Merge pull request #17153 from heisner-tillman/jobs

Create pydantic model for the return of show operation -  get: `/api/jobs/{job_id}`

client/src/api/schema/schema.ts

@@ -4190,7 +4190,7 @@ export interface components {
              * Command Version
              * @description Tool version indicated during job execution.
              */
-            command_version: string;
+            command_version?: string;
             /**
              * Copied from Job-ID
              * @description Reference to cached job if job execution was cached.
@@ -4218,7 +4218,7 @@ export interface components {
              * @description The (major) version of Galaxy used to create this job.
              * @example 21.05
              */
-            galaxy_version: string;
+            galaxy_version?: string;
             /**
              * History ID
              * @description The encoded ID of the history associated with this item.
@@ -6631,7 +6631,7 @@ export interface components {
              * @description The (major) version of Galaxy used to create this job.
              * @example 21.05
              */
-            galaxy_version: string;
+            galaxy_version?: string;
             /**
              * History ID
              * @description The encoded ID of the history associated with this item.
@@ -6756,6 +6756,12 @@ export interface components {
              */
             value: string;
         };
+        /**
+         * JobMetricCollection
+         * @description Collections of metrics provided by `JobInstrumenter` plugins on a particular job.
+         * @default []
+         */
+        JobMetricCollection: components["schemas"]["JobMetric"][];
         /** JobOutput */
         JobOutput: {
             /**
@@ -9020,6 +9026,163 @@ export interface components {
              */
             short_term_storage_request_id: string;
         };
+        /**
+         * ShowFullJobResponse
+         * @description Basic information about a job.
+         */
+        ShowFullJobResponse: {
+            /**
+             * Command Line
+             * @description The command line produced by the job. Users can see this value if allowed in the configuration, administrator can always see this value.
+             */
+            command_line?: string;
+            /**
+             * Command Version
+             * @description Tool version indicated during job execution.
+             */
+            command_version?: string;
+            /**
+             * Copied from Job-ID
+             * @description Reference to cached job if job execution was cached.
+             * @example 0123456789ABCDEF
+             */
+            copied_from_job_id?: string;
+            /**
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
+             */
+            create_time: string;
+            /**
+             * Job dependencies
+             * @description The dependencies of the job.
+             */
+            dependencies?: Record<string, never>[];
+            /**
+             * Exit Code
+             * @description The exit code returned by the tool. Can be unset if the job is not completed yet.
+             */
+            exit_code?: number;
+            /**
+             * External ID
+             * @description The job id used by the external job runner (Condor, Pulsar, etc.)Only administrator can see this value.
+             */
+            external_id?: string;
+            /**
+             * Galaxy Version
+             * @description The (major) version of Galaxy used to create this job.
+             * @example 21.05
+             */
+            galaxy_version?: string;
+            /**
+             * History ID
+             * @description The encoded ID of the history associated with this item.
+             * @example 0123456789ABCDEF
+             */
+            history_id?: string;
+            /**
+             * ID
+             * @description The encoded ID of this entity.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Inputs
+             * @description Dictionary mapping all the tool inputs (by name) to the corresponding data references.
+             * @default {}
+             */
+            inputs?: {
+                [key: string]: components["schemas"]["EncodedDatasetJobInfo"] | undefined;
+            };
+            /**
+             * Job Messages
+             * @description List with additional information and possible reasons for a failed job.
+             */
+            job_messages?: Record<string, never>[];
+            /**
+             * Job Metrics
+             * @description Collections of metrics provided by `JobInstrumenter` plugins on a particular job. Only administrators can see these metrics.
+             */
+            job_metrics?: components["schemas"]["JobMetricCollection"];
+            /**
+             * Job Standard Error
+             * @description The captured standard error of the job execution.
+             */
+            job_stderr?: string;
+            /**
+             * Job Standard Output
+             * @description The captured standard output of the job execution.
+             */
+            job_stdout?: string;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @default Job
+             * @enum {string}
+             */
+            model_class: "Job";
+            /**
+             * Output collections
+             * @default {}
+             */
+            output_collections?: {
+                [key: string]: components["schemas"]["EncodedHdcaSourceId"] | undefined;
+            };
+            /**
+             * Outputs
+             * @description Dictionary mapping all the tool outputs (by name) to the corresponding data references.
+             * @default {}
+             */
+            outputs?: {
+                [key: string]: components["schemas"]["EncodedDatasetJobInfo"] | undefined;
+            };
+            /**
+             * Parameters
+             * @description Object containing all the parameters of the tool associated with this job. The specific parameters depend on the tool itself.
+             */
+            params: Record<string, never>;
+            /**
+             * State
+             * @description Current state of the job.
+             */
+            state: components["schemas"]["JobState"];
+            /**
+             * Standard Error
+             * @description Combined tool and job standard error streams.
+             */
+            stderr?: string;
+            /**
+             * Standard Output
+             * @description Combined tool and job standard output streams.
+             */
+            stdout?: string;
+            /**
+             * Tool ID
+             * @description Identifier of the tool that generated this job.
+             */
+            tool_id: string;
+            /**
+             * Tool Standard Error
+             * @description The captured standard error of the tool executed by the job.
+             */
+            tool_stderr?: string;
+            /**
+             * Tool Standard Output
+             * @description The captured standard output of the tool executed by the job.
+             */
+            tool_stdout?: string;
+            /**
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
+             */
+            update_time: string;
+            /**
+             * User Email
+             * @description The email of the user that owns this job. Only the owner of the job and administrators can see this value.
+             */
+            user_email?: string;
+        };
         /**
          * Src
          * @description An enumeration.
@@ -15792,7 +15955,9 @@ export interface operations {
             /** @description Successful Response */
             200: {
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json":
+                        | components["schemas"]["ShowFullJobResponse"]
+                        | components["schemas"]["EncodedJobDetails"];
                 };
             };
             /** @description Validation Error */

lib/galaxy/model/store/__init__.py

@@ -1550,6 +1550,7 @@ def _set_job_attributes(
             "tool_stderr",
             "job_stdout",
             "job_stderr",
+            "galaxy_version",
         )
         for attribute in ATTRIBUTES:
             value = job_attrs.get(attribute)

lib/galaxy/schema/jobs.py

@@ -23,6 +23,7 @@
     DataItemSourceType,
     EncodedDataItemSourceId,
     EntityIdField,
+    JobMetricCollection,
     JobState,
     JobSummary,
     Model,
@@ -158,7 +159,7 @@ class EncodedDatasetJobInfo(EncodedDataItemSourceId):
 
 class EncodedJobDetails(JobSummary):
     command_version: Optional[str] = Field(
-        ...,
+        default=None,
         title="Command Version",
         description="Tool version indicated during job execution.",
     )
@@ -181,9 +182,15 @@ class EncodedJobDetails(JobSummary):
         description="Dictionary mapping all the tool outputs (by name) to the corresponding data references.",
     )
     copied_from_job_id: Optional[EncodedDatabaseIdField] = Field(
-        default=None, title="Copied from Job-ID", description="Reference to cached job if job execution was cached."
+        default=None,
+        title="Copied from Job-ID",
+        description="Reference to cached job if job execution was cached.",
+    )
+    output_collections: Dict[str, EncodedHdcaSourceId] = Field(
+        default={},
+        title="Output collections",
+        description="",
     )
-    output_collections: Dict[str, EncodedHdcaSourceId] = Field(default={}, title="Output collections", description="")
 
 
 class JobDestinationParams(Model):
@@ -234,3 +241,54 @@ class JobDisplayParametersSummary(Model):
         title="Outputs",
         description="Dictionary mapping all the tool outputs (by name) with the corresponding dataset information in a nested format.",
     )
+
+
+class ShowFullJobResponse(EncodedJobDetails):
+    tool_stdout: Optional[str] = Field(
+        default=None,
+        title="Tool Standard Output",
+        description="The captured standard output of the tool executed by the job.",
+    )
+    tool_stderr: Optional[str] = Field(
+        default=None,
+        title="Tool Standard Error",
+        description="The captured standard error of the tool executed by the job.",
+    )
+    job_stdout: Optional[str] = Field(
+        default=None,
+        title="Job Standard Output",
+        description="The captured standard output of the job execution.",
+    )
+    job_stderr: Optional[str] = Field(
+        default=None,
+        title="Job Standard Error",
+        description="The captured standard error of the job execution.",
+    )
+    stdout: Optional[str] = Field(  # Redundant? it seems to be (tool_stdout + "\n" + job_stdout)
+        default=None,
+        title="Standard Output",
+        description="Combined tool and job standard output streams.",
+    )
+    stderr: Optional[str] = Field(  # Redundant? it seems to be (tool_stderr + "\n" + job_stderr)
+        default=None,
+        title="Standard Error",
+        description="Combined tool and job standard error streams.",
+    )
+    job_messages: Optional[List[Any]] = Field(
+        default=None,
+        title="Job Messages",
+        description="List with additional information and possible reasons for a failed job.",
+    )
+    dependencies: Optional[List[Any]] = Field(
+        default=None,
+        title="Job dependencies",
+        description="The dependencies of the job.",
+    )
+    job_metrics: Optional[JobMetricCollection] = Field(
+        default=None,
+        title="Job Metrics",
+        description=(
+            "Collections of metrics provided by `JobInstrumenter` plugins on a particular job. "
+            "Only administrators can see these metrics."
+        ),
+    )

lib/galaxy/schema/schema.py

@@ -1851,8 +1851,8 @@ class JobBaseModel(Model):
     )
     create_time: datetime = CreateTimeField
     update_time: datetime = UpdateTimeField
-    galaxy_version: str = Field(
-        ...,
+    galaxy_version: Optional[str] = Field(
+        default=None,
         title="Galaxy Version",
         description="The (major) version of Galaxy used to create this job.",
         example="21.05",

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -49,6 +49,7 @@
     JobOutputAssociation,
     ReportJobErrorPayload,
     SearchJobsPayload,
+    ShowFullJobResponse,
 )
 from galaxy.schema.schema import (
     DatasetSourceType,
@@ -500,8 +501,11 @@ def show(
         job_id: Annotated[DecodedDatabaseIdField, JobIdPathParam],
         full: Annotated[Optional[bool], FullShowQueryParam] = False,
         trans: ProvidesUserContext = DependsOnTrans,
-    ) -> Dict[str, Any]:
-        return self.service.show(trans, job_id, bool(full))
+    ) -> Union[ShowFullJobResponse, EncodedJobDetails]:
+        if full:
+            return ShowFullJobResponse(**self.service.show(trans, job_id, bool(full)))
+        else:
+            return EncodedJobDetails(**self.service.show(trans, job_id, bool(full)))
 
     @router.delete(
         "/api/jobs/{job_id}",

lib/galaxy_test/api/test_jobs.py

@@ -353,15 +353,16 @@ def test_show_security(self, history_id):
         assert not job_lock_response.json()["active"]
 
         show_jobs_response = self._get(f"jobs/{job_id}", admin=False)
-        self._assert_not_has_keys(show_jobs_response.json(), "external_id")
+        assert show_jobs_response.json()["external_id"] is None
 
         # TODO: Re-activate test case when API accepts privacy settings
         # with self._different_user():
         #    show_jobs_response = self._get( "jobs/%s" % job_id, admin=False )
         #    self._assert_status_code_is( show_jobs_response, 200 )
 
         show_jobs_response = self._get(f"jobs/{job_id}", admin=True)
-        self._assert_has_keys(show_jobs_response.json(), "command_line", "external_id")
+        assert show_jobs_response.json()["external_id"] is not None
+        assert show_jobs_response.json()["command_line"] is not None
 
     def _run_detect_errors(self, history_id, inputs):
         payload = self.dataset_populator.run_tool_payload(