Added Swagger UI and Dependencies Bumped (#83)

lib/workload/stateless/metadata_manager/src/.gitignore

@@ -136,6 +136,7 @@ dist
 
 dbschema/edgeql-js
 dbschema/queries.*
+dbschema/queriesZodSchema.ts
 dbschema/interfaces.ts
 
 asset/

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

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 -->
+# GraphQL Endpoint
 http://localhost:8080/graphql/explore (UI)
 http://localhost:8080/graphql (Only for graphql POST method)
 ```

lib/workload/stateless/metadata_manager/src/dbschema/queries/audit/updateSystemAuditEvent.edgeql

@@ -5,5 +5,5 @@ filter .id = <uuid>$auditDbId
 set
 {
   actionOutcome := <ActionOutcome>$actionOutcome,
-  details :=  <json>$details,
+  details :=  <optional json>$details,
 }

lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/library/selectAllLibraryQuery.edgeql

@@ -1,3 +1,48 @@
-select metadata::Library{
-  *
+
+with
+
+  # Pagination parameter
+  offset_ := <optional int16>$offset ?? 0,
+  limit_ := <optional int16>$limit ?? 10,
+
+  libraries := (
+    select metadata::Library {
+      *
+    }
+    filter ( 
+      .orcaBusId ?= <optional str>$orcaBusId ?? .orcaBusId
+        AND
+      .internalId ?= <optional str>$internalId ?? .internalId
+        AND
+      .externalId ?= <optional str>$externalId ?? .externalId
+        AND
+      .phenotype ?= <optional str>$phenotype ?? .phenotype
+        AND
+      .assay ?= <optional str>$assay ?? .assay
+        AND
+      .coverage ?= <optional str>$coverage ?? .coverage
+        AND
+      .quality ?= <optional str>$quality ?? .quality
+        AND
+      .type ?= <optional str>$type ?? .type
+        AND
+      .workflow = <optional metadata::WorkflowTypes>$workflow ?? .workflow
+    )
+  )
+select {
+
+  results := (
+    select libraries {
+      *
+    }
+    offset offset_
+    limit limit_
+  ),
+  pagination := {
+    total := count(libraries),
+    `offset` := offset_,
+    `limit` := limit_
+  }
+
 }
+

lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/specimen/selectAllSpecimenQuery.edgeql

@@ -1,3 +1,37 @@
-select metadata::Specimen{
-  *
+with
+
+  # Pagination parameter
+  offset_ := <optional int16>$offset ?? 0,
+  limit_ := <optional int16>$limit ?? 10,
+
+  libraries := (
+    select metadata::Specimen {
+      *
+    }
+    filter ( 
+      .orcaBusId ?= <optional str>$orcaBusId ?? .orcaBusId
+        AND
+      .internalId ?= <optional str>$internalId ?? .internalId
+        AND
+      .externalId ?= <optional str>$externalId ?? .externalId
+        AND
+      .source ?= <optional str>$source ?? .source
+    )
+  )
+select {
+
+  results := (
+    select libraries {
+      *
+    }
+    offset offset_
+    limit limit_
+  ),
+  pagination := {
+    total := count(libraries),
+    `offset` := offset_,
+    `limit` := limit_
+  }
+
 }
+

lib/workload/stateless/metadata_manager/src/dbschema/queries/metadata/subject/selectAllSubjectQuery.edgeql

@@ -1,3 +1,34 @@
-select metadata::Subject{
-  *
+with
+
+  # Pagination parameter
+  offset_ := <optional int16>$offset ?? 0,
+  limit_ := <optional int16>$limit ?? 10,
+
+  libraries := (
+    select metadata::Subject {
+      *
+    }
+    filter (
+      .orcaBusId ?= <optional str>$orcaBusId ?? .orcaBusId
+        AND
+      .internalId ?= <optional str>$internalId ?? .internalId
+        AND
+      .externalId ?= <optional str>$externalId ?? .externalId
+    )
+  )
+select {
+
+  results := (
+    select libraries {
+      *
+    }
+    offset offset_
+    limit limit_
+  ),
+  pagination := {
+    total := count(libraries),
+    `offset` := offset_,
+    `limit` := limit_
+  }
 }
+