staging","x-translator":{"biolink-version":"4.1.6","test-data-location":"https://automat.ci.transltr.io/binding-db/sri_testing_data"},"x-trapi":"1.5"},{"description":"Default server","url":"https://automat.renci.org/binding-db","x-location":"RENCI","x-maturity":"development","x-translator":{"biolink-version":"4.1.6","test-data-location":"https://automat.renci.org/binding-db/sri_testing_data"},"x-trapi":"1.5"}],"tags":[{"name":"translator"},{"name":"Automat"},{"name":"trapi"}]}]} \ No newline at end of file diff --git a/packages/server/docs/smartapi.yaml b/packages/server/docs/smartapi.yaml index 0bfa623..db2abf2 100644 --- a/packages/server/docs/smartapi.yaml +++ b/packages/server/docs/smartapi.yaml @@ -13,7 +13,7 @@ info: team: - Exploring Agent biolink-version: "4.1.6" - infores: "infores:biothings-explorer" + infores: "infores:retriever" x-trapi: version: 1.4.0 asyncquery: true diff --git a/packages/server/package.json b/packages/server/package.json index 4052212..783537e 100644 --- a/packages/server/package.json +++ b/packages/server/package.json @@ -1,7 +1,7 @@ { - "name": "@biothings-explorer/server", + "name": "@retriever/server", "version": "3.0.0", - "description": "The server component of Biothings Explorer", + "description": "The server component of Retriever", "main": "built/server.js", "scripts": { "prepare": "npm run build", @@ -17,21 +17,22 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/bte-server.git" + "url": "git+https://github.com/BioPack-team/retriever" }, "keywords": [ - "bte", + "BioPack", + "retriever", "biothings", "single", "hop", "query" ], - "author": "BioThings Team", + "author": "BioPack Team", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/biothings_explorer/issues" + "url": "https://github.com/BioPack/retriever/issues" }, - "homepage": "https://github.com/biothings/biothings_explorer#readme", + "homepage": "https://github.com/BioPack/retriever#readme", "devDependencies": { "@jest/globals": "^29.7.0", "@types/async": "^3.2.22", @@ -74,10 +75,10 @@ "typescript": "5.2.2" }, "dependencies": { - "@biothings-explorer/query_graph_handler": "workspace:../query_graph_handler", - "@biothings-explorer/smartapi-kg": "workspace:../smartapi-kg", - "@biothings-explorer/types": "workspace:../types", - "@biothings-explorer/utils": "workspace:../utils", + "@retriever/query_graph_handler": "workspace:../query_graph_handler", + "@retriever/smartapi-kg": "workspace:../smartapi-kg", + "@retriever/types": "workspace:../types", + "@retriever/utils": "workspace:../utils", "@bull-board/api": "^5.9.1", "@bull-board/express": "^5.9.1", "@opentelemetry/api": "^1.7.0", diff --git a/packages/server/src/config/api_list.ts b/packages/server/src/config/api_list.ts index 473c236..d14a84a 100644 --- a/packages/server/src/config/api_list.ts +++ b/packages/server/src/config/api_list.ts @@ -1,4 +1,4 @@ -import { APIList } from "@biothings-explorer/types"; +import { APIList } from "@retriever/types"; import { readFileSync } from "fs"; import yaml from "js-yaml"; import path = require("path"); diff --git a/packages/server/src/config/index.ts b/packages/server/src/config/index.ts index ab37741..f0b6a79 100644 --- a/packages/server/src/config/index.ts +++ b/packages/server/src/config/index.ts @@ -7,7 +7,7 @@ import dotenv from "dotenv"; import * as Sentry from "@sentry/node"; import { Express } from "express"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:server-config"); +const debug = Debug("retriever:server-config"); export default class Config { app: Express; diff --git a/packages/server/src/config/smartapi_exclusions.ts b/packages/server/src/config/smartapi_exclusions.ts index 8c75236..f79f928 100644 --- a/packages/server/src/config/smartapi_exclusions.ts +++ b/packages/server/src/config/smartapi_exclusions.ts @@ -1,4 +1,4 @@ -import { APIDefinition } from "@biothings-explorer/types"; +import { APIDefinition } from "@retriever/types"; import { readFileSync } from "fs"; import yaml from "js-yaml"; import path = require("path"); diff --git a/packages/server/src/controllers/association.ts b/packages/server/src/controllers/association.ts index 1c206a7..969176b 100644 --- a/packages/server/src/controllers/association.ts +++ b/packages/server/src/controllers/association.ts @@ -1,10 +1,10 @@ -import meta_kg from "@biothings-explorer/smartapi-kg"; +import meta_kg from "@retriever/smartapi-kg"; import fs from "fs"; import path from "path"; import util from "util"; const readFile = util.promisify(fs.readFile); import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:metakg"); +const debug = Debug("retriever:metakg"); export interface AssocResult { subject: string; diff --git a/packages/server/src/controllers/async/asyncquery.ts b/packages/server/src/controllers/async/asyncquery.ts index 2e6559a..1015c69 100644 --- a/packages/server/src/controllers/async/asyncquery.ts +++ b/packages/server/src/controllers/async/asyncquery.ts @@ -1,19 +1,19 @@ import axios, { AxiosError, AxiosResponse } from "axios"; import { customAlphabet } from "nanoid"; import * as utils from "../../utils/common"; -import { redisClient } from "@biothings-explorer/utils"; -import { LogEntry } from "@biothings-explorer/utils"; +import { redisClient } from "@retriever/utils"; +import { LogEntry } from "@retriever/utils"; import lz4 from "lz4"; import { Readable } from "stream"; import chunker from "stream-chunker"; import { parser } from "stream-json"; import Assembler from "stream-json/Assembler"; -import { Telemetry } from "@biothings-explorer/utils"; +import { Telemetry } from "@retriever/utils"; import ErrorHandler from "../../middlewares/error"; import { Request, Response, NextFunction } from "express"; import { Queue } from "bull"; -import { QueueData, TrapiQueryGraph, TrapiResponse } from "@biothings-explorer/types"; -import TRAPIQueryHandler from "@biothings-explorer/query_graph_handler"; +import { QueueData, TrapiQueryGraph, TrapiResponse } from "@retriever/types"; +import TRAPIQueryHandler from "@retriever/query_graph_handler"; import StatusError from "../../utils/errors/status_error"; export async function asyncquery( diff --git a/packages/server/src/controllers/async/asyncquery_queue.ts b/packages/server/src/controllers/async/asyncquery_queue.ts index c8ea75a..f65b216 100644 --- a/packages/server/src/controllers/async/asyncquery_queue.ts +++ b/packages/server/src/controllers/async/asyncquery_queue.ts @@ -1,11 +1,11 @@ -import "@biothings-explorer/types"; +import "@retriever/types"; import Queue, { Queue as BullQueue, FailedEventCallback } from "bull"; import axios from "axios"; -import { redisClient, getNewRedisClient } from "@biothings-explorer/utils"; +import { redisClient, getNewRedisClient } from "@retriever/utils"; import Debug from "debug"; -import { TrapiLog, TrapiQueryGraph } from "@biothings-explorer/types"; +import { TrapiLog, TrapiQueryGraph } from "@retriever/types"; import { BullJob } from "../../types"; -const debug = Debug("bte:biothings-explorer-trapi:asyncquery_queue"); +const debug = Debug("retriever:asyncquery_queue"); import { Redis } from "ioredis"; import { QueryQueue } from "packages/types/src/global"; diff --git a/packages/server/src/controllers/cron/clear_edge_cache.ts b/packages/server/src/controllers/cron/clear_edge_cache.ts index 0b24f9f..7181499 100644 --- a/packages/server/src/controllers/cron/clear_edge_cache.ts +++ b/packages/server/src/controllers/cron/clear_edge_cache.ts @@ -1,6 +1,6 @@ -import { redisClient } from "@biothings-explorer/utils"; +import { redisClient } from "@retriever/utils"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:cron"); +const debug = Debug("retriever:cron"); import cron from "node-cron"; export default function scheduleClearCache() { diff --git a/packages/server/src/controllers/cron/update_local_smartapi.ts b/packages/server/src/controllers/cron/update_local_smartapi.ts index 558acfa..e555e1e 100644 --- a/packages/server/src/controllers/cron/update_local_smartapi.ts +++ b/packages/server/src/controllers/cron/update_local_smartapi.ts @@ -1,5 +1,5 @@ import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:cron"); +const debug = Debug("retriever:cron"); import axios from "axios"; import fs from "fs/promises"; import path from "path"; diff --git a/packages/server/src/controllers/meta_knowledge_graph.ts b/packages/server/src/controllers/meta_knowledge_graph.ts index e0e573a..76ebd29 100644 --- a/packages/server/src/controllers/meta_knowledge_graph.ts +++ b/packages/server/src/controllers/meta_knowledge_graph.ts @@ -1,8 +1,8 @@ -import meta_kg, { KGQualifiersObject } from "@biothings-explorer/smartapi-kg"; +import meta_kg, { KGQualifiersObject } from "@retriever/smartapi-kg"; import { snakeCase } from "snake-case"; import path from "path"; import PredicatesLoadingError from "../utils/errors/predicates_error"; -const debug = require("debug")("bte:biothings-explorer-trapi:metakg"); +const debug = require("debug")("bte:retriever:metakg"); import apiList from "../config/api_list"; interface PredicateInfo { diff --git a/packages/server/src/controllers/opentelemetry.ts b/packages/server/src/controllers/opentelemetry.ts index 2acf1e9..cc81ead 100644 --- a/packages/server/src/controllers/opentelemetry.ts +++ b/packages/server/src/controllers/opentelemetry.ts @@ -2,7 +2,7 @@ import { NodeSDK } from "@opentelemetry/sdk-node"; import { getNodeAutoInstrumentations } from "@opentelemetry/auto-instrumentations-node"; import { Resource } from "@opentelemetry/resources"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer:otel-init"); +const debug = Debug("retriever:retriever:otel-init"); import { JaegerExporter } from "@opentelemetry/exporter-jaeger"; debug("Initializing Opentelemetry instrumentation..."); @@ -13,7 +13,7 @@ const sdk = new NodeSDK({ }), instrumentations: [getNodeAutoInstrumentations()], resource: new Resource({ - "service.name": "biothings-explorer", + "service.name": "retriever", }), }); sdk.start(); diff --git a/packages/server/src/controllers/threading/taskHandler.ts b/packages/server/src/controllers/threading/taskHandler.ts index f1d0b58..c8a5ac1 100644 --- a/packages/server/src/controllers/threading/taskHandler.ts +++ b/packages/server/src/controllers/threading/taskHandler.ts @@ -3,7 +3,7 @@ import "../opentelemetry"; import { isMainThread, threadId } from "worker_threads"; import Piscina from "piscina"; import Debug from "debug"; -const debug = Debug(`bte:biothings-explorer-trapi:worker${threadId}`); +const debug = Debug(`retriever:worker${threadId}`); if (!isMainThread) { // Log thread start before BioLink model loads @@ -15,8 +15,8 @@ import { getQueryQueue } from "../async/asyncquery_queue"; import * as Sentry from "@sentry/node"; import { ProfilingIntegration } from "@sentry/profiling-node"; import OpenTelemetry, { Span } from "@opentelemetry/api"; -import { Telemetry } from "@biothings-explorer/utils"; -import { InnerTaskData } from "@biothings-explorer/types"; +import { Telemetry } from "@retriever/utils"; +import { InnerTaskData } from "@retriever/types"; // use SENTRY_DSN environment variable try { @@ -29,7 +29,7 @@ try { new Sentry.Integrations.Http({ tracing: true }), ], environment: process.env.INSTANCE_ENV, - debug: true, + debug: false, normalizeDepth: 6, maxBreadcrumbs: 500, // Set tracesSampleRate to 1.0 to capture 100% @@ -51,15 +51,15 @@ export default async function runTask({ route, traceparent, tracestate, - port, + workerSide, job = { jobId: undefined, queueName: undefined }, }: InnerTaskData) { debug(`Worker thread ${threadId} beginning ${Piscina.workerData.queue} task.`); global.SCHEMA_VERSION = "1.4.0"; - global.parentPort = port; - port.postMessage({ threadId, type: "registerId" }); + global.workerSide = workerSide; + workerSide.postMessage({ threadId, type: "registerId" }); global.cachingTasks = []; global.queryInformation = { @@ -91,7 +91,7 @@ export default async function runTask({ }); span = OpenTelemetry.trace - .getTracer("biothings-explorer-thread") + .getTracer("retriever-thread") .startSpan( routeNames[route], undefined, diff --git a/packages/server/src/controllers/threading/threadHandler.ts b/packages/server/src/controllers/threading/threadHandler.ts index bd82235..f24c97d 100644 --- a/packages/server/src/controllers/threading/threadHandler.ts +++ b/packages/server/src/controllers/threading/threadHandler.ts @@ -1,9 +1,9 @@ import { MessageChannel, threadId } from "worker_threads"; import Debug from "debug"; import { context, propagation } from "@opentelemetry/api"; -const debug = Debug("bte:biothings-explorer-trapi:threading"); +const debug = Debug("retriever:threading"); import path from "path"; -import { redisClient } from "@biothings-explorer/utils"; +import { redisClient } from "@retriever/utils"; import Piscina from "piscina"; import os from "os"; import ServerOverloadedError from "../../utils/errors/server_overloaded_error"; @@ -11,7 +11,7 @@ import { customAlphabet } from "nanoid"; import { getQueryQueue } from "../async/asyncquery_queue"; import { tasks } from "../../routes/index"; -import { Telemetry } from "@biothings-explorer/utils"; +import { Telemetry } from "@retriever/utils"; import ErrorHandler from "../../middlewares/error"; import { Request, Response } from "express"; import { BullJob, PiscinaWaitTime, ThreadPool } from "../../types"; @@ -22,9 +22,10 @@ import { InnerTaskData, QueryHandlerOptions, ThreadMessage, -} from "@biothings-explorer/types"; +} from "@retriever/types"; import { Queue } from "bull"; -// import SubqueryRelay from "packages/call-apis/src"; +import SubqueryRelay, { Subquery } from "@retriever/call-apis"; +import { FrozenSubquery } from "packages/call-apis/src/queries/subquery"; const SYNC_MIN_CONCURRENCY = 2; const ASYNC_MIN_CONCURRENCY = 3; @@ -105,11 +106,18 @@ if (!global.threadpool && !Piscina.isWorkerThread && !(process.env.USE_THREADING } as ThreadPool; } -async function queueTaskToWorkers(pool: Piscina, taskInfo: TaskInfo, route: string, job?: BullJob): Promise { +const subqueryRelay = new SubqueryRelay(); + +async function queueTaskToWorkers( + pool: Piscina, + taskInfo: TaskInfo, + route: string, + job?: BullJob, +): Promise { return new Promise((resolve, reject) => { let workerThreadID: string; const abortController = new AbortController(); - const { port1: toWorker, port2: fromWorker } = new MessageChannel(); + const { port1: workerSide, port2: parentSide } = new MessageChannel(); // get otel context @@ -117,11 +125,11 @@ async function queueTaskToWorkers(pool: Piscina, taskInfo: TaskInfo, route: stri propagation.inject(context.active(), otelData); const { traceparent, tracestate } = otelData; - const taskData: InnerTaskData = { req: taskInfo, route, traceparent, tracestate, port: toWorker }; + const taskData: InnerTaskData = { req: taskInfo, route, traceparent, tracestate, workerSide }; // Propagate data between task runner and bull job if (job) taskData.job = { jobId: job.id, queueName: job.queue.name }; - const task = pool.run(taskData, { signal: abortController.signal, transferList: [toWorker] }); + const task = pool.run(taskData, { signal: abortController.signal, transferList: [workerSide] }); if (job) { void job.update({ ...job.data, abortController }); } @@ -160,7 +168,7 @@ async function queueTaskToWorkers(pool: Piscina, taskInfo: TaskInfo, route: stri } = {}; const timeout = parseInt(process.env.REQUEST_TIMEOUT ?? (60 * 5).toString()) * 1000; - fromWorker.on("message", (msg: ThreadMessage) => { + parentSide.on("message", async (msg: ThreadMessage) => { switch (msg.type) { default: debug(`WARNING: received untyped message from thread {msg.threadId}`); @@ -191,6 +199,24 @@ async function queueTaskToWorkers(pool: Piscina, taskInfo: TaskInfo, route: stri case "cacheDone": cacheInProgress = msg.value ? cacheInProgress - 1 : 0; break; + case "subqueryRequest": + const { queries, options } = msg.value as { + queries: FrozenSubquery[]; + options: QueryHandlerOptions; + }; + debug(`Main thread receives ${queries.length} subqueries from worker.`); + subqueryRelay.subscribe( + await Promise.all(queries.map(async query => await Subquery.unfreeze(query))), + options, + ({ hash, records, logs, apiUnavailable }) => { + parentSide.postMessage({ + threadId: 0, + type: "subQueryResult", + value: { hash, records, logs, apiUnavailable }, + } satisfies ThreadMessage); + }, + ); + break; } if (reqDone && cacheInProgress <= 0 && job) { void job.progress(100); @@ -339,8 +365,13 @@ export async function runBullJob(job: BullJob, route: string, useAsync = true) { } export function taskResponse(response: T, status: number = undefined): T { - if (global.parentPort) { - global.parentPort.postMessage({ threadId, type: "result", value: response, status: status } satisfies ThreadMessage); + if (global.workerSide) { + global.workerSide.postMessage({ + threadId, + type: "result", + value: response, + status: status, + } satisfies ThreadMessage); return undefined; } else { return response; @@ -348,11 +379,11 @@ export function taskResponse(response: T, status: number = undefined): T { } export function taskError(error: Error): void { - if (global.parentPort) { + if (global.workerSide) { if (ErrorHandler.shouldHandleError(error)) { Telemetry.captureException(error); } - global.parentPort.postMessage({ threadId, type: "error", value: error }); + global.workerSide.postMessage({ threadId, type: "error", value: error }); return undefined; } else { throw error; diff --git a/packages/server/src/middlewares/error.ts b/packages/server/src/middlewares/error.ts index ea0bfff..e49aff7 100644 --- a/packages/server/src/middlewares/error.ts +++ b/packages/server/src/middlewares/error.ts @@ -1,14 +1,14 @@ import swaggerValidation from "./validate"; -import { InvalidQueryGraphError } from "@biothings-explorer/query_graph_handler"; +import { InvalidQueryGraphError } from "@retriever/types"; import PredicatesLoadingError from "../utils/errors/predicates_error"; import MetaKGLoadingError from "../utils/errors/metakg_error"; import ServerOverloadedError from "../utils/errors/server_overloaded_error"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:error_handler"); +const debug = Debug("retriever:error_handler"); import * as Sentry from "@sentry/node"; import { Express, NextFunction, Request, Response } from "express"; import StatusError from "../utils/errors/status_error"; -import { TrapiResponse } from "@biothings-explorer/types"; +import { TrapiResponse } from "@retriever/types"; class ErrorHandler { shouldHandleError(error: Error) { diff --git a/packages/server/src/middlewares/logging.ts b/packages/server/src/middlewares/logging.ts index b7f05fa..af933e1 100644 --- a/packages/server/src/middlewares/logging.ts +++ b/packages/server/src/middlewares/logging.ts @@ -6,7 +6,7 @@ import { Express, Request, Response } from "express"; class LoggingHandler { setRoutes(app: Express) { const transport = new winston.transports.DailyRotateFile({ - filename: "BioThings-Explorer-TRAPI-%DATE%.log", + filename: "retriever-%DATE%.log", dirname: process.env.LOG || "./log", datePattern: "YYYY-MM-DD", zippedArchive: true, diff --git a/packages/server/src/routes/bullboard.ts b/packages/server/src/routes/bullboard.ts index 33b1fcf..ed1f79d 100644 --- a/packages/server/src/routes/bullboard.ts +++ b/packages/server/src/routes/bullboard.ts @@ -3,8 +3,8 @@ import { createBullBoard } from "@bull-board/api"; import { BullAdapter } from "@bull-board/api/bullAdapter"; import { ExpressAdapter } from "@bull-board/express"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:bullboard"); -import { redisClient } from "@biothings-explorer/utils"; +const debug = Debug("retriever:bullboard"); +import { redisClient } from "@retriever/utils"; import { Express, NextFunction, Request, Response } from "express"; class BullBoardPage { diff --git a/packages/server/src/routes/frontpage.ts b/packages/server/src/routes/frontpage.ts deleted file mode 100644 index ffc09b6..0000000 --- a/packages/server/src/routes/frontpage.ts +++ /dev/null @@ -1,19 +0,0 @@ -import history from "connect-history-api-fallback"; -import express from "express"; -import path from "path"; -import { Express } from "express"; - -class FrontPage { - setRoutes(app: Express) { - const staticFileMiddleware = express.static(path.resolve(__dirname, "../../../web-app/dist")); - app.use(staticFileMiddleware); - app.use( - history({ - disableDotRule: true, - }), - ); - app.use(staticFileMiddleware); - } -} - -export default new FrontPage(); diff --git a/packages/server/src/routes/index.ts b/packages/server/src/routes/index.ts index 96049a4..06e970d 100644 --- a/packages/server/src/routes/index.ts +++ b/packages/server/src/routes/index.ts @@ -1,5 +1,4 @@ import MetaKG from "./metakg"; -import FrontPage from "./frontpage"; import Performance from "./performance"; import V1QueryByAPI from "./v1/query_v1_by_api"; import V1QueryByTeam from "./v1/query_v1_by_team"; @@ -16,7 +15,7 @@ import LoggingHandler from "../middlewares/logging"; import routesBullBoardPage from "./bullboard"; import { Express } from "express"; import { TaskFunction } from "../types"; -import { TaskInfo } from "@biothings-explorer/types"; +import { TaskInfo } from "@retriever/types"; export function setRoutes(app: Express): void { MetaKG.setRoutes(app); @@ -34,7 +33,6 @@ export function setRoutes(app: Express): void { LoggingHandler.setRoutes(app); V1Query.setRoutes(app); ErrorHandler.setRoutes(app); - FrontPage.setRoutes(app); } interface TaskByRoute { diff --git a/packages/server/src/routes/performance.ts b/packages/server/src/routes/performance.ts index 5f3ae83..e3af1a2 100644 --- a/packages/server/src/routes/performance.ts +++ b/packages/server/src/routes/performance.ts @@ -1,7 +1,7 @@ import path from "path"; import fs from "fs"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:performance"); +const debug = Debug("retriever:performance"); import * as utils from "../utils/common"; import { Express } from "express"; diff --git a/packages/server/src/routes/v1/asyncquery_status.ts b/packages/server/src/routes/v1/asyncquery_status.ts index 5e981cb..530b794 100644 --- a/packages/server/src/routes/v1/asyncquery_status.ts +++ b/packages/server/src/routes/v1/asyncquery_status.ts @@ -1,5 +1,5 @@ import path from "path"; -import { LogEntry, redisClient } from "@biothings-explorer/utils"; +import { LogEntry, redisClient } from "@retriever/utils"; import { getQueryQueue } from "../../controllers/async/asyncquery_queue"; import { getQueryResponse } from "../../controllers/async/asyncquery"; import * as utils from "../../utils/common"; @@ -7,9 +7,9 @@ import * as utils from "../../utils/common"; import swaggerValidation from "../../middlewares/validate"; import { runTask, taskResponse, taskError } from "../../controllers/threading/threadHandler"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:async"); +const debug = Debug("retriever:async"); import { Express, NextFunction, Request, RequestHandler, Response } from "express"; -import { TaskInfo, TrapiAsyncStatusResponse, TrapiLog, TrapiResponse } from "@biothings-explorer/types"; +import { TaskInfo, TrapiAsyncStatusResponse, TrapiLog, TrapiResponse } from "@retriever/types"; import { BteRoute } from "../../types"; import { Queue } from "bull"; import StatusError from "../../utils/errors/status_error"; diff --git a/packages/server/src/routes/v1/asyncquery_v1.ts b/packages/server/src/routes/v1/asyncquery_v1.ts index c85a688..fb27bb3 100644 --- a/packages/server/src/routes/v1/asyncquery_v1.ts +++ b/packages/server/src/routes/v1/asyncquery_v1.ts @@ -1,6 +1,6 @@ import path from "path"; import apiList from "../../config/api_list"; -import TRAPIQueryHandler from "@biothings-explorer/query_graph_handler"; +import TRAPIQueryHandler from "@retriever/query_graph_handler"; import swaggerValidation from "../../middlewares/validate"; import { asyncquery, asyncqueryResponse } from "../../controllers/async/asyncquery"; import * as utils from "../../utils/common"; @@ -16,7 +16,7 @@ const predicatesPath = path.resolve( ); import { Express, NextFunction, Request, RequestHandler, Response } from "express"; -import { QueueData, TaskInfo, TrapiQuery } from "@biothings-explorer/types"; +import { QueueData, TaskInfo, TrapiQuery } from "@retriever/types"; interface TypedRequestBody extends Request { body: T; diff --git a/packages/server/src/routes/v1/asyncquery_v1_by_api.ts b/packages/server/src/routes/v1/asyncquery_v1_by_api.ts index 18fc28a..580a3c7 100644 --- a/packages/server/src/routes/v1/asyncquery_v1_by_api.ts +++ b/packages/server/src/routes/v1/asyncquery_v1_by_api.ts @@ -2,7 +2,7 @@ import path from "path"; import swaggerValidation from "../../middlewares/validate"; import { asyncquery, asyncqueryResponse } from "../../controllers/async/asyncquery"; import * as utils from "../../utils/common"; -import TRAPIQueryHandler from "@biothings-explorer/query_graph_handler"; +import TRAPIQueryHandler from "@retriever/query_graph_handler"; import apiList from "../../config/api_list"; import { taskResponse } from "../../controllers/threading/threadHandler"; const smartAPIPath = path.resolve( @@ -14,7 +14,7 @@ const predicatesPath = path.resolve( process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json", ); import { Express, NextFunction, Request, Response } from "express"; -import { QueueData, TaskInfo } from "@biothings-explorer/types"; +import { QueueData, TaskInfo } from "@retriever/types"; import { BteRoute } from "../../types"; class V1AsyncQueryByAPI implements BteRoute { diff --git a/packages/server/src/routes/v1/asyncquery_v1_by_team.ts b/packages/server/src/routes/v1/asyncquery_v1_by_team.ts index a8d64c5..3f5dcb8 100644 --- a/packages/server/src/routes/v1/asyncquery_v1_by_team.ts +++ b/packages/server/src/routes/v1/asyncquery_v1_by_team.ts @@ -1,6 +1,6 @@ import path from "path"; import apiList from "../../config/api_list"; -import TRAPIQueryHandler from "@biothings-explorer/query_graph_handler"; +import TRAPIQueryHandler from "@retriever/query_graph_handler"; import swaggerValidation from "../../middlewares/validate"; import { asyncquery, asyncqueryResponse } from "../../controllers/async/asyncquery"; import * as utils from "../../utils/common"; @@ -16,7 +16,7 @@ const predicatesPath = path.resolve( ); import { Express, NextFunction, Request, RequestHandler, Response } from "express"; -import { QueueData, TaskInfo } from "@biothings-explorer/types"; +import { QueueData, TaskInfo } from "@retriever/types"; class V1AsyncQueryByTeam implements BteRoute { setRoutes(app: Express) { diff --git a/packages/server/src/routes/v1/query_v1.ts b/packages/server/src/routes/v1/query_v1.ts index 893331e..dcbd352 100644 --- a/packages/server/src/routes/v1/query_v1.ts +++ b/packages/server/src/routes/v1/query_v1.ts @@ -1,6 +1,6 @@ import path from "path"; import apiList from "../../config/api_list"; -import TRAPIQueryHandler from "@biothings-explorer/query_graph_handler"; +import TRAPIQueryHandler from "@retriever/query_graph_handler"; import swaggerValidation from "../../middlewares/validate"; const smartAPIPath = path.resolve( __dirname, @@ -13,9 +13,9 @@ const predicatesPath = path.resolve( import * as utils from "../../utils/common"; import { runTask, taskResponse, taskError } from "../../controllers/threading/threadHandler"; import { Express, NextFunction, Request, RequestHandler, Response } from "express"; -import { TrapiResponse } from "@biothings-explorer/types"; +import { TrapiResponse } from "@retriever/types"; import { BteRoute } from "../../types"; -import { TaskInfo } from "@biothings-explorer/types"; +import { TaskInfo } from "@retriever/types"; class V1Query implements BteRoute { setRoutes(app: Express) { diff --git a/packages/server/src/routes/v1/query_v1_by_api.ts b/packages/server/src/routes/v1/query_v1_by_api.ts index fa7bb31..d901993 100644 --- a/packages/server/src/routes/v1/query_v1_by_api.ts +++ b/packages/server/src/routes/v1/query_v1_by_api.ts @@ -1,4 +1,4 @@ -import TRAPIQueryHandler from "@biothings-explorer/query_graph_handler"; +import TRAPIQueryHandler from "@retriever/query_graph_handler"; import swaggerValidation from "../../middlewares/validate"; import path from "path"; const smartAPIPath = path.resolve( @@ -13,7 +13,7 @@ import * as utils from "../../utils/common"; import { runTask, taskResponse, taskError } from "../../controllers/threading/threadHandler"; import apiList from "../../config/api_list"; import { BteRoute } from "../../types"; -import { TaskInfo } from "@biothings-explorer/types"; +import { TaskInfo } from "@retriever/types"; import { Express, NextFunction, Request, RequestHandler, Response } from "express"; class V1QueryByAPI implements BteRoute { diff --git a/packages/server/src/routes/v1/query_v1_by_team.ts b/packages/server/src/routes/v1/query_v1_by_team.ts index 7192925..51fd912 100644 --- a/packages/server/src/routes/v1/query_v1_by_team.ts +++ b/packages/server/src/routes/v1/query_v1_by_team.ts @@ -1,6 +1,6 @@ import path from "path"; import apiList from "../../config/api_list"; -import TRAPIQueryHandler from "@biothings-explorer/query_graph_handler"; +import TRAPIQueryHandler from "@retriever/query_graph_handler"; import swaggerValidation from "../../middlewares/validate"; const smartAPIPath = path.resolve( __dirname, @@ -13,7 +13,7 @@ const predicatesPath = path.resolve( import * as utils from "../../utils/common"; import { runTask, taskResponse, taskError } from "../../controllers/threading/threadHandler"; import { Express, NextFunction, Request, RequestHandler, Response } from "express"; -import { TaskInfo } from "@biothings-explorer/types"; +import { TaskInfo } from "@retriever/types"; class V1QueryByTeam { setRoutes(app: Express) { diff --git a/packages/server/src/server.ts b/packages/server/src/server.ts index 89eb043..2dfb00a 100644 --- a/packages/server/src/server.ts +++ b/packages/server/src/server.ts @@ -1,5 +1,5 @@ import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:server-start"); +const debug = Debug("retriever:server-start"); async function main() { await testRedisConnection(); // must happen before app to avoid issues @@ -15,7 +15,7 @@ async function main() { } async function testRedisConnection() { - const { redisClient } = await import("@biothings-explorer/utils"); + const { redisClient } = await import("@retriever/utils"); if (redisClient.clientEnabled) { // redis enabled diff --git a/packages/server/src/types.ts b/packages/server/src/types.ts index f3f7a9e..f7297ff 100644 --- a/packages/server/src/types.ts +++ b/packages/server/src/types.ts @@ -1,8 +1,8 @@ import Piscina from "piscina"; import Queue from "bull"; -import { TrapiQuery, TrapiResponse } from "@biothings-explorer/types"; +import { TrapiQuery, TrapiResponse } from "@retriever/types"; import { Express, Request } from "express"; -import { TaskInfo, TaskData } from "@biothings-explorer/types"; +import { TaskInfo, TaskData } from "@retriever/types"; export interface ThreadPool { sync: Piscina; diff --git a/packages/server/src/utils/common.ts b/packages/server/src/utils/common.ts index eb7697f..c032f79 100644 --- a/packages/server/src/utils/common.ts +++ b/packages/server/src/utils/common.ts @@ -3,7 +3,7 @@ import { URL } from "url"; import yaml2json from "js-yaml"; import fs from "fs/promises"; import path from "path"; -import { TrapiLog, TrapiSchema, TrapiWorkflow } from "@biothings-explorer/types"; +import { TrapiLog, TrapiSchema, TrapiWorkflow } from "@retriever/types"; import { NextFunction, Request, Response } from "express"; const schema: unknown[] = []; diff --git a/packages/server/src/utils/errors/status_error.ts b/packages/server/src/utils/errors/status_error.ts index e8e2558..0b34eaf 100644 --- a/packages/server/src/utils/errors/status_error.ts +++ b/packages/server/src/utils/errors/status_error.ts @@ -1,4 +1,4 @@ -import { TrapiLog } from "@biothings-explorer/types"; +import { TrapiLog } from "@retriever/types"; export default class StatusError extends Error { statusCode: number; diff --git a/packages/server/tsconfig.json b/packages/server/tsconfig.json index 1116225..ceb9572 100644 --- a/packages/server/tsconfig.json +++ b/packages/server/tsconfig.json @@ -6,9 +6,9 @@ "outDir": "./built", "paths": { "smartapi-kg": ["../smartapi-kg"], - "@biothings-explorer/query_graph_handler": ["../query_graph_handler"], - "@biothings-explorer/utils": ["../utils"], - "@biothings-explorer/types": ["../types"] + "@retriever/query_graph_handler": ["../query_graph_handler"], + "@retriever/utils": ["../utils"], + "@retriever/types": ["../types"] } }, "include": ["./src/**/*", "./src/**/*.json"], diff --git a/packages/smartapi-kg/bundle.js b/packages/smartapi-kg/bundle.js index 90dc10b..0cde8fe 100644 --- a/packages/smartapi-kg/bundle.js +++ b/packages/smartapi-kg/bundle.js @@ -1,2 +1,2 @@ /*! 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s().wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.abrupt("return",P().get(this.constructQueryUrl(n.url),{timeout:5e3}).then((function(t){if(200===t.status){var r=t.data;return e.parsePredicateEndpoint(r,n)}return H("[error]: Unable to get /predicates for ".concat(n.url," due to query failure with status code ").concat(t.status)),[]})).catch((function(t){return H("[error]: Unable to get /predicates for ".concat(n.url," due to error ").concat(t.toString())),[]})));case 1:case"end":return t.stop()}}),t,this)}))),function(t){return i.apply(this,arguments)})},{key:"getOpsFromPredicatesEndpoints",value:(r=n(s().mark((function t(n){var e,r,o=this;return s().wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return e=this.getTRAPIWithPredicatesEndpoint(n),r=[],t.next=4,Promise.allSettled(e.map((function(t){return o.getOpsFromPredicatesEndpoint(t)}))).then((function(t){t.map((function(t){"fulfilled"===t.status&&(t.value,r=[].concat(g(r),g(t.value)))}))}));case 4:return t.abrupt("return",r);case 5:case"end":return t.stop()}}),t,this)}))),function(t){return r.apply(this,arguments)})},{key:"build",value:(e=n(s().mark((function t(){var n,e,r;return s().wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this.load();case 2:return n=t.sent,e=this.loadOpsFromSpecs(n),t.next=6,this.getOpsFromPredicatesEndpoints(n);case 6:return r=t.sent,t.abrupt("return",[].concat(g(e),g(r)));case 8:case"end":return t.stop()}}),t,this)}))),function(){return e.apply(this,arguments)})}]),h}(K),Z=function(){var t=n(s().mark((function t(n,e){var r,o;return s().wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return r=!0===e?new J(n):new K(n),t.next=3,r.build();case 3:return o=t.sent,t.abrupt("return",o);case 5:case"end":return t.stop()}}),t)})));return function(n,e){return t.apply(this,arguments)}}(),V=e(657),X=e.n(V);var Q=R()("bte:smartapi-kg:AllSpecsSyncLoader"),Y=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t){var n;return o(this,i),a(h(n=r.call(this)),"_file_path",void 0),n._file_path=t,n}return u(i,[{key:"fetch",value:function(){Q("Fetching from file path: ".concat(this._file_path));var t,n=X().readFileSync(this._file_path,"utf-8"),e=JSON.parse(n);return t="hits"in e?e:{hits:[e]},Q("Hits in inputs: ".concat("hits"in e)),t}},{key:"parse",value:function(t){return t.hits}},{key:"load",value:function(){var t=this.fetch();return this.parse(t)}}]),i}(T);var tt=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t,n){var e;return o(this,i),a(h(e=r.call(this,n)),"_smartAPIID",void 0),e._smartAPIID=t,e}return u(i,[{key:"parse",value:function(t){var n=this;return t.hits.filter((function(t){return t._id===n._smartAPIID}))}}]),i}(Y);var nt=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t,n){var e;return o(this,i),a(h(e=r.call(this,n)),"_teamName",void 0),e._teamName=t,e}return u(i,[{key:"parse",value:function(t){var n=this;return t.hits.filter((function(t){return"x-translator"in t.info&&"team"in t.info["x-translator"]&&Array.isArray(t.info["x-translator"].team)&&t.info["x-translator"].team.includes(n._teamName)}))}}]),i}(Y);var et=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t,n){var e;return o(this,i),a(h(e=r.call(this,n)),"_tag",void 0),e._tag=t,e}return u(i,[{key:"parse",value:function(t){var n=this;return t.hits.filter((function(t){return t.tags.map((function(t){return t.name})).includes(n._tag)}))}}]),i}(Y);var rt=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t,n){var e;return o(this,i),a(h(e=r.call(this,n)),"_component",void 0),e._component=t,e}return u(i,[{key:"parse",value:function(t){var n=this;return t.hits.filter((function(t){return"x-translator"in t.info&&t.info["x-translator"].component===n._component}))}}]),i}(Y);var ot=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t,n){var e;return o(this,i),a(h(e=r.call(this,n)),"_apiNames",void 0),e._apiNames=t,e}return u(i,[{key:"parse",value:function(t){var n=this;return t.hits.filter((function(t){return n._apiNames.includes(t.info.title)}))}}]),i}(Y),it=R()("bte:smartapi-kg:SyncLoader"),ut=function(){var t,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:void 0,e=arguments.length>1&&void 0!==arguments[1]?arguments[1]:void 0,r=arguments.length>2&&void 0!==arguments[2]?arguments[2]:void 0,o=arguments.length>3&&void 0!==arguments[3]?arguments[3]:void 0,i=arguments.length>4&&void 0!==arguments[4]?arguments[4]:void 0,u=arguments.length>5?arguments[5]:void 0;return void 0!==n?(t=new tt(n,u),it("Using single spec sync loader now.")):void 0!==e?(t=new nt(e,u),it("Using team spec sync loader now.")):void 0!==r?(t=new et(r,u),it("Using tags spec sync loader now.")):void 0!==o?(t=new rt(o,u),it("Using component spec sync loader now.")):Array.isArray(i)?(t=new ot(i,u),it("Using api names spec sync loader now.")):(t=new Y(u),it("Using all specs sync loader now.")),t.load()};var at=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t,n){var e;return o(this,i),a(h(e=r.call(this,t)),"_file_path",void 0),e._file_path=n,e}return u(i,[{key:"build",value:function(){var t=ut(this._options.smartAPIID,this._options.teamName,this._options.tag,this._options.component,this._options.apiNames,this._file_path);return this.loadOpsFromSpecs(t)}}]),i}(j),ct=e(136),st=e.n(ct);var ft=function(t){l(i,t);var n,e,r=(n=i,e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=d(n);if(e){var o=d(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return v(this,t)});function i(t,n,e){var u;return o(this,i),a(h(u=r.call(this,t)),"_file_path",void 0),a(h(u),"_predicates_file_path",void 0),u._file_path=n,u._predicates_file_path=e,u}return u(i,[{key:"removeBioLinkPrefix",value:function(t){if("string"==typeof t)return t.startsWith("biolink:")?t.slice(8):t}},{key:"parsePredicateEndpoint",value:function(t){var n=this,e=[];return"predicates"in t?(Object.keys(t.predicates).map((function(r){Object.keys(t.predicates[r]).map((function(o){Array.isArray(t.predicates[r][o])&&t.predicates[r][o].map((function(i){e.push({association:{input_type:n.removeBioLinkPrefix(r),output_type:n.removeBioLinkPrefix(o),predicate:n.removeBioLinkPrefix(i),api_name:t.association.api_name,smartapi:t.association.smartapi,"x-translator":t.association["x-translator"]},tags:[].concat(g(t.tags),["bte-trapi"]),query_operation:{path:"/query",method:"post",server:t.query_operation.server,pathParams:void 0,params:void 0,request_body:void 0,supportBatch:!0,inputSeparator:",",tags:[].concat(g(t.tags),["bte-trapi"])}})}))}))})),void 0!==this._options.apiNames?e.filter((function(t){return n._options.apiNames.includes(t.association.api_name)})):e):e}},{key:"fetch",value:function(){var t=st().readFileSync(this._predicates_file_path,"utf-8");return JSON.parse(t)}},{key:"build",value:function(){var t=this,n=ut(this._options.smartAPIID,this._options.teamName,this._options.tag,this._options.component,this._options.apiNames,this._file_path),e=this.loadOpsFromSpecs(n),r=this.fetch(),o=[];return r.map((function(n){o=[].concat(g(o),g(t.parsePredicateEndpoint(n)))})),[].concat(g(e),g(o))}}]),i}(j),lt=function(t,n,e,r){return(!0===n?new ft(t,e,r):new at(t,e)).build()},pt=e(486),ht=e.n(pt),vt=e(470),dt=e.n(vt),yt=(R()("bte:smartapi-kg:MetaKG"),function(){function t(){var n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:void 0,e=arguments.length>1&&void 0!==arguments[1]?arguments[1]:void 0;o(this,t),a(this,"_ops",void 0),a(this,"_file_path",void 0),a(this,"_predicates_path",void 0),this._ops=[],this.path=n,this.predicates_path=e}var e;return u(t,[{key:"path",set:function(t){this._file_path=void 0===t?dt().resolve("/","./data/smartapi_specs.json"):t}},{key:"predicates_path",set:function(t){this._predicates_path=void 0===t?dt().resolve("/","./data/predicates.json"):t}},{key:"ops",get:function(){return this._ops}},{key:"constructMetaKG",value:(e=n(s().mark((function t(){var n,e,r=arguments;return s().wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return n=r.length>0&&void 0!==r[0]&&r[0],e=r.length>1&&void 0!==r[1]?r[1]:{},t.next=4,Z(e,n);case 4:return this._ops=t.sent,t.abrupt("return",this._ops);case 6:case"end":return t.stop()}}),t,this)}))),function(){return e.apply(this,arguments)})},{key:"constructMetaKGSync",value:function(){var t=arguments.length>0&&void 0!==arguments[0]&&arguments[0],n=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};return this._ops=lt(n,t,this._file_path,this._predicates_path),this._ops}},{key:"filter",value:function(t){return function(t,n){var e=function(t){var n={};return D.map((function(t){return n[t]=new Set})),t.map((function(t){D.map((function(e){n[e].add(t.association[e])}))})),n}(t),r={};D.map((function(t){if(t in n&&void 0!==n[t]){var o=Array.isArray(n[t])?n[t]:[n[t]];r[t]=new Set(o)}else r[t]=e[t]}));var o=ht().cloneDeep(t);return D.map((function(t){o=o.filter((function(n){return r[t].has(n.association[t])}))})),o}(this.ops,t)}}]),t}())})(),r.default})()})); \ No newline at end of file diff --git a/packages/smartapi-kg/package.json b/packages/smartapi-kg/package.json index 1fe7a93..96aaa2b 100644 --- a/packages/smartapi-kg/package.json +++ b/packages/smartapi-kg/package.json @@ -1,5 +1,5 @@ { - "name": "@biothings-explorer/smartapi-kg", + "name": "@retriever/smartapi-kg", "version": "4.0.0", "description": "create a knowledge graph based on SmartAPI Specifications", "main": "built/index.js", @@ -18,11 +18,12 @@ }, "repository": { "type": "git", - "url": "git+https://github.com/biothings/smartapi-kg.js.git" + "url": "git+https://github.com/BioPack-team/retriever" }, "keywords": [ + "BioPack", + "retriever", "smartapi", - "biothings-explorer", "network", "knowledge graph", "kg" @@ -30,9 +31,9 @@ "author": "Jiwen Xin", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/smartapi-kg.js/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/smartapi-kg.js#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "devDependencies": { "@babel/cli": "^7.23.0", "@babel/core": "^7.23.2", diff --git a/packages/smartapi-kg/src/data/smartapi_specs.json b/packages/smartapi-kg/src/data/smartapi_specs.json index ef8df3f..6feec31 100644 --- a/packages/smartapi-kg/src/data/smartapi_specs.json +++ b/packages/smartapi-kg/src/data/smartapi_specs.json @@ -1 +1 @@ -{"hits":[{"openapi":"3.0.3","info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible developers"},"description":"Documentation of the BioThings SEMMEDDB query web services.","termsOfService":"https://biothings.io/about","title":"BioThings SEMMEDDB API","version":"2.0","x-translator":{"infores":"infores:biothings-semmeddb","component":"KP","team":["Service Provider"],"biolink-version":"3.0.3"}},"servers":[{"description":"Production server","url":"https://biothings.ncats.io/semmeddb","x-maturity":"production"}],"tags":[{"name":"disease"},{"name":"phenotype"},{"name":"gene"},{"name":"chemical"},{"name":"association"},{"name":"query"},{"name":"translator"},{"name":"biothings"},{"name":"ngd"}],"paths":{"/association/{id}":{"get":{"parameters":[{"name":"id","in":"path","required":true,"example":"85213740","schema":{"type":"string"}},{"$ref":"#/components/parameters/raw"},{"$ref":"#/components/parameters/rawquery"},{"$ref":"#/components/parameters/_source"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/_sorted"},{"$ref":"#/components/parameters/always_list"},{"$ref":"#/components/parameters/allow_null"},{"$ref":"#/components/parameters/format"}],"responses":{"200":{"description":"Success"}},"tags":["association"]}},"/association":{"post":{"parameters":[{"$ref":"#/components/parameters/raw"},{"$ref":"#/components/parameters/rawquery"},{"$ref":"#/components/parameters/_source"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/_sorted"},{"$ref":"#/components/parameters/always_list"},{"$ref":"#/components/parameters/allow_null"},{"$ref":"#/components/parameters/format"}],"requestBody":{"content":{"application/json":{"example":{"ids":["85213740","85203385"]},"schema":{"type":"object","properties":{"ids":{"description":"multiple Association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). 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These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nAdditional details on the data can be found in this documentation: (https://github.com/lstillwe/socio-economic-api/blob/master/docs/CensusData.md)\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Socio-Environmental Exposures API","version":"1.0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"By passing in a location specification (lat, lon) and a year range, you can retrieve the the ACS Values for that location and year range\n","operationId":"get_values","parameters":[{"description":"latitude in decimal degrees format, ie: 32.47","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -86.5","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"ACS data year range specification","in":"query","name":"years","required":true,"schema":{"enum":["All (2007-2016)","2007-2011","2012-2016"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"latitude":{"example":"32.47","type":"string"},"longitude":{"example":-86.5,"type":"string"},"values":{"items":{"properties":{"EstPropFemaleHouseholdAnyChild":{"example":"0.154929577","type":"string"},"EstPropFemaleHouseholdAnyChild_SE":{"example":"0.075973316","type":"string"},"EstPropFemaleHouseholdFamilyChild":{"example":"0.227979275","type":"string"},"EstPropFemaleHouseholdFamilyChild_SE":{"example":"0.151408698","type":"string"},"EstPropFemaleHouseholdNoSpouse":{"example":"0.362694301","type":"string"},"EstPropFemaleHouseholdNoSpouse_SE":{"example":"0.108321058","type":"string"},"EstPropHighSchoolDropout":{"example":"n/a","type":"string"},"EstPropHighSchoolDropoutNoWork":{"example":"n/a","type":"string"},"EstPropHighSchoolMaxEducation":{"example":"0.53164557","type":"string"},"EstPropHighSchoolMaxEducation_SE":{"example":"0.076480429","type":"string"},"EstPropHouseholdPA":{"example":"0","type":"string"},"EstPropHouseholdPA_SE":{"example":"0.060887293","type":"string"},"EstPropHouseholdSSI":{"example":"0.088028169","type":"string"},"EstPropHouseholdSSI_SE":{"example":"0.04974414","type":"string"},"EstPropHouseholdsNoAuto":{"example":"0.038732394","type":"string"},"EstPropHouseholdsNoAuto_SE":{"example":"0.039252128","type":"string"},"EstPropMaleLittleWork":{"example":"0.385245902","type":"string"},"EstPropNonHispWhite":{"example":"0.763758389","type":"string"},"EstPropNonHispWhite_SE":{"example":"0.105181283","type":"string"},"EstPropPersons5PlusNoEnglish":{"example":"0.075070822","type":"string"},"EstPropPersons5PlusNoEnglish_SE":{"example":"0.040387049","type":"string"},"EstPropPersonsNoHealthIns":{"example":"0.183892617","type":"string"},"EstPropPersonsNoHealthIns_SE":{"example":"0.063328335","type":"string"},"EstResidentialDensity":{"example":"175.1077206","type":"string"},"EstResidentialDensity_SE":{"example":"32.32567504","type":"string"},"EstTotalPopulation":{"example":"745","type":"string"},"EstTotalPopulation_SE":{"example":"137.5303603","type":"string"},"MedianHouseholdIncome":{"example":"n/a","type":"string"},"MedianHouseholdIncome_SE":{"example":"9888","type":"string"},"geoid":{"example":"15000US010010201001","type":"string"},"years":{"example":"2012-2016","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"content":{},"description":"Invalid parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"provides ACS values","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/socio_environmental_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"openapi":"3.0.3","info":{"contact":{"email":"help@myvariant.info","name":"Chunlei Wu","x-id":"https://github.com/newgene","x-role":"responsible developer"},"description":"Documentation of the MyVariant.info Variant Query web services. Learn more about [MyVariant.info](http://myvariant.info/)","termsOfService":"http://myvariant.info/terms/","title":"MyVariant.info API","version":"1.0","x-translator":{"infores":"infores:myvariant-info","component":"KP","team":["Service Provider"],"biolink-version":"3.0.3"}},"servers":[{"description":"Encrypted Production server","url":"https://myvariant.info/v1","x-maturity":"production"},{"description":"Production server","url":"http://myvariant.info/v1","x-maturity":"production"}],"tags":[{"name":"variant"},{"name":"query"},{"name":"metadata"},{"name":"translator"},{"name":"biothings"}],"paths":{"/metadata":{"get":{"parameters":[{"$ref":"#/components/parameters/callback","in":"query","name":"callback"}],"responses":{"200":{"description":"MyVariant.info metadata object"}},"summary":"Get metadata about the data available from MyVariant.info.","tags":["metadata"]}},"/metadata/fields":{"get":{"parameters":[{"description":"Pass a search term to filter the available fields, e.g. \"search=clinvar\".","in":"query","name":"search","schema":{"type":"string"}},{"description":"Pass a prefix string to filter the available fields, e.g. \"prefix=refseq\".","in":"query","name":"prefix","schema":{"type":"string"}},{"$ref":"#/components/parameters/callback","in":"query","name":"callback"}],"responses":{"200":{"description":"MyVariant.info metadata fields object"}},"summary":"Get metadata about the data fields available from MyVariant.info.","tags":["metadata"]}},"/query":{"get":{"parameters":[{"description":"Query string. Examples \"rs752396467\", \"possibly_damaging\", \"CDK7\". The detailed query syntax can be found from our [docs](http://docs.myvariant.info/en/latest/doc/variant_query_service.html).","example":"CDK7","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"1":"query","$ref":"#/components/parameters/fields","name":"fields"},{"$ref":"#/components/parameters/size","in":"query","name":"size"},{"$ref":"#/components/parameters/from","in":"query","name":"from"},{"$ref":"#/components/parameters/sort","in":"query","name":"sort"},{"description":"a single field or comma-separated fields to return facets, for example, \"facets=clinvar.gene.id\", \"facets=clinvar.gene.id,dbnsfp.uniprot.acc\".","in":"query","name":"facets","schema":{"type":"string"}},{"$ref":"#/components/parameters/callback","in":"query","name":"callback"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/QueryResult"}}},"description":"A query response object with \"hits\" property"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorResult"}}},"description":"A response indicating an improperly formatted query"}},"summary":"Make variant query and return matching variant list. Support JSONP and CORS as well.","tags":["query"]},"post":{"parameters":[{"$ref":"#/components/parameters/fields","in":"query","name":"fields"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"requestBody":{"required":true,"content":{"application/x-www-form-urlencoded":{"schema":{"properties":{"q":{"description":"multiple query terms seperated by comma (also support \"+\" or white space), but no wildcard, e.g., \"q=rs58991260,rs2500\" or \"q=rs58991260+rs2500\"","type":"string"},"scopes":{"description":"Specify one or more fields (separated by comma) as the search \"scopes\", e.g., \"scopes=dbsnp.rsid\". The available \"fields\" that can be passed to \"scopes\" parameter are listed [here](http://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: \"scopes=_id\" (HGVS id).","type":"string"}},"required":["q"]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/QueryPOSTResult"}}},"description":"Query response objects with \"hits\" property"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorResult"}}},"description":"A response indicating an improperly formatted query"}},"summary":"Make variant batch query and return matching variant hits","tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/civic-geneDisease"},{"$ref":"#/components/x-bte-kgs-operations/civic-geneDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/civic-variantDisease"},{"$ref":"#/components/x-bte-kgs-operations/civic-variantDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/dbsnp-variantGene"},{"$ref":"#/components/x-bte-kgs-operations/dbsnp-variantGene-rev"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantGene"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantGene-rev"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-geneDisease"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-geneDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantDisease"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/docm-geneDisease"},{"$ref":"#/components/x-bte-kgs-operations/docm-geneDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/docm-variantDisease"},{"$ref":"#/components/x-bte-kgs-operations/docm-variantDisease-rev"}]}},"/variant":{"post":{"parameters":[{"$ref":"#/components/parameters/fields","in":"query","name":"fields"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"requestBody":{"required":true,"content":{"application/x-www-form-urlencoded":{"schema":{"properties":{"ids":{"description":"multiple variant ids seperated by comma, e.g., \"ids=chr6:g.152708291G>A,chr1:g.35367G>A\" or \"ids=rs5882,rs12190874\". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","type":"string"}},"required":["ids"]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Variant"},"type":"array"}}},"description":"a list of matching variant objects"}},"summary":"For a list of variant ids, return the matching variant objects","tags":["variant"]}},"/variant/{variantid}":{"get":{"parameters":[{"description":"HGVS or rsid, e.g., chr6:g.152708291G>A, rs12190874","example":"chr6:g.152708291G>A","in":"path","name":"variantid","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields","in":"query","name":"fields"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/callback","in":"query","name":"callback"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Variant"}}},"description":"A matching variant object"},"404":{"description":"A response indicating an unknown variant id"}},"summary":"Retrieve variant annotation object based on HGVS or rsid, support JSONP and CORS as well.","tags":["variant"]}}},"components":{"parameters":{"callback":{"description":"you can pass a \"callback\" parameter to make a JSONP call.","in":"query","name":"callback","schema":{"type":"string"}},"dotfield":{"description":"control the format of the returned variant object. If \"true\" or \"1\", all fields will be collapsed into a single level deep structure (all nested objects will be a single level deep, using dotfield notation to signify the nested structure) Default: false.","in":"query","name":"dotfield","schema":{"type":"boolean"}},"email":{"description":"If you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.","in":"query","name":"email","schema":{"type":"string"}},"fields":{"description":"a comma-separated fields to limit the fields returned from the matching variant hits. The supported field names can be found from any variant object (e.g. http://myvariant.info/v1/variant/rs12190874). Note that it supports dot notation as well, e.g., you can pass \"dbsnp.rsid\". If \"fields=all\", all available fields will be returned. Default: \"all\".","in":"query","name":"fields","schema":{"type":"string"}},"from":{"description":"the number of matching variant hits to skip, starting from 0. Combining with \"size\" parameter, this can be useful for paging. Default: 0.","in":"query","name":"from","schema":{"type":"integer"}},"size":{"description":"the maximum number of matching variant hits to return (with a cap of 1000 at the moment). Default: 10.","in":"query","name":"size","schema":{"type":"integer"}},"sort":{"description":"the comma-separated fields to sort on. Prefix with \"-\" for descending order, otherwise in ascending order. 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Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0008974","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns phenotypes associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-phenotype"}]}},"/bioentity/disease/{id}/variants":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0004747","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-variant"}]}},"/bioentity/gene/{id}/anatomy":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:13434","in":"path","required":true,"example":"HGNC:8548","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns anatomies associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-anatomy"}]}},"/bioentity/gene/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:11138","schema":{"type":"string"}},{"name":"association_type","description":"Additional filters: causal, non_causal, both","in":"query","required":false,"example":"causal","schema":{"type":"string","enum":["causal","non_causal","both"],"default":"both"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-disease-1"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease-2"}]}},"/bioentity/gene/{id}/interactions":{"get":{"parameters":[{"name":"id","description":"id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns gene interaction","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-interaction"}]}},"/bioentity/gene/{id}/phenotypes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns phenotypes associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-phenotype"}]}},"/bioentity/gene/{id}/variants":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. HGNC:10896","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-variant"}]}},"/bioentity/pathway/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE any pathway element. E.g. REACT:R-HSA-5387390","in":"path","required":true,"example":"REACT:R-HSA-2644606","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a pathway","tags":["pathway"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/pathway-disease"}]}},"/bioentity/phenotype/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HP:0000272","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-disease"}]}},"/bioentity/phenotype/{id}/genes":{"get":{"parameters":[{"name":"id","description":"Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","in":"path","required":true,"example":"HP:0000183","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-gene"}]}},"/bioentity/phenotype/{id}/variants":{"get":{"parameters":[{"name":"id","description":"Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","in":"path","required":true,"example":"HP:0002944","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-variant"}]}},"/bioentity/variant/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ClinVarVariant:14925","in":"path","required":true,"example":"dbSNP:rs227731","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a variant","tags":["variant"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/variant-disease"}]}},"/bioentity/variant/{id}/genes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783","in":"path","required":true,"example":"dbSNP:rs11879191","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a variant","tags":["variant"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/variant-gene"}]}},"/bioentity/variant/{id}/phenotypes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, 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queryInputs }}","rows":-1,"direct":true,"unselect_evidence":true,"taxon":"NCBITaxon:9606"},"outputs":[{"id":"HGNC","semantic":"Gene"}],"predicate":"expresses","source":"infores:monarchinitiative","response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene-hgnc"}}],"disease-gene-1":[{"supportBatch":false,"useTemplating":true,"inputs":[{"id":"MONDO","semantic":"Disease"}],"parameters":{"id":"{{ queryInputs }}","rows":-1,"direct":true,"unselect_evidence":true,"taxon":"NCBITaxon:9606","association_type":"causal"},"outputs":[{"id":"HGNC","semantic":"Gene"}],"predicate":"caused_by","source":"infores:monarchinitiative","response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene-hgnc"}}],"disease-gene-2":[{"supportBatch":false,"useTemplating":true,"inputs":[{"id":"MONDO","semantic":"Disease"}],"parameters":{"id":"{{ queryInputs 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[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
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These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nAdditional details on the data can be found in this documentation: (https://github.com/lstillwe/socio-economic-api/blob/master/docs/CensusData.md)\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Socio-Environmental Exposures API","version":"1.0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"By passing in a location specification (lat, lon) and a year range, you can retrieve the the ACS Values for that location and year range\n","operationId":"get_values","parameters":[{"description":"latitude in decimal degrees format, ie: 32.47","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -86.5","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"ACS data year range specification","in":"query","name":"years","required":true,"schema":{"enum":["All (2007-2016)","2007-2011","2012-2016"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"latitude":{"example":"32.47","type":"string"},"longitude":{"example":-86.5,"type":"string"},"values":{"items":{"properties":{"EstPropFemaleHouseholdAnyChild":{"example":"0.154929577","type":"string"},"EstPropFemaleHouseholdAnyChild_SE":{"example":"0.075973316","type":"string"},"EstPropFemaleHouseholdFamilyChild":{"example":"0.227979275","type":"string"},"EstPropFemaleHouseholdFamilyChild_SE":{"example":"0.151408698","type":"string"},"EstPropFemaleHouseholdNoSpouse":{"example":"0.362694301","type":"string"},"EstPropFemaleHouseholdNoSpouse_SE":{"example":"0.108321058","type":"string"},"EstPropHighSchoolDropout":{"example":"n/a","type":"string"},"EstPropHighSchoolDropoutNoWork":{"example":"n/a","type":"string"},"EstPropHighSchoolMaxEducation":{"example":"0.53164557","type":"string"},"EstPropHighSchoolMaxEducation_SE":{"example":"0.076480429","type":"string"},"EstPropHouseholdPA":{"example":"0","type":"string"},"EstPropHouseholdPA_SE":{"example":"0.060887293","type":"string"},"EstPropHouseholdSSI":{"example":"0.088028169","type":"string"},"EstPropHouseholdSSI_SE":{"example":"0.04974414","type":"string"},"EstPropHouseholdsNoAuto":{"example":"0.038732394","type":"string"},"EstPropHouseholdsNoAuto_SE":{"example":"0.039252128","type":"string"},"EstPropMaleLittleWork":{"example":"0.385245902","type":"string"},"EstPropNonHispWhite":{"example":"0.763758389","type":"string"},"EstPropNonHispWhite_SE":{"example":"0.105181283","type":"string"},"EstPropPersons5PlusNoEnglish":{"example":"0.075070822","type":"string"},"EstPropPersons5PlusNoEnglish_SE":{"example":"0.040387049","type":"string"},"EstPropPersonsNoHealthIns":{"example":"0.183892617","type":"string"},"EstPropPersonsNoHealthIns_SE":{"example":"0.063328335","type":"string"},"EstResidentialDensity":{"example":"175.1077206","type":"string"},"EstResidentialDensity_SE":{"example":"32.32567504","type":"string"},"EstTotalPopulation":{"example":"745","type":"string"},"EstTotalPopulation_SE":{"example":"137.5303603","type":"string"},"MedianHouseholdIncome":{"example":"n/a","type":"string"},"MedianHouseholdIncome_SE":{"example":"9888","type":"string"},"geoid":{"example":"15000US010010201001","type":"string"},"years":{"example":"2012-2016","type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"OK"},"400":{"content":{},"description":"Invalid parameter"},"404":{"content":{},"description":"No values found"},"500":{"content":{},"description":"Server error"}},"summary":"provides ACS values","x-openapi-router-controller":"swagger_server.controllers.default_controller"}}},"servers":[{"url":"/socio_environmental_exposures_api/v1"}],"tags":[{"name":"translator"}]},{"openapi":"3.0.3","info":{"contact":{"email":"help@myvariant.info","name":"Chunlei Wu","x-id":"https://github.com/newgene","x-role":"responsible developer"},"description":"Documentation of the MyVariant.info Variant Query web services. Learn more about [MyVariant.info](http://myvariant.info/)","termsOfService":"http://myvariant.info/terms/","title":"MyVariant.info API","version":"1.0","x-translator":{"infores":"infores:myvariant-info","component":"KP","team":["Service Provider"],"biolink-version":"3.0.3"}},"servers":[{"description":"Encrypted Production server","url":"https://myvariant.info/v1","x-maturity":"production"},{"description":"Production server","url":"http://myvariant.info/v1","x-maturity":"production"}],"tags":[{"name":"variant"},{"name":"query"},{"name":"metadata"},{"name":"translator"},{"name":"biothings"}],"paths":{"/metadata":{"get":{"parameters":[{"$ref":"#/components/parameters/callback","in":"query","name":"callback"}],"responses":{"200":{"description":"MyVariant.info metadata object"}},"summary":"Get metadata about the data available from MyVariant.info.","tags":["metadata"]}},"/metadata/fields":{"get":{"parameters":[{"description":"Pass a search term to filter the available fields, e.g. \"search=clinvar\".","in":"query","name":"search","schema":{"type":"string"}},{"description":"Pass a prefix string to filter the available fields, e.g. \"prefix=refseq\".","in":"query","name":"prefix","schema":{"type":"string"}},{"$ref":"#/components/parameters/callback","in":"query","name":"callback"}],"responses":{"200":{"description":"MyVariant.info metadata fields object"}},"summary":"Get metadata about the data fields available from MyVariant.info.","tags":["metadata"]}},"/query":{"get":{"parameters":[{"description":"Query string. Examples \"rs752396467\", \"possibly_damaging\", \"CDK7\". The detailed query syntax can be found from our [docs](http://docs.myvariant.info/en/latest/doc/variant_query_service.html).","example":"CDK7","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"1":"query","$ref":"#/components/parameters/fields","name":"fields"},{"$ref":"#/components/parameters/size","in":"query","name":"size"},{"$ref":"#/components/parameters/from","in":"query","name":"from"},{"$ref":"#/components/parameters/sort","in":"query","name":"sort"},{"description":"a single field or comma-separated fields to return facets, for example, \"facets=clinvar.gene.id\", \"facets=clinvar.gene.id,dbnsfp.uniprot.acc\".","in":"query","name":"facets","schema":{"type":"string"}},{"$ref":"#/components/parameters/callback","in":"query","name":"callback"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/QueryResult"}}},"description":"A query response object with \"hits\" property"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorResult"}}},"description":"A response indicating an improperly formatted query"}},"summary":"Make variant query and return matching variant list. Support JSONP and CORS as well.","tags":["query"]},"post":{"parameters":[{"$ref":"#/components/parameters/fields","in":"query","name":"fields"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"requestBody":{"required":true,"content":{"application/x-www-form-urlencoded":{"schema":{"properties":{"q":{"description":"multiple query terms seperated by comma (also support \"+\" or white space), but no wildcard, e.g., \"q=rs58991260,rs2500\" or \"q=rs58991260+rs2500\"","type":"string"},"scopes":{"description":"Specify one or more fields (separated by comma) as the search \"scopes\", e.g., \"scopes=dbsnp.rsid\". The available \"fields\" that can be passed to \"scopes\" parameter are listed [here](http://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: \"scopes=_id\" (HGVS id).","type":"string"}},"required":["q"]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/QueryPOSTResult"}}},"description":"Query response objects with \"hits\" property"},"400":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorResult"}}},"description":"A response indicating an improperly formatted query"}},"summary":"Make variant batch query and return matching variant hits","tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/civic-geneDisease"},{"$ref":"#/components/x-bte-kgs-operations/civic-geneDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/civic-variantDisease"},{"$ref":"#/components/x-bte-kgs-operations/civic-variantDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/dbsnp-variantGene"},{"$ref":"#/components/x-bte-kgs-operations/dbsnp-variantGene-rev"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantGene"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantGene-rev"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-geneDisease"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-geneDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantDisease"},{"$ref":"#/components/x-bte-kgs-operations/clinvar-variantDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/docm-geneDisease"},{"$ref":"#/components/x-bte-kgs-operations/docm-geneDisease-rev"},{"$ref":"#/components/x-bte-kgs-operations/docm-variantDisease"},{"$ref":"#/components/x-bte-kgs-operations/docm-variantDisease-rev"}]}},"/variant":{"post":{"parameters":[{"$ref":"#/components/parameters/fields","in":"query","name":"fields"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"requestBody":{"required":true,"content":{"application/x-www-form-urlencoded":{"schema":{"properties":{"ids":{"description":"multiple variant ids seperated by comma, e.g., \"ids=chr6:g.152708291G>A,chr1:g.35367G>A\" or \"ids=rs5882,rs12190874\". Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","type":"string"}},"required":["ids"]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Variant"},"type":"array"}}},"description":"a list of matching variant objects"}},"summary":"For a list of variant ids, return the matching variant objects","tags":["variant"]}},"/variant/{variantid}":{"get":{"parameters":[{"description":"HGVS or rsid, e.g., chr6:g.152708291G>A, rs12190874","example":"chr6:g.152708291G>A","in":"path","name":"variantid","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields","in":"query","name":"fields"},{"$ref":"#/components/parameters/dotfield","in":"query","name":"dotfield"},{"$ref":"#/components/parameters/callback","in":"query","name":"callback"},{"$ref":"#/components/parameters/email","in":"query","name":"email"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Variant"}}},"description":"A matching variant object"},"404":{"description":"A response indicating an unknown variant id"}},"summary":"Retrieve variant annotation object based on HGVS or rsid, support JSONP and CORS as well.","tags":["variant"]}}},"components":{"parameters":{"callback":{"description":"you can pass a \"callback\" parameter to make a JSONP call.","in":"query","name":"callback","schema":{"type":"string"}},"dotfield":{"description":"control the format of the returned variant object. If \"true\" or \"1\", all fields will be collapsed into a single level deep structure (all nested objects will be a single level deep, using dotfield notation to signify the nested structure) Default: false.","in":"query","name":"dotfield","schema":{"type":"boolean"}},"email":{"description":"If you are regular users of our services, we encourage you to provide us an email, so that we can better track the usage or follow up with you.","in":"query","name":"email","schema":{"type":"string"}},"fields":{"description":"a comma-separated fields to limit the fields returned from the matching variant hits. The supported field names can be found from any variant object (e.g. http://myvariant.info/v1/variant/rs12190874). Note that it supports dot notation as well, e.g., you can pass \"dbsnp.rsid\". If \"fields=all\", all available fields will be returned. Default: \"all\".","in":"query","name":"fields","schema":{"type":"string"}},"from":{"description":"the number of matching variant hits to skip, starting from 0. Combining with \"size\" parameter, this can be useful for paging. Default: 0.","in":"query","name":"from","schema":{"type":"integer"}},"size":{"description":"the maximum number of matching variant hits to return (with a cap of 1000 at the moment). Default: 10.","in":"query","name":"size","schema":{"type":"integer"}},"sort":{"description":"the comma-separated fields to sort on. Prefix with \"-\" for descending order, otherwise in ascending order. 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Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0008974","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns phenotypes associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-phenotype"}]}},"/bioentity/disease/{id}/variants":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0004747","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-variant"}]}},"/bioentity/gene/{id}/anatomy":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:13434","in":"path","required":true,"example":"HGNC:8548","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns anatomies associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-anatomy"}]}},"/bioentity/gene/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:11138","schema":{"type":"string"}},{"name":"association_type","description":"Additional filters: causal, non_causal, both","in":"query","required":false,"example":"causal","schema":{"type":"string","enum":["causal","non_causal","both"],"default":"both"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-disease-1"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease-2"}]}},"/bioentity/gene/{id}/interactions":{"get":{"parameters":[{"name":"id","description":"id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns gene interaction","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-interaction"}]}},"/bioentity/gene/{id}/phenotypes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns phenotypes associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-phenotype"}]}},"/bioentity/gene/{id}/variants":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. HGNC:10896","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-variant"}]}},"/bioentity/pathway/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE any pathway element. E.g. REACT:R-HSA-5387390","in":"path","required":true,"example":"REACT:R-HSA-2644606","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a pathway","tags":["pathway"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/pathway-disease"}]}},"/bioentity/phenotype/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HP:0000272","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-disease"}]}},"/bioentity/phenotype/{id}/genes":{"get":{"parameters":[{"name":"id","description":"Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","in":"path","required":true,"example":"HP:0000183","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-gene"}]}},"/bioentity/phenotype/{id}/variants":{"get":{"parameters":[{"name":"id","description":"Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","in":"path","required":true,"example":"HP:0002944","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-variant"}]}},"/bioentity/variant/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ClinVarVariant:14925","in":"path","required":true,"example":"dbSNP:rs227731","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a variant","tags":["variant"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/variant-disease"}]}},"/bioentity/variant/{id}/genes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783","in":"path","required":true,"example":"dbSNP:rs11879191","schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a variant","tags":["variant"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/variant-gene"}]}},"/bioentity/variant/{id}/phenotypes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, 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queryInputs }}","rows":-1,"direct":true,"unselect_evidence":true,"taxon":"NCBITaxon:9606"},"outputs":[{"id":"HGNC","semantic":"Gene"}],"predicate":"expresses","source":"infores:monarchinitiative","response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene-hgnc"}}],"disease-gene-1":[{"supportBatch":false,"useTemplating":true,"inputs":[{"id":"MONDO","semantic":"Disease"}],"parameters":{"id":"{{ queryInputs }}","rows":-1,"direct":true,"unselect_evidence":true,"taxon":"NCBITaxon:9606","association_type":"causal"},"outputs":[{"id":"HGNC","semantic":"Gene"}],"predicate":"caused_by","source":"infores:monarchinitiative","response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene-hgnc"}}],"disease-gene-2":[{"supportBatch":false,"useTemplating":true,"inputs":[{"id":"MONDO","semantic":"Disease"}],"parameters":{"id":"{{ queryInputs 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[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
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}}","scopes":"part_of.go"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/has_part"},"source":"infores:go","supportBatch":true,"useTemplating":true}],"has_subclass":[{"inputs":[{"id":"GO","semantic":"MolecularActivity"}],"outputs":[{"id":"GO","semantic":"MolecularActivity"}],"parameters":{"fields":"children"},"predicate":"superclass_of","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"_id"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/has_subclass"},"source":"infores:go","supportBatch":true,"useTemplating":true}],"part_of":[{"inputs":[{"id":"GO","semantic":"MolecularActivity"}],"outputs":[{"id":"GO","semantic":"MolecularActivity"}],"parameters":{"fields":"part_of.go"},"predicate":"part_of","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"_id"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/part_of"},"source":"infores:go","supportBatch":true,"useTemplating":true}],"subclass_of":[{"inputs":[{"id":"GO","semantic":"MolecularActivity"}],"outputs":[{"id":"GO","semantic":"MolecularActivity"}],"parameters":{"fields":"parents"},"predicate":"subclass_of","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"_id"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/subclass_of"},"source":"infores:go","supportBatch":true,"useTemplating":true}]},"x-bte-response-mapping":{"has_part":{"GO":"_id"},"has_subclass":{"GO":"children"},"part_of":{"GO":"part_of.go"},"subclass_of":{"GO":"parents"}}},"info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible developers"},"description":"Documentation of the Gene Ontology Molecular Activity query web services.","termsOfService":"https://biothings.io/about","title":"Gene Ontology Molecular Activity API","version":"2020.07","x-translator":{"biolink-version":"2.2.13","component":"KP","infores":"infores:biothings-go-mf","team":["Service 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GO geneset IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"Success"}},"tags":["geneset"]}},"/metadata":{"get":{"parameters":[{"$ref":"#/components/parameters/format"},{"$ref":"#/components/parameters/raw"},{"$ref":"#/components/parameters/dev"}],"responses":{"200":{"description":"Success"}},"summary":"Get metadata about the data available from the API","tags":["metadata"]}},"/metadata/fields":{"get":{"parameters":[{"$ref":"#/components/parameters/format"},{"$ref":"#/components/parameters/raw"},{"$ref":"#/components/parameters/search"},{"$ref":"#/components/parameters/prefix"}],"responses":{"200":{"description":"Success"}},"summary":"Get metadata about the data fields available from a record","tags":["metadata"]}},"/query":{"get":{"parameters":[{"description":"Query string.","example":"go:\"GO:0008613\"","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/aggs"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/userquery"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/explain"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/raw"},{"$ref":"#/components/parameters/rawquery"},{"$ref":"#/components/parameters/_source"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/_sorted"},{"$ref":"#/components/parameters/always_list"},{"$ref":"#/components/parameters/allow_null"},{"$ref":"#/components/parameters/format"}],"responses":{"200":{"description":"Success"}},"tags":["query"]},"post":{"parameters":[{"in":"query","name":"q","required":false,"schema":{"items":{"type":"string"},"type":"array"}},{"in":"query","name":"scopes","required":false,"schema":{"items":{"default":["_id"],"type":"string"},"type":"array"}},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/raw"},{"$ref":"#/components/parameters/rawquery"},{"$ref":"#/components/parameters/_source"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/_sorted"},{"$ref":"#/components/parameters/always_list"},{"$ref":"#/components/parameters/allow_null"},{"$ref":"#/components/parameters/format"}],"requestBody":{"content":{"application/json":{"example":{"q":["GO:0008613","GO:0008510"],"scopes":["go"]},"schema":{"properties":{"from":{"type":"integer"},"q":{"items":{"type":"string"},"type":"array"},"scopes":{"items":{"type":"string"},"type":"array"},"sort":{"items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"Success"}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/has_subclass"},{"$ref":"#/components/x-bte-kgs-operations/subclass_of"},{"$ref":"#/components/x-bte-kgs-operations/part_of"},{"$ref":"#/components/x-bte-kgs-operations/has_part"}]}}},"servers":[{"description":"Encrypted 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object.PATHWAY_NAME,object.PATHWAY_CATEGORIES","size":1000},"predicate":"participates_in","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"subject.GENE_ID"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/pathway"},"source":"infores:bioplanet","supportBatch":true,"useTemplating":true}],"pathway-gene":[{"inputs":[{"id":"ncats.bioplanet","semantic":"Pathway"}],"outputs":[{"id":"NCBIGene","semantic":"Gene"}],"parameters":{"fields":"subject.GENE_ID, object.PATHWAY_NAME,object.PATHWAY_CATEGORIES","size":1000},"predicate":"has_participant","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"object.PATHWAY_ID"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene"},"source":"infores:bioplanet","supportBatch":true,"useTemplating":true}]},"x-bte-response-mapping":{"gene":{"NCBIGene":"subject.GENE_ID","pathway_categories":"object.PATHWAY_CATEGORIES","pathway_name":"object.PATHWAY_NAME"},"pathway":{"ncats.bioplanet":"object.PATHWAY_ID","pathway_categories":"object.PATHWAY_CATEGORIES","pathway_name":"object.PATHWAY_NAME"}}},"info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible developers"},"description":"Documentation of the BioThings API for \n[BioPlanet](https://tripod.nih.gov/bioplanet/#) pathway-gene data.","termsOfService":"https://biothings.io/about","title":"BioThings BioPlanet Pathway-Gene API","version":"1.0","x-translator":{"biolink-version":"2.2.13","component":"KP","infores":"infores:biothings-bioplanet-pathway-gene","team":["Service Provider"]}},"paths":{"/association/{id}":{"get":{"description":"By default, this will return the complete association in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available from the association. Multiple attributes should be separated by commas. If an attribute is not available for a specific association, it will be ignored. Note that the attribute names are case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"bioplanet_465-23118","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["association"]}},"/association":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases, there are some times you might find it easier to batch query (e.g., retrieving multiple associations). Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple association ids separated by commas. Note that currently we only take ids up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["bioplanet_464-10437","bioplanet_465-23118"]},"schema":{"properties":{"ids":{"description":"Accepts multiple association ids. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["association"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained [here for a core BioThings API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"subject.GENE_ID:200150","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases, there are times you might find it more efficient to make batch queries (e.g., retrieving data for multiple inputs). Fortunately, you can also make batch queries via POST requests when you need to.\n\nThe \"query” field in the returned object indicates the matching query term. If a query term has no match, it will return with a “notfound” field with the value “true”.","parameters":[{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"q","required":false,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"Optional, specify one or more fields (separated by commas) to search. Default: _id\n\nThe request body can also be used to provide this information.","in":"query","name":"scopes","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"}],"requestBody":{"content":{"application/json":{"example":{"q":["200150","9672"],"scopes":["subject.GENE_ID"]},"schema":{"properties":{"q":{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"},"scopes":{"description":"Specify one or more fields (separated by commas) to search. Default: _id","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/pathway-gene"},{"$ref":"#/components/x-bte-kgs-operations/gene-pathway"}]}}},"servers":[{"description":"Encrypted Production server","url":"https://biothings.ncats.io/bioplanet_pathway_gene","x-maturity":"production"},{"description":"Production server","url":"http://biothings.ncats.io/bioplanet_pathway_gene","x-maturity":"production"}],"tags":[{"name":"association"},{"name":"pathway"},{"name":"gene"},{"name":"query"},{"name":"translator"},{"name":"biothings"}]}]} \ No newline at end of file diff --git a/packages/smartapi-kg/src/filter.ts b/packages/smartapi-kg/src/filter.ts index b05d063..f1a04e9 100644 --- a/packages/smartapi-kg/src/filter.ts +++ b/packages/smartapi-kg/src/filter.ts @@ -3,7 +3,7 @@ import _ from "lodash"; import { FilterCriteria, ObjectWithValueAsSet, CompactQualifiers } from "./types"; import { SmartAPIKGOperationObject } from "./parser/types"; // import Debug from "debug"; -// const debug = Debug("bte:smartapi-kg:Filter"); +// const debug = Debug("retriever:smartapi-kg:Filter"); const getUniqueValsForEachField = (operations: SmartAPIKGOperationObject[]): ObjectWithValueAsSet => { const allValues = {} as ObjectWithValueAsSet; diff --git a/packages/smartapi-kg/src/index.ts b/packages/smartapi-kg/src/index.ts index b0a6198..52b0c2a 100644 --- a/packages/smartapi-kg/src/index.ts +++ b/packages/smartapi-kg/src/index.ts @@ -5,7 +5,7 @@ import { BuilderOptions, FilterCriteria } from "./types"; import { ft } from "./filter"; import path from "path"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:MetaKG"); +const debug = Debug("retriever:smartapi-kg:MetaKG"); export * from "./types"; export * from "./parser/types"; diff --git a/packages/smartapi-kg/src/load/all_specs_sync_loader.ts b/packages/smartapi-kg/src/load/all_specs_sync_loader.ts index 6e59ba5..ca5aee1 100644 --- a/packages/smartapi-kg/src/load/all_specs_sync_loader.ts +++ b/packages/smartapi-kg/src/load/all_specs_sync_loader.ts @@ -3,7 +3,7 @@ import { SmartAPIQueryResult } from "../types"; import { SmartAPISpec } from "../parser/types"; import fs from "fs"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:AllSpecsSyncLoader"); +const debug = Debug("retriever:smartapi-kg:AllSpecsSyncLoader"); export default class AllSpecsSyncLoader extends BaseLoader { private _file_path: string; diff --git a/packages/smartapi-kg/src/load/api_list_specs_sync_loader.ts b/packages/smartapi-kg/src/load/api_list_specs_sync_loader.ts index 3a2c0ea..40d2bab 100644 --- a/packages/smartapi-kg/src/load/api_list_specs_sync_loader.ts +++ b/packages/smartapi-kg/src/load/api_list_specs_sync_loader.ts @@ -2,7 +2,7 @@ import AllSpecsSyncLoader from "./all_specs_sync_loader"; import { SmartAPIQueryResult, apiListObject } from "../types"; import { SmartAPISpec } from "../parser/types"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:APIListSpecsSyncLoader"); +const debug = Debug("retriever:smartapi-kg:APIListSpecsSyncLoader"); export default class APIListSpecsSyncLoader extends AllSpecsSyncLoader { private _apiList: apiListObject | undefined; diff --git a/packages/smartapi-kg/src/load/base_async_loader.ts b/packages/smartapi-kg/src/load/base_async_loader.ts index ffa0852..15da6d6 100644 --- a/packages/smartapi-kg/src/load/base_async_loader.ts +++ b/packages/smartapi-kg/src/load/base_async_loader.ts @@ -4,7 +4,7 @@ import { SmartAPIQueryResult } from "../types"; import { SmartAPISpec } from "../parser/types"; import BaseLoader from "./base_loader"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:AsyncLoader"); +const debug = Debug("retriever:smartapi-kg:AsyncLoader"); export default abstract class BaseAsyncLoader extends BaseLoader { protected _url: string; diff --git a/packages/smartapi-kg/src/load/single_spec_sync_loader.ts b/packages/smartapi-kg/src/load/single_spec_sync_loader.ts index 0db984a..6d3049d 100644 --- a/packages/smartapi-kg/src/load/single_spec_sync_loader.ts +++ b/packages/smartapi-kg/src/load/single_spec_sync_loader.ts @@ -2,7 +2,7 @@ import AllSpecsSyncLoader from "./all_specs_sync_loader"; import { apiListObject, SmartAPIQueryResult } from "../types"; import { SmartAPISpec } from "../parser/types"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:SingleSpecSyncLoader"); +const debug = Debug("retriever:smartapi-kg:SingleSpecSyncLoader"); export default class SingleSpecSyncLoader extends AllSpecsSyncLoader { private _smartAPIID: string; diff --git a/packages/smartapi-kg/src/load/sync_loader_factory.ts b/packages/smartapi-kg/src/load/sync_loader_factory.ts index 3bc726c..79241c0 100644 --- a/packages/smartapi-kg/src/load/sync_loader_factory.ts +++ b/packages/smartapi-kg/src/load/sync_loader_factory.ts @@ -7,7 +7,7 @@ import APIListSpecsSyncLoader from "./api_list_specs_sync_loader"; import { SmartAPISpec } from "../parser/types"; import { apiListObject } from "../types"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:SyncLoader"); +const debug = Debug("retriever:smartapi-kg:SyncLoader"); export const syncLoaderFactory = ( smartAPIID: string = undefined, diff --git a/packages/smartapi-kg/src/operations_builder/async_operations_builder_with_reasoner.ts b/packages/smartapi-kg/src/operations_builder/async_operations_builder_with_reasoner.ts index 6047848..79f0051 100644 --- a/packages/smartapi-kg/src/operations_builder/async_operations_builder_with_reasoner.ts +++ b/packages/smartapi-kg/src/operations_builder/async_operations_builder_with_reasoner.ts @@ -4,7 +4,7 @@ import { ReasonerPredicatesResponse } from "../types"; import API from "../parser/index"; import axios from "axios"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:OperationsBuilder"); +const debug = Debug("retriever:smartapi-kg:OperationsBuilder"); export default class AsyncOperationsBuilderWithReasoner extends AsyncOperationsBuilder { private getTRAPIWithPredicatesEndpoint(specs: SmartAPISpec[]): ParsedAPIMetadataObject[] { @@ -76,9 +76,9 @@ export default class AsyncOperationsBuilderWithReasoner extends AsyncOperationsB path: "/query", method: "post", server: metadata.url, - path_params: undefined, + pathParams: undefined, params: undefined, - request_body: undefined, + requestBody: undefined, supportBatch: true, inputSeparator: ",", tags: [...metadata.tags, ...["bte-trapi"]], diff --git a/packages/smartapi-kg/src/operations_builder/base_operations_builder.ts b/packages/smartapi-kg/src/operations_builder/base_operations_builder.ts index e470cbb..2fbe12e 100644 --- a/packages/smartapi-kg/src/operations_builder/base_operations_builder.ts +++ b/packages/smartapi-kg/src/operations_builder/base_operations_builder.ts @@ -2,7 +2,7 @@ import { BuilderOptions } from "../types"; import { SmartAPIKGOperationObject, SmartAPISpec } from "../parser/types"; import API from "../parser/index"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:OperationsBuilder"); +const debug = Debug("retriever:smartapi-kg:OperationsBuilder"); export default abstract class BaseOperationsBuilder { protected _options: BuilderOptions; diff --git a/packages/smartapi-kg/src/operations_builder/sync_operations_builder_with_reasoner.ts b/packages/smartapi-kg/src/operations_builder/sync_operations_builder_with_reasoner.ts index b0c3ac1..6e43239 100644 --- a/packages/smartapi-kg/src/operations_builder/sync_operations_builder_with_reasoner.ts +++ b/packages/smartapi-kg/src/operations_builder/sync_operations_builder_with_reasoner.ts @@ -5,7 +5,7 @@ import fs from "fs"; import { SmartAPIKGOperationObject } from "../parser/types"; import { PredicatesMetadata } from "../types"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:SyncOperationsBuilderWithReasoner"); +const debug = Debug("retriever:smartapi-kg:SyncOperationsBuilderWithReasoner"); import { SmartAPISpec } from "../parser/types"; declare global { @@ -77,9 +77,9 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui path: "/query", method: "post", server: metadata.query_operation.server, - path_params: undefined, + pathParams: undefined, params: undefined, - request_body: undefined, + requestBody: undefined, supportBatch: true, inputSeparator: ",", tags: [...metadata.tags, ...["bte-trapi"]], diff --git a/packages/smartapi-kg/src/parser/endpoint.ts b/packages/smartapi-kg/src/parser/endpoint.ts index 3cf4bb4..8095d62 100644 --- a/packages/smartapi-kg/src/parser/endpoint.ts +++ b/packages/smartapi-kg/src/parser/endpoint.ts @@ -46,7 +46,7 @@ export default class Endpoint { const queryOperation = new QueryOperationObject(); queryOperation.xBTEKGSOperation = op; queryOperation.method = method; - queryOperation.path_params = pathParams; + queryOperation.pathParams = pathParams; queryOperation.server = server; queryOperation.path = this.path; queryOperation.tags = this.apiMetadata.tags; diff --git a/packages/smartapi-kg/src/parser/index.ts b/packages/smartapi-kg/src/parser/index.ts index f6c84b4..50cdccf 100644 --- a/packages/smartapi-kg/src/parser/index.ts +++ b/packages/smartapi-kg/src/parser/index.ts @@ -1,7 +1,7 @@ import Components from "./component"; import Endpoint from "./endpoint"; import Debug from "debug"; -const debug = Debug("bte:smartapi-kg:Parser"); +const debug = Debug("retriever:smartapi-kg:Parser"); import { SmartAPISpec, ParsedAPIMetadataObject, SmartAPIKGOperationObject, APIClass } from "./types"; export default class API implements APIClass { diff --git a/packages/smartapi-kg/src/parser/query_operation.ts b/packages/smartapi-kg/src/parser/query_operation.ts index 13bcd37..6ed2733 100644 --- a/packages/smartapi-kg/src/parser/query_operation.ts +++ b/packages/smartapi-kg/src/parser/query_operation.ts @@ -1,100 +1,32 @@ -import { QueryOperationInterface, XBTEKGSOperationObject, XBTEParametersObject } from "./types"; +import { + QueryOperationInterface, + XBTEKGSOperationObject, + XBTEParametersObject, +} from "./types"; export default class QueryOperationObject implements QueryOperationInterface { - private _params: XBTEParametersObject; - private _requestBody: any; - private _requestBodyType: string; - private _supportBatch: boolean; - private _batchSize: number; - private _useTemplating: boolean; - private _inputSeparator: string; - private _path: string; - private _method: string; - private _server: string; - private _tags: string[]; - private _pathParams: string[]; - private _templateInputs: any; + params: XBTEParametersObject; + requestBody: any; + requestBodyType: string; + supportBatch: boolean; + batchSize: number; + useTemplating: boolean; + inputSeparator: string; + path: string; + method: string; + server: string; + tags: string[]; + pathParams: string[]; + templateInputs: any; set xBTEKGSOperation(newOp: XBTEKGSOperationObject) { - this._params = newOp.parameters; - this._requestBody = newOp.requestBody; - this._requestBodyType = newOp.requestBodyType; - this._supportBatch = newOp.supportBatch; - this._useTemplating = newOp.useTemplating; - this._inputSeparator = newOp.inputSeparator; - this._templateInputs = newOp.templateInputs; - this._batchSize = newOp.batchSize; - } - - get templateInputs(): any { - return this._templateInputs; - } - - get params(): XBTEParametersObject { - return this._params; - } - - get request_body(): any { - return this._requestBody; - } - - get requestBodyType(): string { - return this._requestBodyType; - } - - get supportBatch(): boolean { - return this._supportBatch; - } - - get batchSize(): number { - return this._batchSize; - } - - get useTemplating(): boolean { - return this._useTemplating; - } - - get inputSeparator(): string { - return this._inputSeparator; - } - - set path(newPath: string) { - this._path = newPath; - } - - get path(): string { - return this._path; - } - - get method(): string { - return this._method; - } - - set method(newMethod: string) { - this._method = newMethod; - } - - get server(): string { - return this._server; - } - - set server(newServer: string) { - this._server = newServer; - } - - get tags(): string[] { - return this._tags; - } - - set tags(newTags: string[]) { - this._tags = newTags; - } - - get path_params(): string[] { - return this._pathParams; - } - - set path_params(newPathParams: string[]) { - this._pathParams = newPathParams; + this.params = newOp.parameters; + this.requestBody = newOp.requestBody; + this.requestBodyType = newOp.requestBodyType; + this.supportBatch = newOp.supportBatch; + this.useTemplating = newOp.useTemplating; + this.inputSeparator = newOp.inputSeparator; + this.templateInputs = newOp.templateInputs; + this.batchSize = newOp.batchSize; } } diff --git a/packages/smartapi-kg/src/parser/types.ts b/packages/smartapi-kg/src/parser/types.ts index 8cb1e47..e162a86 100644 --- a/packages/smartapi-kg/src/parser/types.ts +++ b/packages/smartapi-kg/src/parser/types.ts @@ -4,7 +4,7 @@ export interface XTranslatorObject { infores?: string; } -interface SmartAIPInfoObject { +export interface SmartAIPInfoObject { title: string; version: string; description?: string; @@ -12,7 +12,7 @@ interface SmartAIPInfoObject { [propName: string]: any; } -interface SmartAPIServerObject { +export interface SmartAPIServerObject { url: string; description?: string; variables?: any; @@ -33,20 +33,20 @@ export interface SmartAPIParameterObject { allowEmptyValue?: boolean; } -interface SmartAPIMediaTypeObject { +export interface SmartAPIMediaTypeObject { example?: any; schema?: any; examples?: any; encoding?: any; } -interface SmartAPIRequestBodyObject { +export interface SmartAPIRequestBodyObject { description?: string; content: SmartAPIMediaTypeObject[]; required?: boolean; } -interface SmartAPIResponsesObject { +export interface SmartAPIResponsesObject { description: string; headers: any; content: any; @@ -91,7 +91,7 @@ export interface SmartAPIPathsObject { [path: string]: SmartAPIPathItemObject; } -interface SmartAPITagObject { +export interface SmartAPITagObject { name: string; description?: string; externalDocs?: any; @@ -173,15 +173,21 @@ export interface QueryOperationInterface { method: string; server: string; tags: string[]; - path_params: string[]; + pathParams: string[]; params: XBTEParametersObject; - request_body: any; + requestBody: any; requestBodyType?: string; supportBatch: boolean; batchSize?: number; inputSeparator: string; useTemplating?: boolean; templateInputs?: any; + transformer?: { + jq: { + wrap: string; + pair: string; + }; + }; } export interface SmartAPIKGOperationObject { diff --git a/packages/types/package.json b/packages/types/package.json index 00c81e9..f2ea90a 100644 --- a/packages/types/package.json +++ b/packages/types/package.json @@ -1,6 +1,6 @@ { "$schema": "https://json.schemastore.org/package.json", - "name": "@biothings-explorer/types", + "name": "@retriever/types", "version": "1.0.0", "description": "A collection of common types used by Biothings Explorer", "main": "./built/index.js", @@ -18,20 +18,22 @@ "test-cov": "jest --coverage" }, "keywords": [ - "bte", + "BioPack", + "retriever", "biothings", "single", "hop", "query" ], - "author": "BioThings Team", + "author": "BioPack Team", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/biothings_explorer/issues" + "url": "https://github.com/BioPack-team/retriever/issues" }, - "homepage": "https://github.com/biothings/biothings_explorer#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "dependencies": { - "@biothings-explorer/smartapi-kg": "workspace:../smartapi-kg" + "@retriever/smartapi-kg": "workspace:../smartapi-kg", + "@retriever/biomedical_id_resolver": "workspace:../biomedical_id_resolver" }, "devDependencies": { "@types/jest": "^29.5.12" diff --git a/packages/types/src/exceptions.ts b/packages/types/src/exceptions.ts new file mode 100644 index 0000000..d19bb4a --- /dev/null +++ b/packages/types/src/exceptions.ts @@ -0,0 +1,31 @@ +export class RetrieverError extends Error { + statusCode: string; + constructor(message = 'Query aborted', name = 'QueryAborted', code = '501', ...params: any) { + super(...params); + + if (Error.captureStackTrace) { + Error.captureStackTrace(this, RetrieverError); + } + + this.name = name; + this.message = message; + this.statusCode = code; + } +} + +export class InvalidQueryGraphError extends Error { + statusCode: number; + constructor(message = 'Your Input Query Graph is invalid.', ...params: string[]) { + super(...params); + + Object.setPrototypeOf(this, InvalidQueryGraphError.prototype); + + if (Error.captureStackTrace) { + Error.captureStackTrace(this, InvalidQueryGraphError); + } + + this.name = 'InvalidQueryGraphError'; + this.message = message; + this.statusCode = 400; + } +} diff --git a/packages/types/src/global.ts b/packages/types/src/global.ts index 209b2ef..203def7 100644 --- a/packages/types/src/global.ts +++ b/packages/types/src/global.ts @@ -1,7 +1,7 @@ // Cursed globals that exist for Reasons import { TrapiQueryGraph } from "./trapi"; -import { SmartAPISpec } from "@biothings-explorer/smartapi-kg"; +import { SmartAPISpec } from "@retriever/smartapi-kg"; import { Queue } from "bull"; import Piscina from "piscina"; import { MessagePort } from "worker_threads"; @@ -33,7 +33,8 @@ declare global { var missingAPIs: SmartAPISpec[]; var BIOLINK_VERSION: string; var SCHEMA_VERSION: string; - var parentPort: MessagePort; + var toParent: MessagePort; + var fromParent: MessagePort; var cachingTasks: Promise[]; var queryInformation: QueryInformation; var job: { diff --git a/packages/types/src/index.ts b/packages/types/src/index.ts index 66f49fc..7840509 100644 --- a/packages/types/src/index.ts +++ b/packages/types/src/index.ts @@ -2,3 +2,5 @@ import "./global"; export * from "./trapi"; export * from "./tasks"; export * from "./misc"; +export * from "./exceptions"; +export * from "./x_bte"; diff --git a/packages/types/src/misc.ts b/packages/types/src/misc.ts index 8018e61..7341ae7 100644 --- a/packages/types/src/misc.ts +++ b/packages/types/src/misc.ts @@ -1,9 +1,12 @@ +import { SRIBioEntity } from "@retriever/biomedical_id_resolver"; + export type APIDefinition = { // Must have one of id or infores id?: string; // SmartAPI ID, takes priority over infores name: string; // Must match name on SmartAPI registry infores?: string; // infores of API primarySource?: boolean; + timeout?: number; } & ({ id: string } | { infores: string }); export interface APIList { @@ -11,3 +14,23 @@ export interface APIList { // takes priority over include, taking into account id/infores prioritization exclude: APIDefinition[]; } + +export interface UnavailableAPITracker { + [server: string]: { skip: boolean; skippedQueries: number }; +} + +export interface SRIResolvedSet { + [originalCurie: string]: SRIBioEntity; +} + +export interface ExpandedCuries { + [originalCurie: string]: string[]; +} + +export type SerializableObject = T extends string | number | boolean | null + ? T + : T extends Function + ? never + : T extends object + ? { [K in keyof T]: SerializableObject } + : never; diff --git a/packages/types/src/tasks.ts b/packages/types/src/tasks.ts index b05406a..a9946d4 100644 --- a/packages/types/src/tasks.ts +++ b/packages/types/src/tasks.ts @@ -57,7 +57,7 @@ export interface InnerTaskData { route: string; traceparent?: string; tracestate?: string; - port: MessagePort; + workerSide: MessagePort; job?: { jobId: string | number; queueName: string; diff --git a/packages/types/src/x_bte.ts b/packages/types/src/x_bte.ts new file mode 100644 index 0000000..aabeef5 --- /dev/null +++ b/packages/types/src/x_bte.ts @@ -0,0 +1,4 @@ +export interface TemplatedInput { + queryInputs: string | string[]; + [additionalProperties: string]: string | string[]; +} diff --git a/packages/types/tsconfig.json b/packages/types/tsconfig.json index aaeb07a..1a50e4f 100644 --- a/packages/types/tsconfig.json +++ b/packages/types/tsconfig.json @@ -5,8 +5,11 @@ "rootDir": "./src", "outDir": "./built", "paths": { - "smartapi-kg": [ + "@retriever/smartapi-kg": [ "../smartapi-kg" + ], + "@retriever/biomedical_id_resolver": [ + "../biomedical_id_resolver" ] } }, @@ -20,6 +23,9 @@ "references": [ { "path": "../smartapi-kg" + }, + { + "path": "../biomedical_id_resolver" } ] } diff --git a/packages/utils/package.json b/packages/utils/package.json index ad2ec80..fd850d9 100644 --- a/packages/utils/package.json +++ b/packages/utils/package.json @@ -1,8 +1,8 @@ { "$schema": "https://json.schemastore.org/package.json", - "name": "@biothings-explorer/utils", + "name": "@retriever/utils", "version": "1.0.0", - "description": "A bundle of commonly-used utilities within other BTE modules", + "description": "A bundle of commonly-used utilities within other Retriever modules", "main": "./built/index.js", "types": "./built/index.d.ts", "scripts": { @@ -18,22 +18,24 @@ "lint:fix": "pnpm lint --fix" }, "keywords": [ + "BioPack", + "retriever", "api", - "biothings", - "explorer" + "biothings" ], "author": "Jackson Callaghan", "license": "ISC", "bugs": { - "url": "https://github.com/biothings/bte-utils/issues" + "url": "https://github.com/BioPack-team/retriever#issues" }, - "homepage": "https://github.com/biothings/bbte-utils#readme", + "homepage": "https://github.com/BioPack-team/retriever#readme", "devDependencies": { "@commitlint/cli": "^18.2.0", "@commitlint/config-conventional": "^11.0.0", "@types/debug": "^4.1.10", "@types/jest": "^29.5.7", "@types/lodash": "^4.14.200", + "@types/lz4": "^0.6.4", "@types/node": "^20.8.10", "@typescript-eslint/eslint-plugin": "^6.8.0", "@typescript-eslint/parser": "^6.8.0", @@ -53,6 +55,8 @@ }, "dependencies": { "@opentelemetry/api": "^1.7.0", + "@retriever/biolink-model": "workspace:../biolink-model", + "@retriever/types": "workspace:../types", "@sentry/node": "^7.74.1", "debug": "^4.3.4", "ioredis": "^5.3.2", diff --git a/packages/query_graph_handler/src/biolink.ts b/packages/utils/src/biolink.ts similarity index 94% rename from packages/query_graph_handler/src/biolink.ts rename to packages/utils/src/biolink.ts index e5bb659..3dd9a52 100644 --- a/packages/query_graph_handler/src/biolink.ts +++ b/packages/utils/src/biolink.ts @@ -1,6 +1,6 @@ -import { BioLink } from 'biolink-model'; +import { BioLink } from '@retriever/biolink-model'; import Debug from 'debug'; -const debug = Debug('bte:biothings-explorer-trapi:EdgeReverse'); +const debug = Debug('retriever:EdgeReverse'); class BioLinkModel { biolink: BioLink; @@ -71,4 +71,4 @@ Object.freeze(biolink); global.BIOLINK_VERSION = biolink.biolink.biolinkJSON.version; -export default biolink; +export { biolink }; diff --git a/packages/utils/src/cache.ts b/packages/utils/src/cache.ts new file mode 100644 index 0000000..c1542c5 --- /dev/null +++ b/packages/utils/src/cache.ts @@ -0,0 +1,242 @@ +import { Readable, Transform } from "stream"; +import lz4 from "lz4"; +import { redisClient } from "./redis-client"; +import Debug from "debug"; +const debug = Debug("retriever:caching"); + +export async function cacheContent( + hash: string, + content: unknown[], +): Promise { + if (!redisClient.clientEnabled) { + debug("redis client unavailable, skipping cache step"); + } + + debug(`Caching ${content.length} items for article ${hash}`); + const cacheID = `retriever:cacheContent:${hash}`; + let success = false; + + await redisClient.client.usingLock( + [`retriever:cachingLock:${hash}`], + 30000, + async () => { + try { + await redisClient.client.delTimeout(cacheID); // delete previous cache to avoid edge cases + await new Promise((resolve, reject) => + streamToCache(hash, content, resolve, reject), + ); + success = true; + } catch (error) { + debug(`Failed to cache article ${hash} due to error ${error}.`); + } + }, + ); + + if (!success) return; + + if (process.env.QEDGE_CACHE_TIME_S !== "0") { + try { + await redisClient.client.expireTimeout( + cacheID, + process.env.QEDGE_CACHE_TIME_S || 1800, + ); + } catch (error) { + debug("Failed to set cache timeout for article ${hash} due to ${error}"); + } + } + + debug(`Successfully cached ${content.length} items for article ${hash}`); +} + +function streamToCache( + hash: string, + content: unknown[], + resolve: () => void, + reject: (reason: any) => void, +) { + let index = 0; + Readable.from(content) + .pipe(new DelimitedChunksEncoder()) + .on( + "data", + async (chunk: string) => await cacheChunk(hash, index++, chunk, reject), + ) + .on("end", () => resolve()); +} +async function cacheChunk( + hash: string, + index: number, + chunk: string, + reject: { (reason: any): void; (arg0: any): void }, +) { + const id = `retriever:cacheContent:${hash}`; + try { + await redisClient.client.hsetTimeout(id, String(index++), chunk); + } catch (error) { + reject(error); + // Attempt cleanup after reporting failure + try { + await redisClient.client.delTimeout(id); + } catch (e) { + debug( + `Unable to remove partial cache article ${id} from redis during cache failure due to error ${error}. This may result in failed or improper cache retrieval of this article.`, + ); + } + } +} + +export async function cacheLookup(hash: string): Promise { + if (!redisClient.clientEnabled) { + debug("redis client unavailable, skipping cache step"); + } + debug(`Beginning cache lookup for article ${hash}`); + const id = `retriever:cacheContent:${hash}`; + + const content = await new Promise(resolve => { + redisClient.client.usingLock( + [`retriever: cachingLock:${hash} `], + 30000, + async () => readFromCache(hash, resolve), + ); + }); + + if (!content) { + debug(`No cached content found for article ${hash}`); + return content; + } + + const message = `Found ${content.length} cached content for article ${hash}.`; + debug(message); + try { + await redisClient.client.expireTimeout( + id, + process.env.QEDGE_CACHE_TIME_S || 1800, + ); + } catch (error) { + debug( + "Failed to re-boost cache timeout for subquery ${hash} due to ${error}", + ); + } + + return content; +} + +async function readFromCache( + hash: string, + resolve: (value: any | null) => void, +): Promise { + const id = `retriever:cacheContent:${hash}`; + try { + const compressedContent = await redisClient.client.hgetallTimeout(id); + if (!(compressedContent && Object.keys(compressedContent).length)) { + resolve(null); + } + + const content = []; + + const sortedPackParts = Object.entries(compressedContent) + .sort(([key1], [key2]) => parseInt(key1) - parseInt(key2)) + .map(([, val]) => val); + + const recordStream = Readable.from(sortedPackParts); + recordStream + .pipe(new DelimitedChunksDecoder()) + .on("data", obj => content.push(obj)) + .on("end", () => resolve(content)); + } catch (error) { + debug( + `Cache lookup / retrieval for subquery ${hash} failed due to ${error}.`, + ); + resolve(null); + } +} + +export class DelimitedChunksEncoder extends Transform { + private _buffer: unknown[]; + constructor() { + super({ + writableObjectMode: true, + writableHighWaterMark: 128, + }); + this._buffer = []; + } + + _transform(obj: unknown, _encoding: unknown, callback: () => void) { + this._buffer.push(obj); // stringify/compress 64 objects at a time limits compress calls + if (this._buffer.length === 64) { + const compressedPart = + lz4 + .encode(Buffer.from(JSON.stringify(this._buffer))) + .toString("base64url") + ","; + this.push(compressedPart); + this._buffer = []; + } + callback(); + } + + _flush(callback: (error?: Error | null | undefined, data?: unknown) => void) { + try { + if (!this._buffer.length) { + callback(); + return; + } + callback( + null, + lz4 + .encode(Buffer.from(JSON.stringify(this._buffer))) + .toString("base64url") + ",", + ); + } catch (error) { + callback(error); + } + } +} + +export class DelimitedChunksDecoder extends Transform { + private _buffer: string; + constructor() { + super({ + readableObjectMode: true, + readableHighWaterMark: 32, // limited output reduces RAM usage slightly + writableHighWaterMark: 100000, + }); + this._buffer = ""; + } + + _transform(chunk: string, _encoding: string, callback: () => void): void { + this._buffer += chunk; + if (this._buffer.includes(",")) { + const parts = this._buffer.split(","); + this._buffer = parts.pop(); + parts.forEach(part => { + const parsedPart = JSON.parse( + lz4.decode(Buffer.from(part, "base64url")).toString(), + ); + if (Array.isArray(parsedPart)) { + parsedPart.forEach(obj => this.push(obj)); + } else { + // backwards compatibility with previous implementation + this.push(parsedPart); + } + }); + } + callback(); // callback *no matter what* + } + + _flush( + callback: (error?: Error | null | undefined, data?: unknown) => void, + ): void { + try { + if (!this._buffer.length) { + callback(); + return; + } + const final = JSON.parse( + lz4.decode(Buffer.from(this._buffer, "base64url")).toString(), + ); + callback(null, final); + } catch (error) { + callback(error); + } + } +} diff --git a/packages/utils/src/index.ts b/packages/utils/src/index.ts index a66de34..534b4c2 100644 --- a/packages/utils/src/index.ts +++ b/packages/utils/src/index.ts @@ -3,3 +3,5 @@ export * from "./log_entry"; export * from "./telemetry"; export * from "./misc"; export * from "./redis-client"; +export * from "./biolink"; +export * from "./cache"; diff --git a/packages/utils/src/log_entry.ts b/packages/utils/src/log_entry.ts index 3b065ff..6f72e55 100644 --- a/packages/utils/src/log_entry.ts +++ b/packages/utils/src/log_entry.ts @@ -5,7 +5,7 @@ import { Telemetry } from "./telemetry"; export interface LogData { type?: string; qEdgeID?: string; - error?: string | number; + error?: string | number | boolean; hits?: number; [additionalInformation: string]: unknown; } @@ -15,6 +15,10 @@ export interface StampedLog extends TrapiLog { toJSON(): TrapiLog; } +export interface SerializableLog extends TrapiLog { + data: LogData; +} + export enum SentryLogSeverity { ERROR = "error", WARNING = "warning", @@ -39,21 +43,39 @@ export class LogEntry { this.data = data; } - getLog(): StampedLog { + getSerializeable(isNewLog = true): SerializableLog { + const log = this.getLog(isNewLog); + delete log.toJSON; + return log as SerializableLog; + } + + static deserialize(logs: SerializableLog[]): StampedLog[] { + return logs.map(log => { + return { + ...log, + toJSON: () => _.omit(log, ["data", "toJSON"]) as StampedLog, + } as StampedLog; + }); + } + + getLog(isNewLog = true): StampedLog { const log = { timestamp: new Date().toISOString(), level: this.level, message: this.message, code: this.code, }; - if (global.job) { - global.job.log(JSON.stringify(log, undefined, 2)); + if (isNewLog) { + if (global.job) { + global.job.log(JSON.stringify(log, undefined, 2)); + } + + Telemetry.addBreadcrumb({ + category: "log", + message: this.message, + level: SentryLogSeverity[this.level.toLowerCase()], + }); } - Telemetry.addBreadcrumb({ - category: "log", - message: this.message, - level: SentryLogSeverity[this.level.toLowerCase()], - }); return { ...log, data: this.data, diff --git a/packages/utils/src/misc.ts b/packages/utils/src/misc.ts index bd41f14..0fb5d84 100644 --- a/packages/utils/src/misc.ts +++ b/packages/utils/src/misc.ts @@ -1,3 +1,5 @@ +import crypto from "crypto"; + export function toArray(input: Type | Type[]): Type[] { if (Array.isArray(input)) { return input; @@ -10,7 +12,7 @@ export function getUnique(input: Type[]): Type[] { } export function removeBioLinkPrefix(input: string): string { - if (input && input.startsWith('biolink:')) { + if (input && input.startsWith("biolink:")) { return input.slice(8); } return input; @@ -19,7 +21,10 @@ export function removeBioLinkPrefix(input: string): string { // This gets the intersection of two sets. // Lodash _.intersection gets the intersection of two arrays. // see https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Set -export function intersection(setA: Set, setB: Set): Set { +export function intersection( + setA: Set, + setB: Set, +): Set { const resultSet: Set = new Set(); for (const elem of setB) { if (setA.has(elem)) { @@ -49,3 +54,7 @@ export function cartesian(a: number[][]): number[][] { } return o; } + +export function hash(toHash: string) { + return crypto.createHash("md5").update(toHash).digest("hex"); +} diff --git a/packages/utils/src/redis-client.ts b/packages/utils/src/redis-client.ts index f4cad3d..ff4844a 100644 --- a/packages/utils/src/redis-client.ts +++ b/packages/utils/src/redis-client.ts @@ -1,6 +1,6 @@ import Redis, { Cluster, RedisKey } from "ioredis"; import Debug from "debug"; -const debug = Debug("bte:biothings-explorer-trapi:redis-client"); +const debug = Debug("retriever:redis-client"); import Redlock, { RedlockAbortSignal } from "redlock"; const prefix = `{BTEHashSlotPrefix}:`; diff --git a/packages/utils/src/telemetry.ts b/packages/utils/src/telemetry.ts index 1515411..b3409e2 100644 --- a/packages/utils/src/telemetry.ts +++ b/packages/utils/src/telemetry.ts @@ -1,7 +1,7 @@ import * as Sentry from "@sentry/node"; import Debug from "debug"; import opentelemetry, { Span as OtelSpan, Context as OtelContext, SpanStatusCode } from '@opentelemetry/api'; -const debug = Debug("bte:telemetry-interface"); +const debug = Debug("retriever:telemetry-interface"); const reassurance = "This doesn't affect execution"; @@ -15,7 +15,7 @@ class Span { ?.getTransaction() ?.startChild(data); - this.otelSpan = opentelemetry.trace.getTracer('biothings-explorer-thread').startSpan((data as any).description ?? "", undefined, opentelemetry.trace.setSpan(opentelemetry.context.active(), Telemetry.getOtelSpan())); + this.otelSpan = opentelemetry.trace.getTracer('retriever-thread').startSpan((data as any).description ?? "", undefined, opentelemetry.trace.setSpan(opentelemetry.context.active(), Telemetry.getOtelSpan())); } catch (error) { debug(`Sentry span start error. ${reassurance}`); debug(error); @@ -25,7 +25,7 @@ class Span { setData(key: string, data: unknown) { try { this.span?.setData(key, data); - this.otelSpan?.setAttribute(`bte.${key}`, typeof data === 'object' ? JSON.stringify(data) : data as any); + this.otelSpan?.setAttribute(`retriever.${key}`, typeof data === 'object' ? JSON.stringify(data) : data as any); } catch (error) { debug(`Sentry setData error. ${reassurance}`); debug(error); diff --git a/packages/utils/tsconfig.json b/packages/utils/tsconfig.json index 77d98cd..5a5b4bd 100644 --- a/packages/utils/tsconfig.json +++ b/packages/utils/tsconfig.json @@ -3,8 +3,20 @@ "extends": "../../tsconfig.base.json", "compilerOptions": { "rootDir": "./src", - "outDir": "./built" + "outDir": "./built", + "paths": { + "@retriever/biolink-model": ["../biolink-model"], + "@retriever/types": ["../types"] + } }, "include": ["./src/**/*"], - "exclude": ["node_modules", "__test__/"] + "exclude": ["node_modules", "__test__/"], + "references": [ + { + "path": "../biolink-model" + }, + { + "path": "../types" + } + ] } diff --git a/packages/web-app/.eslintrc.cjs b/packages/web-app/.eslintrc.cjs deleted file mode 100644 index 45194d0..0000000 --- a/packages/web-app/.eslintrc.cjs +++ /dev/null @@ -1,14 +0,0 @@ -/* eslint-env node */ -require("@rushstack/eslint-patch/modern-module-resolution"); - -module.exports = { - root: true, - env: { - node: true, - }, - extends: [ - "plugin:vue/vue3-essential", - "eslint:recommended", - "@vue/eslint-config-prettier", - ], -}; diff --git a/packages/web-app/.vscode/extensions.json b/packages/web-app/.vscode/extensions.json deleted file mode 100644 index c0a6e5a..0000000 --- a/packages/web-app/.vscode/extensions.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "recommendations": ["Vue.volar", "Vue.vscode-typescript-vue-plugin"] -} diff --git a/packages/web-app/README.md b/packages/web-app/README.md deleted file mode 100644 index 520ed4f..0000000 --- a/packages/web-app/README.md +++ /dev/null @@ -1,52 +0,0 @@ -# BTE Web-app - -## Stack - -- [Vue 3.2](https://vuejs.org/) -- [Pinia 2.0](https://pinia.vuejs.org/) -- [Router 4.1](https://router.vuejs.org/) -- [Tailwind CSS 3.1](https://tailwindcss.com/) -- eslint 8.5 -- prettier 2.5 - -Additionally I added [vite-svg-loader](https://github.com/jpkleemans/vite-svg-loader) for easier SVG imports. - -## Install & Requirements - -Node v.17>= - -``` -pnpm i -``` - -## Run / Develop - -``` - -pnpm run dev - -``` - -## Build - -``` - -pnpm run build - -``` - -## Preview - -``` - -pnpm run preview - -``` - -## Lint - -``` - -pnpm run lint - -``` diff --git a/packages/web-app/index.html b/packages/web-app/index.html deleted file mode 100644 index f34aec4..0000000 --- a/packages/web-app/index.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - BioThings Explorer - - -
- - - diff --git a/packages/web-app/package.json b/packages/web-app/package.json deleted file mode 100644 index f6a59a8..0000000 --- a/packages/web-app/package.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "name": "@marcodarko/btewebapp", - "description": "Vite, Vuex, Vue Router & Tailwind CSS.", - "version": "1.0.8", - "scripts": { - "dev": "vite", - "postinstall": "pnpm run build", - "build": "vite build", - "preview": "vite preview --port 4173", - "lint": "eslint . --ext .vue,.js,.jsx,.cjs,.mjs --fix --ignore-path .gitignore" - }, - "dependencies": { - "@codemirror/autocomplete": "^6.10.2", - "@codemirror/commands": "^6.3.0", - "@codemirror/lang-json": "^6.0.1", - "@codemirror/language": "^6.9.1", - "@codemirror/state": "^6.3.1", - "@codemirror/view": "^6.21.3", - "@tailwindcss/forms": "^0.5.6", - "axios": "^1.5.1", - "codemirror": "^6.0.1", - "cytoscape": "^3.26.0", - "cytoscape-popper": "^2.0.0", - "moment": "^2.29.4", - "pinia": "^2.1.7", - "renderjson": "^1.4.0", - "tippy.js": "^6.3.7", - "vue": "^3.3.6", - "vue-router": "^4.2.5", - "zdog": "^1.1.3" - }, - "devDependencies": { - "@rushstack/eslint-patch": "^1.5.1", - "@types/debug": "^4.1.10", - "@types/lodash": "^4.14.200", - "@types/node": "^20.8.7", - "@vitejs/plugin-vue": "^3.2.0", - "@vue/eslint-config-prettier": "^7.1.0", - "autoprefixer": "^10.4.16", - "cssnano": "^5.1.15", - "eslint": "^8.52.0", - "eslint-plugin-vue": "^9.17.0", - "jest": "^29.7.0", - "postcss": "^8.4.31", - "postcss-import": "^15.1.0", - "prettier": "^2.8.8", - "sass": "^1.69.4", - "tailwindcss": "^3.3.3", - "ts-jest": "^29.1.1", - "vite": "^3.2.10", - "vite-svg-loader": "^3.6.0" - }, - "keywords": [ - "vue", - "vue3", - "vuejs", - "vue3js", - "template", - "router", - "vuerouter", - "vue-router", - "tailwind", - "tailwindcss", - "tailwind-css", - "pinia", - "svg" - ] -} diff --git a/packages/web-app/postcss.config.js b/packages/web-app/postcss.config.js deleted file mode 100644 index 04810b5..0000000 --- a/packages/web-app/postcss.config.js +++ /dev/null @@ -1,7 +0,0 @@ -module.exports = { - plugins: { - tailwindcss: {}, - autoprefixer: {}, - ...(process.env.NODE_ENV === "production" ? { cssnano: {} } : {}), - }, -}; diff --git a/packages/web-app/public/bte.svg b/packages/web-app/public/bte.svg deleted file mode 100644 index 186dc97..0000000 --- a/packages/web-app/public/bte.svg +++ /dev/null @@ -1,115 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/packages/web-app/src/App.vue b/packages/web-app/src/App.vue deleted file mode 100644 index b3481eb..0000000 --- a/packages/web-app/src/App.vue +++ /dev/null @@ -1,42 +0,0 @@ - - - diff --git a/packages/web-app/src/assets/img/biothings-explorer-128.png b/packages/web-app/src/assets/img/biothings-explorer-128.png deleted file mode 100644 index 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Jl7qDG{|9=siO2u| diff --git a/packages/web-app/src/assets/tailwind.css b/packages/web-app/src/assets/tailwind.css deleted file mode 100644 index b612a05..0000000 --- a/packages/web-app/src/assets/tailwind.css +++ /dev/null @@ -1,54 +0,0 @@ -@tailwind base; -@tailwind components; -@tailwind utilities; - - -.route-active{ - @apply font-bold text-orange-500; -} - -.link{ - @apply text-white hover:text-blue-500 hover:underline; -} - -.main-btn{ - @apply p-2 rounded-md outline outline-orange-600 bg-orange-600 hover:bg-orange-500 text-white transition-all duration-100 cursor-pointer min-w-[200px] text-center; -} - -.main-btn-outline{ - @apply p-2 rounded-md bg-none outline outline-2 outline-white hover:bg-orange-500 text-white transition-all duration-100 cursor-pointer min-w-[200px] text-center; -} - -.bg-network{ - background-image: url("./img/network-01.svg"); - background-position: bottom center; - background-repeat: no-repeat; - background-size: contain; -} - -.bg-network-2{ - background-image: url("./img/network-2-01.svg"); - background-position: bottom center; - background-repeat: no-repeat; - background-size: contain; -} - -.cy { - height: 100px; - width: 400px; - margin: 0px !important; -} - -#about-cy { - height: 600px; - width: 900px; - margin: 0px !important; -} - -/* CodeMirror */ -.cm-editor { - @apply sm:h-[500px] md:h-[550px] w-[100%]; - background-color: rgba(0, 0, 0, 0.2); - overflow: scroll; - overflow-y: scroll; -} \ No newline at end of file diff --git a/packages/web-app/src/components/BTE.vue b/packages/web-app/src/components/BTE.vue deleted file mode 100644 index 326149e..0000000 --- a/packages/web-app/src/components/BTE.vue +++ /dev/null @@ -1,105 +0,0 @@ - - - \ No newline at end of file diff --git a/packages/web-app/src/components/BTELogoVertical.vue b/packages/web-app/src/components/BTELogoVertical.vue deleted file mode 100644 index 80d6150..0000000 --- a/packages/web-app/src/components/BTELogoVertical.vue +++ /dev/null @@ -1,409 +0,0 @@ - - - \ No newline at end of file diff --git a/packages/web-app/src/components/CodeEditor.vue b/packages/web-app/src/components/CodeEditor.vue deleted file mode 100644 index 6e42fe5..0000000 --- a/packages/web-app/src/components/CodeEditor.vue +++ /dev/null @@ -1,81 +0,0 @@ - - - \ No newline at end of file diff --git a/packages/web-app/src/components/CytoNetwork.vue b/packages/web-app/src/components/CytoNetwork.vue deleted file mode 100644 index 8ad52a4..0000000 --- a/packages/web-app/src/components/CytoNetwork.vue +++ /dev/null @@ -1,69 +0,0 @@ - - - \ No newline at end of file diff --git a/packages/web-app/src/components/LinkOutIcon.vue b/packages/web-app/src/components/LinkOutIcon.vue deleted file mode 100644 index 82ab8cf..0000000 --- a/packages/web-app/src/components/LinkOutIcon.vue +++ /dev/null @@ -1,5 +0,0 @@ - \ No newline at end of file diff --git a/packages/web-app/src/components/LoadingLogo.vue b/packages/web-app/src/components/LoadingLogo.vue deleted file mode 100644 index fe4fe71..0000000 --- a/packages/web-app/src/components/LoadingLogo.vue +++ /dev/null @@ -1,198 +0,0 @@ - - - - - \ No newline at end of file diff --git a/packages/web-app/src/components/Logo.vue b/packages/web-app/src/components/Logo.vue deleted file mode 100644 index 1d18d2a..0000000 --- a/packages/web-app/src/components/Logo.vue +++ /dev/null @@ -1,118 +0,0 @@ - - - \ No newline at end of file diff --git a/packages/web-app/src/components/Nav.vue b/packages/web-app/src/components/Nav.vue deleted file mode 100644 index cc9a320..0000000 --- a/packages/web-app/src/components/Nav.vue +++ /dev/null @@ -1,15 +0,0 @@ - - - diff --git a/packages/web-app/src/components/QueryBox.vue b/packages/web-app/src/components/QueryBox.vue deleted file mode 100644 index 2626831..0000000 --- a/packages/web-app/src/components/QueryBox.vue +++ /dev/null @@ -1,19 +0,0 @@ - - - \ No newline at end of file diff --git a/packages/web-app/src/main.js b/packages/web-app/src/main.js deleted file mode 100644 index 47bfc7a..0000000 --- a/packages/web-app/src/main.js +++ /dev/null @@ -1,15 +0,0 @@ -import { createApp } from "vue"; -import { createPinia } from "pinia"; - -import App from "./App.vue"; -import router from "./router"; - -import "./assets/tailwind.css"; -import "tippy.js/dist/tippy.css"; - -const app = createApp(App); - -app.use(createPinia()); -app.use(router); - -app.mount("#app"); diff --git a/packages/web-app/src/router/index.js b/packages/web-app/src/router/index.js deleted file mode 100644 index a4ec8e9..0000000 --- a/packages/web-app/src/router/index.js +++ /dev/null @@ -1,32 +0,0 @@ -import { createRouter, createWebHistory } from "vue-router"; -import HomeView from "../views/HomeView.vue"; - -const router = createRouter({ - history: createWebHistory(import.meta.env.BASE_URL), - routes: [ - { - path: "/", - name: "home", - component: HomeView, - }, - { - path: "/about", - name: "about", - // route level code-splitting - // this generates a separate chunk (About.[hash].js) for this route - // which is lazy-loaded when the route is visited. - component: () => import("../views/AboutView.vue"), - }, - { - path: "/try-it", - name: "try", - component: () => import("../views/Try.vue"), - }, - ], - linkActiveClass: "route-active", - scrollBehavior() { - return { x: 0, y: 0 }; - }, -}); - -export default router; diff --git a/packages/web-app/src/stores/examples.js b/packages/web-app/src/stores/examples.js deleted file mode 100644 index 8abb39b..0000000 --- a/packages/web-app/src/stores/examples.js +++ /dev/null @@ -1,225 +0,0 @@ -import moment from "moment"; -import { defineStore } from "pinia"; -import axios from "axios"; -import { useMainStore } from "./general"; - -export const useExamplesStore = defineStore({ - id: "examples", - state: () => ({ - queries: [ - { - selected: false, - name: "Disease (Kartagener syndrome) has phenotypic feature", - id: 423423, - elements: { - nodes: [ - { data: { id: "dis", name: "⭐Disease\n(MONDO:0016575)", color: "#8d5bd4" } }, - { data: { id: "ph", name: "PhenotypicFeature", color: "#2abcbd" } }, - ], - edges: [{ data: { source: "dis", target: "ph", name: "⭐biolink:has_phenotype" } }], - }, - query: { - message: { - query_graph: { - nodes: { - n0: { - categories: ["biolink:Disease"], - ids: ["MONDO:0016575"], - }, - n1: { - categories: ["biolink:PhenotypicFeature"], - }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - predicates: ["biolink:has_phenotype"], - }, - }, - }, - }, - }, - }, - { - selected: false, - name: "Disease (Kartagener syndrome) relation to genes", - id: 428423, - elements: { - nodes: [ - { data: { id: "dis", name: "⭐Disease\n(MONDO:0016575)", color: "#8d5bd4" } }, - { data: { id: "gene", name: "Gene", color: "#369ac1" } }, - ], - edges: [{ data: { source: "dis", target: "gene", name: "" } }], - }, - query: { - message: { - query_graph: { - nodes: { - n0: { - categories: ["biolink:Disease"], - ids: ["MONDO:0005737"], - }, - n1: { - categories: ["biolink:Gene"], - }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - }, - }, - }, - }, - }, - }, - { - selected: false, - name: "Disease (Ebola hemorrhagic fever) gene relation to small molecules", - id: 426654, - elements: { - nodes: [ - { data: { id: "dis", name: "⭐Disease\n(MONDO:0005737)", color: "#8d5bd4" } }, - { data: { id: "gene", name: "Gene", color: "#369ac1" } }, - { data: { id: "sm", name: "SmallMolecule", color: "hotpink" } }, - ], - edges: [ - { data: { source: "dis", target: "gene", name: "" } }, - { data: { source: "gene", target: "sm", name: "" } }, - ], - }, - query: { - message: { - query_graph: { - nodes: { - n0: { - categories: ["biolink:Disease"], - ids: ["MONDO:0005737"], - }, - n1: { - categories: ["biolink:Gene"], - }, - n2: { - categories: ["biolink:SmallMolecule"], - }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - }, - e02: { - subject: "n1", - object: "n2", - }, - }, - }, - }, - }, - }, - { - selected: false, - name: "Gene (NCBIGene:3778) relation to small molecules via other genes", - id: 453423, - elements: { - nodes: [ - { data: { id: "gene", name: "⭐Gene\n(NCBIGene:3778)", color: "#369ac1" } }, - { data: { id: "gene2", name: "Gene", color: "#369ac1" } }, - { data: { id: "sm", name: "SmallMolecule", color: "hotpink" } }, - ], - edges: [ - { data: { source: "gene", target: "gene2", name: "" } }, - { data: { source: "gene2", target: "sm", name: "" } }, - ], - }, - query: { - message: { - query_graph: { - nodes: { - n0: { - categories: ["biolink:Gene"], - ids: ["NCBIGene:3778"], - }, - n1: { - categories: ["biolink:Gene"], - }, - n2: { - categories: ["biolink:SmallMolecule"], - }, - }, - edges: { - e01: { - subject: "n0", - object: "n1", - }, - e02: { - subject: "n1", - object: "n2", - }, - }, - }, - }, - }, - }, - ], - message: "", - jobs: [], - jobPicked: "", - }), - getters: { - selectedQuery: state => state.queries.find(q => q.selected), - }, - actions: { - select(id) { - this.queries.forEach(q => { - if (q.id == id) { - q.selected = !q.selected; - } else { - q.selected = false; - } - }); - }, - async sendRequest(query, description) { - let self = this; - let store = useMainStore(); - store.loading = true; - axios - .post("/v1/asyncquery", JSON.parse(query)) - .then(res => { - store.loading = false; - console.log(res.data); - self.jobs.unshift({ - id: res.data.job_id, - date: this.getDateRightNow(), - url: res.data.job_url, - description: description, - }); - self.message = `A new job ID has been created: ${res.data.job_id} `; - self.updateJobs(); - }) - .catch(err => { - store.loading = false; - console.log(err); - self.message = `Oh no: ${err} `; - throw err; - }); - }, - updateJobs() { - localStorage.setItem("bte-jobs", JSON.stringify(this.jobs)); - }, - getJobs() { - let j = JSON.parse(localStorage.getItem("bte-jobs")); - if (j && j.length) { - this.jobs = j; - } - }, - deleteJobs() { - localStorage.removeItem("bte-jobs"); - this.jobs = []; - }, - getDateRightNow() { - return moment().format("MMMM Do YYYY, h:mm:ss"); - }, - }, -}); diff --git a/packages/web-app/src/stores/general.js b/packages/web-app/src/stores/general.js deleted file mode 100644 index aa06635..0000000 --- a/packages/web-app/src/stores/general.js +++ /dev/null @@ -1,14 +0,0 @@ -import { defineStore } from "pinia"; - -export const useMainStore = defineStore({ - id: "general", - state: () => ({ - loading: false, - }), - getters: {}, - actions: { - setLoading(v) { - this.loading = v; - }, - }, -}); diff --git a/packages/web-app/src/views/AboutView.vue b/packages/web-app/src/views/AboutView.vue deleted file mode 100644 index 43837a3..0000000 --- a/packages/web-app/src/views/AboutView.vue +++ /dev/null @@ -1,194 +0,0 @@ - - - diff --git a/packages/web-app/src/views/HomeView.vue b/packages/web-app/src/views/HomeView.vue deleted file mode 100644 index 66069b6..0000000 --- a/packages/web-app/src/views/HomeView.vue +++ /dev/null @@ -1,28 +0,0 @@ - - - diff --git a/packages/web-app/src/views/Try.vue b/packages/web-app/src/views/Try.vue deleted file mode 100644 index c58e45e..0000000 --- a/packages/web-app/src/views/Try.vue +++ /dev/null @@ -1,63 +0,0 @@ - - - \ No newline at end of file diff --git a/packages/web-app/tailwind.config.js b/packages/web-app/tailwind.config.js deleted file mode 100644 index e367de9..0000000 --- a/packages/web-app/tailwind.config.js +++ /dev/null @@ -1,8 +0,0 @@ -/** @type {import('tailwindcss').Config} */ -module.exports = { - content: ["./index.html", "./src/**/*.{vue,js,ts,jsx,tsx}"], - theme: { - extend: {}, - }, - plugins: [require("@tailwindcss/forms")], -}; diff --git a/packages/web-app/vite.config.js b/packages/web-app/vite.config.js deleted file mode 100644 index 383ca63..0000000 --- a/packages/web-app/vite.config.js +++ /dev/null @@ -1,16 +0,0 @@ -import { fileURLToPath, URL } from "node:url"; - -import { defineConfig } from "vite"; -import vue from "@vitejs/plugin-vue"; - -import svgLoader from "vite-svg-loader"; - -// https://vitejs.dev/config/ -export default defineConfig({ - plugins: [vue(), svgLoader()], - resolve: { - alias: { - "@": fileURLToPath(new URL("./src", import.meta.url)), - }, - }, -}); diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 03055d3..3be7563 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -11,6 +11,9 @@ importers: '@bull-board/express': specifier: ^5.9.1 version: 5.9.1(supports-color@7.2.0) + '@retriever/call-apis': + specifier: workspace:./packages/call-apis + version: link:packages/call-apis '@sentry/node': specifier: ^7.74.1 version: 7.74.1(supports-color@7.2.0) @@ -174,15 +177,24 @@ importers: packages/api-response-transform: dependencies: - '@biothings-explorer/utils': - specifier: workspace:../utils - version: link:../utils '@commitlint/cli': specifier: ^17.8.1 version: 17.8.1 '@commitlint/config-conventional': specifier: ^11.0.0 version: 11.0.0 + '@retriever/graph': + specifier: workspace:../graph + version: link:../graph + '@retriever/smartapi-kg': + specifier: workspace:../smartapi-kg + version: link:../smartapi-kg + '@retriever/types': + specifier: workspace:../types + version: link:../types + '@retriever/utils': + specifier: workspace:../utils + version: link:../utils async: specifier: ^3.2.4 version: 3.2.4 @@ -420,18 +432,27 @@ importers: packages/call-apis: dependencies: - '@biothings-explorer/api-response-transform': + '@retriever/api-response-transform': specifier: workspace:../api-response-transform version: link:../api-response-transform - '@biothings-explorer/smartapi-kg': + '@retriever/graph': + specifier: workspace:../graph + version: link:../graph + '@retriever/smartapi-kg': specifier: workspace:../smartapi-kg version: link:../smartapi-kg - '@biothings-explorer/utils': + '@retriever/types': + specifier: workspace:../types + version: link:../types + '@retriever/utils': specifier: workspace:../utils version: link:../utils '@sentry/node': specifier: ^7.74.1 version: 7.74.1(supports-color@7.2.0) + async: + specifier: ^3.2.4 + version: 3.2.4 axios: specifier: ^0.21.4 version: 0.21.4(debug@4.3.4) @@ -460,6 +481,9 @@ importers: '@commitlint/config-conventional': specifier: ^11.0.0 version: 11.0.0 + '@types/async': + specifier: ^3.2.22 + version: 3.2.24 '@types/debug': specifier: ^4.1.10 version: 4.1.10 @@ -512,6 +536,25 @@ importers: specifier: ^5.2.2 version: 5.2.2 + packages/graph: + dependencies: + '@retriever/biomedical_id_resolver': + specifier: workspace:../biomedical_id_resolver + version: link:../biomedical_id_resolver + '@retriever/smartapi-kg': + specifier: workspace:../smartapi-kg + version: link:../smartapi-kg + '@retriever/types': + specifier: workspace:../types + version: link:../types + '@retriever/utils': + specifier: workspace:../utils + version: link:../utils + devDependencies: + '@types/jest': + specifier: ^29.5.12 + version: 29.5.12 + packages/node-expansion: dependencies: axios: @@ -563,22 +606,25 @@ importers: packages/query_graph_handler: dependencies: - '@biothings-explorer/api-response-transform': + '@retriever/api-response-transform': specifier: workspace:../api-response-transform version: link:../api-response-transform - '@biothings-explorer/call-apis': + '@retriever/call-apis': specifier: workspace:../call-apis version: link:../call-apis - '@biothings-explorer/node-expansion': + '@retriever/graph': + specifier: workspace:../graph + version: link:../graph + '@retriever/node-expansion': specifier: workspace:../node-expansion version: link:../node-expansion - '@biothings-explorer/smartapi-kg': + '@retriever/smartapi-kg': specifier: workspace:../smartapi-kg version: link:../smartapi-kg - '@biothings-explorer/types': + '@retriever/types': specifier: workspace:../types version: link:../types - '@biothings-explorer/utils': + '@retriever/utils': specifier: workspace:../utils version: link:../utils '@sentry/node': @@ -672,18 +718,6 @@ importers: packages/server: dependencies: - '@biothings-explorer/query_graph_handler': - specifier: workspace:../query_graph_handler - version: link:../query_graph_handler - '@biothings-explorer/smartapi-kg': - specifier: workspace:../smartapi-kg - version: link:../smartapi-kg - '@biothings-explorer/types': - specifier: workspace:../types - version: link:../types - '@biothings-explorer/utils': - specifier: workspace:../utils - version: link:../utils '@bull-board/api': specifier: ^5.9.1 version: 5.9.1(@bull-board/ui@5.9.1) @@ -717,6 +751,18 @@ importers: '@opentelemetry/sdk-trace-node': specifier: ^1.18.1 version: 1.23.0(@opentelemetry/api@1.8.0) + '@retriever/query_graph_handler': + specifier: workspace:../query_graph_handler + version: link:../query_graph_handler + '@retriever/smartapi-kg': + specifier: workspace:../smartapi-kg + version: link:../smartapi-kg + '@retriever/types': + specifier: workspace:../types + version: link:../types + '@retriever/utils': + specifier: workspace:../utils + version: link:../utils '@sentry/node': specifier: ^7.74.1 version: 7.74.1(supports-color@7.2.0) @@ -1067,7 +1113,10 @@ importers: packages/types: dependencies: - '@biothings-explorer/smartapi-kg': + '@retriever/biomedical_id_resolver': + specifier: workspace:../biomedical_id_resolver + version: link:../biomedical_id_resolver + '@retriever/smartapi-kg': specifier: workspace:../smartapi-kg version: link:../smartapi-kg devDependencies: @@ -1080,6 +1129,12 @@ importers: '@opentelemetry/api': specifier: ^1.7.0 version: 1.8.0 + '@retriever/biolink-model': + specifier: workspace:../biolink-model + version: link:../biolink-model + '@retriever/types': + specifier: workspace:../types + version: link:../types '@sentry/node': specifier: ^7.74.1 version: 7.74.1(supports-color@7.2.0) @@ -1114,6 +1169,9 @@ importers: '@types/lodash': specifier: ^4.14.200 version: 4.14.200 + '@types/lz4': + specifier: ^0.6.4 + version: 0.6.4 '@types/node': specifier: ^20.8.10 version: 20.9.0 @@ -1148,121 +1206,6 @@ importers: specifier: ^5.2.2 version: 5.2.2 - packages/web-app: - dependencies: - '@codemirror/autocomplete': - specifier: ^6.10.2 - version: 6.10.2(@codemirror/language@6.9.2)(@codemirror/state@6.3.1)(@codemirror/view@6.21.4)(@lezer/common@1.2.1) - '@codemirror/commands': - specifier: ^6.3.0 - version: 6.3.0 - '@codemirror/lang-json': - specifier: ^6.0.1 - version: 6.0.1 - '@codemirror/language': - specifier: ^6.9.1 - version: 6.9.2 - '@codemirror/state': - specifier: ^6.3.1 - version: 6.3.1 - '@codemirror/view': - specifier: ^6.21.3 - version: 6.21.4 - '@tailwindcss/forms': - specifier: ^0.5.6 - version: 0.5.6(tailwindcss@3.3.5) - axios: - specifier: ^1.5.1 - version: 1.5.1(debug@4.3.4) - codemirror: - specifier: ^6.0.1 - version: 6.0.1(@lezer/common@1.2.1) - cytoscape: - specifier: ^3.26.0 - version: 3.26.0 - cytoscape-popper: - specifier: ^2.0.0 - version: 2.0.0(cytoscape@3.26.0) - moment: - specifier: ^2.29.4 - version: 2.29.4 - pinia: - specifier: ^2.1.7 - version: 2.1.7(typescript@5.2.2)(vue@3.3.7) - renderjson: - specifier: ^1.4.0 - version: 1.4.0 - tippy.js: - specifier: ^6.3.7 - version: 6.3.7 - vue: - specifier: ^3.3.6 - version: 3.3.7(typescript@5.2.2) - vue-router: - specifier: ^4.2.5 - version: 4.2.5(vue@3.3.7) - zdog: - specifier: ^1.1.3 - version: 1.1.3 - devDependencies: - '@rushstack/eslint-patch': - specifier: ^1.5.1 - version: 1.5.1 - '@types/debug': - specifier: ^4.1.10 - version: 4.1.10 - '@types/lodash': - specifier: ^4.14.200 - version: 4.14.200 - '@types/node': - specifier: ^20.8.7 - version: 20.8.7 - '@vitejs/plugin-vue': - specifier: ^3.2.0 - version: 3.2.0(vite@3.2.10)(vue@3.3.7) - '@vue/eslint-config-prettier': - specifier: ^7.1.0 - version: 7.1.0(eslint@8.52.0)(prettier@2.8.8) - autoprefixer: - specifier: ^10.4.16 - version: 10.4.16(postcss@8.4.31) - cssnano: - specifier: ^5.1.15 - version: 5.1.15(postcss@8.4.31) - eslint: - specifier: ^8.52.0 - version: 8.52.0(supports-color@7.2.0) - eslint-plugin-vue: - specifier: ^9.17.0 - version: 9.18.0(eslint@8.52.0)(supports-color@7.2.0) - jest: - specifier: ^29.7.0 - version: 29.7.0(@types/node@20.8.7)(supports-color@7.2.0) - postcss: - specifier: ^8.4.31 - version: 8.4.31 - postcss-import: - specifier: ^15.1.0 - version: 15.1.0(postcss@8.4.31) - 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"@biothings-explorer/api-response-transform": ["packages/api-response-transform"], + "@retriever/api-response-transform": ["packages/api-response-transform"], "biolink-model": ["packages/biolink-model"], "biomedical_id_resolver": ["packages/biomedical_id_resolver"], - "@biothings-explorer/call-apis": ["packages/biomedical_id_resolver"], - "@biothings-explorer/node-expansion": ["packages/node-expansion"], - "@biothings-explorer/query_graph_handler": ["packages/query_graph_handler"], - "@biothings-explorer/smartapi-kg": ["packages/smartapi-kg"], - "@biothings-explorer/server": ["packages/server"], - "@biothings-explorer/utils": ["packages/utils"], - "@biothings-explorer/types": ["packages/types"] + "@retriever/call-apis": ["packages/biomedical_id_resolver"], + "@retriever/node-expansion": ["packages/node-expansion"], + "@retriever/query_graph_handler": ["packages/query_graph_handler"], + "@retriever/smartapi-kg": ["packages/smartapi-kg"], + "@retriever/server": ["packages/server"], + "@retriever/utils": ["packages/utils"], + "@retriever/types": ["packages/types"] } }, "files": [], @@ -19,9 +19,6 @@ { "path": "packages/server" }, - { - "paths": "packages/server/web-app" - }, { "path": "packages/biolink-model" }, diff --git a/tsconfig.json b/tsconfig.json index 9fc841d..31b9723 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -13,8 +13,7 @@ "exclude": [ "**/node_modules/**", "**/__test__/**", - "**/packages/**", - "./packages/server/src/web-app/dist/*" + "**/packages/**" ], "references": [] }