Merge pull request #1406 from virtualcell/field-data-bug-fix

Field Data Endpoint Implementation

docker/swarm/README_zeke_stack_on_linux.md

@@ -14,6 +14,11 @@
        ./build.sh --skip-maven --skip-sudo all localhost:5000/virtualcell dev_zeke
        popd
       ```
+   3. ```bash
+       pushd ../build
+       ./build.sh --skip-maven --skip-sudo rest localhost:5000/virtualcell dev_zeke
+       popd
+      ```
 
 3. Run Quarkus in Terminal
    ``` bash 

python-restclient/.github/workflows/python.yml

@@ -16,9 +16,9 @@ jobs:
         python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

python-restclient/.openapi-generator/FILES

@@ -3,17 +3,28 @@
 README.md
 docs/AccesTokenRepresentationRecord.md
 docs/AdminResourceApi.md
+docs/AnalyzedResultsFromFieldData.md
 docs/BatchSystemType.md
 docs/BioModel.md
 docs/BioModelResourceApi.md
 docs/BiomodelRef.md
+docs/DataIdentifier.md
 docs/DetailedState.md
+docs/Domain.md
+docs/Extent.md
+docs/ExternalDataIdentifier.md
+docs/FieldDataReference.md
+docs/FieldDataResourceApi.md
+docs/FieldDataSaveResults.md
+docs/FieldDataShape.md
 docs/HelloWorldApi.md
 docs/HelloWorldMessage.md
 docs/HtcJobID.md
+docs/ISize.md
 docs/Identity.md
 docs/KeyValue.md
 docs/MathmodelRef.md
+docs/Origin.md
 docs/Publication.md
 docs/PublicationResourceApi.md
 docs/SchedulerStatus.md
@@ -32,13 +43,16 @@ docs/UserLoginInfoForMapping.md
 docs/UserRegistrationInfo.md
 docs/UsersResourceApi.md
 docs/VCSimulationIdentifier.md
+docs/VariableDomain.md
+docs/VariableType.md
 pyproject.toml
 test/__init__.py
 tox.ini
 vcell_client/__init__.py
 vcell_client/api/__init__.py
 vcell_client/api/admin_resource_api.py
 vcell_client/api/bio_model_resource_api.py
+vcell_client/api/field_data_resource_api.py
 vcell_client/api/hello_world_api.py
 vcell_client/api/publication_resource_api.py
 vcell_client/api/simulation_resource_api.py
@@ -49,15 +63,25 @@ 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/batch_system_type.py
 vcell_client/models/bio_model.py
 vcell_client/models/biomodel_ref.py
+vcell_client/models/data_identifier.py
 vcell_client/models/detailed_state.py
+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_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/origin.py
 vcell_client/models/publication.py
 vcell_client/models/scheduler_status.py
 vcell_client/models/simulation_execution_status_record.py
@@ -72,6 +96,8 @@ vcell_client/models/user.py
 vcell_client/models/user_identity_json_safe.py
 vcell_client/models/user_login_info_for_mapping.py
 vcell_client/models/user_registration_info.py
+vcell_client/models/variable_domain.py
+vcell_client/models/variable_type.py
 vcell_client/models/vc_simulation_identifier.py
 vcell_client/py.typed
 vcell_client/rest.py

python-restclient/README.md

@@ -89,6 +89,11 @@ 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* | [**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.
 *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
@@ -113,15 +118,25 @@ Class | Method | HTTP request | Description
 ## Documentation For Models
 
  - [AccesTokenRepresentationRecord](docs/AccesTokenRepresentationRecord.md)
+ - [AnalyzedResultsFromFieldData](docs/AnalyzedResultsFromFieldData.md)
  - [BatchSystemType](docs/BatchSystemType.md)
  - [BioModel](docs/BioModel.md)
  - [BiomodelRef](docs/BiomodelRef.md)
+ - [DataIdentifier](docs/DataIdentifier.md)
  - [DetailedState](docs/DetailedState.md)
+ - [Domain](docs/Domain.md)
+ - [Extent](docs/Extent.md)
+ - [ExternalDataIdentifier](docs/ExternalDataIdentifier.md)
+ - [FieldDataReference](docs/FieldDataReference.md)
+ - [FieldDataSaveResults](docs/FieldDataSaveResults.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)
+ - [Origin](docs/Origin.md)
  - [Publication](docs/Publication.md)
  - [SchedulerStatus](docs/SchedulerStatus.md)
  - [SimulationExecutionStatusRecord](docs/SimulationExecutionStatusRecord.md)
@@ -137,6 +152,8 @@ Class | Method | HTTP request | Description
  - [UserLoginInfoForMapping](docs/UserLoginInfoForMapping.md)
  - [UserRegistrationInfo](docs/UserRegistrationInfo.md)
  - [VCSimulationIdentifier](docs/VCSimulationIdentifier.md)
+ - [VariableDomain](docs/VariableDomain.md)
+ - [VariableType](docs/VariableType.md)
 
 
 <a id="documentation-for-authorization"></a>

python-restclient/docs/AnalyzedResultsFromFieldData.md

@@ -0,0 +1,35 @@
+# AnalyzedResultsFromFieldData
+
+
+## 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_results_from_field_data import AnalyzedResultsFromFieldData
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of AnalyzedResultsFromFieldData from a JSON string
+analyzed_results_from_field_data_instance = AnalyzedResultsFromFieldData.from_json(json)
+# print the JSON string representation of the object
+print AnalyzedResultsFromFieldData.to_json()
+
+# convert the object into a dict
+analyzed_results_from_field_data_dict = analyzed_results_from_field_data_instance.to_dict()
+# create an instance of AnalyzedResultsFromFieldData from a dict
+analyzed_results_from_field_data_form_dict = analyzed_results_from_field_data.from_dict(analyzed_results_from_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/BioModelResourceApi.md

@@ -132,7 +132,8 @@ No authorization required
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
-**200** | OK |  -  |
+**200** | return BioModel information in JSON format |  -  |
+**404** | BioModel not found |  -  |
 
 [[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)
 

python-restclient/docs/DataIdentifier.md

@@ -0,0 +1,34 @@
+# DataIdentifier
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**name** | **str** |  | [optional] 
+**display_name** | **str** |  | [optional] 
+**variable_type** | [**VariableType**](VariableType.md) |  | [optional] 
+**domain** | [**Domain**](Domain.md) |  | [optional] 
+**b_function** | **bool** |  | [optional] 
+**function** | **bool** |  | [optional] 
+**visible** | **bool** |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.data_identifier import DataIdentifier
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DataIdentifier from a JSON string
+data_identifier_instance = DataIdentifier.from_json(json)
+# print the JSON string representation of the object
+print DataIdentifier.to_json()
+
+# convert the object into a dict
+data_identifier_dict = data_identifier_instance.to_dict()
+# create an instance of DataIdentifier from a dict
+data_identifier_form_dict = data_identifier.from_dict(data_identifier_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/Simulation.md → python-restclient/docs/Domain.md

@@ -1,4 +1,4 @@
-# Simulation
+# Domain
 
 
 ## Properties
@@ -9,19 +9,19 @@ Name | Type | Description | Notes
 ## Example
 
 ```python
-from vcell_client.models.simulation import Simulation
+from vcell_client.models.domain import Domain
 
 # TODO update the JSON string below
 json = "{}"
-# create an instance of Simulation from a JSON string
-simulation_instance = Simulation.from_json(json)
+# create an instance of Domain from a JSON string
+domain_instance = Domain.from_json(json)
 # print the JSON string representation of the object
-print Simulation.to_json()
+print Domain.to_json()
 
 # convert the object into a dict
-simulation_dict = simulation_instance.to_dict()
-# create an instance of Simulation from a dict
-simulation_form_dict = simulation.from_dict(simulation_dict)
+domain_dict = domain_instance.to_dict()
+# create an instance of Domain from a dict
+domain_form_dict = domain.from_dict(domain_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/Extent.md

@@ -0,0 +1,30 @@
+# Extent
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**x** | **float** |  | [optional] 
+**y** | **float** |  | [optional] 
+**z** | **float** |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.extent import Extent
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of Extent from a JSON string
+extent_instance = Extent.from_json(json)
+# print the JSON string representation of the object
+print Extent.to_json()
+
+# convert the object into a dict
+extent_dict = extent_instance.to_dict()
+# create an instance of Extent from a dict
+extent_form_dict = extent.from_dict(extent_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/ExternalDataIdentifier.md

@@ -0,0 +1,34 @@
+# ExternalDataIdentifier
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**key** | [**KeyValue**](KeyValue.md) |  | [optional] 
+**owner** | [**User**](User.md) |  | [optional] 
+**name** | **str** |  | [optional] 
+**job_index** | **int** |  | [optional] 
+**simulation_key** | [**KeyValue**](KeyValue.md) |  | [optional] 
+**parameter_scan_type** | **bool** |  | [optional] 
+**data_key** | [**KeyValue**](KeyValue.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.external_data_identifier import ExternalDataIdentifier
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ExternalDataIdentifier from a JSON string
+external_data_identifier_instance = ExternalDataIdentifier.from_json(json)
+# print the JSON string representation of the object
+print ExternalDataIdentifier.to_json()
+
+# convert the object into a dict
+external_data_identifier_dict = external_data_identifier_instance.to_dict()
+# create an instance of ExternalDataIdentifier from a dict
+external_data_identifier_form_dict = external_data_identifier.from_dict(external_data_identifier_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

@@ -0,0 +1,30 @@
+# FieldDataReference
+
+
+## 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] 
+
+## Example
+
+```python
+from vcell_client.models.field_data_reference import FieldDataReference
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of FieldDataReference from a JSON string
+field_data_reference_instance = FieldDataReference.from_json(json)
+# print the JSON string representation of the object
+print FieldDataReference.to_json()
+
+# convert the object into a dict
+field_data_reference_dict = field_data_reference_instance.to_dict()
+# create an instance of FieldDataReference from a dict
+field_data_reference_form_dict = field_data_reference.from_dict(field_data_reference_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)
+
+