updates to api and worker specs

biosimulators · Jul 31, 2024 · 2e0ec33 · 2e0ec33
1 parent 7991f9b
commit 2e0ec33
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Showing 4 changed files with 25 additions and 19 deletions.
diff --git a/api/.CONTAINER_VERSION b/api/.CONTAINER_VERSION
@@ -1 +1 @@
-1.0.2
+1.0.3
diff --git a/api/main.py b/api/main.py
@@ -12,7 +12,7 @@
 from starlette.middleware.cors import CORSMiddleware
 
 # from bio_check import MONGO_URI
-from data_model import DbClientResponse, UtcComparisonResult, OmexComparisonSubmission, SbmlComparisonSubmission
+from data_model import DbClientResponse, UtcComparisonResult, PendingOmexJob, PendingSbmlJob
 from shared import save_uploaded_file, upload_blob, MongoDbConnector
 from log_config import setup_logging
 
@@ -111,7 +111,7 @@ def root():
 
 @app.post(
     "/verify-omex",  # "/biosimulators-utc-comparison",
-    response_model=OmexComparisonSubmission,
+    response_model=PendingOmexJob,
     name="Uniform Time Course Comparison from OMEX/COMBINE archive",
     operation_id="verify-omex",
     summary="Compare UTC outputs from a deterministic SBML model within an OMEX/COMBINE archive.")
@@ -124,10 +124,14 @@ async def verify_omex(
         truth: UploadFile = File(default=None, description="reports.h5 file defining the 'ground-truth' to be included in the comparison."),
         rTol: Optional[float] = Query(default=None, description="Relative tolerance to use for proximity comparison."),
         aTol: Optional[float] = Query(default=None, description="Absolute tolerance to use for proximity comparison.")
-) -> OmexComparisonSubmission:
+) -> PendingOmexJob:
     try:
         # request specific params
-        compare_id = comparison_id or "utc_comparison"
+        if comparison_id is None:
+            compare_id = "utc_comparison_omex"
+        else:
+            compare_id = comparison_id
+
         job_id = compare_id + "_" + str(uuid.uuid4())
         _time = db_connector.timestamp()
 
@@ -159,7 +163,6 @@ async def verify_omex(
             job_id=job_id,
             path=uploaded_file_location,
             simulators=simulators,
-            comparison_id=compare_id,
             timestamp=_time,
             ground_truth_report_path=report_location,
             include_outputs=include_outputs,
@@ -173,14 +176,14 @@ async def verify_omex(
         if report_fp:
             os.remove(report_fp)
 
-        return OmexComparisonSubmission(**pending_job_doc)
+        return PendingOmexJob(**pending_job_doc)
     except Exception as e:
         raise HTTPException(status_code=500, detail=str(e))
 
 
 @app.post(
     "/verify-sbml",
-    response_model=SbmlComparisonSubmission,
+    response_model=PendingSbmlJob,
     name="Uniform Time Course Comparison from SBML file",
     operation_id="verify-sbml",
     summary="Compare UTC outputs from a deterministic SBML model.")
@@ -194,10 +197,14 @@ async def verify_sbml(
         rTol: Optional[float] = Query(default=None, description="Relative tolerance to use for proximity comparison."),
         aTol: Optional[float] = Query(default=None, description="Absolute tolerance to use for proximity comparison."),
         selection_list: Optional[List[str]] = Query(default=None, description="List of observables to include in the return data."),
-) -> SbmlComparisonSubmission:
+) -> PendingSbmlJob:
     try:
         # request specific params
-        compare_id = comparison_id or "utc_comparison"
+        if comparison_id is None:
+            compare_id = "utc_comparison_omex"
+        else:
+            compare_id = comparison_id
+
         job_id = compare_id + "_" + str(uuid.uuid4())
         _time = db_connector.timestamp()
 
@@ -220,7 +227,6 @@ async def verify_sbml(
             job_id=job_id,
             path=uploaded_file_location,
             simulators=simulators,
-            comparison_id=compare_id,
             timestamp=_time,
             duration=duration,
             n_steps=number_of_steps,
@@ -233,7 +239,7 @@ async def verify_sbml(
         # clean up local temp files
         os.remove(fp)
 
-        return SbmlComparisonSubmission(**pending_job_doc)
+        return PendingSbmlJob(**pending_job_doc)
     except Exception as e:
         raise HTTPException(status_code=500, detail=str(e))
 

diff --git a/api/spec/openapi_3_1_0_generated.yaml b/api/spec/openapi_3_1_0_generated.yaml
@@ -98,7 +98,7 @@ paths:
           content:
             application/json:
               schema:
-                $ref: '#/components/schemas/OmexComparisonSubmission'
+                $ref: '#/components/schemas/PendingOmexJob'
         '422':
           description: Validation Error
           content:
@@ -204,7 +204,7 @@ paths:
           content:
             application/json:
               schema:
-                $ref: '#/components/schemas/SbmlComparisonSubmission'
+                $ref: '#/components/schemas/PendingSbmlJob'
         '422':
           description: Validation Error
           content:
@@ -274,7 +274,7 @@ components:
           title: Detail
       type: object
       title: HTTPValidationError
-    OmexComparisonSubmission:
+    PendingOmexJob:
       properties:
         job_id:
           type: string
@@ -333,8 +333,8 @@ components:
       - timestamp
       - path
       - simulators
-      title: OmexComparisonSubmission
-    SbmlComparisonSubmission:
+      title: PendingOmexJob
+    PendingSbmlJob:
       properties:
         job_id:
           type: string
@@ -396,7 +396,7 @@ components:
       - duration
       - n_steps
       - simulators
-      title: SbmlComparisonSubmission
+      title: PendingSbmlJob
     UtcComparisonResult:
       properties:
         content:

diff --git a/kustomize/overlays/biochecknet/kustomization.yaml b/kustomize/overlays/biochecknet/kustomization.yaml
@@ -6,7 +6,7 @@ namespace: biochecknet
 
 images:
 - name: ghcr.io/biosimulators/bio-check-api
-  newTag: 1.0.2
+  newTag: 1.0.3
 - name: ghcr.io/biosimulators/bio-check-worker
   newTag: 1.0.0
 - name: mongo