Change BioModel Save Input

Author: Ezequiel-Valencia

python-restclient/.openapi-generator/FILES

@@ -36,7 +36,6 @@ docs/Origin.md
 docs/Publication.md
 docs/PublicationInfo.md
 docs/PublicationResourceApi.md
-docs/SaveBioModel.md
 docs/SchedulerStatus.md
 docs/SimulationExecutionStatusRecord.md
 docs/SimulationJobStatusRecord.md
@@ -110,7 +109,6 @@ 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
 vcell_client/models/simulation_job_status_record.py

python-restclient/README.md

@@ -160,7 +160,6 @@ Class | Method | HTTP request | Description
  - [Origin](docs/Origin.md)
  - [Publication](docs/Publication.md)
  - [PublicationInfo](docs/PublicationInfo.md)
- - [SaveBioModel](docs/SaveBioModel.md)
  - [SchedulerStatus](docs/SchedulerStatus.md)
  - [SimulationExecutionStatusRecord](docs/SimulationExecutionStatusRecord.md)
  - [SimulationJobStatusRecord](docs/SimulationJobStatusRecord.md)

python-restclient/docs/BioModelResourceApi.md

@@ -346,7 +346,7 @@ No authorization required
 [[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)
 
 # **save_bio_model**
-> str save_bio_model(save_bio_model=save_bio_model)
+> str save_bio_model(body, new_name=new_name, sims_requiring_updates=sims_requiring_updates)
 
 Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
 
@@ -356,7 +356,6 @@ Save's the given BioModel. Optional parameters of name and simulations to update
 import time
 import os
 import vcell_client
-from vcell_client.models.save_bio_model import SaveBioModel
 from vcell_client.rest import ApiException
 from pprint import pprint
 
@@ -375,11 +374,13 @@ configuration = vcell_client.Configuration(
 with vcell_client.ApiClient(configuration) as api_client:
     # Create an instance of the API class
     api_instance = vcell_client.BioModelResourceApi(api_client)
-    save_bio_model = vcell_client.SaveBioModel() # SaveBioModel |  (optional)
+    body = 'body_example' # str | BioModelVCML which will be saved.
+    new_name = 'new_name_example' # str | Name to save new BioModel under. Leave blank if re-saving existing BioModel. (optional)
+    sims_requiring_updates = ['sims_requiring_updates_example'] # List[str] | The name of simulations that will be prepared for future execution. (optional)
 
     try:
         # Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
-        api_response = api_instance.save_bio_model(save_bio_model=save_bio_model)
+        api_response = api_instance.save_bio_model(body, new_name=new_name, sims_requiring_updates=sims_requiring_updates)
         print("The response of BioModelResourceApi->save_bio_model:\n")
         pprint(api_response)
     except Exception as e:
@@ -392,7 +393,9 @@ with vcell_client.ApiClient(configuration) as api_client:
 
 Name | Type | Description  | Notes
 ------------- | ------------- | ------------- | -------------
- **save_bio_model** | [**SaveBioModel**](SaveBioModel.md)|  | [optional] 
+ **body** | **str**| BioModelVCML which will be saved. | 
+ **new_name** | **str**| Name to save new BioModel under. Leave blank if re-saving existing BioModel. | [optional] 
+ **sims_requiring_updates** | [**List[str]**](str.md)| The name of simulations that will be prepared for future execution. | [optional] 
 
 ### Return type
 
@@ -404,7 +407,7 @@ Name | Type | Description  | Notes
 
 ### HTTP request headers
 
- - **Content-Type**: application/json
+ - **Content-Type**: application/xml
  - **Accept**: application/xml, application/json
 
 ### HTTP response details

python-restclient/examples/scratch.py

@@ -54,6 +54,7 @@
 final_pubs: list[Publication] = publication_api.get_publications()
 print(f"final publications: {final_pubs}")
 
+BioModelResourceApi(api_client).save_bio_model("")
 
 field = FieldDataResourceApi(api_client)
 

python-restclient/vcell_client/__init__.py

@@ -69,7 +69,6 @@
 from vcell_client.models.origin import Origin
 from vcell_client.models.publication import Publication
 from vcell_client.models.publication_info import PublicationInfo
-from vcell_client.models.save_bio_model import SaveBioModel
 from vcell_client.models.scheduler_status import SchedulerStatus
 from vcell_client.models.simulation_execution_status_record import SimulationExecutionStatusRecord
 from vcell_client.models.simulation_job_status_record import SimulationJobStatusRecord

python-restclient/vcell_client/api/bio_model_resource_api.py

@@ -32,7 +32,6 @@
 
 from vcell_client.models.bio_model import BioModel
 from vcell_client.models.bio_model_summary import BioModelSummary
-from vcell_client.models.save_bio_model import SaveBioModel
 
 from vcell_client.api_client import ApiClient
 from vcell_client.api_response import ApiResponse
@@ -1372,7 +1371,9 @@ def _get_bio_model_vcml_serialize(
     @validate_call
     def save_bio_model(
         self,
-        save_bio_model: Optional[SaveBioModel] = None,
+        body: Annotated[StrictStr, Field(description="BioModelVCML which will be saved.")],
+        new_name: Annotated[Optional[StrictStr], Field(description="Name to save new BioModel under. Leave blank if re-saving existing BioModel.")] = None,
+        sims_requiring_updates: Annotated[Optional[List[StrictStr]], Field(description="The name of simulations that will be prepared for future execution.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -1389,8 +1390,12 @@ def save_bio_model(
         """Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
 
 
-        :param save_bio_model:
-        :type save_bio_model: SaveBioModel
+        :param body: BioModelVCML which will be saved. (required)
+        :type body: str
+        :param new_name: Name to save new BioModel under. Leave blank if re-saving existing BioModel.
+        :type new_name: str
+        :param sims_requiring_updates: The name of simulations that will be prepared for future execution.
+        :type sims_requiring_updates: List[str]
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -1414,7 +1419,9 @@ def save_bio_model(
         """ # noqa: E501
 
         _param = self._save_bio_model_serialize(
-            save_bio_model=save_bio_model,
+            body=body,
+            new_name=new_name,
+            sims_requiring_updates=sims_requiring_updates,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -1443,7 +1450,9 @@ def save_bio_model(
     @validate_call
     def save_bio_model_with_http_info(
         self,
-        save_bio_model: Optional[SaveBioModel] = None,
+        body: Annotated[StrictStr, Field(description="BioModelVCML which will be saved.")],
+        new_name: Annotated[Optional[StrictStr], Field(description="Name to save new BioModel under. Leave blank if re-saving existing BioModel.")] = None,
+        sims_requiring_updates: Annotated[Optional[List[StrictStr]], Field(description="The name of simulations that will be prepared for future execution.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -1460,8 +1469,12 @@ def save_bio_model_with_http_info(
         """Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
 
 
-        :param save_bio_model:
-        :type save_bio_model: SaveBioModel
+        :param body: BioModelVCML which will be saved. (required)
+        :type body: str
+        :param new_name: Name to save new BioModel under. Leave blank if re-saving existing BioModel.
+        :type new_name: str
+        :param sims_requiring_updates: The name of simulations that will be prepared for future execution.
+        :type sims_requiring_updates: List[str]
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -1485,7 +1498,9 @@ def save_bio_model_with_http_info(
         """ # noqa: E501
 
         _param = self._save_bio_model_serialize(
-            save_bio_model=save_bio_model,
+            body=body,
+            new_name=new_name,
+            sims_requiring_updates=sims_requiring_updates,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -1514,7 +1529,9 @@ def save_bio_model_with_http_info(
     @validate_call
     def save_bio_model_without_preload_content(
         self,
-        save_bio_model: Optional[SaveBioModel] = None,
+        body: Annotated[StrictStr, Field(description="BioModelVCML which will be saved.")],
+        new_name: Annotated[Optional[StrictStr], Field(description="Name to save new BioModel under. Leave blank if re-saving existing BioModel.")] = None,
+        sims_requiring_updates: Annotated[Optional[List[StrictStr]], Field(description="The name of simulations that will be prepared for future execution.")] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -1531,8 +1548,12 @@ def save_bio_model_without_preload_content(
         """Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
 
 
-        :param save_bio_model:
-        :type save_bio_model: SaveBioModel
+        :param body: BioModelVCML which will be saved. (required)
+        :type body: str
+        :param new_name: Name to save new BioModel under. Leave blank if re-saving existing BioModel.
+        :type new_name: str
+        :param sims_requiring_updates: The name of simulations that will be prepared for future execution.
+        :type sims_requiring_updates: List[str]
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -1556,7 +1577,9 @@ def save_bio_model_without_preload_content(
         """ # noqa: E501
 
         _param = self._save_bio_model_serialize(
-            save_bio_model=save_bio_model,
+            body=body,
+            new_name=new_name,
+            sims_requiring_updates=sims_requiring_updates,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -1580,7 +1603,9 @@ def save_bio_model_without_preload_content(
 
     def _save_bio_model_serialize(
         self,
-        save_bio_model,
+        body,
+        new_name,
+        sims_requiring_updates,
         _request_auth,
         _content_type,
         _headers,
@@ -1591,6 +1616,7 @@ def _save_bio_model_serialize(
 
         _collection_formats: Dict[str, str] = {
 
+            'simsRequiringUpdates': 'multi',
         }
 
         _path_params: Dict[str, str] = {}
@@ -1602,11 +1628,19 @@ def _save_bio_model_serialize(
 
         # process the path parameters
         # process the query parameters
+        if new_name is not None:
+            
+            _query_params.append(('newName', new_name))
+            
+        if sims_requiring_updates is not None:
+            
+            _query_params.append(('simsRequiringUpdates', sims_requiring_updates))
+            
         # process the header parameters
         # process the form parameters
         # process the body parameter
-        if save_bio_model is not None:
-            _body_params = save_bio_model
+        if body is not None:
+            _body_params = body
 
 
         # set the HTTP header `Accept`
@@ -1624,7 +1658,7 @@ def _save_bio_model_serialize(
             _default_content_type = (
                 self.api_client.select_header_content_type(
                     [
-                        'application/json'
+                        'application/xml'
                     ]
                 )
             )

python-restclient/vcell_client/models/__init__.py

@@ -45,7 +45,6 @@
 from vcell_client.models.origin import Origin
 from vcell_client.models.publication import Publication
 from vcell_client.models.publication_info import PublicationInfo
-from vcell_client.models.save_bio_model import SaveBioModel
 from vcell_client.models.scheduler_status import SchedulerStatus
 from vcell_client.models.simulation_execution_status_record import SimulationExecutionStatusRecord
 from vcell_client.models.simulation_job_status_record import SimulationJobStatusRecord

tools/openapi.yaml

@@ -189,11 +189,31 @@ paths:
       summary: Save's the given BioModel. Optional parameters of name and simulations
         to update due to math changes. Returns saved BioModel as VCML.
       operationId: saveBioModel
+      parameters:
+      - name: newName
+        in: query
+        description: Name to save new BioModel under. Leave blank if re-saving existing
+          BioModel.
+        required: false
+        schema:
+          type: string
+        allowEmptyValue: true
+      - name: simsRequiringUpdates
+        in: query
+        description: The name of simulations that will be prepared for future execution.
+        required: false
+        schema:
+          type: array
+          items:
+            type: string
+        allowEmptyValue: true
       requestBody:
+        description: BioModelVCML which will be saved.
         content:
-          application/json:
+          application/xml:
             schema:
-              $ref: '#/components/schemas/SaveBioModel'
+              type: string
+        required: true
       responses:
         "200":
           description: OK
@@ -1965,22 +1985,6 @@ components:
         theHashCode:
           format: int32
           type: integer
-    SaveBioModel:
-      required:
-      - bioModelXML
-      type: object
-      properties:
-        bioModelXML:
-          pattern: \S
-          type: string
-        name:
-          type: string
-          nullable: true
-        simsRequiringUpdates:
-          type: array
-          items:
-            type: string
-          nullable: true
     SchedulerStatus:
       enum:
       - WAITING

vcell-apiclient/src/main/java/org/vcell/api/messaging/LocalUserMetaDbServerMessaging.java

@@ -889,8 +889,9 @@ public BigString saveBioModel(BigString bioModelXML, String independentSims[]) t
     String savedBioModelXML = null;
     try {
         savedBioModelXML = vCellApiClient.getBioModelApi().saveBioModel(
-                        new SaveBioModel().bioModelXML(bioModelXML.toString())
-                                .simsRequiringUpdates(independentSims == null ? null : Arrays.asList(independentSims))
+				bioModelXML.toString(),
+				null,
+				independentSims == null ? null : Arrays.asList(independentSims)
         );
     } catch (ApiException e) {
         ExceptionHandler.onlyDataAccessException(e);
@@ -909,9 +910,10 @@ public BigString saveBioModelAs(BigString bioModelXML, String newName, String in
     String savedBioModelXML = null;
     try {
         savedBioModelXML = vCellApiClient.getBioModelApi().saveBioModel(
-                        new SaveBioModel().bioModelXML(bioModelXML.toString())
-                                .name(newName)
-                                .simsRequiringUpdates(independentSims == null ? null : Arrays.asList(independentSims)));
+						bioModelXML.toString(),
+						newName,
+						independentSims == null ? null : Arrays.asList(independentSims)
+		);
     } catch (ApiException e) {
         ExceptionHandler.onlyDataAccessException(e);
     }