From f2c6bb59fecdf413b4d3f1acb662d2ff0e79e8da Mon Sep 17 00:00:00 2001 From: "Dr. Ernie Prabhakar" Date: Wed, 18 Dec 2024 16:01:26 -0800 Subject: [PATCH] chore: Xmas24 updates (#29) * Create README_WORKFLOW.md * drop fix_deprecation_warning Not needed, and causes errors * cdk version 173 * split sentinel file into prefix/suffix * explicit omics status * Update poetry.lock * boostrap reminder --------- Co-authored-by: Dr. Ernie Prabhakar <19791+drernie@users.noreply.github.com> --- .github/workflows/upgrade.yml | 3 +- .gitignore | 3 +- .npmignore | 2 + .projen/deps.json | 6 +- .projen/tasks.json | 3 +- .projenrc.ts | 13 +- README.md | 5 +- README_WORKFLOW.md | 16 + package.json | 12 +- src/constants.ts | 3 +- src/omics-quilt.ts | 28 +- src/packager/packager/constants.py | 5 +- src/packager/poetry.lock | 2048 ++++++++++++++------------ src/packager/tests/test_constants.py | 2 +- test/omics-quilt.test.ts | 4 +- tsconfig.dev.json | 1 - yarn.lock | 478 +++--- 17 files changed, 1463 insertions(+), 1169 deletions(-) create mode 100644 README_WORKFLOW.md diff --git a/.github/workflows/upgrade.yml b/.github/workflows/upgrade.yml index 06f7282..85aae7a 100644 --- a/.github/workflows/upgrade.yml +++ b/.github/workflows/upgrade.yml @@ -41,9 +41,8 @@ jobs: steps: - name: Checkout uses: actions/checkout@v3 - with: {} - name: Download patch - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v3 with: name: .repo.patch path: ${{ runner.temp }} diff --git a/.gitignore b/.gitignore index e77feef..2900d78 100644 --- a/.gitignore +++ b/.gitignore @@ -36,7 +36,6 @@ test/__snapshots__/* __pycache__ *.pyc *_metadata.json -!/.projenrc.js /test-reports/ junit.xml /coverage/ @@ -56,4 +55,4 @@ junit.xml /cdk.out/ .cdk.staging/ .parcel-cache/ -package-lock.json +!/.projenrc.ts diff --git a/.npmignore b/.npmignore index 2abb496..ffcd696 100644 --- a/.npmignore +++ b/.npmignore @@ -22,3 +22,5 @@ tsconfig.tsbuildinfo !/assets/ cdk.out/ .cdk.staging/ +/.gitattributes +/.projenrc.ts diff --git a/.projen/deps.json b/.projen/deps.json index c874327..9d77889 100644 --- a/.projen/deps.json +++ b/.projen/deps.json @@ -21,7 +21,7 @@ }, { "name": "aws-cdk", - "version": "^2.114.1", + "version": "^2.173.2", "type": "build" }, { @@ -68,7 +68,7 @@ }, { "name": "@aws-cdk/aws-lambda-python-alpha", - "version": "^2.114.1-alpha.0", + "version": "^2.173.2-alpha.0", "type": "runtime" }, { @@ -93,7 +93,7 @@ }, { "name": "aws-cdk-lib", - "version": "^2.114.1", + "version": "^2.173.2", "type": "runtime" }, { diff --git a/.projen/tasks.json b/.projen/tasks.json index c3c76d9..02ccca9 100644 --- a/.projen/tasks.json +++ b/.projen/tasks.json @@ -119,7 +119,8 @@ "description": "Runs eslint against the codebase", "steps": [ { - "exec": "eslint --ext .ts,.tsx --fix --no-error-on-unmatched-pattern src test build-tools projenrc .projenrc.ts" + "exec": "eslint --ext .ts,.tsx --fix --no-error-on-unmatched-pattern $@ src test build-tools projenrc .projenrc.ts", + "receiveArgs": true } ] }, diff --git a/.projenrc.ts b/.projenrc.ts index c464ec1..ab1ea97 100644 --- a/.projenrc.ts +++ b/.projenrc.ts @@ -1,6 +1,6 @@ import { awscdk } from 'projen'; -const cdkVersion = '2.114.1'; +const cdkVersion = '2.173.2'; const solutionName = 'omics-quilt-demo'; const project = new awscdk.AwsCdkTypeScriptApp({ cdkVersion: cdkVersion, @@ -35,7 +35,6 @@ const project = new awscdk.AwsCdkTypeScriptApp({ ], }); override_file_key('.github/workflows/build.yml', 'jobs.build.env'); -fix_deprecation_warning(); /* const appTestTask = project.addTask('pytest', { cwd: 'src/packager', @@ -58,13 +57,3 @@ function override_file_key(file: string, key: string) { project.tryFindObjectFile(file)?.addOverride(key, opts); } - -// Fix Jest 29 warning about deprecated config in `globals` -function fix_deprecation_warning() { - project.jest!.config.transform ??= {}; - project.jest!.config.transform['\\.ts$'] = [ - 'ts-jest', - project.jest?.config.globals['ts-jest'], - ]; - delete project.jest!.config.globals['ts-jest']; -} diff --git a/README.md b/README.md index 8920338..42d28d5 100644 --- a/README.md +++ b/README.md @@ -7,14 +7,17 @@ Use CDK to create Quilt packages from AWS HealthOmics ### Installation Use CDK to create and deploy the stack. +Note that it requires a large Cloud9 instance to run Docker. ```bash cp example.env .env # and edit +source .env aws configure list-profiles # verify AWS credentials exist # npx npm install # if npm not present (but npx is) npm install yarn -g # if yarn not present (but npm is) yarn install -npx cdk bootstrap # if not yet done for this account/region +# set bootstrap region (if new or changed) +npx cdk bootstrap aws://$CDK_DEFAULT_ACCOUNT/$CDK_DEFAULT_REGION # start Docker if not already running sudo systemctl start docker # e.g. on Linux (requires large Cloud9 instance!) npm run deploy diff --git a/README_WORKFLOW.md b/README_WORKFLOW.md new file mode 100644 index 0000000..03cddeb --- /dev/null +++ b/README_WORKFLOW.md @@ -0,0 +1,16 @@ +# Workflow Sequest + +What happens when you run the workflow? + +1. User uploads (or updates) `input_metadata.json` file in the `fastq/region` folder in the input bucket +2. An `S3EventSource` watching for that files triggers the `fastqLambda` to `run_workflow` and `save_metadata` to the output bucket. +3. When run, FASTQ generates the output file `bqsr_report/*.hg38.recal_data.csv` +4. This acts as a sentinel file to trigger the `packager` lambda, which creates + a package in the output bucket from everything in the parent of + `bqsr_report`. + +## Open Issues + +- Why can't we just use the `omics` events to trigger the packager? +- S3 notifications for the output bucket are not working. + The package is created, but we don't see it the Packages view. diff --git a/package.json b/package.json index 7f4c01b..d75c0e0 100644 --- a/package.json +++ b/package.json @@ -29,7 +29,7 @@ "@types/node": "^18", "@typescript-eslint/eslint-plugin": "^6", "@typescript-eslint/parser": "^6", - "aws-cdk": "^2.121.1", + "aws-cdk": "^2.173.2", "esbuild": "~0.21", "eslint": "^8", "eslint-import-resolver-typescript": "^3.6.1", @@ -42,15 +42,15 @@ "typescript": "^5.3.3" }, "dependencies": { - "@aws-cdk/aws-lambda-python-alpha": "^2.121.1-alpha.0", + "@aws-cdk/aws-lambda-python-alpha": "^2.173.2-alpha.0", "@aws-sdk/client-omics": "^3.490.0", "@aws-sdk/client-s3": "^3.490.0", "@aws-sdk/client-sns": "^3.490.0", "@types/js-yaml": "^4.0.9", "@types/uuid": "^9.0.7", - "aws-cdk-lib": "^2.121.1", + "aws-cdk-lib": "^2.173.2", "aws-lambda": "^1.0.7", - "constructs": "^10.3.0", + "constructs": "^10.0.5", "dotenv": "^16.3.1", "handlebars": "^4.7.8", "js-yaml": "^4.1.0", @@ -91,10 +91,8 @@ } ] ], - "preset": "ts-jest", - "globals": {}, "transform": { - "\\.ts$": [ + "^.+\\.[t]sx?$": [ "ts-jest", { "tsconfig": "tsconfig.dev.json" diff --git a/src/constants.ts b/src/constants.ts index b6c822f..114084d 100644 --- a/src/constants.ts +++ b/src/constants.ts @@ -20,7 +20,8 @@ export class Constants { MANIFEST_SUFFIX: '.json', INPUT_METADATA: 'input_metadata.json', QUILT_METADATA: 'quilt_metadata.json', - FASTQ_SENTINEL: 'out/bqsr_report/NA12878.hg38.recal_data.csv', + FASTQ_PREFIX: 'out/bqsr_report/', + FASTQ_SUFFIX: '.hg38.recal_data.csv', MEMORY_SIZE: 8192, TIMEOUT: '900', }; diff --git a/src/omics-quilt.ts b/src/omics-quilt.ts index 9c5994b..e19fb19 100644 --- a/src/omics-quilt.ts +++ b/src/omics-quilt.ts @@ -52,7 +52,8 @@ export class OmicsQuiltStack extends Stack { public readonly manifest_prefix: string; public readonly manifest_suffix: string; - public readonly packager_sentinel: string; + public readonly packager_prefix: string; + public readonly packager_suffix: string; readonly cc: Constants; readonly lambdaRole: Role; @@ -66,7 +67,8 @@ export class OmicsQuiltStack extends Stack { const manifest_root = this.cc.get('MANIFEST_ROOT'); this.manifest_prefix = `${manifest_root}/${this.cc.region}`; this.manifest_suffix = this.cc.get('MANIFEST_SUFFIX'); - this.packager_sentinel = this.cc.get('FASTQ_SENTINEL'); + this.packager_prefix = this.cc.get('FASTQ_PREFIX'); + this.packager_suffix = this.cc.get('FASTQ_SUFFIX'); // Create Input/Output S3 buckets this.inputBucket = this.makeBucket('input'); @@ -100,7 +102,7 @@ export class OmicsQuiltStack extends Stack { const packagerTrigger = new S3EventSource(this.outputBucket, { events: [EventType.OBJECT_CREATED], filters: [ - { suffix: this.packager_sentinel }, + { prefix: this.packager_prefix, suffix: this.packager_suffix }, ], }); packagerLambda.addEventSource(packagerTrigger); @@ -148,17 +150,15 @@ export class OmicsQuiltStack extends Stack { } private makeOmicsEventRule(ruleName: string) { - const ruleOmics = new Rule(this, ruleName, - { - eventPattern: { - source: ['aws.omics'], - detailType: ['Run Status Change'], - detail: { - status: ['*'], - }, + const ruleOmics = new Rule(this, ruleName, { + eventPattern: { + source: ['aws.omics'], + detailType: ['Run Status Change'], + detail: { + status: ['PENDING', 'STARTING', 'RUNNING', 'COMPLETED', 'FAILED', 'CANCELLED', 'STOPPING', 'DELETED'], }, }, - ); + }); return ruleOmics; } @@ -230,12 +230,14 @@ export class OmicsQuiltStack extends Stack { const output = ['s3:/', this.outputBucket.bucketName, this.cc.app]; const input = ['s3:/', this.inputBucket.bucketName, this.manifest_prefix]; const final_env = { + AWS_NODEJS_CONNECTION_REUSE_ENABLED: '1', ECR_REGISTRY: this.cc.getEcrRegistry(), INPUT_S3_LOCATION: input.join('/'), LOG_LEVEL: 'ALL', OMICS_ROLE: this.omicsRole.roleArn, OUTPUT_S3_LOCATION: output.join('/'), - SENTINEL_FILE: this.packager_sentinel, + SENTINEL_PREFIX: this.packager_prefix, + SENTINEL_SUFFIX: this.packager_suffix, INPUT_METADATA: this.cc.get('INPUT_METADATA'), QUILT_METADATA: this.cc.get('QUILT_METADATA'), WORKFLOW_ID: this.cc.get('READY2RUN_WORKFLOW_ID'), diff --git a/src/packager/packager/constants.py b/src/packager/packager/constants.py index 5896e06..3f6c0ef 100644 --- a/src/packager/packager/constants.py +++ b/src/packager/packager/constants.py @@ -21,14 +21,13 @@ class Constants: "APP_NAME": "packager", "CDK_DEFAULT_EMAIL": "test@example.com", "CDK_DEFAULT_REGION": "us-east-1", - "SENTINEL_BUCKET": "data-yaml-spec-tests", - "SENTINEL_FILE": "quilt_metadata.json", + # "SENTINEL_BUCKET": "data-yaml-spec-tests", + # "SENTINEL_FILE": "quilt_metadata.json", "TIMESTAMP_FILE": "quilt_timestamp.json", "SOURCE_APP": "omics-quilt", "QUILT_METADATA": "quilt_metadata.json", "INPUT_METADATA": "input_metadata.json", "QUILT_SUMMARIZE": "quilt_summarize.json", - "FASTQ_SENTINEL": "out/bqsr_report/NA12878.hg38.recal_data.csv", } @classmethod diff --git a/src/packager/poetry.lock b/src/packager/poetry.lock index 7967dcf..7a515e1 100644 --- a/src/packager/poetry.lock +++ b/src/packager/poetry.lock @@ -1,141 +1,158 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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