diff --git a/compose_api/main.py b/compose_api/main.py index ec1cc77f3..612732797 100644 --- 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 index 25220501f..17f8f79ed 100644 --- 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 index 8e7ad732d..cf1f95b59 100644 --- 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 index d625102cb..d90c65a43 100644 --- 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