update kustomize for api change

biosimulators · Oct 17, 2024 · 802f975 · 802f975
1 parent e52fba9
commit 802f975
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Showing 4 changed files with 18 additions and 26 deletions.
diff --git a/compose_api/main.py b/compose_api/main.py
@@ -33,7 +33,7 @@
 GOOGLE_APPLICATION_CREDENTIALS = os.getenv("GOOGLE_APPLICATION_CREDENTIALS")
 
 APP_TITLE = "bio-compose"
-APP_VERSION = "0.1.1"
+APP_VERSION = "0.1.2"
 # APP_SERVERS = [
 #     {
 #         "url": "https://biochecknet.biosimulations.org",
@@ -213,7 +213,7 @@ async def verify_omex(
         include_outputs: bool = Query(default=True, description="Whether to include the output data on which the comparison is based."),
         selection_list: Optional[List[str]] = Query(default=None, description="List of observables to include in the return data."),
         comparison_id: Optional[str] = Query(default=None, description="Descriptive prefix to be added to this submission's job ID."),
-        expected_results: Optional[UploadFile] = File(default=None, description="reports.h5 file defining the expected results to be included in the comparison."),
+        # expected_results: Optional[UploadFile] = File(default=None, description="reports.h5 file defining the expected results 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.")
 ):
@@ -239,16 +239,16 @@ async def verify_omex(
             uploaded_file_location = blob_dest
 
         # Save uploaded reports file to Google Cloud Storage if applicable
-        report_fp = None
-        report_blob_dest = None
-        if expected_results:
-            # handle incorrect files upload
-            properly_formatted_report = check_upload_file_extension(expected_results, 'expected_results', '.h5')
-            if properly_formatted_report:
-                report_fp = await save_uploaded_file(expected_results, save_dest)
-                report_blob_dest = upload_prefix + report_fp.split("/")[-1]
-            upload_blob(bucket_name=BUCKET_NAME, source_file_name=report_fp, destination_blob_name=report_blob_dest)
-        report_location = report_blob_dest
+        # report_fp = None
+        # report_blob_dest = None
+        # if expected_results:
+        #     # handle incorrect files upload
+        #     properly_formatted_report = check_upload_file_extension(expected_results, 'expected_results', '.h5')
+        #     if properly_formatted_report:
+        #         report_fp = await save_uploaded_file(expected_results, save_dest)
+        #         report_blob_dest = upload_prefix + report_fp.split("/")[-1]
+        #     upload_blob(bucket_name=BUCKET_NAME, source_file_name=report_fp, destination_blob_name=report_blob_dest)
+        # report_location = report_blob_dest
 
         pending_job_doc = await db_connector.insert_job_async(
             collection_name=DatabaseCollections.PENDING_JOBS.value,
@@ -257,7 +257,7 @@ async def verify_omex(
             path=uploaded_file_location,
             simulators=simulators,
             timestamp=_time,
-            expected_results=report_location,
+            # expected_results=report_location,
             include_outputs=include_outputs,
             rTol=rTol,
             aTol=aTol,
@@ -266,8 +266,8 @@ async def verify_omex(
 
         # clean up local temp files
         os.remove(fp)
-        if report_fp:
-            os.remove(report_fp)
+        # if report_fp:
+        # os.remove(report_fp)
 
         # return PendingOmexVerificationJob(**pending_job_doc)
         return pending_job_doc

diff --git a/compose_api/spec/openapi_3_1_0_generated.yaml b/compose_api/spec/openapi_3_1_0_generated.yaml
@@ -1,7 +1,7 @@
 openapi: 3.1.0
 info:
   title: bio-compose
-  version: 0.1.1
+  version: 0.1.2
 paths:
   /:
     get:
@@ -607,14 +607,6 @@ components:
           format: binary
           title: Uploaded File
           description: OMEX/COMBINE archive containing a deterministic SBML model
-        expected_results:
-          anyOf:
-          - type: string
-            format: binary
-          - type: 'null'
-          title: Expected Results
-          description: reports.h5 file defining the expected results to be included
-            in the comparison.
       type: object
       required:
       - uploaded_file

diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -15,7 +15,7 @@ services:
     build:
       context: ./compose_api
       dockerfile: ./Dockerfile-compose_api
-    image: ghcr.io/biosimulators/bio-check-compose_api:1.11.5  # .3
+    image: ghcr.io/biosimulators/bio-check-compose_api:1.11.6  # .3
     container_name: api
     environment:
       - MONGO_URI=mongodb://mongodb:27017/?retryWrites=true&w=majority&appName=bio-compose

diff --git a/kustomize/overlays/biochecknet/kustomization.yaml b/kustomize/overlays/biochecknet/kustomization.yaml
@@ -8,7 +8,7 @@ namespace: biochecknet
 # PREVIOUS (MOST CURRENTLY RELEASED) VERSIONS AS OF 10/17(SMOLDYN BUG): api: 1.11.4, worker: 1.11.6
 images:
 - name: ghcr.io/biosimulators/bio-check-compose_api
-  newTag: 1.11.5
+  newTag: 1.11.6
 - name: ghcr.io/biosimulators/bio-check-compose_worker
   newTag: 1.11.6
 - name: mongo