Merge pull request #21168 from mvdbeek/dev_openapi_typescript

Merge 25.1 into dev, fix openapi schema generation for TypedDict

Author: mvdbeek

Makefile

@@ -203,8 +203,8 @@ remove-api-schema:
 	rm _shed_schema.yaml
 
 update-client-api-schema: client-node-deps build-api-schema ## Update client API schema
-	$(IN_VENV) cd client && npx openapi-typescript ../_schema.yaml > src/api/schema/schema.ts && npx prettier --write src/api/schema/schema.ts
-	$(IN_VENV) cd client && npx openapi-typescript ../_shed_schema.yaml > ../lib/tool_shed/webapp/frontend/src/schema/schema.ts && npx prettier --write ../lib/tool_shed/webapp/frontend/src/schema/schema.ts
+	$(IN_VENV) cd client && yarn openapi-typescript ../_schema.yaml -o src/api/schema/schema.ts && yarn prettier --write src/api/schema/schema.ts
+	$(IN_VENV) cd client && yarn openapi-typescript ../_shed_schema.yaml -o ../lib/tool_shed/webapp/frontend/src/schema/schema.ts && yarn prettier --write ../lib/tool_shed/webapp/frontend/src/schema/schema.ts
 	$(MAKE) remove-api-schema
 
 lint-api-schema: build-api-schema

client/src/api/schema/schema.ts

@@ -43,9 +43,6 @@ export default {
                 reloadEditor = false;
                 this.skipNextReload = false;
             }
-            if (reloadEditor) {
-                this.editorReloadKey += 1;
-            }
 
             this.version = Query.get("version");
             this.storedWorkflowId = Query.get("id");
@@ -59,6 +56,10 @@ export default {
                 const { id: storedWorkflowId } = await getWorkflowInfo(workflowId, this.version, true);
                 this.storedWorkflowId = storedWorkflowId;
             }
+
+            if (reloadEditor) {
+                this.editorReloadKey += 1;
+            }
         },
     },
 };

client/src/entry/analysis/modules/WorkflowEditor.vue

@@ -2,7 +2,7 @@
 psycopg2-binary==2.9.10
 mysqlclient
 fluent-logger
-sentry-sdk[fastapi]
+sentry-sdk
 pbs_python
 drmaa
 statsd

client/yarn.lock

@@ -388,7 +388,8 @@ class LimitedUserModel(Model):
 SampleSheetColumnValueT = Union[int, float, bool, str, NoneType]
 
 
-class SampleSheetColumnDefinition(TypedDict):
+# type ignore because mypy can't handle closed TypedDicts yet
+class SampleSheetColumnDefinition(TypedDict, closed=True):  # type: ignore[call-arg]
     name: str
     description: NotRequired[Optional[str]]
     type: SampleSheetColumnType

lib/galaxy/dependencies/conditional-requirements.txt

@@ -170,7 +170,8 @@ class DrillDownOptionsDict(TypedDict):
 FieldType = Union[CwlType, List[CwlType]]
 
 
-class FieldDict(TypedDict):
+# type ignore because mypy can't handle closed TypedDicts yet
+class FieldDict(TypedDict, closed=True):  # type: ignore[call-arg]
     name: str
     type: FieldType
     format: NotRequired[Optional[str]]

lib/galaxy/schema/schema.py

@@ -380,6 +380,7 @@ class safe_update(NamedTuple):
     "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
     "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
+    "Convert characters1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
@@ -3193,6 +3194,12 @@ class ExpressionTool(Tool):
     tool_type_local = True
     EXPRESSION_INPUTS_NAME = "_expression_inputs_.json"
 
+    def parse(self, tool_source: ToolSource, guid: Optional[str] = None, dynamic: bool = False) -> None:
+        super().parse(tool_source, guid, dynamic)
+        if self.profile < 19.05:
+            # Expression tools were introduced in 19.05 and we don't want crazy stuff like failing on stderr
+            self.profile = 19.05
+
     def parse_command(self, tool_source):
         self.command = f"cd ../; {expressions.EXPRESSION_SCRIPT_CALL}"
         self.interpreter = None

lib/galaxy/tool_util_models/tool_source.py

@@ -596,6 +596,7 @@ def delete_custom_builds(
         "/api/users",
         name="create_user",
         summary="Create a new Galaxy user. Only admins can create users for now.",
+        require_admin=True,
     )
     def create(
         self,

lib/galaxy/tools/__init__.py

@@ -1437,6 +1437,9 @@ export interface components {
              * @default [
              *       "data"
              *     ]
+             * @example txt
+             * @example tabular
+             * @example tiff
              */
             extensions: string[]
             /**
@@ -1998,17 +2001,24 @@ export interface components {
             /**
              * Checksum
              * @description A production (immutable) tool version is required to have a hashcode. Not required otherwise, but might be useful to detect changes.  This exposes the hashcode for specific image versions to verify that the container version pulled is actually the version that was indexed by the registry.
+             * @example {
+             *       "checksum": "77af4d6b9913e693e8d0b4b294fa62ade6054e6b2f1ffb617ac955dd63fb0182",
+             *       "type": "sha256"
+             *     }
              */
             checksum?: components["schemas"]["Checksum"][] | null
             /**
              * Image Name
              * @description Used in conjunction with a registry_url if provided to locate images.
+             * @example quay.io/seqware/seqware_full/1.1
+             * @example ubuntu:latest
              */
             image_name?: string | null
             image_type?: components["schemas"]["ImageType"] | null
             /**
              * Registry Host
              * @description A docker registry or a URL to a Singularity registry. Used along with image_name to locate a specific image.
+             * @example registry.hub.docker.com
              */
             registry_host?: string | null
             /**
@@ -2194,12 +2204,14 @@ export interface components {
             /**
              * Name
              * @description Name of the organization responsible for the service
+             * @example My organization
              */
             name: string
             /**
              * Url
              * Format: uri
              * @description URL of the website of the organization (RFC 3986 format)
+             * @example https://example.com
              */
             url: string
         }
@@ -2793,36 +2805,43 @@ export interface components {
             /**
              * Contacturl
              * @description URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).
+             * @example mailto:[email protected]
              */
             contactUrl?: string | null
             /**
              * Createdat
              * @description Timestamp describing when the service was first deployed and available (RFC 3339 format)
+             * @example 2019-06-04T12:58:19Z
              */
             createdAt?: string | null
             /**
              * Description
              * @description Description of the service. Should be human readable and provide information about the service.
+             * @example This service provides...
              */
             description?: string | null
             /**
              * Documentationurl
              * @description URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.
+             * @example https://docs.myservice.example.com
              */
             documentationUrl?: string | null
             /**
              * Environment
              * @description Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.
+             * @example test
              */
             environment?: string | null
             /**
              * Id
              * @description Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.
+             * @example org.ga4gh.myservice
              */
             id: string
             /**
              * Name
              * @description Name of this service. Should be human readable.
+             * @example My project
              */
             name: string
             /** @description Organization providing the service */
@@ -2831,11 +2850,13 @@ export interface components {
             /**
              * Updatedat
              * @description Timestamp describing when the service was last updated (RFC 3339 format)
+             * @example 2019-06-04T12:58:19Z
              */
             updatedAt?: string | null
             /**
              * Version
              * @description Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.
+             * @example 1.0.0
              */
             version: string
         }
@@ -2844,16 +2865,19 @@ export interface components {
             /**
              * Artifact
              * @description Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.
+             * @example beacon
              */
             artifact: string
             /**
              * Group
              * @description Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization's reverse domain name).
+             * @example org.ga4gh
              */
             group: string
             /**
              * Version
              * @description Version of the API or specification. GA4GH specifications use semantic versioning.
+             * @example 1.0.0
              */
             version: string
         }
@@ -3023,6 +3047,7 @@ export interface components {
             /**
              * Id
              * @description A unique identifier of the tool, scoped to this registry.
+             * @example 123456
              */
             id: string
             /**
@@ -3044,6 +3069,7 @@ export interface components {
             /**
              * Url
              * @description The URL for this tool in this registry.
+             * @example http://agora.broadinstitute.org/tools/123456
              */
             url: string
             /**
@@ -3300,13 +3326,19 @@ export interface components {
             /**
              * Descriptor Type Version
              * @description A map providing information about the language versions used in this tool. The keys should be the same values used in the `descriptor_type` field, and the value should be an array of all the language versions used for the given `descriptor_type`. Depending on the `descriptor_type` (e.g. CWL) multiple version values may be used in a single tool.
+             * @example {
+             *       "WDL": ["1.0", "1.0"],
+             *       "CWL": ["v1.0.2"],
+             *       "NFL": ["DSL2"]
+             *     }
              */
             descriptor_type_version?: {
                 [key: string]: components["schemas"]["DescriptorTypeVersion"][]
             } | null
             /**
              * Id
              * @description An identifier of the version of this tool for this particular tool registry.
+             * @example v1
              */
             id: string
             /**
@@ -3317,6 +3349,8 @@ export interface components {
             /**
              * Included Apps
              * @description An array of IDs for the applications that are stored inside this tool.
+             * @example https://bio.tools/tool/mytum.de/SNAP2/1
+             * @example https://bio.tools/bioexcel_seqqc
              */
             included_apps?: string[] | null
             /**
@@ -3342,6 +3376,7 @@ export interface components {
             /**
              * Url
              * @description The URL for this tool version in this registry.
+             * @example http://agora.broadinstitute.org/tools/123456/versions/1
              */
             url: string
             /**