Merge pull request #1500 from virtualcell/save-biomodel-endpoint

Save BioModel Endpoint

Author: Ezequiel-Valencia

pom.xml

@@ -211,17 +211,17 @@
 		</repository>
 
 		<!-- needed for biomodels.net web services -->
-		<repository>
-			<id>ebi-repo</id>
-			<name>The EBI internal repository</name>
-			<url>https://www.ebi.ac.uk/~maven/m2repo</url>
-			<releases>
-				<enabled>true</enabled>
-			</releases>
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-		</repository>
+<!--		<repository>-->
+<!--			<id>ebi-repo</id>-->
+<!--			<name>The EBI internal repository</name>-->
+<!--			<url>https://www.ebi.ac.uk/~maven/m2repo</url>-->
+<!--			<releases>-->
+<!--				<enabled>true</enabled>-->
+<!--			</releases>-->
+<!--			<snapshots>-->
+<!--				<enabled>false</enabled>-->
+<!--			</snapshots>-->
+<!--		</repository>-->
 
 		<!-- Needed for custom JSBML artifacts we create -->
 		<repository>

python-restclient/.openapi-generator/FILES

@@ -28,6 +28,7 @@ docs/ModelType.md
 docs/Origin.md
 docs/Publication.md
 docs/PublicationResourceApi.md
+docs/SaveBioModel.md
 docs/SchedulerStatus.md
 docs/SimulationExecutionStatusRecord.md
 docs/SimulationJobStatusRecord.md
@@ -87,6 +88,7 @@ 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/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

@@ -6,7 +6,7 @@ This Python package is automatically generated by the [OpenAPI Generator](https:
 - API version: 1.0.1
 - Package version: 1.0.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
-For more information, please visit [http://exampleurl.com/contact](http://exampleurl.com/contact)
+For more information, please visit [https://vcell.org](https://vcell.org)
 
 ## Requirements.
 
@@ -56,10 +56,10 @@ 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
+# Defining the host is optional and defaults to https://vcell.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"
+    host = "https://vcell.cam.uchc.edu"
 )
 
 # The client must configure the authentication and authorization parameters
@@ -85,14 +85,15 @@ with vcell_client.ApiClient(configuration) as api_client:
 
 ## Documentation for API Endpoints
 
-All URIs are relative to *https://vcell-dev.cam.uchc.edu*
+All URIs are relative to *https://vcell.cam.uchc.edu*
 
 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_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.
+*BioModelResourceApi* | [**get_bio_model**](docs/BioModelResourceApi.md#get_bio_model) | **GET** /api/v1/bioModel/{bioModelID} | Get BioModel.
+*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.
 *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.
@@ -149,6 +150,7 @@ Class | Method | HTTP request | Description
  - [ModelType](docs/ModelType.md)
  - [Origin](docs/Origin.md)
  - [Publication](docs/Publication.md)
+ - [SaveBioModel](docs/SaveBioModel.md)
  - [SchedulerStatus](docs/SchedulerStatus.md)
  - [SimulationExecutionStatusRecord](docs/SimulationExecutionStatusRecord.md)
  - [SimulationJobStatusRecord](docs/SimulationJobStatusRecord.md)

python-restclient/docs/AdminResourceApi.md

@@ -1,6 +1,6 @@
 # vcell_client.AdminResourceApi
 
-All URIs are relative to *https://vcell-dev.cam.uchc.edu*
+All URIs are relative to *https://vcell.cam.uchc.edu*
 
 Method | HTTP request | Description
 ------------- | ------------- | -------------
@@ -21,10 +21,10 @@ 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
+# Defining the host is optional and defaults to https://vcell.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"
+    host = "https://vcell.cam.uchc.edu"
 )
 
 # The client must configure the authentication and authorization parameters

python-restclient/docs/BioModelResourceApi.md

@@ -1,12 +1,13 @@
 # vcell_client.BioModelResourceApi
 
-All URIs are relative to *https://vcell-dev.cam.uchc.edu*
+All URIs are relative to *https://vcell.cam.uchc.edu*
 
 Method | HTTP request | Description
 ------------- | ------------- | -------------
 [**delete_bio_model**](BioModelResourceApi.md#delete_bio_model) | **DELETE** /api/v1/bioModel/{bioModelID} | Delete the BioModel from VCell's database.
-[**get_biomodel_by_id**](BioModelResourceApi.md#get_biomodel_by_id) | **GET** /api/v1/bioModel/{bioModelID} | Get BioModel information in JSON format by ID.
-[**upload_bio_model**](BioModelResourceApi.md#upload_bio_model) | **POST** /api/v1/bioModel/upload_bioModel | Upload the BioModel to VCell database. Returns BioModel ID.
+[**get_bio_model**](BioModelResourceApi.md#get_bio_model) | **GET** /api/v1/bioModel/{bioModelID} | Get BioModel.
+[**get_bio_model_vcml**](BioModelResourceApi.md#get_bio_model_vcml) | **GET** /api/v1/bioModel/{bioModelID}/vcml_download | Get the BioModel in VCML format.
+[**save_bio_model**](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.
 
 
 # **delete_bio_model**
@@ -23,10 +24,10 @@ 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
+# Defining the host is optional and defaults to https://vcell.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"
+    host = "https://vcell.cam.uchc.edu"
 )
 
 
@@ -71,10 +72,10 @@ 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)
 
-# **get_biomodel_by_id**
-> BioModel get_biomodel_by_id(bio_model_id)
+# **get_bio_model**
+> BioModel get_bio_model(bio_model_id)
 
-Get BioModel information in JSON format by ID.
+Get BioModel.
 
 ### Example
 
@@ -86,10 +87,10 @@ from vcell_client.models.bio_model import BioModel
 from vcell_client.rest import ApiException
 from pprint import pprint
 
-# Defining the host is optional and defaults to https://vcell-dev.cam.uchc.edu
+# Defining the host is optional and defaults to https://vcell.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"
+    host = "https://vcell.cam.uchc.edu"
 )
 
 
@@ -100,12 +101,12 @@ with vcell_client.ApiClient(configuration) as api_client:
     bio_model_id = 'bio_model_id_example' # str | 
 
     try:
-        # Get BioModel information in JSON format by ID.
-        api_response = api_instance.get_biomodel_by_id(bio_model_id)
-        print("The response of BioModelResourceApi->get_biomodel_by_id:\n")
+        # Get BioModel.
+        api_response = api_instance.get_bio_model(bio_model_id)
+        print("The response of BioModelResourceApi->get_bio_model:\n")
         pprint(api_response)
     except Exception as e:
-        print("Exception when calling BioModelResourceApi->get_biomodel_by_id: %s\n" % e)
+        print("Exception when calling BioModelResourceApi->get_bio_model: %s\n" % e)
 ```
 
 
@@ -132,29 +133,93 @@ No authorization required
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
-**200** | return BioModel information in JSON format |  -  |
-**404** | BioModel not found |  -  |
+**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)
+
+# **get_bio_model_vcml**
+> str get_bio_model_vcml(bio_model_id)
+
+Get the BioModel in VCML format.
+
+### 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.cam.uchc.edu
+# See configuration.py for a list of all supported configuration parameters.
+configuration = vcell_client.Configuration(
+    host = "https://vcell.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.BioModelResourceApi(api_client)
+    bio_model_id = 'bio_model_id_example' # str | 
+
+    try:
+        # Get the BioModel in VCML format.
+        api_response = api_instance.get_bio_model_vcml(bio_model_id)
+        print("The response of BioModelResourceApi->get_bio_model_vcml:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling BioModelResourceApi->get_bio_model_vcml: %s\n" % e)
+```
+
+
+
+### Parameters
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **bio_model_id** | **str**|  | 
+
+### Return type
+
+**str**
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: text/xml
+
+### 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)
 
-# **upload_bio_model**
-> str upload_bio_model(body=body)
+# **save_bio_model**
+> str save_bio_model(save_bio_model=save_bio_model)
 
-Upload the BioModel to VCell database. Returns BioModel ID.
+Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
 
 ### Example
 
 ```python
 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
 
-# Defining the host is optional and defaults to https://vcell-dev.cam.uchc.edu
+# Defining the host is optional and defaults to https://vcell.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"
+    host = "https://vcell.cam.uchc.edu"
 )
 
 # The client must configure the authentication and authorization parameters
@@ -166,15 +231,15 @@ 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)
-    body = 'body_example' # str |  (optional)
+    save_bio_model = vcell_client.SaveBioModel() # SaveBioModel |  (optional)
 
     try:
-        # Upload the BioModel to VCell database. Returns BioModel ID.
-        api_response = api_instance.upload_bio_model(body=body)
-        print("The response of BioModelResourceApi->upload_bio_model:\n")
+        # 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)
+        print("The response of BioModelResourceApi->save_bio_model:\n")
         pprint(api_response)
     except Exception as e:
-        print("Exception when calling BioModelResourceApi->upload_bio_model: %s\n" % e)
+        print("Exception when calling BioModelResourceApi->save_bio_model: %s\n" % e)
 ```
 
 
@@ -183,7 +248,7 @@ with vcell_client.ApiClient(configuration) as api_client:
 
 Name | Type | Description  | Notes
 ------------- | ------------- | ------------- | -------------
- **body** | **str**|  | [optional] 
+ **save_bio_model** | [**SaveBioModel**](SaveBioModel.md)|  | [optional] 
 
 ### Return type
 
@@ -195,8 +260,8 @@ Name | Type | Description  | Notes
 
 ### HTTP request headers
 
- - **Content-Type**: text/xml
- - **Accept**: text/plain
+ - **Content-Type**: application/json
+ - **Accept**: application/xml
 
 ### HTTP response details
 | Status code | Description | Response headers |