Release 1.0.1 (#152)

* Update README and package.json

* Re-generate server for API version 1.0.1

* Comment out required properties of pages to prevent UI issues

* Fix annotation tests (confidence must be specified)

Author: tschaffter

README.md

@@ -26,8 +26,8 @@ This Data Node can be used to:
 
 ### Specification
 
-- Data Node API version: 1.0.0
-- Data Node version: 1.0.0
+- Data Node API version: 1.0.1
+- Data Node version: 1.0.1
 - Docker image: [nlpsandbox/data-node]
 
 ## Usage

docker-compose.yml

@@ -17,7 +17,7 @@ services:
       - "${MONGO_PORT}:27017"
 
   data-node:
-    image: nlpsandbox/data-node:1.0.0
+    image: nlpsandbox/data-node:1.0.1
     build:
       context: server
       dockerfile: Dockerfile

package.json

@@ -4,6 +4,7 @@
     },
     "scripts": {
         "generate:server": "openapi-generator-cli generate -g python-flask -o server -i $npm_config_specification",
+        "generate:server:latest": "openapi-generator-cli generate -g python-flask -o server -i https://nlpsandbox.github.io/nlpsandbox-schemas/data-node/latest/openapi.json",
         "lint": "cd server && flake8",
         "test": "cd server && tox"
     }

server/openapi_server/models/text_annotation.py

@@ -152,6 +152,8 @@ def confidence(self, confidence):
         :param confidence: The confidence of this TextAnnotation.
         :type confidence: float
         """
+        if confidence is None:
+            raise ValueError("Invalid value for `confidence`, must not be `None`")  # noqa: E501
         if confidence is not None and confidence > 100:  # noqa: E501
             raise ValueError("Invalid value for `confidence`, must be a value less than or equal to `100`")  # noqa: E501
         if confidence is not None and confidence < 0:  # noqa: E501

server/openapi_server/models/text_date_annotation.py

@@ -161,6 +161,8 @@ def confidence(self, confidence):
         :param confidence: The confidence of this TextDateAnnotation.
         :type confidence: float
         """
+        if confidence is None:
+            raise ValueError("Invalid value for `confidence`, must not be `None`")  # noqa: E501
         if confidence is not None and confidence > 100:  # noqa: E501
             raise ValueError("Invalid value for `confidence`, must be a value less than or equal to `100`")  # noqa: E501
         if confidence is not None and confidence < 0:  # noqa: E501

server/openapi_server/models/text_person_name_annotation.py

@@ -154,6 +154,8 @@ def confidence(self, confidence):
         :param confidence: The confidence of this TextPersonNameAnnotation.
         :type confidence: float
         """
+        if confidence is None:
+            raise ValueError("Invalid value for `confidence`, must not be `None`")  # noqa: E501
         if confidence is not None and confidence > 100:  # noqa: E501
             raise ValueError("Invalid value for `confidence`, must be a value less than or equal to `100`")  # noqa: E501
         if confidence is not None and confidence < 0:  # noqa: E501

server/openapi_server/models/text_physical_address_annotation.py

@@ -161,6 +161,8 @@ def confidence(self, confidence):
         :param confidence: The confidence of this TextPhysicalAddressAnnotation.
         :type confidence: float
         """
+        if confidence is None:
+            raise ValueError("Invalid value for `confidence`, must not be `None`")  # noqa: E501
         if confidence is not None and confidence > 100:  # noqa: E501
             raise ValueError("Invalid value for `confidence`, must be a value less than or equal to `100`")  # noqa: E501
         if confidence is not None and confidence < 0:  # noqa: E501

server/openapi_server/openapi/openapi.yaml

@@ -8,7 +8,7 @@ info:
     # Overview
 
     The NLP Sandbox Data Node is a repository of data used to benchmark NLP
-    Tools.
+    Tools like the NLP Sandbox Date Annotator and Person Name Annotator.
 
     The resources that can be stored in this Data Node and the operations
     supported are listed below:
@@ -23,7 +23,7 @@ info:
     name: Apache 2.0
     url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE
   title: NLP Sandbox Data Node API
-  version: 1.0.0
+  version: 1.0.1
   x-logo:
     url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png
 servers:
@@ -1403,6 +1403,12 @@ components:
       - $ref: '#/components/schemas/ResponsePageMetadata'
       - $ref: '#/components/schemas/PageOfDatasets_allOf'
       description: A page of datasets
+      # required:
+      # - datasets
+      # - limit
+      # - links
+      # - offset
+      # - totalResults
       type: object
     Error:
       description: Problem details (tools.ietf.org/html/rfc7807)
@@ -1473,6 +1479,12 @@ components:
       - $ref: '#/components/schemas/ResponsePageMetadata'
       - $ref: '#/components/schemas/PageOfAnnotationStores_allOf'
       description: A page of annotation stores
+      # required:
+      # - annotationStores
+      # - limit
+      # - links
+      # - offset
+      # - totalResults
       type: object
     AnnotationStoreId:
       description: The ID of the annotation store
@@ -1549,6 +1561,7 @@ components:
           minimum: 0
           type: number
       required:
+      - confidence
       - length
       - start
       - text
@@ -1657,6 +1670,12 @@ components:
       - $ref: '#/components/schemas/ResponsePageMetadata'
       - $ref: '#/components/schemas/PageOfAnnotations_allOf'
       description: A page of annotations
+      # required:
+      # - annotations
+      # - limit
+      # - links
+      # - offset
+      # - totalResults
       type: object
     AnnotationId:
       description: The ID of the annotation
@@ -1766,6 +1785,12 @@ components:
       - $ref: '#/components/schemas/ResponsePageMetadata'
       - $ref: '#/components/schemas/PageOfFhirStores_allOf'
       description: A page of FHIR stores
+      # required:
+      # - fhirStores
+      # - limit
+      # - links
+      # - offset
+      # - totalResults
       type: object
     FhirStoreCreateRequest:
       description: An empty object
@@ -1819,6 +1844,12 @@ components:
       - $ref: '#/components/schemas/ResponsePageMetadata'
       - $ref: '#/components/schemas/PageOfPatients_allOf'
       description: A page of FHIR patients
+      # required:
+      # - limit
+      # - links
+      # - offset
+      # - patients
+      # - totalResults
       type: object
     PatientCreateRequest:
       description: A FHIR patient
@@ -1898,6 +1929,12 @@ components:
       - $ref: '#/components/schemas/ResponsePageMetadata'
       - $ref: '#/components/schemas/PageOfNotes_allOf'
       description: A page of notes
+      # required:
+      # - limit
+      # - links
+      # - notes
+      # - offset
+      # - totalResults
       type: object
     NoteCreateRequest:
       description: A clinical note

server/openapi_server/test/integration/test_annotation_controller.py

@@ -37,32 +37,38 @@ def test_create_annotation(self):
                 "start": 42,
                 "length": 10,
                 "text": "10/26/2020",
-                "dateFormat": "MM/DD/YYYY"
+                "dateFormat": "MM/DD/YYYY",
+                "confidence": 95.5
             }, {
                 "start": 42,
                 "length": 10,
                 "text": "10/26/2020",
-                "dateFormat": "MM/DD/YYYY"
+                "dateFormat": "MM/DD/YYYY",
+                "confidence": 95.5
             }],
             "textPersonNameAnnotations": [{
                 "start": 42,
                 "length": 11,
-                "text": "Chloe Price"
+                "text": "Chloe Price",
+                "confidence": 95.5
             }, {
                 "start": 42,
                 "length": 11,
-                "text": "Chloe Price"
+                "text": "Chloe Price",
+                "confidence": 95.5
             }],
             "textPhysicalAddressAnnotations": [{
                 "start": 42,
                 "length": 11,
                 "text": "Seattle",
-                "addressType": "city"
+                "addressType": "city",
+                "confidence": 95.5
             }, {
                 "start": 42,
                 "length": 11,
                 "text": "Seattle",
-                "addressType": "city"
+                "addressType": "city",
+                "confidence": 95.5
             }],
             "annotationSource": {
                 "resourceSource": {