Metadata Manager Restructuring (#89)

umccr · Jan 23, 2024 · 346780c · 346780c
1 parent 5b2b5b4
commit 346780c
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Showing 86 changed files with 182 additions and 7,889 deletions.
diff --git a/Makefile b/Makefile
@@ -29,8 +29,8 @@ test:
 # 	Python (conda or venv), Rust and Cargo, TypeScript and Node environment, Docker and Container runtimes
 suite: test
 	@(cd lib/workload/stateless/sequence_run_manager && $(MAKE) test)
+	@(cd lib/workload/stateless/metadata_manager && $(MAKE) test)
 	@#(cd lib/workload/stateless/filemanager && $(MAKE) test)   # FIXME uncomment when ready @Marko
-	@#(cd lib/workload/stateless/metadata_manager && $(MAKE) test)  # FIXME uncomment when ready @William
 
 clean:
 	@yarn clean

diff --git a/...teless/metadata_manager/src/.editorconfig → .../stateless/metadata_manager/.editorconfig b/...teless/metadata_manager/src/.editorconfig → .../stateless/metadata_manager/.editorconfig
diff --git a/...eless/metadata_manager/src/.gitattributes → ...stateless/metadata_manager/.gitattributes b/...eless/metadata_manager/src/.gitattributes → ...stateless/metadata_manager/.gitattributes
diff --git a/...stateless/metadata_manager/src/.gitignore → ...oad/stateless/metadata_manager/.gitignore b/...stateless/metadata_manager/src/.gitignore → ...oad/stateless/metadata_manager/.gitignore
diff --git a/...stateless/metadata_manager/src/Dockerfile → ...oad/stateless/metadata_manager/Dockerfile b/...stateless/metadata_manager/src/Dockerfile → ...oad/stateless/metadata_manager/Dockerfile
@@ -10,5 +10,6 @@ COPY dbschema/migrations ./dbschema/migrations
 COPY dbschema/*.esdl ./dbschema/
 
 RUN make install
+RUN make edgetypes
 
-ENTRYPOINT [ "make", "start", "EDGEDB_HOST=edgedb" ]
+ENTRYPOINT [ "cross-env" "EDGEDB_HOST=edgedb" "yarn" "start" ]
diff --git a/...d/stateless/metadata_manager/src/Makefile → ...kload/stateless/metadata_manager/Makefile b/...d/stateless/metadata_manager/src/Makefile → ...kload/stateless/metadata_manager/Makefile
@@ -1,22 +1,24 @@
 EDGEDB_HOST ?= localhost
 
-# Installation
+# installation
 install:
 	@yarn install
 
-# To run docker compose
+# docker compose shortcut
 up:
-	@docker compose up -d
+	@docker compose up --wait -d
 
 down:
 	@docker compose down
 
 stop:
 	@docker compose down
 
-# Build the app for deployment
+docker-edgedb:
+	@docker compose up --wait -d edgedb
 
-edgetypes:
+# asset build
+edgetypes: | docker-edgedb
 	@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
@@ -35,31 +37,38 @@ build: edgetypes
 	@rm -rf nodejs
 
 # Testing
-test:
+
+# full test pipeline
+test: install docker-edgedb edgetypes suite
+
+suite:
 	@yarn test
 
 # Starting server
-start: edgetypes
-	@yarn start
-start-scenario-1: edgetypes
-	@yarn run insert-scenario-1
+start: up
+
+stop: down 
+
+# development
+start-dev: docker-edgedb edgetypes
 	@yarn start
 
-# Start in watch mode
-watch: edgetypes
+watch-dev: docker-edgedb edgetypes
 	@yarn run insert-scenario-1
 	@yarn watch
 
-# Inserting scenarios
+insert-scenario-1:
+	@yarn run insert-scenario-1
+
 insert-scenario-2:
 	@yarn run insert-scenario-2
 
 # Shortcut of edgedb cli
-edgedb:
+edgedb: | docker-edgedb
 	@edgedb --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
-edgedb-ui:
+edgedb-ui: | docker-edgedb
 	@edgedb ui --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure --no-server-check # pragma: allowlist secret
-edgedb-migrate:
+edgedb-migrate: | docker-edgedb
 	@edgedb migrate --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
-edgedb-migration-create:
+edgedb-migration-create: | docker-edgedb
 	@edgedb migration create --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
diff --git a/.../stateless/metadata_manager/src/README.md → ...load/stateless/metadata_manager/README.md b/.../stateless/metadata_manager/src/README.md → ...load/stateless/metadata_manager/README.md
diff --git a/...ateless/metadata_manager/src/compose.yaml → ...d/stateless/metadata_manager/compose.yaml b/...ateless/metadata_manager/src/compose.yaml → ...d/stateless/metadata_manager/compose.yaml
@@ -12,6 +12,12 @@ services:
       - './dbschema:/dbschema'
     ports:
       - '5656:5656'
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://edgedb:5656/server/status/alive"]
+      interval: 30s
+      timeout: 60s
+      retries: 5
+      start_period: 30s
 
   app:
     build: .
@@ -26,3 +32,6 @@ services:
       - '8080:8080'
     links:
       - edgedb
+    depends_on:
+      edgedb:
+        condition: service_healthy
diff --git a/.../metadata_manager/src/dbschema/audit.esdl → ...less/metadata_manager/dbschema/audit.esdl b/.../metadata_manager/src/dbschema/audit.esdl → ...less/metadata_manager/dbschema/audit.esdl
diff --git a/...tadata_manager/src/dbschema/metadata.esdl → ...s/metadata_manager/dbschema/metadata.esdl b/...tadata_manager/src/dbschema/metadata.esdl → ...s/metadata_manager/dbschema/metadata.esdl
diff --git a/...ager/src/dbschema/migrations/00001.edgeql → ..._manager/dbschema/migrations/00001.edgeql b/...ager/src/dbschema/migrations/00001.edgeql → ..._manager/dbschema/migrations/00001.edgeql
diff --git a/...eries/audit/insertSystemAuditEvent.edgeql → ...eries/audit/insertSystemAuditEvent.edgeql b/...eries/audit/insertSystemAuditEvent.edgeql → ...eries/audit/insertSystemAuditEvent.edgeql
diff --git a/...eries/audit/updateSystemAuditEvent.edgeql → ...eries/audit/updateSystemAuditEvent.edgeql b/...eries/audit/updateSystemAuditEvent.edgeql → ...eries/audit/updateSystemAuditEvent.edgeql
diff --git a/...a/library/deleteLibraryByOrcaBusId.edgeql → ...a/library/deleteLibraryByOrcaBusId.edgeql b/...a/library/deleteLibraryByOrcaBusId.edgeql → ...a/library/deleteLibraryByOrcaBusId.edgeql
diff --git a/...etadata/library/insertLibraryQuery.edgeql → ...etadata/library/insertLibraryQuery.edgeql b/...etadata/library/insertLibraryQuery.edgeql → ...etadata/library/insertLibraryQuery.edgeql
diff --git a/...data/library/selectAllLibraryQuery.edgeql → ...data/library/selectAllLibraryQuery.edgeql b/...data/library/selectAllLibraryQuery.edgeql → ...data/library/selectAllLibraryQuery.edgeql
diff --git a/...ary/selectLibraryByInternalIdQuery.edgeql → ...ary/selectLibraryByInternalIdQuery.edgeql b/...ary/selectLibraryByInternalIdQuery.edgeql → ...ary/selectLibraryByInternalIdQuery.edgeql
diff --git a/...etadata/library/updateLibraryQuery.edgeql → ...etadata/library/updateLibraryQuery.edgeql b/...etadata/library/updateLibraryQuery.edgeql → ...etadata/library/updateLibraryQuery.edgeql
diff --git a/...specimen/deleteSpecimenByOrcaBusId.edgeql → ...specimen/deleteSpecimenByOrcaBusId.edgeql b/...specimen/deleteSpecimenByOrcaBusId.edgeql → ...specimen/deleteSpecimenByOrcaBusId.edgeql
diff --git a/...adata/specimen/insertSpecimenQuery.edgeql → ...adata/specimen/insertSpecimenQuery.edgeql b/...adata/specimen/insertSpecimenQuery.edgeql → ...adata/specimen/insertSpecimenQuery.edgeql
diff --git a/...ta/specimen/selectAllSpecimenQuery.edgeql → ...ta/specimen/selectAllSpecimenQuery.edgeql b/...ta/specimen/selectAllSpecimenQuery.edgeql → ...ta/specimen/selectAllSpecimenQuery.edgeql
diff --git a/...en/selectSpecimenByInternalIdQuery.edgeql → ...en/selectSpecimenByInternalIdQuery.edgeql b/...en/selectSpecimenByInternalIdQuery.edgeql → ...en/selectSpecimenByInternalIdQuery.edgeql
diff --git a/...adata/specimen/updateSpecimenQuery.edgeql → ...adata/specimen/updateSpecimenQuery.edgeql b/...adata/specimen/updateSpecimenQuery.edgeql → ...adata/specimen/updateSpecimenQuery.edgeql
diff --git a/...a/subject/deleteSubjectByOrcaBusId.edgeql → ...a/subject/deleteSubjectByOrcaBusId.edgeql b/...a/subject/deleteSubjectByOrcaBusId.edgeql → ...a/subject/deleteSubjectByOrcaBusId.edgeql
diff --git a/...etadata/subject/insertSubjectQuery.edgeql → ...etadata/subject/insertSubjectQuery.edgeql b/...etadata/subject/insertSubjectQuery.edgeql → ...etadata/subject/insertSubjectQuery.edgeql
diff --git a/...data/subject/selectAllSubjectQuery.edgeql → ...data/subject/selectAllSubjectQuery.edgeql b/...data/subject/selectAllSubjectQuery.edgeql → ...data/subject/selectAllSubjectQuery.edgeql
diff --git a/...ect/selectSubjectByInternalIdQuery.edgeql → ...ect/selectSubjectByInternalIdQuery.edgeql b/...ect/selectSubjectByInternalIdQuery.edgeql → ...ect/selectSubjectByInternalIdQuery.edgeql
diff --git a/...etadata/subject/updateSubjectQuery.edgeql → ...etadata/subject/updateSubjectQuery.edgeql b/...etadata/subject/updateSubjectQuery.edgeql → ...etadata/subject/updateSubjectQuery.edgeql
diff --git a/...ess/metadata_manager/src/deploy/README.md → ...ateless/metadata_manager/deploy/README.md b/...ess/metadata_manager/src/deploy/README.md → ...ateless/metadata_manager/deploy/README.md
diff --git a/...nager/src/deploy/construct/app/Dockerfile → ...a_manager/deploy/construct/app/Dockerfile b/...nager/src/deploy/construct/app/Dockerfile → ...a_manager/deploy/construct/app/Dockerfile
diff --git a/...src/deploy/construct/app/app-construct.ts → ...ger/deploy/construct/app/app-construct.ts b/...src/deploy/construct/app/app-construct.ts → ...ger/deploy/construct/app/app-construct.ts
diff --git a/...r/src/deploy/construct/edge-db/Dockerfile → ...nager/deploy/construct/edge-db/Dockerfile b/...r/src/deploy/construct/edge-db/Dockerfile → ...nager/deploy/construct/edge-db/Dockerfile
diff --git a/...oy/construct/edge-db/edge-db-construct.ts → ...oy/construct/edge-db/edge-db-construct.ts b/...oy/construct/edge-db/edge-db-construct.ts → ...oy/construct/edge-db/edge-db-construct.ts
diff --git a/...ge-db-load-balancer-protocol-construct.ts → ...ge-db-load-balancer-protocol-construct.ts b/...ge-db-load-balancer-protocol-construct.ts → ...ge-db-load-balancer-protocol-construct.ts
diff --git a/...ruct/edge-db/edge-db-service-construct.ts → ...ruct/edge-db/edge-db-service-construct.ts b/...ruct/edge-db/edge-db-service-construct.ts → ...ruct/edge-db/edge-db-service-construct.ts
diff --git a/...y/construct/postgres-rds/base-database.ts → ...y/construct/postgres-rds/base-database.ts b/...y/construct/postgres-rds/base-database.ts → ...y/construct/postgres-rds/base-database.ts
diff --git a/...ds/infrastructure-stack-database-props.ts → ...ds/infrastructure-stack-database-props.ts b/...ds/infrastructure-stack-database-props.ts → ...ds/infrastructure-stack-database-props.ts
diff --git a/...uct/postgres-rds/postgres-db-construct.ts → ...uct/postgres-rds/postgres-db-construct.ts b/...uct/postgres-rds/postgres-db-construct.ts → ...uct/postgres-rds/postgres-db-construct.ts
diff --git a/...er/src/deploy/lib/metadataManagerStack.ts → ...anager/deploy/lib/metadataManagerStack.ts b/...er/src/deploy/lib/metadataManagerStack.ts → ...anager/deploy/lib/metadataManagerStack.ts
diff --git a/...tadata_manager/src/docs/edgedb-schema.png → ...s/metadata_manager/docs/edgedb-schema.png b/...tadata_manager/src/docs/edgedb-schema.png → ...s/metadata_manager/docs/edgedb-schema.png
diff --git a/..._manager/src/docs/relationship.drawio.svg → ...data_manager/docs/relationship.drawio.svg b/..._manager/src/docs/relationship.drawio.svg → ...data_manager/docs/relationship.drawio.svg
diff --git a/...eless/metadata_manager/src/jest.config.js → ...stateless/metadata_manager/jest.config.js b/...eless/metadata_manager/src/jest.config.js → ...stateless/metadata_manager/jest.config.js
diff --git a/...ateless/metadata_manager/src/package.json → ...d/stateless/metadata_manager/package.json b/...ateless/metadata_manager/src/package.json → ...d/stateless/metadata_manager/package.json
diff --git a/...ager/src/src/api/routes/graphql-routes.ts → ..._manager/src/api/routes/graphql-routes.ts b/...ager/src/src/api/routes/graphql-routes.ts → ..._manager/src/api/routes/graphql-routes.ts
diff --git a/...ger/src/src/api/routes/internal-routes.ts → ...manager/src/api/routes/internal-routes.ts b/...ger/src/src/api/routes/internal-routes.ts → ...manager/src/api/routes/internal-routes.ts
diff --git a/...stateless/metadata_manager/src/src/app.ts → ...oad/stateless/metadata_manager/src/app.ts b/...stateless/metadata_manager/src/src/app.ts → ...oad/stateless/metadata_manager/src/app.ts
diff --git a/...src/src/bootstrap/dependency-injection.ts → ...ger/src/bootstrap/dependency-injection.ts b/...src/src/bootstrap/dependency-injection.ts → ...ger/src/bootstrap/dependency-injection.ts
diff --git a/...ata_manager/src/src/bootstrap/settings.ts → ...etadata_manager/src/bootstrap/settings.ts b/...ata_manager/src/src/bootstrap/settings.ts → ...etadata_manager/src/bootstrap/settings.ts
diff --git a/lib/workload/stateless/metadata_manager/src/deploy/.gitignore b/lib/workload/stateless/metadata_manager/src/deploy/.gitignore
diff --git a/lib/workload/stateless/metadata_manager/src/deploy/.npmignore b/lib/workload/stateless/metadata_manager/src/deploy/.npmignore
diff --git a/lib/workload/stateless/metadata_manager/src/deploy/asset/README.md b/lib/workload/stateless/metadata_manager/src/deploy/asset/README.md
diff --git a/lib/workload/stateless/metadata_manager/src/deploy/bin/deploy.ts b/lib/workload/stateless/metadata_manager/src/deploy/bin/deploy.ts
diff --git a/lib/workload/stateless/metadata_manager/src/deploy/cdk.json b/lib/workload/stateless/metadata_manager/src/deploy/cdk.json
diff --git a/lib/workload/stateless/metadata_manager/src/deploy/jest.config.js b/lib/workload/stateless/metadata_manager/src/deploy/jest.config.js