From 932e8e05e697e1b581c47414cf25b99dce70eeb6 Mon Sep 17 00:00:00 2001
From: "spaceBearAmadeus (Alex)" <alexanderpatrie@gmail.com>
Date: Fri, 16 Aug 2024 00:28:12 -0400
Subject: [PATCH] updates for fix of simularium

---
 compose_api/main.py                           | 58 +++++++++----------
 compose_api/spec/openapi_3_1_0_generated.yaml | 40 +++----------
 2 files changed, 37 insertions(+), 61 deletions(-)

diff --git a/compose_api/main.py b/compose_api/main.py
index 1ff8a6901..648931f76 100644
--- a/compose_api/main.py
+++ b/compose_api/main.py
@@ -417,7 +417,7 @@ 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.')
@@ -425,35 +425,33 @@ 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(
diff --git a/compose_api/spec/openapi_3_1_0_generated.yaml b/compose_api/spec/openapi_3_1_0_generated.yaml
index 7939e5f50..7530ec7f8 100644
--- a/compose_api/spec/openapi_3_1_0_generated.yaml
+++ b/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: