From 492c4c456695b97354212fdea97ab77e16d7d861 Mon Sep 17 00:00:00 2001 From: William Putra Intan <61998484+williamputraintan@users.noreply.github.com> Date: Wed, 29 Nov 2023 18:13:52 +1100 Subject: [PATCH] Init for MetadataManager (#67) --- .../stateless/metadata_manager/src/.gitignore | 2 + .../stateless/metadata_manager/src/Dockerfile | 14 + .../stateless/metadata_manager/src/Makefile | 59 + .../stateless/metadata_manager/src/README.md | 177 +- .../metadata_manager/src/compose.yaml | 28 + .../metadata_manager/src/dbschema/audit.esdl | 21 +- .../src/dbschema/metadata.esdl | 47 +- .../src/dbschema/migrations/00001.edgeql | 35 +- .../audit/insertSystemAuditEvent.edgeql | 2 - .../audit/updateSystemAuditEvent.edgeql | 2 - .../library/deleteLibraryByOrcaBusId.edgeql | 2 + .../library/insertLibraryQuery.edgeql | 8 +- .../library/selectAllLibraryQuery.edgeql | 3 + ... => selectLibraryByInternalIdQuery.edgeql} | 0 .../library/updateLibraryQuery.edgeql | 14 +- .../specimen/deleteSpecimenByOrcaBusId.edgeql | 2 + .../specimen/selectAllSpecimenQuery.edgeql | 3 + ...=> selectSpecimenByInternalIdQuery.edgeql} | 0 .../specimen/updateSpecimenQuery.edgeql | 6 +- .../subject/deleteSubjectByOrcaBusId.edgeql | 2 + .../subject/selectAllSubjectQuery.edgeql | 3 + ... => selectSubjectByInternalIdQuery.edgeql} | 0 .../subject/updateSubjectQuery.edgeql | 4 +- .../metadata_manager/src/deploy/.gitignore | 10 + .../metadata_manager/src/deploy/.npmignore | 6 + .../metadata_manager/src/deploy/README.md | 14 + .../src/deploy/asset/README.md | 49 + .../metadata_manager/src/deploy/bin/deploy.ts | 40 + .../metadata_manager/src/deploy/cdk.json | 63 + .../src/deploy/construct/app/Dockerfile | 46 + .../src/deploy/construct/app/app-construct.ts | 174 + .../src/deploy/construct/edge-db/Dockerfile | 8 + .../construct/edge-db/edge-db-construct.ts | 105 + ...dge-db-load-balancer-protocol-construct.ts | 102 + .../edge-db/edge-db-service-construct.ts | 219 + .../construct/postgres-rds/base-database.ts | 64 + .../infrastructure-stack-database-props.ts | 92 + .../postgres-rds/postgres-db-construct.ts | 122 + .../src/deploy/jest.config.js | 8 + .../src/deploy/lib/metadataManagerStack.ts | 105 + .../src/deploy/package-lock.json | 7466 +++++++++++++++++ .../metadata_manager/src/deploy/package.json | 29 + .../src/deploy/test/deploy.test.ts | 16 + .../metadata_manager/src/deploy/tsconfig.json | 31 + .../src/docs/edgedb-schema.png | Bin 0 -> 115496 bytes .../src/docs/relationship.drawio.svg | 87 + .../metadata_manager/src/edgedb.toml | 2 - .../src/{jest.config.ts => jest.config.js} | 3 +- .../metadata_manager/src/package.json | 17 +- .../src/src/api/routes/graphql-routes.ts | 43 + .../src/src/api/routes/internal-routes.ts | 19 +- .../stateless/metadata_manager/src/src/app.ts | 28 +- .../src/src/bootstrap/dependency-injection.ts | 24 +- .../src/src/handler/server.ts | 16 + .../metadata_manager/src/src/handler/sync.ts | 29 + .../metadata_manager/src/src/index.ts | 2 +- .../src/src/service/helpers/audit-helper.ts | 6 +- .../helpers/metadata/library-helper.ts | 10 +- .../src/service/loader-method/googleSheet.ts | 320 +- .../src/src/service/metadata-loader.ts | 11 - .../src/src/service/metadata.ts | 358 + .../src/src/test-data/index.ts | 27 + .../src/src/test-data/scenario-1.ts | 12 - .../src/src/test-data/scenarios/metadata.xlsx | Bin 0 -> 12660 bytes .../src/src/test-data/scenarios/scenario-1.ts | 18 + .../src/src/test-data/scenarios/scenario-2.ts | 37 + .../src/src/test-data/utils.ts | 8 + .../metadata_manager/src/src/utils.ts | 38 + .../src/tests/service/gsheet.test.ts | 94 - .../service/{ => loader}/gsheet.common.ts | 15 +- .../src/tests/service/loader/gsheet.test.ts | 34 + .../src/tests/service/metadata.common.ts | 59 + .../src/tests/service/metadata.test.ts | 153 + .../tests/service/test-dependency.common.ts | 15 +- .../metadata_manager/src/tsconfig.json | 7 +- .../stateless/metadata_manager/src/yarn.lock | 1562 ++-- 76 files changed, 10659 insertions(+), 1598 deletions(-) create mode 100644 lib/workload/stateless/metadata_manager/src/Dockerfile create mode 100644 lib/workload/stateless/metadata_manager/src/Makefile create mode 100644 lib/workload/stateless/metadata_manager/src/compose.yaml create mode 100644 lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/deleteLibraryByOrcaBusId.edgeql create mode 100644 lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectAllLibraryQuery.edgeql rename lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/{selectLibraryByIdQuery.edgeql => selectLibraryByInternalIdQuery.edgeql} (100%) create mode 100644 lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/deleteSpecimenByOrcaBusId.edgeql create mode 100644 lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectAllSpecimenQuery.edgeql rename lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/{selectSpecimenByIdQuery.edgeql => selectSpecimenByInternalIdQuery.edgeql} (100%) create mode 100644 lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/deleteSubjectByOrcaBusId.edgeql create mode 100644 lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectAllSubjectQuery.edgeql rename lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/{selectSubjectByIdQuery.edgeql => selectSubjectByInternalIdQuery.edgeql} (100%) create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/.gitignore create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/.npmignore create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/README.md create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/asset/README.md create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/bin/deploy.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/cdk.json create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/app/Dockerfile create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/app/app-construct.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/Dockerfile create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-construct.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-load-balancer-protocol-construct.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-service-construct.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/base-database.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/infrastructure-stack-database-props.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/postgres-db-construct.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/jest.config.js create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/lib/metadataManagerStack.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/package-lock.json create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/package.json create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/test/deploy.test.ts create mode 100644 lib/workload/stateless/metadata_manager/src/deploy/tsconfig.json create mode 100644 lib/workload/stateless/metadata_manager/src/docs/edgedb-schema.png create mode 100644 lib/workload/stateless/metadata_manager/src/docs/relationship.drawio.svg delete mode 100644 lib/workload/stateless/metadata_manager/src/edgedb.toml rename lib/workload/stateless/metadata_manager/src/{jest.config.ts => jest.config.js} (69%) create mode 100644 lib/workload/stateless/metadata_manager/src/src/api/routes/graphql-routes.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/handler/server.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/handler/sync.ts delete mode 100644 lib/workload/stateless/metadata_manager/src/src/service/metadata-loader.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/service/metadata.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/test-data/index.ts delete mode 100644 lib/workload/stateless/metadata_manager/src/src/test-data/scenario-1.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/metadata.xlsx create mode 100644 lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-1.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-2.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/test-data/utils.ts create mode 100644 lib/workload/stateless/metadata_manager/src/src/utils.ts delete mode 100644 lib/workload/stateless/metadata_manager/src/tests/service/gsheet.test.ts rename lib/workload/stateless/metadata_manager/src/tests/service/{ => loader}/gsheet.common.ts (88%) create mode 100644 lib/workload/stateless/metadata_manager/src/tests/service/loader/gsheet.test.ts create mode 100644 lib/workload/stateless/metadata_manager/src/tests/service/metadata.common.ts create mode 100644 lib/workload/stateless/metadata_manager/src/tests/service/metadata.test.ts diff --git a/lib/workload/stateless/metadata_manager/src/.gitignore b/lib/workload/stateless/metadata_manager/src/.gitignore index 30578c9f3..5385865a2 100644 --- a/lib/workload/stateless/metadata_manager/src/.gitignore +++ b/lib/workload/stateless/metadata_manager/src/.gitignore @@ -137,3 +137,5 @@ dist dbschema/edgeql-js dbschema/queries.* dbschema/interfaces.ts + +asset/ \ No newline at end of file diff --git a/lib/workload/stateless/metadata_manager/src/Dockerfile b/lib/workload/stateless/metadata_manager/src/Dockerfile new file mode 100644 index 000000000..2e79a6598 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/Dockerfile @@ -0,0 +1,14 @@ +FROM node:20 +WORKDIR /app + +COPY Makefile package.json yarn.lock tsconfig.json jest.config.js ./ +COPY src/ ./src/ +COPY tests/ ./tests/ + +COPY dbschema/queries ./dbschema/queries +COPY dbschema/migrations ./dbschema/migrations +COPY dbschema/*.esdl ./dbschema/ + +RUN make install + +ENTRYPOINT [ "make", "start", "EDGEDB_HOST=edgedb" ] diff --git a/lib/workload/stateless/metadata_manager/src/Makefile b/lib/workload/stateless/metadata_manager/src/Makefile new file mode 100644 index 000000000..ce22a2867 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/Makefile @@ -0,0 +1,59 @@ +EDGEDB_HOST ?= localhost + +# Installation +install: + @yarn install + +# To run docker compose +up: + @docker compose up -d + +down: + @docker compose down + +stop: + @docker compose down + +# Build the app for deployment + +edgetypes: + @npx generate queries --target ts --file --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret + @npx generate edgeql-js --target ts --output-dir dbschema/edgeql-js --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret + @npx generate interfaces --file dbschema/interfaces.ts --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret + +build: edgetypes + @rm -rf asset + @mkdir -p asset + @yarn run build-src + @cd dist && zip -r ../asset/src.zip . + + @mkdir -p nodejs + @cp -r node_modules ./nodejs + @zip -r asset/dependency.zip nodejs + @rm -rf nodejs + + +# Testing +test: + @yarn test + +# Starting server +start: edgetypes + @yarn start +start-scenario-1: edgetypes + @yarn run insert-scenario-1 + @yarn start + +# Inserting scenarios +insert-scenario-2: + @yarn run insert-scenario-2 + +# Shortcut of edgedb cli +edgedb: + @edgedb --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret +edgedb-ui: + @edgedb ui --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure --no-server-check # pragma: allowlist secret +edgedb-migrate: + @edgedb migrate --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret +edgedb-migration-create: + @edgedb migration create --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret diff --git a/lib/workload/stateless/metadata_manager/src/README.md b/lib/workload/stateless/metadata_manager/src/README.md index 8c307890f..1ab73fa47 100644 --- a/lib/workload/stateless/metadata_manager/src/README.md +++ b/lib/workload/stateless/metadata_manager/src/README.md @@ -1,46 +1,171 @@ -# Metadata manager +# Metadata Manager for OrcaBus -The `MetadataManager` is one of the microservice within the UMCCR OrcaBus that manages the metadata records used for the -BioInformatics pipelines. The service will be responsible to make records to stay up to date and able to sync records -from multiple sources. +One of the microservices in the Orcabus handles all the metadata information. -## Development +## Schema -### Git Checkout -As this microservice is part of a monorepo from the main OrcaBus project, the process Git Flow process -will follow on the root of this project. +The EdgeDb schema looks like this as follows. You could also open this view with the make command: `make edgedb-ui` (see development +section below) -### Development +![schema](./docs/edgedb-schema.png) + +Relationship between schema + +![relationship](docs/relationship.drawio.svg) + +The mapping between the metadata spreadsheet to the schema are +| Metadata Header | Table | Field Name | +|-------------------|----------------------|------------| +| SubjectID | `metadata::Subject` | internalId | +| ExternalSubjectID | `metadata::Subject` | externalId | +| SampleID | `metadata::Specimen` | internalId | +| ExternalSampleID | `metadata::Specimen` | externalId | +| Source | `metadata::Specimen` | source | +| LibraryID | `metadata::Library` | internalId | +| Phenotype | `metadata::Library` | phenotype | +| Quality | `metadata::Library` | quality | +| Type | `metadata::Library` | type | +| Assay | `metadata::Library` | assay | +| Workflow | `metadata::Library` | workflow | +| Coverage (X) | `metadata::Library` | coverage | + +Notes: + +- The `orcabusId` is constructed uniquely for ocabusId with the structure of prefixes either `spc.`, `lib.`, `sbj.` + (for specimen, library, and subject, respectively) and followed by [ulid](https://github.com/ulid/spec) id. -#### Setup + e.g. `sbj.01HF6B4D6GHCYT3ZVF0S6087W3` +- The audit event schema will record the generation of success/failure of an insertion/deletion. + + ```curl + select audit::AuditEvent {*} filter .id='04ec4232-82be-11ee-870c-6b78b11f565f'; + { + audit::SystemAuditEvent { + id: 04ec4232-82be-11ee-870c-6b78b11f565f, + actionCategory: C, + actionDescription: 'Insert new subject record: sbj.01HF6B4DJPWGYZK8RZDN9BK454', + actionOutcome: success, + details: Json("{\"id\": \"04f3ea1e-82be-11ee-870c-4f6a4d334d37\", \"orcaBusId\": \"sbj.01HF6B4DJPWGYZK8RZDN9BK454\", \"externalId\": \"EXTSUB002\", \"internalId\": \"SBJ220002\"}"), + updatedDateTime: '2023-11-14T07:18:33.366109Z', + }, + } + ``` -Change the terminal directory from the OrcaBus root to this directory: +## Local Deployment + +Requirement: + +- Docker +- Node.js with Yarn + +```bash +docker -v +Docker version 20.10.12, build e91ed5707e + +node -v +v20.9.0 ``` -cd lib/workload/stateless/metadata_manager/src + +### Installation + +To install dependency, yarn is needed for this purpose + +```bash +npm i -g yarn ``` -Requirement for this project: - - nodejs - - edgedb (see ) +To install all dependencies, a make file is provided and can be done by: -To install the dependency of this project +```bash +make install ``` -yarn + +### Start + + +To start the database and server use the following make command. This will run the server and database in +docker-compose. The server will run at port 8080. (http://localhost:8080). +The database used here is [EdgeDb](https://www.edgedb.com/) which is a graph-relational database that uses SQL as their +underlying database. The configuration for this has been bundled up into a docker-compose and could be run as follows. + +```bash +make up ``` -Setup the database + +To start the server up use the following command + +```bash +make start ``` -yarn init-db -yarn migrate-db + +We could also start data by resetting and inserting some mock test data. + +```bash +make start-scenario-1 ``` -#### Build -```yarn edgetypes``` +This should run at localhost port 8080. Valid endpoints are as follows + +```bash + +http://localhost:8080/subject +http://localhost:8080/library +http://localhost:8080/specimen + + + +http://localhost:8080/graphql/explore (UI) +http://localhost:8080/graphql (Only for graphql POST method) +``` + +If you need to serve from existing metadata locally. You could copy and paste +the `.xlsx` file into [./src/test-data/scenarios/metadata.xlsx](./src/test-data/scenarios/metadata.xlsx). +Then to dump and reload with this metadata spreadsheet run the following: + +```bash +make insert-scenario-2 +``` + +### Testing + +```bash +make test + +Test Suites: 2 passed, 2 total +Tests: 6 passed, 6 total +Snapshots: 0 total +Time: 36.073 s +``` + +### Build + +To build for deployment the following will generate assets that could be deployed to lambdas. +For more details on the deployment [deploy-readme](./deploy/README.md). + +```bash +make build +``` + +### Development + +edgedb-cli is expected to be installed in the dev environment. See the [installation guide](https://www.edgedb.com/install#macos-homebrew) for details. + +Homebrew user: + +```curl +brew tap edgedb/tap +brew install edgedb-cli +``` +Since the EdgeDb is running in a container, some EdgeDb commands will need to pass in their connection parameter +to get connected with the container. Some make commands are added in the makefile for convenience. -### Run -```yarn watch``` +List available makefile command equivalent to edgedb-cli: -#### Testing -```yarn test``` +- `make edgedb` (`edgedb`)- to run EdgeDb +- `make edgedb-ui` (`edgedb ui`) - to open EdgeDb UI (username: `orcabus_admin`; password: `admin`) // pragma: allowlist secret +- `make edgedb-migrate` (`edgedb migrate`) - to apply new migration +- `make edgedb-migration-create` (`edgedb migration create`) - to create new migrations +- `make edgetypes` - to make EdgeDb files (e.g. `*.edgeql`) recognizable by typescript diff --git a/lib/workload/stateless/metadata_manager/src/compose.yaml b/lib/workload/stateless/metadata_manager/src/compose.yaml new file mode 100644 index 000000000..d4706e841 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/compose.yaml @@ -0,0 +1,28 @@ +version: '3.8' +services: + edgedb: + image: edgedb/edgedb:3.5 + environment: + EDGEDB_DOCKER_LOG_LEVEL: 'debug' + EDGEDB_SERVER_SECURITY: insecure_dev_mode + EDGEDB_SERVER_ADMIN_UI: enabled + EDGEDB_SERVER_USER: 'orcabus_admin' + EDGEDB_SERVER_PASSWORD: 'admin' # pragma: allowlist secret + volumes: + - './dbschema:/dbschema' + ports: + - '5656:5656' + + app: + build: . + environment: + # EdgedDb related config + EDGEDB_HOST: edgedb + + # Fastify config + PORT: '8080' + HOST: '0.0.0.0' + ports: + - '8080:8080' + links: + - edgedb diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/audit.esdl b/lib/workload/stateless/metadata_manager/src/dbschema/audit.esdl index 729b1acb3..b4d09a7c8 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/audit.esdl +++ b/lib/workload/stateless/metadata_manager/src/dbschema/audit.esdl @@ -1,9 +1,10 @@ +using extension graphql; module audit { # NOTE: TODO How to query deleted library?? # ActionType definition - # Ref: http://hl7.org/fhir/audit-even t-action + # Ref: http://hl7.org/fhir/audit-event-action scalar type ActionType extending enum<'C', 'R', 'U', 'D', 'E'>; # ActionOutcome definition @@ -18,36 +19,18 @@ module audit { # any details will appear later in the details JSON required actionDescription: str; - # when this audit record has been made (should be close to occurredDateTime) - required recordedDateTime: datetime { - default := datetime_current(); - readonly := true; - } - required occurredDateTime: datetime { - default := datetime_current(); - } - required occurredDuration: duration { - rewrite insert, update using ( - select __subject__.occurredDateTime - __subject__.recordedDateTime - ) - } - # when this audit record is last updated (e.g. completion/failure of an event) # Using `rewrite` to re-update this automatically required updatedDateTime: datetime { rewrite insert, update using (datetime_of_statement()) } - # bespoke JSON with details of the event details: json; - # Whether its expected that this audit event will be updated. - required inProgress: bool; } type SystemAuditEvent extending AuditEvent { } - } diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/metadata.esdl b/lib/workload/stateless/metadata_manager/src/dbschema/metadata.esdl index 5d459f8f9..7862b282e 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/metadata.esdl +++ b/lib/workload/stateless/metadata_manager/src/dbschema/metadata.esdl @@ -1,23 +1,28 @@ - +using extension graphql; module metadata { - scalar type Phenotype extending enum<'normal', 'tumor', 'negative-control'>; - scalar type Quality extending enum<'very-poor', 'poor', 'good', 'borderline'>; scalar type WorkflowTypes extending enum<'clinical', 'research', 'qc', 'control', 'bcl', 'manual'>; - scalar type LibraryTypes extending enum< - '10X', - 'ctDNA', - 'ctTSO', - 'exome', - 'Metagenm', - 'MethylSeq', - 'other', - 'TSO-DNA', - 'TSO-RNA', - 'WGS', - 'WTS', - 'BiModal' - >; + + # Apparently GraphQL has some trouble on setting enums that containin hyphens + # and str startswith number + # Regex pattern accepted: /^[_a-zA-Z][_a-zA-Z0-9]*$/ + # + # scalar type Phenotype extending enum<'normal', 'tumor', 'negative-control'>; + # scalar type Quality extending enum<'very-poor', 'poor', 'good', 'borderline'>; + # scalar type LibraryTypes extending enum< + # '10X', + # 'ctDNA', + # 'ctTSO', + # 'exome', + # 'Metagenm', + # 'MethylSeq', + # 'other', + # 'TSO-DNA', + # 'TSO-RNA', + # 'WGS', + # 'WTS', + # 'BiModal' + # >; abstract type MetadataIdentifiable { required orcaBusId: str { @@ -30,12 +35,12 @@ module metadata { } type Library extending MetadataIdentifiable { - phenotype: Phenotype; + phenotype: str; workflow: WorkflowTypes; - quality: Quality; - type: LibraryTypes; + quality: str; + type: str; assay: str; - coverage: decimal; + coverage: str; single link specimen: Specimen { on target delete allow diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/migrations/00001.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/migrations/00001.edgeql index 397bd47e0..d2a37329a 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/migrations/00001.edgeql +++ b/lib/workload/stateless/metadata_manager/src/dbschema/migrations/00001.edgeql @@ -1,6 +1,7 @@ -CREATE MIGRATION m1gwyr7syw4wgds4mz3jflyrnljxi6r64jzvd6ccko6olwo3erqj4a +CREATE MIGRATION m14icr2t2ykpgsskmquyvwoduwtjo7q7qbwfadvqsblckzhdhl7uqq ONTO initial { + CREATE EXTENSION graphql VERSION '1.0'; CREATE MODULE audit IF NOT EXISTS; CREATE MODULE metadata IF NOT EXISTS; CREATE SCALAR TYPE audit::ActionOutcome EXTENDING enum; @@ -10,15 +11,6 @@ CREATE MIGRATION m1gwyr7syw4wgds4mz3jflyrnljxi6r64jzvd6ccko6olwo3erqj4a CREATE REQUIRED PROPERTY actionDescription: std::str; CREATE REQUIRED PROPERTY actionOutcome: audit::ActionOutcome; CREATE PROPERTY details: std::json; - CREATE REQUIRED PROPERTY inProgress: std::bool; - CREATE REQUIRED PROPERTY occurredDateTime: std::datetime { - SET default := (std::datetime_current()); - }; - CREATE REQUIRED PROPERTY occurredDuration: std::duration; - CREATE REQUIRED PROPERTY recordedDateTime: std::datetime { - SET default := (std::datetime_current()); - SET readonly := true; - }; CREATE REQUIRED PROPERTY updatedDateTime: std::datetime { CREATE REWRITE INSERT @@ -27,18 +19,6 @@ CREATE MIGRATION m1gwyr7syw4wgds4mz3jflyrnljxi6r64jzvd6ccko6olwo3erqj4a UPDATE USING (std::datetime_of_statement()); }; - ALTER PROPERTY occurredDuration { - CREATE REWRITE - INSERT - USING (SELECT - (__subject__.occurredDateTime - __subject__.recordedDateTime) - ); - CREATE REWRITE - UPDATE - USING (SELECT - (__subject__.occurredDateTime - __subject__.recordedDateTime) - ); - }; }; CREATE TYPE audit::SystemAuditEvent EXTENDING audit::AuditEvent; CREATE ABSTRACT TYPE metadata::MetadataIdentifiable { @@ -50,16 +30,13 @@ CREATE MIGRATION m1gwyr7syw4wgds4mz3jflyrnljxi6r64jzvd6ccko6olwo3erqj4a CREATE CONSTRAINT std::exclusive ON (std::str_lower(__subject__)); }; }; - CREATE SCALAR TYPE metadata::LibraryTypes EXTENDING enum<`10X`, ctDNA, ctTSO, exome, Metagenm, MethylSeq, other, `TSO-DNA`, `TSO-RNA`, WGS, WTS, BiModal>; - CREATE SCALAR TYPE metadata::Phenotype EXTENDING enum; - CREATE SCALAR TYPE metadata::Quality EXTENDING enum<`very-poor`, poor, good, borderline>; CREATE SCALAR TYPE metadata::WorkflowTypes EXTENDING enum; CREATE TYPE metadata::Library EXTENDING metadata::MetadataIdentifiable { CREATE PROPERTY assay: std::str; - CREATE PROPERTY coverage: std::decimal; - CREATE PROPERTY phenotype: metadata::Phenotype; - CREATE PROPERTY quality: metadata::Quality; - CREATE PROPERTY type: metadata::LibraryTypes; + CREATE PROPERTY coverage: std::str; + CREATE PROPERTY phenotype: std::str; + CREATE PROPERTY quality: std::str; + CREATE PROPERTY type: std::str; CREATE PROPERTY workflow: metadata::WorkflowTypes; }; CREATE TYPE metadata::Specimen EXTENDING metadata::MetadataIdentifiable { diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/insertSystemAuditEvent.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/insertSystemAuditEvent.edgeql index 1fe501c39..453ebb382 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/insertSystemAuditEvent.edgeql +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/insertSystemAuditEvent.edgeql @@ -6,8 +6,6 @@ insert SystemAuditEvent { actionDescription := $actionDescription ?? "", actionOutcome := $actionOutcome ?? ActionOutcome.success, - occurredDateTime := $occurredDateTime ?? datetime_current(), details := $details ?? {}, - inProgress := $inProgress ?? false }; diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/updateSystemAuditEvent.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/updateSystemAuditEvent.edgeql index 7e3af682b..2ccc7ba72 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/updateSystemAuditEvent.edgeql +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/updateSystemAuditEvent.edgeql @@ -6,6 +6,4 @@ set { actionOutcome := $actionOutcome, details := $details, - occurredDateTime := $occurredDateTime, - inProgress := $inProgress } diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/deleteLibraryByOrcaBusId.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/deleteLibraryByOrcaBusId.edgeql new file mode 100644 index 000000000..2cc2664e7 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/deleteLibraryByOrcaBusId.edgeql @@ -0,0 +1,2 @@ +delete metadata::Library +filter .orcaBusId = $orcaBusId diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/insertLibraryQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/insertLibraryQuery.edgeql index 6ee8f5285..bb2c21021 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/insertLibraryQuery.edgeql +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/insertLibraryQuery.edgeql @@ -3,12 +3,12 @@ select ( insert metadata::Library { orcaBusId := $orcaBusId, internalId := $internalId, - phenotype := $phenotype, + phenotype := $phenotype, workflow := $workflow, - quality := $quality, - type := $type, + quality := $quality, + type := $type, assay := $assay, - coverage := $coverage, + coverage := $coverage, specimen := ( select assert_single(( diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectAllLibraryQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectAllLibraryQuery.edgeql new file mode 100644 index 000000000..c82b2c793 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectAllLibraryQuery.edgeql @@ -0,0 +1,3 @@ +select metadata::Library{ + * +} diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectLibraryByIdQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectLibraryByInternalIdQuery.edgeql similarity index 100% rename from lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectLibraryByIdQuery.edgeql rename to lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectLibraryByInternalIdQuery.edgeql diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/updateLibraryQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/updateLibraryQuery.edgeql index 4736279f4..11f902035 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/updateLibraryQuery.edgeql +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/updateLibraryQuery.edgeql @@ -4,14 +4,14 @@ select assert_single(( filter .orcaBusId = $orcaBusId set { - internalId := $internalId ?? .internalId, + internalId := $internalId, - phenotype := $phenotype ?? .phenotype, - workflow := $workflow ?? .workflow, - quality := $quality ?? .quality, - type := $type ?? .type, - assay := $assay ?? .assay, - coverage := $coverage ?? .coverage, + phenotype := $phenotype, + workflow := $workflow, + quality := $quality, + type := $type, + assay := $assay, + coverage := $coverage, specimen := ( select assert_single(( diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/deleteSpecimenByOrcaBusId.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/deleteSpecimenByOrcaBusId.edgeql new file mode 100644 index 000000000..ce28d87f6 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/deleteSpecimenByOrcaBusId.edgeql @@ -0,0 +1,2 @@ +delete metadata::Specimen +filter .orcaBusId = $orcaBusId diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectAllSpecimenQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectAllSpecimenQuery.edgeql new file mode 100644 index 000000000..57663f1e7 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectAllSpecimenQuery.edgeql @@ -0,0 +1,3 @@ +select metadata::Specimen{ + * +} diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectSpecimenByIdQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectSpecimenByInternalIdQuery.edgeql similarity index 100% rename from lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectSpecimenByIdQuery.edgeql rename to lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectSpecimenByInternalIdQuery.edgeql diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/updateSpecimenQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/updateSpecimenQuery.edgeql index 0e578abb5..7e51de960 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/updateSpecimenQuery.edgeql +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/updateSpecimenQuery.edgeql @@ -4,9 +4,9 @@ select assert_single(( filter .orcaBusId = $orcaBusId set { - internalId := $internalId ?? .internalId, - externalId := $externalId ?? .externalId, - source := $source ?? .source, + internalId := $internalId, + externalId := $externalId, + source := $source, subject := ( select assert_single(( diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/deleteSubjectByOrcaBusId.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/deleteSubjectByOrcaBusId.edgeql new file mode 100644 index 000000000..d8ef180d8 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/deleteSubjectByOrcaBusId.edgeql @@ -0,0 +1,2 @@ +delete metadata::Subject +filter .orcaBusId = $orcaBusId diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectAllSubjectQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectAllSubjectQuery.edgeql new file mode 100644 index 000000000..3828799d4 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectAllSubjectQuery.edgeql @@ -0,0 +1,3 @@ +select metadata::Subject{ + * +} diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectSubjectByIdQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectSubjectByInternalIdQuery.edgeql similarity index 100% rename from lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectSubjectByIdQuery.edgeql rename to lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectSubjectByInternalIdQuery.edgeql diff --git a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/updateSubjectQuery.edgeql b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/updateSubjectQuery.edgeql index 9c7cb3622..1ba14b5ef 100644 --- a/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/updateSubjectQuery.edgeql +++ b/lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/updateSubjectQuery.edgeql @@ -3,8 +3,8 @@ select assert_single(( filter .orcaBusId = $orcaBusId set { - internalId := $internalId ?? .internalId, - externalId := $externalId ?? .externalId + internalId := $internalId, + externalId := $externalId } )){ *, diff --git a/lib/workload/stateless/metadata_manager/src/deploy/.gitignore b/lib/workload/stateless/metadata_manager/src/deploy/.gitignore new file mode 100644 index 000000000..581904102 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/.gitignore @@ -0,0 +1,10 @@ +*.js +!jest.config.js +*.d.ts +node_modules + +# CDK asset staging directory +.cdk.staging +cdk.out + +/volume/ \ No newline at end of file diff --git a/lib/workload/stateless/metadata_manager/src/deploy/.npmignore b/lib/workload/stateless/metadata_manager/src/deploy/.npmignore new file mode 100644 index 000000000..c1d6d45dc --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/.npmignore @@ -0,0 +1,6 @@ +*.ts +!*.d.ts + +# CDK asset staging directory +.cdk.staging +cdk.out diff --git a/lib/workload/stateless/metadata_manager/src/deploy/README.md b/lib/workload/stateless/metadata_manager/src/deploy/README.md new file mode 100644 index 000000000..320efc02a --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/README.md @@ -0,0 +1,14 @@ +# Welcome to your CDK TypeScript project + +This is a blank project for CDK development with TypeScript. + +The `cdk.json` file tells the CDK Toolkit how to execute your app. + +## Useful commands + +* `npm run build` compile typescript to js +* `npm run watch` watch for changes and compile +* `npm run test` perform the jest unit tests +* `cdk deploy` deploy this stack to your default AWS account/region +* `cdk diff` compare deployed stack with current state +* `cdk synth` emits the synthesized CloudFormation template diff --git a/lib/workload/stateless/metadata_manager/src/deploy/asset/README.md b/lib/workload/stateless/metadata_manager/src/deploy/asset/README.md new file mode 100644 index 000000000..8df6cd8bd --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/asset/README.md @@ -0,0 +1,49 @@ +# Metadata manager + +The `MetadataManager` is one of the microservices within the UMCCR OrcaBus that manages the metadata records used for the +BioInformatics pipelines. The service will be responsible to make records to stay up to date and able to sync records +from multiple sources. + +## Development + +### Git Checkout +As this microservice is part of a monorepo from the main OrcaBus project, the process Git Flow process +will follow on the root of this project. + +### Development + +#### Setup + +Change the terminal directory from the OrcaBus root to this directory: + +``` +cd lib/workload/stateless/metadata_manager/src +``` + +Requirement for this project: + - nodejs + - edgedb (see ) + +To install the dependency of this project +``` +yarn +``` + +Setup the database +``` +yarn init-db +yarn migrate-db +``` + +#### Build +```yarn edgetypes``` + + +### Run +```yarn watch``` + +#### Testing +```yarn test``` + +### Notes +- If google records have multiple records, the last record will replace the first request. \ No newline at end of file diff --git a/lib/workload/stateless/metadata_manager/src/deploy/bin/deploy.ts b/lib/workload/stateless/metadata_manager/src/deploy/bin/deploy.ts new file mode 100644 index 000000000..1c2ffd841 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/bin/deploy.ts @@ -0,0 +1,40 @@ +#!/usr/bin/env node +import 'source-map-support/register'; +import * as cdk from 'aws-cdk-lib'; +import { MetadataManagerStack } from '../lib/metadataManagerStack'; + +// tags for our stacks +const tags = { + 'umccr-org:Stack': 'orcabusMetadataManager', +}; + +const description = 'MetadataManager for OrcaBus'; + +const app = new cdk.App(); +new MetadataManagerStack(app, 'MetadataManagerStack', { + env: { + region: 'ap-southeast-2', + }, + tags: tags, + description: description, + network: { + vpcName: 'main-vpc', + }, + edgeDb: { + secretPrefix: 'orcabusMetadataManager', // pragma: allowlist secret + version: '3.4', + }, + appConfiguration: { + triggerLoadSchedule: cdk.aws_events.Schedule.cron({ minute: '0', hour: '1' }), + }, + // Ideally this should be reusable RDS across the orcabus microservices + database: { + name: 'orcabus', + adminUser: 'orcabus_admin', + enableMonitoring: { + cloudwatchLogsExports: ['postgresql'], + enablePerformanceInsights: true, + monitoringInterval: cdk.Duration.seconds(60), + }, + }, +}); diff --git a/lib/workload/stateless/metadata_manager/src/deploy/cdk.json b/lib/workload/stateless/metadata_manager/src/deploy/cdk.json new file mode 100644 index 000000000..9fef773d9 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/cdk.json @@ -0,0 +1,63 @@ +{ + "app": "npx ts-node --prefer-ts-exts bin/deploy.ts", + "watch": { + "include": [ + "**" + ], + "exclude": [ + "README.md", + "cdk*.json", + "**/*.d.ts", + "**/*.js", + "tsconfig.json", + "package*.json", + "yarn.lock", + "node_modules", + "test" + ] + }, + "context": { + "@aws-cdk/aws-lambda:recognizeLayerVersion": true, + "@aws-cdk/core:checkSecretUsage": true, + "@aws-cdk/core:target-partitions": [ + "aws", + "aws-cn" + ], + "@aws-cdk-containers/ecs-service-extensions:enableDefaultLogDriver": true, + "@aws-cdk/aws-ec2:uniqueImdsv2TemplateName": true, + "@aws-cdk/aws-ecs:arnFormatIncludesClusterName": true, + "@aws-cdk/aws-iam:minimizePolicies": true, + "@aws-cdk/core:validateSnapshotRemovalPolicy": true, + "@aws-cdk/aws-codepipeline:crossAccountKeyAliasStackSafeResourceName": true, + "@aws-cdk/aws-s3:createDefaultLoggingPolicy": true, + "@aws-cdk/aws-sns-subscriptions:restrictSqsDescryption": true, + "@aws-cdk/aws-apigateway:disableCloudWatchRole": true, + "@aws-cdk/core:enablePartitionLiterals": true, + "@aws-cdk/aws-events:eventsTargetQueueSameAccount": true, + "@aws-cdk/aws-iam:standardizedServicePrincipals": true, + "@aws-cdk/aws-ecs:disableExplicitDeploymentControllerForCircuitBreaker": true, + "@aws-cdk/aws-iam:importedRoleStackSafeDefaultPolicyName": true, + "@aws-cdk/aws-s3:serverAccessLogsUseBucketPolicy": true, + "@aws-cdk/aws-route53-patters:useCertificate": true, + "@aws-cdk/customresources:installLatestAwsSdkDefault": false, + "@aws-cdk/aws-rds:databaseProxyUniqueResourceName": true, + "@aws-cdk/aws-codedeploy:removeAlarmsFromDeploymentGroup": true, + "@aws-cdk/aws-apigateway:authorizerChangeDeploymentLogicalId": true, + "@aws-cdk/aws-ec2:launchTemplateDefaultUserData": true, + "@aws-cdk/aws-secretsmanager:useAttachedSecretResourcePolicyForSecretTargetAttachments": true, + "@aws-cdk/aws-redshift:columnId": true, + "@aws-cdk/aws-stepfunctions-tasks:enableEmrServicePolicyV2": true, + "@aws-cdk/aws-ec2:restrictDefaultSecurityGroup": true, + "@aws-cdk/aws-apigateway:requestValidatorUniqueId": true, + "@aws-cdk/aws-kms:aliasNameRef": true, + "@aws-cdk/aws-autoscaling:generateLaunchTemplateInsteadOfLaunchConfig": true, + "@aws-cdk/core:includePrefixInUniqueNameGeneration": true, + "@aws-cdk/aws-efs:denyAnonymousAccess": true, + "@aws-cdk/aws-opensearchservice:enableOpensearchMultiAzWithStandby": true, + "@aws-cdk/aws-lambda-nodejs:useLatestRuntimeVersion": true, + "@aws-cdk/aws-efs:mountTargetOrderInsensitiveLogicalId": true, + "@aws-cdk/aws-rds:auroraClusterChangeScopeOfInstanceParameterGroupWithEachParameters": true, + "@aws-cdk/aws-appsync:useArnForSourceApiAssociationIdentifier": true, + "@aws-cdk/aws-rds:preventRenderingDeprecatedCredentials": true + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/app/Dockerfile b/lib/workload/stateless/metadata_manager/src/deploy/construct/app/Dockerfile new file mode 100644 index 000000000..5043d808e --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/app/Dockerfile @@ -0,0 +1,46 @@ +FROM alpine:latest as layer-copy + +ARG AWS_ACCESS_KEY_ID +ARG AWS_SECRET_ACCESS_KEY +ARG AWS_SESSION_TOKEN +ENV AWS_DEFAULT_REGION="ap-southeast-2" +ENV AWS_ACCESS_KEY_ID=$AWS_ACCESS_KEY_ID +ENV AWS_SECRET_ACCESS_KEY=$AWS_SECRET_ACCESS_KEY +ENV AWS_SESSION_TOKEN=$AWS_SESSION_TOKEN + +RUN apk add aws-cli curl unzip +RUN mkdir -p /opt + +# Getting AWS managed lambda layer injected in the image +# We are using the extension for access secrets and parameter +# Ref: Ref: https://docs.aws.amazon.com/secretsmanager/latest/userguide/retrieving-secrets_lambda.html +RUN curl $(aws lambda get-layer-version-by-arn --arn arn:aws:lambda:ap-southeast-2:665172237481:layer:AWS-Parameters-and-Secrets-Lambda-Extension-Arm64:11 --query 'Content.Location' --output text) --output layer.zip +RUN unzip layer.zip -d /opt +RUN rm layer.zip + +FROM public.ecr.aws/lambda/nodejs:20-arm64 as builder +WORKDIR /usr/app + +# Copying existing required file to the image +# `make edgetypes` that is for querying edgedb must exist before this +COPY package.json yarn.lock tsconfig.json jest.config.js ./ +COPY dbschema/ ./dbschema/ +COPY src/ ./src/ +COPY tests/ ./tests/ + +# Building necessary file for the lambda +RUN npm install -g yarn +RUN yarn -v +RUN yarn install +RUN yarn run build-src + +FROM public.ecr.aws/lambda/nodejs:20-arm64 + +# Copy the extensions here +WORKDIR /opt +COPY --from=layer-copy /opt/ . + +# Copy the rest of the code +WORKDIR ${LAMBDA_TASK_ROOT} +COPY --from=builder /usr/app/dist/ ./ +COPY --from=builder /usr/app/node_modules/ ./node_modules/ diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/app/app-construct.ts b/lib/workload/stateless/metadata_manager/src/deploy/construct/app/app-construct.ts new file mode 100644 index 000000000..2ecc9b194 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/app/app-construct.ts @@ -0,0 +1,174 @@ +import { + aws_ec2 as ec2, + aws_secretsmanager as secretsmanager, + aws_lambda as lambda, + aws_ssm as ssm, + aws_events as events, + aws_events_targets as targets, + Duration, +} from 'aws-cdk-lib'; +import * as path from 'path'; +import { Construct } from 'constructs'; +import { ISecurityGroup } from 'aws-cdk-lib/aws-ec2'; +import { HttpLambdaIntegration } from '@aws-cdk/aws-apigatewayv2-integrations-alpha'; +import { CorsHttpMethod, HttpApi, HttpMethod } from '@aws-cdk/aws-apigatewayv2-alpha'; +import { EdgeDbConfigurationProps } from '../edge-db/edge-db-construct'; + +export interface appProps { + edgedDb: { + edgeDbConfiguration: EdgeDbConfigurationProps; + secret: secretsmanager.ISecret; + securityGroup: ISecurityGroup; + }; + network: { + vpc: ec2.IVpc; + apiGatewayHttpApiId?: string; + }; + configuration: appConfigurationProps; +} + +export interface appConfigurationProps { + triggerLoadSchedule: events.Schedule; +} + +/** + * A construct wrapping an installation of EdgeDb as a service (assuming + * an existing RDS postgres). + */ +export class AppConstruct extends Construct { + constructor(scope: Construct, id: string, props: appProps) { + super(scope, id); + + // edgeDb environment to make connection the edgeDb instance + const edgeDbConnectionEnv = { + ...props.edgedDb.edgeDbConfiguration, + EDGEDB_CLIENT_TLS_SECURITY: 'insecure', + METADATA_MANAGER_EDGEDB_SECRET_NAME: props.edgedDb.secret.secretName, + }; + + // Lambda would need to access Secret Manager to retrieve edgeDb password + // thus need an outbound traffic from SG to secret manager + const outboundSG = new ec2.SecurityGroup(this, 'OutboundSecurityGroup', { + vpc: props.network.vpc, + allowAllOutbound: true, + description: + 'Security group that allows the app service to reach out over the network (e.g. secret manager)', + }); + + // There are 2 lambdas for this app + // 1. To handle API calls (inc graphql endpoint) + // 2. To sync db with external sources (e.g. metadata in gsheet) + + // (1) Lambda that handles API queries + const apiLambda = new lambda.DockerImageFunction(this, 'APILambda', { + description: 'handles API query for Metadata Manager in OrcaBus', + code: lambda.DockerImageCode.fromImageAsset(path.join(__dirname, '../../../'), { + file: 'deploy/construct/app/Dockerfile', + exclude: ['deploy/cdk.out', 'deploy/asset', '.yarn'], + cmd: ['src/handler/server.handler'], + buildArgs: { + AWS_ACCESS_KEY_ID: process.env.AWS_ACCESS_KEY_ID ?? '', + AWS_SECRET_ACCESS_KEY: process.env.AWS_SECRET_ACCESS_KEY ?? '', + AWS_SESSION_TOKEN: process.env.AWS_SESSION_TOKEN ?? '', + }, + }), + architecture: lambda.Architecture.ARM_64, + timeout: Duration.minutes(15), + environment: { ...edgeDbConnectionEnv }, + securityGroups: [props.edgedDb.securityGroup, outboundSG], + vpc: props.network.vpc, + }); + + // (2) Lambda that handles updates + const trackingSheetCredSSM = ssm.StringParameter.fromSecureStringParameterAttributes( + this, + 'GSheetCredSSM', + { parameterName: '/umccr/google/drive/lims_service_account_json' } + ); + const trackingSheetIdSSM = ssm.StringParameter.fromSecureStringParameterAttributes( + this, + 'TrackingSheetIdSSM', + { parameterName: '/umccr/google/drive/tracking_sheet_id' } + ); + + const loaderLambda = new lambda.DockerImageFunction(this, 'loaderLambda', { + description: 'handles loading metadata to the Metadata Manager', + code: lambda.DockerImageCode.fromImageAsset(path.join(__dirname, '../../../'), { + file: 'deploy/construct/app/Dockerfile', + exclude: ['deploy/cdk.out', 'deploy/asset', '.yarn'], + cmd: ['src/handler/sync.handler'], + buildArgs: { + AWS_ACCESS_KEY_ID: process.env.AWS_ACCESS_KEY_ID ?? '', + AWS_SECRET_ACCESS_KEY: process.env.AWS_SECRET_ACCESS_KEY ?? '', + AWS_SESSION_TOKEN: process.env.AWS_SESSION_TOKEN ?? '', + }, + }), + architecture: lambda.Architecture.ARM_64, + timeout: Duration.seconds(300), + environment: { + ...edgeDbConnectionEnv, + GDRIVE_SERVICE_ACCOUNT_PARAMETER_NAME: trackingSheetCredSSM.parameterName, + TRACKING_SHEET_ID_PARAMETER_NAME: trackingSheetIdSSM.parameterName, + }, + securityGroups: [props.edgedDb.securityGroup, outboundSG], + vpc: props.network.vpc, + }); + // Lambda loader need to able to access parameter store that save google credentials + trackingSheetCredSSM.grantRead(loaderLambda); + trackingSheetIdSSM.grantRead(loaderLambda); + + // The lambda ideally will be on a scheduled interval + new events.Rule(this, 'AutoSyncLambdaRule', { + description: 'this rule is to trigger the metadata load', + schedule: props.configuration.triggerLoadSchedule, + targets: [new targets.LambdaFunction(loaderLambda)], + }); + + // Both lambda would need access for edgeDb password secret for the connection + props.edgedDb.secret.grantRead(apiLambda); + props.edgedDb.secret.grantRead(loaderLambda); + + // The API lambda will have integration with an API Gateway + const metadataApiLambdaIntegration = new HttpLambdaIntegration( + 'metadataManagerApiIntegration', + apiLambda + ); + + if (props.network.apiGatewayHttpApiId) { + throw new Error('Not yet implemented'); + + // Ref: Possible solution is to use HttpRoute, but need to test compatibility + // https://github.com/aws/aws-cdk/issues/12337#issuecomment-991092668 + + // const httpApi = HttpApi.fromHttpApiAttributes(this, 'MetadataManagerOrcabusHttpApi', { + // httpApiId: props.network.apiGatewayHttpApiId, + // }); + + // new HttpRoute(this, id, { + // httpApi: httpApi, + // integration: metadataApiLambdaIntegration, + // routeKey: HttpRouteKey.with('/{proxy+}'), + // }); + } else { + const httpApi = new HttpApi(this, 'MetadataManagerHttpApi', { + corsPreflight: { + allowHeaders: ['Authorization'], + allowMethods: [ + CorsHttpMethod.GET, + CorsHttpMethod.HEAD, + CorsHttpMethod.OPTIONS, + CorsHttpMethod.POST, + ], + allowOrigins: ['*'], // TODO to get this allowed origins from config constant + maxAge: Duration.days(10), + }, + description: 'API for orcabus metadata manager lambda', + }); + httpApi.addRoutes({ + integration: metadataApiLambdaIntegration, + path: '/{proxy+}', + methods: [HttpMethod.ANY], + }); + } + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/Dockerfile b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/Dockerfile new file mode 100644 index 000000000..ceb8fa6c4 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/Dockerfile @@ -0,0 +1,8 @@ +ARG EDGEDB_VERSION + +FROM edgedb/edgedb:${EDGEDB_VERSION} + +# Copy dbschema which contain the migrations to the image +# Migrations will automatically applied +# Ref: https://www.edgedb.com/docs/guides/deployment/docker#schema-migrations +COPY dbschema/ ./dbschema/ diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-construct.ts b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-construct.ts new file mode 100644 index 000000000..1223ee08d --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-construct.ts @@ -0,0 +1,105 @@ +import { aws_ec2 as ec2, aws_secretsmanager as secretsmanager } from 'aws-cdk-lib'; +import { Construct } from 'constructs'; +import { EdgeDbServiceConstruct, EdgeDbServicePassthroughProps } from './edge-db-service-construct'; +import { + EdgeDbLoadBalancerProtocolConstruct, + EdgeDbLoadBalancerProtocolPassthroughProps, +} from './edge-db-load-balancer-protocol-construct'; +import { ISecret } from 'aws-cdk-lib/aws-secretsmanager'; +import { ISecurityGroup } from 'aws-cdk-lib/aws-ec2'; + +export interface EdgeDbProps { + // a prefix that is used for constructing AWS secrets for edgedb + secretsPrefix: string; + + // purely for information/descriptive purposes - the friendly short name of + // the RDS instance we are wrapping + rdsDatabaseDisplayName: string; + + // the underlying network infrastructure that has already + // been set up and that we will be installing into + vpc: ec2.IVpc; + + // the configuration of the fargate service that is edge db itself + edgeDbService: EdgeDbServicePassthroughProps; + + // the configuration of the internal network load balancer that provides EdgeDb protocol access + edgeDbLoadBalancerProtocol: EdgeDbLoadBalancerProtocolPassthroughProps; +} + +export interface EdgeDbConfigurationProps { + EDGEDB_HOST: string; + EDGEDB_PORT: string; + EDGEDB_USER: string; + EDGEDB_DATABASE: string; +} + +/** + * A construct wrapping an installation of EdgeDb as a service (assuming + * an existing RDS postgres). + */ +export class EdgeDbConstruct extends Construct { + private readonly _edgeDbPasswordSecret: ISecret; + private readonly _edgeDbSecurityGroup: ISecurityGroup; + + private readonly host: string; + private readonly port: string; + private readonly user: string; + private readonly dbName: string; + + constructor(scope: Construct, id: string, props: EdgeDbProps) { + super(scope, id); + + this.user = props.edgeDbService.superUser; + this.dbName = props.edgeDbService.databaseName; + this.port = `${props.edgeDbLoadBalancerProtocol.tcpPassthroughPort ?? 5656}`; + + // create a new secret for our edge db database with an autogenerated password + this._edgeDbPasswordSecret = new secretsmanager.Secret(this, 'EdgeDbSecret', { + description: `For database ${props.rdsDatabaseDisplayName} - secret containing EdgeDb super user password`, + secretName: `${props.secretsPrefix}EdgeDb`, + generateSecretString: { + excludePunctuation: true, + }, + }); + + const edgeDbService = new EdgeDbServiceConstruct(this, 'EdgeDbService', { + ...props.edgeDbService, + vpc: props.vpc, + superUserSecret: this._edgeDbPasswordSecret, + }); + + this._edgeDbSecurityGroup = edgeDbService.securityGroup; + + const edgeDbLoadBalancer = new EdgeDbLoadBalancerProtocolConstruct( + this, + 'EdgeDbLoadBalancerProtocol', + { + vpc: props.vpc, + service: edgeDbService.service, + servicePort: edgeDbService.servicePort, + serviceSecurityGroup: edgeDbService.securityGroup, + ...props.edgeDbLoadBalancerProtocol, + } + ); + + this.host = edgeDbLoadBalancer.dnsName; + } + + public get edgeDbConnectionVariable(): EdgeDbConfigurationProps { + return { + EDGEDB_HOST: this.host, + EDGEDB_PORT: this.port, + EDGEDB_USER: this.user, + EDGEDB_DATABASE: this.dbName, + }; + } + + public get passwordSecret(): ISecret { + return this._edgeDbPasswordSecret; + } + + public get securityGroup(): ISecurityGroup { + return this._edgeDbSecurityGroup; + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-load-balancer-protocol-construct.ts b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-load-balancer-protocol-construct.ts new file mode 100644 index 000000000..dce4c9d1e --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-load-balancer-protocol-construct.ts @@ -0,0 +1,102 @@ +import { aws_ec2 as ec2, Duration } from 'aws-cdk-lib'; +import { Construct } from 'constructs'; +import { FargateService } from 'aws-cdk-lib/aws-ecs'; +import { + CfnLoadBalancer, + NetworkLoadBalancer, + Protocol, +} from 'aws-cdk-lib/aws-elasticloadbalancingv2'; +import { ISecurityGroup, SecurityGroup, SubnetType } from 'aws-cdk-lib/aws-ec2'; + +export type EdgeDbLoadBalancerProtocolPassthroughProps = { + // the port that the load balancer will listen on for TCP pass through work - this is the normal + // way for interacting with EdgeDb (i.e. edgedb:// protocol) + tcpPassthroughPort: number; +}; + +type Props = EdgeDbLoadBalancerProtocolPassthroughProps & { + // the VPC that the load balancer back side will live in + vpc: ec2.IVpc; + + // the service we will balance to + service: FargateService; + + // the service port we will balance to + servicePort: number; + + // the security group we need to place the NLB in to access the service + serviceSecurityGroup: ISecurityGroup; +}; + +/** + * A network load balancer that can sit in front of a Fargate EdgeDb service + * and provides direct protocol access. + * https://www.edgedb.com/docs/reference/protocol/index + */ +export class EdgeDbLoadBalancerProtocolConstruct extends Construct { + private readonly _lb: NetworkLoadBalancer; + + constructor(scope: Construct, id: string, props: Props) { + super(scope, id); + + this._lb = new NetworkLoadBalancer(this, 'LoadBalancer', { + vpc: props.vpc, + vpcSubnets: { + subnetType: SubnetType.PRIVATE_WITH_EGRESS, + }, + // the edgeDb can only be accessed internally for protocol access + internetFacing: false, + }); + + const nlbSecurityGroup = new SecurityGroup(this, 'LbProtocolSecurityGroup', { + vpc: props.vpc, + allowAllOutbound: false, + allowAllIpv6Outbound: false, + description: + 'Security group of the NLB (EdgeDb protocol) allowing egress to the EdgeDb service on its port', + }); + nlbSecurityGroup.addEgressRule(props.serviceSecurityGroup, ec2.Port.tcp(props.servicePort)); + + // NLBs now have security groups - but not in CDK yet - this is a workaround - Aug 2023 + // review at some point and replace this with proper CDK usage + const cfnLb = this._lb.node.defaultChild as CfnLoadBalancer; + cfnLb.addPropertyOverride('SecurityGroups', [ + nlbSecurityGroup.securityGroupId, + props.serviceSecurityGroup.securityGroupId, + ]); + + // note for protocol access the NLB does not do *any* TLS handling itself + // it just passes connection through directly + const tcpListener = this._lb.addListener('TcpListener', { + port: props.tcpPassthroughPort, + protocol: Protocol.TCP, + }); + + const tg = tcpListener.addTargets('TcpTargetGroup', { + port: props.servicePort, + protocol: Protocol.TCP, + targets: [props.service], + // the assumption is our code/db will handle reasonably quick shutdown of the + // service and just abort transactions etc (I mean, that's what a database is for) + deregistrationDelay: Duration.seconds(15), + }); + // whilst all the IPs hitting us will be internal IPs - we prefer to be logging the actual IPs + // of the client rather than the NLB interface IPs + tg.setAttribute('preserve_client_ip.enabled', 'true'); + tg.configureHealthCheck({ + enabled: true, + interval: Duration.seconds(10), + timeout: Duration.seconds(5), + healthyThresholdCount: 2, + unhealthyThresholdCount: 2, + }); + } + + public get loadBalancer(): NetworkLoadBalancer { + return this._lb; + } + + public get dnsName(): string { + return this._lb.loadBalancerDnsName; + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-service-construct.ts b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-service-construct.ts new file mode 100644 index 000000000..f7cd89c03 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/edge-db/edge-db-service-construct.ts @@ -0,0 +1,219 @@ +import { + aws_ec2 as ec2, + aws_ecs as ecs, + aws_iam as iam, + aws_logs as logs, + Duration, +} from 'aws-cdk-lib'; +import * as path from 'path'; +import { Construct } from 'constructs'; +import { + CpuArchitecture, + FargateService, + FargateTaskDefinition, + LogDrivers, + OperatingSystemFamily, + Protocol, +} from 'aws-cdk-lib/aws-ecs'; +import { ISecret } from 'aws-cdk-lib/aws-secretsmanager'; +import { ISecurityGroup, IVpc, SecurityGroup } from 'aws-cdk-lib/aws-ec2'; + +/** + * A collection of props that are set in the highest level EdgeDb construct + * but which are then passed through to this construct. + */ +export type EdgeDbServicePassthroughProps = { + // the DSN of the Postgres db it will use for its store (the DSN must include base db user/pw) + postgresDsn: string; + postgresSecurityGroup: ISecurityGroup; + + // the settings for containers of the service + desiredCount: number; + cpu: number; + memory: number; + superUser: string; + databaseName: string; + + // edge db version string for the docker image used for edge db e.g. "3.4" + edgeDbVersion: string; + + // if present and true, enable the EdgeDb feature flag to switch on the UI + // NOTE there are other settings that need to be true for the UI to actually be on the internet! + enableUiFeatureFlag?: boolean; +}; + +/** + * An augmenting of the high level pass through props with other + * settings we have created on the way. + */ +type EdgeDbServiceProps = EdgeDbServicePassthroughProps & { + // the VPC that the service will live in + vpc: ec2.IVpc; + + // the secret holding the EdgeDb superuser password + superUserSecret: ISecret; +}; + +/** + * The EdgeDb service is a Fargate task cluster running the EdgeDb + * Docker image and pointing to an existing Postgres database. + * + * The service is set up to use self-signed certs assuming + * - network load balancer will sit in front of it and that NLB will deal with TLS termination + * - a client will connect and the client will ignore certs + */ +export class EdgeDbServiceConstruct extends Construct { + // this construct is predicated on using the default EdgeDb port + // so if you want to change this then you'll have to add some extra PORT settings in various places + private readonly EDGE_DB_PORT = 5656; + + private readonly _service: FargateService; + private readonly _securityGroup: SecurityGroup; + + constructor(scope: Construct, id: string, props: EdgeDbServiceProps) { + super(scope, id); + + const cluster = new ecs.Cluster(this, 'Cluster', { + vpc: props.vpc, + }); + + const executionRole = new iam.Role(this, 'ExecutionRole', { + assumedBy: new iam.ServicePrincipal('ecs-tasks.amazonaws.com'), + managedPolicies: [ + iam.ManagedPolicy.fromAwsManagedPolicyName('service-role/AmazonECSTaskExecutionRolePolicy'), + ], + }); + + const clusterLogGroup = new logs.LogGroup(this, 'ServiceLog', { + retention: logs.RetentionDays.ONE_WEEK, + }); + + // we do the task definition by hand as we have some specialised settings (ARM64 etc) + const taskDefinition = new FargateTaskDefinition(this, 'TaskDefinition', { + runtimePlatform: { + operatingSystemFamily: OperatingSystemFamily.LINUX, + cpuArchitecture: CpuArchitecture.ARM64, + }, + memoryLimitMiB: props.memory, + cpu: props.cpu, + executionRole: executionRole, + family: 'orcabus-metadata-manager-edge-db', + }); + + const containerName = 'edge-db'; + + const env: { [k: string]: string } = { + EDGEDB_DOCKER_LOG_LEVEL: 'debug', + // the DSN (including postgres user/pw) pointing to the base database + EDGEDB_SERVER_BACKEND_DSN: props.postgresDsn, + // we allow the superuser name to be set + EDGEDB_SERVER_USER: props.superUser, + // we don't do edgedb certs at all - rely on self-signed always + // when putting a TLS terminated network load balancer in front of this - we can + // use a self-signed cert as the internal target TLS + // NLBs are comfortable using self-signed certs purely for traffic encryption + // https://kevin.burke.dev/kevin/aws-alb-validation-tls-reply/ + // that way we can avoid needing to manage custom certs/cas + EDGEDB_SERVER_TLS_CERT_MODE: 'generate_self_signed', + EDGEDB_DATABASE: props.databaseName, + // DO NOT ENABLE + // EDGEDB_SERVER_DEFAULT_AUTH_METHOD: "Trust" + }; + + const secrets: { [k: string]: ecs.Secret } = { + // CDK is smart enough to grant permissions to read these secrets to the execution role + EDGEDB_SERVER_PASSWORD: ecs.Secret.fromSecretsManager(props.superUserSecret), + }; + + taskDefinition.addContainer(containerName, { + image: ecs.ContainerImage.fromAsset(path.join(__dirname, '../../../'), { + file: 'deploy/construct/edge-db/Dockerfile', + exclude: ['deploy/cdk.out', 'deploy/asset', '.yarn'], + buildArgs: { + EDGEDB_VERSION: props.edgeDbVersion, + }, + }), + environment: env, + secrets: secrets, + logging: LogDrivers.awsLogs({ + streamPrefix: 'edge-db', + logGroup: clusterLogGroup, + }), + portMappings: [ + { + containerPort: this.EDGE_DB_PORT, + protocol: Protocol.TCP, + }, + ], + }); + + // the membership security group is a group that defines who is allowed to connect to the EdgeDb + this._securityGroup = this.createMembershipSecurityGroup(props.vpc); + + this._service = new FargateService(this, 'Service', { + // even in dev mode we never want to assign public ips to the fargate service... + // we *ALWAYS* want to access via network load balancer - and that NLB can either be internal or external + assignPublicIp: false, + cluster: cluster, + desiredCount: props.desiredCount, + taskDefinition: taskDefinition, + vpcSubnets: { + // we need egress in order to fetch images?? if we setup with private link maybe avoid? one to investigate? + // again - we are *always* putting the service containers in private - it is our network load balancer + // that can live in public/private + subnetType: ec2.SubnetType.PRIVATE_WITH_EGRESS, + }, + // in practice an EdgeDb startup (from logs) went (timestamps) + // from 10:03:17 + // to 10:03:26 + // i.e. 10 seconds - so allocating 30 seconds to be safe + healthCheckGracePeriod: Duration.seconds(30), + securityGroups: [ + // a security group that allows the EdgeDb to reach the world + new ec2.SecurityGroup(this, 'EgressSecurityGroup', { + vpc: props.vpc, + allowAllOutbound: true, + description: + 'Security group that allows the EdgeDb service to reach out over the network', + }), + // a security group allowing access from the internal IPs (needed for the NLBs) + this._securityGroup, + // a security group that the service needs that gives it the "ability to connect to RDS" + props.postgresSecurityGroup, + ], + }); + } + + private createMembershipSecurityGroup(vpc: IVpc) { + const sg = new SecurityGroup(this, 'MembershipSecurityGroup', { + vpc: vpc, + // databases don't use outbound traffic via a security group unless you are getting them to reach + // out via a stored procedure or something + allowAllOutbound: false, + allowAllIpv6Outbound: false, + description: + 'Security group for resources that can communicate to the contained EdgeDb service', + }); + // the ingress is self-referential - only allowing traffic from itself to the edge port + sg.addIngressRule(sg, ec2.Port.tcp(this.EDGE_DB_PORT)); + // the egress is also self-referential - and allowing outbound traffic to anyone in the same + // group (the all-traffic is safe because the other resources are responsible for setting their + // ingress rules to a set port0 + + sg.addIngressRule(sg, ec2.Port.tcp(80)); + sg.addEgressRule(sg, ec2.Port.allTraffic()); + return sg; + } + + public get service(): FargateService { + return this._service; + } + + public get securityGroup(): ISecurityGroup { + return this._securityGroup; + } + + public get servicePort(): number { + return this.EDGE_DB_PORT; + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/base-database.ts b/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/base-database.ts new file mode 100644 index 000000000..8ba1abede --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/base-database.ts @@ -0,0 +1,64 @@ +import { Construct } from 'constructs'; +import { ISecurityGroup, IVpc, SecurityGroup } from 'aws-cdk-lib/aws-ec2'; +import { aws_ec2 as ec2 } from 'aws-cdk-lib'; +import { ManagedPolicy, Role, ServicePrincipal } from 'aws-cdk-lib/aws-iam'; + +/** + * An abstract concept that helps us wrap the CDK concepts of + * a RDS instance v a RDS cluster v RDS serverless - which + * are all _basically_ the same from our perspective but are + * different enough types in CDK that it is annoying. + */ +export abstract class BaseDatabase extends Construct { + protected constructor(scope: Construct, id: string) { + super(scope, id); + } + + protected createMonitoringRole() { + const monitoringRole = new Role(this, 'DatabaseMonitoringRole', { + assumedBy: new ServicePrincipal('monitoring.rds.amazonaws.com'), + }); + monitoringRole.addManagedPolicy( + ManagedPolicy.fromAwsManagedPolicyName('service-role/AmazonRDSEnhancedMonitoringRole') + ); + return monitoringRole; + } + + protected createMembershipSecurityGroup(vpc: IVpc) { + return new SecurityGroup(this, 'MembershipSecurityGroup', { + vpc: vpc, + // databases don't use outbound traffic via a security group unless you are getting them to reach + // out via a stored procedure or something + allowAllOutbound: false, + allowAllIpv6Outbound: false, + description: + 'Security group for resources that can communicate to the contained RDS instance', + }); + } + + /** + * To the security group apply ingress rules giving access to the database + * (either from the public or from the security group itself) + * + * @param securityGroup + * @param databasePort + * @protected + */ + protected applySecurityGroupRules(securityGroup: ISecurityGroup, databasePort: number) { + securityGroup.addIngressRule(securityGroup, ec2.Port.tcp(databasePort)); + // our membership security group allows outgoing access to things in the SAME SECURITY GROUP + // (we use allTraffic safely for egress here - as those other services will be responsible + // for protected their incoming ports with their own ingress rules) + securityGroup.addEgressRule(securityGroup, ec2.Port.allTraffic()); + } + + public abstract get dsnWithTokens(): string; + + public abstract get dsnNoPassword(): string; + + public abstract get hostname(): string; + + public abstract get port(): number; + + public abstract get securityGroup(): ISecurityGroup; +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/infrastructure-stack-database-props.ts b/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/infrastructure-stack-database-props.ts new file mode 100644 index 000000000..7b414208e --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/infrastructure-stack-database-props.ts @@ -0,0 +1,92 @@ +import { Duration } from 'aws-cdk-lib'; + +// NOTE: this was all set up with some nice typescript types - that separated +// out different postgres settings.. unfortunately - those types are not compatible +// with JSII, so we have had to merge all the fields into one mega Common type. +// Basically this is now all a bit yuck but is necessary to support languages other +// than typescript + +export interface PostgresCommon { + /** + * The name of the database to create + */ + readonly name: string; + + /** + * The name of the admin user to create in the database + */ + readonly adminUser: string; + + /** + * If set will override the allocated storage for the db - otherwise + * we will have this set to smallest database size allowed (20 Gib) + */ + readonly overrideAllocatedStorage?: number; + + /** + * If present switches on monitoring features such as postgres + * logs exported to cloudwatch and performance insights. + */ + readonly enableMonitoring?: PostgresCommonMonitoring; + + // ------------- + // Settings below are only for serverless Postgres + // ------------- + + /** + * The minimum number of ACU - or default to the minimum of 0.5 + */ + readonly minCapacity?: number; + + /** + * The maximum number of ACU - or default to a sensible 4 + */ + readonly maxCapacity?: number; +} + +export interface PostgresCommonMonitoring { + readonly cloudwatchLogsExports: string[]; + readonly enablePerformanceInsights: boolean; + readonly monitoringInterval: Duration; +} + +/** + * Settings that instruct us to connect an EdgeDb + * in front of the given postgres instance + */ +export interface EdgeDbCommon { + /** + * The version string of EdgeDb that will be used for the spun up EdgeDb image + */ + readonly version: string; + + /** + * The memory assigned to the Edge Db service - defaults to a sensible value + */ + readonly memoryLimitMiB?: number; + + /** + * The cpu assigned to the Edge Db service - defaults to a sensible value + */ + readonly cpu?: number; + + /** + * The port number to assign for EdgeDb protocol - defaults to 5656 which + * is what is assumed for edgedb connections + */ + readonly dbPort?: number; +} + +export interface EdgeDbPublic { + /** + * the DNS prefix to expose the EdgeDb UI as + */ + readonly urlPrefix: string; + + /** + * The port number to assign for UI access - defaults to 443. Whilst 443 is + * entirely sensible - I guess you could add a level of security obscurity by + * mapping this to another port. + */ + readonly uiPort?: number; +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/postgres-db-construct.ts b/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/postgres-db-construct.ts new file mode 100644 index 000000000..0207d5cd6 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/construct/postgres-rds/postgres-db-construct.ts @@ -0,0 +1,122 @@ +import { ISecurityGroup, IVpc, SecurityGroup } from 'aws-cdk-lib/aws-ec2'; +import { ISecret } from 'aws-cdk-lib/aws-secretsmanager'; +import { ServerlessCluster } from 'aws-cdk-lib/aws-rds'; +import { Construct } from 'constructs'; +import { aws_ec2 as ec2, aws_rds as rds, RemovalPolicy } from 'aws-cdk-lib'; +import { BaseDatabase } from './base-database'; +import { PostgresCommon } from './infrastructure-stack-database-props'; + +type ServerlessBaseDatabaseProps = PostgresCommon & { + vpc: IVpc; + + databaseName: string; + + secret: ISecret; +}; + +/** + * A construct representing the base database we might use with EdgeDb - in this + * case representing a V2 Serverless Aurora (in postgres mode). + */ +export class ServerlessBaseDatabase extends BaseDatabase { + private readonly _cluster: ServerlessCluster; + private readonly _securityGroup: SecurityGroup; + private readonly _dsnWithTokens: string; + private readonly _dsnNoPassword: string; + + constructor(scope: Construct, id: string, props: ServerlessBaseDatabaseProps) { + super(scope, id); + + // we create a security group and export its id - so we can use that as a security boundary + // for services that "can connect to database" + this._securityGroup = this.createMembershipSecurityGroup(props.vpc); + + this._cluster = new ServerlessCluster(this, 'ServerlessCluster', { + vpc: props.vpc, + securityGroups: [this._securityGroup], + vpcSubnets: { + subnetType: ec2.SubnetType.PRIVATE_WITH_EGRESS, + }, + engine: rds.DatabaseClusterEngine.auroraPostgres({ + version: rds.AuroraPostgresEngineVersion.VER_14_7, + }), + // the default database to create in the cluster - we insist on it being named otherwise no default db is made + defaultDatabaseName: props.databaseName, + credentials: rds.Credentials.fromSecret(props.secret), + // The Db should come from orcaBus master, and if the Db is from this service, it is supposed to be for dev which + // should removed on destroy + removalPolicy: RemovalPolicy.DESTROY, + }); + + // temporary fix to broken CDK constructs + // https://github.com/aws/aws-cdk/issues/20197#issuecomment-1272360016 + { + const cfnDBCluster = this._cluster.node.children.find( + (node) => node instanceof rds.CfnDBCluster + ) as rds.CfnDBCluster; + cfnDBCluster.serverlessV2ScalingConfiguration = { + minCapacity: props.minCapacity ?? 0.5, + maxCapacity: props.maxCapacity ?? rds.AuroraCapacityUnit.ACU_4, + }; + cfnDBCluster.engineMode = undefined; + } + + let enableMonitoring; + if (props.enableMonitoring) { + const monitoringRole = this.createMonitoringRole(); + + enableMonitoring = { + enablePerformanceInsights: props.enableMonitoring.enablePerformanceInsights, + cloudwatchLogsExports: props.enableMonitoring.cloudwatchLogsExports, + monitoringInterval: props.enableMonitoring.monitoringInterval.toSeconds(), + monitoringRoleArn: monitoringRole.roleArn, + }; + } + + new rds.CfnDBInstance(this, 'Writer', { + dbInstanceClass: 'db.serverless', + dbClusterIdentifier: this._cluster.clusterIdentifier, + engine: 'aurora-postgresql', + publiclyAccessible: false, + ...(enableMonitoring && { ...enableMonitoring }), + }); + + this.applySecurityGroupRules(this._securityGroup, this._cluster.clusterEndpoint.port); + + this._dsnWithTokens = + `postgres://` + + `${props.secret.secretValueFromJson('username').unsafeUnwrap()}` + + `:` + + `${props.secret.secretValueFromJson('password').unsafeUnwrap()}` + + `@` + + `${this._cluster.clusterEndpoint.hostname}` + + `:` + + `${this._cluster.clusterEndpoint.port}` + + `/` + + `${props.databaseName}`; + + this._dsnNoPassword = + `postgres://` + + `${props.adminUser}@${this._cluster.clusterEndpoint.hostname}:${this._cluster.clusterEndpoint.port}/${props.databaseName}`; + } + + public get dsnWithTokens(): string { + return this._dsnWithTokens; + } + + public get dsnNoPassword(): string { + return this._dsnNoPassword; + } + + public get hostname(): string { + return this._cluster.clusterEndpoint.hostname; + } + + public get port(): number { + return this._cluster.clusterEndpoint.port; + } + + public get securityGroup(): ISecurityGroup { + return this._securityGroup; + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/jest.config.js b/lib/workload/stateless/metadata_manager/src/deploy/jest.config.js new file mode 100644 index 000000000..44ead8540 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/jest.config.js @@ -0,0 +1,8 @@ +module.exports = { + testEnvironment: 'node', + roots: ['/test'], + testMatch: ['**/*.test.ts'], + transform: { + '^.+\\.tsx?$': 'ts-jest', + }, +}; diff --git a/lib/workload/stateless/metadata_manager/src/deploy/lib/metadataManagerStack.ts b/lib/workload/stateless/metadata_manager/src/deploy/lib/metadataManagerStack.ts new file mode 100644 index 000000000..81f700941 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/lib/metadataManagerStack.ts @@ -0,0 +1,105 @@ +import { Stack, StackProps, aws_ec2 as ec2 } from 'aws-cdk-lib'; +import { Construct } from 'constructs'; +import { EdgeDbConstruct } from '../construct/edge-db/edge-db-construct'; +import { Vpc } from 'aws-cdk-lib/aws-ec2'; +import { Secret } from 'aws-cdk-lib/aws-secretsmanager'; +import { ServerlessBaseDatabase } from '../construct/postgres-rds/postgres-db-construct'; +import { PostgresCommon } from '../construct/postgres-rds/infrastructure-stack-database-props'; +import { AppConstruct, appConfigurationProps } from '../construct/app/app-construct'; + +export interface EdgeDbCommon { + secretPrefix: string; + /** + * The version string of EdgeDb that will be used for the spun up EdgeDb image + */ + readonly version: string; + + /** + * The memory assigned to the Edge Db service - defaults to a sensible value + */ + readonly memoryLimitMiB?: number; + + /** + * The cpu assigned to the Edge Db service - defaults to a sensible value + */ + readonly cpu?: number; + + /** + * The port number to assign for EdgeDb protocol - defaults to 5656 which + * is what is assumed for edgedb connections + */ + readonly dbPort?: number; +} + +export interface MetadataManagerStackProps extends StackProps { + database: PostgresCommon; + edgeDb: EdgeDbCommon; + network: { + vpcName: string; + }; + appConfiguration: appConfigurationProps; +} + +export class MetadataManagerStack extends Stack { + constructor(scope: Construct, id: string, props: MetadataManagerStackProps) { + super(scope, id, props); + + const vpc = Vpc.fromLookup(this, 'mainVpc', { vpcName: props.network.vpcName }); + + // create a new secret for our base database with an autogenerated password + const postgresSecret = new Secret(this, `Secret`, { + description: `For database ${props.database.name} - secret containing RDS details such as admin username and password`, + generateSecretString: { + excludePunctuation: true, + secretStringTemplate: JSON.stringify({ + username: props.database.adminUser, + password: '', + }), + generateStringKey: 'password', + }, + }); + const postgresDb = new ServerlessBaseDatabase(this, 'metadataManagerRds', { + vpc: vpc, + databaseName: props.database.name, + secret: postgresSecret, + ...props.database, + }); + + /** + * Create EdgeDb server + */ + const edgeDb = new EdgeDbConstruct(this, `EdgeDb`, { + vpc: vpc, + rdsDatabaseDisplayName: props.database.name, + secretsPrefix: props.edgeDb.secretPrefix, + edgeDbService: { + // Postgres Config + postgresDsn: postgresDb.dsnWithTokens, + postgresSecurityGroup: postgresDb.securityGroup, + + // edge db Config + databaseName: 'orcabus', + superUser: 'orcabus_superuser', + edgeDbVersion: props.edgeDb.version, + desiredCount: 1, + cpu: props.edgeDb.cpu ?? 1024, + memory: props.edgeDb.memoryLimitMiB ?? 2048, + }, + edgeDbLoadBalancerProtocol: { + tcpPassthroughPort: props.edgeDb.dbPort || 5656, + }, + }); + + new AppConstruct(this, 'app', { + edgedDb: { + edgeDbConfiguration: edgeDb.edgeDbConnectionVariable, + secret: edgeDb.passwordSecret, + securityGroup: edgeDb.securityGroup, + }, + network: { + vpc: vpc, + }, + configuration: props.appConfiguration, + }); + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/package-lock.json b/lib/workload/stateless/metadata_manager/src/deploy/package-lock.json new file mode 100644 index 000000000..df2e597f6 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/package-lock.json @@ -0,0 +1,7466 @@ +{ + "name": "deploy", + 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"constructs": "^10.0.0", + "source-map-support": "^0.5.21" + } +} diff --git a/lib/workload/stateless/metadata_manager/src/deploy/test/deploy.test.ts b/lib/workload/stateless/metadata_manager/src/deploy/test/deploy.test.ts new file mode 100644 index 000000000..c40ef8289 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/test/deploy.test.ts @@ -0,0 +1,16 @@ +// import * as cdk from 'aws-cdk-lib'; +// import { Template } from 'aws-cdk-lib/assertions'; +// import * as Deploy from '../lib/deploy-stack'; + +// example test. To run these tests, uncomment this file along with the +// example resource in lib/deploy-stack.ts +test('SQS Queue Created', () => { + // const app = new cdk.App(); + // // WHEN + // const stack = new Deploy.DeployStack(app, 'MyTestStack'); + // // THEN + // const template = Template.fromStack(stack); + // template.hasResourceProperties('AWS::SQS::Queue', { + // VisibilityTimeout: 300 + // }); +}); diff --git a/lib/workload/stateless/metadata_manager/src/deploy/tsconfig.json b/lib/workload/stateless/metadata_manager/src/deploy/tsconfig.json new file mode 100644 index 000000000..aaa7dc510 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/deploy/tsconfig.json @@ -0,0 +1,31 @@ +{ + "compilerOptions": { + "target": "ES2020", + "module": "commonjs", + "lib": [ + "es2020", + "dom" + ], + "declaration": true, + "strict": true, + "noImplicitAny": true, + "strictNullChecks": true, + "noImplicitThis": true, + "alwaysStrict": true, + "noUnusedLocals": false, + "noUnusedParameters": 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a/lib/workload/stateless/metadata_manager/src/docs/relationship.drawio.svg b/lib/workload/stateless/metadata_manager/src/docs/relationship.drawio.svg new file mode 100644 index 000000000..7da216257 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/docs/relationship.drawio.svg @@ -0,0 +1,87 @@ + + + + + + + + + + +
+
+
+ metadata::Subject +
+
+
+ + + metadata::Subject + + + + + + + +
+
+
+ metadata::Library +
+
+
+ + + metadata::Library + + + + + + + +
+
+
+ metadata::Specimen +
+
+
+ + + metadata::Specimen + + + + + + + + + + +
+
+
+ RELATIONSHIP: +
+
+
+ + + RELATIONSHIP: + + + + + + + + + Text is not SVG - cannot display + + + + \ No newline at end of file diff --git a/lib/workload/stateless/metadata_manager/src/edgedb.toml b/lib/workload/stateless/metadata_manager/src/edgedb.toml deleted file mode 100644 index 5ad3cbd21..000000000 --- a/lib/workload/stateless/metadata_manager/src/edgedb.toml +++ /dev/null @@ -1,2 +0,0 @@ -[edgedb] -server-version = "3.1" diff --git a/lib/workload/stateless/metadata_manager/src/jest.config.ts b/lib/workload/stateless/metadata_manager/src/jest.config.js similarity index 69% rename from lib/workload/stateless/metadata_manager/src/jest.config.ts rename to lib/workload/stateless/metadata_manager/src/jest.config.js index 26379f37a..c865147a9 100644 --- a/lib/workload/stateless/metadata_manager/src/jest.config.ts +++ b/lib/workload/stateless/metadata_manager/src/jest.config.js @@ -1,6 +1,5 @@ module.exports = { preset: 'ts-jest', testEnvironment: 'node', + roots: ['/tests/'], }; - -// jest.setTimeout(30000); diff --git a/lib/workload/stateless/metadata_manager/src/package.json b/lib/workload/stateless/metadata_manager/src/package.json index d15f93672..933386d33 100644 --- a/lib/workload/stateless/metadata_manager/src/package.json +++ b/lib/workload/stateless/metadata_manager/src/package.json @@ -1,34 +1,39 @@ { "name": "src", - "packageManager": "yarn@3.5.1", "scripts": { "watch": "NODE_ENV=development nodemon src/index.ts", "typecheck": "tsc -p tsconfig.json", - "init-db": "edgedb project init", - "migrate-db": "edgedb migration create || true && edgedb migrate", "start": "NODE_ENV=development ts-node src/index.ts", + "insert-scenario-1": "ts-node src/test-data/index.ts insert-scenario-1", + "insert-scenario-2": "ts-node src/test-data/index.ts insert-scenario-2", "//edgetypes": "Generates Typescript classes that match the schema of the *current* project EdgeDb", "edgetypes": "generate queries --file && generate edgeql-js && generate interfaces", - "test": "jest" + "test": "jest --config=jest.config.js", + "build-src": "NODE_OPTIONS='--max-old-space-size=8192' tsc" }, "dependencies": { - "@aws-sdk/client-ssm": "^3.382.0", + "@fastify/aws-lambda": "^3.3.0", + "@fastify/http-proxy": "^9.2.1", + "axios": "^1.5.1", "edgedb": "^1.3.4", "fastify": "^4.20.0", "google-auth-library": "^9.0.0", "google-spreadsheet": "^4.0.2", "lodash": "^4.17.21", + "pino": "^8.15.1", "pino-pretty": "^10.1.0", "reflect-metadata": "^0.1.13", "ts-node": "^10.9.1", "tsyringe": "^4.8.0", - "ulid": "^2.3.0" + "ulid": "^2.3.0", + "xlsx": "^0.18.5" }, "devDependencies": { "@edgedb/generate": "^0.3.1", "@types/jest": "^29.5.3", "@types/lodash": "^4", "@types/node": "^20.4.2", + "esbuild": "^0.19.5", "jest": "^29.6.2", "nodemon": "^3.0.1", "ts-jest": "^29.1.1", diff --git a/lib/workload/stateless/metadata_manager/src/src/api/routes/graphql-routes.ts b/lib/workload/stateless/metadata_manager/src/src/api/routes/graphql-routes.ts new file mode 100644 index 000000000..1627ca1c8 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/api/routes/graphql-routes.ts @@ -0,0 +1,43 @@ +import { FastifyInstance, FastifyRequest } from 'fastify'; +import { fastifyHttpProxy } from '@fastify/http-proxy'; + +export const gqlRoutes = async (fastify: FastifyInstance) => { + const graphQLEndpoint = + `https://` + + `${process.env.EDGEDB_HOST ?? 'localhost'}` + + `:` + + `${process.env.EDGEDB_PORT ?? 5656}` + + `/db/` + + `${process.env.EDGEDB_DATABASE ?? 'edgedb'}` + + `/graphql`; + + fastify.register(fastifyHttpProxy, { + prefix: '/explore', + upstream: `${graphQLEndpoint}/explore`, + httpMethods: ['GET'], + proxyPayloads: false, + preHandler: async (request: FastifyRequest) => { + // It seems that fastify don't like if content-length == 0 while the body is undefined + // (despite of a GET request) and load-balancer/API-Gateway adds this automatically + // So, removing the 'content-length' to resolve this + if (request.headers['content-length']) { + delete request.headers['content-length']; + } + }, + }); + + fastify.register(fastifyHttpProxy, { + upstream: graphQLEndpoint, + httpMethods: ['POST'], + proxyPayloads: false, + preHandler: async (request: FastifyRequest, reply) => { + // We wanted to reject any kind of mutation via the GraphQL endpoint + const body = request.body as Record | undefined; + if (body.query?.includes('mutation')) { + reply + .code(400) + .send({ message: 'mutation is not supported through this graphql endpoint' }); + } + }, + }); +}; diff --git a/lib/workload/stateless/metadata_manager/src/src/api/routes/internal-routes.ts b/lib/workload/stateless/metadata_manager/src/src/api/routes/internal-routes.ts index 7e710428a..31b47e7fa 100644 --- a/lib/workload/stateless/metadata_manager/src/src/api/routes/internal-routes.ts +++ b/lib/workload/stateless/metadata_manager/src/src/api/routes/internal-routes.ts @@ -1,13 +1,22 @@ import { FastifyInstance } from 'fastify'; import { DependencyContainer } from 'tsyringe'; +import { MetadataService } from '../../service/metadata'; export const internalRoutes = async ( fastify: FastifyInstance, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - _opts: { container: DependencyContainer } + opts: { container: DependencyContainer } ) => { - // eslint-disable-next-line @typescript-eslint/no-unused-vars - fastify.get('/hello', async (request, reply) => { - return 'Hello World!\n'; + const metadataService = opts.container.resolve(MetadataService); + + fastify.get('/library', async () => { + return metadataService.getAllLibrary(); + }); + + fastify.get('/specimen', async () => { + return metadataService.getAllSpecimen(); + }); + + fastify.get('/subject', async () => { + return metadataService.getAllSubject(); }); }; diff --git a/lib/workload/stateless/metadata_manager/src/src/app.ts b/lib/workload/stateless/metadata_manager/src/src/app.ts index bfb215671..764ef66c0 100644 --- a/lib/workload/stateless/metadata_manager/src/src/app.ts +++ b/lib/workload/stateless/metadata_manager/src/src/app.ts @@ -1,9 +1,7 @@ import Fastify, { FastifyBaseLogger, FastifyInstance } from 'fastify'; -import e from '../dbschema/edgeql-js'; import { DependencyContainer } from 'tsyringe'; import { internalRoutes } from './api/routes/internal-routes'; -import insertScenario1 from './test-data/scenario-1'; -import { Client } from 'edgedb'; +import { gqlRoutes } from './api/routes/graphql-routes'; export class App { public readonly server: FastifyInstance; @@ -25,23 +23,15 @@ export class App { }); } - public async setupServer(dc: DependencyContainer): Promise { - // register global fastify plugins - // { - // } - const edgeDbClient = dc.resolve('Database'); - - // WARNING: THIS IS DEV MODE - await e.delete(e.metadata.Subject).run(edgeDbClient); - await e.delete(e.metadata.Specimen).run(edgeDbClient); - await e.delete(e.metadata.Library).run(edgeDbClient); - - await insertScenario1(dc); - + public async setupServer(): Promise { // Register Fastify routing - { - this.server.register(internalRoutes); - } + this.server.register(internalRoutes, { + container: this.dc, + }); + this.server.register(gqlRoutes, { + container: this.dc, + prefix: '/graphql', + }); return this.server; } diff --git a/lib/workload/stateless/metadata_manager/src/src/bootstrap/dependency-injection.ts b/lib/workload/stateless/metadata_manager/src/src/bootstrap/dependency-injection.ts index f9a732808..d8041571b 100644 --- a/lib/workload/stateless/metadata_manager/src/src/bootstrap/dependency-injection.ts +++ b/lib/workload/stateless/metadata_manager/src/src/bootstrap/dependency-injection.ts @@ -1,16 +1,30 @@ import { Client, Duration, createClient } from 'edgedb'; import * as tsyringe from 'tsyringe'; -import { SSMClient } from '@aws-sdk/client-ssm'; import { instanceCachingFactory } from 'tsyringe'; import pino, { Logger } from 'pino'; +import { MetadataService } from '../service/metadata'; +import { MetadataGoogleService } from '../service/loader-method/googleSheet'; +import { getSecretManagerWithLayerExtension } from '../utils'; export async function createDependencyContainer() { const dc = tsyringe.container.createChildContainer(); + // Get the edge-db password from SM + const edgeDbPassword = process.env.METADATA_MANAGER_EDGEDB_SECRET_NAME + ? await getSecretManagerWithLayerExtension(process.env.METADATA_MANAGER_EDGEDB_SECRET_NAME) + : undefined; + dc.register('Database', { // https://www.edgedb.com/docs/clients/js/driver#configuring-clients useFactory: instanceCachingFactory(() => - createClient().withConfig({ + createClient({ + host: process.env.EDGEDB_HOST ?? 'localhost', + port: process.env.EDGEDB_PORT ? parseInt(process.env.EDGEDB_PORT) : 5656, + database: process.env.EDGEDB_DATABASE ?? 'edgedb', + tlsSecurity: 'insecure', + password: edgeDbPassword ?? 'admin', + user: process.env.EDGEDB_USER ?? 'orcabus_admin', + }).withConfig({ session_idle_transaction_timeout: Duration.from({ seconds: 60 }), }) ), @@ -24,10 +38,8 @@ export async function createDependencyContainer() { }), }); - dc.register('SSMClient', { - useFactory: () => new SSMClient({}), - }); + dc.registerSingleton(MetadataService); + dc.registerSingleton(MetadataGoogleService); - // Note: dependencies of class constructors must be injected manually when using esbuild. return dc; } diff --git a/lib/workload/stateless/metadata_manager/src/src/handler/server.ts b/lib/workload/stateless/metadata_manager/src/src/handler/server.ts new file mode 100644 index 000000000..5ae9a6846 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/handler/server.ts @@ -0,0 +1,16 @@ +// 'reflect-metadata' must be beginning of the line and before any DI is used +import 'reflect-metadata'; +import { App } from '../app'; +import { createDependencyContainer } from '../bootstrap/dependency-injection'; +import awsLambdaFastify from '@fastify/aws-lambda'; + +export const handler = async (event: unknown, context: unknown) => { + const dc = await createDependencyContainer(); + const app = new App(dc); + + // Setting/registering server routes + const server = await app.setupServer(); + + const proxy = awsLambdaFastify(server); + return proxy(event, context); +}; diff --git a/lib/workload/stateless/metadata_manager/src/src/handler/sync.ts b/lib/workload/stateless/metadata_manager/src/src/handler/sync.ts new file mode 100644 index 000000000..f176a39dc --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/handler/sync.ts @@ -0,0 +1,29 @@ +// 'reflect-metadata' must be beginning of the line and before any DI is used +import 'reflect-metadata'; +import { createDependencyContainer } from '../bootstrap/dependency-injection'; + +import { MetadataService } from '../service/metadata'; +import { MetadataGoogleService } from '../service/loader-method/googleSheet'; +import insertScenario1 from '../test-data/scenarios/scenario-1'; + +export const handler = async () => { + const dc = await createDependencyContainer(); + + if (process.env.NODE_ENV === 'development') { + await insertScenario1(dc); + } else { + const metadataGoogleService = dc.resolve(MetadataGoogleService); + const metadataService = dc.resolve(MetadataService); + + const downloadedMetadata = await metadataGoogleService.downloadGoogleMetadata(); + const convertedRecord = metadataGoogleService.convertToMetadataRecord(downloadedMetadata); + + // Updating Db + await metadataService.upsertMetadataRecords(convertedRecord); + await metadataService.removeDeletedMetadataRecords(convertedRecord); + } + + return { + statusCode: 200, + }; +}; diff --git a/lib/workload/stateless/metadata_manager/src/src/index.ts b/lib/workload/stateless/metadata_manager/src/src/index.ts index 11796b4dc..195ef56ed 100644 --- a/lib/workload/stateless/metadata_manager/src/src/index.ts +++ b/lib/workload/stateless/metadata_manager/src/src/index.ts @@ -12,7 +12,7 @@ import getAppSettings from './bootstrap/settings'; const app = new App(dc); // Setting/registering server routes - const server = await app.setupServer(dc); + const server = await app.setupServer(); server.listen({ host: appSettings.host, port: appSettings.port }, (err, address) => { if (err) { diff --git a/lib/workload/stateless/metadata_manager/src/src/service/helpers/audit-helper.ts b/lib/workload/stateless/metadata_manager/src/src/service/helpers/audit-helper.ts index 5475b08f2..98aeea30a 100644 --- a/lib/workload/stateless/metadata_manager/src/src/service/helpers/audit-helper.ts +++ b/lib/workload/stateless/metadata_manager/src/src/service/helpers/audit-helper.ts @@ -18,7 +18,7 @@ export const systemAuditEventPattern = async ( actionCategory: ActionType = 'E', actionDescription: string, transFunc: (tx: Transaction) => Promise -): Promise => { +): Promise => { const auditEventId = await startSystemAuditEvent(edgeDbClient, actionCategory, actionDescription); try { @@ -53,7 +53,6 @@ export const startSystemAuditEvent = async ( actionDescription: string, // eslint-disable-next-line @typescript-eslint/no-explicit-any details: any = { errorMessage: 'Audit entry not completed' }, - inProgress = true, actionOutcome: ActionOutcomeType = 'error' ): Promise => { return ( @@ -62,7 +61,6 @@ export const startSystemAuditEvent = async ( actionDescription, actionOutcome, details, - inProgress, }) ).id; }; @@ -88,7 +86,5 @@ export const completeSystemAuditEvent = async ( auditDbId: auditEventId, actionOutcome: outcome, details, - occurredDateTime: endDate, - inProgress: false, }); }; diff --git a/lib/workload/stateless/metadata_manager/src/src/service/helpers/metadata/library-helper.ts b/lib/workload/stateless/metadata_manager/src/src/service/helpers/metadata/library-helper.ts index f1ce32a56..6de20e831 100644 --- a/lib/workload/stateless/metadata_manager/src/src/service/helpers/metadata/library-helper.ts +++ b/lib/workload/stateless/metadata_manager/src/src/service/helpers/metadata/library-helper.ts @@ -1,14 +1,14 @@ -import { insertLibraryQuery } from '../../../../dbschema/queries'; +import { insertLibraryQuery, updateLibraryQuery } from '../../../../dbschema/queries'; import { Transaction } from 'edgedb/dist/transaction'; import { MetadataIdentifiableType } from './metadata-helper'; import { metadata } from '../../../../dbschema/interfaces'; import { isEqual } from 'lodash'; export type LibraryType = MetadataIdentifiableType & { - phenotype: metadata.Phenotype | null; + phenotype: string | null; workflow: metadata.WorkflowTypes | null; - quality: metadata.Quality | null; - type: metadata.LibraryTypes | null; + quality: string | null; + type: string | null; assay: string | null; coverage: string | null; specimenOrcaBusId?: string; @@ -61,7 +61,7 @@ export const insertLibraryRecord = async (tx: Transaction, props: LibraryType) = }; export const updateLibraryRecord = async (tx: Transaction, props: LibraryType) => { - await insertLibraryQuery(tx, { + await updateLibraryQuery(tx, { orcaBusId: props.orcaBusId, internalId: props.internalId, phenotype: props.phenotype, diff --git a/lib/workload/stateless/metadata_manager/src/src/service/loader-method/googleSheet.ts b/lib/workload/stateless/metadata_manager/src/src/service/loader-method/googleSheet.ts index cb3e4ffbf..723bd38c2 100644 --- a/lib/workload/stateless/metadata_manager/src/src/service/loader-method/googleSheet.ts +++ b/lib/workload/stateless/metadata_manager/src/src/service/loader-method/googleSheet.ts @@ -1,40 +1,13 @@ -import { Client } from 'edgedb'; -import { ulid } from 'ulid'; import { metadata } from '../../../dbschema/interfaces'; import { inject, injectable } from 'tsyringe'; import { Logger } from 'pino'; import { JWT } from 'google-auth-library'; -import { GetParameterCommand, SSMClient } from '@aws-sdk/client-ssm'; import { GoogleSpreadsheet } from 'google-spreadsheet'; -import { - selectLibraryByIdQuery, - selectSpecimenByIdQuery, - selectSubjectByIdQuery, -} from '../../../dbschema/queries'; -import { - isSubjectIdentical, - insertSubjectRecord, - updateSubjectRecord, -} from '../helpers/metadata/subject-helper'; -import { systemAuditEventPattern } from '../helpers/audit-helper'; -import { Transaction } from 'edgedb/dist/transaction'; -import { - insertSpecimenRecord, - isSpecimenIdentical, - updateSpecimenRecord, -} from '../helpers/metadata/specimen-helper'; -import { - insertLibraryRecord, - isLibraryIdentical, - updateLibraryRecord, -} from '../helpers/metadata/library-helper'; - -const GDRIVE_SERVICE_ACCOUNT = '/umccr/google/drive/lims_service_account_json'; -const TRACKING_SHEET_ID = '/umccr/google/drive/tracking_sheet_id'; -// const LIMS_SHEET_ID = '/umccr/google/drive/lims_sheet_id'; // DEPRECATE? +import { MetadataRecords } from '../metadata'; +import { getParameterDecryptedStoreWithLayerExtension } from '../../utils'; // This will tell from which year the system should query the worksheet -// Note: The title of the sheet are supposed to be th year +// The title of each sheet *SHOULD* be the year const YEAR_START = 2017; type GoogleMetadataTrackingHeader = @@ -56,22 +29,7 @@ type GoogleMetadataTrackingHeader = @injectable() export class MetadataGoogleService { - constructor( - @inject('Database') private readonly edgeDbClient: Client, - @inject('Settings') private readonly settings: Record, - @inject('Logger') private readonly logger: Logger, - @inject('SSMClient') private readonly ssmClient: SSMClient - ) {} - - private async getParameterValue(parameterString: string) { - const input = { - Name: parameterString, - WithDecryption: true, - }; - const command = new GetParameterCommand(input); - return (await this.ssmClient.send(command)).Parameter?.Value; - } - + constructor(@inject('Logger') private readonly logger: Logger) {} /** * Get SpreadSheet values from Google Drive * @param sheetTitle @@ -80,13 +38,18 @@ export class MetadataGoogleService { public async getSheetObject( sheetTitle: string ): Promise[]> { - const googleAuthString = await this.getParameterValue(GDRIVE_SERVICE_ACCOUNT); + const googleAuthString = await getParameterDecryptedStoreWithLayerExtension( + process.env.GDRIVE_SERVICE_ACCOUNT_PARAMETER_NAME + ); if (!googleAuthString) throw new Error('No GDrive credential found!'); - const googleSheetId = await this.getParameterValue(TRACKING_SHEET_ID); + const googleSheetId = await getParameterDecryptedStoreWithLayerExtension( + process.env.TRACKING_SHEET_ID_PARAMETER_NAME + ); if (!googleSheetId) throw new Error('No Google Sheet Id found!'); const googleAuthJson = JSON.parse(googleAuthString); + const jwt = new JWT({ email: googleAuthJson.client_email, key: googleAuthJson.private_key, @@ -100,245 +63,72 @@ export class MetadataGoogleService { if (!sheet) throw new Error(`No sheet found with title: ${sheetTitle}`); const rows = await sheet.getRows(); + return rows.map( (row) => >row.toObject() ); } - /** - * Insert or Update for the subject specified in the properties - * @param props - * @returns - */ - protected async syncSubject(props: { internalId: string; externalId: string | null }) { - const subject = await selectSubjectByIdQuery(this.edgeDbClient, { - internalId: props.internalId, - }); - - // If subject does not exist => insert one - if (!subject) { - return systemAuditEventPattern( - this.edgeDbClient, - 'C', - `Insert new subject record: ${props.internalId}`, - async (tx: Transaction) => { - const r = await insertSubjectRecord(tx, { - orcaBusId: `sbj.${ulid()}`, - internalId: props.internalId, - externalId: props.externalId, - }); - return r; - } - ); - } - - // Check if there it is the same with what we had in record and update if not - if (isSubjectIdentical(subject, props)) { - return systemAuditEventPattern( - this.edgeDbClient, - 'U', - `Update existing subject record: ${props.internalId}`, - async (tx: Transaction) => { - const r = await updateSubjectRecord(tx, { - orcaBusId: subject.orcaBusId, - internalId: props.internalId, - externalId: props.externalId, - }); - return r; - } - ); - } - return subject; - } + public async downloadGoogleMetadata(): Promise< + Record[] + > { + let year = YEAR_START; + let allRecords: Record[] = []; - /** - * Insert or Update for the specimen specified in the properties - * @param props - * @returns - */ - protected async syncSpecimen(props: { - internalId: string; - externalId: string | null; - subjectOrcaBusId?: string; - source: string | null; - }) { - const specimen = await selectSpecimenByIdQuery(this.edgeDbClient, { - internalId: props.internalId, - }); + // eslint-disable-next-line no-constant-condition + while (true) { + this.logger.info(`Retrieving Google Metadata Tracking Sheet year: ${year}`); - // If subject does not exist => insert one - if (!specimen) { - return systemAuditEventPattern( - this.edgeDbClient, - 'C', - `Insert new specimen record: ${props.internalId}`, - async (tx: Transaction) => { - const r = await insertSpecimenRecord(tx, { - orcaBusId: `spc.${ulid()}`, - internalId: props.internalId, - externalId: props.externalId, - subjectOrcaBusId: props.subjectOrcaBusId, - source: props.source, - }); - return r; - } - ); + try { + const yearlyMetadataObject = await this.getSheetObject(year.toString()); + allRecords = [...allRecords, ...yearlyMetadataObject]; + year += 1; + } catch (error) { + break; + } } - // Check if specimen is the same with what we had in record and update if not - if ( - isSpecimenIdentical( - { - internalId: specimen.internalId, - externalId: specimen.externalId, - source: specimen.source, - subjectOrcaBusId: specimen.subjectId, - }, - { ...props } - ) - ) { - return systemAuditEventPattern( - this.edgeDbClient, - 'U', - `Update existing specimen record: ${props.internalId}`, - async (tx: Transaction) => { - const r = await updateSpecimenRecord(tx, { - orcaBusId: specimen.orcaBusId, - internalId: props.internalId, - externalId: props.externalId, - source: props.source, - subjectOrcaBusId: props.subjectOrcaBusId, - }); - return r; - } - ); - } - return specimen; + return allRecords; } - /** - * Insert or Update for the library specified in the properties - * @param props - * @returns - */ - protected async syncLibrary(props: { - internalId: string; - phenotype: metadata.Phenotype | null; - workflow: metadata.WorkflowTypes | null; - quality: metadata.Quality | null; - type: metadata.LibraryTypes | null; - assay: string | null; - coverage: string | null; - specimenId?: string; - }) { - const library = await selectLibraryByIdQuery(this.edgeDbClient, { - libraryId: props.internalId, - }); - // If library does not exist => insert one - if (!library) { - return systemAuditEventPattern( - this.edgeDbClient, - 'C', - `Insert new library record: ${props.internalId}`, - async (tx: Transaction) => { - const r = await insertLibraryRecord(tx, { - orcaBusId: `lib.${ulid()}`, - internalId: props.internalId, - phenotype: props.phenotype, - workflow: props.workflow, - quality: props.quality, - type: props.type, - assay: props.assay, - coverage: props.coverage, - specimenOrcaBusId: props.specimenId, - }); - return r; - } - ); - } + public convertToMetadataRecord( + googleRecArray: Record[] + ): MetadataRecords[] { + this.logger.info('Converting all retrieved metadata to a recognized file format'); - // Check if specimen is the same with what we had in record and update if not - if (isLibraryIdentical(library, props)) { - return systemAuditEventPattern( - this.edgeDbClient, - 'U', - `Update existing specimen record: ${props.internalId}`, - async (tx: Transaction) => { - const r = await updateLibraryRecord(tx, { - orcaBusId: library.orcaBusId, - internalId: props.internalId, - phenotype: props.phenotype, - workflow: props.workflow, - quality: props.quality, - type: props.type, - assay: props.assay, - coverage: props.coverage, - specimenOrcaBusId: props.specimenId, - }); - return r; - } - ); - } - return library; - } + return googleRecArray.map((rec) => { + const val: MetadataRecords = {}; - /** - * Sync Google Metadata record - * - * NOTE (in DEV): Does not handle deletion (from gsheet) and if record is half filled. - * @param sheetRecords - */ - public async syncGoogleMetadataRecords( - sheetRecords: Record[] - ) { - for (const rec of sheetRecords) { - // Sync subject - const subject = rec.SubjectID - ? await this.syncSubject({ - internalId: rec.SubjectID, - externalId: rec.ExternalSubjectID ?? null, - }) - : undefined; + if (rec.SubjectID) { + val.subject = { + internalId: rec.SubjectID, + externalId: rec.ExternalSubjectID ? rec.ExternalSubjectID.toString() : null, + }; + } - // Sync Sample - const sample = rec.SampleID - ? await this.syncSpecimen({ - internalId: rec.SampleID, - externalId: rec.ExternalSampleID ?? null, - subjectOrcaBusId: subject?.orcaBusId, - source: rec.Source ?? null, - }) - : undefined; + if (rec.SampleID) { + val.specimen = { + internalId: rec.SampleID, + externalId: rec.ExternalSampleID ? rec.ExternalSampleID.toString() : null, + source: rec.Source ?? null, + }; + } - // Sync Library if (rec.LibraryID) { - await this.syncLibrary({ + val.library = { internalId: rec.LibraryID, - phenotype: rec.Phenotype ? rec.Phenotype : null, + phenotype: rec.Phenotype ? rec.Phenotype : null, workflow: rec.Workflow ? rec.Workflow : null, - quality: rec.Quality ? rec.Quality : null, - type: rec.Type ? rec.Type : null, + quality: rec.Quality ? rec.Quality : null, + type: rec.Type ? rec.Type : null, assay: rec.Assay ? rec.Assay : null, - coverage: rec['Coverage (X)'] ? rec['Coverage (X)'] : null, - specimenId: sample?.orcaBusId, - }); + coverage: rec['Coverage (X)'] ? rec['Coverage (X)'].toString() : null, + }; } - } - } - public async downloadGoogleMetadata() { - let year = YEAR_START; - for (;;) { - try { - // TODO: Deal with deletion!!! - const metadata_object = await this.getSheetObject(year.toString()); - this.syncGoogleMetadataRecords(metadata_object); - year += 1; - } catch (error) { - break; - } - } + return val; + }); } } diff --git a/lib/workload/stateless/metadata_manager/src/src/service/metadata-loader.ts b/lib/workload/stateless/metadata_manager/src/src/service/metadata-loader.ts deleted file mode 100644 index 84f1f8985..000000000 --- a/lib/workload/stateless/metadata_manager/src/src/service/metadata-loader.ts +++ /dev/null @@ -1,11 +0,0 @@ -import { Client } from 'edgedb'; -import { injectable, inject } from 'tsyringe'; - -@injectable() -export class LibraryLoaderService { - constructor(@inject('Database') private readonly edgeDbClient: Client) {} - - public fetchAndLoad() { - console.log('fetching'); - } -} diff --git a/lib/workload/stateless/metadata_manager/src/src/service/metadata.ts b/lib/workload/stateless/metadata_manager/src/src/service/metadata.ts new file mode 100644 index 000000000..c5b6cb43d --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/service/metadata.ts @@ -0,0 +1,358 @@ +import { Client } from 'edgedb'; +import { injectable, inject } from 'tsyringe'; +import { + isSubjectIdentical, + insertSubjectRecord, + updateSubjectRecord, + SubjectType, +} from './helpers/metadata/subject-helper'; +import { ulid } from 'ulid'; +import { + SpecimenType, + insertSpecimenRecord, + isSpecimenIdentical, + updateSpecimenRecord, +} from './helpers/metadata/specimen-helper'; +import { + LibraryType, + insertLibraryRecord, + isLibraryIdentical, + updateLibraryRecord, +} from './helpers/metadata/library-helper'; +import { + deleteLibraryByOrcaBusId, + deleteSpecimenByOrcaBusId, + deleteSubjectByOrcaBusId, + selectAllLibraryQuery, + selectAllSpecimenQuery, + selectAllSubjectQuery, + selectLibraryByInternalIdQuery, + selectSpecimenByInternalIdQuery, + selectSubjectByInternalIdQuery, +} from '../../dbschema/queries'; +import { Transaction } from 'edgedb/dist/transaction'; +import { systemAuditEventPattern } from './helpers/audit-helper'; +import { Logger } from 'pino'; + +export type MetadataRecords = { + subject?: Omit; + specimen?: Omit; + library?: Omit; +}; + +@injectable() +export class MetadataService { + constructor( + @inject('Database') private readonly edgeDbClient: Client, + @inject('Logger') private readonly logger: Logger + ) {} + + /** + * Update or Insert for the subject specified in the properties + * @param props + * @returns + */ + protected async upsertSubject(props: Omit) { + const subject = await selectSubjectByInternalIdQuery(this.edgeDbClient, { + internalId: props.internalId, + }); + + // If subject does not exist => insert one + if (!subject) { + const assignedOrcaBusId = `sbj.${ulid()}`; + return await systemAuditEventPattern( + this.edgeDbClient, + 'C', + `Insert new subject record: ${assignedOrcaBusId}`, + async (tx: Transaction) => { + const r = await insertSubjectRecord(tx, { + ...props, + orcaBusId: assignedOrcaBusId, + }); + return r; + } + ); + } + + // Check if there it is the same with what we had in record and update if not + if (isSubjectIdentical(subject, props)) { + return await systemAuditEventPattern( + this.edgeDbClient, + 'U', + `Update existing subject record: ${subject.orcaBusId}`, + async (tx: Transaction) => { + const r = await updateSubjectRecord(tx, { + ...props, + orcaBusId: subject.orcaBusId, + }); + return r; + } + ); + } + return subject; + } + + /** + * Check the current records and deletes it if no longer exist in the source truth of data + * @param sourceData The source truth of data + * @returns + */ + protected async checkAndRemoveSubject(sourceInternalIdArray: string[]) { + const allExistingSubject = await selectAllSubjectQuery(this.edgeDbClient); + for (const s of allExistingSubject) { + const shouldRetain = !!sourceInternalIdArray.find( + (sourceInternalId) => sourceInternalId == s.internalId + ); + + if (!shouldRetain) { + await systemAuditEventPattern( + this.edgeDbClient, + 'D', + `Delete subject record: ${s.orcaBusId}`, + async (tx: Transaction) => { + const r = await deleteSubjectByOrcaBusId(tx, { + orcaBusId: s.orcaBusId, + }); + return r; + } + ); + } + } + } + + /** + * Insert or Update for the specimen specified in the properties + * @param props + * @returns + */ + protected async upsertSpecimen( + props: Omit & { + subjectOrcaBusId?: string; + } + ) { + const specimen = await selectSpecimenByInternalIdQuery(this.edgeDbClient, { + internalId: props.internalId, + }); + + // If subject does not exist => insert one + if (!specimen) { + const assignedOrcaBusId = `spc.${ulid()}`; + + return await systemAuditEventPattern( + this.edgeDbClient, + 'C', + `Insert new specimen record: ${assignedOrcaBusId}`, + async (tx: Transaction) => { + const r = await insertSpecimenRecord(tx, { + ...props, + orcaBusId: assignedOrcaBusId, + }); + return r; + } + ); + } + + // Check if specimen is the same with what we had in record and update if not + if ( + isSpecimenIdentical( + { + internalId: specimen.internalId, + externalId: specimen.externalId, + source: specimen.source, + subjectOrcaBusId: specimen.subjectId, + }, + { ...props } + ) + ) { + return await systemAuditEventPattern( + this.edgeDbClient, + 'U', + `Update existing specimen record: ${specimen.orcaBusId}`, + async (tx: Transaction) => { + const r = await updateSpecimenRecord(tx, { + ...props, + orcaBusId: specimen.orcaBusId, + }); + return r; + } + ); + } + return specimen; + } + + /** + * Check the current records and deletes it if no longer exist in source data + * @param sourceData The source truth of data + * @returns + */ + protected async checkAndRemoveSpecimen(sourceInternalIdArray: string[]) { + const allExistingSpc = await selectAllSpecimenQuery(this.edgeDbClient); + for (const s of allExistingSpc) { + const shouldRetain = !!sourceInternalIdArray.find( + (sourceInternalId) => sourceInternalId == s.internalId + ); + + if (!shouldRetain) { + await systemAuditEventPattern( + this.edgeDbClient, + 'D', + `Delete specimen record: ${s.orcaBusId}`, + async (tx: Transaction) => { + const r = await deleteSpecimenByOrcaBusId(tx, { + orcaBusId: s.orcaBusId, + }); + return r; + } + ); + } + } + } + + /** + * Insert or Update for the library specified in the properties + * @param props + * @returns + */ + protected async upsertLibrary( + props: Omit & { + specimenOrcaBusId?: string; + } + ) { + const library = await selectLibraryByInternalIdQuery(this.edgeDbClient, { + libraryId: props.internalId, + }); + // If library does not exist => insert one + if (!library) { + const assignedOrcaBusId = `lib.${ulid()}`; + return await systemAuditEventPattern( + this.edgeDbClient, + 'C', + `Insert new library record: ${assignedOrcaBusId}`, + async (tx: Transaction) => { + const r = await insertLibraryRecord(tx, { + ...props, + orcaBusId: assignedOrcaBusId, + }); + return r; + } + ); + } + + // Check if specimen is the same with what we had in record and update if not + if (isLibraryIdentical(library, props)) { + return await systemAuditEventPattern( + this.edgeDbClient, + 'U', + `Update existing specimen record: ${library.orcaBusId}`, + async (tx: Transaction) => { + const r = await updateLibraryRecord(tx, { + ...props, + orcaBusId: library.orcaBusId, + }); + return r; + } + ); + } + return library; + } + + /** + * Check the current records and deletes it if no longer exist in source data + * @param internalIdArray The internalIds in an array of the truth + * @returns + */ + protected async checkAndRemoveLibrary(sourceInternalIdArray: string[]) { + const allExistingLib = await selectAllLibraryQuery(this.edgeDbClient); + for (const s of allExistingLib) { + const shouldRetain = !!sourceInternalIdArray.find( + (sourceInternalId) => sourceInternalId == s.internalId + ); + + if (!shouldRetain) { + await systemAuditEventPattern( + this.edgeDbClient, + 'D', + `Delete library record: ${s.orcaBusId}`, + async (tx: Transaction) => { + const r = await deleteLibraryByOrcaBusId(tx, { + orcaBusId: s.orcaBusId, + }); + return r; + } + ); + } + } + } + + /** + * Update or Insert record based on the given (source of truth) data + * @param metadataRecords + */ + public async upsertMetadataRecords(metadataRecords: MetadataRecords[]) { + this.logger.info(`Upsert for any new record that doesn't match or exist within the record`); + + for (const rec of metadataRecords) { + // Subject + const subject = rec.subject ? await this.upsertSubject(rec.subject) : undefined; + + // Specimen + const sample = rec.specimen + ? await this.upsertSpecimen({ + ...rec.specimen, + subjectOrcaBusId: subject?.orcaBusId, + }) + : undefined; + + // Library + if (rec.library) { + await this.upsertLibrary({ + ...rec.library, + specimenOrcaBusId: sample?.orcaBusId, + }); + } + } + } + + /** + * Check and delete if internalId is no longer exist in the single source of truth data + * @param metadataRecords the source of true data + */ + public async removeDeletedMetadataRecords(metadataRecords: MetadataRecords[]) { + this.logger.info('Removing any existing record that does not exist in the current dataset'); + const internalIdArrays: { subject: string[]; specimen: string[]; library: string[] } = { + subject: [], + specimen: [], + library: [], + }; + + for (const r of metadataRecords) { + if (r.subject?.internalId) { + internalIdArrays.subject.push(r.subject?.internalId); + } + + if (r.specimen?.internalId) { + internalIdArrays.specimen.push(r.specimen?.internalId); + } + + if (r.library?.internalId) { + internalIdArrays.library.push(r.library?.internalId); + } + } + + await this.checkAndRemoveSubject(internalIdArrays.subject); + await this.checkAndRemoveSpecimen(internalIdArrays.specimen); + await this.checkAndRemoveLibrary(internalIdArrays.library); + } + + public async getAllLibrary() { + return await selectAllLibraryQuery(this.edgeDbClient); + } + + public async getAllSpecimen() { + return await selectAllSpecimenQuery(this.edgeDbClient); + } + + public async getAllSubject() { + return await selectAllSubjectQuery(this.edgeDbClient); + } +} diff --git a/lib/workload/stateless/metadata_manager/src/src/test-data/index.ts b/lib/workload/stateless/metadata_manager/src/src/test-data/index.ts new file mode 100644 index 000000000..afdf39814 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/test-data/index.ts @@ -0,0 +1,27 @@ +// must be first and before any DI is used +import 'reflect-metadata'; +import { createDependencyContainer } from '../bootstrap/dependency-injection'; +import insertScenario1 from './scenarios/scenario-1'; +import insertScenario2 from './scenarios/scenario-2'; + +(async () => { + if (!process.argv || process.argv.length <= 2) { + throw new Error('Invalid argument'); + } + + const arg = process.argv.slice(2).join(' '); + + const dc = await createDependencyContainer(); + + switch (arg) { + case 'insert-scenario-1': + await insertScenario1(dc); + break; + case 'insert-scenario-2': + await insertScenario2(dc); + break; + + default: + throw new Error('Invalid argument'); + } +})(); diff --git a/lib/workload/stateless/metadata_manager/src/src/test-data/scenario-1.ts b/lib/workload/stateless/metadata_manager/src/src/test-data/scenario-1.ts deleted file mode 100644 index 88642065d..000000000 --- a/lib/workload/stateless/metadata_manager/src/src/test-data/scenario-1.ts +++ /dev/null @@ -1,12 +0,0 @@ -import { DependencyContainer } from 'tsyringe'; -import { Logger } from 'pino'; -import { MetadataGoogleService } from '../service/loader-method/googleSheet'; -import { METADATA_GOOGLE_OBJ } from '../../tests/service/gsheet.common'; - -export default async function insertScenario1(dc: DependencyContainer) { - const logger = dc.resolve('Logger'); - const gService = dc.resolve(MetadataGoogleService); - - logger.info('inserting scenario 1'); - await gService.syncGoogleMetadataRecords(METADATA_GOOGLE_OBJ); -} diff --git a/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/metadata.xlsx b/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/metadata.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..95b2bc41cf030d0849a34f99ed858f9ea4cd60fb GIT binary patch literal 12660 zcmeHtg?1fDvh5KwGg-35%*<#pGqWsaW@aXf!D5yyW@eVf7Be%`le_P{?(y{ff;+Wp zWu986A}XtLM@B}(mX!bjMFoHZAOQftM*uSB>WU!{0DuVw0H6RMfi(oJtsIQ39CQ?2 zZH(--Xk08U2y#Jz$+7{!@Av=r_&@vwdJ`tBy6Is1&*E?4l`0f)*6E~B0()L@S@WtP z2C)SRr-{Pg{2Q`xbW;o91NfHm<#3*!ylf2+29ElTDMP-rQVMtMhr(*^)Y)Fix5{K) zamIcmFHF3F7q13F-I}_YwP}X(!7|~b5|%rZG&wVv);pI6B|q9aLQs&{C5hOUZS*2J&ECx3rhFE6C39+vrYLPJ z%8?jaBNUmr5UNI;pi#kwLdnMsLg!BLRqvNlTh+g>0Gbt0I4KXRYGBPijGsvJo=++` zfa48empqfXwfQd}_Ai?OdUs^+TK;bzt#M;!y>zevXMyehQ*E|!ud>4&?&N`O z^~(@+)yTn876!$CKk-4Wei*RJ{7ac>!$ShCn##*G8yq?OCQ2JLO zGz+WkK4e66FlVQlhGobhI`3lldch7oSX-_!X+=i2d*Mu8V8IN9!o+7sQP=pHK5L_^ z0fV__=4i%m^bCNg3GvwCst^@QG=VBSGmh#rG?;hC%p#4!3@Gw&Q|lZ+k{;*R{}73^?bv;!o%LCui#9pQsCE7e2_8A>H6Bw=#N zNWr`3!Ac#1m5uj06NR|v6VrxjfJ4x>Mq6332g$$R8x!VzqJ%d+d!Ae*zZX8gqn_Ud&bGz57JF?E_IxV>ZJEJN5B@O_)=szFBdAF6Xs9>^MCk@{)utnI z<*N>-qEEI;I@K*`0o2^C&M1wqe#ntm(jGhQ6h;_~Vrk6I$RsmKEV+~Pfx4&}dp^Q{ z_O4CW=lsTZ+>TTM1x*9B|l7#*lqyAo$Cw59`>==N8gQc zzgI0rVSd$4+CemtxIV-Dvk>xh^$XAqcetS~%RW#@)U^rHc(7Ohl*$`uiNsi?a(WX= zi^O5#A^QCVS?RidVrC-JAg)BA7&s->(y|8}vIKK#0z--refceCA=1Ka>C5Cq=iv7w7!Ea+cFO3x+f3cD)_Xp` zO*TKn4;sInA+eAdf)HtVj5KmOJpPa}xWmHFkLemSYtD*rVzG>guVxkI|GDKhu|^6A z2_l(ampLC8N6jzlQ))d@zD<)8TNq>qOfh@($J*V~5D`INjLwU>GA3e?sIU|GLy|j7 z5quB#Gmninf9uKGmSqA$E)d5>4G<2{1GsXCl@txjR8GV+{!d#rbhmCjohOA}hqst

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EA7Tf2asU7T literal 0 HcmV?d00001 diff --git a/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-1.ts b/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-1.ts new file mode 100644 index 000000000..6994a106d --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-1.ts @@ -0,0 +1,18 @@ +import { Client } from 'edgedb'; +import { DependencyContainer } from 'tsyringe'; +import { Logger } from 'pino'; +import { blankDb } from '../utils'; +import { MetadataService } from '../../service/metadata'; +import { METADATA_REC_ARR } from '../../../tests/service/metadata.common'; + +export default async function insertScenario1(dc: DependencyContainer) { + const logger = dc.resolve('Logger'); + const metadataService = dc.resolve(MetadataService); + const edgeDbClient = dc.resolve('Database'); + + logger.info('Blank database before inserting scenario-1'); + await blankDb(edgeDbClient); + + logger.info('inserting scenario 1 - from test cases'); + await metadataService.upsertMetadataRecords(METADATA_REC_ARR); +} diff --git a/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-2.ts b/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-2.ts new file mode 100644 index 000000000..98c9b7722 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/test-data/scenarios/scenario-2.ts @@ -0,0 +1,37 @@ +import { Client } from 'edgedb'; +import { DependencyContainer } from 'tsyringe'; +import { Logger } from 'pino'; +import { blankDb } from '../utils'; +import { MetadataService } from '../../service/metadata'; +import * as reader from 'xlsx'; +import * as path from 'path'; +import { MetadataGoogleService } from '../../service/loader-method/googleSheet'; + +const YEAR_START = 2018; +const YEAR_END = new Date().getFullYear(); + +export default async function insertScenario2(dc: DependencyContainer) { + const logger = dc.resolve('Logger'); + const metadataService = dc.resolve(MetadataService); + const metadataGoogleService = dc.resolve(MetadataGoogleService); + const edgeDbClient = dc.resolve('Database'); + + logger.info('Blank database before inserting scenario-2'); + await blankDb(edgeDbClient); + + logger.info('inserting scenario 2 (based on `metadata.xlsx`)'); + const file = reader.readFile(path.join(__dirname, './metadata.xlsx')); + + let data = []; + + for (let index = YEAR_START; index <= YEAR_END; index++) { + const sheetData = reader.utils.sheet_to_json(file.Sheets[index]); + data = data.concat(sheetData); + } + + const convertedRecord = metadataGoogleService.convertToMetadataRecord(data); + + // Updating Db + await metadataService.upsertMetadataRecords(convertedRecord); + await metadataService.removeDeletedMetadataRecords(convertedRecord); +} diff --git a/lib/workload/stateless/metadata_manager/src/src/test-data/utils.ts b/lib/workload/stateless/metadata_manager/src/src/test-data/utils.ts new file mode 100644 index 000000000..6a7cc2602 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/test-data/utils.ts @@ -0,0 +1,8 @@ +import { Client } from 'edgedb'; +import e from '../../dbschema/edgeql-js'; + +export const blankDb = async (edgeDbClient: Client) => { + await e.delete(e.metadata.Subject).run(edgeDbClient); + await e.delete(e.metadata.Specimen).run(edgeDbClient); + await e.delete(e.metadata.Library).run(edgeDbClient); +}; diff --git a/lib/workload/stateless/metadata_manager/src/src/utils.ts b/lib/workload/stateless/metadata_manager/src/src/utils.ts new file mode 100644 index 000000000..43d10b8d4 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/src/utils.ts @@ -0,0 +1,38 @@ +import axios from 'axios'; + +/** + * Use the default lambda layer extension to query secret manager + * Ref: https://docs.aws.amazon.com/secretsmanager/latest/userguide/retrieving-secrets_lambda.html + * @param secretManagerName The name of the secret or ARN + * @returns + */ +export const getSecretManagerWithLayerExtension = async (secretManagerName: string) => { + const apiUrl = `http://localhost:2773/secretsmanager/get?secretId=${encodeURIComponent( + secretManagerName + )}`; + const headers = { 'X-Aws-Parameters-Secrets-Token': process.env.AWS_SESSION_TOKEN }; + const res = await axios.get(apiUrl, { + headers: headers, + }); + + return res.data.SecretString; +}; + +/** + * Use the default lambda layer extension to query system parameter store (WITH decryption) + * Ref: https://docs.aws.amazon.com/systems-manager/latest/userguide/ps-integration-lambda-extensions.html + * @param parameterStoreName The name of the parameterStore or ARN + * @returns + */ +export const getParameterDecryptedStoreWithLayerExtension = async (parameterStoreName: string) => { + const apiUrl = `http://localhost:2773/systemsmanager/parameters/get/?name=${encodeURIComponent( + parameterStoreName + )}&withDecryption=true`; + + const headers = { 'X-Aws-Parameters-Secrets-Token': process.env.AWS_SESSION_TOKEN }; + const res = await axios.get(apiUrl, { + headers: headers, + }); + + return res.data.Parameter.Value; +}; diff --git a/lib/workload/stateless/metadata_manager/src/tests/service/gsheet.test.ts b/lib/workload/stateless/metadata_manager/src/tests/service/gsheet.test.ts deleted file mode 100644 index fb463f720..000000000 --- a/lib/workload/stateless/metadata_manager/src/tests/service/gsheet.test.ts +++ /dev/null @@ -1,94 +0,0 @@ -import e from '../../dbschema/edgeql-js'; -import { registerTypes } from './test-dependency.common'; -import { MetadataGoogleService } from '../../src/service/loader-method/googleSheet'; -import { METADATA_GOOGLE_OBJ, METADATA_REC_1, METADATA_REC_4 } from './gsheet.common'; -import { Client } from 'edgedb'; -import { resetDb } from './utils'; - -const testContainer = registerTypes(); -let edgeDbClient: Client; -let gService: MetadataGoogleService; - -describe('sync metadata from google spreadsheet', () => { - beforeAll(async () => { - gService = testContainer.resolve(MetadataGoogleService); - edgeDbClient = testContainer.resolve('Database'); - }); - - beforeEach(async () => { - await resetDb(edgeDbClient); - // jest.useFakeTimers(); - }); - - it('libraries with the same specimen', async () => { - await gService.syncGoogleMetadataRecords([METADATA_REC_1, METADATA_REC_4]); - - const libraries = await e - .select(e.metadata.Library, () => ({ - ...e.metadata.Library['*'], - specimen: { - internalId: true, - }, - })) - .run(edgeDbClient); - - const specimens = await e - .select(e.metadata.Specimen, () => ({ - ...e.metadata.Specimen['*'], - })) - .run(edgeDbClient); - - // Expecting 2 library record belong to the same subject - expect(specimens.length).toBe(1); - expect(libraries.length).toBe(2); - - // Checks if both libraries belong to the same subject - const subjectId = specimens[0].internalId; - for (const l of libraries) { - expect(l.specimen?.internalId).toBe(subjectId); - } - }); - - it('libraries with both the same specimen and subject', async () => { - await gService.syncGoogleMetadataRecords([METADATA_REC_1, METADATA_REC_4]); - - const specimens = await e - .select(e.metadata.Specimen, () => ({ - ...e.metadata.Specimen['*'], - subject: { internalId: true }, - })) - .run(edgeDbClient); - - const subjects = await e - .select(e.metadata.Subject, () => ({ ...e.metadata.Subject['*'] })) - .run(edgeDbClient); - - expect(subjects.length).toBe(1); - expect(specimens.length).toBe(1); - - expect(specimens[0].subject?.internalId).toBe(subjects[0].internalId); - }); - - it('test insert and update works', async () => { - await gService.syncGoogleMetadataRecords(METADATA_GOOGLE_OBJ); - - const libraries = await e - .select(e.metadata.Library, () => ({ ...e.metadata.Library['*'] })) - .run(edgeDbClient); - - const specimens = await e - .select(e.metadata.Specimen, () => ({ ...e.metadata.Specimen['*'] })) - .run(edgeDbClient); - - const subjects = await e - .select(e.metadata.Subject, () => ({ ...e.metadata.Subject['*'] })) - .run(edgeDbClient); - - // Testing for all google object exist in Db - for (const m of METADATA_GOOGLE_OBJ) { - expect(libraries.find((l) => l.internalId == m.LibraryID)); - expect(specimens.find((s) => s.internalId == m.SampleID)); - expect(subjects.find((s) => s.internalId == m.SubjectID)); - } - }); -}); diff --git a/lib/workload/stateless/metadata_manager/src/tests/service/gsheet.common.ts b/lib/workload/stateless/metadata_manager/src/tests/service/loader/gsheet.common.ts similarity index 88% rename from lib/workload/stateless/metadata_manager/src/tests/service/gsheet.common.ts rename to lib/workload/stateless/metadata_manager/src/tests/service/loader/gsheet.common.ts index 40192de09..ff047c663 100644 --- a/lib/workload/stateless/metadata_manager/src/tests/service/gsheet.common.ts +++ b/lib/workload/stateless/metadata_manager/src/tests/service/loader/gsheet.common.ts @@ -1,4 +1,4 @@ -export const METADATA_REC_1 = { +export const METADATA_GOOGLE_REC_1 = { LibraryID: 'LIB01', SampleName: 'SAMIDA-EXTSAMA', SampleID: 'SAMIDA', @@ -24,7 +24,7 @@ export const METADATA_REC_1 = { 'Sample_ID (SampleSheet)': 'SAMIDA_LIB01', }; -export const METADATA_REC_2 = { +export const METADATA_GOOGLE_REC_2 = { LibraryID: 'LIB02', SampleName: 'SAMIDB-EXTSAMB', SampleID: 'SAMIDB', @@ -50,7 +50,7 @@ export const METADATA_REC_2 = { 'Sample_ID (SampleSheet)': 'SAMIDB_LIB02', }; -export const METADATA_REC_3 = { +export const METADATA_GOOGLE_REC_3 = { LibraryID: 'LIB03', SampleName: 'SAMIDB-EXTSAMB', SampleID: 'SAMIDB', @@ -76,7 +76,7 @@ export const METADATA_REC_3 = { 'Sample_ID (SampleSheet)': 'SAMIDB_LIB03', }; -export const METADATA_REC_4 = { +export const METADATA_GOOGLE_REC_4 = { LibraryID: 'LIB04', SampleName: 'SAMIDA-EXTSAMA', SampleID: 'SAMIDA', @@ -102,4 +102,9 @@ export const METADATA_REC_4 = { 'Sample_ID (SampleSheet)': 'SAMIDA_LIB01', }; -export const METADATA_GOOGLE_OBJ = [METADATA_REC_1, METADATA_REC_2, METADATA_REC_3, METADATA_REC_4]; +export const METADATA_GOOGLE_OBJ = [ + METADATA_GOOGLE_REC_1, + METADATA_GOOGLE_REC_2, + METADATA_GOOGLE_REC_3, + METADATA_GOOGLE_REC_4, +]; diff --git a/lib/workload/stateless/metadata_manager/src/tests/service/loader/gsheet.test.ts b/lib/workload/stateless/metadata_manager/src/tests/service/loader/gsheet.test.ts new file mode 100644 index 000000000..c9b5645aa --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/tests/service/loader/gsheet.test.ts @@ -0,0 +1,34 @@ +import { registerTypes } from '../test-dependency.common'; +import { MetadataGoogleService } from '../../../src/service/loader-method/googleSheet'; +import { METADATA_GOOGLE_REC_1 } from './gsheet.common'; +import { isEqual } from 'lodash'; + +const testContainer = registerTypes(); +let gService: MetadataGoogleService; + +describe('metadata record from GoogleSheet tests', () => { + beforeAll(async () => { + gService = testContainer.resolve(MetadataGoogleService); + }); + + it('google record converted to internal types', async () => { + const convertedResultArr = gService.convertToMetadataRecord([METADATA_GOOGLE_REC_1]); + + expect(convertedResultArr.length).toBe(1); + expect( + isEqual(convertedResultArr[0], { + subject: { internalId: 'SUBIDA', externalId: 'EXTSUBIDA' }, + specimen: { internalId: 'SAMIDA', externalId: null, source: 'FFPE' }, + library: { + internalId: 'LIB01', + phenotype: null, + workflow: 'clinical', + quality: null, + type: 'WTS', + assay: 'NebRNA', + coverage: '6.0', + }, + }) + ).toBe(true); + }); +}); diff --git a/lib/workload/stateless/metadata_manager/src/tests/service/metadata.common.ts b/lib/workload/stateless/metadata_manager/src/tests/service/metadata.common.ts new file mode 100644 index 000000000..07ec2c233 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/tests/service/metadata.common.ts @@ -0,0 +1,59 @@ +import { MetadataRecords } from '../../src/service/metadata'; + +export const METADATA_REC_1: MetadataRecords = { + subject: { internalId: 'SUBIDA', externalId: 'EXTSUBIDA' }, + specimen: { internalId: 'SAMIDA', externalId: '', source: 'FFPE' }, + library: { + internalId: 'LIB01', + phenotype: null, + workflow: 'clinical', + quality: null, + type: 'WTS', + assay: 'NebRNA', + coverage: '6.0', + }, +}; + +export const METADATA_REC_2: MetadataRecords = { + subject: { internalId: 'SUBIDB', externalId: 'EXTSUBIDB' }, + specimen: { internalId: 'SAMIDB', externalId: 'EXTSAMB', source: 'FFPE' }, + library: { + internalId: 'LIB02', + phenotype: 'tumor', + workflow: 'clinical', + quality: 'poor', + type: 'WTS', + assay: 'NebRNA', + coverage: '6.3', + }, +}; + +export const METADATA_REC_3: MetadataRecords = { + subject: { internalId: 'SUBIDB', externalId: 'EXTSUBIDB' }, + specimen: { internalId: 'SAMIDB', externalId: 'EXTSAMB', source: 'FFPE' }, + library: { + internalId: 'LIB03', + phenotype: 'tumor', + workflow: 'clinical', + quality: 'poor', + type: 'WTS', + assay: 'NebRNA', + coverage: '6.0', + }, +}; + +export const METADATA_REC_4: MetadataRecords = { + subject: { internalId: 'SUBIDA', externalId: 'EXTSUBIDA' }, + specimen: { internalId: 'SAMIDA', externalId: 'EXTSAMA', source: 'FFPE' }, + library: { + internalId: 'LIB04', + phenotype: 'tumor', + workflow: 'clinical', + quality: 'poor', + type: 'WTS', + assay: 'NebRNA', + coverage: '6.0', + }, +}; + +export const METADATA_REC_ARR = [METADATA_REC_1, METADATA_REC_2, METADATA_REC_3, METADATA_REC_4]; diff --git a/lib/workload/stateless/metadata_manager/src/tests/service/metadata.test.ts b/lib/workload/stateless/metadata_manager/src/tests/service/metadata.test.ts new file mode 100644 index 000000000..a0d2a14e8 --- /dev/null +++ b/lib/workload/stateless/metadata_manager/src/tests/service/metadata.test.ts @@ -0,0 +1,153 @@ +import e from '../../dbschema/edgeql-js'; +import { registerTypes } from './test-dependency.common'; +import { METADATA_REC_1, METADATA_REC_4, METADATA_REC_ARR } from './metadata.common'; +import { Client } from 'edgedb'; +import { resetDb } from './utils'; +import { MetadataService } from '../../src/service/metadata'; + +const testContainer = registerTypes(); +let edgeDbClient: Client; +let metadataService: MetadataService; + +describe('metadata service test', () => { + beforeAll(async () => { + edgeDbClient = testContainer.resolve('Database'); + metadataService = testContainer.resolve(MetadataService); + }); + + beforeEach(async () => { + await resetDb(edgeDbClient); + }); + + it('two libraries with the same specimen and subject', async () => { + await metadataService.upsertMetadataRecords([METADATA_REC_1, METADATA_REC_4]); + + const libraries = await e + .select(e.metadata.Library, () => ({ + ...e.metadata.Library['*'], + specimen: { + internalId: true, + }, + })) + .run(edgeDbClient); + + const specimens = await e + .select(e.metadata.Specimen, () => ({ + ...e.metadata.Specimen['*'], + subject: { internalId: true }, + })) + .run(edgeDbClient); + + const subjects = await e + .select(e.metadata.Subject, () => ({ ...e.metadata.Subject['*'] })) + .run(edgeDbClient); + + // Expecting 2 library record belong to the same subject and specimen + expect(libraries.length).toBe(2); + expect(subjects.length).toBe(1); + expect(specimens.length).toBe(1); + + // Checks if both libraries belong to the same subject + const specimenId = specimens[0].internalId; + for (const l of libraries) { + expect(l.specimen?.internalId).toBe(specimenId); + } + + // Check if specimen belong to the same subject + const subjectId = subjects[0].internalId; + expect(specimens[0].subject?.internalId).toBe(subjectId); + }); + + it('upsert function works as expected and appear in database', async () => { + await metadataService.upsertMetadataRecords(METADATA_REC_ARR); + + const libraries = await e + .select(e.metadata.Library, () => ({ ...e.metadata.Library['*'] })) + .run(edgeDbClient); + + const specimens = await e + .select(e.metadata.Specimen, () => ({ ...e.metadata.Specimen['*'] })) + .run(edgeDbClient); + + const subjects = await e + .select(e.metadata.Subject, () => ({ ...e.metadata.Subject['*'] })) + .run(edgeDbClient); + + // Testing for all record exist in database + for (const m of METADATA_REC_ARR) { + expect(libraries.find((l) => l.internalId == m.library?.internalId)); + expect(specimens.find((s) => s.internalId == m.specimen?.externalId)); + expect(subjects.find((s) => s.internalId == m.subject?.externalId)); + } + }); + + it('destroy all records works as expected', async () => { + await metadataService.upsertMetadataRecords(METADATA_REC_ARR); + + await metadataService.removeDeletedMetadataRecords([]); + + const libraries = await e + .select(e.metadata.Library, () => ({ ...e.metadata.Library['*'] })) + .run(edgeDbClient); + + const specimens = await e + .select(e.metadata.Specimen, () => ({ ...e.metadata.Specimen['*'] })) + .run(edgeDbClient); + + const subjects = await e + .select(e.metadata.Subject, () => ({ ...e.metadata.Subject['*'] })) + .run(edgeDbClient); + + expect(libraries.length).toBe(0); + expect(specimens.length).toBe(0); + expect(subjects.length).toBe(0); + }); + + it('destroy all records works as expected', async () => { + await metadataService.upsertMetadataRecords(METADATA_REC_ARR); + + await metadataService.removeDeletedMetadataRecords([]); + + const libraries = await e + .select(e.metadata.Library, () => ({ ...e.metadata.Library['*'] })) + .run(edgeDbClient); + + const specimens = await e + .select(e.metadata.Specimen, () => ({ ...e.metadata.Specimen['*'] })) + .run(edgeDbClient); + + const subjects = await e + .select(e.metadata.Subject, () => ({ ...e.metadata.Subject['*'] })) + .run(edgeDbClient); + + expect(libraries.length).toBe(0); + expect(specimens.length).toBe(0); + expect(subjects.length).toBe(0); + }); + + it('removing a library that has the same subject and specimen id', async () => { + await metadataService.upsertMetadataRecords([METADATA_REC_1, METADATA_REC_4]); + + await metadataService.removeDeletedMetadataRecords([METADATA_REC_1]); + + const libraries = await e + .select(e.metadata.Library, () => ({ ...e.metadata.Library['*'] })) + .run(edgeDbClient); + + const specimens = await e + .select(e.metadata.Specimen, () => ({ ...e.metadata.Specimen['*'] })) + .run(edgeDbClient); + + const subjects = await e + .select(e.metadata.Subject, () => ({ ...e.metadata.Subject['*'] })) + .run(edgeDbClient); + + expect(libraries.length).toBe(1); + expect(specimens.length).toBe(1); + expect(subjects.length).toBe(1); + + expect(libraries[0].internalId).toBe(METADATA_REC_1.library?.internalId); + expect(specimens[0].internalId).toBe(METADATA_REC_1.specimen?.internalId); + expect(subjects[0].internalId).toBe(METADATA_REC_1.subject?.internalId); + }); +}); diff --git a/lib/workload/stateless/metadata_manager/src/tests/service/test-dependency.common.ts b/lib/workload/stateless/metadata_manager/src/tests/service/test-dependency.common.ts index 92270c523..0f00027ce 100644 --- a/lib/workload/stateless/metadata_manager/src/tests/service/test-dependency.common.ts +++ b/lib/workload/stateless/metadata_manager/src/tests/service/test-dependency.common.ts @@ -3,7 +3,6 @@ import 'reflect-metadata'; import { container, instanceCachingFactory } from 'tsyringe'; import { Client, Duration, createClient } from 'edgedb'; import { Logger, pino } from 'pino'; -import { SSMClient } from '@aws-sdk/client-ssm'; export function registerTypes() { const dc = container.createChildContainer(); @@ -15,7 +14,14 @@ export function registerTypes() { dc.register('Database', { // https://www.edgedb.com/docs/clients/js/driver#configuring-clients useFactory: instanceCachingFactory(() => - createClient().withConfig({ + createClient({ + host: process.env.EDGEDB_HOST ?? 'localhost', + port: process.env.EDGEDB_PORT ? parseInt(process.env.EDGEDB_PORT) : 5656, + database: process.env.EDGEDB_DATABASE ?? 'edgedb', + tlsSecurity: 'insecure', + password: 'admin', // pragma: allowlist secret + user: process.env.EDGEDB_USER ?? 'orcabus_admin', + }).withConfig({ session_idle_transaction_timeout: Duration.from({ seconds: 60 }), }) ), @@ -29,10 +35,5 @@ export function registerTypes() { }), }); - dc.register('SSMClient', { - useFactory: () => new SSMClient({}), - }); - - // Note: dependencies of class constructors must be injected manually when using esbuild. return dc; } diff --git a/lib/workload/stateless/metadata_manager/src/tsconfig.json b/lib/workload/stateless/metadata_manager/src/tsconfig.json index 0b9690ae0..0c5b60a16 100644 --- a/lib/workload/stateless/metadata_manager/src/tsconfig.json +++ b/lib/workload/stateless/metadata_manager/src/tsconfig.json @@ -58,8 +58,9 @@ // "inlineSourceMap": true, /* Include sourcemap files inside the emitted JavaScript. */ // "outFile": "./", /* Specify a file that bundles all outputs into one JavaScript file. If 'declaration' is true, also designates a file that bundles all .d.ts output. */ // "outDir": "./", /* Specify an output folder for all emitted files. */ + "outDir": "dist", // "removeComments": true, /* Disable emitting comments. */ - "noEmit": true, /* Disable emitting files from a compilation. */ + "noEmit": false, /* Disable emitting files from a compilation. */ // "importHelpers": true, /* Allow importing helper functions from tslib once per project, instead of including them per-file. */ // "importsNotUsedAsValues": "remove", /* Specify emit/checking behavior for imports that are only used for types. */ // "downlevelIteration": true, /* Emit more compliant, but verbose and less performant JavaScript for iteration. */ @@ -84,7 +85,7 @@ "forceConsistentCasingInFileNames": true, /* Ensure that casing is correct in imports. */ /* Type Checking */ - "strict": true, /* Enable all strict type-checking options. */ + // "strict": true, /* Enable all strict type-checking options. */ // "noImplicitAny": true, /* Enable error reporting for expressions and declarations with an implied 'any' type. */ // "strictNullChecks": true, /* When type checking, take into account 'null' and 'undefined'. */ // "strictFunctionTypes": true, /* When assigning functions, check to ensure parameters and the return values are subtype-compatible. */ @@ -109,5 +110,5 @@ "skipLibCheck": true /* Skip type checking all .d.ts files. */ }, "include": ["./src/**/*"], - "exclude": ["node_modules"] + "exclude": ["node_modules","./deploy/cdk.out"] } diff --git a/lib/workload/stateless/metadata_manager/src/yarn.lock b/lib/workload/stateless/metadata_manager/src/yarn.lock index ee4380a6a..591aa7d58 100644 --- a/lib/workload/stateless/metadata_manager/src/yarn.lock +++ b/lib/workload/stateless/metadata_manager/src/yarn.lock @@ -15,491 +15,6 @@ __metadata: languageName: node linkType: hard -"@aws-crypto/crc32@npm:3.0.0": - version: 3.0.0 - resolution: "@aws-crypto/crc32@npm:3.0.0" - dependencies: - 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