update

biosimulators · Aug 19, 2024 · b1f8a1c · b1f8a1c
1 parent 8cd83a7
commit b1f8a1c
Show file tree

Hide file tree

Showing 4 changed files with 54 additions and 12 deletions.
diff --git a/bio_compose/_VERSION b/bio_compose/_VERSION
@@ -1 +1 @@
-0.2.2
+0.2.3
diff --git a/bio_compose/runner.py b/bio_compose/runner.py
@@ -56,6 +56,24 @@ def run_utc_simulation(self, sbml_filepath: str, start: int, end: int, steps: in
         headers = {'Content-Type': multidata.content_type}
 
         return self._execute_request(endpoint=endpoint, headers=headers, multidata=multidata, query_params=query_params)
+
+    def generate_simularium_file(self, smoldyn_output_filepath: str, box_size: float, filename: str = None):
+        endpoint = self._format_endpoint(f'generate-simularium-file')
+
+        # multipart 
+        input_fp = (smoldyn_output_filepath.split('/')[-1], open(smoldyn_output_filepath, 'rb'), 'application/octet-stream')
+        encoder_fields = {'uploaded_file': input_fp}
+        multidata = MultipartEncoder(fields=encoder_fields)
+
+        # query
+        query_params = {'box_size': str(box_size)}
+        if filename is not None:
+            query_params['filename'] = filename
+
+        # headers 
+        headers = {'Content-Type': multidata.content_type}
+
+        return self._execute_request(endpoint=endpoint, headers=headers, multidata=multidata, query_params=query_params)
 
 
 

diff --git a/tests/fixtures/smoldyn/modelouttxt-simulation.simularium b/tests/fixtures/smoldyn/modelouttxt-simulation.simularium
diff --git a/tests/tests.ipynb b/tests/tests.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -11,7 +11,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -28,18 +28,44 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'status': 'PENDING',\n",
+       " 'job_id': 'files-generate-simularium-file75d8bdc8-0bca-4dd4-8983-561a178fecf4',\n",
+       " 'timestamp': '2024-08-19 12:49:43.291403',\n",
+       " 'path': 'file_uploads/files-generate-simularium-file75d8bdc8-0bca-4dd4-8983-561a178fecf4/modelout.txt',\n",
+       " 'filename': 'simulation',\n",
+       " 'box_size': 10.0,\n",
+       " 'translate_output': True,\n",
+       " 'validate_output': True,\n",
+       " 'agent_parameters': {}}"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "simularium_job = runner.generate_simularium_file(smoldyn_output_filepath='./fixtures/smoldyn/modelout.txt', box_size=10.0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
-    "smoldyn_job_id = 'simulation-execution-smoldyn5624b470-ce90-4144-849c-8da896ab1147'\n",
-    "\n",
-    "output = runner.get_output(job_id=smoldyn_job_id, download_dest='./fixtures/smoldyn')"
+    "simularium_job_id = simularium_job['job_id']"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -48,16 +74,14 @@
        "True"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "import os\n",
     "\n",
-    "\n",
-    "simularium_job_id = 'files-generate-simularium-filee58f06f8-98f3-403e-afc2-e34cb86f4151'\n",
     "simularium_output = runner.get_output(job_id=simularium_job_id, download_dest='./fixtures/smoldyn')\n",
     "\n",
     "os.path.exists(simularium_output['results_file'])"