latest worker update and k8

biosimulators · Aug 16, 2024 · 08eac17 · 08eac17
1 parent 865f2e6
commit 08eac17
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Showing 11 changed files with 20 additions and 20 deletions.
diff --git a/api/main.py b/api/main.py
@@ -136,7 +136,7 @@ async def verify_omex(
  _time = db_connector.timestamp()
 
  # bucket params
- upload_prefix = f"uploads/{job_id}/"
+ upload_prefix = f"file_uploads/{job_id}/"
  bucket_prefix = f"gs://{BUCKET_NAME}/" + upload_prefix
 
  save_dest = mkdtemp()
@@ -217,7 +217,7 @@ async def verify_sbml(
  _time = db_connector.timestamp()
 
  # bucket params
- upload_prefix = f"uploads/{job_id}/"
+ upload_prefix = f"file_uploads/{job_id}/"
  bucket_prefix = f"gs://{BUCKET_NAME}/" + upload_prefix
 
  save_dest = mkdtemp()

diff --git a/compose_api/io_api.py b/compose_api/io_api.py
@@ -52,7 +52,7 @@ def upload_blob(bucket_name, source_file_name, destination_blob_name):
 
 async def write_uploaded_file(job_id: str, bucket_name: str, uploaded_file: UploadFile, extension: str) -> str:
  # bucket params
- upload_prefix = f"uploads/{job_id}/"
+ upload_prefix = f"file_uploads/{job_id}/"
  bucket_prefix = f"gs://{bucket_name}/" + upload_prefix
 
  save_dest = mkdtemp()

diff --git a/compose_api/shared.py b/compose_api/shared.py
@@ -27,7 +27,7 @@
 
 def file_upload_prefix(job_id: str):
  # bucket params
- upload_prefix = f"file_uploads/{job_id}/"
+ upload_prefix = f"file_file_uploads/{job_id}/"
  bucket_prefix = f"gs://{BUCKET_NAME}/" + upload_prefix
  return upload_prefix, bucket_prefix
 

diff --git a/compose_worker/.CONTAINER_VERSION b/compose_worker/.CONTAINER_VERSION
@@ -1 +1 @@
-1.2.2
+1.2.3
diff --git a/compose_worker/io_worker.py b/compose_worker/io_worker.py
@@ -27,7 +27,7 @@ def download_file(source_blob_path: str, out_dir: str, bucket_name: str) -> str:
 
 async def write_uploaded_file(job_id: str, bucket_name: str, uploaded_file: UploadFile | str, extension: str) -> str:
  # bucket params
- upload_prefix = f"uploads/{job_id}/"
+ upload_prefix = f"file_uploads/{job_id}/"
  bucket_prefix = f"gs://{bucket_name}/" + upload_prefix
 
  save_dest = mkdtemp()

diff --git a/compose_worker/test.ipynb b/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': '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': 'file_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': 'uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelouttxt-simulation.simularium'}}"
+ "{'results': {'results_file': 'file_uploads/files-generate-simularium-file00f049df-3211-469c-b009-1c95aae5dc11/modelouttxt-simulation.simularium'}}"
  ]
  },
  "execution_count": 3,

diff --git a/compose_worker/tests.py b/compose_worker/tests.py
@@ -25,7 +25,7 @@ async def test_worker(uploaded_file: str, ground_truth_report: str = None, simul
  # save_dest = mkdtemp()
 
  # bucket params
- upload_prefix = f"uploads/{job_id}/"
+ upload_prefix = f"file_uploads/{job_id}/"
  bucket_prefix = f"gs://{BUCKET_NAME}/" + upload_prefix
 
  # Save uploaded omex file to Google Cloud Storage

diff --git a/demos/verification_api_demo.ipynb b/demos/verification_api_demo.ipynb
@@ -265,9 +265,9 @@
  " 'status': 'PENDING',\n",
  " 'timestamp': '2024-08-12 13:54:13.175583',\n",
  " 'comparison_id': None,\n",
- " 'path': 'uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/Elowitz-Nature-2000-Repressilator.omex',\n",
+ " 'path': 'file_uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/Elowitz-Nature-2000-Repressilator.omex',\n",
  " 'simulators': ['amici,copasi,tellurium'],\n",
- " 'expected_results': 'uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/reports.h5',\n",
+ " 'expected_results': 'file_uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/reports.h5',\n",
  " 'include_output': True,\n",
  " 'rTol': None,\n",
  " 'aTol': None,\n",

diff --git a/docs/verification_api_demo.md b/docs/verification_api_demo.md
@@ -95,9 +95,9 @@ submission
   'status': 'PENDING',
   'timestamp': '2024-08-12 13:54:13.175583',
   'comparison_id': None,
-  'path': 'uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/Elowitz-Nature-2000-Repressilator.omex',
+  'path': 'file_uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/Elowitz-Nature-2000-Repressilator.omex',
   'simulators': ['amici,copasi,tellurium'],
-  'expected_results': 'uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/reports.h5',
+  'expected_results': 'file_uploads/bio_check-request-ba8caf28-3350-4e17-905c-8b768b98b517_35987621-19c0-43c1-a83d-2d031d537240/reports.h5',
   'include_output': True,
   'rTol': None,
   'aTol': None,

diff --git a/worker/tests.ipynb b/worker/tests.ipynb
@@ -547,19 +547,19 @@
  "[{'_id': ObjectId('66aa3842d1e5f99d9dd7b8c5'),\n",
  " 'status': 'PENDING',\n",
  " 'job_id': 'localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf',\n",
- " 'path': 'uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/Elowitz-Nature-2000-Repressilator.omex',\n",
+ " 'path': 'file_uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/Elowitz-Nature-2000-Repressilator.omex',\n",
  " 'simulators': ['amici', 'copasi', 'tellurium'],\n",
  " 'comparison_id': 'localomex0',\n",
  " 'timestamp': '2024-07-31 13:12:33.189310',\n",
- " 'ground_truth_report_path': 'uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/reports.h5',\n",
+ " 'ground_truth_report_path': 'file_uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/reports.h5',\n",
  " 'include_outputs': True,\n",
  " 'rTol': None,\n",
  " 'aTol': None,\n",
  " 'selection_list': ['cI mRNA']},\n",
  " {'_id': ObjectId('66aa385dd1e5f99d9dd7b8c6'),\n",
  " 'status': 'PENDING',\n",
  " 'job_id': 'localsbml0_2b484464-691d-48b1-8184-05abe9207d7c',\n",
- " 'path': 'uploads/localsbml0_2b484464-691d-48b1-8184-05abe9207d7c/BIOMD0000000012_url.xml',\n",
+ " 'path': 'file_uploads/localsbml0_2b484464-691d-48b1-8184-05abe9207d7c/BIOMD0000000012_url.xml',\n",
  " 'simulators': ['copasi', 'tellurium'],\n",
  " 'comparison_id': 'localsbml0',\n",
  " 'timestamp': '2024-07-31 13:13:00.724845',\n",
@@ -608,11 +608,11 @@
  "{'_id': ObjectId('66aa3842d1e5f99d9dd7b8c5'),\n",
  " 'status': 'PENDING',\n",
  " 'job_id': 'localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf',\n",
- " 'path': 'uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/Elowitz-Nature-2000-Repressilator.omex',\n",
+ " 'path': 'file_uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/Elowitz-Nature-2000-Repressilator.omex',\n",
  " 'simulators': ['amici', 'copasi', 'tellurium'],\n",
  " 'comparison_id': 'localomex0',\n",
  " 'timestamp': '2024-07-31 13:12:33.189310',\n",
- " 'ground_truth_report_path': 'uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/reports.h5',\n",
+ " 'ground_truth_report_path': 'file_uploads/localomex0_2d35f3a6-9310-4bf3-8635-2f9cafd1b2cf/reports.h5',\n",
  " 'include_outputs': True,\n",
  " 'rTol': None,\n",
  " 'aTol': None,\n",
@@ -2687,7 +2687,7 @@
  "{'_id': ObjectId('66aa385dd1e5f99d9dd7b8c6'),\n",
  " 'status': 'PENDING',\n",
  " 'job_id': 'localsbml0_2b484464-691d-48b1-8184-05abe9207d7c',\n",
- " 'path': 'uploads/localsbml0_2b484464-691d-48b1-8184-05abe9207d7c/BIOMD0000000012_url.xml',\n",
+ " 'path': 'file_uploads/localsbml0_2b484464-691d-48b1-8184-05abe9207d7c/BIOMD0000000012_url.xml',\n",
  " 'simulators': ['copasi', 'tellurium'],\n",
  " 'comparison_id': 'localsbml0',\n",
  " 'timestamp': '2024-07-31 13:13:00.724845',\n",

diff --git a/worker/tests.py b/worker/tests.py
@@ -25,7 +25,7 @@ async def test_worker(uploaded_file: str, ground_truth_report: str = None, simul
  # save_dest = mkdtemp()
 
  # bucket params
- upload_prefix = f"uploads/{job_id}/"
+ upload_prefix = f"file_uploads/{job_id}/"
  bucket_prefix = f"gs://{BUCKET_NAME}/" + upload_prefix
 
  # Save uploaded omex file to Google Cloud Storage