fix to steps for simulariumio

compose_worker/bigraph_steps.py

@@ -1,5 +1,6 @@
 import os
 from tempfile import mkdtemp
+from typing import Dict
 from uuid import uuid4
 from typing import *
 
@@ -285,6 +286,14 @@ class SimulariumSmoldynStep(Step):
  '_default': True,
  '_type': 'boolean'
  },
+ 'write_json': {
+ '_default': True,
+ '_type': 'boolean'
+ },
+ 'run_validation': {
+ '_default': True,
+ '_type': 'boolean'
+ },
  'file_save_name': 'maybe[string]',
  'translation_magnitude': 'maybe[float]',
  'meta_data': 'maybe[tree[string]]',
@@ -296,6 +305,7 @@ def __init__(self, config=None, core=CORE):
 
  # io params
  self.output_dest = self.config['output_dest']
+ self.write_json = self.config['write_json']
  self.filename = self.config.get('file_save_name')
 
  # display params
@@ -310,6 +320,7 @@ def __init__(self, config=None, core=CORE):
 
  # info params
  self.meta_data = self.config.get('meta_data')
+ self.run_validation = self.config['run_validation']
 
  def inputs(self):
  return {'results_file': 'string', 'species_counts': 'tree[integer]'}
@@ -342,11 +353,13 @@ def update(self, inputs):
 
  # write data to simularium file
  if self.filename is None:
- self.filename = f'{in_file.replace(".", "")}-simulation'
- simularium_fp = os.path.join(self.output_dest, self.filename)
- write_simularium_file(data=io_data, simularium_fp=simularium_fp, json=True, validate=True)
+ file_root = os.path.dirname(in_file)
+ self.filename = in_file.split('/')[-1].replace('.', '') + "-simulation"
+
+ save_path = os.path.join(self.output_dest, self.filename)
+ write_simularium_file(data=io_data, simularium_fp=save_path, json=self.write_json, validate=self.run_validation)
 
- return {'simularium_file': simularium_fp}
+ return {'simularium_file': save_path + '.simularium'}
 
  def _generate_display_data(self, species_names) -> Dict | None:
  # user is specifying display data for agents
@@ -390,7 +403,14 @@ def _generate_display_data(self, species_names) -> Dict | None:
  print(f'{process_name} could not be registered because {str(e)}')
 
 
-async def generate_simularium_file(input_fp: str, dest_dir: str, box_size: float):
+async def generate_simularium_file(
+ input_fp: str,
+ dest_dir: str,
+ box_size: float,
+ translate_output: bool = True,
+ write_json: bool = True,
+ run_validation: bool = True
+) -> Dict[str, str]:
  species_names = []
  with open(input_fp, 'r') as f:
  output = [l.strip() for l in f.readlines()]
@@ -399,7 +419,18 @@ async def generate_simularium_file(input_fp: str, dest_dir: str, box_size: float
  if not datum.isdigit():
  species_names.append(datum)
 
- simularium = SimulariumSmoldynStep(config={'output_dest': dest_dir, 'box_size': box_size})
- return simularium.update(inputs={'results_file': input_fp, 'species_names': species_names})
+ simularium = SimulariumSmoldynStep(config={
+ 'output_dest': dest_dir,
+ 'box_size': box_size,
+ 'translate_output': translate_output,
+ 'file_save_name': None,
+ 'write_json': write_json,
+ 'run_validation': run_validation
+ })
+
+ return simularium.update(inputs={
+ 'results_file': input_fp,
+ 'species_names': species_names
+ })
 
 

compose_worker/simularium_utils.py

@@ -114,7 +114,7 @@ def translate_data_object(
 def write_simularium_file(
  data: Union[SmoldynData, TrajectoryData],
  simularium_fp: str,
- json: bool = False,
+ json: bool = True,
  validate: bool = True
 ) -> None:
  """Takes in either a `SmoldynData` or `TrajectoryData` instance and saves a simularium file based on it

compose_worker/test.ipynb

@@ -199,7 +199,7 @@
  }
  },
  "cell_type": "code",
- "source": "job = {'status': 'PENDING', 'job_id': 'files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11', 'timestamp': '2024-08-16 16:09:28.578099', 'path': 'file_uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelout.txt', 'filename': 'simulation', 'box_size': 10.0}",
+ "source": "job = {'status': 'PENDING', 'job_id': 'files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11', 'timestamp': '2024-08-16 16:09:28.578099', 'path': 'uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelout.txt', 'filename': 'simulation', 'box_size': 10.0}",
  "id": "e28c150926800fd6",
  "outputs": [],
  "execution_count": 1
@@ -251,7 +251,7 @@
  {
  "data": {
  "text/plain": [
- "{'results': {'results_file': 'file_uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelouttxt-simulation.simularium'}}"
+ "{'results': {'results_file': 'uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelouttxt-simulation.simularium'}}"
  ]
  },
  "execution_count": 3,
@@ -261,13 +261,107 @@
  ],
  "execution_count": 3
  },
+ {
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-08-16T17:27:17.112917Z",
+ "start_time": "2024-08-16T17:27:17.107988Z"
+ }
+ },
+ "cell_type": "code",
+ "source": [
+ "fp = '../model-examples/smoldyn/modelout.txt'\n",
+ "import os\n",
+ "os.path.exists(fp)"
+ ],
+ "id": "9920ec3288a1bd56",
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 1,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "execution_count": 1
+ },
+ {
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-08-16T17:27:18.048018Z",
+ "start_time": "2024-08-16T17:27:17.113991Z"
+ }
+ },
+ "cell_type": "code",
+ "source": [
+ "from bigraph_steps import generate_simularium_file\n",
+ "\n",
+ "\n"
+ ],
+ "id": "e0f9fcb1045f39d1",
+ "outputs": [],
+ "execution_count": 2
+ },
+ {
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-08-16T17:27:18.487430Z",
+ "start_time": "2024-08-16T17:27:18.049090Z"
+ }
+ },
+ "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)",
+ "id": "c3e8ddfffb7e0ac9",
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Reading Smoldyn Data -------------\n",
+ "Filtering: translation -------------\n",
+ "Converting Trajectory Data to Binary -------------\n",
+ "Writing Binary -------------\n",
+ "saved to ../model-examples/smoldyn/modelouttxt-simulation.simularium\n"
+ ]
+ }
+ ],
+ "execution_count": 3
+ },
+ {
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-08-16T17:27:21.221432Z",
+ "start_time": "2024-08-16T17:27:21.217836Z"
+ }
+ },
+ "cell_type": "code",
+ "source": "result",
+ "id": "1dd577b3febbc71f",
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{'simularium_file': '../model-examples/smoldyn/modelouttxt-simulation.simularium'}"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "execution_count": 4
+ },
  {
  "metadata": {},
  "cell_type": "code",
  "outputs": [],
  "execution_count": null,
  "source": "",
- "id": "9920ec3288a1bd56"
+ "id": "47692e72bd0d19a1"
  }
  ],
  "metadata": {

compose_worker/workers.py

@@ -474,15 +474,18 @@ async def run(self):
  job_id = self.job_params['job_id']
  input_path = self.job_params.get('path')
 
- # is a job related to a client file upload
- if input_path is not None:
- # download the input file
- dest = tempfile.mkdtemp()
- local_input_path = download_file(source_blob_path=input_path, bucket_name=BUCKET_NAME, out_dir=dest)
- print(local_input_path)
- # case: is a smoldyn output file and thus a simularium job
- if input_path.endswith('.txt'):
- await self._run_simularium(job_id=job_id, input_path=local_input_path, dest=dest)
+ try:
+ # is a job related to a client file upload
+ if input_path is not None:
+ # download the input file
+ dest = tempfile.mkdtemp()
+ local_input_path = download_file(source_blob_path=input_path, bucket_name=BUCKET_NAME, out_dir=dest)
+ print(local_input_path)
+ # case: is a smoldyn output file and thus a simularium job
+ if input_path.endswith('.txt'):
+ await self._run_simularium(job_id=job_id, input_path=local_input_path, dest=dest)
+ except Exception as e:
+ self.job_result['results'] = str(e)
 
  return self.job_result