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Updated Java Client
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AvocadoMoon committed Dec 20, 2024
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4 changes: 2 additions & 2 deletions python-restclient/.github/workflows/python.yml
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Expand Up @@ -16,9 +16,9 @@ jobs:
python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]

steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
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63 changes: 63 additions & 0 deletions python-restclient/.openapi-generator/FILES
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Expand Up @@ -3,17 +3,31 @@
README.md
docs/AccesTokenRepresentationRecord.md
docs/AdminResourceApi.md
docs/AnalyzedResultsFromFieldData.md
docs/BatchSystemType.md
docs/BioModel.md
docs/BioModelResourceApi.md
docs/BiomodelRef.md
docs/CartesianMesh.md
docs/Coordinate.md
docs/DetailedState.md
docs/Extent.md
docs/ExternalDataIdentifier.md
docs/FieldDataDBOperationSpec.md
docs/FieldDataExternalDataIDs.md
docs/FieldDataFileOperationSpec.md
docs/FieldDataNoCopyConflict.md
docs/FieldDataResourceApi.md
docs/FieldDataSaveResults.md
docs/GroupAccess.md
docs/HelloWorldApi.md
docs/HelloWorldMessage.md
docs/HtcJobID.md
docs/ISize.md
docs/Identity.md
docs/KeyValue.md
docs/MathmodelRef.md
docs/Origin.md
docs/Publication.md
docs/PublicationResourceApi.md
docs/SchedulerStatus.md
Expand All @@ -26,19 +40,48 @@ docs/SimulationResourceApi.md
docs/SimulationStatusPersistentRecord.md
docs/Status.md
docs/StatusMessage.md
docs/UCDInfo.md
docs/User.md
docs/UserIdentityJSONSafe.md
docs/UserLoginInfoForMapping.md
docs/UserRegistrationInfo.md
docs/UsersResourceApi.md
docs/VCSimulationIdentifier.md
docs/VariableDomain.md
docs/VariableType.md
docs/Version.md
docs/VersionFlag.md
docs/VersionableType.md
docs/VersionableTypeVersion.md
pyproject.toml
test/__init__.py
test/test_analyzed_results_from_field_data.py
test/test_cartesian_mesh.py
test/test_coordinate.py
test/test_extent.py
test/test_external_data_identifier.py
test/test_field_data_db_operation_spec.py
test/test_field_data_external_data_ids.py
test/test_field_data_file_operation_spec.py
test/test_field_data_no_copy_conflict.py
test/test_field_data_resource_api.py
test/test_field_data_save_results.py
test/test_group_access.py
test/test_i_size.py
test/test_origin.py
test/test_ucd_info.py
test/test_variable_domain.py
test/test_variable_type.py
test/test_version.py
test/test_version_flag.py
test/test_versionable_type.py
test/test_versionable_type_version.py
tox.ini
vcell_client/__init__.py
vcell_client/api/__init__.py
vcell_client/api/admin_resource_api.py
vcell_client/api/bio_model_resource_api.py
vcell_client/api/field_data_resource_api.py
vcell_client/api/hello_world_api.py
vcell_client/api/publication_resource_api.py
vcell_client/api/simulation_resource_api.py
Expand All @@ -49,15 +92,28 @@ vcell_client/configuration.py
vcell_client/exceptions.py
vcell_client/models/__init__.py
vcell_client/models/acces_token_representation_record.py
vcell_client/models/analyzed_results_from_field_data.py
vcell_client/models/batch_system_type.py
vcell_client/models/bio_model.py
vcell_client/models/biomodel_ref.py
vcell_client/models/cartesian_mesh.py
vcell_client/models/coordinate.py
vcell_client/models/detailed_state.py
vcell_client/models/extent.py
vcell_client/models/external_data_identifier.py
vcell_client/models/field_data_db_operation_spec.py
vcell_client/models/field_data_external_data_ids.py
vcell_client/models/field_data_file_operation_spec.py
vcell_client/models/field_data_no_copy_conflict.py
vcell_client/models/field_data_save_results.py
vcell_client/models/group_access.py
vcell_client/models/hello_world_message.py
vcell_client/models/htc_job_id.py
vcell_client/models/i_size.py
vcell_client/models/identity.py
vcell_client/models/key_value.py
vcell_client/models/mathmodel_ref.py
vcell_client/models/origin.py
vcell_client/models/publication.py
vcell_client/models/scheduler_status.py
vcell_client/models/simulation_execution_status_record.py
Expand All @@ -68,10 +124,17 @@ vcell_client/models/simulation_queue_id.py
vcell_client/models/simulation_status_persistent_record.py
vcell_client/models/status.py
vcell_client/models/status_message.py
vcell_client/models/ucd_info.py
vcell_client/models/user.py
vcell_client/models/user_identity_json_safe.py
vcell_client/models/user_login_info_for_mapping.py
vcell_client/models/user_registration_info.py
vcell_client/models/variable_domain.py
vcell_client/models/variable_type.py
vcell_client/models/vc_simulation_identifier.py
vcell_client/models/version.py
vcell_client/models/version_flag.py
vcell_client/models/versionable_type.py
vcell_client/models/versionable_type_version.py
vcell_client/py.typed
vcell_client/rest.py
26 changes: 26 additions & 0 deletions python-restclient/README.md
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Expand Up @@ -89,6 +89,12 @@ Class | Method | HTTP request | Description
*BioModelResourceApi* | [**delete_bio_model**](docs/BioModelResourceApi.md#delete_bio_model) | **DELETE** /api/v1/bioModel/{bioModelID} | Delete the BioModel from VCell's database.
*BioModelResourceApi* | [**get_biomodel_by_id**](docs/BioModelResourceApi.md#get_biomodel_by_id) | **GET** /api/v1/bioModel/{bioModelID} | Get BioModel information in JSON format by ID.
*BioModelResourceApi* | [**upload_bio_model**](docs/BioModelResourceApi.md#upload_bio_model) | **POST** /api/v1/bioModel/upload_bioModel | Upload the BioModel to VCell database. Returns BioModel ID.
*FieldDataResourceApi* | [**copy_field_data**](docs/FieldDataResourceApi.md#copy_field_data) | **POST** /api/v1/fieldData/copy | Copy an existing field data entry.
*FieldDataResourceApi* | [**create_new_field_data_from_file_already_analyzed**](docs/FieldDataResourceApi.md#create_new_field_data_from_file_already_analyzed) | **POST** /api/v1/fieldData/createFieldDataFromFileAlreadyAnalyzed |
*FieldDataResourceApi* | [**create_new_field_data_from_simulation**](docs/FieldDataResourceApi.md#create_new_field_data_from_simulation) | **POST** /api/v1/fieldData/createFieldDataFromSimulation | Create new field data from a simulation.
*FieldDataResourceApi* | [**delete_field_data**](docs/FieldDataResourceApi.md#delete_field_data) | **DELETE** /api/v1/fieldData | Delete the selected field data.
*FieldDataResourceApi* | [**generate_field_data_estimate**](docs/FieldDataResourceApi.md#generate_field_data_estimate) | **POST** /api/v1/fieldData/createFieldDataFromFile |
*FieldDataResourceApi* | [**get_all_field_data**](docs/FieldDataResourceApi.md#get_all_field_data) | **GET** /api/v1/fieldData | Get all of the field data for that user.
*HelloWorldApi* | [**get_hello_world**](docs/HelloWorldApi.md#get_hello_world) | **GET** /api/v1/helloworld | Get hello world message.
*PublicationResourceApi* | [**create_publication**](docs/PublicationResourceApi.md#create_publication) | **POST** /api/v1/publications | Create publication
*PublicationResourceApi* | [**delete_publication**](docs/PublicationResourceApi.md#delete_publication) | **DELETE** /api/v1/publications/{id} | Delete publication
Expand All @@ -113,15 +119,28 @@ Class | Method | HTTP request | Description
## Documentation For Models

- [AccesTokenRepresentationRecord](docs/AccesTokenRepresentationRecord.md)
- [AnalyzedResultsFromFieldData](docs/AnalyzedResultsFromFieldData.md)
- [BatchSystemType](docs/BatchSystemType.md)
- [BioModel](docs/BioModel.md)
- [BiomodelRef](docs/BiomodelRef.md)
- [CartesianMesh](docs/CartesianMesh.md)
- [Coordinate](docs/Coordinate.md)
- [DetailedState](docs/DetailedState.md)
- [Extent](docs/Extent.md)
- [ExternalDataIdentifier](docs/ExternalDataIdentifier.md)
- [FieldDataDBOperationSpec](docs/FieldDataDBOperationSpec.md)
- [FieldDataExternalDataIDs](docs/FieldDataExternalDataIDs.md)
- [FieldDataFileOperationSpec](docs/FieldDataFileOperationSpec.md)
- [FieldDataNoCopyConflict](docs/FieldDataNoCopyConflict.md)
- [FieldDataSaveResults](docs/FieldDataSaveResults.md)
- [GroupAccess](docs/GroupAccess.md)
- [HelloWorldMessage](docs/HelloWorldMessage.md)
- [HtcJobID](docs/HtcJobID.md)
- [ISize](docs/ISize.md)
- [Identity](docs/Identity.md)
- [KeyValue](docs/KeyValue.md)
- [MathmodelRef](docs/MathmodelRef.md)
- [Origin](docs/Origin.md)
- [Publication](docs/Publication.md)
- [SchedulerStatus](docs/SchedulerStatus.md)
- [SimulationExecutionStatusRecord](docs/SimulationExecutionStatusRecord.md)
Expand All @@ -132,11 +151,18 @@ Class | Method | HTTP request | Description
- [SimulationStatusPersistentRecord](docs/SimulationStatusPersistentRecord.md)
- [Status](docs/Status.md)
- [StatusMessage](docs/StatusMessage.md)
- [UCDInfo](docs/UCDInfo.md)
- [User](docs/User.md)
- [UserIdentityJSONSafe](docs/UserIdentityJSONSafe.md)
- [UserLoginInfoForMapping](docs/UserLoginInfoForMapping.md)
- [UserRegistrationInfo](docs/UserRegistrationInfo.md)
- [VCSimulationIdentifier](docs/VCSimulationIdentifier.md)
- [VariableDomain](docs/VariableDomain.md)
- [VariableType](docs/VariableType.md)
- [Version](docs/Version.md)
- [VersionFlag](docs/VersionFlag.md)
- [VersionableType](docs/VersionableType.md)
- [VersionableTypeVersion](docs/VersionableTypeVersion.md)


<a id="documentation-for-authorization"></a>
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35 changes: 35 additions & 0 deletions python-restclient/docs/AnalyzedResultsFromFieldData.md
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# AnalyzedResultsFromFieldData


## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**short_spec_data** | **List[List[List[int]]]** | | [optional]
**var_names** | **List[str]** | | [optional]
**times** | **List[float]** | | [optional]
**origin** | [**Origin**](Origin.md) | | [optional]
**extent** | [**Extent**](Extent.md) | | [optional]
**isize** | [**ISize**](ISize.md) | | [optional]
**annotation** | **str** | | [optional]
**name** | **str** | | [optional]

## Example

```python
from vcell_client.models.analyzed_results_from_field_data import AnalyzedResultsFromFieldData

# TODO update the JSON string below
json = "{}"
# create an instance of AnalyzedResultsFromFieldData from a JSON string
analyzed_results_from_field_data_instance = AnalyzedResultsFromFieldData.from_json(json)
# print the JSON string representation of the object
print AnalyzedResultsFromFieldData.to_json()

# convert the object into a dict
analyzed_results_from_field_data_dict = analyzed_results_from_field_data_instance.to_dict()
# create an instance of AnalyzedResultsFromFieldData from a dict
analyzed_results_from_field_data_form_dict = analyzed_results_from_field_data.from_dict(analyzed_results_from_field_data_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)


3 changes: 2 additions & 1 deletion python-restclient/docs/BioModelResourceApi.md
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Expand Up @@ -132,7 +132,8 @@ No authorization required
### HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
**200** | OK | - |
**200** | return BioModel information in JSON format | - |
**404** | BioModel not found | - |

[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)

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43 changes: 43 additions & 0 deletions python-restclient/docs/CartesianMesh.md
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# CartesianMesh


## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**compressed_bytes** | **bytearray** | | [optional]
**u_cd_info** | [**UCDInfo**](UCDInfo.md) | | [optional]
**geometry_dimension** | **int** | | [optional]
**volume_region_map_subvolume** | **Dict[str, int]** | | [optional]
**membrane_region_map_subvolumes_in_out** | **Dict[str, object]** | | [optional]
**num_membrane_elements** | **int** | | [optional]
**num_membrane_regions** | **int** | | [optional]
**num_volume_elements** | **int** | | [optional]
**num_volume_regions** | **int** | | [optional]
**i_size** | [**ISize**](ISize.md) | | [optional]
**size_x** | **int** | | [optional]
**size_y** | **int** | | [optional]
**size_z** | **int** | | [optional]
**membrane_connectivity_ok** | **bool** | | [optional]
**output_fields** | **List[object]** | | [optional]
**chombo_mesh** | **bool** | | [optional]

## Example

```python
from vcell_client.models.cartesian_mesh import CartesianMesh

# TODO update the JSON string below
json = "{}"
# create an instance of CartesianMesh from a JSON string
cartesian_mesh_instance = CartesianMesh.from_json(json)
# print the JSON string representation of the object
print CartesianMesh.to_json()

# convert the object into a dict
cartesian_mesh_dict = cartesian_mesh_instance.to_dict()
# create an instance of CartesianMesh from a dict
cartesian_mesh_form_dict = cartesian_mesh.from_dict(cartesian_mesh_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)


30 changes: 30 additions & 0 deletions python-restclient/docs/Coordinate.md
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# Coordinate


## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**x** | **float** | | [optional]
**y** | **float** | | [optional]
**z** | **float** | | [optional]

## Example

```python
from vcell_client.models.coordinate import Coordinate

# TODO update the JSON string below
json = "{}"
# create an instance of Coordinate from a JSON string
coordinate_instance = Coordinate.from_json(json)
# print the JSON string representation of the object
print Coordinate.to_json()

# convert the object into a dict
coordinate_dict = coordinate_instance.to_dict()
# create an instance of Coordinate from a dict
coordinate_form_dict = coordinate.from_dict(coordinate_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)


30 changes: 30 additions & 0 deletions python-restclient/docs/Extent.md
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# Extent


## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**x** | **float** | | [optional]
**y** | **float** | | [optional]
**z** | **float** | | [optional]

## Example

```python
from vcell_client.models.extent import Extent

# TODO update the JSON string below
json = "{}"
# create an instance of Extent from a JSON string
extent_instance = Extent.from_json(json)
# print the JSON string representation of the object
print Extent.to_json()

# convert the object into a dict
extent_dict = extent_instance.to_dict()
# create an instance of Extent from a dict
extent_form_dict = extent.from_dict(extent_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)


35 changes: 35 additions & 0 deletions python-restclient/docs/ExternalDataIdentifier.md
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# ExternalDataIdentifier


## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**key** | [**KeyValue**](KeyValue.md) | | [optional]
**owner** | [**User**](User.md) | | [optional]
**name** | **str** | | [optional]
**i_d** | **str** | | [optional]
**job_index** | **int** | | [optional]
**simulation_key** | [**KeyValue**](KeyValue.md) | | [optional]
**parameter_scan_type** | **bool** | | [optional]
**data_key** | [**KeyValue**](KeyValue.md) | | [optional]

## Example

```python
from vcell_client.models.external_data_identifier import ExternalDataIdentifier

# TODO update the JSON string below
json = "{}"
# create an instance of ExternalDataIdentifier from a JSON string
external_data_identifier_instance = ExternalDataIdentifier.from_json(json)
# print the JSON string representation of the object
print ExternalDataIdentifier.to_json()

# convert the object into a dict
external_data_identifier_dict = external_data_identifier_instance.to_dict()
# create an instance of ExternalDataIdentifier from a dict
external_data_identifier_form_dict = external_data_identifier.from_dict(external_data_identifier_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)


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