Merge pull request #80 from bento-platform/fix/run-output-model

fix: consolidate run details models + None valid out type

bento_wes/db.py

@@ -14,7 +14,7 @@
 from .backends.backend_types import Command
 from .constants import SERVICE_ARTIFACT
 from .events import get_flask_event_bus
-from .models import RunLog, RunRequest, Run, RunWithDetailsAndOutput
+from .models import RunLog, RunRequest, Run, RunWithDetails
 from .types import RunStream
 from .utils import iso_now
 
@@ -187,13 +187,13 @@ def get_task_logs(c: sqlite3.Cursor, run_id: uuid.UUID | str) -> list:
         return [task_log_dict(task_log) for task_log in c.fetchall()]
 
     @classmethod
-    def run_with_details_and_output_from_row(
+    def run_with_details_from_row(
         cls,
         c: sqlite3.Cursor,
         run: sqlite3.Row,
         stream_content: bool,
-    ) -> RunWithDetailsAndOutput:
-        return RunWithDetailsAndOutput.model_validate(dict(
+    ) -> RunWithDetails:
+        return RunWithDetails.model_validate(dict(
             run_id=run["id"],
             state=run["state"],
             request=run_request_from_row(run),
@@ -218,9 +218,9 @@ def get_run_with_details(
         c: sqlite3.Cursor,
         run_id: uuid.UUID | str,
         stream_content: bool,
-    ) -> RunWithDetailsAndOutput | None:
+    ) -> RunWithDetails | None:
         if run := cls._get_run_row(c, run_id):
-            return cls.run_with_details_and_output_from_row(c, run, stream_content)
+            return cls.run_with_details_from_row(c, run, stream_content)
         return None
 
     def set_run_log_name(self, run: Run, workflow_name: str):

bento_wes/models.py

@@ -10,7 +10,6 @@
     "Run",
     "RunWithDetails",
     "RunOutput",
-    "RunWithDetailsAndOutput",
 ]
 
 
@@ -46,16 +45,13 @@ class Run(BaseModel):
     state: str  # TODO: Literal
 
 
+class RunOutput(BaseModel):  # Bento-specific schema
+    type: str  # WDL / (workflow descriptor language) type
+    value: str | int | float | bool | list | None  # Output value
+
+
 class RunWithDetails(Run):
     request: RunRequest
     run_log: RunLog
     task_logs: list[dict]  # TODO: model
-
-
-class RunOutput(BaseModel):
-    type: str  # WDL / (workflow descriptor language) type
-    value: str | int | float | bool | list  # Output value
-
-
-class RunWithDetailsAndOutput(RunWithDetails):
-    outputs: dict[str, RunOutput]  # Bento-specific extension
+    outputs: dict[str, RunOutput]

bento_wes/runs.py

@@ -315,7 +315,7 @@ def run_list():
     perms_list: list[RunRequest] = []
 
     for r in c.execute("SELECT * FROM runs").fetchall():
-        run = db.run_with_details_and_output_from_row(c, r, stream_content=False)
+        run = db.run_with_details_from_row(c, r, stream_content=False)
         perms_list.append(run.request)
 
         if not public_endpoint or run.state == STATE_COMPLETE: