updates to api and workers for simularium kwargs

compose_api/main.py

@@ -425,6 +425,8 @@ 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."),
+ translate_output: bool = Query(default=True, description="Whether to translate the output trajectory prior to converting to simularium. See simulariumio documentation for more details."),
+ validate_output: bool = Query(default=True, description="Whether to validate the outputs for the simularium file. See simulariumio documentation for more details.")
 ):
  job_id = "files-generate-simularium-file" + str(uuid.uuid4())
  _time = db_connector.timestamp()
@@ -443,6 +445,8 @@ async def generate_simularium_file(
  path=uploaded_file_location,
  filename=filename,
  box_size=box_size,
+ translate_output=translate_output,
+ validate_output=validate_output
  )
  gen_id = new_job_submission.get('_id')
  if gen_id is not None:

compose_worker/test.ipynb

@@ -264,8 +264,8 @@
  {
  "metadata": {
  "ExecuteTime": {
- "end_time": "2024-08-16T17:27:17.112917Z",
- "start_time": "2024-08-16T17:27:17.107988Z"
+ "end_time": "2024-08-16T17:28:27.035927Z",
+ "start_time": "2024-08-16T17:28:27.030441Z"
  }
  },
  "cell_type": "code",
@@ -292,8 +292,8 @@
  {
  "metadata": {
  "ExecuteTime": {
- "end_time": "2024-08-16T17:27:18.048018Z",
- "start_time": "2024-08-16T17:27:17.113991Z"
+ "end_time": "2024-08-16T17:28:28.475098Z",
+ "start_time": "2024-08-16T17:28:27.621723Z"
  }
  },
  "cell_type": "code",
@@ -309,12 +309,12 @@
  {
  "metadata": {
  "ExecuteTime": {
- "end_time": "2024-08-16T17:27:18.487430Z",
- "start_time": "2024-08-16T17:27:18.049090Z"
+ "end_time": "2024-08-16T17:28:29.508622Z",
+ "start_time": "2024-08-16T17:28:29.004458Z"
  }
  },
  "cell_type": "code",
- "source": "result = await generate_simularium_file(input_fp=fp, dest_dir='../model-examples/smoldyn', box_size=10.0, write_json=False, run_validation=False)",
+ "source": "result = await generate_simularium_file(input_fp=fp, dest_dir='../model-examples/smoldyn', box_size=10.0, write_json=True, run_validation=True)",
  "id": "c3e8ddfffb7e0ac9",
  "outputs": [
  {
@@ -323,8 +323,8 @@
  "text": [
  "Reading Smoldyn Data -------------\n",
  "Filtering: translation -------------\n",
- "Converting Trajectory Data to Binary -------------\n",
- "Writing Binary -------------\n",
+ "Converting Trajectory Data to JSON -------------\n",
+ "Writing JSON -------------\n",
  "saved to ../model-examples/smoldyn/modelouttxt-simulation.simularium\n"
  ]
  }

compose_worker/workers.py

@@ -491,7 +491,9 @@ async def run(self):
 
  async def _run_simularium(self, job_id: str, input_path: str, dest: str):
  box_size = self.job_params['box_size']
- result = await generate_simularium_file(input_fp=input_path, dest_dir=dest, box_size=box_size)
+ translate = self.job_params['translate_output']
+ validate = self.job_params['validate_output']
+ result = await generate_simularium_file(input_fp=input_path, dest_dir=dest, box_size=box_size, translate_output=translate, run_validation=validate)
 
  results_file = result.get('simularium_file')
  uploaded_file_location = None