Merge pull request #15105 from mvdbeek/model_class_fix

Fix ``model_class`` field annotations

lib/galaxy/managers/metrics.py

@@ -18,12 +18,7 @@ from galaxy.structured_app import MinimalManagerApp
 log = logging.getLogger(__name__)
 
 
-def datetime_to_iso8601(utc_datetime: datetime) -> str:
-    """
-    Returns the date as string with ISO8601 format.
-    i.e: 2021-01-23T18:25:43.511Z
-    """
-    return f"{utc_datetime.isoformat()}Z"
+SOME_EXAMPLE_DATE = "2021-01-23T18:25:43.511Z"
 
 
 class Metric(BaseModel):
@@ -36,7 +31,7 @@ class Metric(BaseModel):
         ...,  # Required
         title="Timestamp",
         description="The timestamp in ISO format.",
-        example=datetime_to_iso8601(datetime.utcnow()),
+        example=SOME_EXAMPLE_DATE,
     )
     level: int = Field(
         ...,  # Required
@@ -54,11 +49,7 @@ class CreateMetricsPayload(BaseModel):
     metrics: List[Metric] = Field(
         default=[],
         title="List of metrics to be recorded.",
-        example=[
-            Metric(
-                namespace="test-source", time=datetime_to_iso8601(datetime.utcnow()), level=0, args='{"test":"value"}'
-            )
-        ],
+        example=[Metric(namespace="test-source", time=SOME_EXAMPLE_DATE, level=0, args='{"test":"value"}')],
     )
 
 

lib/galaxy/quota/_schema.py

@@ -5,6 +5,10 @@ from typing import (
 )
 
 from pydantic import Field
+from typing_extensions import (
+    Annotated,
+    Literal,
+)
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
@@ -16,10 +20,10 @@ from galaxy.schema.schema import (
     UserModel,
 )
 
-QUOTA_MODEL_CLASS_NAME = "Quota"
-USER_QUOTA_ASSOCIATION_MODEL_CLASS_NAME = "UserQuotaAssociation"
-GROUP_QUOTA_ASSOCIATION_MODEL_CLASS_NAME = "GroupQuotaAssociation"
-DEFAULT_QUOTA_ASSOCIATION_MODEL_CLASS_NAME = "DefaultQuotaAssociation"
+QUOTA = Literal["Quota"]
+USER_QUOTA_ASSOCIATION = Literal["UserQuotaAssociation"]
+GROUP_QUOTA_ASSOCIATION = Literal["GroupQuotaAssociation"]
+DEFAULT_QUOTA_ASSOCIATION = Literal["DefaultQuotaAssociation"]
 
 
 class QuotaOperation(str, Enum):
@@ -66,7 +70,7 @@ QuotaOperationField = Field(
 
 
 class DefaultQuota(Model):  # TODO: should this replace lib.galaxy.model.DefaultQuotaAssociation at some point?
-    model_class: str = ModelClassField(DEFAULT_QUOTA_ASSOCIATION_MODEL_CLASS_NAME)
+    model_class: Annotated[DEFAULT_QUOTA_ASSOCIATION, ModelClassField()]
     type: DefaultQuotaTypes = Field(
         ...,
         title="Type",
@@ -79,7 +83,7 @@ class DefaultQuota(Model):  # TODO: should this replace lib.galaxy.model.Default
 
 
 class UserQuota(Model):
-    model_class: str = ModelClassField(USER_QUOTA_ASSOCIATION_MODEL_CLASS_NAME)
+    model_class: Annotated[USER_QUOTA_ASSOCIATION, ModelClassField()]
     user: UserModel = Field(
         ...,
         title="User",
@@ -88,7 +92,7 @@ class UserQuota(Model):
 
 
 class GroupQuota(Model):
-    model_class: str = ModelClassField(GROUP_QUOTA_ASSOCIATION_MODEL_CLASS_NAME)
+    model_class: Annotated[GROUP_QUOTA_ASSOCIATION, ModelClassField()]
     group: GroupModel = Field(
         ...,
         title="Group",
@@ -99,7 +103,7 @@ class GroupQuota(Model):
 class QuotaBase(Model):
     """Base model containing common fields for Quotas."""
 
-    model_class: str = ModelClassField(QUOTA_MODEL_CLASS_NAME)
+    model_class: Annotated[QUOTA, ModelClassField()]
     id: DecodedDatabaseIdField = Field(
         ...,
         title="ID",

lib/galaxy/schema/fields.py

@@ -94,15 +94,13 @@ class EncodedDatabaseIdField(str, BaseDatabaseIdField):
         return cls.security.decode_id(v)
 
 
-def ModelClassField(class_name: str) -> str:
+def ModelClassField():
     """Represents a database model class name annotated as a constant
     pydantic Field.
     :param class_name: The name of the database class.
     :return: A constant pydantic Field with default annotations for model classes.
     """
     return Field(
-        class_name,
         title="Model class",
         description="The name of the database model class.",
-        const=True,  # Make this field constant
     )

lib/galaxy/schema/schema.py

@@ -50,15 +50,16 @@ from galaxy.schema.types import (
     RelativeUrl,
 )
 
-USER_MODEL_CLASS_NAME = "User"
-GROUP_MODEL_CLASS_NAME = "Group"
-HDA_MODEL_CLASS_NAME = "HistoryDatasetAssociation"
-DC_MODEL_CLASS_NAME = "DatasetCollection"
-DCE_MODEL_CLASS_NAME = "DatasetCollectionElement"
-HDCA_MODEL_CLASS_NAME = "HistoryDatasetCollectionAssociation"
-HISTORY_MODEL_CLASS_NAME = "History"
-JOB_MODEL_CLASS_NAME = "Job"
-STORED_WORKFLOW_MODEL_CLASS_NAME = "StoredWorkflow"
+USER_MODEL_CLASS = Literal["User"]
+GROUP_MODEL_CLASS = Literal["Group"]
+HDA_MODEL_CLASS = Literal["HistoryDatasetAssociation"]
+DC_MODEL_CLASS = Literal["DatasetCollection"]
+DCE_MODEL_CLASS = Literal["DatasetCollectionElement"]
+HDCA_MODEL_CLASS = Literal["HistoryDatasetCollectionAssociation"]
+HISTORY_MODEL_CLASS = Literal["History"]
+JOB_MODEL_CLASS = Literal["Job"]
+STORED_WORKFLOW_MODEL_CLASS = Literal["StoredWorkflow"]
+PAGE_MODEL_CLASS = Literal["Page"]
 
 
 # Generic and common Field annotations that can be reused across models
@@ -204,13 +205,13 @@ class UserModel(Model):
     active: bool = Field(title="Active", description="User is active")
     deleted: bool = Field(title="Deleted", description="User is deleted")
     last_password_change: Optional[datetime] = Field(title="Last password change", description="")
-    model_class: str = ModelClassField(USER_MODEL_CLASS_NAME)
+    model_class: Annotated[USER_MODEL_CLASS, ModelClassField()]
 
 
 class GroupModel(Model):
     """User group model"""
 
-    model_class: str = ModelClassField(GROUP_MODEL_CLASS_NAME)
+    model_class: Annotated[GROUP_MODEL_CLASS, ModelClassField()]
     id: DecodedDatabaseIdField = Field(
         ...,  # Required
         title="ID",
@@ -448,7 +449,7 @@ HdaLddaField = Field(
 class HDADetailed(HDASummary):
     """History Dataset Association detailed information."""
 
-    model_class: str = ModelClassField(HDA_MODEL_CLASS_NAME)
+    model_class: Annotated[HDA_MODEL_CLASS, ModelClassField()]
     hda_ldda: DatasetSourceType = HdaLddaField
     accessible: bool = AccessibleField
     genome_build: Optional[str] = GenomeBuildField
@@ -557,19 +558,21 @@ class HDADetailed(HDASummary):
     )
     annotation: Optional[str] = AnnotationField
     download_url: RelativeUrl = DownloadUrlField
-    type: str = Field(
-        "file",
-        const=True,
-        title="Type",
-        description="This is always `file` for datasets.",
-    )
-    api_type: str = Field(
-        "file",
-        const=True,
-        title="API Type",
-        description="TODO",
-        deprecated=False,  # TODO: Should this field be deprecated as announced in release 16.04?
-    )
+    type: Annotated[
+        Literal["file"],
+        Field(
+            title="Type",
+            description="This is always `file` for datasets.",
+        ),
+    ] = "file"
+    api_type: Annotated[
+        Literal["file"],
+        Field(
+            title="API Type",
+            description="TODO",
+            deprecated=False,  # TODO: Should this field be deprecated as announced in release 16.04?
+        ),
+    ] = "file"
     created_from_basename: Optional[str] = Field(
         None,
         title="Created from basename",
@@ -600,7 +603,7 @@ class HDAExtended(HDADetailed):
 class DCSummary(Model):
     """Dataset Collection summary information."""
 
-    model_class: str = ModelClassField(DC_MODEL_CLASS_NAME)
+    model_class: Annotated[DC_MODEL_CLASS, ModelClassField()]
     id: DecodedDatabaseIdField = EntityIdField
     create_time: datetime = CreateTimeField
     update_time: datetime = UpdateTimeField
@@ -614,7 +617,7 @@ class HDAObject(Model):
     """History Dataset Association Object"""
 
     id: DecodedDatabaseIdField = EntityIdField
-    model_class: str = ModelClassField(HDA_MODEL_CLASS_NAME)
+    model_class: Annotated[HDA_MODEL_CLASS, ModelClassField()]
     state: Dataset.states = DatasetStateField
     hda_ldda: DatasetSourceType = HdaLddaField
     history_id: DecodedDatabaseIdField = HistoryIdField
@@ -627,7 +630,7 @@ class DCObject(Model):
     """Dataset Collection Object"""
 
     id: DecodedDatabaseIdField = EntityIdField
-    model_class: str = ModelClassField(DC_MODEL_CLASS_NAME)
+    model_class: Annotated[DC_MODEL_CLASS, ModelClassField()]
     collection_type: CollectionType = CollectionTypeField
     populated: Optional[bool] = PopulatedField
     element_count: Optional[int] = ElementCountField
@@ -639,7 +642,7 @@ class DCESummary(Model):
     """Dataset Collection Element summary information."""
 
     id: DecodedDatabaseIdField = EntityIdField
-    model_class: str = ModelClassField(DCE_MODEL_CLASS_NAME)
+    model_class: Annotated[DCE_MODEL_CLASS, ModelClassField()]
     element_index: int = Field(
         ...,
         title="Element Index",
@@ -745,15 +748,14 @@ class HDCJobStateSummary(Model):
 class HDCASummary(HistoryItemCommon):
     """History Dataset Collection Association summary information."""
 
-    model_class: str = ModelClassField(
-        HDCA_MODEL_CLASS_NAME
-    )  # TODO: inconsistency? HDASummary does not have model_class only the detailed view has it...
-    type: str = Field(
-        "collection",
-        const=True,
-        title="Type",
-        description="This is always `collection` for dataset collections.",
-    )
+    model_class: Annotated[HDCA_MODEL_CLASS, ModelClassField()]
+    type: Annotated[
+        Literal["collection"],
+        Field(
+            title="Type",
+            description="This is always `collection` for dataset collections.",
+        ),
+    ] = "collection"
     collection_type: CollectionType = CollectionTypeField
     populated_state: DatasetCollection.populated_states = PopulatedStateField
     populated_state_message: Optional[str] = PopulatedStateMessageField
@@ -904,7 +906,7 @@ class UpdateHistoryContentsPayload(HistoryBase):
 class HistorySummary(HistoryBase):
     """History summary information."""
 
-    model_class: str = ModelClassField(HISTORY_MODEL_CLASS_NAME)
+    model_class: Annotated[HISTORY_MODEL_CLASS, ModelClassField()]
     id: DecodedDatabaseIdField = EntityIdField
     name: str = Field(
         ...,
@@ -1467,7 +1469,7 @@ class JobIdResponse(Model):
 
 class JobBaseModel(Model):
     id: DecodedDatabaseIdField = EntityIdField
-    model_class: str = ModelClassField(JOB_MODEL_CLASS_NAME)
+    model_class: Annotated[JOB_MODEL_CLASS, ModelClassField()]
     tool_id: str = Field(
         ...,
         title="Tool ID",
@@ -1506,21 +1508,24 @@ class JobImportHistoryResponse(JobBaseModel):
     )
 
 
-class JobStateSummary(Model):
+class ItemStateSummary(Model):
     id: DecodedDatabaseIdField = EntityIdField
-    model: str = ModelClassField("Job")
     populated_state: DatasetCollection.populated_states = PopulatedStateField
     states: Dict[Job.states, int] = Field(
         {}, title="States", description=("A dictionary of job states and the number of jobs in that state.")
     )
 
 
-class ImplicitCollectionJobsStateSummary(JobStateSummary):
-    model: str = ModelClassField("ImplicitCollectionJobs")
+class JobStateSummary(ItemStateSummary):
+    model: Annotated[Literal["Job"], ModelClassField()]
 
 
-class WorkflowInvocationStateSummary(JobStateSummary):
-    model: str = ModelClassField("WorkflowInvocation")
+class ImplicitCollectionJobsStateSummary(ItemStateSummary):
+    model: Annotated[Literal["ImplicitCollectionJobs"], ModelClassField()]
+
+
+class WorkflowInvocationStateSummary(ItemStateSummary):
+    model: Annotated[Literal["WorkflowInvocation"], ModelClassField()]
 
 
 class JobSummary(JobBaseModel):
@@ -1687,7 +1692,7 @@ class JobFullDetails(JobDetails):
 
 class StoredWorkflowSummary(Model):
     id: DecodedDatabaseIdField = EntityIdField
-    model_class: str = ModelClassField(STORED_WORKFLOW_MODEL_CLASS_NAME)
+    model_class: Annotated[STORED_WORKFLOW_MODEL_CLASS, ModelClassField()]
     create_time: datetime = CreateTimeField
     update_time: datetime = UpdateTimeField
     name: str = Field(
@@ -2176,7 +2181,7 @@ class BasicRoleModel(Model):
 class RoleModel(BasicRoleModel):
     description: Optional[str] = RoleDescriptionField
     url: RelativeUrl = RelativeUrlField
-    model_class: str = ModelClassField("Role")
+    model_class: Annotated[Literal["Role"], ModelClassField()]
 
 
 class RoleDefinitionModel(Model):
@@ -2252,7 +2257,7 @@ class InstalledRepositoryToolShedStatus(Model):
 
 
 class InstalledToolShedRepository(Model):
-    model_class: str = ModelClassField("ToolShedRepository")
+    model_class: Annotated[Literal["ToolShedRepository"], ModelClassField()] = "ToolShedRepository"
     id: EncodedDatabaseIdField = Field(
         ...,
         title="ID",
@@ -2306,7 +2311,7 @@ class LibraryPermissionScope(str, Enum):
 
 
 class LibraryLegacySummary(Model):
-    model_class: str = ModelClassField("Library")
+    model_class: Annotated[Literal["Library"], ModelClassField()]
     id: DecodedDatabaseIdField = Field(
         ...,
         title="ID",
@@ -2553,7 +2558,7 @@ class LibraryFolderPermissionsPayload(LibraryPermissionsPayloadBase):
 
 
 class LibraryFolderDetails(Model):
-    model_class: str = ModelClassField("LibraryFolder")
+    model_class: Annotated[Literal["LibraryFolder"], ModelClassField()]
     id: LibraryFolderDatabaseIdField = Field(
         ...,
         title="ID",
@@ -2811,12 +2816,16 @@ AnyHistoryContentItem = Union[
 ]
 
 
-AnyJobStateSummary = Union[
-    JobStateSummary,
-    ImplicitCollectionJobsStateSummary,
-    WorkflowInvocationStateSummary,
+AnyJobStateSummary = Annotated[
+    Union[
+        JobStateSummary,
+        ImplicitCollectionJobsStateSummary,
+        WorkflowInvocationStateSummary,
+    ],
+    Field(..., discriminator="model"),
 ]
 
+
 HistoryArchiveExportResult = Union[JobExportHistoryArchiveModel, JobIdResponse]
 
 
@@ -3202,12 +3211,7 @@ class PageSummary(PageSummaryBase):
         title="ID",
         description="Encoded ID of the Page.",
     )
-    model_class: str = Field(
-        ...,  # Required
-        title="Model class",
-        description="The class of the model associated with the ID.",
-        example="Page",
-    )
+    model_class: Annotated[PAGE_MODEL_CLASS, ModelClassField()]
     username: str = Field(
         ...,  # Required
         title="Username",

lib/galaxy/webapps/galaxy/services/dataset_collections.py

@@ -12,6 +12,10 @@ from pydantic import (
     Field,
     ValidationError,
 )
+from typing_extensions import (
+    Annotated,
+    Literal,
+)
 
 from galaxy import exceptions
 from galaxy.datatypes.registry import Registry
@@ -64,7 +68,7 @@ class DatasetCollectionAttributesResult(Model):
     dbkey: str = Field(..., description="TODO")
     # Are the following fields really used/needed?
     extension: str = Field(..., description="The dataset file extension.", example="txt")
-    model_class: str = ModelClassField("HistoryDatasetCollectionAssociation")
+    model_class: Annotated[Literal["HistoryDatasetCollectionAssociation"], ModelClassField()]
     dbkeys: Optional[Set[str]]
     extensions: Optional[Set[str]]
     tags: TagCollection