virtualcell · jcschaff · Apr 18, 2026 · Apr 8, 2026 · Apr 8, 2026 · Apr 8, 2026
diff --git a/CLAUDE.md b/CLAUDE.md
@@ -46,14 +46,17 @@ mvn compile test-compile -pl vcell-rest -am
 
 ## OpenAPI Client Generation
 
-OpenAPI spec is generated by Quarkus SmallRye OpenAPI from `vcell-rest` and stored in `tools/openapi.yaml`. Three clients are auto-generated:
+OpenAPI spec is generated by Quarkus SmallRye OpenAPI from `vcell-rest` and stored in `tools/openapi.yaml`. Three clients are auto-generated (Java, Python, TypeScript-Angular) using OpenAPI Generator v7.1.0.
 
 ```bash
-cd tools
-./generate.sh   # Generates Java, Python, and TypeScript-Angular clients
+# Generate clients from existing tools/openapi.yaml (if spec is already up to date)
+./tools/openapi-clients.sh
+
+# Rebuild vcell-rest, regenerate the OpenAPI spec, then generate all clients
+./tools/openapi-clients.sh --update-spec
 ```
 
-- **Java client:** `vcell-restclient/` (OpenAPI Generator v7.1.0)
+- **Java client:** `vcell-restclient/`
 - **Python client:** `python-restclient/`
 - **Angular client:** `webapp-ng/src/app/core/modules/openapi/`
 
@@ -124,7 +127,7 @@ GitHub Actions (`.github/workflows/ci_cd.yml`):
 After major changes (especially removing/renaming user-facing features):
 
 - [ ] Check `vcell-client/UserDocumentation/` for references to changed features. This is an ad-hoc XML format compiled into JavaHelp (in-app help) and HTML published at https://vcell.org/webstart/VCell_Tutorials/VCell_Help/index.html. Update documentation to stay consistent with code.
-- [ ] After regenerating OpenAPI clients (`tools/generate.sh`), compile downstream: `mvn compile test-compile -pl vcell-rest -am`
+- [ ] After regenerating OpenAPI clients (`tools/openapi-clients.sh`), compile downstream: `mvn compile test-compile -pl vcell-rest -am`
 
 ## Conventions
 

diff --git a/docs/parameter-estimation-service.md b/docs/parameter-estimation-service.md
diff --git a/python-restclient/.openapi-generator/FILES b/python-restclient/.openapi-generator/FILES
@@ -15,6 +15,11 @@ docs/BiomodelRef.md
 docs/CompositeCurve.md
 docs/ControlPointCurve.md
 docs/Coordinate.md
+docs/CopasiOptimizationMethod.md
+docs/CopasiOptimizationMethodOptimizationMethodType.md
+docs/CopasiOptimizationParameter.md
+docs/CopasiOptimizationParameterDataType.md
+docs/CopasiOptimizationParameterParamType.md
 docs/Curve.md
 docs/CurveSelectionInfo.md
 docs/DataIdentifier.md
@@ -54,11 +59,21 @@ docs/MathType.md
 docs/MathmodelRef.md
 docs/ModelType.md
 docs/N5ExportRequest.md
+docs/OptJobStatus.md
+docs/OptProblem.md
+docs/OptProgressItem.md
+docs/OptProgressReport.md
+docs/OptResultSet.md
+docs/OptimizationJobStatus.md
+docs/OptimizationResourceApi.md
 docs/Origin.md
+docs/ParameterDescription.md
 docs/Publication.md
 docs/PublicationInfo.md
 docs/PublicationResourceApi.md
 docs/PublishModelsRequest.md
+docs/ReferenceVariable.md
+docs/ReferenceVariableReferenceVariableType.md
 docs/SPECIALCLAIM.md
 docs/SampledCurve.md
 docs/SchedulerStatus.md
@@ -97,9 +112,28 @@ docs/VariableDomain.md
 docs/VariableMode.md
 docs/VariableSpecs.md
 docs/VariableType.md
+docs/Vcellopt.md
+docs/VcelloptStatus.md
 docs/Version.md
 docs/VersionFlag.md
 test/__init__.py
+test/test_copasi_optimization_method.py
+test/test_copasi_optimization_method_optimization_method_type.py
+test/test_copasi_optimization_parameter.py
+test/test_copasi_optimization_parameter_data_type.py
+test/test_copasi_optimization_parameter_param_type.py
+test/test_opt_job_status.py
+test/test_opt_problem.py
+test/test_opt_progress_item.py
+test/test_opt_progress_report.py
+test/test_opt_result_set.py
+test/test_optimization_job_status.py
+test/test_optimization_resource_api.py
+test/test_parameter_description.py
+test/test_reference_variable.py
+test/test_reference_variable_reference_variable_type.py
+test/test_vcellopt.py
+test/test_vcellopt_status.py
 tox.ini
 vcell_client/__init__.py
 vcell_client/api/__init__.py
@@ -110,6 +144,7 @@ vcell_client/api/field_data_resource_api.py
 vcell_client/api/geometry_resource_api.py
 vcell_client/api/hello_world_api.py
 vcell_client/api/math_model_resource_api.py
+vcell_client/api/optimization_resource_api.py
 vcell_client/api/publication_resource_api.py
 vcell_client/api/simulation_resource_api.py
 vcell_client/api/solver_resource_api.py
@@ -132,6 +167,11 @@ vcell_client/models/biomodel_ref.py
 vcell_client/models/composite_curve.py
 vcell_client/models/control_point_curve.py
 vcell_client/models/coordinate.py
+vcell_client/models/copasi_optimization_method.py
+vcell_client/models/copasi_optimization_method_optimization_method_type.py
+vcell_client/models/copasi_optimization_parameter.py
+vcell_client/models/copasi_optimization_parameter_data_type.py
+vcell_client/models/copasi_optimization_parameter_param_type.py
 vcell_client/models/curve.py
 vcell_client/models/curve_selection_info.py
 vcell_client/models/data_identifier.py
@@ -166,10 +206,19 @@ vcell_client/models/math_type.py
 vcell_client/models/mathmodel_ref.py
 vcell_client/models/model_type.py
 vcell_client/models/n5_export_request.py
+vcell_client/models/opt_job_status.py
+vcell_client/models/opt_problem.py
+vcell_client/models/opt_progress_item.py
+vcell_client/models/opt_progress_report.py
+vcell_client/models/opt_result_set.py
+vcell_client/models/optimization_job_status.py
 vcell_client/models/origin.py
+vcell_client/models/parameter_description.py
 vcell_client/models/publication.py
 vcell_client/models/publication_info.py
 vcell_client/models/publish_models_request.py
+vcell_client/models/reference_variable.py
+vcell_client/models/reference_variable_reference_variable_type.py
 vcell_client/models/sampled_curve.py
 vcell_client/models/scheduler_status.py
 vcell_client/models/simulation_execution_status_record.py
@@ -204,6 +253,8 @@ vcell_client/models/variable_type.py
 vcell_client/models/vc_document_type.py
 vcell_client/models/vc_image_summary.py
 vcell_client/models/vc_simulation_identifier.py
+vcell_client/models/vcellopt.py
+vcell_client/models/vcellopt_status.py
 vcell_client/models/version.py
 vcell_client/models/version_flag.py
 vcell_client/py.typed

diff --git a/python-restclient/README.md b/python-restclient/README.md
@@ -118,6 +118,10 @@ Class | Method | HTTP request | Description
 *MathModelResourceApi* | [**get_summary**](docs/MathModelResourceApi.md#get_summary) | **GET** /api/v1/mathModel/summary/{id} | 
 *MathModelResourceApi* | [**get_vcml**](docs/MathModelResourceApi.md#get_vcml) | **GET** /api/v1/mathModel/{id} | 
 *MathModelResourceApi* | [**save_math_model**](docs/MathModelResourceApi.md#save_math_model) | **POST** /api/v1/mathModel | 
+*OptimizationResourceApi* | [**get_optimization_status**](docs/OptimizationResourceApi.md#get_optimization_status) | **GET** /api/v1/optimization/{optId} | Get status, progress, or results of an optimization job
+*OptimizationResourceApi* | [**list_optimization_jobs**](docs/OptimizationResourceApi.md#list_optimization_jobs) | **GET** /api/v1/optimization | List optimization jobs for the authenticated user
+*OptimizationResourceApi* | [**stop_optimization**](docs/OptimizationResourceApi.md#stop_optimization) | **POST** /api/v1/optimization/{optId}/stop | Stop a running optimization job
+*OptimizationResourceApi* | [**submit_optimization**](docs/OptimizationResourceApi.md#submit_optimization) | **POST** /api/v1/optimization | Submit a new parameter estimation optimization job
 *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
 *PublicationResourceApi* | [**get_publication_by_id**](docs/PublicationResourceApi.md#get_publication_by_id) | **GET** /api/v1/publications/{id} | Get publication by ID
@@ -160,6 +164,11 @@ Class | Method | HTTP request | Description
  - [CompositeCurve](docs/CompositeCurve.md)
  - [ControlPointCurve](docs/ControlPointCurve.md)
  - [Coordinate](docs/Coordinate.md)
+ - [CopasiOptimizationMethod](docs/CopasiOptimizationMethod.md)
+ - [CopasiOptimizationMethodOptimizationMethodType](docs/CopasiOptimizationMethodOptimizationMethodType.md)
+ - [CopasiOptimizationParameter](docs/CopasiOptimizationParameter.md)
+ - [CopasiOptimizationParameterDataType](docs/CopasiOptimizationParameterDataType.md)
+ - [CopasiOptimizationParameterParamType](docs/CopasiOptimizationParameterParamType.md)
  - [Curve](docs/Curve.md)
  - [CurveSelectionInfo](docs/CurveSelectionInfo.md)
  - [DataIdentifier](docs/DataIdentifier.md)
@@ -194,10 +203,19 @@ Class | Method | HTTP request | Description
  - [MathmodelRef](docs/MathmodelRef.md)
  - [ModelType](docs/ModelType.md)
  - [N5ExportRequest](docs/N5ExportRequest.md)
+ - [OptJobStatus](docs/OptJobStatus.md)
+ - [OptProblem](docs/OptProblem.md)
+ - [OptProgressItem](docs/OptProgressItem.md)
+ - [OptProgressReport](docs/OptProgressReport.md)
+ - [OptResultSet](docs/OptResultSet.md)
+ - [OptimizationJobStatus](docs/OptimizationJobStatus.md)
  - [Origin](docs/Origin.md)
+ - [ParameterDescription](docs/ParameterDescription.md)
  - [Publication](docs/Publication.md)
  - [PublicationInfo](docs/PublicationInfo.md)
  - [PublishModelsRequest](docs/PublishModelsRequest.md)
+ - [ReferenceVariable](docs/ReferenceVariable.md)
+ - [ReferenceVariableReferenceVariableType](docs/ReferenceVariableReferenceVariableType.md)
  - [SPECIALCLAIM](docs/SPECIALCLAIM.md)
  - [SampledCurve](docs/SampledCurve.md)
  - [SchedulerStatus](docs/SchedulerStatus.md)
@@ -232,6 +250,8 @@ Class | Method | HTTP request | Description
  - [VariableMode](docs/VariableMode.md)
  - [VariableSpecs](docs/VariableSpecs.md)
  - [VariableType](docs/VariableType.md)
+ - [Vcellopt](docs/Vcellopt.md)
+ - [VcelloptStatus](docs/VcelloptStatus.md)
  - [Version](docs/Version.md)
  - [VersionFlag](docs/VersionFlag.md)
 

diff --git a/python-restclient/docs/CopasiOptimizationMethod.md b/python-restclient/docs/CopasiOptimizationMethod.md
@@ -0,0 +1,29 @@
+# CopasiOptimizationMethod
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**optimization_method_type** | [**CopasiOptimizationMethodOptimizationMethodType**](CopasiOptimizationMethodOptimizationMethodType.md) |  | [optional] 
+**optimization_parameter** | [**List[CopasiOptimizationParameter]**](CopasiOptimizationParameter.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.copasi_optimization_method import CopasiOptimizationMethod
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of CopasiOptimizationMethod from a JSON string
+copasi_optimization_method_instance = CopasiOptimizationMethod.from_json(json)
+# print the JSON string representation of the object
+print CopasiOptimizationMethod.to_json()
+
+# convert the object into a dict
+copasi_optimization_method_dict = copasi_optimization_method_instance.to_dict()
+# create an instance of CopasiOptimizationMethod from a dict
+copasi_optimization_method_form_dict = copasi_optimization_method.from_dict(copasi_optimization_method_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)
+
+
diff --git a/python-restclient/docs/CopasiOptimizationMethodOptimizationMethodType.md b/python-restclient/docs/CopasiOptimizationMethodOptimizationMethodType.md
@@ -0,0 +1,10 @@
+# CopasiOptimizationMethodOptimizationMethodType
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+
diff --git a/python-restclient/docs/CopasiOptimizationParameter.md b/python-restclient/docs/CopasiOptimizationParameter.md
@@ -0,0 +1,30 @@
+# CopasiOptimizationParameter
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**data_type** | [**CopasiOptimizationParameterDataType**](CopasiOptimizationParameterDataType.md) |  | [optional] 
+**param_type** | [**CopasiOptimizationParameterParamType**](CopasiOptimizationParameterParamType.md) |  | [optional] 
+**value** | **float** |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.copasi_optimization_parameter import CopasiOptimizationParameter
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of CopasiOptimizationParameter from a JSON string
+copasi_optimization_parameter_instance = CopasiOptimizationParameter.from_json(json)
+# print the JSON string representation of the object
+print CopasiOptimizationParameter.to_json()
+
+# convert the object into a dict
+copasi_optimization_parameter_dict = copasi_optimization_parameter_instance.to_dict()
+# create an instance of CopasiOptimizationParameter from a dict
+copasi_optimization_parameter_form_dict = copasi_optimization_parameter.from_dict(copasi_optimization_parameter_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)
+
+
diff --git a/python-restclient/docs/CopasiOptimizationParameterDataType.md b/python-restclient/docs/CopasiOptimizationParameterDataType.md
@@ -0,0 +1,10 @@
+# CopasiOptimizationParameterDataType
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+
diff --git a/python-restclient/docs/CopasiOptimizationParameterParamType.md b/python-restclient/docs/CopasiOptimizationParameterParamType.md
@@ -0,0 +1,10 @@
+# CopasiOptimizationParameterParamType
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+
diff --git a/python-restclient/docs/OptJobStatus.md b/python-restclient/docs/OptJobStatus.md
@@ -0,0 +1,10 @@
+# OptJobStatus
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+
diff --git a/python-restclient/docs/OptProblem.md b/python-restclient/docs/OptProblem.md
@@ -0,0 +1,33 @@
+# OptProblem
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**copasi_optimization_method** | [**CopasiOptimizationMethod**](CopasiOptimizationMethod.md) |  | [optional] 
+**data_set** | **List[List[float]]** |  | [optional] 
+**math_model_sbml_contents** | **str** |  | [optional] 
+**number_of_optimization_runs** | **int** |  | [optional] 
+**parameter_description_list** | [**List[ParameterDescription]**](ParameterDescription.md) |  | [optional] 
+**reference_variable** | [**List[ReferenceVariable]**](ReferenceVariable.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.opt_problem import OptProblem
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of OptProblem from a JSON string
+opt_problem_instance = OptProblem.from_json(json)
+# print the JSON string representation of the object
+print OptProblem.to_json()
+
+# convert the object into a dict
+opt_problem_dict = opt_problem_instance.to_dict()
+# create an instance of OptProblem from a dict
+opt_problem_form_dict = opt_problem.from_dict(opt_problem_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)
+
+
diff --git a/python-restclient/docs/OptProgressItem.md b/python-restclient/docs/OptProgressItem.md
@@ -0,0 +1,29 @@
+# OptProgressItem
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**num_function_evaluations** | **int** |  | [optional] 
+**obj_func_value** | **float** |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.opt_progress_item import OptProgressItem
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of OptProgressItem from a JSON string
+opt_progress_item_instance = OptProgressItem.from_json(json)
+# print the JSON string representation of the object
+print OptProgressItem.to_json()
+
+# convert the object into a dict
+opt_progress_item_dict = opt_progress_item_instance.to_dict()
+# create an instance of OptProgressItem from a dict
+opt_progress_item_form_dict = opt_progress_item.from_dict(opt_progress_item_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)
+
+
diff --git a/python-restclient/docs/OptProgressReport.md b/python-restclient/docs/OptProgressReport.md
@@ -0,0 +1,29 @@
+# OptProgressReport
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**best_param_values** | **Dict[str, float]** |  | [optional] 
+**progress_items** | [**List[OptProgressItem]**](OptProgressItem.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.opt_progress_report import OptProgressReport
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of OptProgressReport from a JSON string
+opt_progress_report_instance = OptProgressReport.from_json(json)
+# print the JSON string representation of the object
+print OptProgressReport.to_json()
+
+# convert the object into a dict
+opt_progress_report_dict = opt_progress_report_instance.to_dict()
+# create an instance of OptProgressReport from a dict
+opt_progress_report_form_dict = opt_progress_report.from_dict(opt_progress_report_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)
+
+