Merge pull request #1463 from virtualcell/finish-field-data-endpoints

Copy Field Data From BioModel

Author: Ezequiel-Valencia

python-restclient/.openapi-generator/FILES

@@ -3,7 +3,7 @@
 README.md
 docs/AccesTokenRepresentationRecord.md
 docs/AdminResourceApi.md
-docs/AnalyzedResultsFromFieldData.md
+docs/AnalyzedFile.md
 docs/BatchSystemType.md
 docs/BioModel.md
 docs/BioModelResourceApi.md
@@ -15,7 +15,7 @@ docs/Extent.md
 docs/ExternalDataIdentifier.md
 docs/FieldDataReference.md
 docs/FieldDataResourceApi.md
-docs/FieldDataSaveResults.md
+docs/FieldDataSavedResults.md
 docs/FieldDataShape.md
 docs/HelloWorldApi.md
 docs/HelloWorldMessage.md
@@ -24,6 +24,7 @@ docs/ISize.md
 docs/Identity.md
 docs/KeyValue.md
 docs/MathmodelRef.md
+docs/ModelType.md
 docs/Origin.md
 docs/Publication.md
 docs/PublicationResourceApi.md
@@ -36,6 +37,7 @@ docs/SimulationQueueID.md
 docs/SimulationResourceApi.md
 docs/SimulationStatusPersistentRecord.md
 docs/SolverResourceApi.md
+docs/SourceModel.md
 docs/Status.md
 docs/StatusMessage.md
 docs/User.md
@@ -64,7 +66,7 @@ vcell_client/configuration.py
 vcell_client/exceptions.py
 vcell_client/models/__init__.py
 vcell_client/models/acces_token_representation_record.py
-vcell_client/models/analyzed_results_from_field_data.py
+vcell_client/models/analyzed_file.py
 vcell_client/models/batch_system_type.py
 vcell_client/models/bio_model.py
 vcell_client/models/biomodel_ref.py
@@ -74,14 +76,15 @@ vcell_client/models/domain.py
 vcell_client/models/extent.py
 vcell_client/models/external_data_identifier.py
 vcell_client/models/field_data_reference.py
-vcell_client/models/field_data_save_results.py
+vcell_client/models/field_data_saved_results.py
 vcell_client/models/field_data_shape.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/mathmodel_ref.py
+vcell_client/models/model_type.py
 vcell_client/models/origin.py
 vcell_client/models/publication.py
 vcell_client/models/scheduler_status.py
@@ -91,6 +94,7 @@ vcell_client/models/simulation_message.py
 vcell_client/models/simulation_queue_entry_status_record.py
 vcell_client/models/simulation_queue_id.py
 vcell_client/models/simulation_status_persistent_record.py
+vcell_client/models/source_model.py
 vcell_client/models/status.py
 vcell_client/models/status_message.py
 vcell_client/models/user.py

python-restclient/README.md

@@ -93,12 +93,13 @@ 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_field_data_file**](docs/FieldDataResourceApi.md#analyze_field_data_file) | **POST** /api/v1/fieldData/analyzeFieldDataFile | Analyze the field data from the uploaded file. Filenames must be lowercase alphanumeric, and can contain underscores.
-*FieldDataResourceApi* | [**create_field_data_from_analyzed_file**](docs/FieldDataResourceApi.md#create_field_data_from_analyzed_file) | **POST** /api/v1/fieldData/createFieldDataFromAnalyzedFile | Take the analyzed results of the field data, modify it to your liking, then save it on the server.
-*FieldDataResourceApi* | [**create_new_field_data_from_simulation**](docs/FieldDataResourceApi.md#create_new_field_data_from_simulation) | **POST** /api/v1/fieldData/createFieldDataFromSimulation | Create new field data from a simulation.
-*FieldDataResourceApi* | [**delete_field_data**](docs/FieldDataResourceApi.md#delete_field_data) | **DELETE** /api/v1/fieldData/delete/{fieldDataID} | Delete the selected field data.
-*FieldDataResourceApi* | [**get_all_field_data_ids**](docs/FieldDataResourceApi.md#get_all_field_data_ids) | **GET** /api/v1/fieldData/IDs | Get all of the ids used to identify, and retrieve field data.
-*FieldDataResourceApi* | [**get_field_data_shape_from_id**](docs/FieldDataResourceApi.md#get_field_data_shape_from_id) | **GET** /api/v1/fieldData/fieldDataShape/{fieldDataID} | Get the shape of the field data. That is it's size, origin, extent, and data identifiers.
+*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/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.
+*FieldDataResourceApi* | [**get_shape_from_id**](docs/FieldDataResourceApi.md#get_shape_from_id) | **GET** /api/v1/fieldData/shape/{fieldDataID} | Get the shape of the field data. That is it's size, origin, extent, times, and data identifiers.
 *HelloWorldApi* | [**get_hello_world**](docs/HelloWorldApi.md#get_hello_world) | **GET** /api/v1/helloworld | Get hello world message.
 *PublicationResourceApi* | [**create_publication**](docs/PublicationResourceApi.md#create_publication) | **POST** /api/v1/publications | Create publication
 *PublicationResourceApi* | [**delete_publication**](docs/PublicationResourceApi.md#delete_publication) | **DELETE** /api/v1/publications/{id} | Delete publication
@@ -125,7 +126,7 @@ Class | Method | HTTP request | Description
 ## Documentation For Models
 
  - [AccesTokenRepresentationRecord](docs/AccesTokenRepresentationRecord.md)
- - [AnalyzedResultsFromFieldData](docs/AnalyzedResultsFromFieldData.md)
+ - [AnalyzedFile](docs/AnalyzedFile.md)
  - [BatchSystemType](docs/BatchSystemType.md)
  - [BioModel](docs/BioModel.md)
  - [BiomodelRef](docs/BiomodelRef.md)
@@ -135,14 +136,15 @@ Class | Method | HTTP request | Description
  - [Extent](docs/Extent.md)
  - [ExternalDataIdentifier](docs/ExternalDataIdentifier.md)
  - [FieldDataReference](docs/FieldDataReference.md)
- - [FieldDataSaveResults](docs/FieldDataSaveResults.md)
+ - [FieldDataSavedResults](docs/FieldDataSavedResults.md)
  - [FieldDataShape](docs/FieldDataShape.md)
  - [HelloWorldMessage](docs/HelloWorldMessage.md)
  - [HtcJobID](docs/HtcJobID.md)
  - [ISize](docs/ISize.md)
  - [Identity](docs/Identity.md)
  - [KeyValue](docs/KeyValue.md)
  - [MathmodelRef](docs/MathmodelRef.md)
+ - [ModelType](docs/ModelType.md)
  - [Origin](docs/Origin.md)
  - [Publication](docs/Publication.md)
  - [SchedulerStatus](docs/SchedulerStatus.md)
@@ -152,6 +154,7 @@ Class | Method | HTTP request | Description
  - [SimulationQueueEntryStatusRecord](docs/SimulationQueueEntryStatusRecord.md)
  - [SimulationQueueID](docs/SimulationQueueID.md)
  - [SimulationStatusPersistentRecord](docs/SimulationStatusPersistentRecord.md)
+ - [SourceModel](docs/SourceModel.md)
  - [Status](docs/Status.md)
  - [StatusMessage](docs/StatusMessage.md)
  - [User](docs/User.md)

python-restclient/docs/AnalyzedFile.md

@@ -0,0 +1,35 @@
+# AnalyzedFile
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**short_spec_data** | **List[List[List[int]]]** |  | [optional] 
+**var_names** | **List[str]** |  | [optional] 
+**times** | **List[float]** |  | [optional] 
+**origin** | [**Origin**](Origin.md) |  | [optional] 
+**extent** | [**Extent**](Extent.md) |  | [optional] 
+**isize** | [**ISize**](ISize.md) |  | [optional] 
+**annotation** | **str** |  | [optional] 
+**name** | **str** |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.analyzed_file import AnalyzedFile
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of AnalyzedFile from a JSON string
+analyzed_file_instance = AnalyzedFile.from_json(json)
+# print the JSON string representation of the object
+print AnalyzedFile.to_json()
+
+# convert the object into a dict
+analyzed_file_dict = analyzed_file_instance.to_dict()
+# create an instance of AnalyzedFile from a dict
+analyzed_file_form_dict = analyzed_file.from_dict(analyzed_file_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/CopyFieldData.md

@@ -0,0 +1,29 @@
+# CopyFieldData
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**model_id** | **str** |  | [optional] 
+**model_type** | [**ModelType**](ModelType.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.copy_field_data import CopyFieldData
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of CopyFieldData from a JSON string
+copy_field_data_instance = CopyFieldData.from_json(json)
+# print the JSON string representation of the object
+print CopyFieldData.to_json()
+
+# convert the object into a dict
+copy_field_data_dict = copy_field_data_instance.to_dict()
+# create an instance of CopyFieldData from a dict
+copy_field_data_form_dict = copy_field_data.from_dict(copy_field_data_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/FieldDataReference.md

@@ -4,9 +4,9 @@
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
-**external_data_identifier** | [**ExternalDataIdentifier**](ExternalDataIdentifier.md) |  | [optional] 
-**external_data_annotation** | **str** |  | [optional] 
-**external_data_id_sim_refs** | [**List[KeyValue]**](KeyValue.md) |  | [optional] 
+**field_data_id** | [**ExternalDataIdentifier**](ExternalDataIdentifier.md) |  | [optional] 
+**annotation** | **str** |  | [optional] 
+**simulations_referencing_this_id** | [**List[KeyValue]**](KeyValue.md) |  | [optional] 
 
 ## Example