diff --git a/.github/workflows/pr-test.yml b/.github/workflows/pr-test.yml index 399852f8c..dfe0190b7 100644 --- a/.github/workflows/pr-test.yml +++ b/.github/workflows/pr-test.yml @@ -4,6 +4,7 @@ on: pull_request: paths: - api/** + - database/** - ui/** jobs: diff --git a/CHANGELOG.md b/CHANGELOG.md index 8bfe90fff..72e23c9bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,71 @@ +# Release 0.7.0 +- Bump ws from 6.2.1 to 6.2.2 in /ui ([#433](https://github.com/broadinstitute/wfl/pull/433)) +- [GH-1363] Fix Sporadic Firecloud Test Failures ([#437](https://github.com/broadinstitute/wfl/pull/437)) +- [GH-1361] Disable Failing Tests for v0.7.0 Release ([#435](https://github.com/broadinstitute/wfl/pull/435)) +- Move docstring and document when true. ([#436](https://github.com/broadinstitute/wfl/pull/436)) +- Fix broken requirement install command in docs readme ([#434](https://github.com/broadinstitute/wfl/pull/434)) +- [GH-1359] Overwrite Workspace Entity On Sink ([#432](https://github.com/broadinstitute/wfl/pull/432)) +- [GH-1357] Fix failure to sink workflow outputs ([#431](https://github.com/broadinstitute/wfl/pull/431)) +- [GH-1356] Fix Coercion Failure for TDR Snapshots Source ([#429](https://github.com/broadinstitute/wfl/pull/429)) +- [GH-1354] Enforce `snapshotReaders` are email addresses ([#428](https://github.com/broadinstitute/wfl/pull/428)) +- [GH-1325] Get or import snapshot ([#422](https://github.com/broadinstitute/wfl/pull/422)) +- Bump dns-packet from 1.3.1 to 1.3.4 in /ui +- [GH-1350] fix Terra Workspace sink validation ([#427](https://github.com/broadinstitute/wfl/pull/427)) +- [GH-1348] Remove :pipeline from COVID workload request ([#426](https://github.com/broadinstitute/wfl/pull/426)) +- [GH-1344] Enforce valid email addresses in workload `watchers` +- [GH-1341] Fix accepting malformed labels in workload request RR: https://broadinstitute.atlassian.net/browse/GH-1341 Enforce labels are of the form "name:value" where - name starts with a letter followed by any combination of letters, numbers, underscores and dashes - value is any non-blank string not containing `:` +- Add test-covid-workload to parallel test group ([#424](https://github.com/broadinstitute/wfl/pull/424)) +- [GH-1331] document `/stop` and `/workflows` ([#417](https://github.com/broadinstitute/wfl/pull/417)) +- [GH-1339] Prevent Snapshot Job IDs from being clobbered with nils RR: https://broadinstitute.atlassian.net/browse/GH-1339 When we update the status of snapshot creation jobs, we only get the job metadata when the job is complete.As a consequence, `nil`s are propagated up the call stack and the database record is clobbered with nils, including the `snapshot_creation_job_id` column. +- [GH-1338] Fix wfl not discovering new dataset rows RR: https://broadinstitute.atlassian.net/browse/GH-1338 This isn't a complete fix sadly but it at least solves the problem for low ingest rate projects like COVID. For now, only updating `last_checked` when we successfully found new rows in the dataset. +- [GH-1337] fix create snapshot job always failing RR: https://broadinstitute.atlassian.net/browse/GH-1337 Caused by destructuring the tdr job response with the wrong key. +- [GH-1336] Fix continual snapshot creation ([#419](https://github.com/broadinstitute/wfl/pull/419)) +- [GH-1333] Fix NullPointerException in TDR Source ([#418](https://github.com/broadinstitute/wfl/pull/418)) +- [GH-1327] update system tests after /stop changes ([#412](https://github.com/broadinstitute/wfl/pull/412)) +- [GH-1327] Fix Start After Stop ([#411](https://github.com/broadinstitute/wfl/pull/411)) +- GH-1298: TerraWorkspaceSink - verify target entity columns exist ([#410](https://github.com/broadinstitute/wfl/pull/410)) +- [GH-1323] to-edn ([#409](https://github.com/broadinstitute/wfl/pull/409)) +- GH-1316 Create submission within TerraExecutor update ([#406](https://github.com/broadinstitute/wfl/pull/406)) +- [GH-1213] Create covid workload verifications ([#379](https://github.com/broadinstitute/wfl/pull/379)) +- Remove liquibase-core from build dependencies. ([#407](https://github.com/broadinstitute/wfl/pull/407)) +- [GH-1320] add `snapshotReaders` to tdr source ([#405](https://github.com/broadinstitute/wfl/pull/405)) +- GH-1216: [TDR New Work Detection] Extend System Tests for COVID processing ([#395](https://github.com/broadinstitute/wfl/pull/395)) +- [GH-1318] Stop Workload Source ([#400](https://github.com/broadinstitute/wfl/pull/400)) +- [GH-1322] TDR Snapshots Source ([#403](https://github.com/broadinstitute/wfl/pull/403)) +- GH-1307 GH-1312 Update method configuration using snapshot reference ([#402](https://github.com/broadinstitute/wfl/pull/402)) +- TerraExecutor/update-executor should update active, failed workflow statuses ([#398](https://github.com/broadinstitute/wfl/pull/398)) +- [GH-1317] start the workload source ([#399](https://github.com/broadinstitute/wfl/pull/399)) +- [GH-1314] expose workflows via `GET /api/v1/workload/{uuid}/workflows` ([#397](https://github.com/broadinstitute/wfl/pull/397)) +- [GH-1222] Check for new work in TDR ([#371](https://github.com/broadinstitute/wfl/pull/371)) +- [GH-1306] Add `workflows` multimethod for workloads ([#396](https://github.com/broadinstitute/wfl/pull/396)) +- [GH-1215] COVID TerraExecutor/update-executor! +- [GH-1313] TerraWorkspaceSink/update-sink! ([#394](https://github.com/broadinstitute/wfl/pull/394)) +- [GH-1311]: Create/Load COVID workloads ([#389](https://github.com/broadinstitute/wfl/pull/389)) +- Bump lodash from 4.17.19 to 4.17.21 in /ui ([#390](https://github.com/broadinstitute/wfl/pull/390)) +- Bump hosted-git-info from 2.8.8 to 2.8.9 in /ui ([#392](https://github.com/broadinstitute/wfl/pull/392)) +- [GH-1301] Notify Workload Watchers when "User Visible" Exceptions Occur ([#386](https://github.com/broadinstitute/wfl/pull/386)) +- Bump y18n from 4.0.0 to 4.0.1 in /ui ([#352](https://github.com/broadinstitute/wfl/pull/352)) +- Update db schema again based on lasted discussions. ([#387](https://github.com/broadinstitute/wfl/pull/387)) +- Bump url-parse from 1.4.7 to 1.5.1 in /ui ([#388](https://github.com/broadinstitute/wfl/pull/388)) +- GH-1285: [COVID] Launch submissions through Rawls, and keep track of them ([#372](https://github.com/broadinstitute/wfl/pull/372)) +- [GH-1295] Use Rawls to Import Workflow Outputs ([#384](https://github.com/broadinstitute/wfl/pull/384)) +- [GH-1215] Import snapshots within COVID workload ([#376](https://github.com/broadinstitute/wfl/pull/376)) +- Add multimethods for source, executor and sink operations ([#383](https://github.com/broadinstitute/wfl/pull/383)) +- [GH-1213] Update DB schema for COVID workload creation ([#381](https://github.com/broadinstitute/wfl/pull/381)) +- add interactive script ahead of covid-19 demo ([#380](https://github.com/broadinstitute/wfl/pull/380)) +- Bump ssri from 6.0.1 to 6.0.2 in /ui ([#382](https://github.com/broadinstitute/wfl/pull/382)) +- Update documentation and infrastructure for release candidates ([#377](https://github.com/broadinstitute/wfl/pull/377)) +- [GH-1293] fix test-create-submissions-for-entity-set ([#378](https://github.com/broadinstitute/wfl/pull/378)) +- [GH-1215] Add snapshot_reference_id to Sarscov2IlluminaFull table schema ([#375](https://github.com/broadinstitute/wfl/pull/375)) +- Rename rawls/create-snapshot -> create-snapshot-reference ([#373](https://github.com/broadinstitute/wfl/pull/373)) +- Add wfl.service/rawls.clj for interacting directly with Rawls API ([#370](https://github.com/broadinstitute/wfl/pull/370)) +- GH-1272: Lists are not imported correctly into a Terra Workspace Entity ([#368](https://github.com/broadinstitute/wfl/pull/368)) +- Create an interface all COVID work can build on top of. ([#369](https://github.com/broadinstitute/wfl/pull/369)) +- GH-1226 Support entity set creation when creating submissions. ([#353](https://github.com/broadinstitute/wfl/pull/353)) +- util/do-or-nil-silently should move to build.clj ([#367](https://github.com/broadinstitute/wfl/pull/367)) +- bump develop to 0.7.0 ([#360](https://github.com/broadinstitute/wfl/pull/360)) +- Snapshot creation uses datetime rather than date ([#355](https://github.com/broadinstitute/wfl/pull/355)) + # Release 0.6.1 - [GH-1277] Prevent update loop from terminating ([#364](https://github.com/broadinstitute/wfl/pull/364)) - [GH-1284] Fix docker image generation ([#363](https://github.com/broadinstitute/wfl/pull/363)) @@ -121,4 +189,4 @@ - [GH-1013] Item Nesting V2 ([#188](https://github.com/broadinstitute/wfl/pull/188)) - [GH-1034] Fix reference_fasta function ([#194](https://github.com/broadinstitute/wfl/pull/194)) - [GH-771] WGS updates ([#191](https://github.com/broadinstitute/wfl/pull/191)) -- [GH-819] External Exome Reprocessing ([#139](https://github.com/broadinstitute/wfl/pull/139)) +- [GH-819] External Exome Reprocessing ([#139](https://github.com/broadinstitute/wfl/pull/139)) \ No newline at end of file diff --git a/api/build/build.clj b/api/build/build.clj index b673ab87f..ca9cd1a3f 100644 --- a/api/build/build.clj +++ b/api/build/build.clj @@ -1,42 +1,40 @@ (ns build - (:require [clojure.data.xml :as xml] - [clojure.java.io :as io] - [clojure.pprint :refer [pprint]] - [clojure.string :as str] - [wfl.module.aou :as aou] - [wfl.module.wgs :as wgs] - [wfl.module.xx :as xx] - [wfl.module.sg :as sg] + (:require [clojure.data.xml :as xml] + [clojure.java.io :as io] + [clojure.pprint :refer [pprint]] + [clojure.string :as str] [wfl.service.firecloud :as firecloud] - [wfl.util :as util]) + [wfl.util :as util]) (:import [java.time OffsetDateTime] [java.time.temporal ChronoUnit])) +(defmacro do-or-nil-silently + "Value of `body` or `nil` if it throws, without logging exceptions. + See also [[wfl.util/do-or-nil]]." + [& body] + `(try (do ~@body) + (catch Exception x#))) + ;; Java chokes on colons in the version string of the jarfile manifest. ;; And GAE chokes on everything else. ;; (def the-version "A map of version information." - (letfn [(frob [{:keys [release path]}] [(util/basename path) release])] + (delay (let [built (-> (OffsetDateTime/now) (.truncatedTo ChronoUnit/SECONDS) .toInstant .toString) commit (util/shell! "git" "rev-parse" "HEAD") committed (->> commit - (util/shell! "git" "show" "-s" "--format=%cI") - OffsetDateTime/parse .toInstant .toString) - clean? (util/do-or-nil-silently - (util/shell! "git" "diff-index" "--quiet" "HEAD"))] - (into - {:version (or (System/getenv "WFL_VERSION") "devel") - :commit commit - :committed committed - :built built - :user (or (System/getenv "USER") "wfl")} - (map frob [aou/workflow-wdl - sg/workflow-wdl - wgs/workflow-wdl - xx/workflow-wdl]))))) + (util/shell! "git" "show" "-s" "--format=%cI") + OffsetDateTime/parse .toInstant .toString) + clean? (do-or-nil-silently + (util/shell! "git" "diff-index" "--quiet" "HEAD"))] + {:version (or (System/getenv "WFL_VERSION") "devel") + :commit commit + :committed committed + :built built + :user (or (System/getenv "USER") "wfl")}))) (defn write-the-version-file "Write VERSION.edn into the RESOURCES directory." @@ -57,7 +55,7 @@ :groupId (namespace artifactId) :name "WorkFlow Launcher" :url "https://github.com/broadinstitute/wfl.git" - :version (:version the-version)})) + :version (:version @the-version)})) (defn update-the-pom "Update the Project Object Model (pom.xml) file for this program." @@ -97,7 +95,11 @@ (let [derived (str/join "/" [".." "derived" "api"]) resources (io/file derived "resources") test-resources (io/file derived "test" "resources")] - (pprint the-version) - (write-the-version-file resources the-version) - (run! #(write-workflow-description test-resources %) (find-wdls)) - (System/exit 0))) + (try + (pprint @the-version) + (write-the-version-file resources @the-version) + (run! #(write-workflow-description test-resources %) (find-wdls)) + (System/exit 0) + (catch Throwable t + (pprint t) + (System/exit 1))))) diff --git a/api/deps.edn b/api/deps.edn index 806388ee5..d15428daf 100755 --- a/api/deps.edn +++ b/api/deps.edn @@ -5,39 +5,40 @@ "clojars" {:url "https://clojars.org/repo"}} :deps - {org.clojure/clojure {:mvn/version "1.10.1"} + {org.clojure/clojure {:mvn/version "1.10.3"} org.clojure/data.csv {:mvn/version "1.0.0"} - org.clojure/data.json {:mvn/version "0.2.6"} + org.clojure/data.json {:mvn/version "2.3.0"} org.clojure/data.xml {:mvn/version "0.2.0-alpha6"} - org.clojure/data.zip {:mvn/version "0.1.3"} - org.clojure/java.jdbc {:mvn/version "0.7.8"} + org.clojure/data.zip {:mvn/version "1.0.0"} + org.clojure/java.jdbc {:mvn/version "0.7.12"} org.clojure/tools.logging {:mvn/version "1.1.0"} - amperity/vault-clj {:mvn/version "1.0.1"} - clj-http/clj-http {:mvn/version "3.7.0"} - clj-time/clj-time {:mvn/version "0.15.1"} + amperity/vault-clj {:mvn/version "1.0.3"} + clj-http/clj-http {:mvn/version "3.9.1"} + clj-time/clj-time {:mvn/version "0.15.2"} javax.servlet/servlet-api {:mvn/version "2.5"} - javax/javaee-api {:mvn/version "7.0"} - metosin/reitit {:mvn/version "0.5.10" :exclusions [metosin/ring-swagger-ui]} - metosin/ring-http-response {:mvn/version "0.9.1"} - mysql/mysql-connector-java {:mvn/version "8.0.12"} + javax/javaee-api {:mvn/version "8.0.1"} + metosin/reitit {:mvn/version "0.5.13" :exclusions [metosin/ring-swagger-ui]} + metosin/ring-http-response {:mvn/version "0.9.2"} + mysql/mysql-connector-java {:mvn/version "8.0.25"} ojdbc14/ojdbc14 {:mvn/version "10.2.0.1.0"} - org.apache.tika/tika-core {:mvn/version "1.19.1"} - org.apache.logging.log4j/log4j-api {:mvn/version "2.13.3"} - org.apache.logging.log4j/log4j-core {:mvn/version "2.13.3"} - org.apache.logging.log4j/log4j-slf4j-impl {:mvn/version "2.13.3"} - org.postgresql/postgresql {:mvn/version "42.2.9"} + org.apache.commons/commons-lang3 {:mvn/version "3.8.1"} + org.apache.tika/tika-core {:mvn/version "1.26"} + org.apache.logging.log4j/log4j-api {:mvn/version "2.14.1"} + org.apache.logging.log4j/log4j-core {:mvn/version "2.14.1"} + org.apache.logging.log4j/log4j-slf4j-impl {:mvn/version "2.14.1"} + org.postgresql/postgresql {:mvn/version "42.2.20"} org.slf4j/slf4j-api {:mvn/version "1.7.30"} - ring-oauth2/ring-oauth2 {:mvn/version "0.1.4"} - ring/ring-core {:mvn/version "1.7.1"} + ring-oauth2/ring-oauth2 {:mvn/version "0.1.5"} + ring/ring-core {:mvn/version "1.9.3"} ring/ring-defaults {:mvn/version "0.3.2"} - ring/ring-devel {:mvn/version "1.7.1"} - ring/ring-jetty-adapter {:mvn/version "1.8.2"} - ring/ring-json {:mvn/version "0.5.0"} - ring/ring-servlet {:mvn/version "1.7.1"} - com.google.auth/google-auth-library-oauth2-http {:mvn/version "0.23.0"} - com.google.cloud.sql/mysql-socket-factory-connector-j-8 {:mvn/version "1.0.11"} - com.google.cloud.sql/postgres-socket-factory {:mvn/version "1.0.15"} - com.google.cloud.sql/jdbc-socket-factory-core {:mvn/version "1.0.15"}} + ring/ring-devel {:mvn/version "1.9.3"} + ring/ring-jetty-adapter {:mvn/version "1.9.3"} + ring/ring-json {:mvn/version "0.5.1"} + ring/ring-servlet {:mvn/version "1.9.3"} + com.google.auth/google-auth-library-oauth2-http {:mvn/version "0.25.5"} + com.google.cloud.sql/mysql-socket-factory-connector-j-8 {:mvn/version "1.2.3"} + com.google.cloud.sql/postgres-socket-factory {:mvn/version "1.2.3"} + com.google.cloud.sql/jdbc-socket-factory-core {:mvn/version "1.2.3"}} ;; derived/api/src must come first so environment.clj is found before ;; placeholder in src/. @@ -56,15 +57,15 @@ :main-opts ["-m" "cljfmt.main" "fix"]} :kondo - {:extra-deps {clj-kondo/clj-kondo {:mvn/version "2020.02.28-1"}} + {:extra-deps {clj-kondo/clj-kondo {:mvn/version "2021.04.23"}} :main-opts ["-m" "clj-kondo.main"]} :kibit - {:extra-deps {jonase/kibit {:mvn/version "0.1.6"}} + {:extra-deps {jonase/kibit {:mvn/version "0.1.8"}} :main-opts ["-e" "(use,'kibit.driver),(external-run,[\"src\"],nil)"]} :liquibase - {:extra-deps {org.liquibase/liquibase-core {:mvn/version "4.0.0" + {:extra-deps {org.liquibase/liquibase-core {:mvn/version "4.3.5" :exclusions [ch.qos.logback/logback-classic]}} :extra-paths ["test"] :main-opts ["-m" "wfl.tools.liquibase"]} @@ -73,20 +74,28 @@ {:main-opts ["-m" "wfl.main"]} :test - {:extra-deps {lambdaisland/kaocha {:mvn/version "1.0.632"} + {:extra-deps {lambdaisland/kaocha {:mvn/version "1.0.829"} org.apache.commons/commons-io {:mvn/version "1.3.2"} - org.liquibase/liquibase-core {:mvn/version "4.0.0" + org.liquibase/liquibase-core {:mvn/version "4.3.5" :exclusions [ch.qos.logback/logback-classic]}} :extra-paths ["test" "../derived/api/test/resources"] :main-opts ["-m" "kaocha.runner"]} :parallel-test - {:extra-deps {org.liquibase/liquibase-core {:mvn/version "4.0.0" + {:extra-deps {org.liquibase/liquibase-core {:mvn/version "4.3.5" :exclusions [ch.qos.logback/logback-classic]}} :extra-paths ["test"] :main-opts ["-m" "wfl.tools.parallel-runner"]} - :uberjar {:extra-deps {uberdeps/uberdeps {:mvn/version "1.0.3"}}} + :demo + {:extra-deps + {org.apache.commons/commons-io {:mvn/version "1.3.2"} + org.liquibase/liquibase-core {:mvn/version "4.3.5" + :exclusions [ch.qos.logback/logback-classic]}} + :extra-paths ["test" "../derived/api/test/resources"] + :main-opts ["-m" "wfl.system.cdc-covid19-surveillance-demo"]} + + :uberjar {:extra-deps {uberdeps/uberdeps {:mvn/version "1.0.4"}}} :prebuild {:extra-paths ["./build"] :exec-fn build/prebuild} diff --git a/api/module.mk b/api/module.mk index a95fd1dcd..9218dd858 100644 --- a/api/module.mk +++ b/api/module.mk @@ -76,10 +76,17 @@ $(SYSTEM): $(TEST_SCM_SRC) $(TEE) $(DERIVED_MODULE_DIR)/system.log @$(TOUCH) $@ -DOCKER_API_IMAGE := broadinstitute/workflow-launcher-$(MODULE):$(WFL_VERSION) +DOCKER_IMAGE_NAME := broadinstitute/workflow-launcher-$(MODULE) $(IMAGES): $(MODULE_DIR)/Dockerfile $(MODULE_DIR)/.dockerignore - $(DOCKER) build --file $< --tag $(DOCKER_API_IMAGE) $(PROJECT_DIR) + $(DOCKER) build \ + --file $< \ + --tag $(DOCKER_IMAGE_NAME):latest \ + --tag $(DOCKER_IMAGE_NAME):$(WFL_VERSION) \ + $(PROJECT_DIR) @$(TOUCH) $@ $(CLEAN): - -$(DOCKER) image rm -f $(DOCKER_API_IMAGE) + -$(DOCKER) image rm -f $(DOCKER_IMAGE_NAME):$(WFL_VERSION) + +$(DISTCLEAN): + -$(DOCKER) image rm -f $(DOCKER_IMAGE_NAME):latest diff --git a/api/src/wfl/api/handlers.clj b/api/src/wfl/api/handlers.clj index b7cc6e203..7b7faf7c0 100644 --- a/api/src/wfl/api/handlers.clj +++ b/api/src/wfl/api/handlers.clj @@ -1,19 +1,21 @@ (ns wfl.api.handlers - "Define handlers for API endpoints. Note that pipeline modules MUST be required here." - (:require [clojure.set :refer [rename-keys]] + "Define handlers for API endpoints. Require wfl.module namespaces here." + (:require [clojure.set :refer [rename-keys]] + [clojure.tools.logging :as log] [clojure.tools.logging.readable :as logr] - [ring.util.http-response :as response] - [wfl.api.workloads :as workloads] - [wfl.module.aou :as aou] + [ring.util.http-response :as response] + [wfl.api.workloads :as workloads] + [wfl.jdbc :as jdbc] + [wfl.module.aou :as aou] [wfl.module.arrays] [wfl.module.copyfile] + [wfl.module.covid] + [wfl.module.sg] [wfl.module.wgs] [wfl.module.xx] - [wfl.module.sg] - [wfl.jdbc :as jdbc] - [wfl.service.google.storage :as gcs] - [wfl.service.postgres :as postgres] - [wfl.util :as util])) + [wfl.service.google.storage :as gcs] + [wfl.service.postgres :as postgres] + [wfl.util :as util])) (defn succeed "A successful response with BODY." @@ -25,14 +27,8 @@ [body] (constantly (succeed body))) -(defn strip-internals - "Strip internal properties from the `workload` and its `workflows`." - [workload] - (let [prune #(apply dissoc % [:id :items])] - (prune (update workload :workflows (partial mapv prune))))) - (defn append-to-aou-workload - "Append new workflows to an existing started AoU workload describe in BODY of REQUEST." + "Append workflows described in BODY of REQUEST to a started AoU workload." [request] (let [{:keys [notifications uuid]} (get-in request [:parameters :body])] (logr/infof "appending %s samples to workload %s" (count notifications) uuid) @@ -51,7 +47,7 @@ (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (->> (assoc workload-request :creator email) (workloads/create-workload! tx) - strip-internals + util/to-edn succeed)))) (defn get-workload @@ -60,12 +56,23 @@ (let [{:keys [uuid project] :as query} (get-in request [:parameters :query])] (logr/info "GET /api/v1/workload with query: " query) (succeed - (map strip-internals + (map util/to-edn (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (cond uuid [(workloads/load-workload-for-uuid tx uuid)] project (workloads/load-workloads-with-project tx project) :else (workloads/load-workloads tx))))))) +(defn get-workflows + "Return the workflows managed by the workload." + [request] + (let [uuid (get-in request [:path-params :uuid])] + (log/infof "GET /api/v1/workload/%s/workflows" uuid) + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (workloads/load-workload-for-uuid tx uuid) + (workloads/workflows tx) + (mapv util/to-edn) + succeed)))) + (defn post-start "Start the workload with UUID in REQUEST." [request] @@ -75,7 +82,7 @@ (let [{:keys [started] :as workload} (workloads/load-workload-for-uuid tx uuid)] (-> (if-not started (workloads/start-workload! tx workload) workload) - strip-internals + util/to-edn succeed))))) (defn post-stop @@ -86,7 +93,7 @@ (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (->> (workloads/load-workload-for-uuid tx uuid) (workloads/stop-workload! tx) - strip-internals + util/to-edn succeed)))) (defn post-exec @@ -100,5 +107,5 @@ :email (assoc workload-request :creator) (workloads/execute-workload! tx) - strip-internals + util/to-edn succeed)))) diff --git a/api/src/wfl/api/routes.clj b/api/src/wfl/api/routes.clj index d324d7ded..bc4e6ea30 100644 --- a/api/src/wfl/api/routes.clj +++ b/api/src/wfl/api/routes.clj @@ -1,5 +1,5 @@ (ns wfl.api.routes - "Define routes for API endpoints" + "Define routes for API endpoints." (:require [clojure.string :as str] [clojure.tools.logging :as log] [clojure.tools.logging.readable :as logr] @@ -14,10 +14,12 @@ [reitit.swagger :as swagger] [wfl.api.handlers :as handlers] [wfl.api.workloads :as workloads] - [wfl.environment :as env] + [wfl.environment :as env] [wfl.api.spec :as spec] [wfl.wfl :as wfl]) - (:import (java.sql SQLException))) + (:import [java.sql SQLException] + [wfl.util UserException] + [org.apache.commons.lang3.exception ExceptionUtils])) (def endpoints "Endpoints exported by the server." @@ -55,6 +57,11 @@ :parameters {:query ::spec/workload-query} :responses {200 {:body ::spec/workload-responses}} :handler handlers/get-workload}}] + ["/api/v1/workload/:uuid/workflows" + {:get {:summary "Get workflows managed by the workload." + :parameters {:path {:uuid ::spec/uuid}} + :responses {200 {:body ::spec/workflows}} + :handler handlers/get-workflows}}] ["/api/v1/create" {:post {:summary "Create a new workload." :parameters {:body ::spec/workload-request} @@ -66,7 +73,7 @@ :responses {200 {:body ::spec/workload-response}} :handler handlers/post-start}}] ["/api/v1/stop" - {:post {:summary "Stop managing workflows for the workload specified by 'request'." + {:post {:summary "Stop managing the workload specified by 'request'." :parameters {:body ::spec/uuid-kv} :responses {200 {:body ::spec/workload-response}} :handler handlers/post-stop}}] @@ -95,10 +102,15 @@ [endpoints] (let [security-info {:swagger {:tags ["Authenticated"] :security [{:googleoauth []}]}}] - (letfn [(needs-security? [endpoint] (str/starts-with? (first endpoint) "/api")) - (write-security-info [method-description] (merge-with merge security-info method-description)) - (modify-method [method] (zipmap (keys method) (map write-security-info (vals method))))] - (vec (map #(if (needs-security? %) (apply vector (first %) (map modify-method (rest %))) %) + (letfn [(needs-security? [endpoint] + (str/starts-with? (first endpoint) "/api")) + (write-security-info [method-description] + (merge-with merge security-info method-description)) + (modify-method [method] + (zipmap (keys method) + (map write-security-info (vals method))))] + (vec (map #(if (needs-security? %) + (apply vector (first %) (map modify-method (rest %))) %) endpoints))))) ;; https://cljdoc.org/d/metosin/reitit/0.5.10/doc/ring/exception-handling-with-ring#exceptioncreate-exception-middleware @@ -106,12 +118,13 @@ (defn exception-handler "Top level exception handler. Prefer to use status and message from EXCEPTION and fallback to the provided STATUS and MESSAGE." - [status message exception request] + [status message exception {:keys [uri] :as _request}] {:status (or (:status (ex-data exception)) status) - :body {:message (or (.getMessage exception) message) - :exception (str (.getClass exception)) - :data (ex-data exception) - :uri (:uri request)}}) + :body (-> (when-let [cause (.getCause exception)] + {:cause (ExceptionUtils/getRootCauseMessage cause)}) + (merge {:uri uri + :message (or (.getMessage exception) message) + :details (-> exception ex-data (dissoc :status))}))}) (defn logging-exception-handler "Like [[exception-handler]] but also log information about the exception." @@ -129,6 +142,7 @@ {;; ex-data with :type :wfl/exception ::workloads/invalid-pipeline (partial exception-handler 400 "") ::workloads/workload-not-found (partial exception-handler 404 "") + UserException (partial exception-handler 400 "") ;; SQLException and all its child classes SQLException (partial logging-exception-handler 500 "SQL Exception") ;; handle clj-http Slingshot stone exceptions @@ -141,25 +155,25 @@ (ring/router (endpoint-swagger-auth-processor endpoints) {;; uncomment for easier debugging with coercion and middleware transformations - ;; :reitit.middleware/transform dev/print-request-diffs - ;; :exception pretty/exception + ;; :reitit.middleware/transform dev/print-request-diffs + ;; :exception pretty/exception :data {:coercion reitit.coercion.spec/coercion :muuntaja muuntaja-core/instance :middleware [exception-middleware ;; query-params & form-params parameters/parameters-middleware - ;; content-negotiation + ;; content-negotiation muuntaja/format-negotiate-middleware - ;; encoding response body + ;; encoding response body muuntaja/format-response-middleware - ;; decoding request body + ;; decoding request body muuntaja/format-request-middleware - ;; coercing response bodys + ;; coercing response bodys coercion/coerce-response-middleware - ;; coercing request parameters + ;; coercing request parameters coercion/coerce-request-middleware multipart/multipart-middleware]}}) - ;; get more correct http error responses on routes + ;; get more correct http error responses on routes (ring/create-default-handler {:not-found (fn [m] {:status 404 :body (format "Route %s not found" (:uri m))}) :method-not-allowed (fn [m] {:status 405 :body (format "Method %s not allowed" (name (:request-method m)))})}))) diff --git a/api/src/wfl/api/spec.clj b/api/src/wfl/api/spec.clj index 35b939b37..5523dd6a4 100644 --- a/api/src/wfl/api/spec.clj +++ b/api/src/wfl/api/spec.clj @@ -1,12 +1,20 @@ (ns wfl.api.spec "Define specs used in routes" - (:require [wfl.service.cromwell :as cromwell] - [clojure.spec.alpha :as s] - [wfl.util :as util] - [clojure.string :as str]) - (:import [java.util UUID])) + (:require [clojure.spec.alpha :as s] + [clojure.string :as str] + [wfl.service.cromwell :as cromwell] + [wfl.util :as util]) + (:import [java.time OffsetDateTime] + [java.util UUID] + [javax.mail.internet InternetAddress])) (defn uuid-string? [s] (uuid? (util/do-or-nil (UUID/fromString s)))) +(defn datetime-string? [s] (util/do-or-nil (OffsetDateTime/parse s))) + +(defn email-address? + "True if `s` is an email address." + [s] + (util/do-or-nil (or (.validate (InternetAddress. s)) true))) ;; shared (s/def ::base_file_name string?) @@ -15,14 +23,14 @@ (s/def ::contamination_vcf_index string?) (s/def ::cram_ref_fasta string?) (s/def ::cram_ref_fasta_index string?) -(s/def ::created inst?) -(s/def ::creator string?) +(s/def ::timestamp (s/or :instant inst? :datetime datetime-string?)) +(s/def ::created ::timestamp) +(s/def ::creator email-address?) (s/def ::cromwell string?) (s/def ::dbsnp_vcf string?) (s/def ::dbsnp_vcf_index string?) (s/def ::environment string?) -(s/def ::executor string?) -(s/def ::finished inst?) +(s/def ::finished ::timestamp) (s/def ::input string?) (s/def ::input_bam #(str/ends-with? % ".bam")) (s/def ::input_cram #(str/ends-with? % ".cram")) @@ -31,10 +39,10 @@ (s/def ::project string?) (s/def ::release string?) (s/def ::status (set (conj cromwell/statuses "skipped"))) -(s/def ::started inst?) -(s/def ::stopped inst?) -(s/def ::updated inst?) -(s/def ::uuid (s/and string? uuid-string?)) +(s/def ::started ::timestamp) +(s/def ::stopped ::timestamp) +(s/def ::updated ::timestamp) +(s/def ::uuid uuid-string?) (s/def ::uuid-kv (s/keys :req-un [::uuid])) (s/def ::version string?) (s/def ::wdl string?) @@ -42,30 +50,6 @@ (s/def ::common map?) (s/def ::workload-query (s/and (s/keys :opt-un [::uuid ::project]) #(not (and (:uuid %) (:project %))))) -(s/def ::workload-request (s/keys :opt-un [::common - ::input - ::items] - :req-un [(or ::executor ::cromwell) - ::output - ::pipeline - ::project])) -(s/def ::workload-response (s/keys :opt-un [::finished - ::input - ::started - ::stopped - ::wdl - ::workflows] - :req-un [::commit - ::created - ::creator - ::executor - ::output - ::pipeline - ::project - ::release - ::uuid - ::version])) -(s/def ::workload-responses (s/* ::workload-response)) ;; compound (s/def ::items (s/* ::workload-inputs)) @@ -76,12 +60,12 @@ :copyfile ::copyfile-workflow-inputs :wgs ::wgs-workflow-inputs :xx ::xx-workflow-inputs - :sg ::sg-workflow-inputs)) + :sg ::sg-workflow-inputs + :other map?)) +(s/def ::workflow (s/keys :req-un [::inputs] + :opt-un [::status ::updated ::uuid ::options])) (s/def ::workflows (s/* ::workflow)) -(s/def ::workflow - (s/keys :req-un [::inputs] - :opt-un [::status ::updated ::uuid ::options])) ;; aou (s/def ::analysis_version_number integer?) @@ -122,9 +106,108 @@ ::dbsnp_vcf_index ::input_cram])) -;; /api/v1/workflows -(s/def ::start string?) -(s/def ::end string?) -(s/def ::workflow-request (s/keys :req-un [::end - ::environment - ::start])) +(s/def ::column string?) +(s/def ::dataset string?) +(s/def ::entityType string?) +(s/def ::identifier string?) +(s/def ::fromOutputs map?) +(s/def ::fromSource string?) +(s/def ::labels (s/* util/label?)) +(s/def ::name string?) +(s/def ::methodConfiguration (s/and string? util/terra-namespaced-name?)) +(s/def ::methodConfigurationVersion integer?) +(s/def ::table string?) +(s/def ::snapshotReaders (s/* email-address?)) +(s/def ::watchers (s/* email-address?)) +(s/def ::workspace (s/and string? util/terra-namespaced-name?)) +(s/def ::snapshots (s/* ::uuid)) + +(s/def :batch/executor string?) +(s/def :covid/executor (s/keys :req-un [::name + ::fromSource + ::methodConfiguration + ::methodConfigurationVersion + ::workspace])) + +(s/def ::sink (s/keys :req-un [::name + ::entityType + ::fromOutputs + ::identifier + ::workspace])) + +(s/def ::tdr-source + (s/keys :req-un [::name + ::column + ::dataset + ::table + ::snapshotReaders] + :opt-un [::snapshots])) + +(s/def ::snapshot-list-source + (s/keys :req-un [::name ::snapshots])) + +(s/def ::source (s/or :dataset ::tdr-source + :snapshots ::snapshot-list-source)) + +;; This is the wrong thing to do. See [1] for more information. +;; As a consequence, I've included the keys for a covid pipeline as optional +;; inputs for batch workloads so that these keys are not removed during +;; coercion. +;; [1]: https://github.com/metosin/reitit/issues/494 +(s/def ::batch-workload-request + (s/keys :opt-un [::common + ::input + ::items + ::labels + ::output + ::sink + ::source + ::watchers] + :req-un [(or ::cromwell :batch/executor) + ::pipeline + ::project])) + +(s/def ::batch-workload-response (s/keys :opt-un [::finished + ::input + ::started + ::stopped + ::wdl] + :req-un [::commit + ::created + ::creator + :batch/executor + ::output + ::pipeline + ::project + ::release + ::uuid + ::version])) + +(s/def ::covid-workload-request (s/keys :req-un [:covid/executor + ::project + ::sink + ::source] + :opt-un [::labels + ::watchers])) + +(s/def ::covid-workload-response (s/keys :req-un [::created + ::creator + :covid/executor + ::labels + ::sink + ::source + ::uuid + ::version + ::watchers] + :opt-un [::finished + ::started + ::stopped + ::updated])) + +(s/def ::workload-request (s/or :batch ::batch-workload-request + :covid ::covid-workload-request)) + +(s/def ::workload-response (s/or :batch ::batch-workload-response + :covid ::covid-workload-response)) + +(s/def ::workload-responses (s/* ::workload-response)) diff --git a/api/src/wfl/api/workloads.clj b/api/src/wfl/api/workloads.clj index 92dd94997..c07eb4c8c 100644 --- a/api/src/wfl/api/workloads.clj +++ b/api/src/wfl/api/workloads.clj @@ -1,9 +1,8 @@ (ns wfl.api.workloads - (:require [clojure.string :as str] - [wfl.jdbc :as jdbc] - [wfl.service.postgres :as postgres] - [wfl.util :as util] - [clojure.tools.logging :as log])) + (:require [clojure.string :as str] + [clojure.tools.logging :as log] + [wfl.jdbc :as jdbc] + [wfl.util :as util])) ;; always derive from base :wfl/exception (derive ::invalid-pipeline :wfl/exception) @@ -30,6 +29,14 @@ "(transaction workload) -> workload" (fn [_ body] (:pipeline body))) +(defmulti workflows + "Use `tx` to return the workflows managed by the `workload`." + (fn [tx workload] (:pipeline workload))) + +(defmulti to-edn + "Return an EDN representation of the `workload` that will be shown to users." + (fn [workload] (:pipeline workload))) + ;; loading utilities (defmulti load-workload-impl "Load the workload given a TRANSACTION and a partially loaded WORKLOAD. @@ -91,27 +98,30 @@ ;; :default implementations (defmethod create-workload! :default - [_ body] + [_ {:keys [pipeline] :as request}] (throw (ex-info "Failed to create workload - no such pipeline" - {:cause body - :type ::invalid-pipeline}))) + {:request request + :pipeline pipeline + :type ::invalid-pipeline}))) (defmethod start-workload! :default - [_ body] + [_ {:keys [pipeline] :as workload}] (throw (ex-info "Failed to start workload - no such pipeline" - {:cause body - :type ::invalid-pipeline}))) + {:workload workload + :pipeline pipeline + :type ::invalid-pipeline}))) (defmethod stop-workload! :default - [_ body] + [_ {:keys [pipeline] :as workload}] (throw (ex-info "Failed to stop workload - no such pipeline" - {:cause body - :type ::invalid-pipeline}))) + {:workload workload + :pipeline pipeline + :type ::invalid-pipeline}))) (defmethod execute-workload! :default @@ -120,27 +130,34 @@ (defmethod update-workload! :default - [_ body] + [_ {:keys [pipeline] :as workload}] (throw (ex-info "Failed to update workload - no such pipeline" - {:cause body - :type ::invalid-pipeline}))) - -(defn default-load-workload-impl - [tx workload] - (letfn [(unnilify [m] (into {} (filter second m))) - (split-inputs [m] - (let [keep [:id :finished :status :updated :uuid :options]] - (assoc (select-keys m keep) :inputs (apply dissoc m keep)))) - (load-options [m] (update m :options (fnil util/parse-json "null")))] - (->> (postgres/get-table tx (:items workload)) - (mapv (comp unnilify split-inputs load-options)) - (assoc workload :workflows) - unnilify))) - -(defoverload load-workload-impl :default default-load-workload-impl) + {:workload workload + :pipeline pipeline + :type ::invalid-pipeline}))) + +(defmethod to-edn + :default + [{:keys [pipeline] :as workload}] + (throw + (ex-info "Failed to coerce workload to EDN - no such pipeline" + {:workload workload + :pipeline pipeline + :type ::invalid-pipeline}))) + +(defmethod load-workload-impl + :default + [_ {:keys [pipeline] :as workload}] + (throw + (ex-info "Failed to load workload - no such pipeline" + {:workload workload + :pipeline pipeline + :type ::invalid-pipeline}))) ;; Common workload operations +(defoverload util/to-edn :workload to-edn) + (defn saved-before? "Test if the `_workload` was saved before the `reference` version string. Version strings must be in the form \"major.minor.patch\"." diff --git a/api/src/wfl/environment.clj b/api/src/wfl/environment.clj index eeb7eb6c9..f0871797f 100644 --- a/api/src/wfl/environment.clj +++ b/api/src/wfl/environment.clj @@ -8,9 +8,6 @@ (declare getenv) -;; TODO: `is-known-cromwell-url?` in modules means new projects require new releases -;; since this is baked in code. Can we improve this? - (defn ^:private vault-secrets "Return the secrets at `path` in vault." [path] @@ -48,6 +45,8 @@ #(-> nil) "WFL_FIRECLOUD_URL" #(-> "https://api.firecloud.org") + "WFL_RAWLS_URL" + #(-> "https://rawls.dsde-dev.broadinstitute.org") ;; -- variables used in test code below this line -- "WFL_CROMWELL_URL" diff --git a/api/src/wfl/jdbc.clj b/api/src/wfl/jdbc.clj index 6c124982e..47efa19b8 100644 --- a/api/src/wfl/jdbc.clj +++ b/api/src/wfl/jdbc.clj @@ -1,7 +1,9 @@ (ns wfl.jdbc "clojure.tools.logging wrapping for clojure.java.jdbc" - (:require [clojure.java.jdbc :as jdbc] - [clojure.tools.logging.readable :as log])) + (:require [clojure.java.jdbc :as jdbc] + [clojure.tools.logging.readable :as log]) + (:import (clojure.lang IPersistentVector) + (java.sql PreparedStatement Array))) (def ^:private remember-db "Memoized helper to only print the db out the first time" @@ -21,99 +23,117 @@ (defmacro query "Logged alias for [[clojure.java.jdbc/query]]" ([db sql-params] - `(do - (log/trace "JDBC SQL query (without opts):" (format-db ~db) ~sql-params) - (jdbc/query ~db ~sql-params))) + `(let [db# ~db + sql-params# ~sql-params] + (log/trace "jdbc/query:" (format-db db#) sql-params#) + (jdbc/query db# sql-params#))) ([db sql-params opts] - `(do - (log/trace "JDBC SQL query:" (format-db ~db) ~sql-params ~opts) - (jdbc/query ~db ~sql-params ~opts)))) + `(let [db# ~db + sql-params# ~sql-params + opts# ~opts] + (log/trace "jdbc/query:" (format-db db#) sql-params# opts#) + (jdbc/query db# sql-params# opts#)))) (defmacro update! "Logged alias for [[clojure.java.jdbc/update!]]" ([db table set-map where-clause] - `(do - (log/info "JDBC SQL update! (without opts):" - (format-db ~db) ~table ~set-map ~where-clause) - (jdbc/update! ~db ~table ~set-map ~where-clause))) + `(let [db# ~db + table# ~table + set-map# ~set-map + where-clause# ~where-clause] + (log/info "jdbc/update!" (format-db db#) table# set-map# where-clause#) + (jdbc/update! db# table# set-map# where-clause#))) ([db table set-map where-clause opts] - `(do - (log/info "JDBC SQL update!:" - (format-db ~db) ~table ~set-map ~where-clause ~opts) - (jdbc/update! ~db ~table ~set-map ~where-clause ~opts)))) + `(let [db# ~db + table# ~table + set-map# ~set-map + where-clause# ~where-clause + opts# ~opts] + (log/info "jdbc/update!" (format-db db#) table# set-map# where-clause# opts#) + (jdbc/update! db# table# set-map# where-clause# opts#)))) (defmacro insert-multi! "Logged alias for [[clojure.java.jdbc/insert-multi!]]" ([db table rows] - `(do - (log/info "JDBC SQL insert-rows! (without opts):" - (format-db ~db) ~table ~rows) - (jdbc/insert-multi! ~db ~table ~rows))) + `(let [db# ~db + table# ~table + rows# ~rows] + (log/info "jdbc/insert-multi!" (format-db db#) table# rows#) + (jdbc/insert-multi! db# table# rows#))) ([db table cols-or-rows values-or-opts] - `(do - (if (map? values-or-opts) - (log/info "JDBC SQL insert-rows!:" - (format-db ~db) ~table ~cols-or-rows ~values-or-opts) - (log/info "JDBC SQL insert-cols! (without opts):" - (format-db ~db) ~table ~cols-or-rows ~values-or-opts)) - (jdbc/insert-multi! ~db ~table ~cols-or-rows ~values-or-opts))) + `(let [db# ~db + table# ~table + cols-or-rows# ~cols-or-rows + values-or-opts# ~values-or-opts] + (log/info "jdbc/insert-multi!" (format-db db#) table# cols-or-rows# values-or-opts#) + (jdbc/insert-multi! db# table# cols-or-rows# values-or-opts#))) ([db table cols values opts] - `(do - (log/info "JDBC SQL insert-cols!:" - (format-db ~db) ~table ~cols ~values ~opts) - (jdbc/insert-multi! ~db ~table ~cols ~values ~opts)))) + `(let [db# ~db + table# ~table + cols# ~cols + values# ~values + opts# ~opts] + (log/info "jdbc/insert-multi!" (format-db db#) table# cols# values# opts#) + (jdbc/insert-multi! db# table# cols# values# opts#)))) (defmacro execute! "Logged alias for [[clojure.java.jdbc/execute!]]" ([db sql-params] - `(do - (log/info "JDBC SQL execute! (without opts):" (format-db ~db) ~sql-params) - (jdbc/execute! ~db ~sql-params))) + `(let [db# ~db + sql-params# ~sql-params] + (log/info "jdbc/execute!" (format-db db#) sql-params#) + (jdbc/execute! db# sql-params#))) ([db sql-params opts] - `(do - (log/info "JDBC SQL execute!:" (format-db ~db) ~sql-params ~opts) - (jdbc/execute! ~db ~sql-params ~opts)))) + `(let [db# ~db + sql-params# ~sql-params + opts# ~opts] + (log/info "jdbc/execute!" (format-db db#) sql-params# opts#) + (jdbc/execute! db# sql-params# opts#)))) (defmacro db-do-commands "Logged alias for [[clojure.java.jdbc/db-do-commands]]" ([db sql-commands] - `(do - (log/info "JDBC SQL db-do-commands:" (format-db ~db) ~sql-commands) - (jdbc/db-do-commands ~db ~sql-commands))) + `(let [db# ~db + sql-commands# ~sql-commands] + (log/info "jbs/db-do-commands" (format-db db#) sql-commands#) + (jdbc/db-do-commands db# sql-commands#))) ([db transaction? sql-commands] - `(do - (log/info "JDBC SQL db-do-commands:" - (format-db ~db) ~transaction? ~sql-commands) - (jdbc/db-do-commands ~db ~transaction? ~sql-commands)))) + `(let [db# ~db + transaction?# ~transaction? + sql-commands# ~sql-commands] + (log/info "jbs/db-do-commands" (format-db db#) transaction?# sql-commands#) + (jdbc/db-do-commands db# transaction?# sql-commands#)))) (defmacro insert! "Logged alias for [[clojure.java.jdbc/insert!]]" ([db table row] - `(do - (log/info "JDBC SQL insert-rows! (without opts):" - (format-db ~db) ~table [~row]) - (jdbc/insert! ~db ~table ~row))) + `(let [db# ~db + table# ~table + row# ~row] + (log/info "jdbc/insert" (format-db db#) table# row#) + (jdbc/insert! db# table# row#))) ([db table cols-or-row values-or-opts] - `(do - (if (map? values-or-opts) - (log/info "JDBC SQL insert-rows!:" - (format-db ~db) ~table [~cols-or-row] ~values-or-opts) - (log/info "JDBC SQL insert-cols! (without opts):" - (format-db ~db) ~table ~cols-or-row [~values-or-opts])) - (jdbc/insert! ~db ~table ~cols-or-row ~values-or-opts))) + `(let [db# ~db + table# ~table + cols-or-row# ~cols-or-row + values-or-opts# ~values-or-opts] + (log/info "jdbc/insert" (format-db db#) table# cols-or-row# values-or-opts#) + (jdbc/insert! db# table# cols-or-row# values-or-opts#))) ([db table cols values opts] - `(do - (log/info "JDBC SQL insert-cols!:" - (format-db ~db) ~table ~cols [~values] ~opts) - (jdbc/insert! ~db ~table ~cols ~values ~opts)))) + `(let [db# ~db + table# ~table + cols# ~cols + values# ~values] + (log/info "jdbc/insert" (format-db db#) table# cols# values# opts) + "jdbc/insert" db# table# cols# values# opts))) (defmacro with-db-transaction "Logged alias for [[clojure.java.jdbc/with-db-transaction]]" [binding & body] - `(let [id# (rand-int 10000)] - (log/info "JDBC SQL transaction" id# "started to" - (format-db ~(second binding))) - (let [exe# (jdbc/with-db-transaction ~binding ~@body)] + `(let [id# (rand-int 10000) + init# ~(second binding)] + (log/info "JDBC transaction" id# "started to" (format-db init#)) + (let [exe# (jdbc/with-db-transaction [~(first binding) init#] ~@body)] (log/info "JDBC SQL transaction" id# "ended") exe#))) @@ -135,3 +155,20 @@ `(do (log/info "JBDC SQL connection made:" (format-db ~db-spec) ~opts) (jdbc/get-connection ~db-spec ~opts)))) + +;; Expertly copied and pasted from Stack Overflow: +;; https://stackoverflow.com/a/25786990 +(extend-protocol clojure.java.jdbc/ISQLParameter + IPersistentVector + (set-parameter [v ^PreparedStatement stmt ^long i] + (let [conn (.getConnection stmt) + meta (.getParameterMetaData stmt) + [head & rest] (.getParameterTypeName meta i)] + (if-let [elem-type (when (= head \_) (apply str rest))] + (.setObject stmt i (.createArrayOf conn elem-type (to-array v))) + (.setObject stmt i v))))) + +(extend-protocol clojure.java.jdbc/IResultSetReadColumn + Array + (result-set-read-column [val _ _] + (into [] (.getArray val)))) diff --git a/api/src/wfl/module/aou.clj b/api/src/wfl/module/aou.clj index 9c8f3509c..245c2628d 100644 --- a/api/src/wfl/module/aou.clj +++ b/api/src/wfl/module/aou.clj @@ -1,16 +1,15 @@ (ns wfl.module.aou "Process Arrays for the All Of Us project." - (:require [clojure.string :as str] - [clojure.tools.logging :as log] - [wfl.api.workloads :as workloads :refer [defoverload]] - [wfl.jdbc :as jdbc] - [wfl.module.batch :as batch] - [wfl.references :as references] - [wfl.service.cromwell :as cromwell] + (:require [clojure.string :as str] + [clojure.tools.logging :as log] + [wfl.api.workloads :as workloads :refer [defoverload]] + [wfl.jdbc :as jdbc] + [wfl.module.batch :as batch] + [wfl.references :as references] + [wfl.service.cromwell :as cromwell] [wfl.service.google.storage :as gcs] - [wfl.service.postgres :as postgres] - [wfl.util :as util] - [wfl.wfl :as wfl]) + [wfl.util :as util] + [wfl.wfl :as wfl]) (:import [java.sql Timestamp] [java.time OffsetDateTime] [java.util UUID])) @@ -280,8 +279,12 @@ pipeline [tx {:keys [started finished] :as workload}] (letfn [(update! [{:keys [id] :as workload}] - (postgres/update-workflow-statuses! tx workload) + (batch/update-workflow-statuses! tx workload) (when (:stopped workload) - (postgres/update-workload-status! tx workload)) + (batch/update-workload-status! tx workload)) (workloads/load-workload-for-id tx id))] (if (and started (not finished)) (update! workload) workload))) + +(defoverload workloads/workflows pipeline batch/pre-v0_4_0-load-workflows) +(defoverload workloads/load-workload-impl pipeline batch/load-batch-workload-impl) +(defoverload workloads/to-edn pipeline batch/workload-to-edn) diff --git a/api/src/wfl/module/arrays.clj b/api/src/wfl/module/arrays.clj index d71400729..7aed59d01 100644 --- a/api/src/wfl/module/arrays.clj +++ b/api/src/wfl/module/arrays.clj @@ -1,14 +1,14 @@ (ns wfl.module.arrays "Process Arrays for the Broad Genomics Platform." - (:require [clojure.data.json :as json] - [clojure.string :as str] - [wfl.api.workloads :as workloads :refer [defoverload]] - [wfl.jdbc :as jdbc] - [wfl.module.batch :as batch] - [wfl.references :as references] + (:require [clojure.data.json :as json] + [clojure.string :as str] + [wfl.api.workloads :as workloads :refer [defoverload]] + [wfl.jdbc :as jdbc] + [wfl.module.batch :as batch] + [wfl.references :as references] [wfl.service.firecloud :as firecloud] - [wfl.service.postgres :as postgres] - [wfl.util :as util]) + [wfl.service.postgres :as postgres] + [wfl.util :as util]) (:import [java.time OffsetDateTime])) (def pipeline "GPArrays") @@ -119,22 +119,26 @@ (defn start-arrays-workload! "Use transaction TX to start the WORKLOAD." [tx {:keys [items project uuid] :as workload}] - (let [now (OffsetDateTime/now) - methodconfig-ns (first (str/split project #"/"))] + (let [now (OffsetDateTime/now) + methodconfig-ns (first (str/split project #"/")) + methodconfig (str/join "/" [methodconfig-ns methodconfig-name])] (letfn [(submit! [{:keys [id inputs] :as _workflow}] - [id (firecloud/create-submission - project - (str/join "/" [methodconfig-ns methodconfig-name]) - (mapv inputs [:entity-type :entity-name]))]) - (update! [tx [id uuid]] - (when uuid - (jdbc/update! tx items - {:updated now :uuid uuid :status "Submitted"} - ["id = ?" id])))] - (let [ids-uuids (map submit! (:workflows workload))] + (let [entity (mapv inputs [:entity-type :entity-name])] + [id (firecloud/create-submission project methodconfig entity)])) + (update! [tx [id {:keys [submissionId]}]] + (jdbc/update! tx items + {:updated now :uuid submissionId :status "Submitted"} + ["id = ?" id]))] + (let [ids-uuids (map submit! (workloads/workflows tx workload))] (run! (partial update! tx) ids-uuids) (jdbc/update! tx :workload {:started now} ["uuid = ?" uuid]))))) +(def update-terra-workflow-statuses! + "Use `tx` to update `status` of Terra `workflows` in a `workload`." + (letfn [(get-terra-status [{:keys [project]} workflow] + (firecloud/get-workflow-status-by-entity project workflow))] + (batch/make-update-workflows get-terra-status))) + (defmethod workloads/create-workload! pipeline [tx request] @@ -144,25 +148,19 @@ (defmethod workloads/start-workload! pipeline [tx {:keys [id] :as workload}] - (do (start-arrays-workload! tx workload) - (workloads/load-workload-for-id tx id))) + (start-arrays-workload! tx workload) + (workloads/load-workload-for-id tx id)) (defmethod workloads/update-workload! pipeline [tx {:keys [started finished] :as workload}] (letfn [(update! [{:keys [id] :as workload}] - (postgres/update-terra-workflow-statuses! tx workload) - (postgres/update-workload-status! tx workload) + (update-terra-workflow-statuses! tx workload) + (batch/update-workload-status! tx workload) (workloads/load-workload-for-id tx id))] (if (and started (not finished)) (update! workload) workload))) -(defmethod workloads/load-workload-impl - pipeline - [tx {:keys [items] :as workload}] - (letfn [(unnilify [m] (into {} (filter second m)))] - (->> (postgres/get-table tx items) - (mapv (comp #(update % :inputs util/parse-json) unnilify)) - (assoc workload :workflows) - unnilify))) - -(defoverload workloads/stop-workload! pipeline batch/stop-workload!) +(defoverload workloads/load-workload-impl pipeline batch/load-batch-workload-impl) +(defoverload workloads/stop-workload! pipeline batch/stop-workload!) +(defoverload workloads/workflows pipeline batch/workflows) +(defoverload workloads/to-edn pipeline batch/workload-to-edn) diff --git a/api/src/wfl/module/batch.clj b/api/src/wfl/module/batch.clj index 43777e5c1..b65a24517 100644 --- a/api/src/wfl/module/batch.clj +++ b/api/src/wfl/module/batch.clj @@ -1,13 +1,78 @@ (ns wfl.module.batch "Some utilities shared between batch workloads in cromwell." - (:require [wfl.api.workloads :as workloads] - [wfl.jdbc :as jdbc] + (:require [clj-http.client :as http] + [clojure.string :as str] + [wfl.api.workloads :as workloads] + [wfl.auth :as auth] + [wfl.jdbc :as jdbc] [wfl.service.cromwell :as cromwell] [wfl.service.postgres :as postgres] - [wfl.util :as util] - [wfl.wfl :as wfl]) + [wfl.util :as util] + [wfl.wfl :as wfl]) (:import [java.time OffsetDateTime] - [java.util UUID])) + [java.util UUID] + [wfl.util UserException])) + +(defn ^:private cromwell-status + "`status` of the workflow with `uuid` in `cromwell`." + [cromwell uuid] + (-> (str/join "/" [cromwell "api" "workflows" "v1" uuid "status"]) + (http/get {:headers (auth/get-auth-header)}) + :body + util/parse-json + :status)) + +(def ^:private finished? + "Test if a workflow `:status` is in a terminal state." + (set (conj cromwell/final-statuses "skipped"))) + +(defn make-update-workflows [get-status!] + (fn [tx {:keys [items] :as workload}] + (letfn [(update! [{:keys [id uuid]} status] + (jdbc/update! tx items + {:status status + :updated (OffsetDateTime/now) + :uuid uuid} + ["id = ?" id]))] + (->> (workloads/workflows tx workload) + (remove (comp nil? :uuid)) + (remove (comp finished? :status)) + (run! #(update! % (get-status! workload %))))))) + +(def update-workflow-statuses! + "Use `tx` to update `status` of Cromwell `workflows` in a `workload`." + (letfn [(get-cromwell-status [{:keys [executor]} {:keys [uuid]}] + (if (util/uuid-nil? uuid) + "skipped" + (cromwell-status executor uuid)))] + (make-update-workflows get-cromwell-status))) + +(defn batch-update-workflow-statuses! + "Use `tx` to update the `status` of the workflows in `_workload`." + [tx {:keys [executor uuid items] :as _workoad}] + (let [uuid->status (->> {:label (str "workload:" uuid) :includeSubworkflows "false"} + (cromwell/query executor) + (map (juxt :id :status)))] + (letfn [(update! [[uuid status]] + (jdbc/update! tx items + {:status status :updated (OffsetDateTime/now)} + ["uuid = ?" uuid]))] + (run! update! uuid->status)))) + +(defn active-workflows + "Use `tx` to query all the workflows in `_workload` whose :status is not in + `finished?`" + [tx {:keys [items] :as _workload}] + (let [query "SELECT id FROM %s WHERE status IS NULL OR status NOT IN %s"] + (->> (util/to-quoted-comma-separated-list finished?) + (format query items) + (jdbc/query tx)))) + +(defn update-workload-status! + "Use `tx` to mark `workload` finished when all `workflows` are finished." + [tx {:keys [id] :as workload}] + (when (empty? (active-workflows tx workload)) + (jdbc/update! tx :workload {:finished (OffsetDateTime/now)} ["id = ?" id]))) (defn add-workload-table! "Use transaction `tx` to add a `CromwellWorkflow` table @@ -19,7 +84,7 @@ setter "UPDATE workload SET pipeline = ?::pipeline WHERE id = ?" [{:keys [id]}] (-> workload-request - (select-keys [:creator :executor :input :output :project]) + (select-keys [:creator :executor :input :output :project :watchers :labels]) (update :executor util/de-slashify) (merge (select-keys (wfl/get-the-version) [:commit :version])) (assoc :release release :wdl path :uuid (UUID/randomUUID)) @@ -31,52 +96,108 @@ [id table])) (defn load-batch-workload-impl - "Use transaction `tx` to load and associate the workflows in the `workload` - stored in a CromwellWorkflow table." - [tx {:keys [items] :as workload}] - (letfn [(unnilify [m] (into {} (filter second m))) - (load-inputs [m] (update m :inputs (fnil util/parse-json "null"))) + "Load workload metadata + trim any unused vars." + [_ workload] + (into {:type :workload} (filter second workload))) + +(defn pre-v0_4_0-load-workflows + [tx workload] + (letfn [(split-inputs [m] + (let [keep [:id :finished :status :updated :uuid :options]] + (assoc (select-keys m keep) :inputs (apply dissoc m keep)))) + (load-options [m] (update m :options (fnil util/parse-json "null")))] + (->> (postgres/get-table tx (:items workload)) + (mapv (comp util/unnilify split-inputs load-options))))) + +(defn ^:private load-batch-workflows + "Use transaction `tx` to load the workflows in the `_workload` stored in a + CromwellWorkflow table." + [tx {:keys [items] :as _workload}] + (letfn [(load-inputs [m] (update m :inputs (fnil util/parse-json "null"))) (load-options [m] (update m :options (fnil util/parse-json "null")))] (->> (postgres/get-table tx items) - (mapv (comp unnilify load-options load-inputs)) - (assoc workload :workflows) - load-options - unnilify))) + (mapv (comp util/unnilify load-options load-inputs))))) (defn submit-workload! - "Use transaction TX to start the WORKLOAD." - ([{:keys [uuid workflows]} url workflow-wdl make-cromwell-inputs! cromwell-label default-options] - (letfn [(update-workflow [workflow cromwell-uuid] - (assoc workflow :uuid cromwell-uuid - :status "Submitted" - :updated (OffsetDateTime/now))) - (submit-batch! [[options workflows]] - (map update-workflow - workflows - (cromwell/submit-workflows - url - workflow-wdl - (map (partial make-cromwell-inputs! url) workflows) - (util/deep-merge default-options options) - (merge cromwell-label {:workload uuid}))))] - (mapcat submit-batch! (group-by :options workflows))))) + "Submit the `workflows` to Cromwell with `url`." + [{:keys [uuid labels] :as _workload} + workflows + url + workflow-wdl + make-cromwell-inputs! + cromwell-label + default-options] + (letfn [(update-workflow [workflow cromwell-uuid] + (merge workflow {:uuid cromwell-uuid + :status "Submitted" + :updated (OffsetDateTime/now)})) + (submit-batch! [[options workflows]] + (map update-workflow + workflows + (cromwell/submit-workflows + url + workflow-wdl + (map (partial make-cromwell-inputs! url) workflows) + (util/deep-merge default-options options) + (merge + cromwell-label + {:workload uuid} + (into {} (map #(-> (str/split % #":" 2) (update 0 keyword)) labels))))))] + (->> workflows + (group-by :options) + (mapcat submit-batch!)))) (defn update-workload! "Use transaction TX to batch-update WORKLOAD statuses." [tx {:keys [started finished] :as workload}] (letfn [(update! [{:keys [id] :as workload}] - (postgres/batch-update-workflow-statuses! tx workload) - (postgres/update-workload-status! tx workload) + (batch-update-workflow-statuses! tx workload) + (update-workload-status! tx workload) (workloads/load-workload-for-id tx id))] (if (and started (not finished)) (update! workload) workload))) (defn stop-workload! "Use transaction TX to stop the WORKLOAD." - [tx {:keys [stopped finished id] :as workload}] + [tx {:keys [started stopped finished id] :as workload}] (letfn [(patch! [cols] (jdbc/update! tx :workload cols ["id = ?" id])) (stop! [{:keys [id] :as workload}] (let [now (OffsetDateTime/now)] (patch! {:stopped now}) (when-not (:started workload) (patch! {:finished now})) (workloads/load-workload-for-id tx id)))] + (when-not started + (throw (UserException. "Cannot stop workload before it's been started." + {:workload workload}))) (if-not (or stopped finished) (stop! workload) workload))) + +(defn workflows + "Return the workflows managed by the `workload`." + [tx workload] + (map + #(assoc % :type :batch-workflow) + (if (workloads/saved-before? "0.4.0" workload) + (pre-v0_4_0-load-workflows tx workload) + (load-batch-workflows tx workload)))) + +(defmethod util/to-edn :batch-workflow [workflow] (dissoc workflow :id :type)) + +(defn workload-to-edn + "Return a user-friendly EDN representation of the batch `workload`" + [workload] + (util/select-non-nil-keys + workload + [:commit + :created + :creator + :executor + :finished + :input + :output + :pipeline + :project + :release + :started + :stopped + :uuid + :version + :wdl])) diff --git a/api/src/wfl/module/copyfile.clj b/api/src/wfl/module/copyfile.clj index b8805b593..eb8939db4 100644 --- a/api/src/wfl/module/copyfile.clj +++ b/api/src/wfl/module/copyfile.clj @@ -1,12 +1,12 @@ (ns wfl.module.copyfile "A dummy module for smoke testing wfl/cromwell auth." - (:require [clojure.data.json :as json] - [clojure.string :as str] - [wfl.api.workloads :as workloads :refer [defoverload]] - [wfl.jdbc :as jdbc] - [wfl.module.batch :as batch] + (:require [clojure.data.json :as json] + [clojure.string :as str] + [wfl.api.workloads :as workloads :refer [defoverload]] + [wfl.jdbc :as jdbc] + [wfl.module.batch :as batch] [wfl.service.cromwell :as cromwell] - [wfl.util :as util]) + [wfl.util :as util]) (:import [java.time OffsetDateTime])) (def pipeline "copyfile") @@ -118,7 +118,7 @@ (defn start-copyfile-workload! "Use transaction TX to start _WORKLOAD." [tx {:keys [items uuid executor] :as workload}] - (let [executor (is-known-cromwell-url? executor) + (let [executor (is-known-cromwell-url? executor) default-options (make-workflow-options executor)] (letfn [(submit! [{:keys [id inputs options]}] [id (submit-workflow executor inputs @@ -128,7 +128,7 @@ (jdbc/update! tx items {:updated (OffsetDateTime/now) :uuid uuid :status "Submitted"} ["id = ?" id]))] - (run! (comp (partial update! tx) submit!) (:workflows workload)) + (run! (comp (partial update! tx) submit!) (workloads/workflows tx workload)) (jdbc/update! tx :workload {:started (OffsetDateTime/now)} ["uuid = ?" uuid])))) @@ -141,12 +141,8 @@ (start-copyfile-workload! tx workload) (workloads/load-workload-for-id tx id))) -(defoverload workloads/update-workload! pipeline batch/update-workload!) -(defoverload workloads/stop-workload! pipeline batch/stop-workload!) - -(defmethod workloads/load-workload-impl - pipeline - [tx workload] - (if (workloads/saved-before? "0.4.0" workload) - (workloads/default-load-workload-impl tx workload) - (batch/load-batch-workload-impl tx workload))) +(defoverload workloads/update-workload! pipeline batch/update-workload!) +(defoverload workloads/stop-workload! pipeline batch/stop-workload!) +(defoverload workloads/load-workload-impl pipeline batch/load-batch-workload-impl) +(defoverload workloads/workflows pipeline batch/workflows) +(defoverload workloads/to-edn pipeline batch/workload-to-edn) diff --git a/api/src/wfl/module/covid.clj b/api/src/wfl/module/covid.clj new file mode 100644 index 000000000..83eb1e75c --- /dev/null +++ b/api/src/wfl/module/covid.clj @@ -0,0 +1,1053 @@ +(ns wfl.module.covid + "Manage the Sarscov2IlluminaFull pipeline." + (:require [clojure.data :as data] + [clojure.edn :as edn] + [clojure.set :as set] + [clojure.string :as str] + [clojure.tools.logging :as log] + [wfl.api.workloads :as workloads :refer [defoverload]] + [wfl.jdbc :as jdbc] + [wfl.service.datarepo :as datarepo] + [wfl.service.firecloud :as firecloud] + [wfl.service.postgres :as postgres] + [wfl.service.rawls :as rawls] + [wfl.util :as util :refer [do-or-nil]] + [wfl.wfl :as wfl]) + (:import [clojure.lang ExceptionInfo] + [java.sql Timestamp] + [java.time OffsetDateTime ZoneId] + [java.time.format DateTimeFormatter] + [java.util UUID] + [wfl.util UserException])) + +(def pipeline nil) + +;; interfaces +;; queue operations +(defmulti peek-queue! + "Peek the first object from the `queue`, if one exists." + (fn [queue] (:type queue))) + +(defmulti pop-queue! + "Pop the first object from the `queue`. Throws if none exists." + (fn [queue] (:type queue))) + +(defmulti queue-length! + "Return the number of objects in the queue." + (fn [queue] (:type queue))) + +;; validation operations +(defmulti validate-or-throw + "Validate the `request` request." + (fn [request] (:name request))) + +(defmethod validate-or-throw :default + [{:keys [name] :as request}] + (throw (UserException. "Invalid request - unknown name" + (util/make-map name request)))) + +;; source operations +(defmulti create-source! + "Use `tx` and workload `id` to write the source to persisted storage and + return a [type item] pair to be written into the parent table." + (fn [tx id source-request] (:name source-request))) + +(defmulti load-source! + "Use `tx` to load the workload source with `source_type`." + (fn [tx workload] (:source_type workload))) + +(defmulti start-source! + "Use `tx` to start accepting data from the `source`." + (fn [tx source] (:type source))) + +(defmulti update-source! + "Update the source." + (fn [source] (:type source))) + +(defmulti stop-source! + "Use `tx` to stop accepting new data from the `source`." + (fn [tx source] (:type source))) + +;; executor operations +(defmulti create-executor! + "Use `tx` and workload `id` to write the executor to persisted storage and + return a [type item] pair to be written into the parent table." + (fn [tx id executor-request] (:name executor-request))) + +(defmulti update-executor! + "Update the executor with the `source`" + (fn [source executor] (:type executor))) + +(defmulti executor-workflows + "Use `tx` to return the workflows created by the `executor" + (fn [tx executor] (:type executor))) + +(defmulti load-executor! + "Use `tx` to load the workload executor with `executor_type`." + (fn [tx workload] (:executor_type workload))) + +;; sink operations +(defmulti create-sink! + "Use `tx` and workload `id` to write the sink to persisted storage and + return a [type item] pair to be written into the parent table." + (fn [tx id sink-request] (:name sink-request))) + +(defmulti update-sink! + "Update the sink with the `executor`" + (fn [executor sink] (:type sink))) + +(defmulti load-sink! + "Use `tx` to load the workload sink with `sink_type`." + (fn [tx workload] (:sink_type workload))) + +;; Processing "stage" operations +(defmulti done? + "Test if the processing stage is complete and will not process any more data" + (fn [stage] (:type stage))) + +;; Generic helpers +(defn ^:private utc-now + "Return OffsetDateTime/now in UTC." + [] + (OffsetDateTime/now (ZoneId/of "UTC"))) + +(defn ^:private load-record-by-id! [tx table id] + (let [query "SELECT * FROM %s WHERE id = ? LIMIT 1" + [record & _] (jdbc/query tx [(format query table) id])] + (when-not record + (throw (ex-info (str "No such record") {:id id :table table}))) + record)) + +;; Workload + +(defn ^:private patch-workload [tx {:keys [id]} colls] + (jdbc/update! tx :workload colls ["id = ?" id])) + +(def ^:private workload-metadata-keys + [:commit + :created + :creator + :executor + :finished + :labels + :sink + :source + :started + :stopped + :updated + :uuid + :version + :watchers]) + +(defn ^:private add-workload-metadata + "Use `tx` to record the workload metadata in `request` in the workload table + and return the ID the of the new row." + [tx {:keys [project] :as request}] + (letfn [(combine-labels [labels] + (->> (str "project:" project) + (conj labels) + set + sort + vec))] + (-> (update request :labels combine-labels) + (select-keys [:creator :watchers :labels :project]) + (merge (select-keys (wfl/get-the-version) [:commit :version])) + (assoc :executor "" + :output "" + :release "" + :wdl "" + :uuid (UUID/randomUUID)) + (->> (jdbc/insert! tx :workload) first :id)))) + +(def ^:private update-workload-query + "UPDATE workload + SET source_type = ?::source + , source_items = ? + , executor_type = ?::executor + , executor_items = ? + , sink_type = ?::sink + , sink_items = ? + WHERE id = ?") + +(defn ^:private create-covid-workload + [tx {:keys [source executor sink] :as request}] + (let [[source executor sink] (mapv validate-or-throw [source executor sink]) + id (add-workload-metadata tx request)] + (jdbc/execute! + tx + (concat [update-workload-query] + (create-source! tx id source) + (create-executor! tx id executor) + (create-sink! tx id sink) + [id])) + (workloads/load-workload-for-id tx id))) + +(defn ^:private load-covid-workload-impl [tx {:keys [id] :as workload}] + (let [src-exc-sink {:source (load-source! tx workload) + :executor (load-executor! tx workload) + :sink (load-sink! tx workload)}] + (as-> workload $ + (select-keys $ workload-metadata-keys) + (merge $ src-exc-sink) + (filter second $) + (into {:type :workload :id id} $)))) + +(defn ^:private start-covid-workload + "Start creating and managing workflows from the source." + [tx {:keys [started] :as workload}] + (letfn [(start [{:keys [id source] :as workload} now] + (start-source! tx source) + (patch-workload tx workload {:started now :updated now}) + (workloads/load-workload-for-id tx id))] + (if-not started (start workload (utc-now)) workload))) + +(defn ^:private update-covid-workload + "Use transaction `tx` to update `workload` statuses." + [tx {:keys [started finished] :as workload}] + (letfn [(update! [{:keys [id source executor sink] :as workload} now] + (-> (update-source! source) + (update-executor! executor) + (update-sink! sink)) + (patch-workload tx workload {:updated now}) + (when (every? done? [source executor sink]) + (patch-workload tx workload {:finished now})) + (workloads/load-workload-for-id tx id))] + (if (and started (not finished)) (update! workload (utc-now)) workload))) + +(defn ^:private stop-covid-workload + "Use transaction `tx` to stop the `workload` looking for new data." + [tx {:keys [started stopped finished] :as workload}] + (letfn [(stop! [{:keys [id source] :as workload} now] + (stop-source! tx source) + (patch-workload tx workload {:stopped now :updated now}) + (when-not (:started workload) + (patch-workload tx workload {:finished now})) + (workloads/load-workload-for-id tx id))] + (when-not started + (throw (UserException. "Cannot stop workload before it's been started." + {:workload workload}))) + (if-not (or stopped finished) (stop! workload (utc-now)) workload))) + +(defn ^:private workload-to-edn [workload] + (-> workload + (util/select-non-nil-keys workload-metadata-keys) + (dissoc :pipeline) + (update :source util/to-edn) + (update :executor util/to-edn) + (update :sink util/to-edn))) + +(defoverload workloads/create-workload! pipeline create-covid-workload) +(defoverload workloads/start-workload! pipeline start-covid-workload) +(defoverload workloads/update-workload! pipeline update-covid-workload) +(defoverload workloads/stop-workload! pipeline stop-covid-workload) +(defoverload workloads/load-workload-impl pipeline load-covid-workload-impl) +(defmethod workloads/workflows pipeline + [tx {:keys [executor] :as _workload}] + (executor-workflows tx executor)) +(defoverload workloads/to-edn pipeline workload-to-edn) + +;; Terra Data Repository Source +(def ^:private tdr-source-name "Terra DataRepo") +(def ^:private tdr-source-type "TerraDataRepoSource") +(def ^:private tdr-source-table "TerraDataRepoSource") +(def ^:private tdr-source-serialized-fields + {:dataset :dataset + :table :dataset_table + :column :table_column_name + :snapshotReaders :snapshot_readers}) + +(defn ^:private create-tdr-source [tx id request] + (let [create "CREATE TABLE %s OF TerraDataRepoSourceDetails (PRIMARY KEY (id))" + alter "ALTER TABLE %s ALTER COLUMN id ADD GENERATED ALWAYS AS IDENTITY" + details (format "%s_%09d" tdr-source-type id)] + (jdbc/db-do-commands tx [(format create details) (format alter details)]) + [tdr-source-type + (-> (select-keys request (keys tdr-source-serialized-fields)) + (update :dataset pr-str) + (set/rename-keys tdr-source-serialized-fields) + (assoc :details details) + (->> (jdbc/insert! tx tdr-source-table) first :id str))])) + +(defn ^:private load-tdr-source [tx {:keys [source_items] :as workload}] + (if-let [id (util/parse-int source_items)] + (-> (load-record-by-id! tx tdr-source-table id) + (set/rename-keys (set/map-invert tdr-source-serialized-fields)) + (assoc :type tdr-source-type) + (update :dataset edn/read-string)) + (throw (ex-info "source_items is not an integer" {:workload workload})))) + +(defn ^:private id-and-name [dataset] + (select-keys dataset [:id :name])) + +(defn ^:private throw-unless-column-exists + "Throw if `table` does not have `column` in `dataset`." + [table column dataset] + (when (->> table :columns (filter (comp #{column} :name)) empty?) + (throw (UserException. "Column not found" + {:column column + :table table + :dataset (id-and-name dataset)})))) + +(defn ^:private get-table-or-throw + "Throw or return the table from `dataset`" + [table-name dataset] + (let [[table & _] (->> (get-in dataset [:schema :tables]) + (filter (comp #{table-name} :name)))] + (when-not table + (throw (UserException. "Table not found" + {:table table-name + :dataset (id-and-name dataset)}))) + table)) + +(defn ^:private get-dataset-or-throw + "Return the dataset with `dataset-id` or throw" + [dataset-id] + (try + (datarepo/dataset dataset-id) + (catch ExceptionInfo e + (throw + (UserException. "Cannot access dataset" + {:dataset dataset-id :status (-> e ex-data :status)} + e))))) + +(defn verify-data-repo-source! + "Verify that the `dataset` exists and that WFL has the necessary permissions + to read it." + [{:keys [dataset table column skipValidation] :as source}] + (if skipValidation + source + (let [dataset (get-dataset-or-throw dataset)] + (-> (get-table-or-throw table dataset) + (throw-unless-column-exists column dataset)) + (assoc source :dataset dataset)))) + +(defn ^:private find-new-rows + "Find new rows in TDR by querying the dataset between the `interval`." + [{:keys [dataset table column] :as _source} interval] + (-> dataset + (datarepo/query-table-between table column interval [:datarepo_row_id]) + :rows + flatten)) + +(defn ^:private go-create-snapshot! + "Create snapshot in TDR from `dataset` body, `table` and `row-ids` then + write job info as well as rows into `source-details-name` table. + Snapshots will be readable by members of the `snapshotReaders` list. + `suffix` will be appended to the snapshot names." + [suffix {:keys [dataset table snapshotReaders] :as _source} row-ids] + (let [columns (->> (datarepo/all-columns dataset table) + (mapv :name) + (cons "datarepo_row_id"))] + (-> (datarepo/make-snapshot-request dataset columns table row-ids) + (update :name #(str % suffix)) + (assoc :readers snapshotReaders) + datarepo/create-snapshot-job))) + +(defn ^:private create-snapshots + "Create uniquely named snapshots in TDR with max partition size of 500, + using the frozen `now-obj`, from `row-ids`, return shards and TDR job-ids." + [source now-obj row-ids] + (let [dt-format (DateTimeFormatter/ofPattern "YYYYMMdd'T'HHmmss") + compact-now (.format now-obj dt-format)] + (letfn [(create-snapshot [idx shard] + [shard (-> (format "_%s_%s" compact-now idx) + (go-create-snapshot! source shard))])] + (->> row-ids + (partition-all 500) + (map vec) + (map-indexed create-snapshot))))) + +(defn ^:private get-pending-tdr-jobs [{:keys [details] :as _source}] + (let [query "SELECT id, snapshot_creation_job_id FROM %s + WHERE snapshot_creation_job_status = 'running' + ORDER BY id ASC"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (format query details) + (jdbc/query tx) + (map (juxt :id :snapshot_creation_job_id)))))) + +(defn ^:private check-tdr-job + "Check TDR job status for `job-id`, return a map with job-id, + snapshot_id and job_status if job has failed or succeeded, otherwise nil." + [job-id] + (let [{:keys [job_status] :as result} (datarepo/get-job-metadata job-id)] + (case job_status + "running" result + "succeeded" (assoc result :snapshot_id (:id (datarepo/get-job-result job-id))) + (do (log/warnf "Snapshot creation job %s failed!" job-id) + result)))) + +(defn ^:private write-snapshot-id + "Write `snapshot_id` and `job_status` into source `details` table + from the `_tdr-job-metadata` map, update timestamp with real now." + [{:keys [details] :as _source} + [id {:keys [job_status snapshot_id] :as _tdr-job-metadata}]] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (jdbc/update! tx details {:snapshot_creation_job_status job_status + :snapshot_id snapshot_id + :updated (utc-now)} + ["id = ?" id]))) + +(defn ^:private write-snapshots-creation-jobs + "Write the shards and corresponding snapshot creation jobs from + `shards->snapshot-jobs` into source `details` table, with the frozen `now`. + Also initialize all jobs statuses to running." + [{:keys [last_checked details] :as _source} now shards->snapshot-jobs] + (letfn [(make-record [[shard id]] + {:snapshot_creation_job_id id + :snapshot_creation_job_status "running" + :datarepo_row_ids shard + :start_time last_checked + :end_time now})] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (map make-record shards->snapshot-jobs) + (jdbc/insert-multi! tx details))))) + +(defn ^:private update-last-checked + "Update the `last_checked` field in source table with + the frozen `now`." + ([tx {:keys [id] :as _source} now] + (jdbc/update! tx tdr-source-table {:last_checked now} ["id = ?" id])) + ([source now] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (update-last-checked tx source now)))) + +(defn ^:private timestamp-to-offsetdatetime [^Timestamp t] + "Parse the Timestamp `t` into an `OffsetDateTime`." + (OffsetDateTime/ofInstant (.toInstant t) (ZoneId/of "UTC"))) + +(def ^:private bigquery-datetime-format + (DateTimeFormatter/ofPattern "yyyy-MM-dd'T'HH:mm:ss")) + +(defn ^:private find-and-snapshot-new-rows + "Create and enqueue snapshots from new rows in the `source` dataset." + [{:keys [last_checked] :as source} utc-now] + (let [shards->jobs (->> [(timestamp-to-offsetdatetime last_checked) utc-now] + (mapv #(.format % bigquery-datetime-format)) + (find-new-rows source) + (create-snapshots source utc-now))] + (when (seq shards->jobs) + (write-snapshots-creation-jobs source utc-now shards->jobs) + (update-last-checked source utc-now)))) + +(defn ^:private update-pending-snapshot-jobs + "Update the status of TDR snapshot jobs that are still 'running'." + [source] + (->> (get-pending-tdr-jobs source) + (map #(update % 1 check-tdr-job)) + (run! #(write-snapshot-id source %)))) + +(defn ^:private update-tdr-source + "Check for new data in TDR from `source`, create new snapshots, + insert resulting job creation ids into database and update the + timestamp for next time." + [{:keys [stopped] :as source}] + (when-not stopped + (find-and-snapshot-new-rows source (utc-now))) + (update-pending-snapshot-jobs source) + ;; load and return the source table + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (load-tdr-source tx {:source_items (str (:id source))}))) + +(defn ^:private start-tdr-source [tx source] + (update-last-checked tx source (utc-now))) + +(defn ^:private stop-tdr-source [tx {:keys [id] :as _source}] + (jdbc/update! tx tdr-source-table {:stopped (utc-now)} ["id = ?" id])) + +(defn ^:private peek-tdr-source-details + "Get first unconsumed snapshot record from `details` table." + [{:keys [details] :as _source}] + (let [query "SELECT * FROM %s + WHERE consumed IS NULL + AND snapshot_id IS NOT NULL + ORDER BY id ASC + LIMIT 1"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (format query details) + (jdbc/query tx) + first)))) + +(defn ^:private peek-tdr-source-queue + "Get first unconsumed snapshot from `source` queue." + [source] + (if-let [{:keys [snapshot_id] :as _record} (peek-tdr-source-details source)] + (datarepo/snapshot snapshot_id))) + +(defn ^:private tdr-source-queue-length + "Return the number of unconsumed snapshot records from `details` table." + [{:keys [details] :as _source}] + (let [query "SELECT COUNT(*) FROM %s + WHERE consumed IS NULL + AND snapshot_creation_job_status <> 'failed'"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (format query details) + (jdbc/query tx) + first + :count)))) + +(defn ^:private pop-tdr-source-queue + "Consume first unconsumed snapshot record in `details` table, or throw if none." + [{:keys [details] :as source}] + (if-let [{:keys [id] :as _record} (peek-tdr-source-details source)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (let [now (utc-now)] + (jdbc/update! tx details {:consumed now :updated now} ["id = ?" id]))) + (throw (ex-info "No snapshots in queue" {:source source})))) + +(defn ^:private tdr-source-done? [{:keys [stopped] :as source}] + (and stopped (zero? (queue-length! source)))) + +(defn ^:private tdr-source-to-edn [source] + (-> source + (util/select-non-nil-keys (keys tdr-source-serialized-fields)) + (update :dataset :id) + (assoc :name tdr-source-name))) + +(defoverload validate-or-throw tdr-source-name verify-data-repo-source!) + +(defoverload create-source! tdr-source-name create-tdr-source) +(defoverload start-source! tdr-source-type start-tdr-source) +(defoverload update-source! tdr-source-type update-tdr-source) +(defoverload stop-source! tdr-source-type stop-tdr-source) + +(defoverload load-source! tdr-source-type load-tdr-source) +(defoverload peek-queue! tdr-source-type peek-tdr-source-queue) +(defoverload pop-queue! tdr-source-type pop-tdr-source-queue) +(defoverload queue-length! tdr-source-type tdr-source-queue-length) + +(defoverload done? tdr-source-type tdr-source-done?) + +(defoverload util/to-edn tdr-source-type tdr-source-to-edn) + +;; TDR Snapshot List Source +(def ^:private tdr-snapshot-list-name "TDR Snapshots") +(def ^:private tdr-snapshot-list-type "TDRSnapshotListSource") + +(defn ^:private validate-tdr-snapshot-list + [{:keys [skipValidation] :as source}] + (letfn [(snapshot-or-throw [snapshot-id] + (try + (datarepo/snapshot snapshot-id) + (catch ExceptionInfo e + (throw (UserException. "Cannot access snapshot" + {:snapshot snapshot-id + :status (-> e ex-data :status)} + e)))))] + (if skipValidation + source + (update source :snapshots #(mapv snapshot-or-throw %))))) + +(defn ^:private create-tdr-snapshot-list [tx id {:keys [snapshots] :as _request}] + (let [create "CREATE TABLE %s OF ListSource (PRIMARY KEY (id))" + alter "ALTER TABLE %s ALTER COLUMN id ADD GENERATED ALWAYS AS IDENTITY" + details (format "%s_%09d" tdr-snapshot-list-type id)] + (jdbc/db-do-commands tx [(format create details) (format alter details)]) + (jdbc/insert-multi! tx details (map #(-> {:item (pr-str %)}) snapshots)) + [tdr-snapshot-list-type details])) + +(defn ^:private load-tdr-snapshot-list + [tx {:keys [source_items] :as _workload}] + (when-not (postgres/table-exists? tx source_items) + (throw (ex-info "Failed to load tdr-snapshot-list: no such table" + {:table source_items}))) + {:type tdr-snapshot-list-type + :items source_items + :snapshots (postgres/get-table tx source_items)}) + +(defn ^:private start-tdr-snapshot-list [_ source] source) +(defn ^:private stop-tdr-snapshot-list [_ source] source) +(defn ^:private update-tdr-snapshot-list [source] source) + +(defn ^:private peek-tdr-snapshot-list [{:keys [items] :as _source}] + (let [query "SELECT * FROM %s + WHERE consumed IS NULL + ORDER BY id ASC + LIMIT 1"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (format query items) + (jdbc/query tx) + first)))) + +(defn ^:private tdr-snapshot-list-queue-length [{:keys [items] :as _source}] + (let [query "SELECT COUNT (*) FROM %s WHERE consumed IS NULL"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (format query items) + (jdbc/query tx) + first + :count)))) + +(defn ^:private pop-tdr-snapshot-list [{:keys [items] :as source}] + (if-let [{:keys [id]} (peek-tdr-snapshot-list source)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (jdbc/update! tx items {:consumed (utc-now)} ["id = ?" id])) + (throw (ex-info "Attempt to pop empty queue" {:source source})))) + +(defn ^:private tdr-snapshot-list-done? [source] + (zero? (queue-length! source))) + +(defn ^:private tdr-snapshot-list-to-edn [source] + (let [read-snapshot-id (comp :id edn/read-string :item)] + (-> (select-keys source [:snapshots]) + (assoc :name tdr-snapshot-list-name) + (update :snapshots #(map read-snapshot-id %))))) + +(defoverload validate-or-throw tdr-snapshot-list-name validate-tdr-snapshot-list) + +(defoverload create-source! tdr-snapshot-list-name create-tdr-snapshot-list) +(defoverload start-source! tdr-snapshot-list-type start-tdr-snapshot-list) +(defoverload stop-source! tdr-snapshot-list-type stop-tdr-snapshot-list) +(defoverload update-source! tdr-snapshot-list-type update-tdr-snapshot-list) +(defoverload load-source! tdr-snapshot-list-type load-tdr-snapshot-list) + +(defoverload peek-queue! tdr-snapshot-list-type (comp edn/read-string :item peek-tdr-snapshot-list)) +(defoverload queue-length! tdr-snapshot-list-type tdr-snapshot-list-queue-length) +(defoverload pop-queue! tdr-snapshot-list-type pop-tdr-snapshot-list) + +(defoverload done? tdr-snapshot-list-type tdr-snapshot-list-done?) + +(defoverload util/to-edn tdr-snapshot-list-type tdr-snapshot-list-to-edn) + +;; Terra Executor +(def ^:private terra-executor-name "Terra") +(def ^:private terra-executor-type "TerraExecutor") +(def ^:private terra-executor-table "TerraExecutor") +(def ^:private terra-executor-serialized-fields + {:workspace :workspace + :methodConfiguration :method_configuration + :methodConfigurationVersion :method_configuration_version + :fromSource :from_source}) + +(defn ^:private create-terra-executor [tx id request] + (let [create "CREATE TABLE %s OF TerraExecutorDetails (PRIMARY KEY (id))" + alter "ALTER TABLE %s ALTER COLUMN id ADD GENERATED ALWAYS AS IDENTITY" + details (format "%s_%09d" terra-executor-type id)] + (jdbc/db-do-commands tx [(format create details) (format alter details)]) + [terra-executor-type + (-> (select-keys request (keys terra-executor-serialized-fields)) + (update :fromSource pr-str) + (set/rename-keys terra-executor-serialized-fields) + (assoc :details details) + (->> (jdbc/insert! tx terra-executor-table) first :id str))])) + +(defn ^:private load-terra-executor [tx {:keys [executor_items] :as workload}] + (if-let [id (util/parse-int executor_items)] + (-> (load-record-by-id! tx terra-executor-table id) + (assoc :type terra-executor-type) + (set/rename-keys (set/map-invert terra-executor-serialized-fields)) + (update :fromSource edn/read-string)) + (throw (ex-info "Invalid executor_items" {:workload workload})))) + +(defn ^:private workspace-or-throw [workspace] + (try + (firecloud/workspace workspace) + (catch ExceptionInfo cause + (throw (UserException. + "Cannot access workspace" + {:workspace workspace + :status (-> cause ex-data :status)} + cause))))) + +(defn ^:private method-config-or-throw [workspace methodconfig] + (try + (firecloud/get-method-configuration workspace methodconfig) + (catch ExceptionInfo cause + (throw (UserException. + "Cannot access method configuration in workspace" + {:workspace workspace + :methodConfiguration methodconfig + :status (-> cause ex-data :status)} + cause))))) + +(defn ^:private throw-on-method-config-version-mismatch + [{:keys [methodConfigVersion] :as methodconfig} expected] + (when-not (== expected methodConfigVersion) + (throw (UserException. + "Unexpected method configuration version" + {:methodConfiguration methodconfig + :expected expected + :actual methodConfigVersion})))) + +(defn verify-terra-executor + "Verify the method-configuration exists." + [{:keys [skipValidation + workspace + methodConfiguration + methodConfigurationVersion + fromSource] :as executor}] + (when-not skipValidation + (workspace-or-throw workspace) + (when-not (= "importSnapshot" fromSource) + (throw + (UserException. "Unsupported coercion" (util/make-map fromSource)))) + (-> (method-config-or-throw workspace methodConfiguration) + (throw-on-method-config-version-mismatch methodConfigurationVersion))) + executor) + +(defn ^:private from-source + "Coerce `source-item` to form understood by `executor` via `fromSource`." + [{:keys [workspace fromSource] :as executor} + {:keys [name id] :as _source-item}] + (cond (= "importSnapshot" fromSource) + (rawls/create-or-get-snapshot-reference workspace id name) + :else + (throw (ex-info "Unknown fromSource" {:executor executor})))) + +(defn ^:private update-method-configuration! + "Update `methodConfiguration` in `workspace` with snapshot reference `name` + as :dataReferenceName via Firecloud. + Update executor table record ID with incremented `methodConfigurationVersion`." + [{:keys [id + workspace + methodConfiguration + methodConfigurationVersion] :as _executor} + {:keys [name] :as _reference}] + (let [current (method-config-or-throw workspace methodConfiguration) + _ (throw-on-method-config-version-mismatch + current methodConfigurationVersion) + inc'd (inc methodConfigurationVersion)] + (->> (assoc current :dataReferenceName name :methodConfigVersion inc'd) + (firecloud/update-method-configuration workspace methodConfiguration)) + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (jdbc/update! tx terra-executor-table + {:method_configuration_version inc'd} + ["id = ?" id])))) + +(defn ^:private create-submission! + "Update `methodConfiguration` to use `reference`. + Create and return submission in `workspace` for `methodConfiguration` via Firecloud." + [{:keys [workspace methodConfiguration] :as executor} reference] + (update-method-configuration! executor reference) + (firecloud/submit-method workspace methodConfiguration)) + +(defn ^:private allocate-submission + "Write or allocate workflow records for `submission` in `details` table." + [{:keys [details] :as _executor} + {:keys [referenceId] :as _reference} + {:keys [submissionId workflows] :as _submission}] + (letfn [(to-row [now {:keys [status workflowId entityName] :as _workflow}] + {:reference referenceId + :submission submissionId + :workflow workflowId + :entity entityName + :status status + :updated now})] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (map (partial to-row (utc-now)) workflows) + (jdbc/insert-multi! tx details))))) + +;; Workflows in newly created firecloud submissions may not have been scheduled +;; yet and thus do not have a workflow uuid. Thus, we first "allocate" the +;; workflow in the database and then later assign workflow uuids. +(defn ^:private update-unassigned-workflow-uuids! + "Assign workflow uuids from previous submissions" + [{:keys [workspace details] :as executor}] + (letfn [(read-a-submission-without-workflows [] + (let [query "SELECT id, submission, entity FROM %s + WHERE submission IN ( + SELECT submission FROM %s WHERE workflow IS NULL + LIMIT 1 + )"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (let [records (jdbc/query tx (format query details details))] + (when-first [{:keys [submission]} records] + [submission records]))))) + (zip-record [{:keys [entity] :as record} + {:keys [workflowId workflowEntity status]}] + (when-not (= entity workflowEntity) + (throw (ex-info "Failed to write workflow uuid: entity did not match" + {:expected entity + :actual workflowEntity + :executor executor}))) + (assoc record :workflow workflowId :status status)) + (write-workflow-statuses [now records] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (run! + (fn [{:keys [id workflow status]}] + (jdbc/update! tx details + {:status status :workflow workflow :updated now} + ["id = ?" id])) + records)))] + (when-let [[submission records] (read-a-submission-without-workflows)] + (let [{:keys [workflows]} (firecloud/get-submission workspace submission)] + (when-not (== (count records) (count workflows)) + (throw (ex-info "Allocated more records than created workflows" + {:submission submission :executor executor}))) + (->> workflows + (map #(update % :workflowEntity :entityName)) + (sort-by :workflowEntity) + (map zip-record (sort-by :entity records)) + (write-workflow-statuses (utc-now))))))) + +(defn ^:private update-terra-workflow-statuses! + "Update statuses in DETAILS table for active or failed WORKSPACE workflows. + Return EXECUTOR." + [{:keys [workspace details] :as _executor}] + (letfn [(read-active-or-failed-workflows [] + (let [query "SELECT * FROM %s + WHERE submission IS NOT NULL + AND workflow IS NOT NULL + AND status NOT IN ('Succeeded', 'Aborted') + ORDER BY id ASC"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (jdbc/query tx (format query details))))) + (update-status-from-firecloud + [{:keys [submission workflow] :as record}] + (->> (firecloud/get-workflow workspace submission workflow) + :status + (assoc record :status))) + (write-workflow-statuses [now records] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (run! + (fn [{:keys [id status] :as _record}] + (jdbc/update! tx details {:status status :updated now} + ["id = ?" id])) + (sort-by :entity records))))] + (->> (read-active-or-failed-workflows) + (mapv update-status-from-firecloud) + (write-workflow-statuses (utc-now))))) + +(defn ^:private update-terra-executor + "Create new submission from new `source` snapshot if available, + writing its workflows to `details` table. + Update statuses for active or failed workflows in `details` table. + Return `executor`." + [source executor] + (when-let [snapshot (peek-queue! source)] + (let [reference (from-source executor snapshot) + submission (create-submission! executor reference)] + (allocate-submission executor reference submission) + (pop-queue! source))) + (update-unassigned-workflow-uuids! executor) + (update-terra-workflow-statuses! executor) + executor) + +(defn ^:private combine-record-workflow-and-outputs + [{:keys [updated] :as _record} + {:keys [workflowName] :as workflow} + firecloud-outputs] + (let [prefix (str workflowName ".") + outputs (-> firecloud-outputs + (get-in [:tasks (keyword workflowName) :outputs]) + (util/unprefix-keys prefix))] + (-> (assoc workflow :updated updated :outputs outputs) + (update :inputs #(util/unprefix-keys % prefix)) + (set/rename-keys {:id :uuid}) + (util/select-non-nil-keys [:inputs :uuid :status :outputs :updated])))) + +(defn ^:private peek-terra-executor-details + "Get first unconsumed successful workflow record from `details` table." + [{:keys [details] :as _executor}] + (let [query "SELECT * FROM %s + WHERE consumed IS NULL + AND status = 'Succeeded' + ORDER BY id ASC + LIMIT 1"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (format query details) + (jdbc/query tx) + first)))) + +(defn ^:private peek-terra-executor-queue + "Get first unconsumed successful workflow from `executor` queue." + [{:keys [workspace] :as executor}] + (when-let [{:keys [submission workflow] :as record} + (peek-terra-executor-details executor)] + (combine-record-workflow-and-outputs + record + (firecloud/get-workflow workspace submission workflow) + (firecloud/get-workflow-outputs workspace submission workflow)))) + +(defn ^:private pop-terra-executor-queue + "Consume first unconsumed successful workflow record in `details` table, + or throw if none." + [{:keys [details] :as executor}] + (if-let [{:keys [id] :as _record} (peek-terra-executor-details executor)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (let [now (utc-now)] + (jdbc/update! tx details {:consumed now :updated now} ["id = ?" id]))) + (throw (ex-info "No successful workflows in queue" {:executor executor})))) + +(defn ^:private terra-executor-queue-length + "Return the number workflows in the `_executor` queue that are yet to be + consumed." + [{:keys [details] :as _executor}] + (let [query "SELECT COUNT(*) FROM %s + WHERE consumed IS NULL + AND status NOT IN ('Failed', 'Aborted')"] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> (format query details) + (jdbc/query tx) + first + :count)))) + +(defn ^:private terra-executor-workflows + [tx {:keys [workspace details] :as _executor}] + (when-not (postgres/table-exists? tx details) + (throw (ex-info "Missing executor details table" {:table details}))) + (letfn [(from-record [{:keys [workflow submission status] :as record}] + (combine-record-workflow-and-outputs + record + (firecloud/get-workflow workspace submission workflow) + (when (= "Succeeded" status) + (firecloud/get-workflow-outputs workspace submission workflow))))] + (let [query "SELECT * FROM %s WHERE workflow IS NOT NULL ORDER BY id ASC"] + (map from-record (jdbc/query tx (format query details)))))) + +(defn ^:private terra-executor-done? [executor] + (zero? (queue-length! executor))) + +(defn ^:private terra-executor-to-edn [executor] + (-> executor + (util/select-non-nil-keys (keys terra-executor-serialized-fields)) + (assoc :name terra-executor-name))) + +(defoverload validate-or-throw terra-executor-name verify-terra-executor) + +(defoverload create-executor! terra-executor-name create-terra-executor) +(defoverload update-executor! terra-executor-type update-terra-executor) +(defoverload load-executor! terra-executor-type load-terra-executor) +(defoverload executor-workflows terra-executor-type terra-executor-workflows) + +(defoverload peek-queue! terra-executor-type peek-terra-executor-queue) +(defoverload pop-queue! terra-executor-type pop-terra-executor-queue) +(defoverload queue-length! terra-executor-type terra-executor-queue-length) + +(defoverload done? terra-executor-type terra-executor-done?) + +(defoverload util/to-edn terra-executor-type terra-executor-to-edn) + +;; Terra Workspace Sink +(def ^:private terra-workspace-sink-name "Terra Workspace") +(def ^:private terra-workspace-sink-type "TerraWorkspaceSink") +(def ^:private terra-workspace-sink-table "TerraWorkspaceSink") +(def ^:private terra-workspace-sink-serialized-fields + {:workspace :workspace + :entityType :entity_type + :fromOutputs :from_outputs + :identifier :identifier}) + +(defn ^:private create-terra-workspace-sink [tx id request] + (let [create "CREATE TABLE %s OF TerraWorkspaceSinkDetails (PRIMARY KEY (id))" + alter "ALTER TABLE %s ALTER COLUMN id ADD GENERATED ALWAYS AS IDENTITY" + details (format "%s_%09d" terra-workspace-sink-type id)] + (jdbc/db-do-commands tx [(format create details) (format alter details)]) + [terra-workspace-sink-type + (-> (select-keys request (keys terra-workspace-sink-serialized-fields)) + (update :fromOutputs pr-str) + (set/rename-keys terra-workspace-sink-serialized-fields) + (assoc :details details) + (->> (jdbc/insert! tx terra-workspace-sink-table) first :id str))])) + +(defn ^:private load-terra-workspace-sink [tx {:keys [sink_items] :as workload}] + (if-let [id (util/parse-int sink_items)] + (-> (load-record-by-id! tx terra-workspace-sink-table id) + (set/rename-keys (set/map-invert terra-workspace-sink-serialized-fields)) + (update :fromOutputs edn/read-string) + (assoc :type terra-workspace-sink-type)) + (throw (ex-info "Invalid sink_items" {:workload workload})))) + +(def unknown-entity-type-error-message + "The entityType was not found in workspace.") + +(def malformed-from-outputs-error-message + (str/join " " ["fromOutputs must define a mapping from workflow outputs" + "to the attributes of entityType."])) + +(def unknown-attributes-error-message + (str/join " " ["Found additional attributes in fromOutputs that are not" + "present in the entityType."])) + +(defn ^:private verify-terra-sink! + "Verify that the WFL has access the `workspace`." + [{:keys [entityType fromOutputs skipValidation workspace] :as sink}] + (when-not skipValidation + (workspace-or-throw workspace) + (let [entity-type (keyword entityType) + entity-types (firecloud/list-entity-types workspace) + types (-> entity-types keys set)] + (when-not (types entity-type) + (throw (UserException. unknown-entity-type-error-message + (util/make-map entityType types workspace)))) + (when-not (map? fromOutputs) + (throw (UserException. malformed-from-outputs-error-message + (util/make-map entityType fromOutputs)))) + (let [attributes (->> (get-in entity-types [entity-type :attributeNames]) + (cons (str entityType "_id")) + (mapv keyword)) + [missing _ _] (data/diff (set (keys fromOutputs)) (set attributes))] + (when (seq missing) + (throw (UserException. unknown-attributes-error-message + {:entityType entityType + :attributes (sort attributes) + :missing (sort missing) + :fromOutputs fromOutputs})))))) + sink) + +;; visible for testing +(defn rename-gather + "Transform the `values` using the transformation defined in `mapping`." + [values mapping] + (letfn [(literal? [x] (str/starts-with? x "$")) + (go! [v] + (cond (literal? v) (subs v 1 (count v)) + (string? v) (values (keyword v)) + (map? v) (rename-gather values v) + (coll? v) (keep go! v) + :else (throw (ex-info "Unknown operation" + {:operation v}))))] + (into {} (for [[k v] mapping] [k (go! v)])))) + +(defn ^:private terra-workspace-sink-to-attributes + [{:keys [outputs] :as workflow} fromOutputs] + (when-not (map? fromOutputs) + (throw (IllegalStateException. "fromOutputs is malformed"))) + (try + (rename-gather outputs fromOutputs) + (catch Exception cause + (throw (ex-info "Failed to coerce workflow outputs to attribute values" + {:fromOutputs fromOutputs :workflow workflow} + cause))))) + +(defn ^:private entity-exists? + "True when the `entity` exists in the `workspace`." + [workspace entity] + (try + (firecloud/get-entity workspace entity) + (catch ExceptionInfo ex + (when (not= (-> ex ex-data :status) 404) + (throw ex))))) + +(defn ^:private update-terra-workspace-sink + [executor {:keys [fromOutputs workspace entityType identifier details] :as _sink}] + (when-let [{:keys [uuid outputs] :as workflow} (peek-queue! executor)] + (log/debug "coercing workflow" uuid "outputs to" entityType) + (let [attributes (terra-workspace-sink-to-attributes workflow fromOutputs) + [_ name :as entity] [entityType (outputs (keyword identifier))]] + (when (entity-exists? workspace entity) + (log/debug "entity" name "already exists - deleting previous entity.") + (firecloud/delete-entities workspace [entity])) + (log/debug "upserting workflow" uuid "outputs as" name) + (rawls/batch-upsert workspace [(conj entity attributes)]) + (pop-queue! executor) + (log/info "sunk workflow" uuid "to" workspace "as" name) + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> {:entity name :workflow uuid :updated (utc-now)} + (jdbc/insert! tx details)))))) + +(defn ^:private terra-workspace-sink-done? [_sink] true) + +(defn ^:private terra-workspace-sink-to-edn [sink] + (-> sink + (util/select-non-nil-keys (keys terra-workspace-sink-serialized-fields)) + (assoc :name terra-workspace-sink-name))) + +(defoverload validate-or-throw terra-workspace-sink-name verify-terra-sink!) + +(defoverload create-sink! terra-workspace-sink-name create-terra-workspace-sink) +(defoverload load-sink! terra-workspace-sink-type load-terra-workspace-sink) +(defoverload update-sink! terra-workspace-sink-type update-terra-workspace-sink) + +(defoverload done? terra-workspace-sink-type terra-workspace-sink-done?) + +(defoverload util/to-edn terra-workspace-sink-type terra-workspace-sink-to-edn) diff --git a/api/src/wfl/module/sg.clj b/api/src/wfl/module/sg.clj index 800a7d872..0a1e7ebf1 100644 --- a/api/src/wfl/module/sg.clj +++ b/api/src/wfl/module/sg.clj @@ -1,19 +1,18 @@ (ns wfl.module.sg "Handle Somatic Genomes." - (:require [clojure.data.json :as json] - [clojure.set :as set] - [clojure.string :as str] + (:require [clojure.data.json :as json] + [clojure.set :as set] + [clojure.string :as str] [clojure.tools.logging.readable :as log] - [wfl.api.workloads :as workloads :refer [defoverload]] - [wfl.jdbc :as jdbc] - [wfl.module.batch :as batch] - [wfl.references :as references] - [wfl.service.clio :as clio] - [wfl.service.cromwell :as cromwell] - [wfl.service.google.storage :as gcs] - [wfl.service.postgres :as postgres] - [wfl.util :as util] - [wfl.wfl :as wfl]) + [wfl.api.workloads :as workloads :refer [defoverload]] + [wfl.jdbc :as jdbc] + [wfl.module.batch :as batch] + [wfl.references :as references] + [wfl.service.clio :as clio] + [wfl.service.cromwell :as cromwell] + [wfl.service.google.storage :as gcs] + [wfl.util :as util] + [wfl.wfl :as wfl]) (:import [java.time OffsetDateTime])) (def pipeline "GDCWholeGenomeSomaticSingleSample") @@ -86,6 +85,7 @@ (let [now (OffsetDateTime/now)] (run! update-record! (batch/submit-workload! workload + (workloads/workflows tx workload) executor workflow-wdl cromwellify-workflow-inputs @@ -190,20 +190,22 @@ ;; visible for testing (defn register-workload-in-clio - "Register `_workload` outputs with Clio." - [{:keys [executor output workflows] :as _workload}] + "Register `workload` outputs with Clio." + [{:keys [executor output] :as _workload} workflows] (run! (partial register-workflow-in-clio executor output) workflows)) (defn update-sg-workload! "Use transaction `tx` to batch-update `workload` statuses." [tx {:keys [started finished] :as workload}] (letfn [(update! [{:keys [id] :as workload}] - (postgres/batch-update-workflow-statuses! tx workload) - (postgres/update-workload-status! tx workload) + (batch/batch-update-workflow-statuses! tx workload) + (batch/update-workload-status! tx workload) (workloads/load-workload-for-id tx id))] (if (and started (not finished)) (let [workload' (update! workload)] - (when (:finished workload') (register-workload-in-clio workload')) + (when (:finished workload') + (->> (workloads/workflows tx workload') + (register-workload-in-clio workload'))) workload') workload))) @@ -211,5 +213,6 @@ (defoverload workloads/start-workload! pipeline start-sg-workload!) (defoverload workloads/update-workload! pipeline update-sg-workload!) (defoverload workloads/stop-workload! pipeline batch/stop-workload!) -(defoverload workloads/load-workload-impl pipeline - batch/load-batch-workload-impl) +(defoverload workloads/load-workload-impl pipeline batch/load-batch-workload-impl) +(defoverload workloads/workflows pipeline batch/workflows) +(defoverload workloads/to-edn pipeline batch/workload-to-edn) diff --git a/api/src/wfl/module/wgs.clj b/api/src/wfl/module/wgs.clj index 0f1605a7b..01565ca3a 100644 --- a/api/src/wfl/module/wgs.clj +++ b/api/src/wfl/module/wgs.clj @@ -1,15 +1,14 @@ (ns wfl.module.wgs "Reprocess (External) Whole Genomes." - (:require [clojure.data.json :as json] - [clojure.string :as str] - [wfl.api.workloads :as workloads :refer [defoverload]] - [wfl.jdbc :as jdbc] - [wfl.module.all :as all] - [wfl.references :as references] + (:require [clojure.data.json :as json] + [clojure.string :as str] + [wfl.api.workloads :as workloads :refer [defoverload]] + [wfl.jdbc :as jdbc] + [wfl.module.batch :as batch] + [wfl.references :as references] [wfl.service.google.storage :as gcs] - [wfl.util :as util] - [wfl.wfl :as wfl] - [wfl.module.batch :as batch]) + [wfl.util :as util] + [wfl.wfl :as wfl]) (:import [java.time OffsetDateTime])) (def pipeline "ExternalWholeGenomeReprocessing") @@ -186,18 +185,21 @@ (letfn [(update-record! [{:keys [id] :as workflow}] (let [values (select-keys workflow [:uuid :status :updated])] (jdbc/update! tx items values ["id = ?" id])))] - (let [now (OffsetDateTime/now) + (let [now (OffsetDateTime/now) executor (is-known-cromwell-url? executor)] - (run! update-record! (batch/submit-workload! workload executor workflow-wdl make-workflow-inputs cromwell-label (make-workflow-options executor))) + (run! update-record! + (batch/submit-workload! workload + (workloads/workflows tx workload) + executor + workflow-wdl + make-workflow-inputs + cromwell-label + (make-workflow-options executor))) (jdbc/update! tx :workload {:started now} ["id = ?" id])) (workloads/load-workload-for-id tx id))) -(defoverload workloads/update-workload! pipeline batch/update-workload!) -(defoverload workloads/stop-workload! pipeline batch/stop-workload!) - -(defmethod workloads/load-workload-impl - pipeline - [tx workload] - (if (workloads/saved-before? "0.4.0" workload) - (workloads/default-load-workload-impl tx workload) - (batch/load-batch-workload-impl tx workload))) +(defoverload workloads/update-workload! pipeline batch/update-workload!) +(defoverload workloads/stop-workload! pipeline batch/stop-workload!) +(defoverload workloads/load-workload-impl pipeline batch/load-batch-workload-impl) +(defoverload workloads/workflows pipeline batch/workflows) +(defoverload workloads/to-edn pipeline batch/workload-to-edn) diff --git a/api/src/wfl/module/xx.clj b/api/src/wfl/module/xx.clj index cc7fcb1be..d128f80a3 100644 --- a/api/src/wfl/module/xx.clj +++ b/api/src/wfl/module/xx.clj @@ -1,16 +1,15 @@ (ns wfl.module.xx - "Reprocess External Exomes, whatever they are." - (:require [clojure.data.json :as json] - [clojure.string :as str] - [wfl.api.workloads :refer [defoverload]] - [wfl.api.workloads :as workloads] - [wfl.jdbc :as jdbc] - [wfl.module.all :as all] - [wfl.module.batch :as batch] - [wfl.references :as references] + "Reprocess eXternal eXomes." + (:require [clojure.data.json :as json] + [clojure.string :as str] + [wfl.api.workloads :refer [defoverload]] + [wfl.api.workloads :as workloads] + [wfl.jdbc :as jdbc] + [wfl.module.batch :as batch] + [wfl.references :as references] [wfl.service.google.storage :as gcs] - [wfl.util :as util] - [wfl.wfl :as wfl]) + [wfl.util :as util] + [wfl.wfl :as wfl]) (:import [java.time OffsetDateTime])) (def pipeline "ExternalExomeReprocessing") @@ -164,12 +163,21 @@ (jdbc/update! tx items values ["id = ?" id])))] (let [now (OffsetDateTime/now) executor (is-known-cromwell-url? executor)] - (run! update-record! (batch/submit-workload! workload executor workflow-wdl cromwellify-workflow-inputs cromwell-label (make-workflow-options executor))) + (run! update-record! + (batch/submit-workload! workload + (workloads/workflows tx workload) + executor + workflow-wdl + cromwellify-workflow-inputs + cromwell-label + (make-workflow-options executor))) (jdbc/update! tx :workload {:started now} ["id = ?" id])) (workloads/load-workload-for-id tx id))) -(defoverload workloads/create-workload! pipeline create-xx-workload!) -(defoverload workloads/start-workload! pipeline start-xx-workload!) -(defoverload workloads/update-workload! pipeline batch/update-workload!) -(defoverload workloads/stop-workload! pipeline batch/stop-workload!) +(defoverload workloads/create-workload! pipeline create-xx-workload!) +(defoverload workloads/start-workload! pipeline start-xx-workload!) +(defoverload workloads/update-workload! pipeline batch/update-workload!) +(defoverload workloads/stop-workload! pipeline batch/stop-workload!) (defoverload workloads/load-workload-impl pipeline batch/load-batch-workload-impl) +(defoverload workloads/workflows pipeline batch/workflows) +(defoverload workloads/to-edn pipeline batch/workload-to-edn) diff --git a/api/src/wfl/server.clj b/api/src/wfl/server.clj index cc4d8234c..8f0dc883f 100644 --- a/api/src/wfl/server.clj +++ b/api/src/wfl/server.clj @@ -1,24 +1,25 @@ (ns wfl.server "An HTTP API server." - (:require [clojure.pprint :refer [pprint]] - [clojure.stacktrace :refer [print-throwable]] - [clojure.string :as str] - [clojure.tools.logging :as log] - [clj-time.coerce :as tc] - [ring.adapter.jetty :as jetty] - [ring.middleware.defaults :as defaults] - [ring.middleware.json :refer [wrap-json-response]] - [ring.middleware.params :refer [wrap-params]] - [ring.middleware.reload :as reload] + (:require [clojure.pprint :refer [pprint]] + [clojure.stacktrace :refer [print-throwable]] + [clojure.string :as str] + [clojure.tools.logging :as log] + [clj-time.coerce :as tc] + [ring.adapter.jetty :as jetty] + [ring.middleware.defaults :as defaults] + [ring.middleware.json :refer [wrap-json-response]] + [ring.middleware.params :refer [wrap-params]] + [ring.middleware.reload :as reload] [ring.middleware.session.cookie :as cookie] - [wfl.api.routes :as routes] - [wfl.api.workloads :as workloads] - [wfl.environment :as env] - [wfl.jdbc :as jdbc] - [wfl.service.postgres :as postgres] - [wfl.util :as util] - [wfl.wfl :as wfl]) - (:import (java.util.concurrent Future TimeUnit))) + [wfl.api.routes :as routes] + [wfl.api.workloads :as workloads] + [wfl.environment :as env] + [wfl.jdbc :as jdbc] + [wfl.service.postgres :as postgres] + [wfl.util :as util] + [wfl.wfl :as wfl]) + (:import (java.util.concurrent Future TimeUnit) + (wfl.util UserException))) (def description "The purpose of this command." @@ -77,31 +78,47 @@ wrap-internal-error (wrap-json-response {:pretty true}))) +(defn notify-watchers [watchers uuid exception] + {:pre [(some? watchers)]} + (log/info "notifying: " watchers)) + (defn ^:private start-workload-manager "Update the workload database, then start a `future` to manage the state of workflows in the background. Dereference the future to wait for the background task to finish (when an error occurs)." [] (letfn [(do-update! [{:keys [id uuid]}] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (let [{:keys [watchers] :as workload} + (workloads/load-workload-for-id tx id)] + (try + (workloads/update-workload! tx workload) + (catch UserException e + (log/warnf "Error updating workload %s" uuid) + (log/warn e) + (notify-watchers watchers uuid e)))))) + (try-update [{:keys [uuid] :as workload}] + (try + (do-update! workload) + (catch Throwable t + (log/error "Failed to update workload %s" uuid) + (log/error t)))) + (update-workloads [] (try - (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] - (->> (workloads/load-workload-for-id tx id) - (workloads/update-workload! tx))) + (log/info "updating workloads") + (run! try-update + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (jdbc/query tx "SELECT id,uuid FROM workload + WHERE started IS NOT NULL + AND finished IS NULL"))) (catch Throwable t - (log/warnf "Failed to update workload %s" uuid) - (log/warn t)))) - (update-workloads! [] - (log/info "updating workloads") - (run! do-update! - (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] - (jdbc/query tx [(str/join " " ["SELECT id,uuid FROM workload" - "WHERE started IS NOT NULL" - "AND finished IS NULL"])]))))] + (log/error "Failed to update workloads") + (log/error t))))] (log/info "starting workload update loop") - (update-workloads!) + (update-workloads) (future (while true - (update-workloads!) + (update-workloads) (.sleep TimeUnit/SECONDS 20))))) (defn ^:private start-webserver diff --git a/api/src/wfl/service/datarepo.clj b/api/src/wfl/service/datarepo.clj index 977f3165e..80c4d768f 100644 --- a/api/src/wfl/service/datarepo.clj +++ b/api/src/wfl/service/datarepo.clj @@ -27,6 +27,7 @@ (defn dataset "Query the DataRepo for the Dataset with `dataset-id`." [dataset-id] + {:pre [(some? dataset-id)]} (get-repository-json "datasets" dataset-id)) (defn ^:private ingest @@ -96,6 +97,17 @@ ([job-id] (poll-job job-id 5))) +(defn get-job-metadata + "Return the metadata of job with `job-id` when done." + [job-id] + {:pre [(some? job-id)]} + (get-repository-json "jobs" job-id)) + +(defn get-job-result + "Get the result of job with `job-id`." + [job-id] + (get-repository-json "jobs" job-id "result")) + (defn create-dataset "Create a dataset with EDN `dataset-request` and return the id of the created dataset. See `DatasetRequestModel` in the @@ -122,6 +134,18 @@ :id poll-job)) +(defn create-snapshot-job + "Return snapshot creation job-id defined by `snapshot-request` right away. + See `SnapshotRequestModel` in the DataRepo swagger page for more information. + https://jade.datarepo-dev.broadinstitute.org/swagger-ui.html#/" + [snapshot-request] + (-> (repository "snapshots") + (http/post {:headers (auth/get-service-account-header) + :content-type :application/json + :form-params snapshot-request}) + util/response-body-json + :id)) + ;; Note the TDR is under active development, the endpoint spec is getting ;; changed so the spec in this function is not consistent with the TDR Swagger ;; page in order to make the request work. @@ -131,12 +155,8 @@ See `SnapshotRequestModel` in the DataRepo swagger page for more information. https://jade.datarepo-dev.broadinstitute.org/swagger-ui.html#/" [snapshot-request] - (-> (repository "snapshots") - (http/post {:headers (auth/get-service-account-header) - :content-type :application/json - :form-params snapshot-request}) - util/response-body-json - :id + (-> snapshot-request + create-snapshot-job poll-job :id)) @@ -176,7 +196,8 @@ (get-repository-json "snapshots" snapshot-id)) (defn all-columns - "Return all of the columns of `table` in `dataset` content." + "Helper function to parse all of the columns + of `table` in `dataset` body." [dataset table] (->> (get-in dataset [:schema :tables]) (filter #(= (:name %) table)) @@ -189,15 +210,14 @@ "Return a snapshot request for `row-ids`and `columns` from `table` name in `_dataset`." [{:keys [name defaultProfileId description] :as _dataset} columns table row-ids] - (let [row-ids (vec row-ids)] - {:contents [{:datasetName name - :mode "byRowId" - :rowIdSpec {:tables [{:columns columns - :rowIds row-ids - :tableName table}]}}] - :description description - :name name - :profileId defaultProfileId})) + {:contents [{:datasetName name + :mode "byRowId" + :rowIdSpec {:tables [{:columns columns + :rowIds row-ids + :tableName table}]}}] + :description description + :name name + :profileId defaultProfileId}) ;; hack - TDR adds the "datarepo_" prefix to the dataset name in BigQuery ;; They plan to expose this name via `GET /api/repository/v1/datasets/{id}` @@ -224,22 +244,24 @@ (query-table-impl dataset table)))) (defn ^:private query-table-between-impl - [{:keys [dataProject] :as dataset} table [start end] col-spec] - (let [bq-name (bigquery-name dataset) - query "SELECT %s - FROM `%s.%s.%s` - WHERE datarepo_ingest_date > '%s' - AND datarepo_ingest_date <= '%s'"] - (->> (format query col-spec dataProject bq-name table start end) - (bigquery/query-sync dataProject)))) + [{:keys [dataProject] :as dataset} table between [start end] col-spec] + (let [[table between] (map name [table between]) + bq-name (bigquery-name dataset) + query (str/join \newline ["SELECT %s" + "FROM `%s.%s.%s`" + "WHERE %s BETWEEN '%s' AND '%s'"])] + (-> query + (format col-spec dataProject bq-name table between start end) + (->> (bigquery/query-sync dataProject))))) (defn query-table-between - "Query everything or optionally the `columns` in `table` in the Terra DataRepo - `dataset` in the open-closed `interval` of `datarepo_ingest_date`, where - `dataset` is a DataRepo dataset or a snapshot of a dataset. If no rows match - the `interval`, TDR will respond with error 400." - ([dataset table interval] - (query-table-between-impl dataset table interval "*")) - ([dataset table interval columns] - (->> (util/to-comma-separated-list (map name columns)) - (query-table-between-impl dataset table interval)))) + "Return rows from `table` of `dataset`, where `dataset` can name a + snapshot and values in the `between` column fall within `interval`. + Select `columns` from matching rows when specified. A 400 response + means no rows matched the query." + ([dataset table between interval] + (query-table-between-impl dataset table between interval "*")) + ([dataset table between interval columns] + (->> (map name columns) + util/to-comma-separated-list + (query-table-between-impl dataset table between interval)))) diff --git a/api/src/wfl/service/firecloud.clj b/api/src/wfl/service/firecloud.clj index f2cc00631..2a4eb4cba 100644 --- a/api/src/wfl/service/firecloud.clj +++ b/api/src/wfl/service/firecloud.clj @@ -1,11 +1,12 @@ (ns wfl.service.firecloud "Analyze data in Terra using the Firecloud/Terra API." - (:require [clj-http.client :as http] + (:require [clj-http.client :as http] [clojure.data.json :as json] - [clojure.string :as str] - [wfl.auth :as auth] - [wfl.environment :as env] - [wfl.util :as util])) + [clojure.string :as str] + [wfl.auth :as auth] + [wfl.environment :as env] + [wfl.util :as util]) + (:import [java.util UUID])) (defn ^:private firecloud-url [& parts] (let [url (util/de-slashify (env/getenv "WFL_FIRECLOUD_URL"))] @@ -19,6 +20,10 @@ (http/get {:headers (auth/get-auth-header)}) util/response-body-json)) +(defn workspace [workspace] + {:pre [(some? workspace)]} + (get-workspace-json workspace)) + (defn abort-submission "Abort the submission with `submission-id` in the Terra `workspace`." [workspace submission-id] @@ -27,22 +32,38 @@ (defn create-submission "Submit samples in a workspace for analysis with a method configuration in Terra." - [workspace methodconfig [entity-type entity-name :as _entity]] + ([workspace methodconfig [entity-type entity-name :as _entity] body-override] + {:pre [(map? body-override)]} + (let [[mcns mcn] (str/split methodconfig #"/") + payload (util/deep-merge {:methodConfigurationNamespace mcns + :methodConfigurationName mcn + :entityType entity-type + :entityName entity-name + :useCallCache true} + body-override)] + (-> (workspace-api-url workspace "submissions") + (http/post {:headers (auth/get-auth-header) + :content-type :application/json + :body (json/write-str payload + :escape-slash false)}) + util/response-body-json))) + ([workspace methodconfig entity] + (create-submission workspace methodconfig entity {}))) + +(defn submit-method + "Submit the`methodconfig` for processing in the Terra `workspace`." + [workspace methodconfig] + {:pre [(every? string? [workspace methodconfig])]} (let [[mcns mcn] (str/split methodconfig #"/")] - (-> {:method :post - :url (workspace-api-url workspace "submissions") - :headers (auth/get-auth-header) - :content-type :application/json - :body (json/write-str - {:methodConfigurationNamespace mcns - :methodConfigurationName mcn - :entityType entity-type - :entityName entity-name - :useCallCache true} - :escape-slash false)} - http/request - util/response-body-json - :submissionId))) + (-> (workspace-api-url workspace "submissions") + (http/post {:headers (auth/get-auth-header) + :content-type :application/json + :body (json/write-str + {:methodConfigurationNamespace mcns + :methodConfigurationName mcn + :useCallCache true} + :escape-slash false)}) + util/response-body-json))) (defn create-workspace "Create an empty Terra workspace with the fully-qualified `workspace` name, @@ -59,6 +80,22 @@ :body (json/write-str payload)}) util/response-body-json))) +(defn clone-workspace + "Clone the Terra workspace `workspace-to-clone` as `workspace` and grant + access to the `firecloud-group`." + [workspace-to-clone workspace firecloud-group] + {:pre [(every? string? [workspace-to-clone workspace firecloud-group])]} + (let [[namespace name] (str/split workspace #"/") + payload {:namespace namespace + :name name + :attributes {:description ""} + :authorizationDomain [{:membersGroupName firecloud-group}]}] + (-> (workspace-api-url workspace-to-clone "clone") + (http/post {:headers (auth/get-auth-header) + :content-type :application/json + :body (json/write-str payload)}) + util/response-body-json))) + (defn delete-workspace "Delete the terra `workspace` and all data within." [workspace] @@ -93,6 +130,11 @@ first :status))) +(defn get-entity + "Fetch the `entity` metadata from the `workspace`." + [workspace [type name :as _entity]] + (get-workspace-json workspace "entities" type name)) + (defn delete-entities "Delete the `entities` from the Terra `workspace`. Parameters @@ -100,7 +142,7 @@ workspace - Terra Workspace to delete entities from entities - list of entity `[type name]` pairs" [workspace entities] - (letfn [(make-entity [[type name]] {:entityType type :entityName name})] + (let [make-entity (partial zipmap [:entityType :entityName])] (-> (workspace-api-url workspace "entities" "delete") (http/post {:headers (auth/get-auth-header) :content-type :application/json @@ -126,6 +168,79 @@ {:Content/type "text/tab-separated-values" :entities (slurp file)})}))) +(defn import-entity-set + " + Format existing same-typed ENTITIES into a Terra-compatible tsv. + Upload to \"_set\" table in WORKSPACE under ENTITY-SET-NAME. + + Parameters + ---------- + workspace - Terra Workspace \"namespace/name\" + entity-set-name - Identifier for the entity set + entities - List of same-typed entity [Type Name] pairs + + Example + ------- + (import-entity-set \"workspace-namespace/workspace-name\" + \"c25ee04b-...\" + [[\"sample\" \"NA12878\"] [\"sample\" \"NA12879\"]]) + " + [workspace entity-set-name [[entity-type _] & _ :as entities]] + (->> (for [[_ entity-name] entities] [entity-set-name entity-name]) + (util/columns-rows->terra-tsv :membership [entity-type entity-type]) + .getBytes + (import-entities workspace))) + +(defn create-submission-for-entity-set + " + Consolidate ENTITIES into an entity set and use it to create a + submission in WORKSPACE with METHODCONFIG. + + Parameters + ---------- + workspace - Terra Workspace \"namespace/name\" + methodconfig - Terra Method Configuration \"namespace/name\" + entities - List of 1+ entity [Type Name] pairs + entity-set-name - [Optional] ID for entity set entry, or + random UUID if unspecified. + + Example + ------- + (create-submission-for-entity-set \"w-namespace/w-name\" + \"mc-namespace/mc-name\" + [[\"sample\" \"NA12878\"] [\"sample\" \"NA12879\"]]) + " + ([workspace methodconfig entities entity-set-name] + ;; TODO: refactor create-submission to support entity set specification. + {:pre [(seq entities)]} + (let [entity-set-type ((import-entity-set workspace entity-set-name entities) :body)] + (->> (str "this." (util/unsuffix entity-set-type "_set") "s") + (array-map :expression) + (create-submission workspace methodconfig [entity-set-type entity-set-name])))) + ([workspace methodconfig entities] + (create-submission-for-entity-set workspace methodconfig entities (str (UUID/randomUUID))))) + +(defn list-method-configurations + "List all method configurations in the `workspace`." + [workspace] + (get-workspace-json workspace "methodconfigs?allRepos=true")) + +(defn get-method-configuration + "Return the `methodconfig` in the `workspace`." + [workspace methodconfig] + {:pre [(every? some? [workspace methodconfig])]} + (get-workspace-json workspace "method_configs" methodconfig)) + +(defn update-method-configuration + "Update the method-configuration `method-config-name` to be `methodconfig` in + the `workspace`." + [workspace method-config-name methodconfig] + (-> (workspace-api-url workspace "method_configs" method-config-name) + (http/put {:headers (auth/get-auth-header) + :content-type :application/json + :body (json/write-str methodconfig)}) + (util/response-body-json))) + (defn list-entities "List all entities with `entity-type` in `workspace`." [workspace entity-type] @@ -148,3 +263,17 @@ :workflowSource) workflow})}) util/response-body-json))) + +(defn ^:private get-groups + "Return the groups caller is in." + [] + (-> (str/join "/" [(firecloud-url) "api" "groups"]) + (http/get {:headers (auth/get-auth-header)}) + util/response-body-json)) + +(defn ^:private get-group-members + "Return the members of group." + [group] + (-> (str/join "/" [(firecloud-url) "api" "groups" group]) + (http/get {:headers (auth/get-auth-header)}) + util/response-body-json)) diff --git a/api/src/wfl/service/google/bigquery.clj b/api/src/wfl/service/google/bigquery.clj index fabe75153..557dceda9 100644 --- a/api/src/wfl/service/google/bigquery.clj +++ b/api/src/wfl/service/google/bigquery.clj @@ -1,13 +1,11 @@ (ns wfl.service.google.bigquery "Wrappers for Google Cloud BigQuery REST APIs. See https://cloud.google.com/bigquery/docs/reference/rest." - (:require [clj-http.client :as http] - [clojure.data.csv :as csv] - [clojure.java.io :as io] + (:require [clj-http.client :as http] [clojure.data.json :as json] - [clojure.string :as str] - [wfl.auth :as auth] - [wfl.util :as util]) + [clojure.string :as str] + [wfl.auth :as auth] + [wfl.util :as util]) (:import [java.io StringWriter])) (def ^:private bigquery-url @@ -75,12 +73,6 @@ "Dump a BigQuery TABLE/view into a tsv FILE that's supported by Terra. Will dump the tsv contents to bytes if no FILE is provided. - The first column of the table must be the table primary key, - i.e. [entity-type]_id. For example, 'entity:sample_id' will upload the tsv - data into a `sample` table in the workspace (or create one if it does not - exist). If the table already contains a sample with that id, it will get - overwritten. - Parameters ---------- table - BigQuery table/view body with the rows field flatten. @@ -91,12 +83,7 @@ (dump-table->tsv table \"dumped.tsv\") (dump-table->tsv table)" ([table file] - (letfn [(format-entity-type [[head & rest]] - (cons (format "entity:%s" head) rest))] - (let [columns (map :name (get-in table [:schema :fields]))] - (with-open [writer (io/writer file)] - (csv/write-csv writer [(format-entity-type columns)] :separator \tab) - (csv/write-csv writer (:rows table) :separator \tab) - file)))) + (let [columns (map :name (get-in table [:schema :fields]))] + (util/columns-rows->terra-tsv :entity columns (:rows table) file))) ([table] (str (dump-table->tsv table (StringWriter.))))) diff --git a/api/src/wfl/service/google/storage.clj b/api/src/wfl/service/google/storage.clj index e1de27b9d..c95bd6dd9 100644 --- a/api/src/wfl/service/google/storage.clj +++ b/api/src/wfl/service/google/storage.clj @@ -6,7 +6,6 @@ [clojure.data.json :as json] [clojure.java.io :as io] [clojure.pprint :refer [pprint]] - [clojure.set :as set] [clojure.spec.alpha :as s] [clojure.string :as str] [clojure.tools.logging.readable :as logr] @@ -117,13 +116,12 @@ ([url] (apply list-objects (parse-gs-url url)))) -(def _-? (set "_-")) -(def digit? (set "0123456789")) -(def lowercase? (set "abcdefghijklmnopqrstuvwxyz")) +(def ^:private _-? (set "_-")) +(def ^:private bucket-allowed? (into _-? (concat util/digit? util/lowercase?))) (s/def ::bucket-name (s/and string? - (partial every? (set/union _-? digit? lowercase?)) + (partial every? bucket-allowed?) (complement (comp _-? first)) (complement (comp _-? last)) (comp (partial > 64) count) diff --git a/api/src/wfl/service/postgres.clj b/api/src/wfl/service/postgres.clj index babeaf786..930db803a 100644 --- a/api/src/wfl/service/postgres.clj +++ b/api/src/wfl/service/postgres.clj @@ -1,32 +1,34 @@ (ns wfl.service.postgres "Talk to the Postgres database." - (:require [clojure.string :as str] - [clj-http.client :as http] - [wfl.environment :as env] - [wfl.jdbc :as jdbc] - [wfl.auth :as auth] - [wfl.service.cromwell :as cromwell] - [wfl.service.firecloud :as firecloud] - [wfl.util :as util]) - (:import [java.time OffsetDateTime])) + (:require [clojure.string :as str] + [wfl.environment :as env] + [wfl.jdbc :as jdbc])) + +(def ^:private testing-db-overrides + "Override the configuration used by `wfl-db-config` for testing. Use + `wfl.tools.fixtures/temporary-postgresql-database` instead of this." + (atom {})) (defn wfl-db-config "Get the database configuration." [] - (assoc {:classname "org.postgresql.Driver" - :db-name "wfl" - :instance-name "zero-postgresql" - ;; https://www.postgresql.org/docs/9.1/transaction-iso.html - :isolation-level :serializable - :subprotocol "postgresql"} - :connection-uri (env/getenv "WFL_POSTGRES_URL") - :password (env/getenv "WFL_POSTGRES_PASSWORD") - :user (or (env/getenv "WFL_POSTGRES_USERNAME") (env/getenv "USER") "postgres"))) + (-> {:classname "org.postgresql.Driver" + :db-name "wfl" + :instance-name "zero-postgresql" + ;; https://www.postgresql.org/docs/9.1/transaction-iso.html + :isolation-level :serializable + :subprotocol "postgresql"} + (assoc :connection-uri (env/getenv "WFL_POSTGRES_URL") + :password (env/getenv "WFL_POSTGRES_PASSWORD") + :user (or (env/getenv "WFL_POSTGRES_USERNAME") (env/getenv "USER") "postgres")) + (merge @testing-db-overrides))) (defn table-exists? "Check if TABLE exists using transaction TX." [tx table] - (->> ["SELECT * FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_NAME = ?" (str/lower-case table)] + (->> (name table) + str/lower-case + (conj ["SELECT * FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_NAME = ?"]) (jdbc/query tx) (count) (not= 0))) @@ -38,69 +40,23 @@ (jdbc/query tx (format "SELECT * FROM %s" table)) (throw (ex-info (format "Table %s does not exist" table) {:cause "no-such-table"})))) -(defn ^:private cromwell-status - "`status` of the workflow with `uuid` in `cromwell`." - [cromwell uuid] - (-> (str/join "/" [cromwell "api" "workflows" "v1" uuid "status"]) - (http/get {:headers (auth/get-auth-header)}) - :body - util/parse-json - :status)) - -(def ^:private finished? - "Test if a workflow `:status` is in a terminal state." - (set (conj cromwell/final-statuses "skipped"))) - -(defn ^:private make-update-workflows [get-status!] - (fn [tx {:keys [items workflows] :as workload}] - (letfn [(update! [{:keys [id uuid]} status] - (jdbc/update! tx items - {:status status - :updated (OffsetDateTime/now) - :uuid uuid} - ["id = ?" id]))] - (->> workflows - (remove (comp nil? :uuid)) - (remove (comp finished? :status)) - (run! #(update! % (get-status! workload %))))))) - -(def update-workflow-statuses! - "Use `tx` to update `status` of Cromwell `workflows` in a `workload`." - (letfn [(get-cromwell-status [{:keys [executor]} {:keys [uuid]}] - (if (util/uuid-nil? uuid) - "skipped" - (cromwell-status executor uuid)))] - (make-update-workflows get-cromwell-status))) - -(def update-terra-workflow-statuses! - "Use `tx` to update `status` of Terra `workflows` in a `workload`." - (letfn [(get-terra-status [{:keys [project]} workflow] - (firecloud/get-workflow-status-by-entity project workflow))] - (make-update-workflows get-terra-status))) - -(defn batch-update-workflow-statuses! - "Use `tx` to update the `status` of the workflows in `_workload`." - [tx {:keys [executor uuid items] :as _workoad}] - (let [uuid->status (->> {:label (str "workload:" uuid) :includeSubworkflows "false"} - (cromwell/query executor) - (map (juxt :id :status)))] - (letfn [(update! [[uuid status]] - (jdbc/update! tx items - {:status status :updated (OffsetDateTime/now)} - ["uuid = ?" uuid]))] - (run! update! uuid->status)))) - -(defn active-workflows - "Use `tx` to query all the workflows in `_workload` whose :status is not in - `finished?`" - [tx {:keys [items] :as _workload}] - (let [query "SELECT id FROM %s WHERE status IS NULL OR status NOT IN %s"] - (->> (util/to-quoted-comma-separated-list finished?) - (format query items) - (jdbc/query tx)))) - -(defn update-workload-status! - "Use `tx` to mark `workload` finished when all `workflows` are finished." - [tx {:keys [id] :as workload}] - (when (empty? (active-workflows tx workload)) - (jdbc/update! tx :workload {:finished (OffsetDateTime/now)} ["id = ?" id]))) +(defn table-length + "Use `tx` to return the number of records in `table-name`." + [tx table-name] + (when-not (table-exists? tx table-name) + (throw (ex-info "No such table" {:table table-name}))) + (->> (format "SELECT COUNT(*) FROM %s" table-name) + (jdbc/query tx) + first + :count)) + +(defn table-max + "Use `tx` to return the maximum value of `column` in `table-name`." + [tx table-name column] + (when-not (table-exists? tx table-name) + (throw (ex-info "No such table" {:table table-name}))) + (-> (format "SELECT MAX(%s) FROM %s" (name column) (name table-name)) + (->> (jdbc/query tx)) + first + :max + (or 0))) diff --git a/api/src/wfl/service/rawls.clj b/api/src/wfl/service/rawls.clj new file mode 100644 index 000000000..7fd81bc92 --- /dev/null +++ b/api/src/wfl/service/rawls.clj @@ -0,0 +1,137 @@ +(ns wfl.service.rawls + "Analyze and manipulate Terra Workspaces using the Rawls API. + Note that firecloud exposes a subset of Rawls' API." + (:require [clj-http.client :as http] + [clojure.data.json :as json] + [clojure.string :as str] + [wfl.auth :as auth] + [wfl.environment :as env] + [wfl.util :as util]) + (:import [clojure.lang ExceptionInfo])) + +(defn ^:private rawls-url [& parts] + (let [url (util/de-slashify (env/getenv "WFL_RAWLS_URL"))] + (str/join "/" (cons url parts)))) + +(def ^:private workspace-api-url + (partial rawls-url "api/workspaces")) + +(defn ^:private get-workspace-json [& parts] + (-> (apply workspace-api-url parts) + (http/get {:headers (auth/get-auth-header)}) + util/response-body-json)) + +(def ^:private snapshot-endpoint + "snapshots") + +(defn create-snapshot-reference + "Link `snapshot-id` to `workspace` as `name` with `description`." + ([workspace snapshot-id name description] + (-> (workspace-api-url workspace snapshot-endpoint) + (http/post {:headers (auth/get-auth-header) + :content-type :application/json + :body (json/write-str {:snapshotId snapshot-id + :name name + :description description} + :escape-slash false)}) + util/response-body-json)) + ([workspace snapshot-id name] + (create-snapshot-reference workspace snapshot-id name ""))) + +(defn get-snapshot-reference + "Return the snapshot reference in `workspace` with `reference-id`." + [workspace reference-id] + (get-workspace-json workspace snapshot-endpoint reference-id)) + +(defn get-snapshot-references + "Lazily returns the snapshot references in `workspace` + with `limit` resources per page (default: 100)." + ([workspace limit] + (letfn + [(page [offset] + (let [{:keys [resources] :as _response} + (-> (workspace-api-url workspace snapshot-endpoint) + (http/get {:headers (auth/get-auth-header) + :query-params {:offset offset + :limit limit}}) + (util/response-body-json)) + total (+ offset (count resources))] + (lazy-cat resources (when (seq resources) (page total)))))] + (util/lazy-unchunk (page 0)))) + ([workspace] + (get-snapshot-references workspace 100))) + +(defn ^:private get-reference-for-snapshot-id + "Return first snapshot reference for `snapshot-id` in `workspace`." + [workspace snapshot-id] + (->> (get-snapshot-references workspace) + (filter #(= (get-in % [:reference :snapshot]) snapshot-id)) + first)) + +(def ^:private reference-creation-failed-message + (str/join " " ["Could not create snapshot reference" + "and found no snapshot reference" + "matching the snapshot id."])) + +(defn create-or-get-snapshot-reference + "Return first snapshot reference for `snapshot-id` in `workspace`, + creating it as `name` with `description` if it does not yet exist." + ([workspace snapshot-id name description] + (try + (create-snapshot-reference workspace snapshot-id name description) + (catch ExceptionInfo cause + (when-not (== 409 (:status (ex-data cause))) + (throw cause)) + (or (get-reference-for-snapshot-id workspace snapshot-id) + (throw (ex-info reference-creation-failed-message + {:workspace workspace + :snapshot-id snapshot-id + :name name} + cause)))))) + ([workspace snapshot-id name] + (create-or-get-snapshot-reference workspace snapshot-id name ""))) + +(defn delete-snapshot-reference + "Delete the snapshot reference in `workspace` with `reference-id`." + [workspace reference-id] + (-> (workspace-api-url workspace snapshot-endpoint reference-id) + (http/delete {:headers (auth/get-auth-header)}) + util/response-body-json)) + +(defn batch-upsert + "Batch update and insert entities into a `workspace`." + [workspace [[_type _name _attributes] & _ :as entities]] + {:pre [(string? workspace) (not-empty entities)]} + (letfn [(add-scalar [k v] + [{:op "AddUpdateAttribute" + :attributeName (name k) + :addUpdateAttribute v}]) + (add-list [k v] + (let [list-name (name k) + init {:op "CreateAttributeValueList" + :attributeName list-name} + template {:op "AddListMember" + :attributeListName list-name} + make-member (partial assoc template :newMember)] + (reduce #(conj %1 (make-member %2)) [init] v))) + (no-op [] []) + (on-unhandled-attribute [name value] + (throw (ex-info "No method to make upsert operation for attribute" + {:name name :value value}))) + (to-operations [attributes] + (flatten + (for [[k v] (seq attributes)] + (cond (number? v) (add-scalar k v) + (string? v) (add-scalar k v) + (map? v) (add-scalar k v) + (coll? v) (add-list k v) + (nil? v) (no-op) + :else (on-unhandled-attribute k v))))) + (make-request [[type name attributes]] + {:entityType type :name name :operations (to-operations attributes)})] + (-> (workspace-api-url workspace "entities/batchUpsert") + (http/post {:headers (auth/get-auth-header) + :content-type :application/json + :body (json/write-str (map make-request entities) + :escape-slash false)}) + util/response-body-json))) diff --git a/api/src/wfl/tsv.clj b/api/src/wfl/tsv.clj new file mode 100644 index 000000000..2f6755dd8 --- /dev/null +++ b/api/src/wfl/tsv.clj @@ -0,0 +1,122 @@ +(ns wfl.tsv + "Read and write Terra's tab-separated value (.tsv) files." + (:refer-clojure :exclude [read]) + (:require [clojure.data.csv :as csv] + [clojure.data.json :as json] + [clojure.edn :as edn] + [clojure.java.io :as io]) + (:import [java.io Reader StringReader StringWriter Writer])) + +(defprotocol TsvField + "One field of a row or line in a .tsv file." + (-write [field ^Writer out] + "Write FIELD to java.io.Writer OUT as a .tsv value.")) + +(extend-protocol TsvField + clojure.lang.Named + (^:private -write [field out] + (.write out (name field))) + java.lang.Object + (^:private -write [field out] + (.write out (json/write-str field :escape-slash false))) + java.lang.String + (^:private -write [field out] + (.write out field))) + +;; BUG: Do not quote or escape \tab or \newline. +;; +(defn ^:private write-fields + "Write the sequence of .tsv FIELDS to WRITER." + [fields ^Writer writer] + (loop [fields fields separator ""] + (when-first [field fields] + (-write separator writer) + (-write field writer) + (recur (rest fields) "\t")))) + +(defn ^:private read-field + "Guess what S is to avoid writing a full-blown scanner." + [s] + (case (first s) + (\[ \{) (json/read-str s) + (or (try (let [x (edn/read-string s)] + (when (and (number? x) + (= s (str x))) x)) + (catch Throwable _ignored)) + s))) + +;; HACK: Post-process CSV to avoid writing a full-blown parser. +;; +(defn read + "Read a .tsv table, a sequence of sequences, from READER." + [^Reader reader] + (-> reader + (csv/read-csv :separator \tab) + (->> (map (partial map read-field))))) + +(defn read-str + "Read a .tsv table, a sequence of sequences, from string S." + [s] + (read (StringReader. s))) + +(defn read-file + "Return a lazy .tsv table from FILE." + [file] + (read (io/reader file))) + +(defn write + "Write TABLE, a sequence of .tsv field sequences, to WRITER." + [table ^Writer writer] + (when-first [line table] + (write-fields line writer) + (.write writer "\n") + (recur (rest table) writer))) + +(defn write-str + "Return TABLE, a sequence of .tsv field sequences, in a string." + [table] + (let [writer (StringWriter.)] + (write table writer) + (.toString writer))) + +(defn write-file + "Write TABLE, a sequence of .tsv field sequences, to FILE." + [table file] + (with-open [writer (io/writer file)] + (write table writer))) + +(defn ^:private assert-mapulatable! + "Throw when (mapulate TABLE) would lose information." + [table] + (letfn [(repeated? [[label n]] (when-not (== 1 n) label))] + (let [repeats (keep repeated? (frequencies (first table)))] + (when (seq repeats) + (throw (ex-info "TABLE.tsv has repeated column labels." + {:repeats repeats}))))) + (let [counts (set (map count table))] + (when-not (== 1 (count counts)) + (throw (ex-info "TABLE.tsv has multiple column counts." + {:counts counts}))))) + +(defn mapulate + "Return a sequence of maps from TABLE, a sequence of sequences." + [table] + (assert-mapulatable! table) + (let [[header & rows] table] + (map (partial zipmap header) rows))) + +(defn ^:private assert-tabulatable! + "Throw when (tabulate EDN) would lose information." + [edn] + (let [counts (set (map count edn))] + (when-not (== 1 (count counts)) + (throw (ex-info "TABLE.tsv has multiple column counts." + {:counts counts}))))) + +(defn tabulate + "Return a table, sequence of sequences, from EDN, a sequence of maps." + [edn] + (assert-tabulatable! edn) + (let [header (keys (first edn))] + (letfn [(extract [row] (map row header))] + (cons header (map extract edn))))) diff --git a/api/src/wfl/util.clj b/api/src/wfl/util.clj index 8d9809d2f..fc7e259e6 100644 --- a/api/src/wfl/util.clj +++ b/api/src/wfl/util.clj @@ -1,15 +1,17 @@ (ns wfl.util "Some utilities shared across this program." - (:require [clojure.data.json :as json] + (:require [clojure.data.csv :as csv] + [clojure.data.json :as json] [clojure.java.io :as io] [clojure.java.shell :as shell] + [clojure.spec.alpha :as s] [clojure.string :as str] [clojure.tools.logging :as log] [wfl.wfl :as wfl]) - (:import [java.io File Writer IOException] + (:import [java.io File IOException StringWriter Writer] [java.nio.file Files] [java.nio.file.attribute FileAttribute] - [java.time OffsetDateTime Clock LocalDate] + [java.time OffsetDateTime] [java.time.temporal ChronoUnit] [java.util ArrayList Collections Random UUID] [java.util.concurrent TimeUnit TimeoutException] @@ -21,14 +23,7 @@ [& body] `(try (do ~@body) (catch Exception x# - (log/warn x# "Swallowed exception and returned nil in wfl.util/do-or-nil")))) - -(defmacro do-or-nil-silently - "Value of `body` or `nil` if it throws, without logging exceptions. - See also [[do-or-nil]]." - [& body] - `(try (do ~@body) - (catch Exception x#))) + (log/warn x# "from wfl.util/do-or-nil")))) ;; Parsers that will not throw. ;; @@ -229,6 +224,18 @@ [coll key] (not (contains? coll key))) +(defn unnilify + "Return a map containing only those non-nil entries in `map`." + [map] + {:pre [(map? map)]} + (into {} (filter second map))) + +(defn select-non-nil-keys + "Returns a map containing only those non-nil entries in `map` whose key is + in `keyseq`." + [map keyseq] + (unnilify (select-keys map keyseq))) + (defn on "Apply the function `g` `on` the results of mapping the unary function `f` over each of the input arguments in `xs`. @@ -389,17 +396,6 @@ (letfn [(make-part [[k v]] {:name (name k) :content v})] (map make-part parts))) -(defn today - "Return a ^LocalDate of today's date in UTC." - [] - (LocalDate/now (Clock/systemUTC))) - -(defn days-from-today - "Return n-days from today's date in ^LocalDate, either - backward or forward depends on the sign of n." - [^Integer n] - (.plus (today) n ChronoUnit/DAYS)) - (defn randomize "Append a random suffix to `string`." [string] @@ -421,7 +417,7 @@ [default: 3]." ([task! seconds max-attempts] (loop [attempt 1] - (if-let [result (task!)] + (if-some [result (task!)] result (do (when (<= max-attempts attempt) (throw (TimeoutException. "Max number of attempts exceeded"))) @@ -432,3 +428,152 @@ (poll task seconds 3)) ([task] (poll task 1))) + +"A set of all mutually supported TSV file types (by FireCloud and WFL)" +(s/def ::tsv-type #{:entity :membership}) + +(defn terra-id + " + Generate a Terra-compatible primary key column name for the specified TSV-TYPE and base COL. + + The first column of the table must be its primary key, and named accordingly: + entity:[entity-type]_id + membership:[entity-type]_set_id + + For tsv-type :entity, 'entity:sample_id' will upload the .tsv data into a `sample` table + in the workspace (or create one if it does not exist). + If the table already contains a sample with that id, it will get overwritten. + + For tsv-type :membership, 'membership:sample_set_id' will append sample names to a `sample_set` table + in the workspace (or create one if it does not exist). + If the table already contains a sample set with that id, it will be appended to and not overwritten. + + Parameters + ---------- + tsv-type - A member of ::tsv-type + col - Entity name or primary key column base + + Examples + -------- + (terra_id :entity \"flowcell\") + (terra_id :membership \"flowcell\") + " + [tsv-type col] + {:pre [(s/valid? ::tsv-type tsv-type)]} + (let [stripped (-> (unsuffix col "_id") (unsuffix "_set"))] + (str (name tsv-type) ":" stripped (when (= :membership tsv-type) "_set") "_id"))) + +(defn columns-rows->tsv + " + Write COLUMNS and ROWS to a .tsv named FILE, or to bytes if FILE not specified. + + Examples + -------- + (columns-rows->tsv [c1 c2 c3] [[x1 x2 x3] [y1 y2 y3] ...]) + (columns-rows->tsv [c1 c2 c3] [[x1 x2 x3] [y1 y2 y3] ...] \"destination.tsv\") + " + ([columns rows file] + (with-open [writer (io/writer file)] + (csv/write-csv writer columns :separator \tab) + (csv/write-csv writer rows :separator \tab) + file)) + ([columns rows] + (str (columns-rows->tsv columns rows (StringWriter.))))) + +(defn columns-rows->terra-tsv + " + Write COLUMNS and ROWS to a .tsv named FILE in a Terra-compatible format + as dictated by TSV-TYPE, or to bytes if FILE not specified. + + Parameters + ---------- + tsv-type - A member of ::tsv-type + columns - Column names (first will be formatted as primary key identifier) + rows - Rows with element counts matching the column count + file - [optional] TSV file name to dump + + Examples + -------- + (columns-rows->terra-tsv :entity [c1 c2 c3] [[x1 x2 x3] [y1 y2 y3] ...]) + (columns-rows->terra-tsv :membership [c1 c2 c3] [[x1 x2 x3] [y1 y2 y3] ...] \"dest.tsv\") + " + ([tsv-type columns rows file] + {:pre [(s/valid? ::tsv-type tsv-type)]} + (letfn [(format-entity-type [[head & rest]] + (cons (terra-id tsv-type head) rest))] + (columns-rows->tsv [(format-entity-type columns)] rows file))) + ([tsv-type columns rows] + (str (columns-rows->terra-tsv tsv-type columns rows (StringWriter.))))) + +(gen-class + :name wfl.util.UserException + :extends java.lang.Exception + :implements [clojure.lang.IExceptionInfo] + :constructors {[String] [String] + [String clojure.lang.IPersistentMap] [String] + [String clojure.lang.IPersistentMap Throwable] [String Throwable]} + :state data + :prefix user-exception- + :init init) + +(defn ^:private user-exception-init + ([message] [[message] {}]) + ([message data] [[message] data]) + ([message data cause] [[message cause] data])) + +(defn ^:private user-exception-getData [this] + (.data this)) + +(defn ^:private user-exception-toString [this] + (let [data (.getData this) + cause (.getCause this)] + (cond-> (str (-> this .getClass .getName) ": " (.getMessage this)) + (and data (seq data)) (str " " data) + cause (str " caused by " cause)))) + +(defmulti to-edn + "Return an EDN representation of the `object` that will be shown to users." + (fn [object] (:type object))) + +(defmethod to-edn :default [x] x) + +(def digit? (set "0123456789")) +(def lowercase? (set "abcdefghijklmnopqrstuvwxyz")) +(def uppercase? (set (map #(Character/toUpperCase %) lowercase?))) +(def letter? (into lowercase? uppercase?)) +(def alphanumeric? (into letter? digit?)) +(def spaceunderdash? (set " _-")) +(def terra-allowed? (into alphanumeric? spaceunderdash?)) +(def terra-name? (partial every? terra-allowed?)) + +(defn terra-namespaced-name? + "Return nil or the Terra [namespace name] pair in NAMESPACE-NAME." + [namespace-name] + (let [[namespace name & more] (str/split namespace-name #"/" 3)] + (when (and (nil? more) + (seq namespace) (seq name) + (terra-name? namespace) (terra-name? name)) + [namespace name]))) + +(defmacro make-map + "Map SYMBOLS as keywords to their values in the environment." + [& symbols] + (zipmap (map keyword symbols) symbols)) + +(let [alphanumunderdash? (into (set "-_") alphanumeric?)] + (defn ^:private label-name? + "True if `_s` starts with a letter followed by any number of letters, numbers + underscores or dashes." + [[first & rest :as _s]] + (and (letter? first) (every? alphanumunderdash? rest)))) + +(defn ^:private label-value? + "True if `s` is not a blank string." + [^String s] + (not (str/blank? s))) + +(defn label? + "True if `s` is a string of the form \"name:value\"." + [s] + (let [[name value & rest] (str/split s #":" 3)] + (and (label-name? name) (label-value? value) (nil? rest)))) diff --git a/api/test/resources/workflows/sarscov2_illumina_full/entity-from-outputs.edn b/api/test/resources/workflows/sarscov2_illumina_full/entity-from-outputs.edn new file mode 100644 index 000000000..90ae36dbb --- /dev/null +++ b/api/test/resources/workflows/sarscov2_illumina_full/entity-from-outputs.edn @@ -0,0 +1,52 @@ +{:submission_xml "submission_xml", + :assembled_ids "assembled_ids", + :num_failed_assembly "num_failed_assembly", + :ivar_trim_stats_png "ivar_trim_stats_png", + :read_counts_raw "read_counts_raw", + :num_samples "num_samples", + :vadr_outputs "vadr_outputs", + :cleaned_reads_unaligned_bams "cleaned_reads_unaligned_bams", + :demux_commonBarcodes "demux_commonBarcodes", + :submission_zip "submission_zip", + :cleaned_bams_tiny "cleaned_bams_tiny", + :data_tables_out "data_tables_out", + :ntc_rejected_batches "ntc_rejected_batches", + :picard_metrics_alignment "picard_metrics_alignment", + :failed_assembly_ids "failed_assembly_ids", + :ivar_trim_stats_html "ivar_trim_stats_html", + :assembly_stats_tsv "assembly_stats_tsv", + :failed_annotation_ids "failed_annotation_ids", + :run_date "run_date", + :genbank_source_table "genbank_source_table", + :num_read_files "num_read_files", + :ntc_rejected_lanes "ntc_rejected_lanes", + :gisaid_meta_csv "gisaid_meta_csv", + :primer_trimmed_read_count "primer_trimmed_read_count", + :gisaid_fasta "gisaid_fasta", + :num_submittable "num_submittable", + :submit_ready "submit_ready", + :passing_fasta "passing_fasta", + :nextclade_auspice_json "nextclade_auspice_json", + :read_counts_depleted "read_counts_depleted", + :cleaned_bam_uris "cleaned_bam_uris", + :num_assembled "num_assembled", + :max_ntc_bases "max_ntc_bases", + :genbank_fasta "genbank_fasta", + :multiqc_report_cleaned "multiqc_report_cleaned", + :num_failed_annotation "num_failed_annotation", + :meta_by_filename_json "meta_by_filename_json", + :primer_trimmed_read_percent "primer_trimmed_read_percent", + :assembly_stats_final_tsv "assembly_stats_final_tsv", + :demux_metrics "demux_metrics", + :submittable_ids "submittable_ids", + :sra_metadata "sra_metadata", + :spikein_counts "spikein_counts", + :raw_reads_unaligned_bams "raw_reads_unaligned_bams", + :ivar_trim_stats_tsv "ivar_trim_stats_tsv", + :picard_metrics_wgs "picard_metrics_wgs", + :nextclade_all_json "nextclade_all_json", + :multiqc_report_raw "multiqc_report_raw", + :sequencing_reports "sequencing_reports", + :demux_outlierBarcodes "demux_outlierBarcodes", + :nextmeta_tsv "nextmeta_tsv", + :assemblies_fasta "assemblies_fasta"} diff --git a/api/test/resources/workflows/sarscov2_illumina_full/outputs.edn b/api/test/resources/workflows/sarscov2_illumina_full/outputs.edn index 47f6dc100..7e8edb998 100644 --- a/api/test/resources/workflows/sarscov2_illumina_full/outputs.edn +++ b/api/test/resources/workflows/sarscov2_illumina_full/outputs.edn @@ -1,2252 +1,7682 @@ -{:spikein_counts "gs://broad-gotc-dev-wfl-ptc-test-inputs/sarscov2_illumina_full/outputs/call-demux_deplete/demux_deplete/955c74b3-854a-4075-839f-856d0f41e020/call-spike_summary/cacheCopy/count_summary.tsv", - 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:cleaned_bam_uris "gs://broad-gotc-dev-wfl-ptc-test-inputs/sarscov2_illumina_full/outputs/call-demux_deplete/demux_deplete/955c74b3-854a-4075-839f-856d0f41e020/call-sra_meta_prep/write_lines_bc5302b8fdd987961b17ced77e1da4ab.tmp", - :data_table_status "Upload complete. Check your workspace for new assemblies table! - Upload complete. Check your workspace for new reads table!", - :assembled_ids ["MA_DPH_00361" - "MA_DPH_00362" - "MA_DPH_00363" - "MA_DPH_00365" - "MA_DPH_00366" - "MA_DPH_00368" - "MA_DPH_00369" - "MA_DPH_00370" - "MA_DPH_00371" - "MA_DPH_00372" - "MA_DPH_00373" - "MA_DPH_00374" - "MA_MGH_02716" - "MA_MGH_02719" - "USA/MA-MGH-02662/2020" - "USA/MA-MGH-02688/2020" - "USA/MA-MGH-02690/2020" - "USA/MA-MGH-02691/2020" - "USA/MA-MGH-02692/2020" - "USA/MA-MGH-02694/2020" - "USA/MA-MGH-02695/2020" - "USA/MA-MGH-02696/2020" - "USA/MA-MGH-02699/2020" - "USA/MA-MGH-02702/2020" - "USA/MA-MGH-02703/2020" - "USA/MA-MGH-02705/2020" - "USA/MA-MGH-02707/2020" - "USA/MA-MGH-02709/2020" - "USA/MA-MGH-02711/2020" - "USA/MA-MGH-02714/2020" - "USA/MA-MGH-02715/2020" - "USA/MA-MGH-02718/2020" - "USA/MA-MGH-02721/2020" - "USA/MA-MGH-02725/2020" - "USA/MA-MGH-02726/2020" - "USA/MA-MGH-02727/2020" - "USA/MA-MGH-02728/2020" - "USA/MA-MGH-02730/2020" - "USA/MA-MGH-02731/2020" - "USA/MA-MGH-02732/2020" - "USA/MA-MGH-02733/2020" 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a/api/test/resources/workflows/sarscov2_illumina_full/sarscov2_illumina_full.wdl b/api/test/resources/workflows/sarscov2_illumina_full/sarscov2_illumina_full.wdl index 8b9edbe72..6d19c8a04 100644 --- a/api/test/resources/workflows/sarscov2_illumina_full/sarscov2_illumina_full.wdl +++ b/api/test/resources/workflows/sarscov2_illumina_full/sarscov2_illumina_full.wdl @@ -1 +1 @@ -https://cdn.jsdelivr.net/gh/broadinstitute/viral-pipelines@07868f432c421a66ce1c5affdf5fa4d7cc5504a3/pipes/WDL/workflows/sarscov2_illumina_full.wdl +https://cdn.jsdelivr.net/gh/broadinstitute/viral-pipelines@f288aaf8c135a63ff7caa2b286a45bc6327ea609/pipes/WDL/workflows/sarscov2_illumina_full.wdl diff --git a/api/test/wfl/integration/datarepo_test.clj b/api/test/wfl/integration/datarepo_test.clj index 047f56037..d880aa471 100644 --- a/api/test/wfl/integration/datarepo_test.clj +++ b/api/test/wfl/integration/datarepo_test.clj @@ -2,6 +2,7 @@ (:require [clojure.data.json :as json] [clojure.test :refer [deftest is testing]] [wfl.environment :as env] + [wfl.module.covid :as covid] [wfl.service.datarepo :as datarepo] [wfl.service.firecloud :as firecloud] [wfl.service.google.storage :as gcs] @@ -60,8 +61,7 @@ workflows/make-object-type) workflow-id (UUID/randomUUID)] (fixtures/with-fixtures - [(fixtures/with-temporary-cloud-storage-folder - "broad-gotc-dev-wfl-ptc-test-inputs") + [(fixtures/with-temporary-cloud-storage-folder fixtures/gcs-test-bucket) (fixtures/with-temporary-dataset (datasets/unique-dataset-request tdr-profile dataset-json))] (fn [[temp dataset]] @@ -69,7 +69,7 @@ (-> (->> (workflows/get-files outputs-type outputs) (datasets/ingest-files tdr-profile dataset workflow-id)) (replace-urls-with-file-ids outputs-type outputs) - (datasets/rename-gather from-outputs) + (covid/rename-gather from-outputs) (json/write-str :escape-slash false) (gcs/upload-content table-url)) (let [{:keys [bad_row_count row_count]} @@ -78,17 +78,19 @@ (is (= 1 row_count)) (is (= 0 bad_row_count)))))))) -(def ^:private testing-dataset "ff6e2b40-6497-4340-8947-2f52a658f561") +(def ^:private testing-dataset "85efdfea-52fb-4698-bee6-eef76104a7f4") ;; Get row-ids from BigQuery and use them to create a snapshot. -(deftest test-create-snapshot +;; excluded, the testing-dataset has been removed from dev-TDR +(deftest ^:excluded test-create-snapshot (let [tdr-profile (env/getenv "WFL_TDR_DEFAULT_PROFILE") dataset (datarepo/dataset testing-dataset) - table "flowcell" + table "sample" row-ids (-> (datarepo/query-table-between dataset table - ["2021-03-30" "2021-03-31"] + "datarepo_ingest_date" + ["2021-01-05" "2021-01-07"] [:datarepo_row_id]) :rows flatten)] @@ -97,8 +99,10 @@ #(let [snapshot (datarepo/snapshot %)] (is (= % (:id snapshot))))))) +(def ^:private testing-snapshot-id "7cb392d8-949b-419d-b40b-d039617d2fc7") + (deftest test-flattened-query-result - (let [samplesheets (-> (datarepo/dataset testing-dataset) + (let [samplesheets (-> (datarepo/snapshot testing-snapshot-id) (datarepo/query-table "flowcell" [:samplesheets]) :rows (->> (mapcat first)))] @@ -120,7 +124,7 @@ (defn ^:private make-entity-import-request-tsv [from-dataset columns maps] - (-> (map #(datasets/rename-gather % from-dataset) maps) + (-> (map #(covid/rename-gather % from-dataset) maps) (maps->table columns) bigquery/dump-table->tsv)) @@ -135,8 +139,6 @@ (firecloud/import-entities workspace)) (map #(% primary-key) maps))) -(def ^:private snapshot-id "7cb392d8-949b-419d-b40b-d039617d2fc7") - (def ^:private entity-columns "Return the columns in the `entity-type`." (>>> (juxt :idName :attributeNames) @@ -147,12 +149,12 @@ (let [dataset-table "flowcell" entity "flowcell" from-dataset (resources/read-resource "entity-from-dataset.edn") - columns (-> (firecloud/list-entity-types "wfl-dev/SARSCoV2-Illumina-Full") + columns (-> (firecloud/list-entity-types "pathogen-genomic-surveillance/CDC_Viral_Sequencing_dev") :flowcell entity-columns)] (fixtures/with-temporary-workspace (fn [workspace] - (let [entities (-> (datarepo/snapshot snapshot-id) + (let [entities (-> (datarepo/snapshot testing-snapshot-id) (datarepo/query-table dataset-table) (import-table workspace columns from-dataset)) names (->> #(firecloud/list-entities workspace entity) diff --git a/api/test/wfl/integration/firecloud_test.clj b/api/test/wfl/integration/firecloud_test.clj index c745a3686..25b725e0f 100644 --- a/api/test/wfl/integration/firecloud_test.clj +++ b/api/test/wfl/integration/firecloud_test.clj @@ -1,8 +1,10 @@ (ns wfl.integration.firecloud-test - (:require [clojure.test :refer [deftest is testing]] - [wfl.service.cromwell :as cromwell] + (:require [clojure.string :as str] + [clojure.test :refer [deftest is testing]] + [wfl.service.cromwell :as cromwell] [wfl.service.firecloud :as firecloud] - [wfl.util :as util])) + [wfl.util :as util]) + (:import [java.util UUID])) ;; Of the form NAMESPACE/NAME (def workspace "wfl-dev/Illumina-Genotyping-Array") @@ -12,6 +14,7 @@ ;; An entity is a pair [Type Name] (def entity ["sample" "NA12878"]) +(def entity-set-type (str (first entity) "_set")) ;; A submission that was manually created (def well-known-submission "12ea8b91-737d-4838-972e-05f3c80f3881") @@ -27,17 +30,60 @@ (deftest test-create-submission (util/bracket - #(firecloud/create-submission workspace method-configuration entity) + (comp :submissionId #(firecloud/create-submission workspace method-configuration entity)) #(firecloud/abort-submission workspace %) - #(let [workflow (-> (firecloud/get-submission workspace %) :workflows first)] + #(let [get-workflows (fn [] (:workflows (firecloud/get-submission workspace %))) + workflow (first (get-workflows))] (is (= (second entity) (get-in workflow [:workflowEntity :entityName]))) - (is (#{"Queued" "Submitted"} - ;; GH-1212: `get-submission` can return the workflow before it has - ;; been queued. In such cases :status is nil so try again - (or (:status workflow) (-> (firecloud/get-submission workspace %) - :workflows - first - :status))))))) + (is (not (str/blank? (util/poll (comp :status first get-workflows)))))))) + +(deftest test-create-submissions-for-entity-set + (testing "Empty entity list throws AssertionError" + (is (thrown? AssertionError + (firecloud/create-submission-for-entity-set workspace + method-configuration + [])))) + (doseq [entity-count (range 1 4)] + (testing (str "Submission with " entity-count " matching entit(ies) yields 1 workflow") + (let [entity-set-name (str (UUID/randomUUID))] + (util/bracket + (comp :submissionId + #(firecloud/create-submission-for-entity-set + workspace + method-configuration + (repeat entity-count entity) + entity-set-name)) + #((firecloud/abort-submission workspace %) + (firecloud/delete-entities workspace [[entity-set-type entity-set-name]])) + #(let [get-workflows (fn [] (:workflows (firecloud/get-submission workspace %))) + [workflow & rest] (get-workflows)] + (is (empty? rest)) + (is (= (second entity) (get-in workflow [:workflowEntity :entityName]))) + (is (not (str/blank? (util/poll (comp :status first get-workflows))))))))))) + +(defn ^:private with-entity? + "Check if entity name is found in HTTP response." + [name] (fn [response] (= (:name response) name))) + +(defn ^:private matches-entity? + "Check if entity reference [Type Name] matches item from HTTP response." + [[ref-type ref-name]] (fn [{response-type :entityType response-name :entityName}] + (and (= ref-type response-type) (= ref-name response-name)))) + +(deftest test-import-entity-set + (doseq [entity-count (range 1 4)] + (testing (str "Import entity set with " entity-count " matching entit(ies)") + (let [entity-set-name (str (UUID/randomUUID))] + (util/bracket + #(-> (firecloud/import-entity-set workspace entity-set-name (repeat entity-count entity)) + :body) + #(firecloud/delete-entities workspace [[% entity-set-name]]) + #(let [[entity-response & rest] (->> (firecloud/list-entities workspace %) + (filter (with-entity? entity-set-name))) + items (get-in entity-response [:attributes :samples :items])] + (is (empty? rest)) + (is (= entity-count (count items))) + (is (every? (matches-entity? entity) items)))))))) (defmacro ^:private using-assemble-refbased-workflow-bindings "Define a set of workflow bindings for use in `body`. The values refer to a diff --git a/api/test/wfl/integration/google/bigquery_test.clj b/api/test/wfl/integration/google/bigquery_test.clj index fc68502d2..27a18e227 100644 --- a/api/test/wfl/integration/google/bigquery_test.clj +++ b/api/test/wfl/integration/google/bigquery_test.clj @@ -3,7 +3,7 @@ [wfl.service.google.bigquery :as bigquery])) (def ^:private google-project "broad-jade-dev-data") -(def ^:private dr-dataset "zerosnapshot") +(def ^:private dr-dataset "datarepo_zerotest_partition") (def ^:private dr-view "sample") (deftest test-list-datasets diff --git a/api/test/wfl/integration/jdbc_test.clj b/api/test/wfl/integration/jdbc_test.clj new file mode 100644 index 000000000..c8bcb1087 --- /dev/null +++ b/api/test/wfl/integration/jdbc_test.clj @@ -0,0 +1,24 @@ +(ns wfl.integration.jdbc-test + (:require [clojure.test :refer :all :as clj-test] + [clojure.test] + [wfl.jdbc :as jdbc] + [wfl.service.postgres :as postgres] + [wfl.tools.fixtures :as fixtures])) + +(clj-test/use-fixtures :once fixtures/temporary-postgresql-database) + +(deftest test-jdbc-protocol-extensions + (let [create "CREATE TABLE %s (id SERIAL, arr text[])" + table "test_protocols" + rows ["dog" "cat" "panda"]] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (jdbc/db-do-commands tx [(format create table)]) + + (testing "Insert supports native clojure vector and psql array" + (let [insert-res (jdbc/insert! tx table {:id 1 :arr rows})] + (is (= rows (:arr (first insert-res)))))) + + (testing "Query supports native clojure vector and psql array" + (let [query "SELECT * FROM %s;" + query-res (jdbc/query tx (format query table))] + (is (= rows (:arr (first query-res))))))))) diff --git a/api/test/wfl/integration/modules/aou_test.clj b/api/test/wfl/integration/modules/aou_test.clj index 96864bae3..0ce91ec0a 100644 --- a/api/test/wfl/integration/modules/aou_test.clj +++ b/api/test/wfl/integration/modules/aou_test.clj @@ -1,21 +1,23 @@ (ns wfl.integration.modules.aou-test - (:require [clojure.spec.alpha :as s] - [clojure.test :refer [testing is deftest use-fixtures]] + (:require [clojure.spec.alpha :as s] + [clojure.test :refer [testing is deftest use-fixtures]] [wfl.api.spec] [wfl.integration.modules.shared :as shared] - [wfl.jdbc :as jdbc] - [wfl.module.aou :as aou] - [wfl.tools.fixtures :as fixtures] - [wfl.tools.workloads :as workloads] - [wfl.service.postgres :as postgres] - [wfl.util :as util]) - (:import (java.util UUID))) + [wfl.jdbc :as jdbc] + [wfl.module.aou :as aou] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.workloads :as workloads] + [wfl.util :as util] + [wfl.module.batch :as batch]) + (:import [java.util UUID])) (use-fixtures :once fixtures/temporary-postgresql-database) (defn mock-submit-workload [& _] (UUID/randomUUID)) -(defn mock-update-statuses! [tx {:keys [items workflows]}] - (run! (fn [{:keys [id]}] (jdbc/update! tx items {:status "Succeeded"} ["id = ?" id])) workflows)) +(defn mock-update-statuses! [tx {:keys [items] :as workload}] + (letfn [(f [{:keys [id]}] + (jdbc/update! tx items {:status "Succeeded"} ["id = ?" id]))] + (run! f (workloads/workflows workload)))) (defn ^:private make-aou-workload-request [] (-> (workloads/aou-workload-request (UUID/randomUUID)) @@ -70,17 +72,17 @@ (shared/run-stop-workload-state-transition-test! (make-aou-workload-request))) (deftest test-aou-workload-not-finished-until-stopped - (with-redefs-fn {#'aou/submit-aou-workflow mock-submit-workload - #'postgres/update-workflow-statuses! mock-update-statuses!} + (with-redefs-fn {#'aou/submit-aou-workflow mock-submit-workload + #'batch/update-workflow-statuses! mock-update-statuses!} #(let [workload (-> (make-aou-workload-request) (workloads/execute-workload!) (workloads/update-workload!))] (is (not (:finished workload))) (workloads/append-to-workload! [workloads/aou-sample] workload) (let [workload (workloads/load-workload-for-uuid (:uuid workload))] - (is (every? (comp #{"Submitted"} :status) (:workflows workload))) + (is (every? (comp #{"Submitted"} :status) (workloads/workflows workload))) (let [workload (workloads/update-workload! workload)] - (is (every? (comp #{"Succeeded"} :status) (:workflows workload))) + (is (every? (comp #{"Succeeded"} :status) (workloads/workflows workload))) (is (not (:finished workload)))))))) ;; rr: GH-1071 diff --git a/api/test/wfl/integration/modules/arrays_test.clj b/api/test/wfl/integration/modules/arrays_test.clj index 5a8f9b634..dc4a4d3a1 100644 --- a/api/test/wfl/integration/modules/arrays_test.clj +++ b/api/test/wfl/integration/modules/arrays_test.clj @@ -4,7 +4,7 @@ [wfl.service.firecloud :as terra] [wfl.tools.fixtures :as fixtures] [wfl.tools.workloads :as workloads]) - (:import (java.util UUID))) + (:import [java.util UUID])) (use-fixtures :once @@ -12,7 +12,8 @@ (fixtures/temporary-environment {"WFL_FIRECLOUD_URL" "https://firecloud-orchestration.dsde-dev.broadinstitute.org"})) -(defn ^:private mock-terra-create-submission [& _] (UUID/randomUUID)) +(defn ^:private mock-terra-create-submission [& _] + {:submissionId (UUID/randomUUID)}) (defn ^:private mock-get-workflow-status-by-entity [& _] "Succeeded") @@ -38,7 +39,7 @@ (deftest test-create-arrays-workload! (let [workload (-> (make-arrays-workload-request) workloads/create-workload!)] - (run! check-inputs (:workflows workload)))) + (run! check-inputs (workloads/workflows workload)))) (deftest test-workload-state-transition (with-redefs-fn @@ -57,24 +58,26 @@ workloads/create-workload! workloads/start-workload!)] (is (:started workload)) - (run! check-inputs (:workflows workload)) - (run! check-workflow (:workflows workload))))) + (let [workflows (workloads/workflows workload)] + (run! check-inputs workflows) + (run! check-workflow workflows))))) (deftest test-exec-arrays-workload! (with-redefs-fn {#'terra/create-submission mock-terra-create-submission} #(let [workload (-> (make-arrays-workload-request) workloads/execute-workload!)] (is (:started workload)) - (run! check-inputs (:workflows workload)) - (run! check-workflow (:workflows workload))))) + (let [workflows (workloads/workflows workload)] + (run! check-inputs workflows) + (run! check-workflow workflows))))) -(deftest test-update-arrays-workload! +(deftest ^:excluded test-update-arrays-workload! (letfn [(check-status [status workflow] (is (= status (:status workflow))))] (with-redefs-fn {#'terra/get-workflow-status-by-entity mock-get-workflow-status-by-entity} #(let [workload (-> (make-arrays-workload-request) workloads/execute-workload!)] - (run! (partial check-status "Submitted") (:workflows workload)) + (run! (partial check-status "Submitted") (workloads/workflows workload)) (let [updated-workload (workloads/update-workload! workload)] - (run! (partial check-status "Succeeded") (:workflows updated-workload)) + (run! (partial check-status "Succeeded") (workloads/workflows updated-workload)) (is (:finished updated-workload))))))) diff --git a/api/test/wfl/integration/modules/copyfile_test.clj b/api/test/wfl/integration/modules/copyfile_test.clj index 9ac2940e7..7e8bf1c74 100644 --- a/api/test/wfl/integration/modules/copyfile_test.clj +++ b/api/test/wfl/integration/modules/copyfile_test.clj @@ -1,19 +1,20 @@ (ns wfl.integration.modules.copyfile-test - (:require [clojure.test :refer [deftest testing is] :as clj-test] - [clojure.string :as str] + (:require [clojure.test :refer [deftest testing is use-fixtures]] + [clojure.string :as str] [wfl.integration.modules.shared :as shared] - [wfl.jdbc :as jdbc] - [wfl.module.all :as all] - [wfl.module.copyfile :as copyfile] - [wfl.service.cromwell :as cromwell] - [wfl.service.postgres :as postgres] - [wfl.tools.fixtures :as fixtures] - [wfl.tools.workloads :as workloads] - [wfl.util :as util]) - (:import (java.util UUID) - (java.time OffsetDateTime))) + [wfl.jdbc :as jdbc] + [wfl.module.all :as all] + [wfl.module.batch :as batch] + [wfl.module.copyfile :as copyfile] + [wfl.service.cromwell :as cromwell] + [wfl.service.postgres :as postgres] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.workloads :as workloads] + [wfl.util :as util]) + (:import [java.util UUID] + [java.time OffsetDateTime])) -(clj-test/use-fixtures :once fixtures/temporary-postgresql-database) +(use-fixtures :once fixtures/temporary-postgresql-database) (defn ^:private make-copyfile-workload-request [src dst] @@ -22,7 +23,7 @@ (defn ^:private old-create-copyfile-workload! [] (let [request (make-copyfile-workload-request "gs://fake/input" "gs://fake/output")] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (let [[id table] (all/add-workload-table! tx copyfile/workflow-wdl request) add-id (fn [m id] (assoc (:inputs m) :id id))] (jdbc/insert-multi! tx table (map add-id (:items request) (range))) @@ -55,7 +56,7 @@ (partial map #(assoc % :options {:supports_options true :overwritten true}))) workloads/execute-workload! - :workflows + workloads/workflows (->> (map (comp verify-workflow-options :options)))))))) (deftest test-submitted-workflow-inputs @@ -89,20 +90,20 @@ (assoc-in [:common :options] {}) (update :items (partial map #(assoc % :options {}))) workloads/create-workload! - :workflows)))) + workloads/workflows)))) (defn mock-batch-update-workflow-statuses! - [tx {:keys [workflows items] :as _workload}] + [tx {:keys [items] :as workload}] (letfn [(update! [{:keys [id]}] (jdbc/update! tx items {:status "Succeeded" :updated (OffsetDateTime/now)} ["id = ?" id]))] - (run! update! workflows))) + (run! update! (workloads/workflows workload)))) (deftest test-workload-state-transition (with-redefs-fn {#'cromwell/submit-workflow (fn [& _] (UUID/randomUUID)) - #'postgres/batch-update-workflow-statuses! mock-batch-update-workflow-statuses!} + #'batch/batch-update-workflow-statuses! mock-batch-update-workflow-statuses!} #(shared/run-workload-state-transition-test! (make-copyfile-workload-request "gs://b/in" "gs://b/out")))) diff --git a/api/test/wfl/integration/modules/covid_test.clj b/api/test/wfl/integration/modules/covid_test.clj new file mode 100644 index 000000000..0b9089363 --- /dev/null +++ b/api/test/wfl/integration/modules/covid_test.clj @@ -0,0 +1,751 @@ +(ns wfl.integration.modules.covid-test + "Test the Sarscov2IlluminaFull COVID pipeline." + (:require [clojure.test :refer :all] + [clojure.set :as set] + [clojure.spec.alpha :as s] + [clojure.string :as str] + [reitit.coercion.spec] + [reitit.ring :as ring] + [reitit.ring.coercion :as coercion] + [wfl.api.spec :as spec] + [wfl.api.spec :as spec] + [wfl.integration.modules.shared :as shared] + [wfl.jdbc :as jdbc] + [wfl.module.covid :as covid] + [wfl.service.firecloud :as firecloud] + [wfl.service.postgres :as postgres] + [wfl.service.rawls :as rawls] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.workloads :as workloads] + [wfl.tools.resources :as resources] + [wfl.util :as util]) + (:import [java.lang Math] + [java.time LocalDateTime] + [java.util ArrayDeque UUID] + [wfl.util UserException])) + +;; Snapshot creation mock +(def ^:private mock-new-rows-size 2021) +(defn ^:private mock-find-new-rows [_ interval] + (is (every? #(LocalDateTime/parse % @#'covid/bigquery-datetime-format) interval)) + (take mock-new-rows-size (range))) +(defn ^:private mock-create-snapshots [_ _ row-ids] + (letfn [(f [idx shard] [(vec shard) (format "mock_job_id_%s" idx)])] + (->> (partition-all 500 row-ids) + (map-indexed f)))) + +;; Note this mock only covers happy paths of TDR jobs +(defn ^:private mock-check-tdr-job [job-id] + {:snapshot_id (str (UUID/randomUUID)) + :job_status "succeeded" + :id job-id}) + +(def ^:private testing-dataset "cd25d59e-1451-44d0-8a24-7669edb9a8f8") +(def ^:private testing-snapshot "e8f1675e-1e7c-48b4-92ab-3598425c149d") +(def ^:private testing-workspace "wfl-dev/CDC_Viral_Sequencing") +(def ^:private testing-method-name "sarscov2_illumina_full") +(def ^:private testing-method-configuration (str "cdc-covid-surveillance/" testing-method-name)) +(def ^:private testing-method-configuration-version 2) +(def ^:private testing-table-name "flowcells") +(def ^:private testing-column-name "run_date") + +;; Queue mocks +(def ^:private testing-queue-type "TestQueue") +(defn ^:private make-queue-from-list [items] + {:type testing-queue-type :queue (ArrayDeque. items)}) + +(defn ^:private testing-queue-peek [this] + (-> this :queue .getFirst)) + +(defn ^:private testing-queue-pop [this] + (-> this :queue .removeFirst)) + +(defn ^:private testing-queue-length [this] + (-> this :queue .size)) + +(defn ^:private testing-queue-done? [this] + (-> this :queue .empty)) + +(let [new-env {"WFL_FIRECLOUD_URL" "https://api.firecloud.org" + "WFL_TDR_URL" "https://data.terra.bio" + "WFL_RAWLS_URL" "https://rawls.dsde-prod.broadinstitute.org"}] + + (use-fixtures :once + (fixtures/temporary-environment new-env) + fixtures/temporary-postgresql-database + (fixtures/method-overload-fixture + covid/peek-queue! testing-queue-type testing-queue-peek) + (fixtures/method-overload-fixture + covid/pop-queue! testing-queue-type testing-queue-pop) + (fixtures/method-overload-fixture + covid/queue-length! testing-queue-type testing-queue-length) + (fixtures/method-overload-fixture + covid/done? testing-queue-type testing-queue-done?))) + +(deftest test-create-workload + (letfn [(verify-source [{:keys [type last_checked details]}] + (is (= type "TerraDataRepoSource")) + (is (not last_checked) "The TDR should not have been checked yet") + (is (str/starts-with? details "TerraDataRepoSource_"))) + (verify-executor [{:keys [type details]}] + (is (= type "TerraExecutor")) + (is (str/starts-with? details "TerraExecutor_"))) + (verify-sink [{:keys [type details]}] + (is (= type "TerraWorkspaceSink")) + (is (str/starts-with? details "TerraWorkspaceSink_")))] + (let [{:keys [created creator source executor sink labels watchers] :as workload} + (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:skipValidation true}))] + (is created "workload is missing :created timestamp") + (is creator "workload is missing :creator field") + (is (and source (verify-source source))) + (is (and executor (verify-executor executor))) + (is (and sink (verify-sink sink))) + (is (seq labels) "workload did not contain any labels") + (is (contains? (set labels) (str "project:" @workloads/project))) + (is (util/absent? workload :pipeline) ":pipeline should not be defined") + (is (vector? watchers))))) + +(deftest test-workload-to-edn + (let [request (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:skipValidation true}) + _ (is (s/valid? ::spec/workload-request request) + (s/explain-str ::spec/workload-request request)) + workload (util/to-edn (workloads/create-workload! request))] + (is (not-any? workload [:id + :items + :source_type + :source_items + :executor_type + :executor_items + :sink_type + :sink_items + :type])) + (is (not-any? (:source workload) [:id :details :type :last_checked])) + (is (not-any? (:executor workload) [:id :details :type])) + (is (not-any? (:sink workload) [:id :details :type])))) + +(deftest test-create-covid-workload-with-misnamed-source + (is (thrown-with-msg? + UserException #"Invalid request" + (workloads/create-workload! + (workloads/covid-workload-request + {:name "bad name"} + {:skipValidation true} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-valid-source-request + (is (workloads/create-workload! + (workloads/covid-workload-request + {:dataset testing-dataset + :table testing-table-name + :column testing-column-name} + {:skipValidation true} + {:skipValidation true})))) + +(deftest test-create-covid-workload-with-non-existent-dataset + (is (thrown-with-msg? + UserException #"Cannot access dataset" + (workloads/create-workload! + (workloads/covid-workload-request + {:dataset util/uuid-nil} + {:skipValidation true} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-invalid-dataset-table + (is (thrown-with-msg? + UserException #"Table not found" + (workloads/create-workload! + (workloads/covid-workload-request + {:dataset testing-dataset + :table "no_such_table"} + {:skipValidation true} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-invalid-dataset-column + (is (thrown-with-msg? + UserException #"Column not found" + (workloads/create-workload! + (workloads/covid-workload-request + {:dataset testing-dataset + :table testing-table-name + :column "no_such_column"} + {:skipValidation true} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-empty-snapshot-list + (is (workloads/create-workload! + (workloads/covid-workload-request + {:name "TDR Snapshots" + :snapshots [testing-snapshot]} + {:skipValidation true} + {:skipValidation true})))) + +(deftest test-create-covid-workload-with-invalid-snapshot + (is (thrown-with-msg? + UserException #"Cannot access snapshot" + (workloads/create-workload! + (workloads/covid-workload-request + {:name "TDR Snapshots" + :snapshots [util/uuid-nil]} + {:skipValidation true} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-valid-executor-request + (is (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:workspace testing-workspace + :methodConfiguration testing-method-configuration + :methodConfigurationVersion testing-method-configuration-version + :fromSource "importSnapshot"} + {:skipValidation true})))) + +(deftest test-create-covid-workload-with-misnamed-executor + (is (thrown-with-msg? + UserException #"Invalid request" + (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:name "bad name"} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-valid-executor-request + (is (thrown-with-msg? + UserException #"Unsupported coercion" + (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:workspace testing-workspace + :methodConfiguration testing-method-configuration + :methodConfigurationVersion testing-method-configuration-version + :fromSource "frobnicate"} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-wrong-method-configuration + (is (thrown-with-msg? + UserException #"Method configuration version mismatch" + (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:workspace testing-workspace + :methodConfiguration testing-method-configuration + :methodConfigurationVersion -1 + :fromSource "importSnapshot"} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-wrong-method-configuration + (is (thrown-with-msg? + UserException #"Cannot access method configuration" + (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:workspace testing-workspace + :methodConfiguration "no_such/method_configuration" + :fromSource "importSnapshot"} + {:skipValidation true}))))) + +(deftest test-create-covid-workload-with-valid-sink-request + (is (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:workspace testing-workspace + :entityType "assemblies" + :identity "Who cares?" + :fromOutputs {:assemblies_id "foo"}})))) + +(deftest test-create-covid-workload-with-invalid-sink-entity-type + (let [request (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:workspace testing-workspace + :entityType "does_not_exist" + :identity "Who cares?" + :fromOutputs {}})] + (is (thrown-with-msg? + UserException (re-pattern covid/unknown-entity-type-error-message) + (workloads/create-workload! request))))) + +(deftest test-create-covid-workload-with-malformed-fromOutputs + (let [request (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:workspace testing-workspace + :entityType "assemblies" + :identity "Who cares?" + :fromOutputs "geoff"})] + (is (thrown-with-msg? + UserException (re-pattern covid/malformed-from-outputs-error-message) + (workloads/create-workload! request))))) + +(deftest test-create-covid-workload-with-unknown-attributes-listed-in-fromOutputs + (let [request (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:workspace testing-workspace + :entityType "assemblies" + :identity "Who cares?" + :fromOutputs {:does_not_exist "genbank_source_table"}})] + (is (thrown-with-msg? + UserException (re-pattern covid/unknown-attributes-error-message) + (workloads/create-workload! request))))) + +(deftest test-create-covid-workload-with-invalid-sink-workspace + (is (thrown-with-msg? + UserException #"Cannot access workspace" + (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:workspace "moo/moo" + :entityType "moo" + :identity "reads_id" + :fromOutputs {:submission_xml "submission_xml"}}))))) + +(deftest test-start-workload + (let [workload (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:skipValidation true}))] + (is (not (:started workload))) + (is (:started (workloads/start-workload! workload))))) + +;; Mocks + +(def ^:private fake-method-name "method-name") +(def ^:private fake-method-config (str "method-namespace/" fake-method-name)) +;; Snapshot and snapshot reference mocks +(def ^:private snapshot + {:name "test-snapshot-name" :id (str (UUID/randomUUID))}) + +(def ^:private snapshot-reference-id (str (UUID/randomUUID))) +(def ^:private snapshot-reference-name (str (:name snapshot) "-ref")) +(defn ^:private mock-rawls-create-snapshot-reference [& _] + {:referenceId snapshot-reference-id + :name snapshot-reference-name}) + +(def ^:private method-config-version-mock 1) + +(defn ^:private mock-firecloud-get-method-configuration [& _] + {:methodConfigVersion method-config-version-mock}) + +(defn ^:private mock-firecloud-update-method-configuration + [_ _ {:keys [dataReferenceName methodConfigVersion]}] + (is (= dataReferenceName snapshot-reference-name) + "Snapshot reference name should be passed to method config update") + (is (= methodConfigVersion (inc method-config-version-mock)) + "Incremented version should be passed to method config update") + nil) + +(def ^:private submission-id-mock (str (UUID/randomUUID))) + +(def ^:private running-workflow-mock + {:entityName "entity" + :id (str (UUID/randomUUID)) + :inputs {:input "value"} + :status "Running" + :workflowName fake-method-name}) + +(def ^:private succeeded-workflow-mock + {:entityName "entity" + :id (str (UUID/randomUUID)) + :inputs {:input "value"} + :status "Succeeded" + :workflowName fake-method-name}) + +;; when we create submissions, workflows have been queued for execution +(defn ^:private mock-firecloud-create-submission [& _] + (let [enqueue #(-> % (dissoc :id) (assoc :staus "Queued"))] + {:submissionId submission-id-mock + :workflows (map enqueue [running-workflow-mock succeeded-workflow-mock])})) + +;; when we get the submission later, the workflows may have a uuid assigned +(defn ^:private mock-firecloud-get-submission [& _] + (letfn [(add-workflow-entity [{:keys [entityName] :as workflow}] + (-> workflow + (set/rename-keys {:id :workflowId}) + (assoc :workflowEntity {:entityType "test" :entityName entityName}) + (dissoc :entityName)))] + {:submissionId submission-id-mock + :workflows (map add-workflow-entity [running-workflow-mock succeeded-workflow-mock])})) + +(defn ^:private mock-firecloud-create-failed-submission [& _] + {:submissionId submission-id-mock + :workflows [{:status "Failed" + :uuid (str (UUID/randomUUID)) + :entityName "failed"} + {:status "Aborted" + :uuid (str (UUID/randomUUID)) + :entityName "aborted"}]}) + +;; Workflow fetch mocks within update-workflow-statuses! +(defn ^:private mock-workflow-update-status [_ _ workflow-id] + (is (not (= (:workflowId succeeded-workflow-mock) workflow-id)) + "Successful workflow records should be filtered out before firecloud fetch") + {:status "Succeeded" :id workflow-id :workflowName fake-method-name}) + +(defn ^:private mock-workflow-keep-status [_ _ workflow-id] + (is (not (= (:workflowId succeeded-workflow-mock) workflow-id)) + "Successful workflow records should be filtered out before firecloud fetch") + running-workflow-mock) + +(defn ^:private mock-firecloud-get-workflow-outputs [_ _ workflow] + (is (= (:id succeeded-workflow-mock) workflow)) + {:tasks + {:noise + {} + (keyword fake-method-name) + {:outputs + (util/prefix-keys {:output "value"} (str fake-method-name "."))}}}) + +(defn ^:private create-tdr-source [] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> {:name "Terra DataRepo", + :dataset "this" + :table "is" + :column "fun" + :skipValidation true} + (covid/create-source! tx (rand-int 1000000)) + (zipmap [:source_type :source_items]) + (covid/load-source! tx)))) + +(defn ^:private reload-source [tx {:keys [type id] :as _source}] + (covid/load-source! tx {:source_type type :source_items (str id)})) + +(deftest test-start-tdr-source + (let [source (create-tdr-source)] + (is (-> source :last_checked nil?)) + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (covid/start-source! tx source) + (is (:last_checked (reload-source tx source)) + ":last_checked was not updated")))) + +(deftest test-update-tdr-source + (let [source (create-tdr-source) + expected-num-records (int (Math/ceil (/ mock-new-rows-size 500)))] + (with-redefs-fn + {#'covid/create-snapshots mock-create-snapshots + #'covid/find-new-rows mock-find-new-rows + #'covid/check-tdr-job mock-check-tdr-job} + (fn [] + (covid/update-source! + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (covid/start-source! tx source) + (reload-source tx source))) + (is (== expected-num-records (covid/queue-length! source)) + "snapshots should be enqueued") + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (let [records (->> source :details (postgres/get-table tx))] + (letfn [(record-updated? [record] + (and (= "succeeded" (:snapshot_creation_job_status record)) + (not (nil? (:snapshot_creation_job_id record))) + (not (nil? (:snapshot_id record)))))] + (testing "source details got updated with correct number of snapshot jobs" + (is (= expected-num-records (count records)))) + (testing "all snapshot jobs were updated and corresponding snapshot ids were inserted" + (is (every? record-updated? records)))))) + (covid/update-source! + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (covid/stop-source! tx source) + (reload-source tx source))) + (is (== expected-num-records (covid/queue-length! source)) + "no more snapshots should be enqueued") + (is (not (covid/done? source)) "the tdr source was done before snapshots were consumed"))))) + +(deftest test-stop-tdr-sourced + (let [source (create-tdr-source)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (covid/start-source! tx source) + (covid/stop-source! tx source) + (let [source (reload-source tx source)] + (is (:stopped (reload-source tx source)) ":stopped was not written"))))) + +(defn ^:private create-tdr-snapshot-list [snapshots] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> {:name "TDR Snapshots" + :snapshots snapshots + :skipValidation true} + (covid/create-source! tx (rand-int 1000000)) + (zipmap [:source_type :source_items]) + (covid/load-source! tx)))) + +(defn ^:private create-terra-executor [id] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> {:name "Terra" + :workspace "workspace-ns/workspace-name" + :methodConfiguration fake-method-config + :methodConfigurationVersion method-config-version-mock + :fromSource "importSnapshot" + :skipValidation true} + (covid/create-executor! tx id) + (zipmap [:executor_type :executor_items]) + (covid/load-executor! tx)))) + +(deftest test-update-terra-executor + (let [source (create-tdr-snapshot-list [snapshot]) + executor (create-terra-executor (rand-int 1000000))] + (letfn [(verify-record-against-workflow [record workflow idx] + (is (= idx (:id record)) + "The record ID was incorrect given the workflow order in mocked submission") + (is (= (:id workflow) (:workflow record)) + "The workflow ID was incorrect and should match corresponding record"))] + (with-redefs-fn + {#'rawls/create-snapshot-reference mock-rawls-create-snapshot-reference + #'firecloud/get-method-configuration mock-firecloud-get-method-configuration + #'firecloud/update-method-configuration mock-firecloud-update-method-configuration + #'firecloud/submit-method mock-firecloud-create-submission + #'firecloud/get-submission mock-firecloud-get-submission + #'firecloud/get-workflow mock-workflow-update-status} + #(covid/update-executor! source executor)) + (is (zero? (covid/queue-length! source)) "The snapshot was not consumed.") + (is (== 2 (covid/queue-length! executor)) "Two workflows should be enqueued") + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (let [[running-record succeeded-record & _ :as records] + (->> executor :details (postgres/get-table tx) (sort-by :id)) + executor-record + (#'covid/load-record-by-id! tx "TerraExecutor" (:id executor))] + (is (== 2 (count records)) + "Exactly 2 workflows should have been written to the database") + (is (every? #(= snapshot-reference-id (:reference %)) records) + "The snapshot reference ID was incorrect and should match all records") + (is (every? #(= submission-id-mock (:submission %)) records) + "The submission ID was incorrect and should match all records") + (is (every? #(= "Succeeded" (:status %)) records) + "Status update mock should have marked running workflow as succeeded") + (is (every? #(nil? (:consumed %)) records) + "All records should be unconsumed") + (is (not (covid/done? executor)) "executor should not have finished processing") + (verify-record-against-workflow running-record running-workflow-mock 1) + (verify-record-against-workflow succeeded-record succeeded-workflow-mock 2) + (is (== (inc method-config-version-mock) (:method_configuration_version executor-record)) + "Method configuration version was not incremented.")))))) + +(deftest test-peek-terra-executor-queue + (let [succeeded? #{"Succeeded"} + source (create-tdr-snapshot-list [snapshot]) + executor (create-terra-executor (rand-int 1000000))] + (with-redefs-fn + {#'rawls/create-snapshot-reference mock-rawls-create-snapshot-reference + #'firecloud/get-method-configuration mock-firecloud-get-method-configuration + #'firecloud/update-method-configuration mock-firecloud-update-method-configuration + #'firecloud/submit-method mock-firecloud-create-submission + #'firecloud/get-submission mock-firecloud-get-submission + #'firecloud/get-workflow mock-workflow-keep-status} + #(covid/update-executor! source executor)) + (with-redefs-fn + {#'firecloud/get-workflow (constantly succeeded-workflow-mock) + #'firecloud/get-workflow-outputs mock-firecloud-get-workflow-outputs} + #(let [workflow (covid/peek-queue! executor)] + (is (succeeded? (:status workflow))) + (is (= (:id succeeded-workflow-mock) (:uuid workflow))) + (is (contains? workflow :updated)) + (is (= "value" (-> workflow :inputs :input))) + (is (= "value" (-> workflow :outputs :output))) + (is (not (-> workflow :outputs :noise))) + (covid/pop-queue! executor) + (is (nil? (covid/peek-queue! executor))) + (is (== 1 (covid/queue-length! executor))) + (is (not (covid/done? executor))))))) + +(def ^:private fake-entity-type "flowcell") +(def ^:private fake-entity-name "test") + +(deftest test-update-terra-workspace-sink + (let [workflow {:uuid "2768b29e-c808-4bd6-a46b-6c94fd2a67aa" + :status "Succeeded" + :outputs (-> "sarscov2_illumina_full/outputs.edn" + resources/read-resource + (assoc :flowcell_id fake-entity-name))} + executor (make-queue-from-list [workflow]) + sink (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> {:name "Terra Workspace" + :workspace "workspace-ns/workspace-name" + :entityType fake-entity-type + :fromOutputs (resources/read-resource + "sarscov2_illumina_full/entity-from-outputs.edn") + :identifier "flowcell_id" + :skipValidation true} + (covid/create-sink! tx (rand-int 1000000)) + (zipmap [:sink_type :sink_items]) + (covid/load-sink! tx)))] + (letfn [(verify-upsert-request [workspace [[type name _]]] + (is (= "workspace-ns/workspace-name" workspace)) + (is (= type fake-entity-type)) + (is (= name fake-entity-name))) + (throw-if-called [fname & args] + (throw (ex-info (str fname " should not have been called") + {:called-with args})))] + (with-redefs-fn + {#'rawls/batch-upsert verify-upsert-request + #'covid/entity-exists? (constantly false) + #'firecloud/delete-entities (partial throw-if-called "delete-entities")} + #(covid/update-sink! executor sink)) + (is (zero? (covid/queue-length! executor)) "The workflow was not consumed") + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (let [[record & rest] (->> sink :details (postgres/get-table tx))] + (is record "The record was not written to the database") + (is (empty? rest) "More than one record was written") + (is (= (:uuid workflow) (:workflow record)) + "The workflow UUID was not written") + (is (= fake-entity-name (:entity record)) + "The entity was not correct")))))) + +(deftest test-sinking-resubmitted-workflow + (fixtures/with-temporary-workspace + (fn [workspace] + (let [workflow1 {:uuid "2768b29e-c808-4bd6-a46b-6c94fd2a67aa" + :status "Succeeded" + :outputs {:run_id fake-entity-name + :results ["aligned-thing.cram"]}} + workflow2 {:uuid "2768b29e-c808-4bd6-a46b-6c94fd2a67ab" + :status "Succeeded" + :outputs {:run_id fake-entity-name + :results ["another-aligned-thing.cram"]}} + executor (make-queue-from-list [workflow1 workflow2]) + sink (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (->> {:name "Terra Workspace" + :workspace workspace + :entityType fake-entity-type + :fromOutputs {:aligned_crams "results"} + :identifier "run_id" + :skipValidation true} + (covid/create-sink! tx (rand-int 1000000)) + (zipmap [:sink_type :sink_items]) + (covid/load-sink! tx)))] + (covid/update-sink! executor sink) + (is (== 1 (covid/queue-length! executor)) + "one workflow should have been consumed") + (let [{:keys [entityType name attributes]} + (firecloud/get-entity workspace [fake-entity-type fake-entity-name])] + (is (= fake-entity-type entityType)) + (is (= fake-entity-name name)) + (is (== 1 (count attributes))) + (is (= [:aligned_crams {:itemsType "AttributeValue" :items ["aligned-thing.cram"]}] + (first attributes)))) + (covid/update-sink! executor sink) + (is (zero? (covid/queue-length! executor)) + "one workflow should have been consumed") + (let [entites (firecloud/list-entities workspace fake-entity-type)] + (is (== 1 (count entites)) + "No new entities should have been added")) + (let [{:keys [entityType name attributes]} + (firecloud/get-entity workspace [fake-entity-type fake-entity-name])] + (is (= fake-entity-type entityType)) + (is (= fake-entity-name name)) + (is (== 1 (count attributes))) + (is (= [:aligned_crams {:itemsType "AttributeValue" :items ["another-aligned-thing.cram"]}] + (first attributes)) + "attributes should have been overwritten")))))) + +(deftest test-tdr-snapshot-list-to-edn + (let [source (util/to-edn (create-tdr-snapshot-list [snapshot]))] + (is (not-any? source [:id :type])) + (is (= (:snapshots source) [(:id snapshot)])) + (is (s/valid? ::spec/snapshot-list-source source)))) + +(deftest test-get-workflows-empty + (let [workload (workloads/create-workload! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:skipValidation true}))] + (is (empty? (workloads/workflows workload))))) + +(deftest test-workload-state-transition + (with-redefs-fn + {#'covid/find-new-rows mock-find-new-rows + #'covid/create-snapshots mock-create-snapshots + #'covid/check-tdr-job mock-check-tdr-job + #'rawls/create-snapshot-reference mock-rawls-create-snapshot-reference + #'firecloud/get-method-configuration mock-firecloud-get-method-configuration + #'firecloud/update-method-configuration mock-firecloud-update-method-configuration + #'firecloud/submit-method mock-firecloud-create-submission + #'firecloud/get-submission mock-firecloud-get-submission + #'firecloud/get-workflow mock-workflow-keep-status} + #(shared/run-workload-state-transition-test! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:skipValidation true})))) + +(deftest test-batch-workload-state-transition + (shared/run-workload-state-transition-test! + (workloads/covid-workload-request + {:name "TDR Snapshots" + :snapshots []} + {:skipValidation true} + {:skipValidation true}))) + +(deftest test-stop-workload-state-transition + (shared/run-stop-workload-state-transition-test! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:skipValidation true}))) + +(deftest test-workload-state-transition-with-failed-workflow + (with-redefs-fn + {#'covid/find-new-rows mock-find-new-rows + #'covid/create-snapshots mock-create-snapshots + #'covid/check-tdr-job mock-check-tdr-job + #'rawls/create-snapshot-reference mock-rawls-create-snapshot-reference + #'firecloud/get-method-configuration mock-firecloud-get-method-configuration + #'firecloud/update-method-configuration mock-firecloud-update-method-configuration + #'firecloud/submit-method mock-firecloud-create-submission + #'firecloud/get-workflow (constantly {:status "Failed"})} + #(shared/run-workload-state-transition-test! + (workloads/covid-workload-request + {:skipValidation true} + {:skipValidation true} + {:skipValidation true})))) + +(defn ^:private create-app [input-spec output-spec handler] + (let [app + (ring/ring-handler + (ring/router + [["/test" {:post {:parameters {:body input-spec} + :responses {200 {:body output-spec}} + :handler (fn [{:keys [body-params]}] + {:status 200 + :body (handler body-params)})}}]] + {:data {:coercion reitit.coercion.spec/coercion + :middleware [coercion/coerce-exceptions-middleware + coercion/coerce-request-middleware + coercion/coerce-response-middleware]}}))] + (fn [request] + (app {:request-method :post + :uri "/test" + :body-params request})))) + +(deftest test-create-workload-coercion + (let [app (create-app ::spec/workload-request + ::spec/workload-response + (comp util/to-edn workloads/create-workload!)) + request (workloads/covid-workload-request + {} + {:skipValidation true} + {:skipValidation true})] + (testing "Workload with a TDR Source" + (let [{:keys [status body]} + (->> {:name "Terra DataRepo" + :dataset testing-dataset + :table testing-table-name + :column testing-column-name + :snapshotReaders ["workflow-launcher-dev@firecloud.org"]} + (assoc request :source) + app)] + (is (== 200 status) body))) + (testing "Workload with a TDR Snapshots Source" + (let [{:keys [status body]} + (->> {:name "TDR Snapshots" + :snapshots [testing-snapshot]} + (assoc request :source) + app)] + (is (== 200 status) body))))) diff --git a/api/test/wfl/integration/modules/sg_test.clj b/api/test/wfl/integration/modules/sg_test.clj index 617a9556a..1b6542e9b 100644 --- a/api/test/wfl/integration/modules/sg_test.clj +++ b/api/test/wfl/integration/modules/sg_test.clj @@ -1,19 +1,18 @@ (ns wfl.integration.modules.sg-test - (:require [clojure.string :as str] - [clojure.test :refer [deftest is testing use-fixtures]] + (:require [clojure.string :as str] + [clojure.test :refer :all] [wfl.integration.modules.shared :as shared] - [wfl.module.batch :as batch] - [wfl.module.sg :as sg] - [wfl.service.clio :as clio] - [wfl.service.cromwell :as cromwell] - [wfl.service.google.storage :as gcs] - [wfl.tools.fixtures :as fixtures] - [wfl.tools.workloads :as workloads] - [wfl.util :as util :refer [absent?]] - [wfl.service.postgres :as postgres] - [wfl.jdbc :as jdbc]) - (:import (java.time OffsetDateTime) - (java.util UUID))) + [wfl.jdbc :as jdbc] + [wfl.module.batch :as batch] + [wfl.module.sg :as sg] + [wfl.service.clio :as clio] + [wfl.service.cromwell :as cromwell] + [wfl.service.google.storage :as gcs] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.workloads :as workloads] + [wfl.util :as util :refer [absent?]]) + (:import [java.time OffsetDateTime] + [java.util UUID])) (use-fixtures :once fixtures/temporary-postgresql-database) @@ -46,7 +45,7 @@ :creator @workloads/email}) (defn mock-submit-workload - [{:keys [workflows]} _ _ _ _ _] + [_ workflows _ _ _ _ _] (let [now (OffsetDateTime/now)] (letfn [(submit [workflow uuid] (assoc workflow :status "Submitted" @@ -64,7 +63,7 @@ (is (:created workload)) (is (absent? workload :started)) (is (absent? workload :finished)) - (run! verify-workflow (:workflows workload))))] + (run! verify-workflow (workloads/workflows workload))))] (testing "single-sample workload-request" (go! (the-sg-workload-request))))) @@ -75,7 +74,8 @@ (is (= expected (select-keys inputs (keys expected)))))] (run! ok (-> (the-sg-workload-request) (assoc-in [:common :inputs] expected) - workloads/create-workload! :workflows + workloads/create-workload! + workloads/workflows (->> (map :inputs))))))) (deftest test-start-workload! @@ -84,12 +84,11 @@ (is (:status workflow)) (is (:updated workflow)))] (with-redefs-fn {#'batch/submit-workload! mock-submit-workload} - #(-> (the-sg-workload-request) - workloads/create-workload! - workloads/start-workload! - (as-> workload - (is (:started workload)) - (run! go! (:workflows workload))))))) + #(let [workload (-> (the-sg-workload-request) + workloads/create-workload! + workloads/start-workload!)] + (is (:started workload)) + (run! go! (workloads/workflows workload)))))) (deftest test-hidden-inputs (testing "google_account_vault_path and vault_token_path are not in inputs" @@ -98,7 +97,7 @@ (is (absent? inputs :google_account_vault_path)))] (->> (the-sg-workload-request) workloads/create-workload! - :workflows + workloads/workflows (run! (comp go! :inputs)))))) (deftest test-submitted-workflow-inputs @@ -142,7 +141,8 @@ (assoc-in [:common :options] {:overwritten false :supports_common_options true}) (update :items (partial map overmap)) - workloads/execute-workload! :workflows + workloads/execute-workload! + workloads/workflows (->> (map (comp verify-workflow-options :options)))))))) (deftest test-empty-workflow-options @@ -151,7 +151,8 @@ (run! go! (-> (the-sg-workload-request) (assoc-in [:common :options] {}) (update :items (partial map empty-options)) - workloads/create-workload! :workflows)))) + workloads/create-workload! + workloads/workflows)))) (defn ^:private mock-clio-add-bam-found "Fail because a `_clio` BAM record already exists for `_md`" @@ -316,10 +317,10 @@ workloads/execute-workload! workloads/update-workload! (as-> workload - (let [{:keys [finished pipeline workflows]} workload] + (let [{:keys [finished pipeline]} workload] (is finished) (is (= sg/pipeline pipeline)) - (is (= (count items) (count workflows)))))))) + (is (= (count items) (-> workload workloads/workflows count)))))))) (deftest test-clio-updates-bam-found (testing "Clio not updated if outputs already known." @@ -365,24 +366,24 @@ (is (seq (clio/query-bam @workloads/clio-url {:bam_path bam_path}))))) (defmethod workloads/postcheck sg/pipeline postcheck-sg-workload - [{:keys [output workflows] :as _workload}] - (run! (partial workflow-postcheck output) workflows)) + [{:keys [output] :as workload}] + (run! (partial workflow-postcheck output) (workloads/workflows workload))) (defn ^:private mock-batch-update-workflow-statuses! - [tx {:keys [workflows items] :as _workload}] + [tx {:keys [items] :as workload}] (letfn [(update! [{:keys [id]}] (jdbc/update! tx items {:status "Succeeded" :updated (OffsetDateTime/now)} ["id = ?" id]))] - (run! update! workflows))) + (run! update! (wfl.api.workloads/workflows tx workload)))) (deftest test-workload-state-transition (let [count (atom 0) - increment-count (fn [_] (swap! count inc))] + increment-count (fn [& _] (swap! count inc))] (with-redefs-fn - {#'cromwell/submit-workflows mock-cromwell-submit-workflows - #'postgres/batch-update-workflow-statuses! mock-batch-update-workflow-statuses! - #'sg/register-workload-in-clio increment-count} + {#'cromwell/submit-workflows mock-cromwell-submit-workflows + #'batch/batch-update-workflow-statuses! mock-batch-update-workflow-statuses! + #'sg/register-workload-in-clio increment-count} #(shared/run-workload-state-transition-test! (the-sg-workload-request))) (is (== 1 @count) "Clio was updated more than once"))) diff --git a/api/test/wfl/integration/modules/shared.clj b/api/test/wfl/integration/modules/shared.clj index 76a89f54c..576c21ef3 100644 --- a/api/test/wfl/integration/modules/shared.clj +++ b/api/test/wfl/integration/modules/shared.clj @@ -1,7 +1,8 @@ (ns wfl.integration.modules.shared (:require [clojure.test :refer [deftest is]] [wfl.tools.workloads :as workloads] - [wfl.util :refer [absent?]])) + [wfl.util :refer [absent?]]) + (:import [wfl.util UserException])) (defn ^:private verify-workload-states [workload states] (doseq [[key test?] states] (is (test? workload key))) @@ -36,14 +37,13 @@ :finished contains?}))) (defn run-stop-workload-state-transition-test! [workload-request] - (-> workload-request - workloads/create-workload! - (verify-workload-states {:created contains? - :started absent? - :stopped absent? - :finished absent?}) - workloads/stop-workload! - (verify-workload-states {:created contains? - :started absent? - :stopped contains? - :finished contains?}))) + (let [workload (workloads/create-workload! workload-request)] + (verify-workload-states + workload + {:created contains? + :started absent? + :stopped absent? + :finished absent?}) + (is (thrown-with-msg? + UserException #"Cannot stop workload" + (workloads/stop-workload! workload))))) diff --git a/api/test/wfl/integration/modules/wgs_test.clj b/api/test/wfl/integration/modules/wgs_test.clj index 4ea23faf3..f3f9f52df 100644 --- a/api/test/wfl/integration/modules/wgs_test.clj +++ b/api/test/wfl/integration/modules/wgs_test.clj @@ -1,19 +1,20 @@ (ns wfl.integration.modules.wgs-test - (:require [clojure.set :refer [rename-keys]] + (:require [clojure.set :refer [rename-keys]] [clojure.test :refer [deftest testing is] :as clj-test] + [clojure.string :as str] [wfl.integration.modules.shared :as shared] - [wfl.service.cromwell :as cromwell] - [wfl.tools.fixtures :as fixtures] - [wfl.tools.workloads :as workloads] - [wfl.module.wgs :as wgs] - [wfl.jdbc :as jdbc] - [wfl.module.all :as all] - [wfl.util :as util] - [wfl.references :as references] - [clojure.string :as str] - [wfl.service.postgres :as postgres]) - (:import (java.util UUID) - (java.time OffsetDateTime))) + [wfl.jdbc :as jdbc] + [wfl.module.all :as all] + [wfl.module.batch :as batch] + [wfl.module.wgs :as wgs] + [wfl.references :as references] + [wfl.service.cromwell :as cromwell] + [wfl.service.postgres :as postgres] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.workloads :as workloads] + [wfl.util :as util]) + (:import [java.util UUID] + [java.time OffsetDateTime])) (clj-test/use-fixtures :once fixtures/temporary-postgresql-database) @@ -41,7 +42,7 @@ (-> (make-wgs-workload-request) (assoc-in [:common :inputs] {:reference_fasta_prefix prefix}) workloads/create-workload! - :workflows))))) + workloads/workflows))))) (deftest test-create-with-reference-fasta-prefix-override (let [prefix "gs://fake-input-bucket/ref-fasta"] @@ -57,7 +58,7 @@ (assoc-in [:common :inputs] {:reference_fasta_prefix "gs://ignore/this/ref-fasta"}) (update :items (partial map #(update % :inputs (fn [xs] (assoc xs :reference_fasta_prefix prefix))))) workloads/create-workload! - :workflows))))) + workloads/workflows))))) (deftest test-start-wgs-workload! (with-redefs-fn {#'cromwell/submit-workflows mock-submit-workflows} @@ -69,11 +70,11 @@ (is (not-any? (partial contains? workflow) (keys workloads/wgs-inputs)) "Inputs are not at the top-level"))] - (run! check-nesting (:workflows workload)))))) + (run! check-nesting (workloads/workflows workload)))))) (defn ^:private old-create-wgs-workload! [] (let [request (make-wgs-workload-request)] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (let [[id table] (all/add-workload-table! tx wgs/workflow-wdl request) add-id (fn [m id] (assoc (:inputs m) :id id))] (jdbc/insert-multi! tx table (map add-id (:items request) (range))) @@ -111,12 +112,12 @@ inputs))] (with-redefs-fn {#'cromwell/submit-workflows verify-inputs} - #(-> (make-wgs-workload-request) - (update :items use-input_bam) - (workloads/execute-workload!) - (as-> workload - (is (:started workload)) - (run! go! (:workflows workload))))))) + #(let [workload (-> (make-wgs-workload-request) + (update :items use-input_bam) + workloads/execute-workload!)] + + (is (:started workload)) + (run! go! (workloads/workflows workload)))))) (deftest test-submitted-workflow-inputs (letfn [(prefixed? [prefix key] (str/starts-with? (str key) (str prefix))) @@ -187,7 +188,7 @@ (partial map #(assoc % :options {:supports_options true :overwritten true}))) workloads/execute-workload! - :workflows + workloads/workflows (->> (map (comp verify-workflow-options :options)))))))) (deftest test-empty-workflow-options @@ -196,20 +197,20 @@ (assoc-in [:common :options] {}) (update :items (partial map #(assoc % :options {}))) workloads/create-workload! - :workflows)))) + workloads/workflows)))) (defn mock-batch-update-workflow-statuses! - [tx {:keys [workflows items] :as _workload}] + [tx {:keys [items] :as workload}] (letfn [(update! [{:keys [id]}] (jdbc/update! tx items {:status "Succeeded" :updated (OffsetDateTime/now)} ["id = ?" id]))] - (run! update! workflows))) + (run! update! (wfl.api.workloads/workflows tx workload)))) (deftest test-workload-state-transition (with-redefs-fn - {#'cromwell/submit-workflows mock-submit-workflows - #'postgres/batch-update-workflow-statuses! mock-batch-update-workflow-statuses!} + {#'cromwell/submit-workflows mock-submit-workflows + #'batch/batch-update-workflow-statuses! mock-batch-update-workflow-statuses!} #(shared/run-workload-state-transition-test! (make-wgs-workload-request)))) (deftest test-stop-workload-state-transition diff --git a/api/test/wfl/integration/modules/xx_test.clj b/api/test/wfl/integration/modules/xx_test.clj index c397189fb..6fa4e2eb6 100644 --- a/api/test/wfl/integration/modules/xx_test.clj +++ b/api/test/wfl/integration/modules/xx_test.clj @@ -1,16 +1,16 @@ (ns wfl.integration.modules.xx-test (:require [clojure.test :refer [deftest testing is use-fixtures]] - [clojure.string :as str] + [clojure.string :as str] [wfl.integration.modules.shared :as shared] - [wfl.module.xx :as xx] - [wfl.service.cromwell :as cromwell] - [wfl.service.postgres :as postgres] - [wfl.tools.fixtures :as fixtures] - [wfl.tools.workloads :as workloads] - [wfl.util :as util :refer [absent?]] - [wfl.jdbc :as jdbc]) - (:import (java.time OffsetDateTime) - (java.util UUID))) + [wfl.module.batch :as batch] + [wfl.module.xx :as xx] + [wfl.service.cromwell :as cromwell] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.workloads :as workloads] + [wfl.util :as util :refer [absent?]] + [wfl.jdbc :as jdbc]) + (:import [java.time OffsetDateTime] + [java.util UUID])) (use-fixtures :once fixtures/temporary-postgresql-database) @@ -32,7 +32,7 @@ (is (:created workload)) (is (absent? workload :started)) (is (absent? workload :finished)) - (run! verify-workflow (:workflows workload))))] + (run! verify-workflow (workloads/workflows workload))))] (testing "single-sample workload-request" (go! (make-xx-workload-request))))) @@ -46,7 +46,7 @@ (run! (comp go! :inputs) (-> (make-xx-workload-request) (assoc-in [:common :inputs] common-inputs) workloads/create-workload! - :workflows))))) + workloads/workflows))))) (deftest test-start-workload! (letfn [(go! [workflow] @@ -54,12 +54,11 @@ (is (:status workflow)) (is (:updated workflow)))] (with-redefs-fn {#'cromwell/submit-workflows mock-submit-workflows} - #(-> (make-xx-workload-request) - workloads/create-workload! - workloads/start-workload! - (as-> workload - (is (:started workload)) - (run! go! (:workflows workload))))))) + #(let [workload (-> (make-xx-workload-request) + workloads/create-workload! + workloads/start-workload!)] + (is (:started workload)) + (run! go! (workloads/workflows workload)))))) (deftest test-hidden-inputs (testing "google_account_vault_path and vault_token_path are not in inputs" @@ -68,7 +67,7 @@ (is (absent? inputs :google_account_vault_path)))] (->> (make-xx-workload-request) workloads/create-workload! - :workflows + workloads/workflows (run! (comp go! :inputs)))))) (deftest test-create-empty-workload @@ -136,7 +135,7 @@ (partial map #(assoc % :options {:supports_options true :overwritten true}))) workloads/execute-workload! - :workflows + workloads/workflows (->> (map (comp verify-workflow-options :options)))))))) (deftest test-empty-workflow-options @@ -145,20 +144,20 @@ (assoc-in [:common :options] {}) (update :items (partial map #(assoc % :options {}))) workloads/create-workload! - :workflows)))) + workloads/workflows)))) (defn mock-batch-update-workflow-statuses! - [tx {:keys [workflows items] :as _workload}] + [tx {:keys [items] :as workload}] (letfn [(update! [{:keys [id]}] (jdbc/update! tx items {:status "Succeeded" :updated (OffsetDateTime/now)} ["id = ?" id]))] - (run! update! workflows))) + (run! update! (workloads/workflows workload)))) (deftest test-workload-state-transition (with-redefs-fn - {#'cromwell/submit-workflows mock-submit-workflows - #'postgres/batch-update-workflow-statuses! mock-batch-update-workflow-statuses!} + {#'cromwell/submit-workflows mock-submit-workflows + #'batch/batch-update-workflow-statuses! mock-batch-update-workflow-statuses!} #(shared/run-workload-state-transition-test! (make-xx-workload-request)))) (deftest test-stop-workload-state-transition diff --git a/api/test/wfl/integration/rawls_test.clj b/api/test/wfl/integration/rawls_test.clj new file mode 100644 index 000000000..5a33d4c6d --- /dev/null +++ b/api/test/wfl/integration/rawls_test.clj @@ -0,0 +1,69 @@ +(ns wfl.integration.rawls-test + (:require [clojure.test :refer [deftest is testing use-fixtures]] + [wfl.service.firecloud :as firecloud] + [wfl.service.rawls :as rawls] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.resources :as resources] + [wfl.util :as util]) + (:import [clojure.lang ExceptionInfo])) + +;; A known TDR Dev snapshot ID +(def snapshot-id "7cb392d8-949b-419d-b40b-d039617d2fc7") + +(let [new-env {"WFL_FIRECLOUD_URL" + "https://firecloud-orchestration.dsde-dev.broadinstitute.org"}] + (use-fixtures :once (fixtures/temporary-environment new-env))) + +(deftest test-snapshot-references + (fixtures/with-temporary-workspace + "general-dev-billing-account/test-workspace" + "hornet-eng" + (fn [workspace] + (letfn [(make-reference [snapshot-name] + (rawls/create-snapshot-reference workspace snapshot-id snapshot-name)) + (verify-snapshot [[snapshot snapshot-name]] + (is (= "DATA_REPO_SNAPSHOT" (:referenceType snapshot))) + (is (= snapshot-id (get-in snapshot [:reference :snapshot]))) + (is (= snapshot-name (:name snapshot)))) + (verify-snapshots [snapshots snapshot-names] + (->> (map list snapshots snapshot-names) + (run! verify-snapshot)))] + (let [names ["snapshot1" "snapshot2"] + reference-ids + (testing "Create" + (let [snapshots (map make-reference names)] + (verify-snapshots snapshots names) + (map :referenceId snapshots)))] + (testing "Get" + (let [snapshots + (map #(rawls/get-snapshot-reference workspace %) reference-ids)] + (verify-snapshots snapshots names))) + (testing "Get all" + (let [[_first _second & rest :as snapshots] + (rawls/get-snapshot-references workspace 10)] + (is (empty? rest)) + (verify-snapshots snapshots names))) + (testing "Create or get" + (let [snapshot (rawls/create-or-get-snapshot-reference workspace + snapshot-id + (first names))] + (verify-snapshot [snapshot (first names)]))) + (testing "Create already exists" + (is (thrown-with-msg? ExceptionInfo #"clj-http: status 409" + (make-reference (first names)))))))))) + +(deftest test-batch-upsert-entities + (let [entity-type "outputs" + entity-name "test" + outputs (resources/read-resource "sarscov2_illumina_full/outputs.edn")] + (fixtures/with-temporary-workspace + "general-dev-billing-account/test-workspace" + "hornet-eng" + (fn [workspace] + (rawls/batch-upsert workspace [[entity-type entity-name outputs]]) + (let [[{:keys [name attributes]} & _] + (util/poll + #(not-empty (firecloud/list-entities workspace entity-type)))] + (is (= name entity-name) "The test entity was not created") + (is (= (util/map-vals #(if (map? %) (:items %) %) attributes) + (into {} (filter second outputs))))))))) diff --git a/api/test/wfl/integration/workloads_test.clj b/api/test/wfl/integration/workloads_test.clj index ae8492ab5..f9b088e0a 100644 --- a/api/test/wfl/integration/workloads_test.clj +++ b/api/test/wfl/integration/workloads_test.clj @@ -1,6 +1,5 @@ (ns wfl.integration.workloads-test (:require [clojure.test :refer [deftest testing is] :as clj-test] - [clojure.test :refer :all] [wfl.module.copyfile :as copyfile] [wfl.tools.fixtures :as fixtures] [wfl.tools.workloads :as workloads])) diff --git a/api/test/wfl/system/automation_test.clj b/api/test/wfl/system/automation_test.clj index 0a52c580b..903ce1e0d 100644 --- a/api/test/wfl/system/automation_test.clj +++ b/api/test/wfl/system/automation_test.clj @@ -1,84 +1,74 @@ (ns wfl.system.automation-test - (:require [clojure.data.json :as json] - [clojure.test :refer [deftest is]] - [wfl.environment :as env] - [wfl.service.datarepo :as datarepo] - [wfl.service.google.storage :as storage] - [wfl.tools.datasets :as datasets] - [wfl.tools.fixtures :as fixtures] - [wfl.tools.resources :as resources] - [wfl.tools.workflows :as workflows]) - (:import (java.util UUID))) + (:require [clojure.pprint :as pprint] + [clojure.test :refer [deftest is]] + [wfl.environment :as env] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.resources :as resources] + [wfl.tools.workflows :as workflows] + [wfl.service.firecloud :as firecloud] + [wfl.util :as util] + [wfl.tools.endpoints :as endpoints] + [wfl.tools.workloads :as workloads])) (defn ^:private replace-urls-with-file-ids [file->fileid type value] (-> (fn [type value] (case type ("Boolean" "Float" "Int" "Number" "String") value - "File" (file->fileid value) + "File" (file->fileid value) (throw (ex-info "Unknown type" {:type type :value value})))) (workflows/traverse type value))) +(def workspace-to-clone "wfl-dev/CDC_Viral_Sequencing") +(def firecloud-group "workflow-launcher-dev") +(def snapshot-readers ["cdc-covid-surveillance@firecloud.org"]) +(def source-dataset "cd25d59e-1451-44d0-8a24-7669edb9a8f8") +(def source-table "flowcells") +(def snapshot-column "run_date") +(def source-dataset-profile "395f5921-d2d9-480d-b302-f856d787c9d9") +(def method-configuration "cdc-covid-surveillance/sarscov2_illumina_full") + +(def workspace-table "flowcell") + +(defn clone-workspace [] + (println "Cloning workspace" workspace-to-clone) + (let [clone-name (util/randomize "wfl-dev/CDC_Viral_Sequencing_GP")] + (firecloud/clone-workspace workspace-to-clone clone-name firecloud-group) + (println "Cloned new workspace " clone-name) + clone-name)) + +(defn delete-workspace [workspace] + (println "Deleting" workspace) + (firecloud/delete-workspace workspace)) + +(defn ^:private covid-workload-request [workspace] + "Build a covid workload request." + {:source {:name "TDR Snapshots" + :snapshots ["f9242ab8-c522-4305-966d-7c51419377ab"]} + :executor {:name "Terra" + :workspace workspace + :methodConfiguration "cdc-covid-surveillance/sarscov2_illumina_full" + :methodConfigurationVersion 1 + :fromSource "importSnapshot"} + :sink {:name "Terra Workspace" + :workspace workspace + :entityType "run_date" + :identifier "run_date" + :fromOutputs (resources/read-resource + "sarscov2_illumina_full/entity-from-outputs.edn") + :skipValidation true} + :project @workloads/project + :creator @workloads/email + :labels ["hornet:test"]}) + (deftest test-automate-sarscov2-illumina-full (let [tdr-profile (env/getenv "WFL_TDR_DEFAULT_PROFILE")] (fixtures/with-fixtures - [(fixtures/with-temporary-cloud-storage-folder fixtures/gcs-test-bucket) - (fixtures/with-temporary-dataset - (datasets/unique-dataset-request - tdr-profile - "sarscov2-illumina-full-inputs.json")) - (fixtures/with-temporary-dataset - (datasets/unique-dataset-request - tdr-profile - "sarscov2-illumina-full-outputs.json"))] - (fn [[temp source sink]] - ;; TODO: create + start the workload - ;; upload a sample - (let [;; This defines how we'll convert the inputs of the pipeline into - ;; a form that can be ingested as a new row in the dataset. - ;; I think a user would specify something like this in the initial - ;; workload request, one mapping for dataset to workspace entity - ;; names and one for outputs to dataset. - from-inputs (resources/read-resource "sarscov2_illumina_full/dataset-from-inputs.edn") - inputs (-> (resources/read-resource "sarscov2_illumina_full/inputs.edn") - (select-keys (map keyword (vals from-inputs)))) - inputs-type (-> "sarscov2_illumina_full.edn" - resources/read-resource - :inputs - workflows/make-object-type) - table-name "flowcell" - unique-prefix (UUID/randomUUID) - table-url (str temp "inputs.json")] - (-> (->> (workflows/get-files inputs-type inputs) - (datasets/ingest-files tdr-profile source unique-prefix)) - (replace-urls-with-file-ids inputs-type inputs) - (datasets/rename-gather from-inputs) - (json/write-str :escape-slash false) - (storage/upload-content table-url)) - (let [{:keys [bad_row_count row_count]} - (datarepo/poll-job - (datarepo/ingest-table source table-url table-name))] - (is (= 1 row_count)) - (is (= 0 bad_row_count)))) - ;; At this point, workflow-launcher should run the workflow. The code - ;; below simulates this effect. - (let [outputs (resources/read-resource "sarscov2_illumina_full/outputs.edn") - outputs-type (-> "sarscov2_illumina_full.edn" - resources/read-resource - :outputs - workflows/make-object-type) - table-name "sarscov2_illumina_full_outputs" - unique-prefix (UUID/randomUUID) - table-url (str temp "outputs.json")] - (-> (->> (workflows/get-files outputs-type outputs) - (datasets/ingest-files tdr-profile sink unique-prefix)) - (replace-urls-with-file-ids outputs-type outputs) - (json/write-str :escape-slash false) - (storage/upload-content table-url)) - (let [{:keys [bad_row_count row_count]} - (datarepo/poll-job - (datarepo/ingest-table sink table-url table-name))] - (is (= 1 row_count)) - (is (= 0 bad_row_count)))) - ;; TODO: verify the outputs have been written to TDR - )))) + [(util/bracket clone-workspace delete-workspace)] + (fn [[workspace]] + (let [workload (endpoints/create-workload + (covid-workload-request workspace))] + (endpoints/start-workload workload) + (workloads/when-done + (comp pprint/pprint endpoints/get-workflows) + workload)))))) diff --git a/api/test/wfl/system/cdc_covid19_surveillance_demo.clj b/api/test/wfl/system/cdc_covid19_surveillance_demo.clj new file mode 100644 index 000000000..55d741f86 --- /dev/null +++ b/api/test/wfl/system/cdc_covid19_surveillance_demo.clj @@ -0,0 +1,144 @@ +(ns wfl.system.cdc-covid19-surveillance-demo + (:require [wfl.module.covid :as covid] + [wfl.service.datarepo :as datarepo] + [wfl.service.firecloud :as firecloud] + [wfl.service.rawls :as rawls] + [wfl.tools.fixtures :as fixtures] + [wfl.tools.snapshots :as snapshots] + [wfl.tools.resources :as resources] + [wfl.util :as util])) + +(def workspace-to-clone "wfl-dev/CDC_Viral_Sequencing") +(def firecloud-group "workflow-launcher-dev") +(def snapshot-readers ["cdc-covid-surveillance@firecloud.org"]) +(def source-dataset "cd25d59e-1451-44d0-8a24-7669edb9a8f8") +(def source-table "flowcells") +(def snapshot-column "run_date") +(def source-dataset-profile "395f5921-d2d9-480d-b302-f856d787c9d9") +(def method-configuration "cdc-covid-surveillance/sarscov2_illumina_full") + +;; for demonstrating writing outputs back to the workspace +(def well-known-submission "475d0a1d-20c0-42a1-968a-7540b79fcf0c") +(def well-known-workflow "2768b29e-c808-4bd6-a46b-6c94fd2a67aa") +(def workspace-table "flowcell") + +(defn wait-for-user [] + (println "Press Enter to continue...") + (read-line)) + +(defn clone-workspace [] + (println "Cloning workspace" workspace-to-clone) + (let [clone-name (util/randomize "wfl-dev/CDC_Viral_Sequencing_GP")] + (firecloud/clone-workspace workspace-to-clone clone-name firecloud-group) + (println "Cloned new workspace " clone-name) + clone-name)) + +(defn look-for-new-dataset-rows [{:keys [name] :as dataset}] + (println "Looking for rows to snapshot in dataset" name) + (let [row-ids (-> (datarepo/query-table-between + dataset source-table + snapshot-column + ["2021-04-27T03:59:59" "2021-04-27T04:00:01"] + [:datarepo_row_id]) + :rows + flatten)] + (println "Found rows" row-ids) + row-ids)) + +(defn snapshot-new-dataset-rows [{:keys [name] :as dataset} row-ids] + (println "Snapshotting rows" row-ids "in dataset" name) + (let [{:keys [name] :as snapshot} + (-> (snapshots/unique-snapshot-request + source-dataset-profile + dataset + source-table + row-ids) + (assoc :readers snapshot-readers) + datarepo/create-snapshot + datarepo/snapshot)] + (println "Created snapshot" name) + snapshot)) + +(defn create-snapshot [] + (let [dataset (datarepo/dataset source-dataset)] + (snapshot-new-dataset-rows dataset (look-for-new-dataset-rows dataset)))) + +(defn import-snapshot-into-workspace [workspace {:keys [name id] :as _snapshot}] + (println "Importing snapshot" name "into" workspace) + (let [{:keys [name] :as ref} (rawls/create-snapshot-reference workspace id name)] + (println "Created snapshot reference" name) + ref)) + +(defn update-method-configuration + [workspace {:keys [name] :as _snapshot-reference}] + (println "Updating" method-configuration "to use" name) + (-> (firecloud/get-method-configuration workspace method-configuration) + (assoc :dataReferenceName name) + (->> (firecloud/update-method-configuration workspace method-configuration)))) + +(defn submit-snapshot-reference + [workspace {:keys [name] :as _snapshot-reference}] + (println "Submitting" name "in" workspace) + (let [submission (firecloud/submit-method workspace method-configuration) + [id count] ((juxt :submissionId (comp count :workflows)) submission)] + (println "Created submission" id "-" count "workflow(s)") + submission)) + +(defn abort-submission [workspace {:keys [submissionId] :as _submission}] + (println "Aborting" submissionId "in" workspace) + (firecloud/abort-submission workspace submissionId)) + +;; TODO demonstrate copying form one workspace to another +;; Need to get the WDL description to extract file from the outputs, however. +(defn write-known-outputs-to-workspace [workspace] + (println "Writing outputs to flowcell table in" workspace) + (let [from-outputs (resources/read-resource "sarscov2_illumina_full/entity-from-outputs.edn") + pipeline (:name (firecloud/get-method-configuration workspace method-configuration)) + outputs (-> workspace-to-clone + (firecloud/get-workflow-outputs well-known-submission well-known-workflow) + (get-in [:tasks (keyword pipeline) :outputs]) + (util/unprefix-keys (keyword (str pipeline ".")))) + attributes (covid/rename-gather outputs from-outputs) + entity-name "test"] + (rawls/batch-upsert workspace [[workspace-table entity-name attributes]]))) + +(defn delete-snapshot [{:keys [name id] :as _snapshot}] + (println "Deleting snapshot" name) + (datarepo/delete-snapshot id)) + +(defn delete-workspace [workspace] + (println "Deleting" workspace) + (firecloud/delete-workspace workspace)) + +(defn demo [] + (println "CDC COVID-19 Surveillance Demo") + (println "Demonstrating sarscov2_illumina_full automation") + (wait-for-user) + (fixtures/with-fixtures + [(util/bracket clone-workspace delete-workspace) + (util/bracket #(wait-for-user) (constantly nil)) + (util/bracket create-snapshot delete-snapshot)] + (fn [[workspace _ snapshot]] + (wait-for-user) + (let [reference (import-snapshot-into-workspace workspace snapshot) + _ (wait-for-user) + _ (update-method-configuration workspace reference) + submission (submit-snapshot-reference workspace reference)] + (wait-for-user) + (abort-submission workspace submission)) + (wait-for-user) + (write-known-outputs-to-workspace workspace) + (wait-for-user) + (println "Cleaning up")))) + +(def prod-env + {"WFL_TDR_URL" "https://data.terra.bio" + "WFL_RAWLS_URL" "https://rawls.dsde-prod.broadinstitute.org"}) + +(defn -main [] + (try + (fixtures/with-temporary-environment prod-env demo) + (catch Throwable t + (binding [*out* *err*] + (println t) + (System/exit 1))))) diff --git a/api/test/wfl/system/v1_endpoint_test.clj b/api/test/wfl/system/v1_endpoint_test.clj index 36ada92e3..cb82abc48 100644 --- a/api/test/wfl/system/v1_endpoint_test.clj +++ b/api/test/wfl/system/v1_endpoint_test.clj @@ -1,15 +1,19 @@ (ns wfl.system.v1-endpoint-test - (:require [clojure.set :as set] + (:require [clojure.test :refer :all] + [clojure.instant :as instant] + [clojure.set :as set] + [clojure.spec.alpha :as s] [clojure.string :as str] - [clojure.test :refer [deftest testing is]] + [wfl.api.spec :as spec] [wfl.service.cromwell :as cromwell] [wfl.service.google.storage :as gcs] [wfl.tools.endpoints :as endpoints] [wfl.tools.fixtures :as fixtures] [wfl.tools.workloads :as workloads] + [wfl.tools.resources :as resources] [wfl.util :as util]) - (:import (clojure.lang ExceptionInfo) - (java.util UUID))) + (:import [clojure.lang ExceptionInfo] + [java.util UUID])) (defn make-create-workload [make-request] (fn [] (endpoints/create-workload (make-request (UUID/randomUUID))))) @@ -24,24 +28,25 @@ (endpoints/create-workload (workloads/copyfile-workload-request src dst))) (defn ^:private verify-succeeded-workflow - [{:keys [inputs labels status updated uuid] :as workflow}] + [{:keys [inputs labels status updated uuid] :as _workflow}] (is (map? inputs) "Every workflow should have nested inputs") (is updated) (is uuid) (is (= "Succeeded" status))) (defn ^:private verify-succeeded-workload - [{:keys [pipeline workflows] :as workload}] - (run! verify-succeeded-workflow workflows) + [workload] + (run! verify-succeeded-workflow (endpoints/get-workflows workload)) (workloads/postcheck workload)) (defn ^:private verify-internal-properties-removed [workload] - (letfn [(go! [key] - (is (util/absent? workload key) - (format "workload should not contain %s" key)) - (is (every? #(util/absent? % key) (:workflows workload)) - (format "workflows should not contain %s" key)))] - (run! go! [:id :items]))) + (let [workflows (endpoints/get-workflows workload)] + (letfn [(go! [key] + (is (util/absent? workload key) + (format "workload should not contain %s" key)) + (is (every? #(util/absent? % key) workflows) + (format "workflows should not contain %s" key)))] + (run! go! [:id :items])))) (deftest test-oauth2-endpoint (testing "The `oauth2_id` endpoint indeed provides an ID" @@ -95,7 +100,7 @@ (let [workload (endpoints/start-workload workload)] (is (= uuid (:uuid workload))) (is (:started workload)) - (let [{:keys [workflows]} workload] + (let [workflows (endpoints/get-workflows workload)] (is (every? :updated workflows)) (is (every? :uuid workflows))) (verify-internal-properties-removed workload) @@ -122,18 +127,16 @@ (test-start-workload (create-copyfile-workload src dst)))))) (defn ^:private test-stop-workload - [{:keys [uuid pipeline] :as workload}] - (letfn [(verify-no-workflows-run [{:keys [workflows] :as workload}] - (is (:finished workload)) - (is (every? (comp nil? :uuid) workflows)) - (is (every? (comp nil? :status) workflows)))] - (testing (format "calling api/v1/start with %s workload" pipeline) - (let [workload (endpoints/stop-workload workload)] - (is (= uuid (:uuid workload))) - (is (not (:started workload))) - (is (:stopped workload)) - (verify-internal-properties-removed workload) - (workloads/when-done verify-no-workflows-run workload))))) + [{:keys [pipeline] :as workload}] + (testing (format "calling /stop with %s workload before /start" pipeline) + (is (thrown-with-msg? + ExceptionInfo #"400" + (endpoints/stop-workload workload))) + (testing (format "calling /stop with %s workload after /start" pipeline) + (let [workload (endpoints/stop-workload + (endpoints/start-workload workload))] + (is (:started workload)) + (is (:stopped workload)))))) (deftest ^:parallel test-stop-wgs-workload (test-stop-workload (create-wgs-workload))) @@ -149,7 +152,7 @@ (defn ^:private test-exec-workload [{:keys [pipeline] :as request}] (testing (format "calling api/v1/exec with %s workload request" pipeline) - (let [{:keys [created creator started uuid workflows] :as workload} + (let [{:keys [created creator started uuid] :as workload} (endpoints/exec-workload request)] (is uuid "workloads should have a uuid") (is created "should have a created timestamp") @@ -158,8 +161,9 @@ "creator inferred from auth token") (letfn [(included [m] (select-keys m [:pipeline :project]))] (is (= (included request) (included workload)))) - (is (every? :updated workflows)) - (is (every? :uuid workflows)) + (let [workflows (endpoints/get-workflows workload)] + (is (every? :updated workflows)) + (is (every? :uuid workflows))) (verify-internal-properties-removed workload) (workloads/when-done verify-succeeded-workload workload)))) @@ -212,3 +216,75 @@ (testing "exec-workload! fails (400) with bad request" (is (thrown-with-msg? ExceptionInfo #"clj-http: status 400" (endpoints/exec-workload request)))))) + +(defn ^:private covid-workload-request [] + "Build a covid workload request." + (let [terra-ns (comp (partial str/join "/") (partial vector "wfl-dev")) + workspace (terra-ns "CDC_Viral_Sequencing") + source {:name "Terra DataRepo" + :dataset "79fc88f5-dcf4-48b0-8c01-615dfbc1c63a" + :table "flowcells" + :column "last_modified_date" + :snapshotReaders ["hornet@firecloud.org"]} + executor {:name "Terra" + :workspace workspace + :methodConfiguration (terra-ns "sarscov2_illumina_full") + :methodConfigurationVersion 1 + :fromSource "importSnapshot"} + sink {:name "Terra Workspace" + :workspace workspace + :entityType "assemblies" + :identifier "flowcell_id" + :fromOutputs (resources/read-resource + "sarscov2_illumina_full/entity-from-outputs.edn") + :skipValidation true}] + (workloads/covid-workload-request source executor sink))) + +(defn instantify-timestamps + "Replace timestamps at keys KS of map M with parsed #inst values." + [m & ks] + (reduce (fn [m k] (update m k instant/read-instant-timestamp)) m ks)) + +(deftest ^:parallel test-covid-workload + (testing "/create covid workload" + (let [workload-request (covid-workload-request) + {:keys [creator started uuid] :as workload} + (-> workload-request + endpoints/create-workload + (update :created instant/read-instant-timestamp))] + (is (s/valid? ::spec/covid-workload-request workload-request)) + (is (s/valid? ::spec/covid-workload-response workload)) + (verify-internal-properties-removed workload) + (is (not started)) + (is (= @workloads/email creator)) + (testing "/workload status" + (let [{:keys [started] :as response} + (-> uuid endpoints/get-workload-status + (instantify-timestamps :created))] + (is (not started)) + (verify-internal-properties-removed response) + (is (s/valid? ::spec/covid-workload-response response)))) + (testing "/workload all" + (let [{:keys [started] :as response} + (-> (endpoints/get-workloads) + (->> (filter (comp #{uuid} :uuid))) + first + (instantify-timestamps :created))] + (is (not started)) + (verify-internal-properties-removed response) + (is (s/valid? ::spec/covid-workload-response response)))) + (testing "/start covid workload" + (let [{:keys [created started] :as response} + (-> workload endpoints/start-workload + (instantify-timestamps :created :started))] + (is (s/valid? ::spec/covid-workload-response response)) + (is (inst? created)) + (is (inst? started)))) + (testing "/stop covid workload" + (let [{:keys [created started stopped] :as response} + (-> workload endpoints/stop-workload + (instantify-timestamps :created :started :stopped))] + (is (s/valid? ::spec/covid-workload-response response)) + (is (inst? created)) + (is (inst? started)) + (is (inst? stopped))))))) diff --git a/api/test/wfl/tools/datasets.clj b/api/test/wfl/tools/datasets.clj index 7e64f1827..db5e8f5b2 100644 --- a/api/test/wfl/tools/datasets.clj +++ b/api/test/wfl/tools/datasets.clj @@ -35,17 +35,3 @@ (mapcat #(-> % datarepo/poll-job :loadFileResults)) (map (juxt :sourcePath :fileId)) (into {})))) - -(defn rename-gather - "Transform the `values` using the transformation defined in `mapping`." - [values mapping] - (letfn [(literal? [x] (str/starts-with? x "$")) - (go! [v] - (cond (literal? v) (subs v 1 (count v)) - (string? v) (values (keyword v)) - (map? v) (json/write-str (rename-gather values v) - :escape-slash false) - (coll? v) (keep go! v) - :else (throw (ex-info "Unknown operation" - {:operation v}))))] - (into {} (for [[k v] mapping] [k (go! v)])))) diff --git a/api/test/wfl/tools/endpoints.clj b/api/test/wfl/tools/endpoints.clj index 3a6f1ef5b..a102b4406 100644 --- a/api/test/wfl/tools/endpoints.clj +++ b/api/test/wfl/tools/endpoints.clj @@ -1,15 +1,16 @@ (ns wfl.tools.endpoints - (:require [clj-http.client :as http] - [clojure.data.json :as json] - [wfl.auth :as auth] - [wfl.environment :as env] - [wfl.util :as util])) + (:require [clojure.data.json :as json] + [clojure.string :as str] + [clj-http.client :as http] + [wfl.auth :as auth] + [wfl.environment :as env] + [wfl.util :as util])) (defn ^:private wfl-url "The WFL server URL to test." [& parts] - (let [url (env/getenv "WFL_WFL_URL")] - (apply str url parts))) + (let [url (util/de-slashify (env/getenv "WFL_WFL_URL"))] + (str/join "/" (cons url parts)))) (defn get-oauth2-id "Query oauth2 ID that the server is currently using" @@ -33,14 +34,20 @@ (http/get {:headers (auth/get-auth-header)}) util/response-body-json)) +(defn get-workflows + "Query v1 api for all workflows managed by `_workload`." + [{:keys [uuid] :as _workload}] + (-> (wfl-url "/api/v1/workload/" uuid "/workflows") + (http/get {:headers (auth/get-auth-header)}) + util/response-body-json)) + (defn create-workload "Create workload defined by WORKLOAD" [workload] (-> (wfl-url "/api/v1/create") (http/post {:headers (auth/get-auth-header) :content-type :application/json - :body (json/write-str workload - :escape-slash false)}) + :body (json/write-str workload :escape-slash false)}) util/response-body-json)) (defn start-workload diff --git a/api/test/wfl/tools/fixtures.clj b/api/test/wfl/tools/fixtures.clj index 879884e7d..629ac7729 100644 --- a/api/test/wfl/tools/fixtures.clj +++ b/api/test/wfl/tools/fixtures.clj @@ -1,70 +1,69 @@ (ns wfl.tools.fixtures - (:require [clojure.string :as str] - [wfl.service.datarepo :as datarepo] - [wfl.service.google.pubsub :as pubsub] + (:require [wfl.service.datarepo :as datarepo] + [wfl.service.google.pubsub :as pubsub] [wfl.service.google.storage :as gcs] - [wfl.service.postgres :as postgres] - [wfl.tools.liquibase :as liquibase] - [wfl.jdbc :as jdbc] - [wfl.util :as util] - [wfl.environment :as env] - [wfl.service.firecloud :as firecloud]) - (:import [java.util UUID] - (java.nio.file Files) - (org.apache.commons.io FileUtils) - (java.nio.file.attribute FileAttribute))) + [wfl.service.postgres :as postgres] + [wfl.tools.liquibase :as liquibase] + [wfl.jdbc :as jdbc] + [wfl.util :as util] + [wfl.environment :as env] + [wfl.service.firecloud :as firecloud]) + (:import [java.nio.file.attribute FileAttribute] + [java.nio.file Files] + [java.util UUID] + [org.apache.commons.io FileUtils])) + +(defn with-temporary-overload + "Temporarily dispatch MULTIFN to OVERLOAD on DISPATCH-VAL" + [multifn dispatch-val overload f] + (defmethod multifn dispatch-val [& xs] (apply overload xs)) + (try + (f) + (finally + (remove-method multifn dispatch-val)))) (defn method-overload-fixture "Temporarily dispatch MULTIFN to OVERLOAD on DISPATCH-VAL" [multifn dispatch-val overload] - (fn [run-test] - (defmethod multifn dispatch-val [& xs] (apply overload xs)) - (run-test) - (remove-method multifn dispatch-val))) + (partial with-temporary-overload multifn dispatch-val overload)) (def gcs-test-bucket "broad-gotc-dev-wfl-ptc-test-outputs") (def delete-test-object (partial gcs/delete-object gcs-test-bucket)) (defn ^:private postgres-db-config [] (-> (postgres/wfl-db-config) - (dissoc :instance-name) (merge {:connection-uri "jdbc:postgresql:postgres" - :db-name "postgres"}))) - -(def ^:private test-db-name - (str "wfltest" (str/replace (UUID/randomUUID) "-" ""))) + :db-name "postgres" + :instance-name nil}))) -(defn testing-db-config - [] - (-> (postgres/wfl-db-config) - (dissoc :instance-name) - (merge {:connection-uri (str "jdbc:postgresql:" test-db-name) - :db-name test-db-name}))) +(def testing-db-name + "The name of the test database" + (util/randomize "wfltest")) (defn ^:private create-local-database "Create a local PostgreSQL database with DBNAME." [dbname] - (clojure.java.jdbc/with-db-connection [conn (postgres-db-config)] - (jdbc/db-do-commands conn false (format "CREATE DATABASE %s" dbname)))) + (let [config (postgres-db-config)] + (clojure.java.jdbc/with-db-connection [conn config] + (jdbc/db-do-commands conn false (format "CREATE DATABASE %s" dbname)) + (merge config {:connection-uri (str "jdbc:postgresql:" dbname) + :db-name dbname})))) (defn ^:private setup-local-database - "Run liquibase migrations on the local PostgreSQL database `dbname`." - [dbname] - (let [changelog "../database/changelog.xml" - url (format "jdbc:postgresql:%s" dbname) - {:keys [user password]} (postgres/wfl-db-config)] - (liquibase/run-liquibase url changelog user password))) + "Run liquibase migrations using PostgreSQL database `config`." + [config] + (liquibase/run-liquibase "../database/changelog.xml" config)) (defn ^:private drop-local-db "Drop the local PostgreSQL database `dbname`." - [dbname] + [{:keys [db-name]}] (clojure.java.jdbc/with-db-connection [conn (postgres-db-config)] - (jdbc/db-do-commands conn false (format "DROP DATABASE %s" dbname)))) + (jdbc/db-do-commands conn false (format "DROP DATABASE %s" db-name)))) (defn temporary-postgresql-database - "Create a temporary PostgreSQL database whose configuration is - `testing-db-config` for testing. Assumes that the database does not - already exist. + "Create a temporary PostgreSQL database named `testing-db-name` and + reconfigure `postgres/wfl-db-config` to use it for testing. Assumes that + the database does not already exist. Example ------- @@ -73,28 +72,29 @@ (clj-test/use-fixtures :once temporary-postgresql-database) (deftest test-requiring-database-access - (jdbc/with-db-transaction [tx (testing-db-config)] + (jdbc/with-db-transaction [tx (wfl-db-config)] #_(use tx)))" [f] - (let [name (:db-name (testing-db-config))] - (create-local-database name) - (try - (setup-local-database name) - (f) - (finally - (drop-local-db name))))) + (util/bracket + #(create-local-database testing-db-name) + drop-local-db + (fn [config] + (setup-local-database config) + (let [prev @@#'postgres/testing-db-overrides] + (swap! @#'postgres/testing-db-overrides merge config) + (try + (f) + (finally + (reset! @#'postgres/testing-db-overrides prev))))))) (defn create-local-database-for-testing - "Create and run liquibase on a PostgreSQL database whose configuration is - `config` for testing. Assumes that the database `(:db-name config)` does - not already exist. + "Create and run liquibase on a PostgreSQL database named `dbname`. Assumes + that `dbname` does not already exist. Notes: - This is intended for interactive development in a REPL. - The new database will NOT be cleaned up automatically." - [config] - (let [name (:db-name config)] - (create-local-database name) - (setup-local-database name))) + [dbname] + (-> dbname create-local-database setup-local-database)) (defmacro with-fixtures "Use 0 or more `fixtures` in `use-fixtures`. @@ -200,12 +200,13 @@ (defn with-temporary-workspace "Create and use a temporary Terra Workspace." - [f] - (util/bracket - #(doto (util/randomize "wfl-dev/test-workspace") - (firecloud/create-workspace "workflow-launcher-dev")) - firecloud/delete-workspace - f)) + ([workspace-prefix group f] + (util/bracket + #(doto (util/randomize workspace-prefix) (firecloud/create-workspace group)) + firecloud/delete-workspace + f)) + ([f] + (with-temporary-workspace "wfl-dev/test-workspace" "workflow-launcher-dev" f))) (defn with-temporary-environment "Temporarily override the environment with the key-value mapping in `env`. diff --git a/api/test/wfl/tools/liquibase.clj b/api/test/wfl/tools/liquibase.clj index a3b44c173..2c39a73df 100644 --- a/api/test/wfl/tools/liquibase.clj +++ b/api/test/wfl/tools/liquibase.clj @@ -1,27 +1,29 @@ (ns wfl.tools.liquibase - (:require [wfl.environment :as env]) - (:import [liquibase.integration.commandline Main])) + (:require [wfl.service.postgres :as postgres]) + (:import [liquibase.integration.commandline Main] + [clojure.lang ExceptionInfo])) (defn run-liquibase "Migrate the database schema using Liquibase." - ([url changelog username password] - (let [status (Main/run - (into-array - String - [(str "--url=" url) - (str "--changeLogFile=" changelog) - (str "--username=" username) - (str "--password=" password) - "update"]))] - (when-not (zero? status) - (throw - (Exception. - (format "Liquibase failed with: %s" status)))))) - ([url changelog username] - (run-liquibase url changelog username nil))) + [changelog {:keys [user password connection-uri]}] + (let [status (Main/run + (into-array + String + [(str "--url=" connection-uri) + (str "--changeLogFile=" changelog) + (str "--username=" user) + (str "--password=" password) + "update"]))] + (when-not (zero? status) + (throw (ex-info "Liquibase migration failed" {:status status}))))) (defn -main "Migrate the local database schema using Liquibase." [] - (let [user (env/getenv "USER")] - (run-liquibase "jdbc:postgresql:wfl" "../database/changelog.xml" user))) + (try + (run-liquibase "../database/changelog.xml" (postgres/wfl-db-config)) + (System/exit 0) + (catch ExceptionInfo e + (binding [*out* *err*] + (-> e .getMessage println) + (-> e .getData :status System/exit))))) diff --git a/api/test/wfl/tools/snapshots.clj b/api/test/wfl/tools/snapshots.clj index a35a38992..7ce508279 100644 --- a/api/test/wfl/tools/snapshots.clj +++ b/api/test/wfl/tools/snapshots.clj @@ -4,29 +4,11 @@ [wfl.util :as util])) (defn unique-snapshot-request - "Wrap `table` from `dataset` in a snapshot with a unique name for `tdr-profile`." + "Return a snapshot request of `table` from `dataset` for `tdr-profile`." [tdr-profile dataset table row-ids] - (let [columns (-> (datarepo/all-columns dataset table) - (->> (map :name) set) - (conj "datarepo_row_id"))] + (let [columns (-> (datarepo/all-columns dataset (name table)) + (->> (map :name) set) + (conj "datarepo_row_id"))] (-> (datarepo/make-snapshot-request dataset columns table row-ids) (update :name util/randomize) - (update :profileId (constantly tdr-profile))))) - -;; Partition row IDs into batches of 500 to keep TDR happy. -;; Ask Ruchi for the reference to the bug ticket if there's one. -(defn create-snapshots - "Return snapshot requests of up to 500 row ID - from `table` in `dataset` for `tdr-profile`. - - Note the dataset row query time range is set to (yesterday, today] - for testing purposes for now." - [tdr-profile dataset table] - (let [today (util/today) - yesterday (util/days-from-today -1) - unique-request-batch (partial unique-snapshot-request tdr-profile dataset table)] - (->> (datarepo/query-table-between dataset table [yesterday today] [:datarepo_row_id]) - flatten - (partition-all 500) - (map unique-request-batch) - (map (partial unique-snapshot-request tdr-profile dataset table))))) + (assoc :profileId tdr-profile)))) diff --git a/api/test/wfl/tools/workloads.clj b/api/test/wfl/tools/workloads.clj index 04ccf3c4a..5ae727026 100644 --- a/api/test/wfl/tools/workloads.clj +++ b/api/test/wfl/tools/workloads.clj @@ -1,24 +1,24 @@ (ns wfl.tools.workloads - (:require [clojure.string :as str] + (:require [clojure.string :as str] [clojure.tools.logging.readable :as log] - [wfl.auth :as auth] - [wfl.environment :as env] - [wfl.jdbc :as jdbc] - [wfl.module.aou :as aou] - [wfl.module.arrays :as arrays] - [wfl.module.copyfile :as cp] - [wfl.module.sg :as sg] - [wfl.module.wgs :as wgs] - [wfl.module.xx :as xx] - [wfl.service.clio :as clio] - [wfl.service.cromwell :as cromwell] - [wfl.service.google.storage :as gcs] - [wfl.tools.endpoints :as endpoints] - [wfl.tools.fixtures :as fixtures] - [wfl.util :as util :refer [shell!]]) - (:import (java.time OffsetDateTime) - (java.util.concurrent TimeoutException) - (java.util UUID))) + [wfl.auth :as auth] + [wfl.environment :as env] + [wfl.jdbc :as jdbc] + [wfl.module.aou :as aou] + [wfl.module.arrays :as arrays] + [wfl.module.copyfile :as cp] + [wfl.module.sg :as sg] + [wfl.module.wgs :as wgs] + [wfl.module.xx :as xx] + [wfl.service.clio :as clio] + [wfl.service.cromwell :as cromwell] + [wfl.service.google.storage :as gcs] + [wfl.service.postgres :as postgres] + [wfl.tools.endpoints :as endpoints] + [wfl.util :as util :refer [shell!]]) + (:import [java.time OffsetDateTime] + [java.util.concurrent TimeoutException] + [java.util UUID])) (def clio-url (delay (env/getenv "WFL_CLIO_URL"))) @@ -124,6 +124,36 @@ :project @project :items [{:inputs {:src src :dst dst}}]}) +(defn covid-workload-request + "Make a COVID Sarscov2IlluminaFull workload creation request." + ([source executor sink] + {:source (merge + {:name "Terra DataRepo" + :dataset (str util/uuid-nil) + :table "table" + :column "column" + :snapshotReaders []} + source) + :executor (merge + {:name "Terra" + :workspace "namespace/name" + :methodConfiguration "namespace/name" + :methodConfigurationVersion 0 + :fromSource "importSnapshot"} + executor) + :sink (merge + {:name "Terra Workspace" + :workspace "namespace/name" + :entityType "entity" + :identifier "foo" + :fromOutputs {}} + sink) + :project @project + :creator @email + :labels ["hornet:test"]}) + ([] + (covid-workload-request {} {} {}))) + (defn xx-workload-request [identifier] "A whole genome sequencing workload used for testing." @@ -223,13 +253,13 @@ (letfn [(finished? [{:keys [status] :as workflow}] (let [skipped? #(-> % :uuid util/uuid-nil?)] (or (skipped? workflow) ((set cromwell/final-statuses) status))))] - (let [interval 10 - timeout 3600] ; 1 hour + (let [interval 60 + timeout 4800] ; 80 minutes (loop [elapsed 0 wl workload] (when (> elapsed timeout) (throw (TimeoutException. (format "Timed out waiting for workload %s" uuid)))) - (if (or (:finished workload) (every? finished? (:workflows wl))) + (if (or (:finished workload) (every? finished? (endpoints/get-workflows wl))) (done! wl) (do (log/infof "Waiting for workload %s to complete" uuid) @@ -238,42 +268,46 @@ (endpoints/get-workload-status uuid)))))))) (defn create-workload! [workload-request] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/create-workload! tx workload-request))) (defn start-workload! [workload] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/start-workload! tx workload))) (defn stop-workload! [workload] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/stop-workload! tx workload))) (defn execute-workload! [workload-request] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/execute-workload! tx workload-request))) (defn update-workload! [workload] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/update-workload! tx workload))) +(defn workflows [workload] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] + (wfl.api.workloads/workflows tx workload))) + (defn load-workload-for-uuid [uuid] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/load-workload-for-uuid tx uuid))) (defn load-workload-for-id [id] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/load-workload-for-id tx id))) (defn load-workloads-with-project [project] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (wfl.api.workloads/load-workloads-with-project tx project))) (defn append-to-workload! [samples workload] - (jdbc/with-db-transaction [tx (fixtures/testing-db-config)] + (jdbc/with-db-transaction [tx (postgres/wfl-db-config)] (aou/append-to-workload! tx samples workload))) -(defmulti postcheck +(defmulti postcheck "Implement this to validate `workload` after all workflows complete." (fn [workload] (:pipeline workload))) diff --git a/api/test/wfl/unit/api_handlers_test.clj b/api/test/wfl/unit/api_handlers_test.clj deleted file mode 100644 index cfa7288fd..000000000 --- a/api/test/wfl/unit/api_handlers_test.clj +++ /dev/null @@ -1,12 +0,0 @@ -(ns wfl.unit.api-handlers-test - (:require [clojure.test :refer [deftest is]] - [wfl.api.handlers :as handlers])) - -(deftest test-strip-internals - (let [workload (handlers/strip-internals - {:id 0 - :items "ExampleTable_0000001" - :workflows [{:id 0} {:id 1}]})] - (is (wfl.util/absent? workload :id)) - (is (wfl.util/absent? workload :items)) - (is (every? #(wfl.util/absent? % :id) (:workflows workload))))) diff --git a/api/test/wfl/unit/datasets_test.clj b/api/test/wfl/unit/datasets_test.clj deleted file mode 100644 index b4305be2b..000000000 --- a/api/test/wfl/unit/datasets_test.clj +++ /dev/null @@ -1,18 +0,0 @@ -(ns wfl.unit.datasets-test - (:require [clojure.test :refer :all] - [wfl.tools.datasets :as datasets] - [wfl.tools.resources :as resources])) - -(deftest test-rename-gather - (let [inputs (resources/read-resource "sarscov2_illumina_full/inputs.edn")] - (is (= {:workspace_name "SARSCoV2-Illumina-Full"} - (datasets/rename-gather inputs {:workspace_name "$SARSCoV2-Illumina-Full"}))) - (is (= {:instrument_model "Illumina NovaSeq 6000"} - (datasets/rename-gather inputs {:instrument_model "instrument_model"}))) - (is (= {:extra ["broad_gcid-srv"]} - (datasets/rename-gather inputs {:extra ["package_genbank_ftp_submission.account_name"]}))) - (is (= {:extra "{\"account_name\":\"broad_gcid-srv\",\"workspace_name\":\"SARSCoV2-Illumina-Full\"}"} - (datasets/rename-gather - inputs - {:extra {:account_name "package_genbank_ftp_submission.account_name" - :workspace_name "$SARSCoV2-Illumina-Full"}}))))) diff --git a/api/test/wfl/unit/mime_type_test.clj b/api/test/wfl/unit/mime_type_test.clj index 155a6180e..23591851f 100644 --- a/api/test/wfl/unit/mime_type_test.clj +++ b/api/test/wfl/unit/mime_type_test.clj @@ -20,7 +20,7 @@ (str filename " does not have the expected mime-type"))))) (deftest test-workflow-mime-types - (let [exclude? #{"gs://broad-gotc-dev-wfl-ptc-test-inputs/sarscov2_illumina_full/outputs/call-demux_deplete/demux_deplete/955c74b3-854a-4075-839f-856d0f41e020/call-sra_meta_prep/write_lines_bc5302b8fdd987961b17ced77e1da4ab.tmp"} + (let [exclude? #{"gs://fc-f9083173-1e35-4c1b-9d80-d837d6d12283/475d0a1d-20c0-42a1-968a-7540b79fcf0c/sarscov2_illumina_full/2768b29e-c808-4bd6-a46b-6c94fd2a67aa/call-demux_deplete/demux_deplete/7045e3bd-cf81-401d-b7da-4eee334cc937/call-sra_meta_prep/cacheCopy/write_lines_0128f217b922021a3b05cdc678f982d2.tmp"} cases [[(resources/read-resource "assemble_refbased/outputs.edn") (-> "assemble_refbased.edn" resources/read-resource :outputs)] [(resources/read-resource "sarscov2_illumina_full/outputs.edn") diff --git a/api/test/wfl/unit/modules/all_test.clj b/api/test/wfl/unit/modules/all_test.clj deleted file mode 100644 index 7dce45bba..000000000 --- a/api/test/wfl/unit/modules/all_test.clj +++ /dev/null @@ -1,16 +0,0 @@ -(ns wfl.unit.modules.all-test - (:require [clojure.test :refer [deftest testing is]] - [wfl.module.aou :as aou] - [wfl.module.sg :as sg] - [wfl.module.wgs :as wgs] - [wfl.module.xx :as xx] - [wfl.util :refer [basename]] - [wfl.wfl :as wfl])) - -(deftest test-version-edn-contains-wdl-version - (let [edn (wfl/get-the-version) - has-version? #(= (:release %) (-> % :path basename edn))] - (is (every? has-version? [aou/workflow-wdl - sg/workflow-wdl - wgs/workflow-wdl - xx/workflow-wdl])))) diff --git a/api/test/wfl/unit/modules/covid_test.clj b/api/test/wfl/unit/modules/covid_test.clj new file mode 100644 index 000000000..2962822c2 --- /dev/null +++ b/api/test/wfl/unit/modules/covid_test.clj @@ -0,0 +1,59 @@ +(ns wfl.unit.modules.covid-test + (:require [clojure.spec.alpha :as s] + [clojure.test :refer :all] + [wfl.api.spec :as spec] + [wfl.module.covid :as covid] + [wfl.service.datarepo :as datarepo] + [wfl.tools.resources :as resources] + [wfl.tools.workloads :as workloads]) + (:import [java.time OffsetDateTime ZoneId] + [java.lang Math])) + +(deftest test-rename-gather + (let [inputs (resources/read-resource "sarscov2_illumina_full/inputs.edn")] + (is (= {:workspace_name "SARSCoV2-Illumina-Full"} + (covid/rename-gather inputs {:workspace_name "$SARSCoV2-Illumina-Full"}))) + (is (= {:instrument_model "Illumina NovaSeq 6000"} + (covid/rename-gather inputs {:instrument_model "instrument_model"}))) + (is (= {:extra ["broad_gcid-srv"]} + (covid/rename-gather inputs {:extra ["package_genbank_ftp_submission.account_name"]}))) + (is (= {:extra {:account_name "broad_gcid-srv" :workspace_name "SARSCoV2-Illumina-Full"}} + (covid/rename-gather + inputs + {:extra {:account_name "package_genbank_ftp_submission.account_name" + :workspace_name "$SARSCoV2-Illumina-Full"}}))))) + +(def ^:private readers-list ["hornet@firecloud.org"]) + +;; Snapshot creation mock +(defn mock-create-snapshot-job + [snapshot-request] + (is (= readers-list (:readers snapshot-request))) + (-> snapshot-request + (select-keys [:name]) + (assoc :id "mock-job-id"))) + +(deftest test-create-snapshots + (let [mock-new-rows-size 2021 + expected-num-shards (int (Math/ceil (/ mock-new-rows-size 500))) + source {:dataset {} + :table "flowcell" + :snapshotReaders readers-list} + row-ids (take mock-new-rows-size (range)) + now-obj (OffsetDateTime/now (ZoneId/of "UTC")) + shards->snapshot-requests + (with-redefs-fn + {#'datarepo/create-snapshot-job mock-create-snapshot-job} + #(vec (#'covid/create-snapshots source now-obj row-ids)))] + (testing "snapshot requests are properly partitioned and made unique" + (is (= expected-num-shards (count shards->snapshot-requests)) + "requests are not partitioned correctly!") + (is (apply distinct? (map #(get-in % [1 :name]) shards->snapshot-requests)) + "requests are not made unique!")))) + +(deftest test-tdr-source-spec + (let [valid? (partial s/valid? ::spec/tdr-source) + {:keys [source]} (workloads/covid-workload-request)] + (is (valid? source) (s/explain-str ::spec/tdr-source source)) + (is (not (valid? (assoc source :snapshotReaders ["geoff"]))) + "snapshotReaders should be a list of email addresses"))) diff --git a/api/test/wfl/unit/spec_test.clj b/api/test/wfl/unit/spec_test.clj index 6524558d7..f5d24a5a5 100644 --- a/api/test/wfl/unit/spec_test.clj +++ b/api/test/wfl/unit/spec_test.clj @@ -1,10 +1,9 @@ (ns wfl.unit.spec-test - (:require [clojure.test :refer [deftest testing is]] - [wfl.tools.workloads :as workloads] - [wfl.api.spec :as spec] - [clojure.spec.alpha :as s] - [clojure.walk :as walk]) - (:import (java.util UUID))) + (:require [clojure.spec.alpha :as s] + [clojure.test :refer [deftest testing is]] + [wfl.api.spec :as spec] + [wfl.tools.workloads :as workloads]) + (:import [java.util UUID])) (deftest request-spec-test (testing "Requests are valid" @@ -14,16 +13,6 @@ workloads/aou-workload-request workloads/xx-workload-request]))))) -(deftest request-spec-negative-test - (testing "Mismatched cram/bam inputs cannot pass spec validation" - (letfn [(invalid? [req] (is (not (s/valid? ::spec/workload-request req))))] - (let [requests (map #(% (UUID/randomUUID)) - [workloads/wgs-workload-request - workloads/xx-workload-request]) - mismatched-requests (map #(walk/postwalk-replace {:input_cram :input_bam} %) - requests)] - (run! invalid? mismatched-requests))))) - (deftest workload-query-spec-test (letfn [(invalid? [req] (is (not (s/valid? ::spec/workload-query req)))) (valid? [req] (is (s/valid? ::spec/workload-query req)))] @@ -39,3 +28,29 @@ (let [uuid-request {:uuid uuid} proj-request {:project project}] (run! valid? [uuid-request proj-request])))))) + +(deftest test-labels-spec + (let [valid? s/valid? + invalid? (comp not s/valid?)] ;; i die + (doseq [[test? label] + [[valid? "test:label"] + [valid? "te_-st:l ab31 "] + [valid? "test:00000000-0000-0000-0000-000000000000"] + [invalid? ":"] + [invalid? "::"] + [invalid? "test:"] + [invalid? "test :"] + [invalid? ":label"] + [invalid? "label"] + [invalid? "test:label:bad"]]] + (is (test? ::spec/labels [label]) (format "failed: %s" label))))) + +(deftest test-watchers-spec + (let [valid? s/valid? + invalid? (comp not s/valid?)] ;; i die + (doseq [[test? email] + [[valid? "hornet-eng@broadinstitute.org"] + ;; From tbl: https://www.netmeister.org/blog/email.html + [valid? "'*+-/=?^_`{|}~#$@[IPv6:2001:470:30:84:e276:63ff:fe72:3900]"] + [invalid? "foo"]]] + (is (test? ::spec/watchers [email]) (format "failed: %s" email))))) diff --git a/api/test/wfl/unit/tsv_test.clj b/api/test/wfl/unit/tsv_test.clj new file mode 100644 index 000000000..edff26549 --- /dev/null +++ b/api/test/wfl/unit/tsv_test.clj @@ -0,0 +1,100 @@ +(ns wfl.unit.tsv-test + "Test the wfl.tsv utility namespace." + (:require [clojure.test :refer [deftest is testing]] + [clojure.java.io :as io] + [clojure.set :as set] + [clojure.walk :as walk] + [wfl.tools.resources :as resources] + [wfl.tsv :as tsv]) + (:import [java.util UUID])) + +(def ^:private the-edn + "More EDN than can be represented in a Terra (.tsv) file." + [{:boolean false + :integer 23 + :keyword :keyword + :map {:a "map"} + :set #{:a "set" 5} + :string "a frayed knot" + :vector ["one thing"] + :jason-rose [:made "a" :good "joke"]} + {:boolean true + :integer 5 + :keyword :lockletter + :map {:b "map"} + :set #{:b "set" 23} + :string "23 skiddoo" + :vector ["or another thing"] + :jason-rose ["and" 23 "skiddoo" :fnord]}]) + +(deftest round-trip-table-map + (testing "Map to table does not lose information." + (is (= the-edn (tsv/mapulate (tsv/tabulate the-edn)))) + (let [keywords (keys (first the-edn)) + renames (zipmap keywords (map name keywords))] + (letfn [(rename [m] (set/rename-keys m renames))] + (let [keywordless (map rename the-edn)] + (is (= keywordless (tsv/mapulate (tsv/tabulate keywordless))))))))) + +(deftest manipulators-throw + (testing "TABLE.tsv has multiple column counts." + (is (thrown-with-msg? + Throwable #"TABLE.tsv has multiple column counts." + (tsv/tabulate [{:a 0} {:a 0 :b 1}])))) + (testing "TABLE.tsv has repeated column labels." + (is (thrown-with-msg? + Throwable #"TABLE.tsv has repeated column labels." + (tsv/mapulate [[:a :a] [:b :b]])))) + (testing "TABLE.tsv has multiple column counts." + (is (thrown-with-msg? + Throwable #"TABLE.tsv has multiple column counts." + (tsv/mapulate [[:a :b] [:b]]))))) + +(defn ^:private hack-terrafy + "Make TREE safe for Terra's TSV format." + [tree] + (letfn [(terrify [x] (cond (boolean? x) (if x "true" "false") + (keyword? x) (name x) + (set? x) (vec x) + :else x))] + (walk/postwalk terrify tree))) + +(defn ^:private hack-unterrafy + "Recover sets in THE-EDN from the resulting Terra TSV map." + [tsv] + (letfn [(fix? [[k v]] (when (set? v) k))] + (let [set-keys (map name (keep fix? (first the-edn)))] + (letfn [(up-set [m k] (update m k set)) + (re-set [m] (into {} (map (partial up-set m) set-keys)))] + (map re-set tsv))))) + +(deftest round-trip-string + (testing "Round-trip THE-EDN to string and back." + (is (= (-> the-edn + hack-terrafy + hack-unterrafy) + (-> the-edn + tsv/tabulate + tsv/write-str + tsv/read-str + tsv/mapulate + hack-unterrafy))))) + +(deftest round-trip-file + (testing "Round-trip THE-EDN to file.tsv and back." + (let [file (io/file (str (UUID/randomUUID) ".tsv"))] + (try (is (= (-> the-edn hack-terrafy hack-unterrafy) + (do (-> the-edn tsv/tabulate (tsv/write-file file)) + (-> file tsv/read-file tsv/mapulate hack-unterrafy)))) + (finally (io/delete-file file)))))) + +(deftest round-trip-inputs + (testing "Round-trip inputs.edn to TSV string and back." + (let [file "sarscov2_illumina_full/inputs.edn" + inputs [(resources/read-resource file)]] + (is (= (-> inputs hack-terrafy) + (-> inputs + tsv/tabulate + tsv/write-str + tsv/read-str + tsv/mapulate)))))) diff --git a/api/test/wfl/unit/utils_test.clj b/api/test/wfl/unit/utils_test.clj index 9cf3d96d0..875123c1c 100644 --- a/api/test/wfl/unit/utils_test.clj +++ b/api/test/wfl/unit/utils_test.clj @@ -60,3 +60,17 @@ (deftest test-assoc-when (is (= {:a 2} (util/assoc-when {:a 1} contains? :a 2))) (is (= {:a 1} (util/assoc-when {:a 1} (constantly false) :a 2)))) + +(deftest test-terra-id + (is (thrown? AssertionError (util/terra-id "not-in-tsv-type-spec" "flowcell"))) + (letfn [(go [[first second expected]] + (is (= expected (util/terra-id first second))))] + (let [entity "entity:flowcell_id" + membership "membership:flowcell_set_id" + parameters [[:entity "flowcell" entity] + [:entity "flowcell_id" entity] + [:membership "flowcell" membership] + [:membership "flowcell_id" membership] + [:membership "flowcell_set" membership] + [:membership "flowcell_set_id" membership]]] + (run! go parameters)))) diff --git a/database/changelog.xml b/database/changelog.xml index a89715ab5..ca01ff523 100644 --- a/database/changelog.xml +++ b/database/changelog.xml @@ -8,21 +8,35 @@ http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.8.xsd" logicalFilePath="changelog.xml" > - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/database/changesets/20210422_AddSourceSinkExecutorToWorkload.xml b/database/changesets/20210422_AddSourceSinkExecutorToWorkload.xml new file mode 100644 index 000000000..603f66430 --- /dev/null +++ b/database/changesets/20210422_AddSourceSinkExecutorToWorkload.xml @@ -0,0 +1,26 @@ + + + + + ALTER TABLE workload + ADD COLUMN source_type SOURCE, -- type of this source + ADD COLUMN source_items TEXT, -- the identifier of the source table + ADD COLUMN executor_type EXECUTOR, -- type of this executor + ADD COLUMN executor_items TEXT, -- the identifier of the executor table + ADD COLUMN sink_type SINK, -- type of this sink + ADD COLUMN sink_items TEXT, -- the identifier of the sink table + ADD COLUMN updated TIMESTAMPTZ; -- when was this workload updated in utc + + + diff --git a/database/changesets/20210422_SourceExecutorSinkEnums.xml b/database/changesets/20210422_SourceExecutorSinkEnums.xml new file mode 100644 index 000000000..c41743222 --- /dev/null +++ b/database/changesets/20210422_SourceExecutorSinkEnums.xml @@ -0,0 +1,39 @@ + + + + + CREATE TYPE source AS ENUM () + + Add a new value for each new 'source' type. + The 'source_type' column for sources of this kind. + + + + + CREATE TYPE executor AS ENUM () + + Add a new value for each new 'executor' type. + The 'executor_type' column for executors of this kind. + + + + + CREATE TYPE sink AS ENUM () + + Add a new value for each new 'sink' type. + The 'sink_type' column for sinks of this kind. + + + + diff --git a/database/changesets/20210422_TerraDataRepoSourceDetailsTable.xml b/database/changesets/20210422_TerraDataRepoSourceDetailsTable.xml new file mode 100644 index 000000000..36c353a4b --- /dev/null +++ b/database/changesets/20210422_TerraDataRepoSourceDetailsTable.xml @@ -0,0 +1,32 @@ + + + + + the details table of 'Terra DataRepo' source + + + CREATE TYPE TerraDataRepoSourceDetails AS ( + id BIGINT, -- unique to this table + start_time TIMESTAMPTZ, -- start timestamp of the TDR data query interval + end_time TIMESTAMPTZ, -- end timestamp of the TDR data query interval + datarepo_row_ids TEXT[], -- array of datarepo row ids for snapshot creation + snapshot_creation_job_id TEXT, -- id of the TDR snapshot creation job + snapshot_creation_job_status TEXT, -- status of the TDR snapshot creation job + snapshot_id TEXT, -- id of the TDR snapshot + updated TIMESTAMPTZ, -- status update time + consumed TIMESTAMPTZ -- time when consumed, null otherwise + ) + + + diff --git a/database/changesets/20210422_TerraDataRepoSourceEnum.xml b/database/changesets/20210422_TerraDataRepoSourceEnum.xml new file mode 100644 index 000000000..62da58f0a --- /dev/null +++ b/database/changesets/20210422_TerraDataRepoSourceEnum.xml @@ -0,0 +1,19 @@ + + + + + ALTER TYPE source ADD VALUE 'TerraDataRepoSource' + + + diff --git a/database/changesets/20210422_TerraDataRepoSourceTable.xml b/database/changesets/20210422_TerraDataRepoSourceTable.xml new file mode 100644 index 000000000..acb766796 --- /dev/null +++ b/database/changesets/20210422_TerraDataRepoSourceTable.xml @@ -0,0 +1,32 @@ + + + + + the 'Terra DataRepo' source table schema + + + CREATE TABLE TerraDataRepoSource ( + id BIGINT GENERATED BY DEFAULT AS IDENTITY NOT NULL, -- primary key + dataset TEXT NOT NULL, -- the serialized EDN of the TDR dataset schema + dataset_table TEXT NOT NULL, -- the name of the dataset table + table_column_name TEXT NOT NULL, -- name of a column in table containing orderable and strictly increasing data + snapshot_readers TEXT[] DEFAULT '{}', -- list of accounts to be made watchers of the snapshots this source creates + details TEXT NOT NULL, -- the identifier of the source details table + last_checked TIMESTAMPTZ, -- when WFL last checked TDR for new data + stopped TIMESTAMPTZ, -- when WFL stopped checking for new data + CONSTRAINT TERRADATAREPOSOURCE_PKEY PRIMARY KEY (id) + ) + + + diff --git a/database/changesets/20210422_TerraExecutorDetailsTable.xml b/database/changesets/20210422_TerraExecutorDetailsTable.xml new file mode 100644 index 000000000..53ef21e65 --- /dev/null +++ b/database/changesets/20210422_TerraExecutorDetailsTable.xml @@ -0,0 +1,31 @@ + + + + + the details table of 'Terra' executor + + + CREATE TYPE TerraExecutorDetails AS ( + id BIGINT, -- unique to this table + reference TEXT, -- id of the snapshot reference in the workspace + submission TEXT, -- id of the Rawls submission + workflow TEXT, -- id of the Terra workflow + entity TEXT, -- name of the workflow entity + status TEXT, -- status of the Terra workflow + updated TIMESTAMPTZ, -- status update time + consumed TIMESTAMPTZ -- time when consumed, null otherwise + ) + + + diff --git a/database/changesets/20210422_TerraExecutorEnum.xml b/database/changesets/20210422_TerraExecutorEnum.xml new file mode 100644 index 000000000..60d879dc3 --- /dev/null +++ b/database/changesets/20210422_TerraExecutorEnum.xml @@ -0,0 +1,19 @@ + + + + + ALTER TYPE executor ADD VALUE 'TerraExecutor' + + + diff --git a/database/changesets/20210422_TerraExecutorTable.xml b/database/changesets/20210422_TerraExecutorTable.xml new file mode 100644 index 000000000..3378c6ca6 --- /dev/null +++ b/database/changesets/20210422_TerraExecutorTable.xml @@ -0,0 +1,30 @@ + + + + + the 'Terra' executor table schema + + + CREATE TABLE TerraExecutor ( + id BIGINT GENERATED BY DEFAULT AS IDENTITY NOT NULL, -- primary key + workspace TEXT NOT NULL, -- the fully-qualified 'Namespace/Name' of the Terra workspace to execute workflows in + method_configuration TEXT NOT NULL, -- the fully-qualified 'Namespace/Name' of the method configuration used to create submissions + method_configuration_version INTEGER NOT NULL, -- the version of the method configuration + details TEXT NOT NULL, -- the identifier of the executor details table + from_source TEXT NOT NULL, -- mapping of how to coerce the output of source to executor in serialized EDN + CONSTRAINT TERRAEXECUTOR_PKEY PRIMARY KEY (id) + ) + + + diff --git a/database/changesets/20210422_TerraWorkspaceSinkEnum.xml b/database/changesets/20210422_TerraWorkspaceSinkEnum.xml new file mode 100644 index 000000000..a30fd8376 --- /dev/null +++ b/database/changesets/20210422_TerraWorkspaceSinkEnum.xml @@ -0,0 +1,20 @@ + + + + + ALTER TYPE sink ADD VALUE 'TerraWorkspaceSink' + + + + diff --git a/database/changesets/20210422_TerraWorkspaceSinkTable.xml b/database/changesets/20210422_TerraWorkspaceSinkTable.xml new file mode 100644 index 000000000..a33c19752 --- /dev/null +++ b/database/changesets/20210422_TerraWorkspaceSinkTable.xml @@ -0,0 +1,30 @@ + + + + + the 'Terra Workspace' sink table schema + + + CREATE TABLE TerraWorkspaceSink ( + id BIGINT GENERATED BY DEFAULT AS IDENTITY NOT NULL, -- primary key + workspace TEXT NOT NULL, -- the fully-qualified 'Namespace/Name' of the Terra workspace to execute workflows in + entity_type TEXT NOT NULL, -- the entity type to import data from the source as + from_outputs TEXT NOT NULL, -- mapping of how to coerce the output of executor to whatever the sink understands in serialized EDN + details TEXT NOT NULL, -- the identifier of the sink details table + identifier TEXT NOT NULL, -- the name of the output uniquely identifying the entity + CONSTRAINT TERRAWORKSPACESINK_PKEY PRIMARY KEY (id) + ) + + + diff --git a/database/changesets/20210507_AddWatchersAndLabelsToWorkload.xml b/database/changesets/20210507_AddWatchersAndLabelsToWorkload.xml new file mode 100644 index 000000000..e96040403 --- /dev/null +++ b/database/changesets/20210507_AddWatchersAndLabelsToWorkload.xml @@ -0,0 +1,24 @@ + + + + + Add a few new columns to the `workload` table + + + ALTER TABLE workload + ADD labels TEXT[] DEFAULT '{}', + ADD watchers TEXT[] DEFAULT '{}'; + + + diff --git a/database/changesets/20210510_TerraWorkspaceSinkDetailsTable.xml b/database/changesets/20210510_TerraWorkspaceSinkDetailsTable.xml new file mode 100644 index 000000000..aa2029572 --- /dev/null +++ b/database/changesets/20210510_TerraWorkspaceSinkDetailsTable.xml @@ -0,0 +1,27 @@ + + + + + the details table of 'Terra' executor + + + CREATE TYPE TerraWorkspaceSinkDetails AS ( + id BIGINT, -- unique to this table + workflow TEXT, -- workflow id + entity TEXT, -- name the entity created + updated TIMESTAMPTZ -- status update time + ) + + + diff --git a/database/changesets/20210519_ListSourceType.xml b/database/changesets/20210519_ListSourceType.xml new file mode 100644 index 000000000..b86676d42 --- /dev/null +++ b/database/changesets/20210519_ListSourceType.xml @@ -0,0 +1,26 @@ + + + + + A List of Items Used as A Workload Source + + + CREATE TYPE ListSource AS ( + id BIGINT, -- unique to this table + item TEXT, -- item on the queue + consumed TIMESTAMPTZ -- time when consumed, null otherwise + ) + + + diff --git a/database/changesets/20210519_TDRSnapshotListSourceEnum.xml b/database/changesets/20210519_TDRSnapshotListSourceEnum.xml new file mode 100644 index 000000000..8a53129f9 --- /dev/null +++ b/database/changesets/20210519_TDRSnapshotListSourceEnum.xml @@ -0,0 +1,19 @@ + + + + + ALTER TYPE source ADD VALUE 'TDRSnapshotListSource' + + + diff --git a/docs/md/dev-process.md b/docs/md/dev-process.md index cd2d5a75c..b8ef735d6 100644 --- a/docs/md/dev-process.md +++ b/docs/md/dev-process.md @@ -5,13 +5,17 @@ encourage ourselves to follow in most cases. ## The Swagger page -WFL ships with a swagger UI that documents all available endpoints. It's -available at path `/swagger`, e.g. -https://dev-wfl.gotc-dev.broadinstitute.org/swagger +WFL ships with a Swagger UI that documents all available endpoints. It's +available at path `/swagger`. At present, we cannot hit it directly +without logging in first because it is bundled with the UI and not the API. + +- Log into WFL UI, e.g. https://dev-wfl.gotc-dev.broadinstitute.org/login +- Navigate to `/swagger` via Swagger API button in top right !!! tip -To access the swagger page locally, you'll need to start a development server -and access via the UI. See the development tips below for more information. + To access the swagger page locally, you'll need to start a development + server and access via the UI. See the development tips below for more + information. ## Development Setup @@ -23,10 +27,14 @@ Get a demonstration from someone familiar with Clojure development before you spend too much time trying to figure things out on your own. Find a local Cursive user for guidance if you like IntelliJ. -[Rex Wang](mailto:chengche@broadinstitute.org) and -[Saman Ehsan](mailto:sehsan@broadinstitute.org) know how to use it. +[Rex Wang](mailto:chengche@broadinstitute.org) knows how to use it. + Cursive licences are available [here](https://broadinstitute.atlassian.net/wiki/spaces/DSDE/pages/48234557/Software%2BLicenses%2B-%2BCursive). +If none are available, free +[non-commercial licenses](https://cursive-ide.com/buy.html) are suitable for +open-source development. + The steps for getting this project set up with very recent versions of IntelliJ differ from Cursive's docs: @@ -57,7 +65,7 @@ used to Emacs. (I can help if CIDER gives you trouble.) We base feature branches off `develop`, make pull requests, ask for reviews and merge back to `develop` on Github. -For the release process, please refer to the [release guide](../dev-release/) +For the release process, please refer to the [release guide](./dev-release.md). 1. Clone the repo ``` @@ -72,7 +80,7 @@ For the release process, please refer to the [release guide](../dev-release/) 3. Create a feature branch - _It is highly recommend that you follow the naming convention + _It is highly recommended that you follow the naming convention shown below so JIRA could pick up the branch and link it to our JIRA board._ ``` @@ -85,7 +93,7 @@ For the release process, please refer to the [release guide](../dev-release/) git commit -m "Update the readme file." ``` -5. [Optional] Rebase onto lastest develop if you want to get updates +5. [Optional] Rebase onto latest develop if you want to get updates ``` git checkout develop git pull origin develop --ff @@ -131,6 +139,66 @@ Here are some tips for WFL development. Some of this advice might help when testing Liquibase migration or other changes that affect WFL's Postgres database. +### setting up a local Postgres + +You can test against a local Postgres before running Liquibase or SQL against a +shared database in `gotc-dev` or *gasp* production. + +1. Install Postgres locally. + You need version 11 because that is what Google's hosted service supports, + and there are differences in the SQL syntax. + + ``` + brew install postgresql@11 + ``` + +2. Start Postgres. + + ``` + pg_ctl -D /usr/local/var/postgresql@11 start + ``` + !!! tip + It might be useful to set up some an alias for postgres if you are using + zsh, for example: + ``` + alias pq="pg_ctl -D /usr/local/var/postgresql@11" + ``` + thus you could use `pq start` or `pq stop` to easily spin up and turn down + the db. + +3. [Optional] Create wfl DB. + + If you see errors like this when launching a local WFL server + or applying liquibase updates: + + ``` + FATAL: database "wfl" does not exist + ``` + + You should do as instructed within your terminal: + + ``` + createdb wfl + ``` + + Or to recreate an existing wfl DB: + + ``` + dropdb wfl + createdb wfl + ``` + +You are now free to launch a local WFL server pointing to your local DB. + +Assuming that `WFL_POSTGRES_URL` in `(wfl.environment/defaults)` is set to +point at a running local Postgres (e.g. `jdbc:postgresql:wfl`), running +`./ops/server.sh` (or however you launch a local WFL server) will +connect the server to that running local Postgres. + +Now any changes to WFL state will affect only your local database. +That includes running Liquibase, so don't forget to reset `:debug` to `env` +before deploying your changes after merging a PR. + ### migrating a database @@ -157,45 +225,7 @@ silently fail or the Swagger page will fail to render. Check the `clojure.spec.alpha/def`s in `wfl.api.routes` for typos before tearing your hair out. -### hacking a scratch database - -You can test against a local Postgres before running Liquibase or SQL against a -shared database in `gotc-dev` or *gasp* production. - -First install Postgres locally. - -``` shell -brew install postgresql@11 -``` - -You need version 11 because that is what Google's hosted service supports, -and there are differences in the SQL syntax. - -Modify the value of `WFL_POSTGRES_URL` in `(postgres/wfl-db-config)` to redirect -the WFL server's database to a local Postgres server. With that hack in place, -running `./ops/server.sh` (or however you launch a local WFL server) will -connect the server to a local Postgres. - -Now any changes to WFL state will affect only your local database. -That includes running Liquibase, so don't forget to reset `:debug` to `env` -before deploying your changes after merging a PR. - -### Useful hacks for debugging Postgres/Liquibase locally - -Starting `postgres`: -```bash -pg_ctl -D /usr/local/var/postgresql@11 start -``` - -!!! tip - It might be useful to set up some an alias for postgres if you are using - zsh, for example: - ``` - alias pq="pg_ctl -D /usr/local/var/postgresql@11" - ``` - thus you could use `pq start` or `pq stop` to easily spin up and turn down - the db. - +### debugging Liquibase locally Running `liquibase update`: ```bash @@ -221,4 +251,35 @@ You can use `--password=$ENV_SOMETHING` to supply it. ``` clojure -M:liquibase ``` - if you are working with a local database. + if you are working with a local database. + +### Override ENVIRONMENT variables for local development + +WFL uses `src/wfl/api/environment.clj` to read and process environment variables. +Most of the variables have their default values, which can be overwritten for development +purposes. For example, if we want to run system tests in parallel against a local +WFL instance, use below under `api/` directory: + +```shell +WFL_WFL_URL=http://localhost:3000 clojure -M:parallel-test wfl.system.v1-endpoint-test +``` + +### REPL testing with fixtures. + +Now that we're using fixtures, +and so on, +in our tests, +it is no longer good enough +to run `deftest` vars as functions. +Running a test like this `(test-something)` +does not set up the necessary fixtures. + +However, +`clojure.test/test-vars` can run a test +with all the surrounding `clojure.test` +mechanism in place. +It takes a vector of `var`s like this. + +``` clojure +(comment (test-vars [#'test-something])) +``` diff --git a/docs/md/dev-release.md b/docs/md/dev-release.md index b17e3fa75..46347768f 100644 --- a/docs/md/dev-release.md +++ b/docs/md/dev-release.md @@ -8,18 +8,55 @@ in order to release a new version of WFL: - the version string should match that specified in `version` 2. Identify and cherry-pick additional commits from `develop` that you want to release (e.g. late features and bug fixes). -3. Create a pull request into `main`. You will need to run +3. Create a release candidate and deploy to a testing environment. See + instructions bellow. +4. [Bash](https://broadinstitute.atlassian.net/wiki/spaces/GHConfluence/pages/1731658083/Feature+Bashes) + the release candidate. Add/cherry-pick any bug fixes that result. +5. Create a pull request into `main`. You will need to run `./ops/cli.py release` to generate the changelog for this release (the `-d` flag can be used to do a dry run without writing to the `CHANGELOG.md`file). -5. When the PR is approved, merge it into `main`. The release action will run +6. When the PR is approved, merge it into `main`. The release action will run automatically to build, test and build and push the tagged docker images of WFL to [DockerHub](https://hub.docker.com/repository/docker/broadinstitute/workflow-launcher-api). Please merge PRs that have passed all automated tests only. !!! tip - It can take up to 30 minutes for the Github Action to finish! Please be + It can take up to 30 minutes for the Github Action to finish! Please be patient! !!! tip Remember to create a PR to bump the version string in `version` in - `develop` for the next release. + `develop` for the next release, including changes to `CHANGELOG.md` + from the release. + +## Creating a Release Candidate + +In this example, we will create a release candidate for vX.Y.Z. We will assume +the existence of a release branch `release/X.Y.Z-rc`. From `wfl`'s root +directory: + +1. Ensure your local repository clone is clean + ``` + $ make distclean + ``` + +2. Prepare sources + ```bash + $ git checkout release/X.Y.Z-rc + $ git pull origin release/X.Y.Z-rc --ff + ``` + +4. Build the docker images locally + ```bash + $ make TARGET=images + ``` + +5. Tag the commit and release the images to dockerhub with the release + candidate tag. Let us assume that this is the Mth release candidate. + ```bash + $ ./ops/cli.py tag-and-push-images --version=X.Y.Z-rcN + ``` + +!!! tip + You can run `make` in parallel by adding `-jN` to the end of your `make` + command, where `N` is the number of concurrent jobs to run. diff --git a/docs/md/index.md b/docs/md/index.md index e27132cea..e9a276ae6 100644 --- a/docs/md/index.md +++ b/docs/md/index.md @@ -1,6 +1,6 @@ # Welcome to WorkFlow Launcher -[![Build Board](https://img.shields.io/badge/-The%20Build%20Boad%20(VPN)-blue)](https://internal.broadinstitute.org/~chengche/green-hornet-status.html) +[![Build Board](https://img.shields.io/badge/-The%20Build%20Board%20(VPN)-blue)](https://internal.broadinstitute.org/~chengche/green-hornet-status.html) ![Docsite Build](https://github.com/broadinstitute/wfl/workflows/Publish%20docs%20via%20GitHub%20Pages/badge.svg?branch=main) ![Build on Main](https://github.com/broadinstitute/wfl/workflows/Tests%20on%20Pull%20Requests%20and%20Main/badge.svg?branch=main) [![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/broadinstitute/wfl?label=Latest%20Release)](https://github.com/broadinstitute/wfl/blob/main/CHANGELOG.md) @@ -21,7 +21,7 @@ on Kubernetes clusters. !!! info "" For more on Workflow Launcher's role in the Terra infrastructure - see [Workflow Launcher's role in Terra](/docs/md/terra.md). + see [Workflow Launcher's role in Terra](./terra.md). ## Quickstart @@ -29,18 +29,19 @@ on Kubernetes clusters. ???+ tip This is the Quickstart section, which should cover the most frequent uses cases that interact with WFL. For more detailed information, please - check other sections such as the [development guide](/docs/md/dev-process.md) - or [modules design principles](/docs/md/modules-general.md). + check other sections such as the [development guide](./dev-process.md) + or [modules design principles](./modules-general.md). ### Build -The easiest way to build WFL is via `make` (or `gmake` on macOS), in addition, the -following prerequisites are needed: +The easiest way to build WFL is via `make`, in addition, the following +prerequisites are needed: - [The Docker daemon](https://www.docker.com/products/docker-desktop) - Clojure (`brew install clojure` on macOS) -- Python3 (`brew install python@3.8` on macOS) +- Python3 (`brew install python@3.9` on macOS) - NodeJS (`brew install node` on macOS) +- Google Cloud SDK (`brew install --cask google-cloud-sdk` on macOS) !!! tip "Arch Linux tips" - Install [clojure](https://www.archlinux.org/packages/?name=clojure) @@ -176,18 +177,15 @@ clojure -M:parallel-test wfl.system.v1-endpoint-test Currently, we mainly deploy WFL to `broad-gotc-dev` and `broad-gotc-prod` projects. When it's time to deploy WFL, for most of the time developers need to -release a new version following the steps in [Release Guide](/docs/md/dev-release.md) +release a new version following the steps in [Release Guide](./dev-release.md) After which, the developers who have broad VPN connected can go to the [Jenkins Page](https://gotc-jenkins.dsp-techops.broadinstitute.org/job/deploy-wfl/build?delay=0sec) to deploy applicable versions of WFL to various available cloud projects. -Learn more about the deployment details in -[Deployment of WorkFlow Launcher](/docs/md/dev-deployment.md). - ## Implementation -For frontend details, check [Frontend Section](/docs/md/dev-frontend.md) +For frontend details, check [Frontend Section](./dev-frontend.md) ### Top-level files diff --git a/docs/md/modules-arrays.md b/docs/md/modules-arrays.md index e3e4e6b03..05810d511 100644 --- a/docs/md/modules-arrays.md +++ b/docs/md/modules-arrays.md @@ -21,15 +21,15 @@ caller. It supports the following API endpoints: -| Verb | Endpoint | Description | -|------|------------------------------|----------------------------------------------------------------| -| GET | `/api/v1/workload` | List all workloads | -| GET | `/api/v1/workload/{uuid}` | Query for a workload by its UUID | -| GET | `/api/v1/workload/{project}` | Query for a workload by its Project name | -| POST | `/api/v1/create` | Create a new workload | -| POST | `/api/v1/start` | Start a workload | -| POST | `/api/v1/exec` | Create and start (execute) a workload | -| POST | `/api/v1/append_to_aou` | Append a new or multiple sample(s) to an existing AOU workload | +| Verb | Endpoint | Description | +|------|-------------------------------------|--------------------------------------------------------------------------| +| GET | `/api/v1/workload` | List all workloads, optionally filtering by uuid or project | +| GET | `/api/v1/workload/{uuid}/workflows` | List all workflows for a specified workload uuid | +| POST | `/api/v1/create` | Create a new workload | +| POST | `/api/v1/start` | Start a workload | +| POST | `/api/v1/stop` | Stop a running workload | +| POST | `/api/v1/exec` | Create and start (execute) a workload | +| POST | `/api/v1/append_to_aou` | Append one or more sample(s) to an existing AOU workload, unless stopped | Different from the fixed workload types that caller only needs to create a workload with a series of sample inputs and then simply start the workload, `aou-arrays` module requires the caller to manage the life cycle of a workload on their @@ -50,27 +50,27 @@ To give more information, here are some example inputs to the above endpoints: === "Request" ```shell - curl "http://localhost:8080/api/v1/workload" \ + curl 'http://localhost:8080/api/v1/workload' \ -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ -H 'Accept: application/json' ``` -**GET /api/v1/workload/{uuid}** +**GET /api/v1/workload?uuid={uuid}** === "Request" ```shell - curl "http://localhost:8080/api/v1/workload?uuid=00000000-0000-0000-0000-000000000000" \ + curl 'http://localhost:8080/api/v1/workload?uuid=00000000-0000-0000-0000-000000000000' \ -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ -H 'Accept: application/json' ``` -**GET /api/v1/workload/{project}** +**GET /api/v1/workload?project={project}** === "Request" ```shell - curl "http://localhost:8080/api/v1/workload?project=(Test)%20WFL%20Local%20Testing" \ + curl 'http://localhost:8080/api/v1/workload?project=(Test)%20WFL%20Local%20Testing' \ -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ -H 'Accept: application/json' ``` @@ -80,47 +80,69 @@ To give more information, here are some example inputs to the above endpoints: hitting this endpoint without them will return all workloads. However, they cannot be specified together. -**GET /api/v1/workload/create** +**GET /api/v1/workload/{uuid}/workflows** === "Request" ```shell - curl -X "POST" "http://localhost:8080/api/v1/create" \ - -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ - -H 'Accept: application/json' \ - -H 'Content-Type: application/json' \ - -d '{ - "executor": "https://cromwell-gotc-auth.gotc-dev.broadinstitute.org", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/aou-test-output/", - "project": "Example Project", - "pipeline": "AllOfUsArrays" - }' + curl 'http://localhost:8080/api/v1/workload/00000000-0000-0000-0000-000000000000/workflows' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) ``` -**GET /api/v1/workload/start** +**POST /api/v1/create** === "Request" ```shell - curl -X "POST" "http://localhost:8080/api/v1/start" \ - -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ - -H 'Accept: application/json' \ - -H 'Content-Type: application/json' \ - -d $'{ - "uuid": "00000000-0000-0000-0000-000000000000" - }' + curl -X POST 'http://localhost:8080/api/v1/create' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Accept: application/json' \ + -H 'Content-Type: application/json' \ + -d '{ + "executor": "https://cromwell-gotc-auth.gotc-dev.broadinstitute.org", + "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/aou-test-output/", + "project": "Example Project", + "pipeline": "AllOfUsArrays" + }' ``` -**GET /api/v1/workload/append_to_aou** +**POST /api/v1/start** === "Request" ```shell - curl -X "POST" "http://localhost:8080/api/v1/append_to_aou" \ - -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ - -H 'Accept: application/json' \ - -H 'Content-Type: application/json' \ - -d $'{ + curl -X POST 'http://localhost:8080/api/v1/start' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Accept: application/json' \ + -H 'Content-Type: application/json' \ + -d $'{ "uuid": "00000000-0000-0000-0000-000000000000" }' + ``` + +**POST /api/v1/stop** + +Stops the workload from accepting new samples. +See also: `/api/v1/append_to_aou`. + +=== "Request" + + ```shell + curl -X POST 'http://localhost:8080/api/v1/stop' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Accept: application/json' \ + -H 'Content-Type: application/json' \ + -d $'{ "uuid": "00000000-0000-0000-0000-000000000000" }' + ``` + +**POST /api/v1/workload/append_to_aou** + +=== "Request" + + ```shell + curl -X POST 'http://localhost:8080/api/v1/append_to_aou' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Accept: application/json' \ + -H 'Content-Type: application/json' \ + -d $'{ "uuid": "00000000-0000-0000-0000-000000000000", "notifications": [ { @@ -185,7 +207,7 @@ Note that different from the fixed workload types, `input`, `output` and `items` since these fields vary from sample to sample. Any information the caller provided to these fields will stored as placeholders. -More importantly, eve though `id` is the `primary` key here, `(pipeline, project, release)` works as the +More importantly, even though `id` is the `primary` key here, `(pipeline, project, release)` works as the unique identifier for arrays workloads, for instance, if there's already a workload with values: `(AllOfUsArrays, gotc-dev, Arrays_v1.9)`, any further attempts to create a new workload with exact the same values will return the information of this existing workload rather than create a new row. diff --git a/docs/md/modules-external-exome-reprocessing.md b/docs/md/modules-external-exome-reprocessing.md index 5b2d45524..9bfca3e78 100644 --- a/docs/md/modules-external-exome-reprocessing.md +++ b/docs/md/modules-external-exome-reprocessing.md @@ -16,21 +16,21 @@ below for all options. External Exome Reprocessing workload supports the following API endpoints: -| Verb | Endpoint | Description | -|------|------------------------------|----------------------------------------------------------------| -| GET | `/api/v1/workload` | List all workloads | -| GET | `/api/v1/workload/{uuid}` | Query for a workload by its UUID | -| GET | `/api/v1/workload/{project}` | Query for a workload by its Project name | -| POST | `/api/v1/create` | Create a new workload | -| POST | `/api/v1/start` | Start a workload | -| POST | `/api/v1/exec` | Create and start (execute) a workload | +| Verb | Endpoint | Description | +|------|-------------------------------------|----------------------------------------------------------------| +| GET | `/api/v1/workload` | List all workloads, optionally filtering by uuid or project | +| GET | `/api/v1/workload/{uuid}/workflows` | List all workflows for a specified workload uuid | +| POST | `/api/v1/create` | Create a new workload | +| POST | `/api/v1/start` | Start a workload | +| POST | `/api/v1/stop` | Stop a running workload | +| POST | `/api/v1/exec` | Create and start (execute) a workload | ???+ warning "Permissions in production" External Exome Reprocessing in `gotc-prod` uses a set of execution projects, please refer to [this page](https://github.com/broadinstitute/gotc-deploy/blob/master/deploy/gotc-prod/helm/WFL_README.md) when you have questions about permissions. -### Create Workload: `/api/v1/create` +### Create Workload: `POST /api/v1/create` Create a new workload. Ensure that `workflow-launcher` and `cromwell`'s service accounts have at least read access to the input files. @@ -63,15 +63,6 @@ accounts have at least read access to the input files. "release" : "ExternalExomeReprocessing_vX.Y.Z", "created" : "YYYY-MM-DDTHH:MM:SSZ", "output" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/", - "workflows" : [ { - "inputs" : { - "input_cram" : "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "destination_cloud_path" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/8600be1a-48df-4a51-bdba-0044e0af8d33/single_sample/plumbing/truth/develop/20k", - "sample_name" : "NA12878_PLUMBING", - "base_file_name" : "NA12878_PLUMBING.cram", - "final_gvcf_base_name" : "NA12878_PLUMBING.cram" - } - } ], "commit" : "commit-ish", "project" : "Example Project", "uuid" : "1337254e-f7d8-438d-a2b3-a74b199fee3c", @@ -84,7 +75,7 @@ Note that the ExternalExomeReprocessing pipeline supports specifying cromwell "workflowOptions" via the `options` map. See the [reference page](./usage-workflow-options) for more information. -### Start Workload: `/api/v1/start` +### Start Workload: `POST /api/v1/start` Starts a Cromwell workflow for each item in the workload. If an output already exists in the output bucket for a particular input cram, WFL will not re-submit that workflow. @@ -109,18 +100,6 @@ particular input cram, WFL will not re-submit that workflow. "created" : "YYYY-MM-DDTHH:MM:SSZ", "started" : "YYYY-MM-DDTHH:MM:SSZ", "output" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/", - "workflows" : [ { - "status" : "Submitted", - "updated" : "YYYY-MM-DDTHH:MM:SSZ", - "uuid" : "bb0d93e3-1a6a-4816-82d9-713fa58fb235", - "inputs" : { - "input_cram" : "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "destination_cloud_path" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/8600be1a-48df-4a51-bdba-0044e0af8d33/single_sample/plumbing/truth/develop/20k", - "sample_name" : "NA12878_PLUMBING", - "base_file_name" : "NA12878_PLUMBING.cram", - "final_gvcf_base_name" : "NA12878_PLUMBING.cram" - } - } ], "commit" : "commit-ish", "project" : "Example Project", "uuid" : "1337254e-f7d8-438d-a2b3-a74b199fee3c", @@ -129,7 +108,40 @@ particular input cram, WFL will not re-submit that workflow. } ``` -### Exec Workload: `/api/v1/exec` +### Stop Workload: `POST /api/v1/stop` + +Included for compatibility with continuous workloads. + +=== "Request" + + ```bash + curl -X POST 'https://gotc-prod-wfl.gotc-prod.broadinstitute.org/api/v1/stop' \ + -H "Authorization: Bearer $(gcloud auth print-access-token)" \ + -H 'Content-Type: application/json' \ + -d '{ "uuid": "1337254e-f7d8-438d-a2b3-a74b199fee3c" }' + ``` + +=== "Response" + + ```json + { + "creator" : "user@domain", + "pipeline" : "ExternalExomeReprocessing", + "executor" : "https://cromwell-gotc-auth.gotc-prod.broadinstitute.org", + "release" : "ExternalExomeReprocessing_vX.Y.Z", + "created" : "YYYY-MM-ddTHH:mm:ssZ", + "started" : "YYYY-MM-ddTHH:mm:ssZ", + "stopped" : "YYYY-MM-ddTHH:mm:ssZ", + "output" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/", + "commit" : "commit-ish", + "project" : "Example Project", + "uuid" : "1337254e-f7d8-438d-a2b3-a74b199fee3c", + "wdl" : "pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl", + "version" : "X.Y.Z" + } + ``` + +### Exec Workload: `POST /api/v1/exec` Creates and then starts a Cromwell workflow for each item in the workload. @@ -163,18 +175,6 @@ Creates and then starts a Cromwell workflow for each item in the workload. "created" : "YYYY-MM-DDTHH:MM:SSZ", "started" : "YYYY-MM-DDTHH:MM:SSZ", "output" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/", - "workflows" : [ { - "status" : "Submitted", - "updated" : "YYYY-MM-DDTHH:MM:SSZ", - "uuid" : "bb0d93e3-1a6a-4816-82d9-713fa58fb235", - "inputs" : { - "input_cram" : "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "destination_cloud_path" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/8600be1a-48df-4a51-bdba-0044e0af8d33/single_sample/plumbing/truth/develop/20k", - "sample_name" : "NA12878_PLUMBING", - "base_file_name" : "NA12878_PLUMBING.cram", - "final_gvcf_base_name" : "NA12878_PLUMBING.cram" - } - } ], "commit" : "commit-ish", "project" : "Example Project", "uuid" : "1337254e-f7d8-438d-a2b3-a74b199fee3c", @@ -183,7 +183,7 @@ Creates and then starts a Cromwell workflow for each item in the workload. } ``` -### Query Workload: `/api/v1/workload?uuid=` +### Query Workload: `GET /api/v1/workload?uuid=` Queries the WFL database for workloads. Specify the uuid to query for a specific workload. @@ -205,18 +205,6 @@ Queries the WFL database for workloads. Specify the uuid to query for a specific "created" : "YYYY-MM-DDTHH:MM:SSZ", "started" : "YYYY-MM-DDTHH:MM:SSZ", "output" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/", - "workflows" : [ { - "status" : "Submitted", - "updated" : "YYYY-MM-DDTHH:MM:SSZ", - "uuid" : "bb0d93e3-1a6a-4816-82d9-713fa58fb235", - "inputs" : { - "input_cram" : "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "destination_cloud_path" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/8600be1a-48df-4a51-bdba-0044e0af8d33/single_sample/plumbing/truth/develop/20k", - "sample_name" : "NA12878_PLUMBING", - "base_file_name" : "NA12878_PLUMBING.cram", - "final_gvcf_base_name" : "NA12878_PLUMBING.cram" - } - } ], "commit" : "commit-ish", "project" : "Example Project", "uuid" : "1337254e-f7d8-438d-a2b3-a74b199fee3c", @@ -225,12 +213,7 @@ Queries the WFL database for workloads. Specify the uuid to query for a specific }] ``` -The "workflows" field lists out each Cromwell workflow that was started, and -includes their status information. It is also possible to use the Job Manager -to check workflow progress and easily see information about any workflow -failures. - -### Query Workload with project: `/api/v1/workload?project=` +### Query Workload with project: `GET /api/v1/workload?project=` Queries the WFL database for workloads. Specify the project name to query for a list of specific workload(s). @@ -252,18 +235,6 @@ Queries the WFL database for workloads. Specify the project name to query for a "created" : "YYYY-MM-DDTHH:MM:SSZ", "started" : "YYYY-MM-DDTHH:MM:SSZ", "output" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/", - "workflows" : [ { - "status" : "Submitted", - "updated" : "YYYY-MM-DDTHH:MM:SSZ", - "uuid" : "bb0d93e3-1a6a-4816-82d9-713fa58fb235", - "inputs" : { - "input_cram" : "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "destination_cloud_path" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/8600be1a-48df-4a51-bdba-0044e0af8d33/single_sample/plumbing/truth/develop/20k", - "sample_name" : "NA12878_PLUMBING", - "base_file_name" : "NA12878_PLUMBING.cram", - "final_gvcf_base_name" : "NA12878_PLUMBING.cram" - } - } ], "commit" : "commit-ish", "project" : "Example Project", "uuid" : "1337254e-f7d8-438d-a2b3-a74b199fee3c", @@ -272,16 +243,44 @@ Queries the WFL database for workloads. Specify the project name to query for a }] ``` -The "workflows" field lists out each Cromwell workflow that was started, and -includes their status information. It is also possible to use the Job Manager -to check workflow progress and easily see information about any workflow -failures. - !!! warning "Note" - `project` and `uuid` are optional path parameters to the `/api/v1/workload` endpoint, + `project` and `uuid` are optional query parameters to the `/api/v1/workload` endpoint, hitting this endpoint without them will return all workloads. However, they cannot be specified together. +### List Workflows in a Workload: `GET /api/v1/workload/{uuid}/workflows` + +Returns the workflows created and managed by the workload with `uuid`. + +=== "Request" + + ```bash + curl -X GET 'https://gotc-prod-wfl.gotc-prod.broadinstitute.org/api/v1/workload/1337254e-f7d8-438d-a2b3-a74b199fee3c/workflows' \ + -H "Authorization: Bearer $(gcloud auth print-access-token)" + ``` + +=== "Response" + + ```json + [{ + "status" : "Submitted", + "updated" : "YYYY-MM-DDTHH:MM:SSZ", + "uuid" : "bb0d93e3-1a6a-4816-82d9-713fa58fb235", + "inputs" : { + "input_cram" : "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", + "destination_cloud_path" : "gs://broad-gotc-dev-wfl-ptc-test-outputs/xx-test-output/8600be1a-48df-4a51-bdba-0044e0af8d33/single_sample/plumbing/truth/develop/20k", + "sample_name" : "NA12878_PLUMBING", + "base_file_name" : "NA12878_PLUMBING.cram", + "final_gvcf_base_name" : "NA12878_PLUMBING.cram" + } + }] + ``` + +"workflows" lists out each workflow managed by this workload, +including their status. It is also possible to use the Job Manager +to check workflow progress and easily see information about any workflow +failures. + ## A1 External Exome Workload-Request JSON Spec ```json { diff --git a/docs/md/modules-gp-arrays.md b/docs/md/modules-gp-arrays.md deleted file mode 100644 index d0169799d..000000000 --- a/docs/md/modules-gp-arrays.md +++ /dev/null @@ -1,275 +0,0 @@ -# GPArrays workload - -The "GPArrays" workload launches workflows in Terra. Because Terra submits workflows to Cromwell -using the RAWLs API, both the input data and pipeline must be imported into a Terra workspace -prior to analysis. - -In addition, the workload differs from the other WFL modules in several ways: -- The `executor` field is the Terra API URL (instead of the Cromwell URL) -- The `project` is the Terra workspace to use for processing, and must follow the format -"{workspaceNamespace}/{workspaceName}". - -## Inputs -A `GPArrays` workload specifies the following inputs for each workflow: -- `entity_name` -- `entity_type` - -#### `entity_name` (required) -- The unique id of the sample in the Terra data table. The id field follows -the format "{table_name}_id". - -#### `entity_type` (required) - -- The name of the Terra workspace data table containing the sample -(e.g the `entity_type` of a row in the "sample" table is "sample") - -## Usage - -A `GPArrays` workload supports the following API endpoints: - -| Verb | Endpoint | Description | -|------|------------------------------|----------------------------------------------------------------| -| GET | `/api/v1/workload` | List all workloads | -| GET | `/api/v1/workload/{uuid}` | Query for a workload by its UUID | -| GET | `/api/v1/workload/{project}` | Query for a workload by its Project name | -| POST | `/api/v1/create` | Create a new workload | -| POST | `/api/v1/start` | Start a workload | -| POST | `/api/v1/exec` | Create and start (execute) a workload | - -### Create Workload: `/api/v1/create` -Creates a WFL workload. Before processing, confirm that the Terra proxy SA for the -wfl-non-prod SA has at least read access to the input files, and -the vault token path used by the Arrays pipeline. - -=== "Request" - - ```bash - curl --location --request POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/create' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) \ - --header 'Content-Type: application/json' \ - --data-raw '{ - "executor": "https://firecloud-orchestration.dsde-dev.broadinstitute.org", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/arrays-test-output/", - "pipeline": "GPArrays", - "project": "general-dev-billing-account/arrays", - "items": [ - { - "inputs": { - "entity_name": "200598830050_R07C01-1", - "entity_type": "sample" - } - } - ] - }' - ``` - -=== "Response" - - ```json - { - "creator": "user@domain", - "pipeline": "GPArrays", - "executor": "https://firecloud-orchestration.dsde-dev.broadinstitute.org", - "release": "Arrays_v2.3.0", - "created": "YYYY-MM-DDTHH:MM:SSZ", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/arrays-test-output/", - "project": "general-dev-billing-account/arrays", - "commit": "commit-ish", - "wdl": "pipelines/broad/arrays/single_sample/Arrays.wdl", - "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", - "version": "X.Y.Z" - } - ``` - -Note that the GPArrays module does NOT support specifying -Cromwell "workflowOptions" via the `options` map, since this functionality -is not exposed via the Terra API. - -### Start Workload: `/api/v1/start` - -Creates a new "submission" in Terra, which starts a Cromwell workflow for each item in the workload. -Note that the workflow `uuid` in the response is the Terra submission uuid, not the Cromwell workflow uuid. - -=== "Request" - - ```bash - curl --location --request POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/start' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) \ - --header 'Content-Type: application/json' \ - --data-raw '{"uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e"}' - ``` - -=== "Response" - - ```json - { - "started": "YYYY-MM-DDTHH:MM:SSZ", - "creator": "user@domain", - "pipeline": "GPArrays", - "executor": "https://firecloud-orchestration.dsde-dev.broadinstitute.org", - "release": "Arrays_v2.3.0", - "created": "YYYY-MM-DDTHH:MM:SSZ", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/arrays-test-output/", - "workflows": [ - { - "updated": "YYYY-MM-DDTHH:MM:SSZ", - "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", - "inputs": { - "entity_name": "200598830050_R07C01-1", - "entity_type": "sample" - } - } - ], - "project": "general-dev-billing-account/arrays", - "commit": "commit-ish", - "wdl": "pipelines/broad/arrays/single_sample/Arrays.wdl", - "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", - "version": "X.Y.Z" - } - ``` - -### Exec Workload: `/api/v1/exec` - -Creates and then starts a WFL workload. - -=== "Request" - - ```bash - curl --location --request POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/exec' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) \ - --header 'Content-Type: application/json' \ - --data-raw '{ - "executor": "https://firecloud-orchestration.dsde-dev.broadinstitute.org", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/arrays-test-output/", - "pipeline": "GPArrays", - "project": "general-dev-billing-account/arrays", - "items": [ - { - "inputs": { - "entity_name": "200598830050_R07C01-1", - "entity_type": "sample" - } - } - ] - }' - ``` - -=== "Response" - - ```json - { - "started": "YYYY-MM-DDTHH:MM:SSZ", - "creator": "user@domain", - "pipeline": "GPArrays", - "executor": "https://firecloud-orchestration.dsde-dev.broadinstitute.org", - "release": "Arrays_v2.3.0", - "created": "YYYY-MM-DDTHH:MM:SSZ", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/arrays-test-output/", - "workflows": [ - { - "updated": "YYYY-MM-DDTHH:MM:SSZ", - "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", - "inputs": { - "entity_name": "200598830050_R07C01-1", - "entity_type": "sample" - } - } - ], - "project": "general-dev-billing-account/arrays", - "commit": "commit-ish", - "wdl": "pipelines/broad/arrays/single_sample/Arrays.wdl", - "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", - "version": "X.Y.Z" - } - ``` - -### Query Workload: `/api/v1/workload?uuid=` - -Queries the WFL database for workloads. Specify the uuid to query for a specific workload. - -=== "Request" - - ```bash - curl --location --request GET 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/workload?uuid=2c543b29-2db9-4643-b81b-b16a0654c5cc' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) - ``` - -=== "Response" - - ```json - [{ - "creator": "user@domain", - "pipeline": "GPArrays", - "executor": "https://firecloud-orchestration.dsde-dev.broadinstitute.org", - "release": "Arrays_v2.3.0", - "created": "YYYY-MM-DDTHH:MM:SSZ", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/arrays-test-output/", - "workflows": [ - { - "updated": "YYYY-MM-DDTHH:MM:SSZ", - "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", - "inputs": { - "entity_name": "200598830050_R07C01-1", - "entity_type": "sample" - } - } - ], - "project": "general-dev-billing-account/arrays", - "commit": "commit-ish", - "wdl": "pipelines/broad/arrays/single_sample/Arrays.wdl", - "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", - "version": "X.Y.Z" - }] - ``` - -The "workflows" field lists out each Terra submission, and includes the status information -of the workflow that was started for that sample. It is also possible to use the Terra UI -to check workflow progress and easily see information about any workflow failures. - -### Query Workload with project: `/api/v1/workload?project=` - -Queries the WFL database for workloads. Specify the project name to query for a list of specific workload(s). - -=== "Request" - - ```bash - curl --location --request GET 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/workload?project=general-dev-billing-account/arrays' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) - ``` - -=== "Response" - - ```json - [{ - "creator": "user@domain", - "pipeline": "GPArrays", - "executor": "https://firecloud-orchestration.dsde-dev.broadinstitute.org", - "release": "Arrays_v2.3.0", - "created": "YYYY-MM-DDTHH:MM:SSZ", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/arrays-test-output/", - "workflows": [ - { - "updated": "YYYY-MM-DDTHH:MM:SSZ", - "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", - "inputs": { - "entity_name": "200598830050_R07C01-1", - "entity_type": "sample" - } - } - ], - "project": "general-dev-billing-account/arrays", - "commit": "commit-ish", - "wdl": "pipelines/broad/arrays/single_sample/Arrays.wdl", - "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", - "version": "X.Y.Z" - }] - ``` - -The "workflows" field lists out each Terra submission, and includes the status information -of the workflow that was started for that sample. It is also possible to use the Terra UI -to check workflow progress and easily see information about any workflow failures. - -!!! warning "Note" - `project` and `uuid` are optional path parameters to the `/api/v1/workload` endpoint, - hitting this endpoint without them will return all workloads. However, they cannot be specified - together. diff --git a/docs/md/modules-sg.md b/docs/md/modules-sg.md index e7433332d..8814abc76 100644 --- a/docs/md/modules-sg.md +++ b/docs/md/modules-sg.md @@ -82,14 +82,14 @@ specified as an `input_cram`. GDCWholeGenomeSomaticSingleSample workload supports the following API endpoints: -| Verb | Endpoint | Description | -|------|------------------------------|----------------------------------------------------------------| -| GET | `/api/v1/workload` | List all workloads | -| GET | `/api/v1/workload/{uuid}` | Query for a workload by its UUID | -| GET | `/api/v1/workload/{project}` | Query for a workload by its Project name | -| POST | `/api/v1/create` | Create a new workload | -| POST | `/api/v1/start` | Start a workload | -| POST | `/api/v1/exec` | Create and start (execute) a workload | +| Verb | Endpoint | Description | +|------|-------------------------------------|----------------------------------------------------------------| +| GET | `/api/v1/workload` | List all workloads, optionally filtering by uuid or project | +| GET | `/api/v1/workload/{uuid}/workflows` | List all workflows for a specified workload uuid | +| POST | `/api/v1/create` | Create a new workload | +| POST | `/api/v1/start` | Start a workload | +| POST | `/api/v1/stop` | Stop a running workload | +| POST | `/api/v1/exec` | Create and start (execute) a workload | ???+ warning "Permissions in production" External Whole Genome Reprocessing in `gotc-prod` uses a set of execution projects, please refer to @@ -147,28 +147,8 @@ https://gotc-prod-wfl.gotc-prod.broadinstitute.org/api/v1/create \ "release": "GDCWholeGenomeSomaticSingleSample_v1.1.0", "started": "2021-04-05T16:02:32Z", "uuid": "efb00901-378e-4365-86e7-edd0fbdaaab2", - "version": "0.6.0", - "wdl": "pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl", - "workflows": [ - { - "status": "Submitted", - "updated": "2021-04-05T16:02:32Z", - "uuid": "8c1f586e-036b-4690-87c2-2af5d7e00450", - "inputs": { - "base_file_name": "27B-6", - "contamination_vcf": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz", - "contamination_vcf_index": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz.tbi", - "cram_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", - "cram_ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", - "dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz", - "dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz.tbi", - "input_cram": "gs://broad-gotc-prod-storage/pipeline/PO-1234/27B-6/v1/27B-6.cram" - }, - "options": { - "monitoring_script": "gs://broad-gotc-prod-storage/scripts/monitoring_script.sh" - } - } - ] + "version": "0.7.0", + "wdl": "pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" } ``` @@ -206,28 +186,41 @@ https://gotc-prod-wfl.gotc-prod.broadinstitute.org/api/v1/start \ "release": "GDCWholeGenomeSomaticSingleSample_v1.1.0", "started": "2021-04-05T16:02:32Z", "uuid": "efb00901-378e-4365-86e7-edd0fbdaaab2", - "version": "0.6.0", - "wdl": "pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl", - "workflows": [ - { - "status": "Submitted", - "updated": "2021-04-05T16:02:32Z", - "uuid": "8c1f586e-036b-4690-87c2-2af5d7e00450", - "inputs": { - "base_file_name": "27B-6", - "contamination_vcf": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz", - "contamination_vcf_index": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz.tbi", - "cram_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", - "cram_ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", - "dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz", - "dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz.tbi", - "input_cram": "gs://broad-gotc-prod-storage/pipeline/PO-1234/27B-6/v1/27B-6.cram" - }, - "options": { - "monitoring_script": "gs://broad-gotc-prod-storage/scripts/monitoring_script.sh" - } - } - ] + "version": "0.7.0", + "wdl": "pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" +} +``` + +### Start Workload: `/api/v1/start` + +Included for compatibility with continuous workloads. + +=== "Request" + +```bash +curl -X POST 'https://gotc-prod-wfl.gotc-prod.broadinstitute.org/api/v1/stop' \ + -X "Authorization: Bearer $(gcloud auth print-access-token)" \ + -X 'Content-Type: application/json' \ + -d '{ "uuid": "efb00901-378e-4365-86e7-edd0fbdaaab2" }' +``` + +=== "Response" + +```json +{ + "commit": "477bb195c40cc5f5afb81ca1b57e97c9cc18fa2c", + "created": "2021-04-05T16:02:31Z", + "creator": "tbl@broadinstitute.org", + "executor": "https://cromwell-gotc-auth.gotc-prod.broadinstitute.org", + "output": "gs://broad-prod-somatic-genomes-output", + "pipeline": "GDCWholeGenomeSomaticSingleSample", + "project": "PO-1234", + "release": "GDCWholeGenomeSomaticSingleSample_v1.1.0", + "started": "2021-04-05T16:02:32Z", + "stopped": "2021-04-05T16:02:33Z", + "uuid": "efb00901-378e-4365-86e7-edd0fbdaaab2", + "version": "0.7.0", + "wdl": "pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" } ``` @@ -278,35 +271,12 @@ but specifying a UUID returns only one. "release": "GDCWholeGenomeSomaticSingleSample_v1.1.0", "started": "2021-04-05T16:02:32Z", "uuid": "efb00901-378e-4365-86e7-edd0fbdaaab2", - "version": "0.6.0", - "wdl": "pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl", - "workflows": [ - { - "status": "Submitted", - "updated": "2021-04-05T16:02:32Z", - "uuid": "8c1f586e-036b-4690-87c2-2af5d7e00450", - "inputs": { - "base_file_name": "27B-6", - "contamination_vcf": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz", - "contamination_vcf_index": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz.tbi", - "cram_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", - "cram_ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", - "dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz", - "dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz.tbi", - "input_cram": "gs://broad-gotc-prod-storage/pipeline/PO-1234/27B-6/v1/27B-6.cram" - }, - "options": { - "monitoring_script": "gs://broad-gotc-prod-storage/scripts/monitoring_script.sh" - } - } - ] + "version": "0.7.0", + "wdl": "pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl" } ] ``` -The `workflows` field -lists each Cromwell workflow and its status. - ### Query Workload with project: `/api/v1/workload?project=` Query WFL for all workloads @@ -330,3 +300,39 @@ that share the same `project` value. that WFL knows about. That response might be large and take a while to process. + + +### List workflows managed by the workload `GET /api/v1/workload/{uuid}/workflows` + +=== "Request" + +```bash +curl -X GET '/api/v1/workload/efb00901-378e-4365-86e7-edd0fbdaaab2/workflows' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) +``` + +=== "Response" + +A successful response from `/api/v1/workload/{uuid}/workload` +is always an array of Cromwell workflows with their statuses. + +```json +[{ + "status": "Submitted", + "updated": "2021-04-05T16:02:32Z", + "uuid": "8c1f586e-036b-4690-87c2-2af5d7e00450", + "inputs": { + "base_file_name": "27B-6", + "contamination_vcf": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz", + "contamination_vcf_index": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz.tbi", + "cram_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", + "cram_ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", + "dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz", + "dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/gdc/dbsnp_144.hg38.vcf.gz.tbi", + "input_cram": "gs://broad-gotc-prod-storage/pipeline/PO-1234/27B-6/v1/27B-6.cram" + }, + "options": { + "monitoring_script": "gs://broad-gotc-prod-storage/scripts/monitoring_script.sh" + } +}] +``` diff --git a/docs/md/modules-wgs.md b/docs/md/modules-wgs.md index 141040fea..65438abee 100644 --- a/docs/md/modules-wgs.md +++ b/docs/md/modules-wgs.md @@ -48,49 +48,47 @@ at the workload level through `common` or individually via `items`. ExternalWholeGenomeReprocessing workload supports the following API endpoints: -| Verb | Endpoint | Description | -|------|------------------------------|----------------------------------------------------------------| -| GET | `/api/v1/workload` | List all workloads | -| GET | `/api/v1/workload/{uuid}` | Query for a workload by its UUID | -| GET | `/api/v1/workload/{project}` | Query for a workload by its Project name | -| POST | `/api/v1/create` | Create a new workload | -| POST | `/api/v1/start` | Start a workload | -| POST | `/api/v1/exec` | Create and start (execute) a workload | +| Verb | Endpoint | Description | +|------|-------------------------------------|----------------------------------------------------------------| +| GET | `/api/v1/workload` | List all workloads, optionally filtering by uuid or project | +| GET | `/api/v1/workload/{uuid}/workflows` | List all workflows for a specified workload uuid | +| POST | `/api/v1/create` | Create a new workload | +| POST | `/api/v1/start` | Start a workload | +| POST | `/api/v1/stop` | Stop a running workload | +| POST | `/api/v1/exec` | Create and start (execute) a workload | ???+ warning "Permissions in production" External Whole Genome Reprocessing in `gotc-prod` uses a set of execution projects, please refer to [this page](https://github.com/broadinstitute/gotc-deploy/blob/master/deploy/gotc-prod/helm/WFL_README.md) when you have questions about permissions. -### Create Workload: `/api/v1/create` +### Create Workload: `POST /api/v1/create` Creates a WFL workload. Before processing, confirm that the WFL and Cromwell service accounts have at least read access to the input files. === "Request" - ```bash - curl --location --request POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/create' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) \ - --header 'Content-Type: application/json' \ - --data-raw '{ - "executor": "https://cromwell-gotc-auth.gotc-dev.broadinstitute.org", - "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/wgs-test-output/", - "pipeline": "ExternalWholeGenomeReprocessing", - "project": "PO-1234", - "items": [ - { - "inputs": { - "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "sample_name": "TestSample1234" - } - } - ] - }' - ``` +```bash +curl -X POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/create' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Content-Type: application/json' \ + -d '{ + "executor": "https://cromwell-gotc-auth.gotc-dev.broadinstitute.org", + "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/wgs-test-output/", + "pipeline": "ExternalWholeGenomeReprocessing", + "project": "PO-1234", + "items": [{ + "inputs": { + "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", + "sample_name": "TestSample1234" + } + }] + }' +``` === "Response" - ```json +```json { "creator": "sehsan@broadinstitute.org", "pipeline": "ExternalWholeGenomeReprocessing", @@ -103,31 +101,31 @@ at least read access to the input files. "wdl": "pipelines/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl", "input": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth", "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", - "version": "0.3.2" + "version": "0.7.0" } - ``` +``` Note that the ExternalWholeGenomeReprocessing pipeline supports specifying cromwell "workflowOptions" via the `options` map. See the [reference page](./usage-workflow-options) for more information. -### Start Workload: `/api/v1/start` +### Start Workload: `POST /api/v1/start` Starts a Cromwell workflow for each item in the workload. If an output already exists in the output bucket for a particular input cram, WFL will not re-submit that workflow. === "Request" - ```bash - curl --location --request POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/start' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) \ - --header 'Content-Type: application/json' \ - --data-raw '{"uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e"}' - ``` +```bash +curl -X POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/start' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Content-Type: application/json' \ + -d '{ "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e" }' +``` === "Response" - ```json +```json { "started": "2020-10-05T15:50:51Z", "creator": "username@broadinstitute.org", @@ -136,54 +134,75 @@ particular input cram, WFL will not re-submit that workflow. "release": "ExternalWholeGenomeReprocessing_v1.0", "created": "2020-10-05T15:50:01Z", "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/wgs-test-output/", - "workflows": [ - { - "updated": "2020-10-05T16:15:32Z", - "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", - "inputs": { - "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "sample_name": "TestSample1234" - } - } - ], "project": "PO-1234", "commit": "d65371ca983b4f0d4fa06868e2946a8e3cab291b", "wdl": "pipelines/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl", "input": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth", "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", - "version": "0.3.2" + "version": "0.7.0" } - ``` +``` -### Exec Workload: `/api/v1/exec` +### Stop Workload: `POST /api/v1/stop` -Creates and then starts a Cromwell workflow for each item in the workload. +Included for compatibility with continuous workloads. === "Request" - ```bash - curl --location --request POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/exec' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) \ - --header 'Content-Type: application/json' \ - --data-raw '{ +```bash +curl -X POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/start' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Content-Type: application/json' \ + -d '{ "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e" }' +``` + +=== "Response" + + ```json + { + "started": "2020-10-05T15:50:51Z", + "creator": "username@broadinstitute.org", + "pipeline": "ExternalWholeGenomeReprocessing", "executor": "https://cromwell-gotc-auth.gotc-dev.broadinstitute.org", + "release": "ExternalWholeGenomeReprocessing_v1.0", + "created": "2020-10-05T15:50:01Z", "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/wgs-test-output/", - "pipeline": "ExternalWholeGenomeReprocessing", "project": "PO-1234", - "items": [ - { - "inputs": { - "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "sample_name": "TestSample1234" - } - } - ] - }' - ``` + "commit": "d65371ca983b4f0d4fa06868e2946a8e3cab291b", + "wdl": "pipelines/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl", + "input": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth", + "uuid": "74d96a04-fea7-4270-a02b-a319dae2dd5e", + "version": "0.7.0" + } +``` + +### Exec Workload: `POST /api/v1/exec` + +Creates and then starts a Cromwell workflow for each item in the workload. + +=== "Request" + +```bash +curl -X POST 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/exec' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) \ + -H 'Content-Type: application/json' \ + -d '{ + "executor": "https://cromwell-gotc-auth.gotc-dev.broadinstitute.org", + "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/wgs-test-output/", + "pipeline": "ExternalWholeGenomeReprocessing", + "project": "PO-1234", + "items": [{ + "inputs": { + "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", + "sample_name": "TestSample1234" + } + }] + }' +``` === "Response" - ```json +```json { "started": "2020-10-05T16:15:32Z", "creator": "username@broadinstitute.org", @@ -192,39 +211,29 @@ Creates and then starts a Cromwell workflow for each item in the workload. "release": "ExternalWholeGenomeReprocessing_v1.0", "created": "2020-10-05T16:15:32Z", "output": "gs://broad-gotc-dev-wfl-ptc-test-outputs/wgs-test-output/", - "workflows": [ - { - "updated": "2020-10-05T16:15:32Z", - "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", - "inputs": { - "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "sample_name": "TestSample1234" - } - } - ], "project": "PO-1234", "commit": "d65371ca983b4f0d4fa06868e2946a8e3cab291b", "wdl": "pipelines/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl", "input": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth", "uuid": "3a13f732-9743-47a9-ab83-c467b3bf0ca4", - "version": "0.3.2" + "version": "0.7.0" } - ``` +``` -### Query Workload: `/api/v1/workload?uuid=` +### Query Workload: `GET /api/v1/workload?uuid=` Queries the WFL database for workloads. Specify the uuid to query for a specific workload. === "Request" - ```bash - curl --location --request GET 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/workload?uuid=813e3c38-9c11-4410-9888-435569d91d1d' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) - ``` +```bash +curl -X GET 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/workload?uuid=813e3c38-9c11-4410-9888-435569d91d1d' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) +``` === "Response" - ```json +```json [{ "creator": "username", "pipeline": "ExternalWholeGenomeReprocessing", @@ -247,28 +256,24 @@ Queries the WFL database for workloads. Specify the uuid to query for a specific "wdl": "pipelines/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl", "input": "gs://broad-gotc-test-storage/single_sample/plumbing/truth", "uuid": "813e3c38-9c11-4410-9888-435569d91d1d", - "version": "0.1.7" + "version": "0.7.0" }] - ``` +``` -The "workflows" field lists out each Cromwell workflow that was started, and includes their -status information. It is also possible to use the Job Manager to check workflow progress and -easily see information about any workflow failures. - -### Query Workload with project: `/api/v1/workload?project=` +### Query Workload with project: `GET /api/v1/workload?project=` Queries the WFL database for workloads. Specify the project name to query for a list of specific workload(s). === "Request" - ```bash - curl --location --request GET 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/workload?project=wgs-dev' \ - --header 'Authorization: Bearer '$(gcloud auth print-access-token) - ``` +```bash +curl -X GET 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/workload?project=wgs-dev' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) +``` === "Response" - ```json +```json [{ "creator": "username", "pipeline": "ExternalWholeGenomeReprocessing", @@ -276,24 +281,14 @@ Queries the WFL database for workloads. Specify the project name to query for a "release": "ExternalWholeGenomeReprocessing_v1.0", "created": "2020-08-27T16:26:59Z", "output": "gs://broad-gotc-dev-zero-test/wgs-test-output", - "workflows": [ - { - "updated": "2020-10-05T16:15:32Z", - "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", - "inputs": { - "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", - "sample_name": "TestSample1234" - } - } - ], "project": "wgs-dev", "commit": "d2fc38c61c62c44f4fd4d24bdee3121138e6c09e", "wdl": "pipelines/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl", "input": "gs://broad-gotc-test-storage/single_sample/plumbing/truth", "uuid": "813e3c38-9c11-4410-9888-435569d91d1d", - "version": "0.1.7" + "version": "0.7.0" }] - ``` +``` The "workflows" field lists out each Cromwell workflow that was started, and includes their status information. It is also possible to use the Job Manager @@ -304,3 +299,29 @@ failures. `project` and `uuid` are optional path parameters to the `/api/v1/workload` endpoint, hitting this endpoint without them will return all workloads. However, they cannot be specified together. + +### List workflows managed by a workload `GET /api/v1/workload/{uuid}/workflows` + +=== "Request" + +```bash +curl -X GET 'https://dev-wfl.gotc-dev.broadinstitute.org/api/v1/workload/813e3c38-9c11-4410-9888-435569d91d1d/workflows' \ + -H 'Authorization: Bearer '$(gcloud auth print-access-token) +``` + +=== "Response" + +```json +[{ + "updated": "2020-10-05T16:15:32Z", + "uuid": "2c543b29-2db9-4643-b81b-b16a0654c5cc", + "inputs": { + "input_cram": "gs://broad-gotc-dev-wfl-ptc-test-inputs/single_sample/plumbing/truth/develop/20k/NA12878_PLUMBING.cram", + "sample_name": "TestSample1234" + } +}] +``` + +The "workflows" endpoint lists out each Cromwell workflow that was started, and includes their +status information. It is also possible to use the Job Manager to check workflow progress and +easily see information about any workflow failures. diff --git a/docs/md/usage-abort.md b/docs/md/usage-abort.md index 0ff2c7ded..cb74b19a7 100644 --- a/docs/md/usage-abort.md +++ b/docs/md/usage-abort.md @@ -17,19 +17,49 @@ Here's a script that can help with that: # THREADS is optionally the number of threads to use to talk to Cromwell # Default is 2 -WORKLOAD=$(curl -X GET "${2:-https://gotc-prod-wfl.gotc-prod.broadinstitute.org}/api/v1/workload?$1" \ - -H "Authorization: Bearer $(gcloud auth print-access-token)" \ - -H 'Content-Type: application/json' | jq) - -CROMWELL=$(jq -r 'map(.executor) | .[0]' <<< "$WORKLOAD") - -jq -r 'map(.workflows) - | flatten - | map(select(.status != "Failed" and .status != "Succeeded") | .uuid) - | .[]' <<< "$WORKLOAD" \ - | xargs -I % -n 1 -P ${3:-2} curl -w "\n" -s -X POST "$CROMWELL/api/workflows/v1/%/abort" \ - -H "Authorization: Bearer $(gcloud auth print-access-token)" \ - -H "Content-Type: application/json" +# Usage: bash abort.sh QUERY [WFL_URL] +# QUERY is either like `project=PO-123` or `uuid=1a2b3c4d` +# WFL_URL is the WFL instance to abort workflows from [default: gotc-prod] + +WFL_URL="${2:-https://gotc-prod-wfl.gotc-prod.broadinstitute.org}" +AUTH_HEADER="Authorization: Bearer $(gcloud auth print-access-token)" + +getWorkloads () { + # Query -> [Workload] + curl -s -X GET "${WFL_URL}/api/v1/workload?$1" \ + -H "${AUTH_HEADER}" \ + | jq +} + +getWorkflows() { + # Workload -> [Workflow] + uuid=$(jq -r .uuid <<< "$1") + curl -s -X GET "${WFL_URL}/api/v1/workload/${uuid}/workflows" \ + -H "${AUTH_HEADER}" \ + | jq +} + +mapjq () { + jq -c '.[]' <<< "${2}" \ + | while read elem; do ${1} "${elem}"; done \ + | jq '[ .[] ]' +} + +main() { + # Query -> () + workloads=$(getWorkloads "${1}") + cromwell=$(jq -r 'map(.executor) | .[0]' <<< "$WORKLOAD") + + mapjq getWorkflows "${workloads}" + | jq -s 'flatten + | map(select(.status != "Failed" and .status != "Succeeded") | .uuid) + | .[]' \ + | xargs -I % -n 1 -P ${3:-2} curl -w "\n" -s -X POST "$CROMWELL/api/workflows/v1/%/abort" \ + -H "${AUTH_HEADER}" \ + -H "Content-Type: application/json" +} + +main "$1" ``` The 'QUERY' part is like you'd pass to [retry.sh](./usage-retry). diff --git a/docs/md/usage-retry.md b/docs/md/usage-retry.md index e91128436..59ab69478 100644 --- a/docs/md/usage-retry.md +++ b/docs/md/usage-retry.md @@ -22,27 +22,74 @@ Usage: `bash retry.sh QUERY` Ex: `bash retry.sh project=PO-29619` ```bash -WORKLOAD=$(curl -X GET "https://gotc-prod-wfl.gotc-prod.broadinstitute.org/api/v1/workload?$1" \ - -H "Authorization: Bearer $(gcloud auth print-access-token)" \ - -H 'Content-Type: application/json' | jq) - -jq '{ - executor: .[0].executor, - output: .[0].output, - input: .[0].input, - pipeline: .[0].pipeline, - project: .[0].project, - items: .[].workflows - | group_by({inputs: .inputs, options: .options}) - | map(select(all(.status=="Failed")) | .[0] - | {inputs: .inputs, options: .options}) +# Usage: bash abort.sh QUERY [WFL_URL] +# QUERY is either like `project=PO-123` or `uuid=1a2b3c4d` +# WFL_URL is the WFL instance to abort workflows from [default: gotc-prod] + +WFL_URL="${2:-https://gotc-prod-wfl.gotc-prod.broadinstitute.org}" +AUTH_HEADER="Authorization: Bearer $(gcloud auth print-access-token)" + +getWorkloads () { + # Query -> [Workload] + curl -s -X GET "${WFL_URL}/api/v1/workload?$1" \ + -H "${AUTH_HEADER}" \ + | jq +} + +getWorkflows() { + # Workload -> [Workflow] + uuid=$(jq -r .uuid <<< "$1") + curl -s -X GET "${WFL_URL}/api/v1/workload/${uuid}/workflows" \ + -H "${AUTH_HEADER}" \ + | jq +} + +removeSucceeded() { + # [[Workflow]] -> [Workflow] + jq 'flatten + | group_by( {inputs: .inputs, options: .options} ) + | map( select( all(.status=="Succeeded") ) + | .[0] + | {inputs: .inputs, options: .options} ) | del(.[][] | nulls) -} | del(.[] | nulls)' <<< "$WORKLOAD" > retry.json - -curl -X POST "https://gotc-prod-wfl.gotc-prod.broadinstitute.org/api/v1/exec" \ - -H "Authorization: Bearer $(gcloud auth print-access-token)" \ - -H 'Content-Type: application/json' \ - -d "@retry.json" + ' <<< "$1" +} + +makeRetryRequest() { + # [Workload], [Workflow] -> Request + jq --argjson 'workflows' "$2" \ + '.[0] + | { executor: .executor + , input: .input + , output: .output + , pipeline: .pipeline + , project: .project + , items: $workflows + } + | del(.[] | nulls) + ' <<< "$1" +} + +mapjq () { + jq -c '.[]' <<< "${2}" \ + | while read elem; do ${1} "${elem}"; done \ + | jq -s '[ .[] ]' +} + +main() { + # Query -> () + workloads=$(getWorkloads "${1}") + workflows=$(mapjq getWorkflows "${workloads}") + toSubmit=$(removeSucceeded "${workflows}") + makeRetryRequest "${workloads[0]}" "${toSubmit}" > /tmp/retry.json + + curl -X POST "${WFL_URL}/api/v1/exec" \ + -H "${AUTH_HEADER}" \ + -H "Content-Type: application/json" \ + -d @/tmp/retry.json +} + +main "$1" ``` ## Tips @@ -54,7 +101,7 @@ you can do that with a `common` block. For example, replace this: ``` jq '{ - executor: .[0].executor, + executor: .executor, ``` with this: @@ -62,7 +109,7 @@ with this: ``` jq '{ common: { inputs: { "WholeGenomeReprocessing.WholeGenomeGermlineSingleSample.BamToCram.ValidateCram.memory_multiplier": 2 } }, - executor: .[0].executor, + executor: .executor, ``` That example uses WFL's arbitrary input feature to bump up the memory multiplier @@ -71,27 +118,3 @@ for a particular WGS task. - Nested inputs will have periods in them, you'll need to use quotes around it - You can't override inputs or options that the workflows originally had (the `common` block has lower precedence) - - -### "Simpler" Retries - -The script tries to be a bit intelligent about not making multiple resubmissions -for the same sets of inputs/options. If you don't want that logic for whatever -reason, replace this: - -``` - items: .[].workflows - | group_by({inputs: .inputs, options: .options}) - | map(select(all(.status=="Failed")) | .[0] - | {inputs: .inputs, options: .options}) - | del(.[][] | nulls) -``` - -with this: - -``` - items: .[].workflows - | map(select(.status=="Failed") - | {inputs: .inputs, options: .options}) - | del(.[][] | nulls) -``` diff --git a/docs/md/usage-workflow-options.md b/docs/md/usage-workflow-options.md index d80bb6151..4f6a2948b 100644 --- a/docs/md/usage-workflow-options.md +++ b/docs/md/usage-workflow-options.md @@ -102,35 +102,29 @@ resolve the options for individual workflows. You can see this in WFL's response, which includes all workflow options calculated for each workflow: ```json +[{ + "inputs": { + "input_cram": "develop/20k/NA12878_PLUMBING.cram", + "sample_name": "TestSample1234" + }, + "options": { + "jes_gcs_root": "gs://broad-gotc-something-execution", + "write_to_cache": false, + "google_project": "broad-google-project" + } +}, { - "pipeline": "ExternalWholeGenomeReprocessing", - "created": "2020-10-05T15:50:01Z", - "workflows": [ - { - "inputs": { - "input_cram": "develop/20k/NA12878_PLUMBING.cram", - "sample_name": "TestSample1234" - }, - "options": { - "jes_gcs_root": "gs://broad-gotc-something-execution", - "write_to_cache": false, - "google_project": "broad-google-project" - } - }, - { - "inputs": { - "input_cram": "develop/20k/NA12878_PLUMBING.cram", - "sample_name": "TestSample5678" - }, - "options": { - "jes_gcs_root": "gs://broad-gotc-different-execution", - "default_runtime_attributes": {"maxRetries": 3}, - "write_to_cache": false, - "google_project": "broad-google-project-2" - } - } - ] -} + "inputs": { + "input_cram": "develop/20k/NA12878_PLUMBING.cram", + "sample_name": "TestSample5678" + }, + "options": { + "jes_gcs_root": "gs://broad-gotc-different-execution", + "default_runtime_attributes": {"maxRetries": 3}, + "write_to_cache": false, + "google_project": "broad-google-project-2" + } +}] ``` One note is that WFL already has some default values it passes for diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index bd8279e8e..bfba417aa 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -33,14 +33,11 @@ nav: - Development Guide: - Development Process and Tips: dev-process.md - Release Process: dev-release.md - - Local Development SandBox: dev-sandbox.md - Logging: dev-logging.md - - Deployment: dev-deployment.md - Frontend: dev-frontend.md - Module-Specific Usage: - Overview: modules-general.md - Arrays: modules-arrays.md - - GPArrays: modules-gp-arrays.md - Whole Genome: modules-wgs.md - External Exome: modules-external-exome-reprocessing.md - Somatic Genomes: modules-sg.md diff --git a/docs/readme.md b/docs/readme.md new file mode 100644 index 000000000..2cff59cdb --- /dev/null +++ b/docs/readme.md @@ -0,0 +1,37 @@ +# WorkFlow Launcher Documentation + +**GitHub Pages [documentation website](https://broadinstitute.github.io/wfl)** + +## Rendering locally + +You may wish to launch a local version of our documentation website +to test changes for formatting, link resolution, etc. + +Python 3 is required: +``` +cd /path/to/wfl/docs +python3 -m pip install -r requirements.txt +mkdocs serve +``` + +Logging output will indicate that changes are being detected, +and point you to where documentation is served (e.g. http://127.0.0.1:8000). +``` +INFO - Building documentation... +INFO - Cleaning site directory +INFO - Documentation built in 1.46 seconds +[I 210423 14:27:04 server:335] Serving on http://127.0.0.1:8000 +INFO - Serving on http://127.0.0.1:8000 +[I 210423 14:27:04 handlers:62] Start watching changes +INFO - Start watching changes +[I 210423 14:27:04 handlers:64] Start detecting changes +INFO - Start detecting changes +[I 210423 14:27:05 handlers:135] Browser Connected: http://localhost:8000/dev-process/ +INFO - Browser Connected: http://localhost:8000/dev-process/ +... +``` + +## GitHub Pages Resources +[Relative links in markup files](https://github.blog/2013-01-31-relative-links-in-markup-files/) +allow intra-doc links to work within GitHub Pages website as well as the +repository view. \ No newline at end of file diff --git a/ops/cli.py b/ops/cli.py index e98a52e55..de226534e 100755 --- a/ops/cli.py +++ b/ops/cli.py @@ -39,10 +39,13 @@ def exit_if_dry_run(config: WflInstanceConfig) -> None: def publish_docker_images(config: WflInstanceConfig) -> None: - """Publish existing docker images for the stored version.""" + """Publish latest docker images for the stored version.""" info(f"=> Publishing Docker images for version {config.version}") for module in ["api", "ui"]: - shell(f"docker push broadinstitute/workflow-launcher-{module}:{config.version}") + image = f"broadinstitute/workflow-launcher-{module}" + # re-tag the image in case the version is being overwritten. + shell(f"docker tag {image}:latest {image}:{config.version}") + shell(f"docker push {image}:{config.version}") success("Published Docker images") @@ -119,6 +122,8 @@ def cli() -> WflInstanceConfig: parser.add_argument("-d", "--dry-run", action="store_true", help="exit before COMMAND makes any remote changes") + parser.add_argument("-v", "--version", + help="specify the version to use instead of the 'version' file") return WflInstanceConfig(**vars(parser.parse_args())) diff --git a/ops/server.sh b/ops/server.sh index 861f6c3cb..be3764fa3 100755 --- a/ops/server.sh +++ b/ops/server.sh @@ -5,6 +5,9 @@ set -ex # export GOOGLE_APPLICATION_CREDENTIALS=/Users/tbl/Broad/wfl/api/wfl-non-prod-sa.json # export WFL_CLIO_URL=https://clio.gotc-dev.broadinstitute.org # export WFL_CROMWELL_URL=https://cromwell-gotc-auth.gotc-dev.broadinstitute.org +export WFL_FIRECLOUD_URL="https://api.firecloud.org" +export WFL_TDR_URL="https://data.terra.bio" +export WFL_RAWLS_URL="https://rawls.dsde-prod.broadinstitute.org" declare -r WFL=${0%/*} diff --git a/readme.md b/readme.md index d00c9dfd6..b6cfc26ee 100644 --- a/readme.md +++ b/readme.md @@ -1,6 +1,6 @@ # WorkFlow Launcher -[![Build Board](https://img.shields.io/badge/-The%20Build%20Boad%20(VPN)-blue)](https://internal.broadinstitute.org/~chengche/green-hornet-status.html) +[![Build Board](https://img.shields.io/badge/-The%20Build%20Board%20(VPN)-blue)](https://internal.broadinstitute.org/~chengche/green-hornet-status.html) ![Docsite Build](https://github.com/broadinstitute/wfl/workflows/Publish%20docs%20via%20GitHub%20Pages/badge.svg?branch=main) ![Build on Main Branch](https://github.com/broadinstitute/wfl/workflows/Tests%20on%20Pull%20Requests%20and%20Main/badge.svg?branch=main) [![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/broadinstitute/wfl?label=Latest%20Release)](https://github.com/broadinstitute/wfl/blob/main/CHANGELOG.md) diff --git a/ui/module.mk b/ui/module.mk index 5618f6326..51078aa08 100644 --- a/ui/module.mk +++ b/ui/module.mk @@ -27,14 +27,21 @@ $(BUILD): $(DERIVED_SRC) $(NPM) run build --prefix $(DERIVED_MODULE_DIR) @$(TOUCH) $@ -DOCKER_UI_IMAGE := broadinstitute/workflow-launcher-$(MODULE):$(WFL_VERSION) +DOCKER_IMAGE_NAME := broadinstitute/workflow-launcher-$(MODULE) $(IMAGES): $(MODULE_DIR)/Dockerfile $(MODULE_DIR)/.dockerignore $(CP) $(MODULE_DIR)/.dockerignore $(DERIVED_MODULE_DIR) - $(DOCKER) build --file $< --tag $(DOCKER_UI_IMAGE) $(DERIVED_MODULE_DIR) + $(DOCKER) build \ + --file $< \ + --tag $(DOCKER_IMAGE_NAME):latest \ + --tag $(DOCKER_IMAGE_NAME):$(WFL_VERSION) \ + $(DERIVED_MODULE_DIR) @$(TOUCH) $@ $(CLEAN): - -$(DOCKER) image rm -f $(DOCKER_UI_IMAGE) + -$(DOCKER) image rm -f $(DOCKER_IMAGE_NAME):$(WFL_VERSION) + +$(DISTCLEAN): + -$(DOCKER) image rm -f $(DOCKER_IMAGE_NAME):latest $(DERIVED_NPM_CONFIG): $(DERIVED_MODULE_DIR)/%.json : $(MODULE_DIR)/%.json $(JQ) '.version="$(WFL_VERSION)"' $< > $@ diff --git a/ui/package-lock.json b/ui/package-lock.json index b27b563bd..609e3402a 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -1978,9 +1978,9 @@ } }, "ssri": { - "version": "6.0.1", - "resolved": "https://registry.npmjs.org/ssri/-/ssri-6.0.1.tgz", - "integrity": "sha512-3Wge10hNcT1Kur4PDFwEieXSCMCJs/7WvSACcrMYrNp+b8kDL1/0wJch5Ni2WrtwEa2IO8OsVfeKIciKCDx/QA==", + "version": "6.0.2", + "resolved": "https://registry.npmjs.org/ssri/-/ssri-6.0.2.tgz", + "integrity": "sha512-cepbSq/neFK7xB6A50KHN0xHDotYzq58wWCa5LeWqnPrHG8GzfEjO/4O8kpmcGW+oaxkvhEJCWgbgNk4/ZV93Q==", "dev": true, "requires": { "figgy-pudding": "^3.5.1" @@ -4405,9 +4405,9 @@ "dev": true }, "ssri": { - 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