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fix: added builder to cobra notebook and process init
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@AlexPatrie
AlexPatrie committed Feb 29, 2024
1 parent c57e576 commit d612c3e
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Showing 3 changed files with 16 additions and 17 deletions.
2 changes: 1 addition & 1 deletion biosimulator_processes/processes/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
process_class = getattr(process_module, class_name)

# Register the process
BIOSIMULATOR_PROCESS_BUILDER.register_process(process_name, process_class)
BIOSIMULATOR_PROCESS_BUILDER.register_process(class_name, process_class)
print(f"{class_name} registered successfully.")
except ImportError as e:
print(f"{class_name} not available. Error: {e}")
7 changes: 4 additions & 3 deletions biosimulator_processes/processes/cobra_process.py
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Expand Up @@ -5,7 +5,8 @@

import cobra.io
from cobra.io import read_sbml_model
from process_bigraph import Process, core, Composite, pf, pp
from process_bigraph import Process, Composite, pf, pp
from biosimulator_processes.processes import BIOSIMULATOR_PROCESS_BUILDER


def check_sbml(state, schema, core):
Expand All @@ -32,8 +33,8 @@ def check_sbml(state, schema, core):
}

# register new types
core.register('bounds', bounds_type)
core.register('sbml', sbml_type)
BIOSIMULATOR_PROCESS_BUILDER.register_type('bounds', bounds_type)
BIOSIMULATOR_PROCESS_BUILDER.register_type('sbml', sbml_type)


class CobraProcess(Process):
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24 changes: 11 additions & 13 deletions notebooks/copasi_process_composer.ipynb
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Expand Up @@ -16,8 +16,8 @@
"id": "initial_id",
"metadata": {
"ExecuteTime": {
"end_time": "2024-02-29T19:54:21.729902Z",
"start_time": "2024-02-29T19:54:21.723041Z"
"end_time": "2024-02-29T20:05:02.946437Z",
"start_time": "2024-02-29T20:05:02.937522Z"
}
},
"outputs": [],
Expand All @@ -34,21 +34,19 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-02-29T19:54:23.693482Z",
"start_time": "2024-02-29T19:54:22.908092Z"
"end_time": "2024-02-29T20:05:06.292184Z",
"start_time": "2024-02-29T20:05:03.585162Z"
}
},
"outputs": [
{
"ename": "ImportError",
"evalue": "cannot import name 'process_registry' from 'process_bigraph' (/Users/alex/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/__init__.py)",
"output_type": "error",
"traceback": [
"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
"\u001B[0;31mImportError\u001B[0m Traceback (most recent call last)",
"Cell \u001B[0;32mIn[2], line 5\u001B[0m\n\u001B[1;32m 3\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mprocess_bigraph\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m Composite, pf \n\u001B[1;32m 4\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbuilder\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m Builder, Process \u001B[38;5;28;01mas\u001B[39;00m builderProcess, ProcessTypes\n\u001B[0;32m----> 5\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbiosimulator_processes\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mprocesses\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mcopasi_process\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m CopasiProcess\n\u001B[1;32m 6\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbiosimulator_processes\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mprocess_types\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m MODEL_TYPE, CHANGES_SCHEMA\n\u001B[1;32m 7\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbiosimulator_processes\u001B[39;00m\u001B[38;5;21;01m.\u001B[39;00m\u001B[38;5;21;01mutils\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m play_composition\n",
"File \u001B[0;32m~/Desktop/uchc_work/biosimulator-processes/notebooks/../biosimulator_processes/processes/__init__.py:1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mprocess_bigraph\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m process_registry\n\u001B[1;32m 4\u001B[0m \u001B[38;5;66;03m# Define a list of processes to attempt to import and register\u001B[39;00m\n\u001B[1;32m 5\u001B[0m processes_to_register \u001B[38;5;241m=\u001B[39m [\n\u001B[1;32m 6\u001B[0m (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcobra\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcobra_process.CobraProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m 7\u001B[0m (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcopasi\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcopasi_process.CopasiProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m 8\u001B[0m (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124msmoldyn\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124msmoldyn_process.SmoldynProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m 9\u001B[0m (\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mtellurium\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mtellurium_process.TelluriumProcess\u001B[39m\u001B[38;5;124m'\u001B[39m),\n\u001B[1;32m 10\u001B[0m ]\n",
"\u001B[0;31mImportError\u001B[0m: cannot import name 'process_registry' from 'process_bigraph' (/Users/alex/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-KVuYbFzt-py3.10/lib/python3.10/site-packages/process_bigraph/__init__.py)"
"name": "stdout",
"output_type": "stream",
"text": [
"CobraProcess registered successfully.\n",
"CopasiProcess registered successfully.\n",
"SmoldynProcess registered successfully.\n",
"TelluriumProcess registered successfully.\n"
]
}
],
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