Clarify API

Author: Ezequiel-Valencia

python-restclient/README.md

@@ -93,9 +93,9 @@ Class | Method | HTTP request | Description
 *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.
-*FieldDataResourceApi* | [**analyze_file**](docs/FieldDataResourceApi.md#analyze_file) | **POST** /api/v1/fieldData/analyzeFile | Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
+*FieldDataResourceApi* | [**analyze_file**](docs/FieldDataResourceApi.md#analyze_file) | **POST** /api/v1/fieldData/analyzeFile | Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.
-*FieldDataResourceApi* | [**create_from_analyzed_file**](docs/FieldDataResourceApi.md#create_from_analyzed_file) | **POST** /api/v1/fieldData/createFromAnalyzedFile | Take the Analyzed results of the field data, and save them to the server. User may adjust the analyzed file before uploading to edit defaults.
+*FieldDataResourceApi* | [**create_from_analyzed_file**](docs/FieldDataResourceApi.md#create_from_analyzed_file) | **POST** /api/v1/fieldData/createFromSpecification | Take the field data specification, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
 *FieldDataResourceApi* | [**create_from_simulation**](docs/FieldDataResourceApi.md#create_from_simulation) | **POST** /api/v1/fieldData/createFromSimulation | Create new field data from existing simulation results.
 *FieldDataResourceApi* | [**delete**](docs/FieldDataResourceApi.md#delete) | **DELETE** /api/v1/fieldData/delete/{fieldDataID} | Delete the selected field data.
 *FieldDataResourceApi* | [**get_all_ids**](docs/FieldDataResourceApi.md#get_all_ids) | **GET** /api/v1/fieldData/IDs | Get all of the ids used to identify, and retrieve field data.

python-restclient/docs/FieldDataResourceApi.md

@@ -4,9 +4,9 @@ All URIs are relative to *https://vcell-dev.cam.uchc.edu*
 
 Method | HTTP request | Description
 ------------- | ------------- | -------------
-[**analyze_file**](FieldDataResourceApi.md#analyze_file) | **POST** /api/v1/fieldData/analyzeFile | Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
+[**analyze_file**](FieldDataResourceApi.md#analyze_file) | **POST** /api/v1/fieldData/analyzeFile | Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.
 [**copy_models_field_data**](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.
-[**create_from_analyzed_file**](FieldDataResourceApi.md#create_from_analyzed_file) | **POST** /api/v1/fieldData/createFromAnalyzedFile | Take the Analyzed results of the field data, and save them to the server. User may adjust the analyzed file before uploading to edit defaults.
+[**create_from_analyzed_file**](FieldDataResourceApi.md#create_from_analyzed_file) | **POST** /api/v1/fieldData/createFromSpecification | Take the field data specification, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
 [**create_from_simulation**](FieldDataResourceApi.md#create_from_simulation) | **POST** /api/v1/fieldData/createFromSimulation | Create new field data from existing simulation results.
 [**delete**](FieldDataResourceApi.md#delete) | **DELETE** /api/v1/fieldData/delete/{fieldDataID} | Delete the selected field data.
 [**get_all_ids**](FieldDataResourceApi.md#get_all_ids) | **GET** /api/v1/fieldData/IDs | Get all of the ids used to identify, and retrieve field data.
@@ -16,7 +16,7 @@ Method | HTTP request | Description
 # **analyze_file**
 > AnalyzedFile analyze_file(file=file, file_name=file_name)
 
-Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
+Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.
 
 ### Example
 
@@ -47,7 +47,7 @@ with vcell_client.ApiClient(configuration) as api_client:
     file_name = 'file_name_example' # str |  (optional)
 
     try:
-        # Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
+        # Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.
         api_response = api_instance.analyze_file(file=file, file_name=file_name)
         print("The response of FieldDataResourceApi->analyze_file:\n")
         pprint(api_response)
@@ -161,7 +161,7 @@ Name | Type | Description  | Notes
 # **create_from_analyzed_file**
 > FieldDataSavedResults create_from_analyzed_file(analyzed_file=analyzed_file)
 
-Take the Analyzed results of the field data, and save them to the server. User may adjust the analyzed file before uploading to edit defaults.
+Take the field data specification, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
 
 ### Example
 
@@ -192,7 +192,7 @@ with vcell_client.ApiClient(configuration) as api_client:
     analyzed_file = vcell_client.AnalyzedFile() # AnalyzedFile |  (optional)
 
     try:
-        # Take the Analyzed results of the field data, and save them to the server. User may adjust the analyzed file before uploading to edit defaults.
+        # Take the field data specification, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
         api_response = api_instance.create_from_analyzed_file(analyzed_file=analyzed_file)
         print("The response of FieldDataResourceApi->create_from_analyzed_file:\n")
         pprint(api_response)

python-restclient/vcell_client/api/field_data_resource_api.py

@@ -71,7 +71,7 @@ def analyze_file(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> AnalyzedFile:
-        """Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
+        """Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.
 
 
         :param file:
@@ -144,7 +144,7 @@ def analyze_file_with_http_info(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> ApiResponse[AnalyzedFile]:
-        """Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
+        """Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.
 
 
         :param file:
@@ -217,7 +217,7 @@ def analyze_file_without_preload_content(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> RESTResponseType:
-        """Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
+        """Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.
 
 
         :param file:
@@ -641,7 +641,7 @@ def create_from_analyzed_file(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> FieldDataSavedResults:
-        """Take the Analyzed results of the field data, and save them to the server. User may adjust the analyzed file before uploading to edit defaults.
+        """Take the field data specification, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
 
 
         :param analyzed_file:
@@ -710,7 +710,7 @@ def create_from_analyzed_file_with_http_info(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> ApiResponse[FieldDataSavedResults]:
-        """Take the Analyzed results of the field data, and save them to the server. User may adjust the analyzed file before uploading to edit defaults.
+        """Take the field data specification, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
 
 
         :param analyzed_file:
@@ -779,7 +779,7 @@ def create_from_analyzed_file_without_preload_content(
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> RESTResponseType:
-        """Take the Analyzed results of the field data, and save them to the server. User may adjust the analyzed file before uploading to edit defaults.
+        """Take the field data specification, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
 
 
         :param analyzed_file:
@@ -886,7 +886,7 @@ def _create_from_analyzed_file_serialize(
 
         return self.api_client.param_serialize(
             method='POST',
-            resource_path='/api/v1/fieldData/createFromAnalyzedFile',
+            resource_path='/api/v1/fieldData/createFromSpecification',
             path_params=_path_params,
             query_params=_query_params,
             header_params=_header_params,

tools/openapi.yaml

@@ -212,10 +212,10 @@ paths:
     post:
       tags:
       - Field Data Resource
-      summary: "Analyze the field data from supported files (Tiff, Zip, and Non-GPL\
-        \ BioFormats). Please don't use color mapped images for the files (the colors\
-        \ in those images will be interpreted as separate channels). Filenames must\
-        \ be lowercase alphanumeric, and can contain underscores."
+      summary: "Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and\
+        \ create default field data specification. 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."
       operationId: analyzeFile
       requestBody:
         content:
@@ -270,32 +270,6 @@ paths:
       security:
       - openId:
         - user
-  /api/v1/fieldData/createFromAnalyzedFile:
-    post:
-      tags:
-      - Field Data Resource
-      summary: "Take the Analyzed results of the field data, and save them to the\
-        \ server. User may adjust the analyzed file before uploading to edit defaults."
-      operationId: createFromAnalyzedFile
-      requestBody:
-        content:
-          application/json:
-            schema:
-              $ref: '#/components/schemas/AnalyzedFile'
-      responses:
-        "200":
-          description: OK
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/FieldDataSavedResults'
-        "401":
-          description: Not Authorized
-        "403":
-          description: Not Allowed
-      security:
-      - openId:
-        - user
   /api/v1/fieldData/createFromSimulation:
     post:
       tags:
@@ -325,6 +299,32 @@ paths:
       security:
       - openId:
         - user
+  /api/v1/fieldData/createFromSpecification:
+    post:
+      tags:
+      - Field Data Resource
+      summary: "Take the field data specification, and save it to the server. User\
+        \ may adjust the analyzed file before uploading to edit defaults."
+      operationId: createFromAnalyzedFile
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/AnalyzedFile'
+      responses:
+        "200":
+          description: OK
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/FieldDataSavedResults'
+        "401":
+          description: Not Authorized
+        "403":
+          description: Not Allowed
+      security:
+      - openId:
+        - user
   /api/v1/fieldData/delete/{fieldDataID}:
     delete:
       tags:

vcell-rest/src/main/java/org/vcell/restq/handlers/FieldData/FieldDataResource.java

@@ -101,7 +101,7 @@ public void createNewFieldDataFromSimulation(@RestForm String simKeyReference, @
     @RolesAllowed("user")
     @Produces(MediaType.APPLICATION_JSON)
     @Consumes(MediaType.MULTIPART_FORM_DATA)
-    @Operation(operationId = "analyzeFile", summary = "Analyze the field data from supported files (Tiff, Zip, and Non-GPL BioFormats). Please don't use color mapped images for the files (the colors in those images will be interpreted as separate channels). " +
+    @Operation(operationId = "analyzeFile", summary = "Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and create default field data specification. 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.")
     public AnalyzedFile analyzeFieldData(@RestForm File file, @RestForm String fileName){
         try{
@@ -116,13 +116,13 @@ public AnalyzedFile analyzeFieldData(@RestForm File file, @RestForm String fileN
     }
 
     @POST
-    @Path("/createFromAnalyzedFile")
+    @Path("/createFromSpecification")
     @RolesAllowed("user")
     @Produces(MediaType.APPLICATION_JSON)
     @Consumes(MediaType.APPLICATION_JSON)
-    @Operation(operationId = "createFromAnalyzedFile", summary = "Take the Analyzed results of the field data, and save them to the server. " +
+    @Operation(operationId = "createFromAnalyzedFile", summary = "Take the field data specification, and save it to the server. " +
             "User may adjust the analyzed file before uploading to edit defaults.")
-    public FieldDataSavedResults createNewFieldDataFromFile(AnalyzedFile saveFieldData){
+    public FieldDataSavedResults createNewFieldDataFromSpecification(AnalyzedFile saveFieldData){
         FieldDataSavedResults fieldDataSavedResults;
         try{
             User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
@@ -155,7 +155,9 @@ public Hashtable<String, ExternalDataIdentifier> copyFieldData(SourceModel sourc
     @Operation(operationId = "delete", summary = "Delete the selected field data.")
     public void deleteFieldData(@PathParam("fieldDataID") String fieldDataID){
         try{
-            fieldDataDB.deleteFieldData(userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER), fieldDataID);
+            ExternalDataIdentifier edi = new ExternalDataIdentifier(new KeyValue(fieldDataID), userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER),
+                    null);
+            fieldDataDB.deleteFieldData(edi);
         } catch (DataAccessException e) {
             throw new WebApplicationException(e.getMessage(), HTTP.INTERNAL_SERVER_ERROR);
         }