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updates to verifier and not implemented
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@AlexPatrie
AlexPatrie committed Aug 2, 2024
1 parent 56423ed commit f34eb4f
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Showing 2 changed files with 24 additions and 35 deletions.
2 changes: 1 addition & 1 deletion bio_check/verifier.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ def verify_sbml(
endpoint = self._format_endpoint('verify-sbml')

# TODO: fix and remove this
raise NotImplementedError("This feature is currently under development.")
raise NotImplementedError("Submission of jobs with a SBML file is currently under development.")

# configure params
_id = comparison_id or "bio_check-request-" + str(uuid4())
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57 changes: 23 additions & 34 deletions demos/bio_check_demo.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-02T04:06:48.397693Z",
"start_time": "2024-08-02T04:06:48.396009Z"
"end_time": "2024-08-02T04:14:16.250142Z",
"start_time": "2024-08-02T04:14:16.247335Z"
}
},
"cell_type": "code",
Expand All @@ -24,8 +24,8 @@
"metadata": {
"collapsed": true,
"ExecuteTime": {
"end_time": "2024-08-02T04:06:48.503175Z",
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"end_time": "2024-08-02T04:14:16.647386Z",
"start_time": "2024-08-02T04:14:16.544912Z"
}
},
"source": [
Expand All @@ -38,8 +38,8 @@
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-02T04:06:48.506855Z",
"start_time": "2024-08-02T04:06:48.504802Z"
"end_time": "2024-08-02T04:14:16.936657Z",
"start_time": "2024-08-02T04:14:16.934482Z"
}
},
"cell_type": "code",
Expand All @@ -60,8 +60,8 @@
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-02T04:06:48.752308Z",
"start_time": "2024-08-02T04:06:48.507472Z"
"end_time": "2024-08-02T04:14:18.105549Z",
"start_time": "2024-08-02T04:14:17.854669Z"
}
},
"cell_type": "code",
Expand All @@ -81,8 +81,8 @@
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-02T04:00:11.775107Z",
"start_time": "2024-08-02T04:00:11.773068Z"
"end_time": "2024-08-02T04:14:18.629123Z",
"start_time": "2024-08-02T04:14:18.627180Z"
}
},
"cell_type": "code",
Expand Down Expand Up @@ -119,8 +119,8 @@
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-07-31T20:33:03.274795Z",
"start_time": "2024-07-31T20:33:02.885073Z"
"end_time": "2024-08-02T04:14:19.421769Z",
"start_time": "2024-08-02T04:14:19.261974Z"
}
},
"cell_type": "code",
Expand All @@ -130,32 +130,21 @@
"submission_1 = verify.verify_sbml(sbml_filepath=sbml_fp, comparison_id=comparison_id, duration=duration, number_of_steps=nsteps, simulators=simulators)"
],
"id": "54fa1033a7c27056",
"outputs": [],
"execution_count": 6
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-07-31T20:33:03.911224Z",
"start_time": "2024-07-31T20:33:03.905608Z"
}
},
"cell_type": "code",
"source": "submission_1",
"id": "cc025e89e140d68a",
"outputs": [
{
"data": {
"text/plain": [
"RequestError(error='422 Client Error: Unprocessable Entity for url: https://biochecknet.biosimulations.org/verify-sbml')"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
"ename": "NotImplementedError",
"evalue": "Submission of jobs with a SBML file is currently under development.",
"output_type": "error",
"traceback": [
"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
"\u001B[0;31mNotImplementedError\u001B[0m Traceback (most recent call last)",
"Cell \u001B[0;32mIn[6], line 3\u001B[0m\n\u001B[1;32m 1\u001B[0m \u001B[38;5;66;03m# submit a new verification \u001B[39;00m\n\u001B[0;32m----> 3\u001B[0m submission_1 \u001B[38;5;241m=\u001B[39m \u001B[43mverify\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mverify_sbml\u001B[49m\u001B[43m(\u001B[49m\u001B[43msbml_filepath\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43msbml_fp\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mcomparison_id\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mcomparison_id\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mduration\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mduration\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mnumber_of_steps\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mnsteps\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43msimulators\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43msimulators\u001B[49m\u001B[43m)\u001B[49m\n",
"File \u001B[0;32m~/Desktop/repos/bio-check/demos/../bio_check/verifier.py:125\u001B[0m, in \u001B[0;36mVerifier.verify_sbml\u001B[0;34m(self, sbml_filepath, duration, number_of_steps, simulators, include_outputs, comparison_id, rTol, aTol, selection_list)\u001B[0m\n\u001B[1;32m 122\u001B[0m endpoint \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_format_endpoint(\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mverify-sbml\u001B[39m\u001B[38;5;124m'\u001B[39m)\n\u001B[1;32m 124\u001B[0m \u001B[38;5;66;03m# TODO: fix and remove this\u001B[39;00m\n\u001B[0;32m--> 125\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mNotImplementedError\u001B[39;00m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mSubmission of jobs with a SBML file is currently under development.\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m 127\u001B[0m \u001B[38;5;66;03m# configure params\u001B[39;00m\n\u001B[1;32m 128\u001B[0m _id \u001B[38;5;241m=\u001B[39m comparison_id \u001B[38;5;129;01mor\u001B[39;00m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mbio_check-request-\u001B[39m\u001B[38;5;124m\"\u001B[39m \u001B[38;5;241m+\u001B[39m \u001B[38;5;28mstr\u001B[39m(uuid4())\n",
"\u001B[0;31mNotImplementedError\u001B[0m: Submission of jobs with a SBML file is currently under development."
]
}
],
"execution_count": 7
"execution_count": 6
},
{
"metadata": {
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