Federate sample for report (#155)

Co-authored-by: Erin Hoops <[email protected]> Co-authored-by: Julie Han <[email protected]> Co-authored-by: Jerry Fu <[email protected]> Co-authored-by: bchu1 <[email protected]> Co-authored-by: czi-github-helper[bot] <95879977+czi-github-helper[bot]@users.noreply.github.com> Co-authored-by: rzlim08 <[email protected]>
chanzuckerberg · Mar 7, 2024 · 45407c6 · 45407c6
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diff --git a/.github/workflows/deploy-sandbox.yml b/.github/workflows/deploy-sandbox.yml
@@ -37,6 +37,18 @@ jobs:
           app_config_name: API_URL
           app_config_value: ${{ vars.API_URL}}
           happy_env: sandbox
+      - name: Set CZ ID Entities URL
+        uses: chanzuckerberg/czid-graphql-federation-server/.github/actions/happy-config-set@main
+        with:
+          app_config_name: NEXTGEN_ENTITIES_URL
+          app_config_value: ${{ vars.NEXTGEN_ENTITIES_URL}}
+          happy_env: sandbox
+      - name: Set CZ ID Workflows URL
+        uses: chanzuckerberg/czid-graphql-federation-server/.github/actions/happy-config-set@main
+        with:
+          app_config_name: NEXTGEN_WORKFLOWS_URL
+          app_config_value: ${{ vars.NEXTGEN_WORKFLOWS_URL}}
+          happy_env: sandbox
       - name: Set allowed CORS origins
         uses: chanzuckerberg/czid-graphql-federation-server/.github/actions/happy-config-set@main
         with:

diff --git a/.github/workflows/deploy-staging.yml b/.github/workflows/deploy-staging.yml
@@ -62,6 +62,18 @@ jobs:
           app_config_name: API_URL
           app_config_value: ${{ vars.API_URL}}
           happy_env: staging
+      - name: Set CZ ID Entities URL
+        uses: chanzuckerberg/czid-graphql-federation-server/.github/actions/happy-config-set@main
+        with:
+          app_config_name: NEXTGEN_ENTITIES_URL
+          app_config_value: ${{ vars.NEXTGEN_ENTITIES_URL}}
+          happy_env: staging
+      - name: Set CZ ID Workflows URL
+        uses: chanzuckerberg/czid-graphql-federation-server/.github/actions/happy-config-set@main
+        with:
+          app_config_name: NEXTGEN_WORKFLOWS_URL
+          app_config_value: ${{ vars.NEXTGEN_WORKFLOWS_URL}}
+          happy_env: staging
       - name: Set allowed CORS origins
         uses: chanzuckerberg/czid-graphql-federation-server/.github/actions/happy-config-set@main
         with:

diff --git a/.happy/terraform/envs/sandbox/main.tf b/.happy/terraform/envs/sandbox/main.tf
@@ -33,10 +33,6 @@ module "stack" {
   stack_prefix     = "/${var.stack_name}"
   app_name         = var.app
   k8s_namespace    = var.k8s_namespace
-  additional_env_vars = {
-    NEXTGEN_ENTITIES_URL = "http://entities-entities:8008"
-    NEXTGEN_WORKFLOWS_URL = "http://workflows-workflows:8042"
-  }
   services = {
     gql = merge(local.routing_config[local.service_type], {
       name              = "graphql-federation"

diff --git a/.meshrc.yaml b/.meshrc.yaml
@@ -96,6 +96,12 @@ sources:
             requestSample: { pipelineVersion: "8.0" }
             responseSchema: ./json-schemas/sampleMetadata.json
             responseTypeName: SampleMetadata
+          - type: Query
+            field: SampleForReport
+            method: GET
+            path: /pub/{args.snapshotLinkId}/samples/{args.railsSampleId}.json
+            responseSchema: ./json-schemas/sampleForReportResponse.json
+            responseTypeName: SampleForReport
           - type: Query
             field: MngsWorkflowResults
             path: /pub/{args.snapshotLinkId}/samples/{args.sampleId}.json
@@ -176,8 +182,8 @@ sources:
             field: fedWorkflowRuns
             path: /workflow_runs.json
             method: POST
-            requestSchema: ./json-schemas/fedWorkflowRunsRequest.json
-            responseSchema: ./json-schemas/fedWorkflowRunsResponse.json
+            requestSchema: ./json-schemas/workflowRunsRequest.json
+            responseSchema: ./json-schemas/workflowRunsResponse.json
             responseTypeName: fedWorkflowRuns
           - type: Query
             field: fedWorkflowRunsAggregate

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,25 @@
 # Changelog
 
 
+## [2.14.0](https://github.com/chanzuckerberg/czid-graphql-federation-server/compare/v2.13.0...v2.14.0) (2024-03-07)
+
+
+### Features
+
+* update staging env variables urls ([#153](https://github.com/chanzuckerberg/czid-graphql-federation-server/issues/153)) ([26afdd7](https://github.com/chanzuckerberg/czid-graphql-federation-server/commit/26afdd7888752856d13d3fa255cb94dfcde6c23b))
+
+## [2.13.0](https://github.com/chanzuckerberg/czid-graphql-federation-server/compare/v2.12.0...v2.13.0) (2024-03-06)
+
+
+### Features
+
+* Integrate fedWorkflowRuns and fedSequencingReads with NextGen ([#146](https://github.com/chanzuckerberg/czid-graphql-federation-server/issues/146)) ([8f51783](https://github.com/chanzuckerberg/czid-graphql-federation-server/commit/8f51783d81050e059eb11f475fbc03238c222c51))
+
+
+### Bug Fixes
+
+* createBulkDownload Change workflowRunIdsStrings type and remove required for workflowRunIds ([#145](https://github.com/chanzuckerberg/czid-graphql-federation-server/issues/145)) ([256173d](https://github.com/chanzuckerberg/czid-graphql-federation-server/commit/256173dd1b8aaa8794daea7d0527656496238021))
+
 ## [2.12.0](https://github.com/chanzuckerberg/czid-graphql-federation-server/compare/v2.11.1...v2.12.0) (2024-03-04)
 
 

diff --git a/Makefile b/Makefile
@@ -2,18 +2,17 @@
 help: ## display help for this makefile
 	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 
-.PHONY: build 
+.PHONY: build
 build: ## Build docker images
 	docker compose build
 
-.PHONY: update-schema
-update-schema: ## Update schema
-	rm tests/__snapshots__/UnifiedSchema.test.ts.snap
+.PHONY: update-schema-snapshot
+update-schema-snapshot: ## Update test schema snapshot
 	docker compose run gql npm test -- tests/UnifiedSchema.test.ts -u
 
 .PHONY: test
 test: ## Run tests
-	docker compose run --rm gql npm test 
+	docker compose run --rm gql npm test
 
 .PHONY: local-init
 local-init: ## Build & start the service

diff --git a/example-queries/sample-for-report-query.graphql b/example-queries/sample-for-report-query.graphql
@@ -0,0 +1,55 @@
+query SampleViewSampleQuery($railsSampleId: String, $snapshotLinkId: String) {
+    SampleForReport(
+      railsSampleId: $railsSampleId
+      snapshotLinkId: $snapshotLinkId
+    ) {
+      id
+      created_at
+      default_background_id
+      default_pipeline_run_id
+      editable
+      host_genome_id
+      initial_workflow
+      name
+      pipeline_runs {
+        adjusted_remaining_reads
+        alignment_config_name
+        assembled
+        created_at
+        id
+        pipeline_version
+        run_finalized
+        total_ercc_reads
+        wdl_version
+      }
+      project {
+        id
+        name
+      }
+      project_id
+      railsSampleId
+      status
+      updated_at
+      upload_error
+      user_id
+      workflow_runs {
+        deprecated
+        executed_at
+        id
+        input_error
+        inputs {
+          accession_id
+          accession_name
+          creation_source
+          ref_fasta
+          taxon_id
+          taxon_name
+          technology
+        }
+        run_finalized
+        status
+        wdl_version
+        workflow
+      }
+    }
+  }
diff --git a/example-queries/workflow-runs-query-order-by.graphql b/example-queries/workflow-runs-query-order-by.graphql
@@ -1,7 +1,11 @@
 query TestQuery {
     fedWorkflowRuns(input: {
         orderBy: {
-            startedAt: "ASC"
+            startedAt: "asc"
+        },
+        todoRemove: {
+            orderBy: "createdAt"
+            orderDir: "ASC"
         }
     }) {
         id

diff --git a/json-schemas/consensusGenomesResponse.json b/json-schemas/consensusGenomesResponse.json
@@ -21,17 +21,6 @@
                 },
                 "required": ["name"]
             },
-            "referenceGenome": {
-                "type": "object",
-                "properties": {
-                    "accessionId": {
-                        "type": "string"
-                    },
-                    "accessionName": {
-                        "type": "string"
-                    }
-                }
-            },
             "accession": {
                 "type": "object",
                 "properties": {
@@ -41,7 +30,8 @@
                     "accessionName": {
                         "type": "string"
                     }
-                }
+                },
+                "required": ["accessionId", "accessionName"]
             },
             "metrics": {
                 "type": "object",

diff --git a/json-schemas/fedWorkflowRunsRequest.json b/json-schemas/fedWorkflowRunsRequest.json