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added maybe to model units
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@AlexPatrie
AlexPatrie committed Mar 1, 2024
1 parent e218542 commit 83e062a
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Showing 2 changed files with 28 additions and 44 deletions.
2 changes: 1 addition & 1 deletion biosimulator_processes/data_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -276,7 +276,7 @@ class SedModel(FromDict):
'global_parameter_changes': 'maybe[tree[string]]', # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs
'reaction_changes': 'maybe[tree[string]]'
},
'model_units': 'tree[string]'
'model_units': 'maybe[tree[string]]'
}

def __init__(self, _type: Dict = MODEL_TYPE):
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70 changes: 27 additions & 43 deletions notebooks/builder_composer.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,9 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": null,
"id": "b385dca6-942d-472c-9963-13b8cb33843c",
"metadata": {
"ExecuteTime": {
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"start_time": "2024-03-01T18:50:04.260886Z"
}
},
"metadata": {},
"outputs": [],
"source": [
"from builder import Builder, Process\n",
Expand All @@ -41,8 +36,8 @@
"id": "b6260555-2bad-4834-adc5-e6d358063579",
"metadata": {
"ExecuteTime": {
"end_time": "2024-03-01T18:45:09.801100Z",
"start_time": "2024-03-01T18:45:09.797541Z"
"end_time": "2024-03-01T19:01:08.039180Z",
"start_time": "2024-03-01T19:01:08.035424Z"
}
},
"outputs": [],
Expand All @@ -56,14 +51,14 @@
"id": "40cde984-cfdf-4571-af9c-3a3755e3763c",
"metadata": {
"ExecuteTime": {
"end_time": "2024-03-01T18:45:10.172978Z",
"start_time": "2024-03-01T18:45:10.169400Z"
"end_time": "2024-03-01T19:01:08.768333Z",
"start_time": "2024-03-01T19:01:08.764889Z"
}
},
"outputs": [
{
"data": {
"text/plain": "['ram-emitter',\n 'CopasiProcess',\n 'SmoldynProcess',\n 'console-emitter',\n 'CobraProcess',\n 'TelluriumProcess']"
"text/plain": "['console-emitter',\n 'CobraProcess',\n 'ram-emitter',\n 'TelluriumProcess',\n 'SmoldynProcess',\n 'CopasiProcess']"
},
"execution_count": 3,
"metadata": {},
Expand All @@ -89,8 +84,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-03-01T18:45:12.715567Z",
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"start_time": "2024-03-01T19:01:10.952929Z"
}
},
"id": "9279a6fec5ad0c48",
Expand All @@ -115,8 +110,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-03-01T18:45:12.736247Z",
"start_time": "2024-03-01T18:45:12.717370Z"
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"start_time": "2024-03-01T19:01:13.802137Z"
}
},
"id": "da6096ec3e0daa85",
Expand Down Expand Up @@ -164,12 +159,12 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-03-01T18:51:15.399056Z",
"start_time": "2024-03-01T18:51:15.392102Z"
"end_time": "2024-03-01T19:01:15.365004Z",
"start_time": "2024-03-01T19:01:15.359117Z"
}
},
"id": "2b1c1bdd6864a771",
"execution_count": 23
"execution_count": 6
},
{
"cell_type": "code",
Expand All @@ -189,7 +184,8 @@
" 'model_id': 'simple_copasi_process',\n",
" 'model_language': 'sbml',\n",
" 'model_name': 'Simple Composite Process',\n",
" 'model_source': {'value': 'BIOMD0000000861'}}\n"
" 'model_source': {'value': 'BIOMD0000000861'},\n",
" 'model_units': None}\n"
]
}
],
Expand All @@ -209,22 +205,22 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-03-01T18:52:11.944029Z",
"start_time": "2024-03-01T18:52:11.940871Z"
"end_time": "2024-03-01T19:01:21.177545Z",
"start_time": "2024-03-01T19:01:21.172957Z"
}
},
"id": "8d0566183a2d1c1f",
"execution_count": 25
"execution_count": 7
},
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 8,
"id": "b79dc6639a17e353",
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-03-01T18:53:12.797999Z",
"start_time": "2024-03-01T18:53:12.791670Z"
"end_time": "2024-03-01T19:01:28.308684Z",
"start_time": "2024-03-01T19:01:28.304148Z"
}
},
"outputs": [
Expand All @@ -244,7 +240,8 @@
" 'model_id': 'simple_copasi_process',\n",
" 'model_language': 'sbml',\n",
" 'model_name': 'Simple Composite Process',\n",
" 'model_source': {'value': 'BIOMD0000000861'}}}\n"
" 'model_source': {'value': 'BIOMD0000000861'},\n",
" 'model_units': None}}\n"
]
}
],
Expand All @@ -263,28 +260,15 @@
},
{
"cell_type": "code",
"outputs": [
{
"data": {
"text/plain": "['__abstractmethods__',\n '__annotations__',\n '__class__',\n '__class_getitem__',\n '__class_vars__',\n '__copy__',\n '__deepcopy__',\n '__delattr__',\n '__dict__',\n '__dir__',\n '__doc__',\n '__eq__',\n '__fields__',\n '__fields_set__',\n '__format__',\n '__ge__',\n '__get_pydantic_core_schema__',\n '__get_pydantic_json_schema__',\n '__getattr__',\n '__getattribute__',\n '__getstate__',\n '__gt__',\n '__hash__',\n '__init__',\n '__init_subclass__',\n '__iter__',\n '__le__',\n '__lt__',\n '__module__',\n '__ne__',\n '__new__',\n '__pretty__',\n '__private_attributes__',\n '__pydantic_complete__',\n '__pydantic_core_schema__',\n '__pydantic_custom_init__',\n '__pydantic_decorators__',\n '__pydantic_extra__',\n '__pydantic_fields_set__',\n '__pydantic_generic_metadata__',\n '__pydantic_init_subclass__',\n '__pydantic_parent_namespace__',\n '__pydantic_post_init__',\n '__pydantic_private__',\n '__pydantic_root_model__',\n '__pydantic_serializer__',\n '__pydantic_validator__',\n '__reduce__',\n '__reduce_ex__',\n '__repr__',\n '__repr_args__',\n '__repr_name__',\n '__repr_str__',\n '__rich_repr__',\n '__setattr__',\n '__setstate__',\n '__signature__',\n '__sizeof__',\n '__slots__',\n '__str__',\n '__subclasshook__',\n '__weakref__',\n '_abc_impl',\n '_calculate_keys',\n '_check_frozen',\n '_copy_and_set_values',\n '_get_value',\n '_iter',\n 'construct',\n 'copy',\n 'dict',\n 'from_orm',\n 'json',\n 'method',\n 'model',\n 'model_computed_fields',\n 'model_config',\n 'model_construct',\n 'model_copy',\n 'model_dump',\n 'model_dump_json',\n 'model_extra',\n 'model_fields',\n 'model_fields_set',\n 'model_json_schema',\n 'model_parametrized_name',\n 'model_post_init',\n 'model_rebuild',\n 'model_validate',\n 'model_validate_json',\n 'model_validate_strings',\n 'parse_file',\n 'parse_obj',\n 'parse_raw',\n 'schema',\n 'schema_json',\n 'serialize_model',\n 'update_forward_refs',\n 'validate']"
},
"execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"dir(process_config)"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-03-01T18:55:44.251693Z",
"start_time": "2024-03-01T18:55:44.243963Z"
}
"collapsed": false
},
"id": "a8bc9415d6ac47ad",
"execution_count": 28
"execution_count": null
},
{
"cell_type": "code",
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