Merge pull request #1431 from virtualcell/sbml-to-finite-volume-input

Sbml to finite volume input

python-restclient/.openapi-generator-ignore

@@ -7,4 +7,5 @@ setup.cfg
 setup.py
 test-requirements.txt
 .gitlab-ci.yml
-.travis.yml
+.travis.yml
+pyproject.toml

python-restclient/.openapi-generator/FILES

@@ -35,6 +35,7 @@ docs/SimulationQueueEntryStatusRecord.md
 docs/SimulationQueueID.md
 docs/SimulationResourceApi.md
 docs/SimulationStatusPersistentRecord.md
+docs/SolverResourceApi.md
 docs/Status.md
 docs/StatusMessage.md
 docs/User.md
@@ -45,7 +46,6 @@ docs/UsersResourceApi.md
 docs/VCSimulationIdentifier.md
 docs/VariableDomain.md
 docs/VariableType.md
-pyproject.toml
 test/__init__.py
 tox.ini
 vcell_client/__init__.py
@@ -56,6 +56,7 @@ 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
+vcell_client/api/solver_resource_api.py
 vcell_client/api/users_resource_api.py
 vcell_client/api_client.py
 vcell_client/api_response.py

python-restclient/README.md

@@ -107,6 +107,7 @@ Class | Method | HTTP request | Description
 *SimulationResourceApi* | [**get_simulation_status**](docs/SimulationResourceApi.md#get_simulation_status) | **GET** /api/v1/Simulation/{simID}/simulationStatus | Get the status of simulation running
 *SimulationResourceApi* | [**start_simulation**](docs/SimulationResourceApi.md#start_simulation) | **POST** /api/v1/Simulation/{simID}/startSimulation | Start a simulation.
 *SimulationResourceApi* | [**stop_simulation**](docs/SimulationResourceApi.md#stop_simulation) | **POST** /api/v1/Simulation/{simID}/stopSimulation | Stop a simulation.
+*SolverResourceApi* | [**get_fv_solver_input**](docs/SolverResourceApi.md#get_fv_solver_input) | **GET** /api/v1/solver/getFVSolverInput | Retrieve finite volume input from SBML spatial model.
 *UsersResourceApi* | [**forgot_legacy_password**](docs/UsersResourceApi.md#forgot_legacy_password) | **POST** /api/v1/users/forgotLegacyPassword | The end user has forgotten the legacy password they used for VCell, so they will be emailed it.
 *UsersResourceApi* | [**get_guest_legacy_api_token**](docs/UsersResourceApi.md#get_guest_legacy_api_token) | **POST** /api/v1/users/guestBearerToken | Method to get legacy tokens for guest users
 *UsersResourceApi* | [**get_legacy_api_token**](docs/UsersResourceApi.md#get_legacy_api_token) | **POST** /api/v1/users/bearerToken | Get token for legacy API

python-restclient/docs/SolverResourceApi.md

@@ -0,0 +1,73 @@
+# vcell_client.SolverResourceApi
+
+All URIs are relative to *https://vcell-dev.cam.uchc.edu*
+
+Method | HTTP request | Description
+------------- | ------------- | -------------
+[**get_fv_solver_input**](SolverResourceApi.md#get_fv_solver_input) | **GET** /api/v1/solver/getFVSolverInput | Retrieve finite volume input from SBML spatial model.
+
+
+# **get_fv_solver_input**
+> bytearray get_fv_solver_input(sbml_file=sbml_file)
+
+Retrieve finite volume input from SBML spatial model.
+
+### Example
+
+```python
+import time
+import os
+import vcell_client
+from vcell_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to https://vcell-dev.cam.uchc.edu
+# See configuration.py for a list of all supported configuration parameters.
+configuration = vcell_client.Configuration(
+    host = "https://vcell-dev.cam.uchc.edu"
+)
+
+
+# Enter a context with an instance of the API client
+with vcell_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = vcell_client.SolverResourceApi(api_client)
+    sbml_file = None # bytearray |  (optional)
+
+    try:
+        # Retrieve finite volume input from SBML spatial model.
+        api_response = api_instance.get_fv_solver_input(sbml_file=sbml_file)
+        print("The response of SolverResourceApi->get_fv_solver_input:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling SolverResourceApi->get_fv_solver_input: %s\n" % e)
+```
+
+
+
+### Parameters
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **sbml_file** | **bytearray**|  | [optional] 
+
+### Return type
+
+**bytearray**
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: multipart/form-data
+ - **Accept**: application/octet-stream
+
+### HTTP response details
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | OK |  -  |
+
+[[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)
+

python-restclient/docs/SpatialResourceApi.md

@@ -0,0 +1,73 @@
+# vcell_client.SpatialResourceApi
+
+All URIs are relative to *https://vcell-dev.cam.uchc.edu*
+
+Method | HTTP request | Description
+------------- | ------------- | -------------
+[**retrieve_finite_volume_input_from_spatial_model**](SpatialResourceApi.md#retrieve_finite_volume_input_from_spatial_model) | **GET** /api/v1/spatial/retrieveFiniteVolumeInputFromSpatialModel | Retrieve finite volume input from spatial model
+
+
+# **retrieve_finite_volume_input_from_spatial_model**
+> bytearray retrieve_finite_volume_input_from_spatial_model(sbml_file=sbml_file)
+
+Retrieve finite volume input from spatial model
+
+### Example
+
+```python
+import time
+import os
+import vcell_client
+from vcell_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to https://vcell-dev.cam.uchc.edu
+# See configuration.py for a list of all supported configuration parameters.
+configuration = vcell_client.Configuration(
+    host = "https://vcell-dev.cam.uchc.edu"
+)
+
+
+# Enter a context with an instance of the API client
+with vcell_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = vcell_client.SpatialResourceApi(api_client)
+    sbml_file = None # bytearray |  (optional)
+
+    try:
+        # Retrieve finite volume input from spatial model
+        api_response = api_instance.retrieve_finite_volume_input_from_spatial_model(sbml_file=sbml_file)
+        print("The response of SpatialResourceApi->retrieve_finite_volume_input_from_spatial_model:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling SpatialResourceApi->retrieve_finite_volume_input_from_spatial_model: %s\n" % e)
+```
+
+
+
+### Parameters
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **sbml_file** | **bytearray**|  | [optional] 
+
+### Return type
+
+**bytearray**
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: multipart/form-data
+ - **Accept**: application/octet-stream
+
+### HTTP response details
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | OK |  -  |
+
+[[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)
+

python-restclient/test/test_solver_resource_api.py

@@ -0,0 +1,39 @@
+# coding: utf-8
+
+"""
+    VCell API
+
+    VCell API
+
+    The version of the OpenAPI document: 1.0.1
+    Contact: [email protected]
+    Generated by OpenAPI Generator (https://openapi-generator.tech)
+
+    Do not edit the class manually.
+"""  # noqa: E501
+
+
+import unittest
+
+from vcell_client.api.solver_resource_api import SolverResourceApi
+
+
+class TestSolverResourceApi(unittest.TestCase):
+    """SolverResourceApi unit test stubs"""
+
+    def setUp(self) -> None:
+        self.api = SolverResourceApi()
+
+    def tearDown(self) -> None:
+        pass
+
+    def test_get_fv_solver_input(self) -> None:
+        """Test case for get_fv_solver_input
+
+        Retrieve finite volume input from SBML spatial model.
+        """
+        pass
+
+
+if __name__ == '__main__':
+    unittest.main()

python-restclient/test/test_spatial_resource_api.py

@@ -0,0 +1,39 @@
+# coding: utf-8
+
+"""
+    VCell API
+
+    VCell API
+
+    The version of the OpenAPI document: 1.0.1
+    Contact: [email protected]
+    Generated by OpenAPI Generator (https://openapi-generator.tech)
+
+    Do not edit the class manually.
+"""  # noqa: E501
+
+
+import unittest
+
+from vcell_client.api.spatial_resource_api import SpatialResourceApi
+
+
+class TestSpatialResourceApi(unittest.TestCase):
+    """SpatialResourceApi unit test stubs"""
+
+    def setUp(self) -> None:
+        self.api = SpatialResourceApi()
+
+    def tearDown(self) -> None:
+        pass
+
+    def test_retrieve_finite_volume_input_from_spatial_model(self) -> None:
+        """Test case for retrieve_finite_volume_input_from_spatial_model
+
+        Retrieve finite volume input from spatial model
+        """
+        pass
+
+
+if __name__ == '__main__':
+    unittest.main()

python-restclient/vcell_client/__init__.py

@@ -24,6 +24,7 @@
 from vcell_client.api.hello_world_api import HelloWorldApi
 from vcell_client.api.publication_resource_api import PublicationResourceApi
 from vcell_client.api.simulation_resource_api import SimulationResourceApi
+from vcell_client.api.solver_resource_api import SolverResourceApi
 from vcell_client.api.users_resource_api import UsersResourceApi
 
 # import ApiClient

python-restclient/vcell_client/api/__init__.py

@@ -7,5 +7,6 @@
 from vcell_client.api.hello_world_api import HelloWorldApi
 from vcell_client.api.publication_resource_api import PublicationResourceApi
 from vcell_client.api.simulation_resource_api import SimulationResourceApi
+from vcell_client.api.solver_resource_api import SolverResourceApi
 from vcell_client.api.users_resource_api import UsersResourceApi