Merge pull request #1477 from virtualcell/fix-field-data-algorithim

Fix field data algorithim

Author: Ezequiel-Valencia

docker/swarm/README_zeke_stack_on_linux.md

@@ -30,6 +30,7 @@
    -Dvcellapi.privateKey.file=/Users/evalencia/Documents/VCellDummyFiles/apiKeys \
    -Dvcell.mongodb.database=test \
    -Dvcell.mongodb.host.internal=localhost \
-   -Dvcell.mongodb.port.internal=27020
+   -Dvcell.mongodb.port.internal=27020 \
+   -Dvcell.primarySimdatadir.internal=/Users/evalencia/Documents/TempStorage
    popd
    ```

python-restclient/README.md

@@ -94,6 +94,7 @@ Class | Method | HTTP request | Description
 *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 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* | [**analyze_file_and_create**](docs/FieldDataResourceApi.md#analyze_file_and_create) | **POST** /api/v1/fieldData/analyzeAndCreateFromFile | For advanced users, combines the two separate requests of Analyze File and Create From Analyzed File. The following files are accepted: .tif and .zip.
 *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/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.

python-restclient/docs/FieldDataResourceApi.md

@@ -5,6 +5,7 @@ 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 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.
+[**analyze_file_and_create**](FieldDataResourceApi.md#analyze_file_and_create) | **POST** /api/v1/fieldData/analyzeAndCreateFromFile | For advanced users, combines the two separate requests of Analyze File and Create From Analyzed File. The following files are accepted: .tif and .zip.
 [**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/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.
@@ -86,6 +87,94 @@ Name | Type | Description  | Notes
 
 [[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)
 
+# **analyze_file_and_create**
+> FieldDataSavedResults analyze_file_and_create(file=file, file_name=file_name, extent=extent, i_size=i_size, channel_names=channel_names, times=times, annotation=annotation, origin=origin)
+
+For advanced users, combines the two separate requests of Analyze File and Create From Analyzed File. The following files are accepted: .tif and .zip.
+
+### Example
+
+```python
+import time
+import os
+import vcell_client
+from vcell_client.models.extent import Extent
+from vcell_client.models.field_data_saved_results import FieldDataSavedResults
+from vcell_client.models.i_size import ISize
+from vcell_client.models.origin import Origin
+from vcell_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to https://vcell-dev.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"
+)
+
+# The client must configure the authentication and authorization parameters
+# in accordance with the API server security policy.
+# Examples for each auth method are provided below, use the example that
+# satisfies your auth use case.
+
+# 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.FieldDataResourceApi(api_client)
+    file = None # bytearray |  (optional)
+    file_name = 'file_name_example' # str |  (optional)
+    extent = vcell_client.Extent() # Extent |  (optional)
+    i_size = vcell_client.ISize() # ISize |  (optional)
+    channel_names = ['channel_names_example'] # List[str] |  (optional)
+    times = [3.4] # List[float] |  (optional)
+    annotation = 'annotation_example' # str |  (optional)
+    origin = vcell_client.Origin() # Origin |  (optional)
+
+    try:
+        # For advanced users, combines the two separate requests of Analyze File and Create From Analyzed File. The following files are accepted: .tif and .zip.
+        api_response = api_instance.analyze_file_and_create(file=file, file_name=file_name, extent=extent, i_size=i_size, channel_names=channel_names, times=times, annotation=annotation, origin=origin)
+        print("The response of FieldDataResourceApi->analyze_file_and_create:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling FieldDataResourceApi->analyze_file_and_create: %s\n" % e)
+```
+
+
+
+### Parameters
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **file** | **bytearray**|  | [optional] 
+ **file_name** | **str**|  | [optional] 
+ **extent** | [**Extent**](Extent.md)|  | [optional] 
+ **i_size** | [**ISize**](ISize.md)|  | [optional] 
+ **channel_names** | [**List[str]**](str.md)|  | [optional] 
+ **times** | [**List[float]**](float.md)|  | [optional] 
+ **annotation** | **str**|  | [optional] 
+ **origin** | [**Origin**](Origin.md)|  | [optional] 
+
+### Return type
+
+[**FieldDataSavedResults**](FieldDataSavedResults.md)
+
+### Authorization
+
+[openId](../README.md#openId)
+
+### HTTP request headers
+
+ - **Content-Type**: multipart/form-data
+ - **Accept**: application/json
+
+### HTTP response details
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | OK |  -  |
+**401** | Not Authorized |  -  |
+**403** | Not Allowed |  -  |
+
+[[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)
+
 # **copy_models_field_data**
 > Dict[str, ExternalDataIdentifier] copy_models_field_data(source_model=source_model)