Merge pull request #1514 from virtualcell/biomodel-get-info

Introduce Retrieval of BioModel Info Objects From Quarkus

Author: Ezequiel-Valencia

docker/swarm/README_zeke_stack_on_linux.md

@@ -33,4 +33,15 @@
    -Dvcell.mongodb.port.internal=27020 \
    -Dvcell.primarySimdatadir.internal=/Users/evalencia/Documents/TempStorage
    popd
-   ```
+   ```
+
+---
+Build and Generate Clients
+
+``` bash 
+    pushd ../../
+    mvn clean install dependency:copy-dependencies -DskipTests=true
+    cp ./vcell-rest/target/generated/openapi.yaml ./tools/openapi.yaml
+    ./tools/generate.sh
+    popd
+ ```

pom.xml

@@ -158,6 +158,7 @@
 		<log4j2-jboss-logmanager.version>1.1.2.Final</log4j2-jboss-logmanager.version>
 		<log4j-layout-template-json.version>2.24.0</log4j-layout-template-json.version>
 		<lz4.version>1.8.0</lz4.version>
+		<microprofile-openapi.version>3.1</microprofile-openapi.version>
 		<mongodb-driver-sync.version>5.0.0</mongodb-driver-sync.version>
 		<n5.version>3.0.0</n5.version>
 		<netcdf.version>4.3.22</netcdf.version>

python-restclient/.openapi-generator/FILES

@@ -3,9 +3,12 @@
 README.md
 docs/AccesTokenRepresentationRecord.md
 docs/AdminResourceApi.md
+docs/ApplicationInfo.md
 docs/BatchSystemType.md
 docs/BioModel.md
+docs/BioModelChildSummary.md
 docs/BioModelResourceApi.md
+docs/BioModelSummary.md
 docs/BiomodelRef.md
 docs/DataIdentifier.md
 docs/DetailedState.md
@@ -17,16 +20,22 @@ docs/FieldDataReference.md
 docs/FieldDataResourceApi.md
 docs/FieldDataSavedResults.md
 docs/FieldDataShape.md
+docs/GroupAccess.md
+docs/GroupAccessAll.md
+docs/GroupAccessNone.md
+docs/GroupAccessSome.md
 docs/HelloWorldApi.md
 docs/HelloWorldMessage.md
 docs/HtcJobID.md
 docs/ISize.md
 docs/Identity.md
 docs/KeyValue.md
+docs/MathType.md
 docs/MathmodelRef.md
 docs/ModelType.md
 docs/Origin.md
 docs/Publication.md
+docs/PublicationInfo.md
 docs/PublicationResourceApi.md
 docs/SaveBioModel.md
 docs/SchedulerStatus.md
@@ -46,10 +55,15 @@ docs/UserIdentityJSONSafe.md
 docs/UserLoginInfoForMapping.md
 docs/UserRegistrationInfo.md
 docs/UsersResourceApi.md
+docs/VCDocumentType.md
 docs/VCSimulationIdentifier.md
 docs/VCellHTTPError.md
+docs/VCellSite.md
+docs/VCellSoftwareVersion.md
 docs/VariableDomain.md
 docs/VariableType.md
+docs/Version.md
+docs/VersionFlag.md
 test/__init__.py
 tox.ini
 vcell_client/__init__.py
@@ -68,8 +82,11 @@ vcell_client/configuration.py
 vcell_client/exceptions.py
 vcell_client/models/__init__.py
 vcell_client/models/acces_token_representation_record.py
+vcell_client/models/application_info.py
 vcell_client/models/batch_system_type.py
 vcell_client/models/bio_model.py
+vcell_client/models/bio_model_child_summary.py
+vcell_client/models/bio_model_summary.py
 vcell_client/models/biomodel_ref.py
 vcell_client/models/data_identifier.py
 vcell_client/models/detailed_state.py
@@ -80,15 +97,21 @@ vcell_client/models/field_data.py
 vcell_client/models/field_data_reference.py
 vcell_client/models/field_data_saved_results.py
 vcell_client/models/field_data_shape.py
+vcell_client/models/group_access.py
+vcell_client/models/group_access_all.py
+vcell_client/models/group_access_none.py
+vcell_client/models/group_access_some.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/math_type.py
 vcell_client/models/mathmodel_ref.py
 vcell_client/models/model_type.py
 vcell_client/models/origin.py
 vcell_client/models/publication.py
+vcell_client/models/publication_info.py
 vcell_client/models/save_bio_model.py
 vcell_client/models/scheduler_status.py
 vcell_client/models/simulation_execution_status_record.py
@@ -105,8 +128,13 @@ 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/v_cell_http_error.py
+vcell_client/models/v_cell_site.py
+vcell_client/models/v_cell_software_version.py
 vcell_client/models/variable_domain.py
 vcell_client/models/variable_type.py
+vcell_client/models/vc_document_type.py
 vcell_client/models/vc_simulation_identifier.py
+vcell_client/models/version.py
+vcell_client/models/version_flag.py
 vcell_client/py.typed
 vcell_client/rest.py

python-restclient/README.md

@@ -92,8 +92,10 @@ Class | Method | HTTP request | Description
 *AdminResourceApi* | [**get_usage**](docs/AdminResourceApi.md#get_usage) | **GET** /api/v1/admin/usage | Get usage summary
 *BioModelResourceApi* | [**delete_bio_model**](docs/BioModelResourceApi.md#delete_bio_model) | **DELETE** /api/v1/bioModel/{bioModelID} | Delete the BioModel from VCell's database.
 *BioModelResourceApi* | [**get_bio_model**](docs/BioModelResourceApi.md#get_bio_model) | **GET** /api/v1/bioModel/{bioModelID} | Get BioModel.
+*BioModelResourceApi* | [**get_bio_model_summaries**](docs/BioModelResourceApi.md#get_bio_model_summaries) | **GET** /api/v1/bioModel/summaries | Return BioModel summaries.
+*BioModelResourceApi* | [**get_bio_model_summary**](docs/BioModelResourceApi.md#get_bio_model_summary) | **GET** /api/v1/bioModel/{bioModelID}/summary | All of the text based information about a BioModel (summary, version, publication status, etc...), but not the actual BioModel itself.
 *BioModelResourceApi* | [**get_bio_model_vcml**](docs/BioModelResourceApi.md#get_bio_model_vcml) | **GET** /api/v1/bioModel/{bioModelID}/vcml_download | Get the BioModel in VCML format.
-*BioModelResourceApi* | [**save_bio_model**](docs/BioModelResourceApi.md#save_bio_model) | **POST** /api/v1/bioModel/save | Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
+*BioModelResourceApi* | [**save_bio_model**](docs/BioModelResourceApi.md#save_bio_model) | **POST** /api/v1/bioModel | Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
 *FieldDataResourceApi* | [**advanced_create**](docs/FieldDataResourceApi.md#advanced_create) | **POST** /api/v1/fieldData/advancedCreate | Create Field Data with granular detail in one request.The following files are accepted: .tif and .zip.
 *FieldDataResourceApi* | [**analyze_file**](docs/FieldDataResourceApi.md#analyze_file) | **POST** /api/v1/fieldData/analyzeFile | Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and return field data. Color mapped images not supported (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
 *FieldDataResourceApi* | [**copy_models_field_data**](docs/FieldDataResourceApi.md#copy_models_field_data) | **POST** /api/v1/fieldData/copyModelsFieldData | Copy all existing field data from a BioModel/MathModel that you have access to, but don't own.
@@ -129,8 +131,11 @@ Class | Method | HTTP request | Description
 ## Documentation For Models
 
  - [AccesTokenRepresentationRecord](docs/AccesTokenRepresentationRecord.md)
+ - [ApplicationInfo](docs/ApplicationInfo.md)
  - [BatchSystemType](docs/BatchSystemType.md)
  - [BioModel](docs/BioModel.md)
+ - [BioModelChildSummary](docs/BioModelChildSummary.md)
+ - [BioModelSummary](docs/BioModelSummary.md)
  - [BiomodelRef](docs/BiomodelRef.md)
  - [DataIdentifier](docs/DataIdentifier.md)
  - [DetailedState](docs/DetailedState.md)
@@ -141,15 +146,21 @@ Class | Method | HTTP request | Description
  - [FieldDataReference](docs/FieldDataReference.md)
  - [FieldDataSavedResults](docs/FieldDataSavedResults.md)
  - [FieldDataShape](docs/FieldDataShape.md)
+ - [GroupAccess](docs/GroupAccess.md)
+ - [GroupAccessAll](docs/GroupAccessAll.md)
+ - [GroupAccessNone](docs/GroupAccessNone.md)
+ - [GroupAccessSome](docs/GroupAccessSome.md)
  - [HelloWorldMessage](docs/HelloWorldMessage.md)
  - [HtcJobID](docs/HtcJobID.md)
  - [ISize](docs/ISize.md)
  - [Identity](docs/Identity.md)
  - [KeyValue](docs/KeyValue.md)
+ - [MathType](docs/MathType.md)
  - [MathmodelRef](docs/MathmodelRef.md)
  - [ModelType](docs/ModelType.md)
  - [Origin](docs/Origin.md)
  - [Publication](docs/Publication.md)
+ - [PublicationInfo](docs/PublicationInfo.md)
  - [SaveBioModel](docs/SaveBioModel.md)
  - [SchedulerStatus](docs/SchedulerStatus.md)
  - [SimulationExecutionStatusRecord](docs/SimulationExecutionStatusRecord.md)
@@ -165,10 +176,15 @@ Class | Method | HTTP request | Description
  - [UserIdentityJSONSafe](docs/UserIdentityJSONSafe.md)
  - [UserLoginInfoForMapping](docs/UserLoginInfoForMapping.md)
  - [UserRegistrationInfo](docs/UserRegistrationInfo.md)
+ - [VCDocumentType](docs/VCDocumentType.md)
  - [VCSimulationIdentifier](docs/VCSimulationIdentifier.md)
  - [VCellHTTPError](docs/VCellHTTPError.md)
+ - [VCellSite](docs/VCellSite.md)
+ - [VCellSoftwareVersion](docs/VCellSoftwareVersion.md)
  - [VariableDomain](docs/VariableDomain.md)
  - [VariableType](docs/VariableType.md)
+ - [Version](docs/Version.md)
+ - [VersionFlag](docs/VersionFlag.md)
 
 
 <a id="documentation-for-authorization"></a>

python-restclient/docs/ApplicationInfo.md

@@ -0,0 +1,31 @@
+# ApplicationInfo
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**name** | **str** |  | [optional] 
+**type** | [**MathType**](MathType.md) |  | [optional] 
+**dimensions** | **int** |  | [optional] 
+**geometry_name** | **str** |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.application_info import ApplicationInfo
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ApplicationInfo from a JSON string
+application_info_instance = ApplicationInfo.from_json(json)
+# print the JSON string representation of the object
+print ApplicationInfo.to_json()
+
+# convert the object into a dict
+application_info_dict = application_info_instance.to_dict()
+# create an instance of ApplicationInfo from a dict
+application_info_form_dict = application_info.from_dict(application_info_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)
+
+

python-restclient/docs/BioModelChildSummary.md

@@ -0,0 +1,39 @@
+# BioModelChildSummary
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**sc_names** | **List[str]** |  | [optional] 
+**sc_annots** | **List[str]** |  | [optional] 
+**geo_names** | **List[str]** |  | [optional] 
+**geo_dims** | **List[int]** |  | [optional] 
+**app_types** | [**List[MathType]**](MathType.md) |  | [optional] 
+**sim_names** | **List[List[str]]** |  | [optional] 
+**sim_annots** | **List[List[str]]** |  | [optional] 
+**geometry_dimensions** | **List[int]** |  | [optional] 
+**geometry_names** | **List[str]** |  | [optional] 
+**simulation_context_annotations** | **List[str]** |  | [optional] 
+**simulation_context_names** | **List[str]** |  | [optional] 
+**application_info** | [**List[ApplicationInfo]**](ApplicationInfo.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.bio_model_child_summary import BioModelChildSummary
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of BioModelChildSummary from a JSON string
+bio_model_child_summary_instance = BioModelChildSummary.from_json(json)
+# print the JSON string representation of the object
+print BioModelChildSummary.to_json()
+
+# convert the object into a dict
+bio_model_child_summary_dict = bio_model_child_summary_instance.to_dict()
+# create an instance of BioModelChildSummary from a dict
+bio_model_child_summary_form_dict = bio_model_child_summary.from_dict(bio_model_child_summary_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)
+
+

python-restclient/docs/BioModelContext.md

@@ -0,0 +1,31 @@
+# BioModelContext
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**version** | [**Version**](Version.md) |  | [optional] 
+**summary** | [**BioModelChildSummary**](BioModelChildSummary.md) |  | [optional] 
+**publication_information** | [**List[PublicationInfo]**](PublicationInfo.md) |  | [optional] 
+**v_cell_software_version** | [**VCellSoftwareVersion**](VCellSoftwareVersion.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.bio_model_context import BioModelContext
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of BioModelContext from a JSON string
+bio_model_context_instance = BioModelContext.from_json(json)
+# print the JSON string representation of the object
+print BioModelContext.to_json()
+
+# convert the object into a dict
+bio_model_context_dict = bio_model_context_instance.to_dict()
+# create an instance of BioModelContext from a dict
+bio_model_context_form_dict = bio_model_context.from_dict(bio_model_context_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)
+
+