From c7692de428a0c87a020251bdab510c123b3b432d Mon Sep 17 00:00:00 2001 From: William Putra Intan <61998484+williamputraintan@users.noreply.github.com> Date: Fri, 19 Jan 2024 12:47:30 +1100 Subject: [PATCH] Added Swagger UI and Dependencies Bumped (#83) --- .../stateless/metadata_manager/src/.gitignore | 1 + .../stateless/metadata_manager/src/Makefile | 14 +- .../stateless/metadata_manager/src/README.md | 4 +- .../audit/updateSystemAuditEvent.edgeql | 2 +- .../library/selectAllLibraryQuery.edgeql | 49 +- .../specimen/selectAllSpecimenQuery.edgeql | 38 +- .../subject/selectAllSubjectQuery.edgeql | 35 +- .../src/deploy/package-lock.json | 112 +- .../metadata_manager/src/package.json | 41 +- .../src/src/api/routes/internal-routes.ts | 92 +- .../stateless/metadata_manager/src/src/app.ts | 52 +- .../src/src/bootstrap/settings.ts | 4 +- .../metadata_manager/src/src/index.ts | 1 - .../src/src/service/metadata.ts | 26 +- .../stateless/metadata_manager/src/yarn.lock | 2693 ++++++++++------- 15 files changed, 1937 insertions(+), 1227 deletions(-) diff --git a/lib/workload/stateless/metadata_manager/src/.gitignore b/lib/workload/stateless/metadata_manager/src/.gitignore index 5385865a2..b8c865810 100644 --- a/lib/workload/stateless/metadata_manager/src/.gitignore +++ b/lib/workload/stateless/metadata_manager/src/.gitignore @@ -136,6 +136,7 @@ dist dbschema/edgeql-js dbschema/queries.* +dbschema/queriesZodSchema.ts dbschema/interfaces.ts asset/ \ No newline at end of file diff --git a/lib/workload/stateless/metadata_manager/src/Makefile b/lib/workload/stateless/metadata_manager/src/Makefile index ce22a2867..f6dcfbead 100644 --- a/lib/workload/stateless/metadata_manager/src/Makefile +++ b/lib/workload/stateless/metadata_manager/src/Makefile @@ -17,9 +17,11 @@ stop: # 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@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret + @yarn run -B generate queries --target ts --file --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret + @yarn run -B generate edgeql-js --target ts --output-dir dbschema/edgeql-js --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret + @yarn run -B generate interfaces --file dbschema/interfaces.ts --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret + @yarn run ts-to-zod dbschema/queries.ts dbschema/queriesZodSchema.ts + build: edgetypes @rm -rf asset @@ -32,7 +34,6 @@ build: edgetypes @zip -r asset/dependency.zip nodejs @rm -rf nodejs - # Testing test: @yarn test @@ -44,6 +45,11 @@ start-scenario-1: edgetypes @yarn run insert-scenario-1 @yarn start +# Start in watch mode +watch: edgetypes + @yarn run insert-scenario-1 + @yarn watch + # Inserting scenarios insert-scenario-2: @yarn run insert-scenario-2 diff --git a/lib/workload/stateless/metadata_manager/src/README.md b/lib/workload/stateless/metadata_manager/src/README.md index 1ab73fa47..0bfacb31b 100644 --- a/lib/workload/stateless/metadata_manager/src/README.md +++ b/lib/workload/stateless/metadata_manager/src/README.md @@ -114,8 +114,10 @@ http://localhost:8080/subject http://localhost:8080/library http://localhost:8080/specimen +# Swagger Endpoint +http://localhost:8080/documentation - +# GraphQL Endpoint http://localhost:8080/graphql/explore (UI) http://localhost:8080/graphql (Only for graphql POST method) ``` 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 2ccc7ba72..fcf8c951f 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 @@ -5,5 +5,5 @@ filter .id = $auditDbId set { actionOutcome := $actionOutcome, - details := $details, + details := $details, } 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 index c82b2c793..db3c0cffa 100644 --- 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 @@ -1,3 +1,48 @@ -select metadata::Library{ - * + +with + + # Pagination parameter + offset_ := $offset ?? 0, + limit_ := $limit ?? 10, + + libraries := ( + select metadata::Library { + * + } + filter ( + .orcaBusId ?= $orcaBusId ?? .orcaBusId + AND + .internalId ?= $internalId ?? .internalId + AND + .externalId ?= $externalId ?? .externalId + AND + .phenotype ?= $phenotype ?? .phenotype + AND + .assay ?= $assay ?? .assay + AND + .coverage ?= $coverage ?? .coverage + AND + .quality ?= $quality ?? .quality + AND + .type ?= $type ?? .type + AND + .workflow = $workflow ?? .workflow + ) + ) +select { + + results := ( + select libraries { + * + } + offset offset_ + limit limit_ + ), + pagination := { + total := count(libraries), + `offset` := offset_, + `limit` := limit_ + } + } + 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 index 57663f1e7..3fd1d275e 100644 --- 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 @@ -1,3 +1,37 @@ -select metadata::Specimen{ - * +with + + # Pagination parameter + offset_ := $offset ?? 0, + limit_ := $limit ?? 10, + + libraries := ( + select metadata::Specimen { + * + } + filter ( + .orcaBusId ?= $orcaBusId ?? .orcaBusId + AND + .internalId ?= $internalId ?? .internalId + AND + .externalId ?= $externalId ?? .externalId + AND + .source ?= $source ?? .source + ) + ) +select { + + results := ( + select libraries { + * + } + offset offset_ + limit limit_ + ), + pagination := { + total := count(libraries), + `offset` := offset_, + `limit` := limit_ + } + } + 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 index 3828799d4..80564ac51 100644 --- 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 @@ -1,3 +1,34 @@ -select metadata::Subject{ - * +with + + # Pagination parameter + offset_ := $offset ?? 0, + limit_ := $limit ?? 10, + + libraries := ( + select metadata::Subject { + * + } + filter ( + .orcaBusId ?= $orcaBusId ?? .orcaBusId + AND + .internalId ?= $internalId ?? .internalId + AND + .externalId ?= $externalId ?? .externalId + ) + ) +select { + + results := ( + select libraries { + * + } + offset offset_ + limit limit_ + ), + pagination := { + total := count(libraries), + `offset` := offset_, + `limit` := limit_ + } } + diff --git a/lib/workload/stateless/metadata_manager/src/deploy/package-lock.json b/lib/workload/stateless/metadata_manager/src/deploy/package-lock.json index df2e597f6..53785bbd5 100644 --- a/lib/workload/stateless/metadata_manager/src/deploy/package-lock.json +++ b/lib/workload/stateless/metadata_manager/src/deploy/package-lock.json @@ -81,12 +81,12 @@ } }, "node_modules/@babel/code-frame": { - "version": "7.22.13", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.22.13.tgz", - "integrity": "sha512-XktuhWlJ5g+3TJXc5upd9Ks1HutSArik6jf2eAjYFyIOf4ej3RN+184cZbzDvbPnuTJIUhPKKJE3cIsYTiAT3w==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.4.tgz", + "integrity": "sha512-r1IONyb6Ia+jYR2vvIDhdWdlTGhqbBoFqLTQidzZ4kepUFH15ejXvFHxCVbtl7BOXIudsIubf4E81xeA3h3IXA==", "dev": true, "dependencies": { - "@babel/highlight": "^7.22.13", + "@babel/highlight": "^7.23.4", "chalk": "^2.4.2" }, "engines": { @@ -204,12 +204,12 @@ } }, "node_modules/@babel/generator": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.0.tgz", - "integrity": "sha512-lN85QRR+5IbYrMWM6Y4pE/noaQtg4pNiqeNGX60eqOfo6gtEj6uw/JagelB8vVztSd7R6M5n1+PQkDbHbBRU4g==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.4.tgz", + "integrity": "sha512-esuS49Cga3HcThFNebGhlgsrVLkvhqvYDTzgjfFFlHJcIfLe5jFmRRfCQ1KuBfc4Jrtn3ndLgKWAKjBE+IraYQ==", "dev": true, "dependencies": { - "@babel/types": "^7.23.0", + "@babel/types": "^7.23.4", "@jridgewell/gen-mapping": "^0.3.2", "@jridgewell/trace-mapping": "^0.3.17", "jsesc": "^2.5.1" @@ -333,9 +333,9 @@ } }, "node_modules/@babel/helper-string-parser": { - "version": "7.22.5", - "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.22.5.tgz", - "integrity": "sha512-mM4COjgZox8U+JcXQwPijIZLElkgEpO5rsERVDJTc2qfCDfERyob6k5WegS14SX18IIjv+XD+GrqNumY5JRCDw==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.23.4.tgz", + "integrity": "sha512-803gmbQdqwdf4olxrX4AJyFBV/RTr3rSmOj0rKwesmzlfhYNDEs+/iOcznzpNWlJlIlTJC2QfPFcHB6DlzdVLQ==", "dev": true, "engines": { "node": ">=6.9.0" @@ -374,9 +374,9 @@ } }, "node_modules/@babel/highlight": { - "version": "7.22.20", - "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.22.20.tgz", - "integrity": "sha512-dkdMCN3py0+ksCgYmGG8jKeGA/8Tk+gJwSYYlFGxG5lmhfKNoAy004YpLxpS1W2J8m/EK2Ew+yOs9pVRwO89mg==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.23.4.tgz", + "integrity": "sha512-acGdbYSfp2WheJoJm/EBBBLh/ID8KDc64ISZ9DYtBmC8/Q204PZJLHyzeB5qMzJ5trcOkybd78M4x2KWsUq++A==", "dev": true, "dependencies": { "@babel/helper-validator-identifier": "^7.22.20", @@ -459,9 +459,9 @@ } }, "node_modules/@babel/parser": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.23.0.tgz", - "integrity": "sha512-vvPKKdMemU85V9WE/l5wZEmImpCtLqbnTvqDS2U1fJ96KrxoW7KrXhNsNCblQlg8Ck4b85yxdTyelsMUgFUXiw==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.23.4.tgz", + "integrity": "sha512-vf3Xna6UEprW+7t6EtOmFpHNAuxw3xqPZghy+brsnusscJRW5BMUzzHZc5ICjULee81WeUV2jjakG09MDglJXQ==", "dev": true, "bin": { "parser": "bin/babel-parser.js" @@ -662,19 +662,19 @@ } }, "node_modules/@babel/traverse": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.23.0.tgz", - "integrity": "sha512-t/QaEvyIoIkwzpiZ7aoSKK8kObQYeF7T2v+dazAYCb8SXtp58zEVkWW7zAnju8FNKNdr4ScAOEDmMItbyOmEYw==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.23.4.tgz", + "integrity": "sha512-IYM8wSUwunWTB6tFC2dkKZhxbIjHoWemdK+3f8/wq8aKhbUscxD5MX72ubd90fxvFknaLPeGw5ycU84V1obHJg==", "dev": true, "dependencies": { - "@babel/code-frame": "^7.22.13", - "@babel/generator": "^7.23.0", + "@babel/code-frame": "^7.23.4", + "@babel/generator": "^7.23.4", "@babel/helper-environment-visitor": "^7.22.20", "@babel/helper-function-name": "^7.23.0", "@babel/helper-hoist-variables": "^7.22.5", "@babel/helper-split-export-declaration": "^7.22.6", - "@babel/parser": "^7.23.0", - "@babel/types": "^7.23.0", + "@babel/parser": "^7.23.4", + "@babel/types": "^7.23.4", "debug": "^4.1.0", "globals": "^11.1.0" }, @@ -683,12 +683,12 @@ } }, "node_modules/@babel/types": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.23.0.tgz", - "integrity": "sha512-0oIyUfKoI3mSqMvsxBdclDwxXKXAUA8v/apZbc+iSyARYou1o8ZGDxbUYyLFoW2arqS2jDGqJuZvv1d/io1axg==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.23.4.tgz", + "integrity": "sha512-7uIFwVYpoplT5jp/kVv6EF93VaJ8H+Yn5IczYiaAi98ajzjfoZfslet/e0sLh+wVBjb2qqIut1b0S26VSafsSQ==", "dev": true, "dependencies": { - "@babel/helper-string-parser": "^7.22.5", + "@babel/helper-string-parser": "^7.23.4", "@babel/helper-validator-identifier": "^7.22.20", "to-fast-properties": "^2.0.0" }, @@ -4344,12 +4344,12 @@ "requires": {} }, "@babel/code-frame": { - "version": "7.22.13", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.22.13.tgz", - "integrity": "sha512-XktuhWlJ5g+3TJXc5upd9Ks1HutSArik6jf2eAjYFyIOf4ej3RN+184cZbzDvbPnuTJIUhPKKJE3cIsYTiAT3w==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.4.tgz", + "integrity": "sha512-r1IONyb6Ia+jYR2vvIDhdWdlTGhqbBoFqLTQidzZ4kepUFH15ejXvFHxCVbtl7BOXIudsIubf4E81xeA3h3IXA==", "dev": true, "requires": { - "@babel/highlight": "^7.22.13", + "@babel/highlight": "^7.23.4", "chalk": "^2.4.2" }, "dependencies": { @@ -4441,12 +4441,12 @@ } }, "@babel/generator": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.0.tgz", - "integrity": "sha512-lN85QRR+5IbYrMWM6Y4pE/noaQtg4pNiqeNGX60eqOfo6gtEj6uw/JagelB8vVztSd7R6M5n1+PQkDbHbBRU4g==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.4.tgz", + "integrity": "sha512-esuS49Cga3HcThFNebGhlgsrVLkvhqvYDTzgjfFFlHJcIfLe5jFmRRfCQ1KuBfc4Jrtn3ndLgKWAKjBE+IraYQ==", "dev": true, "requires": { - "@babel/types": "^7.23.0", + "@babel/types": "^7.23.4", "@jridgewell/gen-mapping": "^0.3.2", "@jridgewell/trace-mapping": "^0.3.17", "jsesc": "^2.5.1" @@ -4537,9 +4537,9 @@ } }, "@babel/helper-string-parser": { - "version": "7.22.5", - "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.22.5.tgz", - "integrity": "sha512-mM4COjgZox8U+JcXQwPijIZLElkgEpO5rsERVDJTc2qfCDfERyob6k5WegS14SX18IIjv+XD+GrqNumY5JRCDw==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.23.4.tgz", + "integrity": "sha512-803gmbQdqwdf4olxrX4AJyFBV/RTr3rSmOj0rKwesmzlfhYNDEs+/iOcznzpNWlJlIlTJC2QfPFcHB6DlzdVLQ==", "dev": true }, "@babel/helper-validator-identifier": { @@ -4566,9 +4566,9 @@ } }, "@babel/highlight": { - "version": "7.22.20", - "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.22.20.tgz", - "integrity": "sha512-dkdMCN3py0+ksCgYmGG8jKeGA/8Tk+gJwSYYlFGxG5lmhfKNoAy004YpLxpS1W2J8m/EK2Ew+yOs9pVRwO89mg==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.23.4.tgz", + "integrity": "sha512-acGdbYSfp2WheJoJm/EBBBLh/ID8KDc64ISZ9DYtBmC8/Q204PZJLHyzeB5qMzJ5trcOkybd78M4x2KWsUq++A==", "dev": true, "requires": { "@babel/helper-validator-identifier": "^7.22.20", @@ -4635,9 +4635,9 @@ } }, "@babel/parser": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.23.0.tgz", - "integrity": "sha512-vvPKKdMemU85V9WE/l5wZEmImpCtLqbnTvqDS2U1fJ96KrxoW7KrXhNsNCblQlg8Ck4b85yxdTyelsMUgFUXiw==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.23.4.tgz", + "integrity": "sha512-vf3Xna6UEprW+7t6EtOmFpHNAuxw3xqPZghy+brsnusscJRW5BMUzzHZc5ICjULee81WeUV2jjakG09MDglJXQ==", "dev": true }, "@babel/plugin-syntax-async-generators": { @@ -4778,30 +4778,30 @@ } }, "@babel/traverse": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.23.0.tgz", - "integrity": "sha512-t/QaEvyIoIkwzpiZ7aoSKK8kObQYeF7T2v+dazAYCb8SXtp58zEVkWW7zAnju8FNKNdr4ScAOEDmMItbyOmEYw==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.23.4.tgz", + "integrity": "sha512-IYM8wSUwunWTB6tFC2dkKZhxbIjHoWemdK+3f8/wq8aKhbUscxD5MX72ubd90fxvFknaLPeGw5ycU84V1obHJg==", "dev": true, "requires": { - "@babel/code-frame": "^7.22.13", - "@babel/generator": "^7.23.0", + "@babel/code-frame": "^7.23.4", + "@babel/generator": "^7.23.4", "@babel/helper-environment-visitor": "^7.22.20", "@babel/helper-function-name": "^7.23.0", "@babel/helper-hoist-variables": "^7.22.5", "@babel/helper-split-export-declaration": "^7.22.6", - "@babel/parser": "^7.23.0", - "@babel/types": "^7.23.0", + "@babel/parser": "^7.23.4", + "@babel/types": "^7.23.4", "debug": "^4.1.0", "globals": "^11.1.0" } }, "@babel/types": { - "version": "7.23.0", - "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.23.0.tgz", - "integrity": "sha512-0oIyUfKoI3mSqMvsxBdclDwxXKXAUA8v/apZbc+iSyARYou1o8ZGDxbUYyLFoW2arqS2jDGqJuZvv1d/io1axg==", + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.23.4.tgz", + "integrity": "sha512-7uIFwVYpoplT5jp/kVv6EF93VaJ8H+Yn5IczYiaAi98ajzjfoZfslet/e0sLh+wVBjb2qqIut1b0S26VSafsSQ==", "dev": true, "requires": { - "@babel/helper-string-parser": "^7.22.5", + "@babel/helper-string-parser": "^7.23.4", "@babel/helper-validator-identifier": "^7.22.20", "to-fast-properties": "^2.0.0" } diff --git a/lib/workload/stateless/metadata_manager/src/package.json b/lib/workload/stateless/metadata_manager/src/package.json index 933386d33..4d9953b15 100644 --- a/lib/workload/stateless/metadata_manager/src/package.json +++ b/lib/workload/stateless/metadata_manager/src/package.json @@ -12,32 +12,33 @@ "build-src": "NODE_OPTIONS='--max-old-space-size=8192' tsc" }, "dependencies": { - "@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", + "@fastify/aws-lambda": "^3.5.0", + "@fastify/http-proxy": "^9.3.0", + "@fastify/swagger": "^8.14.0", + "@fastify/swagger-ui": "^2.1.0", + "axios": "^1.6.5", + "edgedb": "^1.4.1", + "fastify": "^4.25.2", + "fastify-type-provider-zod": "^1.1.9", + "google-auth-library": "^9.4.2", + "google-spreadsheet": "^4.1.1", "lodash": "^4.17.21", - "pino": "^8.15.1", - "pino-pretty": "^10.1.0", - "reflect-metadata": "^0.1.13", - "ts-node": "^10.9.1", + "pino": "^8.17.2", + "pino-pretty": "^10.3.1", + "reflect-metadata": "^0.2.1", + "ts-node": "^10.9.2", "tsyringe": "^4.8.0", "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", + "@edgedb/generate": "^0.4.1", + "@types/lodash": "^4.14.202", + "@types/node": "^20.11.5", + "jest": "^29.7.0", + "nodemon": "^3.0.3", "ts-jest": "^29.1.1", - "tsx": "^3.12.7", - "typescript": "^5.1.6" + "ts-to-zod": "^3.6.1", + "typescript": "^5.3.3" } } 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 31b47e7fa..a390ceb43 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 @@ -1,6 +1,32 @@ +import { z } from 'zod'; import { FastifyInstance } from 'fastify'; import { DependencyContainer } from 'tsyringe'; import { MetadataService } from '../../service/metadata'; +import { + selectAllLibraryQueryArgsSchema, + selectAllLibraryQueryReturnsSchema, + selectAllSpecimenQueryArgsSchema, + selectAllSpecimenQueryReturnsSchema, + selectAllSubjectQueryArgsSchema, + selectAllSubjectQueryReturnsSchema, +} from '../../../dbschema/queriesZodSchema'; + +/** + * Query parameter only accept string where pagination needs to be number, this function will + * add coerce to zod schema to convert these pagination value to numbers + * + * @param zodSchema The raw ZodSchema (that is not coerce) + * @returns + */ + +const coercePaginationType = >(zodSchema: Z) => { + const paginationSchema = z.object({ + offset: z.coerce.number().optional().nullable(), + limit: z.coerce.number().optional().nullable(), + }); + + return zodSchema.omit({ offset: true, limit: true }).merge(paginationSchema); +}; export const internalRoutes = async ( fastify: FastifyInstance, @@ -8,15 +34,63 @@ export const internalRoutes = async ( ) => { const metadataService = opts.container.resolve(MetadataService); - fastify.get('/library', async () => { - return metadataService.getAllLibrary(); - }); + fastify.get( + '/library', + { + schema: { + tags: ['library'], + query: coercePaginationType(selectAllLibraryQueryArgsSchema), + response: { + 200: { + description: 'Successful', + type: 'object', + properties: selectAllLibraryQueryReturnsSchema, + }, + }, + }, + }, + async (req, res) => { + return metadataService.getAllLibrary(req.query); + } + ); - fastify.get('/specimen', async () => { - return metadataService.getAllSpecimen(); - }); + fastify.get( + '/specimen', + { + schema: { + tags: ['specimen'], + query: coercePaginationType(selectAllSpecimenQueryArgsSchema), + response: { + 200: { + description: 'Successful', + type: 'object', + properties: selectAllSpecimenQueryReturnsSchema, + }, + }, + }, + }, + async (req, res) => { + return metadataService.getAllSpecimen(req.query); + } + ); - fastify.get('/subject', async () => { - return metadataService.getAllSubject(); - }); + fastify.get( + '/subject', + { + schema: { + tags: ['subject'], + query: coercePaginationType(selectAllSubjectQueryArgsSchema), + response: { + 200: { + description: 'Successful', + type: 'object', + properties: selectAllSubjectQueryReturnsSchema, + }, + }, + }, + }, + async (req, res) => { + return metadataService.getAllSubject(req.query); + } + ); }; diff --git a/lib/workload/stateless/metadata_manager/src/src/app.ts b/lib/workload/stateless/metadata_manager/src/src/app.ts index 764ef66c0..7a0acc247 100644 --- a/lib/workload/stateless/metadata_manager/src/src/app.ts +++ b/lib/workload/stateless/metadata_manager/src/src/app.ts @@ -1,7 +1,16 @@ import Fastify, { FastifyBaseLogger, FastifyInstance } from 'fastify'; +import fastifySwagger from '@fastify/swagger'; +import fastifySwaggerUi from '@fastify/swagger-ui'; import { DependencyContainer } from 'tsyringe'; import { internalRoutes } from './api/routes/internal-routes'; import { gqlRoutes } from './api/routes/graphql-routes'; +import { + jsonSchemaTransform, + createJsonSchemaTransform, + serializerCompiler, + validatorCompiler, + ZodTypeProvider, +} from 'fastify-type-provider-zod'; export class App { public readonly server: FastifyInstance; @@ -24,11 +33,48 @@ export class App { } public async setupServer(): Promise { - // Register Fastify routing - this.server.register(internalRoutes, { + // TypeProvider + this.server.setValidatorCompiler(validatorCompiler); + this.server.setSerializerCompiler(serializerCompiler); + this.server.withTypeProvider(); + + // OpenAPI + await this.server.register(fastifySwagger, { + // openapi 3.0.3 options + openapi: { + info: { + title: 'OrcaBus - Metadata Manager', + description: 'one of the microservice in OrcaBus that handles on metadata', + version: '0.0.1', + license: { name: 'MIT License' }, + }, + components: { + securitySchemes: { + apiKey: { + type: 'apiKey', + name: 'Authorization', + in: 'header', + }, + }, + }, + }, + hideUntagged: true, + transform: jsonSchemaTransform, + }); + + await this.server.register(fastifySwaggerUi, { + routePrefix: '/documentation', + uiConfig: { + docExpansion: 'full', + deepLinking: false, + }, + }); + + // Register API Routing for the app + await this.server.register(internalRoutes, { container: this.dc, }); - this.server.register(gqlRoutes, { + await this.server.register(gqlRoutes, { container: this.dc, prefix: '/graphql', }); diff --git a/lib/workload/stateless/metadata_manager/src/src/bootstrap/settings.ts b/lib/workload/stateless/metadata_manager/src/src/bootstrap/settings.ts index 753b9397c..c27a4354a 100644 --- a/lib/workload/stateless/metadata_manager/src/src/bootstrap/settings.ts +++ b/lib/workload/stateless/metadata_manager/src/src/bootstrap/settings.ts @@ -1,9 +1,9 @@ -export type SettingsType = { +export type SettingType = { port: number; host: string; }; -export default function getAppSettings(): SettingsType { +export default function getAppSettings(): SettingType { const isDevelopment = process.env.NODE_ENV === 'development'; if (isDevelopment) { diff --git a/lib/workload/stateless/metadata_manager/src/src/index.ts b/lib/workload/stateless/metadata_manager/src/src/index.ts index 195ef56ed..45a284583 100644 --- a/lib/workload/stateless/metadata_manager/src/src/index.ts +++ b/lib/workload/stateless/metadata_manager/src/src/index.ts @@ -11,7 +11,6 @@ import getAppSettings from './bootstrap/settings'; const dc = await createDependencyContainer(); const app = new App(dc); - // Setting/registering server routes const server = await app.setupServer(); server.listen({ host: appSettings.host, port: appSettings.port }, (err, address) => { diff --git a/lib/workload/stateless/metadata_manager/src/src/service/metadata.ts b/lib/workload/stateless/metadata_manager/src/src/service/metadata.ts index c5b6cb43d..2b8c58af9 100644 --- a/lib/workload/stateless/metadata_manager/src/src/service/metadata.ts +++ b/lib/workload/stateless/metadata_manager/src/src/service/metadata.ts @@ -20,6 +20,8 @@ import { updateLibraryRecord, } from './helpers/metadata/library-helper'; import { + SelectAllLibraryQueryArgs, + SelectAllSubjectQueryArgs, deleteLibraryByOrcaBusId, deleteSpecimenByOrcaBusId, deleteSubjectByOrcaBusId, @@ -98,8 +100,8 @@ export class MetadataService { * @returns */ protected async checkAndRemoveSubject(sourceInternalIdArray: string[]) { - const allExistingSubject = await selectAllSubjectQuery(this.edgeDbClient); - for (const s of allExistingSubject) { + const allExistingSubject = await selectAllSubjectQuery(this.edgeDbClient, {}); + for (const s of allExistingSubject.results) { const shouldRetain = !!sourceInternalIdArray.find( (sourceInternalId) => sourceInternalId == s.internalId ); @@ -186,8 +188,8 @@ export class MetadataService { * @returns */ protected async checkAndRemoveSpecimen(sourceInternalIdArray: string[]) { - const allExistingSpc = await selectAllSpecimenQuery(this.edgeDbClient); - for (const s of allExistingSpc) { + const allExistingSpc = await selectAllSpecimenQuery(this.edgeDbClient, {}); + for (const s of allExistingSpc.results) { const shouldRetain = !!sourceInternalIdArray.find( (sourceInternalId) => sourceInternalId == s.internalId ); @@ -262,8 +264,8 @@ export class MetadataService { * @returns */ protected async checkAndRemoveLibrary(sourceInternalIdArray: string[]) { - const allExistingLib = await selectAllLibraryQuery(this.edgeDbClient); - for (const s of allExistingLib) { + const allExistingLib = await selectAllLibraryQuery(this.edgeDbClient, {}); + for (const s of allExistingLib.results) { const shouldRetain = !!sourceInternalIdArray.find( (sourceInternalId) => sourceInternalId == s.internalId ); @@ -344,15 +346,15 @@ export class MetadataService { await this.checkAndRemoveLibrary(internalIdArrays.library); } - public async getAllLibrary() { - return await selectAllLibraryQuery(this.edgeDbClient); + public async getAllLibrary(libraryQuery: SelectAllLibraryQueryArgs) { + return await selectAllLibraryQuery(this.edgeDbClient, libraryQuery); } - public async getAllSpecimen() { - return await selectAllSpecimenQuery(this.edgeDbClient); + public async getAllSpecimen(specimenQuery: SelectAllSubjectQueryArgs) { + return await selectAllSpecimenQuery(this.edgeDbClient, specimenQuery); } - public async getAllSubject() { - return await selectAllSubjectQuery(this.edgeDbClient); + public async getAllSubject(subjectQuery: SelectAllSubjectQueryArgs) { + return await selectAllSubjectQuery(this.edgeDbClient, subjectQuery); } } diff --git a/lib/workload/stateless/metadata_manager/src/yarn.lock b/lib/workload/stateless/metadata_manager/src/yarn.lock index 591aa7d58..e25333626 100644 --- a/lib/workload/stateless/metadata_manager/src/yarn.lock +++ b/lib/workload/stateless/metadata_manager/src/yarn.lock @@ -496,352 +496,21 @@ __metadata: languageName: node 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