updates for fix of simularium

compose_api/main.py

@@ -417,43 +417,41 @@ async def fetch_results(job_id: str):
 
 @app.post(
  "/generate-simularium-file",
- response_model=PendingSimulariumJob,
+ # response_model=PendingSimulariumJob,
  operation_id='generate-simularium-file',
  tags=["Files"],
  summary='Generate a simularium file with a compatible simulation results file from either Smoldyn, SpringSaLaD, or ReaDDy.')
 async def generate_simularium_file(
  uploaded_file: UploadFile = File(..., description="A file containing results that can be parse by Simularium (spatial)."),
  box_size: float = Query(..., description="Size of the simulation box as a floating point number."),
  filename: str = Query(default=None, description="Name desired for the simularium file. NOTE: pass only the file name without an extension."),
-) -> PendingSimulariumJob:
- try:
- job_id = "files-generate-simularium-file" + str(uuid.uuid4())
- _time = db_connector.timestamp()
- upload_prefix = f"uploads/{job_id}/"
- bucket_prefix = f"gs://{BUCKET_NAME}/" + upload_prefix
- uploaded_file_location = await write_uploaded_file(job_id=job_id, uploaded_file=uploaded_file, bucket_name=BUCKET_NAME, extension='.txt')
-
- # new simularium job in db
- if filename is None:
- filename = 'simulation'
-
- new_job_submission = await db_connector.insert_job_async(
- collection_name=DatabaseCollections.PENDING_JOBS.value,
- status=JobStatus.PENDING.value,
- job_id=job_id,
- timestamp=_time,
- path=uploaded_file_location,
- filename=filename,
- box_size=box_size,
- )
-
- gen_id = new_job_submission.get('_id')
- if gen_id is not None:
- new_job_submission.pop('_id')
-
- return PendingSimulariumJob(**new_job_submission)
- except Exception as e:
- raise HTTPException(status_code=404, detail=f"A simularium file cannot be parsed from your input. Please check your input file and refer to the simulariumio documentation for more details.")
+):
+ job_id = "files-generate-simularium-file" + str(uuid.uuid4())
+ _time = db_connector.timestamp()
+ upload_prefix = f"uploads/{job_id}/"
+ bucket_prefix = f"gs://{BUCKET_NAME}/" + upload_prefix
+ uploaded_file_location = await write_uploaded_file(job_id=job_id, uploaded_file=uploaded_file, bucket_name=BUCKET_NAME, extension='.txt')
+
+ # new simularium job in db
+ if filename is None:
+ filename = 'simulation'
+
+ new_job_submission = await db_connector.insert_job_async(
+ collection_name=DatabaseCollections.PENDING_JOBS.value,
+ status=JobStatus.PENDING.value,
+ job_id=job_id,
+ timestamp=_time,
+ path=uploaded_file_location,
+ filename=filename,
+ box_size=box_size,
+ )
+ gen_id = new_job_submission.get('_id')
+ if gen_id is not None:
+ new_job_submission.pop('_id')
+
+ return new_job_submission
+ # except Exception as e:
+ # raise HTTPException(status_code=404, detail=f"A simularium file cannot be parsed from your input. Please check your input file and refer to the simulariumio documentation for more details.")
 
 
 @app.post(

compose_api/spec/openapi_3_1_0_generated.yaml

@@ -392,6 +392,14 @@ paths:
  from either Smoldyn, SpringSaLaD, or ReaDDy.
  operationId: generate-simularium-file
  parameters:
+ - name: box_size
+ in: query
+ required: true
+ schema:
+ type: number
+ description: Size of the simulation box as a floating point number.
+ title: Box Size
+ description: Size of the simulation box as a floating point number.
  - name: filename
  in: query
  required: false
@@ -413,8 +421,7 @@ paths:
  description: Successful Response
  content:
  application/json:
- schema:
- $ref: '#/components/schemas/PendingSimulariumJob'
+ schema: {}
  '422':
  description: Validation Error
  content:
@@ -803,35 +810,6 @@ components:
  - steps
  - simulators
  title: PendingSbmlVerificationJob
- PendingSimulariumJob:
- properties:
- job_id:
- type: string
- title: Job Id
- status:
- type: string
- title: Status
- default: PENDING
- timestamp:
- type: string
- title: Timestamp
- comparison_id:
- type: string
- title: Comparison Id
- input_file:
- type: string
- title: Input File
- filename:
- type: string
- title: Filename
- type: object
- required:
- - job_id
- - timestamp
- - comparison_id
- - input_file
- - filename
- title: PendingSimulariumJob
  Simulator:
  properties:
  name: