Update nlpsandboxsdk to nlpsandbox (#174)

* Update nlpsandboxsdk to nlpsandbox * Update
nlpsandbox · Jun 5, 2021 · 7e95d3d · 7e95d3d
1 parent b8abb58
commit 7e95d3d
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Showing 117 changed files with 215 additions and 56 deletions.
diff --git a/.openapi-generator/FILES b/.openapi-generator/FILES
@@ -199,6 +199,5 @@ nlpsandbox/model/tool_dependencies.py
 nlpsandbox/model/tool_type.py
 nlpsandbox/model_utils.py
 nlpsandbox/models/__init__.py
-nlpsandbox/models/__init__.py
 nlpsandbox/rest.py
 test/__init__.py
diff --git a/.openapi-generator/VERSION b/.openapi-generator/VERSION
@@ -1 +1 @@
-5.0.1
+5.1.1
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -113,22 +113,6 @@ The Python SDK client `nlpsandbox` is now automatically updated when there is a
   openapi-generator generate -g python -o . --package-name nlpsandbox -i https://nlpsandbox.github.io/nlpsandbox-schemas/_internal/nlpsandbox/edge/openapi.json
   ```
 
-<!-- - `datanode` package
-  ```
-  openapi-generator generate -g python -o . --package-name datanode -i https://nlpsandbox.github.io/nlpsandbox-schemas/data-node/edge/openapi.json
-  ```
-
-- `annotator` package
-  Use the `merge-annotator` branch in the `nlpsandbox-schemas` to view a merged [openapi.yaml](https://github.com/nlpsandbox/nlpsandbox-schemas/blob/merge-annotators/openapi/annotator/openapi.yaml).  Follow instructions in the schemas github repository to validate the `annotators` folder. This file merges all of the annotators together.
-  ```
-  # Create merged openapi.yaml
-  git clone -b merge-annotator https://github.com/nlpsandbox/nlpsandbox-schemas.git
-  cd nlpsandbox-schemas
-  npm run validate --api=annotator  # This command will create a complete openapi.yaml
-  # navigate back into the nlpsandbox-client directory
-  openapi-generator generate -g python -o . --package-name annotator -i nlpsandbox-schemas/openapi.yaml
-  ``` -->
-
 ### Testing
 
 Please add tests for new code. These might include unit tests (to test specific functionality of code that was added to support fixing the bug or feature), integration tests (to test that the feature is usable - e.g., it should have complete the expected behavior as reported in the feature request or bug report), or both.

diff --git a/docs/Annotation.md b/docs/Annotation.md
@@ -1,6 +1,7 @@
 # Annotation
 
 An annotation record
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationApi.md b/docs/AnnotationApi.md
@@ -88,6 +88,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationApi->create_annotation: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -110,6 +111,7 @@ No authorization required
  - **Content-Type**: application/json
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -162,6 +164,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationApi->delete_annotation: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -183,6 +186,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -235,6 +239,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationApi->get_annotation: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -256,6 +261,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -319,6 +325,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationApi->list_annotations: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -341,6 +348,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|

diff --git a/docs/AnnotationCreateRequest.md b/docs/AnnotationCreateRequest.md
@@ -1,6 +1,7 @@
 # AnnotationCreateRequest
 
 An annotation record
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationCreateResponse.md b/docs/AnnotationCreateResponse.md
@@ -1,6 +1,7 @@
 # AnnotationCreateResponse
 
 The reference to the annotation created
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationId.md b/docs/AnnotationId.md
@@ -1,6 +1,7 @@
 # AnnotationId
 
 The ID of the annotation
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationName.md b/docs/AnnotationName.md
@@ -1,6 +1,7 @@
 # AnnotationName
 
 The resource name of the annotation record, of the form datasets/{datasetId}/annotationStores/{annotationStoreId}/annotations/{annotationId}
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationSet.md b/docs/AnnotationSet.md
@@ -1,6 +1,7 @@
 # AnnotationSet
 
 Set of annotations of all types for a text
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationSource.md b/docs/AnnotationSource.md
@@ -1,6 +1,7 @@
 # AnnotationSource
 
 The source of an annotation record
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationStore.md b/docs/AnnotationStore.md
@@ -1,6 +1,7 @@
 # AnnotationStore
 
 An annotation store
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationStoreApi.md b/docs/AnnotationStoreApi.md
@@ -61,6 +61,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationStoreApi->create_annotation_store: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -82,6 +83,7 @@ No authorization required
  - **Content-Type**: application/json
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -132,6 +134,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationStoreApi->delete_annotation_store: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -152,6 +155,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -202,6 +206,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationStoreApi->get_annotation_store: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -222,6 +227,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -283,6 +289,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling AnnotationStoreApi->list_annotation_stores: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -304,6 +311,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|

diff --git a/docs/AnnotationStoreCreateResponse.md b/docs/AnnotationStoreCreateResponse.md
@@ -1,6 +1,7 @@
 # AnnotationStoreCreateResponse
 
 The reference to the annotation store created
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationStoreId.md b/docs/AnnotationStoreId.md
@@ -1,6 +1,7 @@
 # AnnotationStoreId
 
 The ID of the annotation store
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/AnnotationStoreName.md b/docs/AnnotationStoreName.md
@@ -1,6 +1,7 @@
 # AnnotationStoreName
 
 The resource name of the annotation store, of the form datasets/{datasetId}/annotationStores/{annotationStoreId}
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/Dataset.md b/docs/Dataset.md
@@ -1,6 +1,7 @@
 # Dataset
 
 A dataset
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/DatasetApi.md b/docs/DatasetApi.md
@@ -59,6 +59,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling DatasetApi->create_dataset: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -79,6 +80,7 @@ No authorization required
  - **Content-Type**: application/json
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -127,6 +129,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling DatasetApi->delete_dataset: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -146,6 +149,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -194,6 +198,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling DatasetApi->get_dataset: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -213,6 +218,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
@@ -264,6 +270,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling DatasetApi->list_datasets: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -284,6 +291,7 @@ No authorization required
  - **Content-Type**: Not defined
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|

diff --git a/docs/DatasetCreateResponse.md b/docs/DatasetCreateResponse.md
@@ -1,6 +1,7 @@
 # DatasetCreateResponse
 
 The reference of the dataset created
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/DatasetId.md b/docs/DatasetId.md
@@ -1,6 +1,7 @@
 # DatasetId
 
 The ID of the dataset
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/DatasetName.md b/docs/DatasetName.md
@@ -1,6 +1,7 @@
 # DatasetName
 
 The name of the dataset
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/DateOffsetConfig.md b/docs/DateOffsetConfig.md
@@ -1,6 +1,7 @@
 # DateOffsetConfig
 
 Configuration for the \"date offset\" strategy. E.g. \"John Smith visited on 1 January 2020\" -> \"John Smith visited on 29 October 2025\". Note, can only be set with the \"text_date\" annotation type.
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/DeidentificationStep.md b/docs/DeidentificationStep.md
@@ -1,6 +1,7 @@
 # DeidentificationStep
 
 The configuration of a deidentification step
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/DeidentifiedNoteApi.md b/docs/DeidentifiedNoteApi.md
@@ -70,6 +70,7 @@ with nlpsandbox.ApiClient() as api_client:
         print("Exception when calling DeidentifiedNoteApi->create_deidentified_notes: %s\n" % e)
 ```
 
+
 ### Parameters
 
 Name | Type | Description  | Notes
@@ -89,6 +90,7 @@ No authorization required
  - **Content-Type**: application/json
  - **Accept**: application/json
 
+
 ### HTTP response details
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|

diff --git a/docs/DeidentifyRequest.md b/docs/DeidentifyRequest.md
@@ -1,6 +1,7 @@
 # DeidentifyRequest
 
 A request to de-identify a clinical note
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------

diff --git a/docs/DeidentifyResponse.md b/docs/DeidentifyResponse.md
@@ -1,6 +1,7 @@
 # DeidentifyResponse
 
 The response to a deidentification request
+
 ## Properties
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------