Update to API version 1.0.2 (#98)

* Update to API version 1.0.2

* Bump tool version to 1.0.2

README.md

@@ -21,8 +21,8 @@ note.
 
 ### Specification
 
-- Date Annotator API version: 1.0.1
-- Tool version: 1.0.1
+- Date Annotator API version: 1.0.2
+- Tool version: 1.0.2
 - Docker image: [nlpsandbox/date-annotator-example]
 
 ## Model

docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.8"
 
 services:
   date-annotator:
-    image: nlpsandbox/date-annotator-example:1.0.1
+    image: nlpsandbox/date-annotator-example:1.0.2
     build:
       context: server
       dockerfile: Dockerfile

server/openapi_server/controllers/tool_controller.py

@@ -13,15 +13,15 @@ def get_tool():  # noqa: E501
     """
     tool = Tool(
         name="date-annotator-example",
-        version="1.0.1",
+        version="1.0.2",
         license=License.APACHE_2_0,
         repository="github:nlpsandbox/date-annotator-example",
         description="Example implementation of the NLP Sandbox Date Annotator",
         author="The NLP Sandbox Team",
         author_email="thomas.schaffter@sagebionetworks.org",
         url="https://github.com/nlpsandbox/date-annotator-example",
-        tool_type="nlpsandbox:date-annotator",
-        tool_api_version="1.0.1"
+        type="nlpsandbox:date-annotator",
+        api_version="1.0.2"
     )
     return tool, 200
 

server/openapi_server/models/note.py

@@ -17,35 +17,35 @@ class Note(Model):
     Do not edit the class manually.
     """
 
-    def __init__(self, identifier=None, text=None, note_type=None, patient_id=None):  # noqa: E501
+    def __init__(self, identifier=None, text=None, type=None, patient_id=None):  # noqa: E501
         """Note - a model defined in OpenAPI
 
         :param identifier: The identifier of this Note.  # noqa: E501
         :type identifier: str
         :param text: The text of this Note.  # noqa: E501
         :type text: str
-        :param note_type: The note_type of this Note.  # noqa: E501
-        :type note_type: str
+        :param type: The type of this Note.  # noqa: E501
+        :type type: str
         :param patient_id: The patient_id of this Note.  # noqa: E501
         :type patient_id: str
         """
         self.openapi_types = {
             'identifier': str,
             'text': str,
-            'note_type': str,
+            'type': str,
             'patient_id': str
         }
 
         self.attribute_map = {
             'identifier': 'identifier',
             'text': 'text',
-            'note_type': 'noteType',
+            'type': 'type',
             'patient_id': 'patientId'
         }
 
         self._identifier = identifier
         self._text = text
-        self._note_type = note_type
+        self._type = type
         self._patient_id = patient_id
 
     @classmethod
@@ -116,29 +116,29 @@ def text(self, text):
         self._text = text
 
     @property
-    def note_type(self):
-        """Gets the note_type of this Note.
+    def type(self):
+        """Gets the type of this Note.
 
         The note type (LOINC concept)  # noqa: E501
 
-        :return: The note_type of this Note.
+        :return: The type of this Note.
         :rtype: str
         """
-        return self._note_type
+        return self._type
 
-    @note_type.setter
-    def note_type(self, note_type):
-        """Sets the note_type of this Note.
+    @type.setter
+    def type(self, type):
+        """Sets the type of this Note.
 
         The note type (LOINC concept)  # noqa: E501
 
-        :param note_type: The note_type of this Note.
-        :type note_type: str
+        :param type: The type of this Note.
+        :type type: str
         """
-        if note_type is None:
-            raise ValueError("Invalid value for `note_type`, must not be `None`")  # noqa: E501
+        if type is None:
+            raise ValueError("Invalid value for `type`, must not be `None`")  # noqa: E501
 
-        self._note_type = note_type
+        self._type = type
 
     @property
     def patient_id(self):

server/openapi_server/models/tool.py

@@ -19,7 +19,7 @@ class Tool(Model):
     Do not edit the class manually.
     """
 
-    def __init__(self, name=None, version=None, license=None, repository=None, description=None, author=None, author_email=None, url=None, tool_type=None, tool_api_version=None):  # noqa: E501
+    def __init__(self, name=None, version=None, license=None, repository=None, description=None, author=None, author_email=None, url=None, type=None, api_version=None):  # noqa: E501
         """Tool - a model defined in OpenAPI
 
         :param name: The name of this Tool.  # noqa: E501
@@ -38,10 +38,10 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
         :type author_email: str
         :param url: The url of this Tool.  # noqa: E501
         :type url: str
-        :param tool_type: The tool_type of this Tool.  # noqa: E501
-        :type tool_type: str
-        :param tool_api_version: The tool_api_version of this Tool.  # noqa: E501
-        :type tool_api_version: str
+        :param type: The type of this Tool.  # noqa: E501
+        :type type: str
+        :param api_version: The api_version of this Tool.  # noqa: E501
+        :type api_version: str
         """
         self.openapi_types = {
             'name': str,
@@ -52,8 +52,8 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
             'author': str,
             'author_email': str,
             'url': str,
-            'tool_type': str,
-            'tool_api_version': str
+            'type': str,
+            'api_version': str
         }
 
         self.attribute_map = {
@@ -65,8 +65,8 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
             'author': 'author',
             'author_email': 'authorEmail',
             'url': 'url',
-            'tool_type': 'toolType',
-            'tool_api_version': 'toolApiVersion'
+            'type': 'type',
+            'api_version': 'apiVersion'
         }
 
         self._name = name
@@ -77,8 +77,8 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
         self._author = author
         self._author_email = author_email
         self._url = url
-        self._tool_type = tool_type
-        self._tool_api_version = tool_api_version
+        self._type = type
+        self._api_version = api_version
 
     @classmethod
     def from_dict(cls, dikt) -> 'Tool':
@@ -302,61 +302,61 @@ def url(self, url):
         self._url = url
 
     @property
-    def tool_type(self):
-        """Gets the tool_type of this Tool.
+    def type(self):
+        """Gets the type of this Tool.
 
         The type of this tool  # noqa: E501
 
-        :return: The tool_type of this Tool.
+        :return: The type of this Tool.
         :rtype: str
         """
-        return self._tool_type
+        return self._type
 
-    @tool_type.setter
-    def tool_type(self, tool_type):
-        """Sets the tool_type of this Tool.
+    @type.setter
+    def type(self, type):
+        """Sets the type of this Tool.
 
         The type of this tool  # noqa: E501
 
-        :param tool_type: The tool_type of this Tool.
-        :type tool_type: str
+        :param type: The type of this Tool.
+        :type type: str
         """
-        if tool_type is None:
-            raise ValueError("Invalid value for `tool_type`, must not be `None`")  # noqa: E501
-        if tool_type is not None and len(tool_type) > 60:
-            raise ValueError("Invalid value for `tool_type`, length must be less than or equal to `60`")  # noqa: E501
-        if tool_type is not None and len(tool_type) < 3:
-            raise ValueError("Invalid value for `tool_type`, length must be greater than or equal to `3`")  # noqa: E501
-        if tool_type is not None and not re.search(r'^[a-z0-9]+(?:-[a-z0-9]+)*(:)[a-z0-9]+(?:-[a-z0-9]+)*$', tool_type):  # noqa: E501
-            raise ValueError("Invalid value for `tool_type`, must be a follow pattern or equal to `/^[a-z0-9]+(?:-[a-z0-9]+)*(:)[a-z0-9]+(?:-[a-z0-9]+)*$/`")  # noqa: E501
+        if type is None:
+            raise ValueError("Invalid value for `type`, must not be `None`")  # noqa: E501
+        if type is not None and len(type) > 60:
+            raise ValueError("Invalid value for `type`, length must be less than or equal to `60`")  # noqa: E501
+        if type is not None and len(type) < 3:
+            raise ValueError("Invalid value for `type`, length must be greater than or equal to `3`")  # noqa: E501
+        if type is not None and not re.search(r'^[a-z0-9]+(?:-[a-z0-9]+)*(:)[a-z0-9]+(?:-[a-z0-9]+)*$', type):  # noqa: E501
+            raise ValueError("Invalid value for `type`, must be a follow pattern or equal to `/^[a-z0-9]+(?:-[a-z0-9]+)*(:)[a-z0-9]+(?:-[a-z0-9]+)*$/`")  # noqa: E501
 
-        self._tool_type = tool_type
+        self._type = type
 
     @property
-    def tool_api_version(self):
-        """Gets the tool_api_version of this Tool.
+    def api_version(self):
+        """Gets the api_version of this Tool.
 
         The version of the tool OpenAPI specification  # noqa: E501
 
-        :return: The tool_api_version of this Tool.
+        :return: The api_version of this Tool.
         :rtype: str
         """
-        return self._tool_api_version
+        return self._api_version
 
-    @tool_api_version.setter
-    def tool_api_version(self, tool_api_version):
-        """Sets the tool_api_version of this Tool.
+    @api_version.setter
+    def api_version(self, api_version):
+        """Sets the api_version of this Tool.
 
         The version of the tool OpenAPI specification  # noqa: E501
 
-        :param tool_api_version: The tool_api_version of this Tool.
-        :type tool_api_version: str
+        :param api_version: The api_version of this Tool.
+        :type api_version: str
         """
-        if tool_api_version is None:
-            raise ValueError("Invalid value for `tool_api_version`, must not be `None`")  # noqa: E501
-        if tool_api_version is not None and len(tool_api_version) < 1:
-            raise ValueError("Invalid value for `tool_api_version`, length must be greater than or equal to `1`")  # noqa: E501
-        if tool_api_version is not None and not re.search(r'^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$', tool_api_version):  # noqa: E501
-            raise ValueError("Invalid value for `tool_api_version`, must be a follow pattern or equal to `/^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$/`")  # noqa: E501
-
-        self._tool_api_version = tool_api_version
+        if api_version is None:
+            raise ValueError("Invalid value for `api_version`, must not be `None`")  # noqa: E501
+        if api_version is not None and len(api_version) < 1:
+            raise ValueError("Invalid value for `api_version`, length must be greater than or equal to `1`")  # noqa: E501
+        if api_version is not None and not re.search(r'^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$', api_version):  # noqa: E501
+            raise ValueError("Invalid value for `api_version`, must be a follow pattern or equal to `/^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$/`")  # noqa: E501
+
+        self._api_version = api_version

server/openapi_server/openapi/openapi.yaml

@@ -27,7 +27,7 @@ info:
     name: Apache 2.0
     url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE
   title: NLP Sandbox Date Annotator API
-  version: 1.0.1
+  version: 1.0.2
   x-logo:
     url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png
 servers:
@@ -233,7 +233,7 @@ components:
       example:
         identifier: awesome-note
         text: On 12/26/2020, Ms. Chloe Price met with Dr. Prescott in Seattle.
-        noteType: loinc:LP29684-5
+        type: loinc:LP29684-5
         patientId: awesome-patient
       properties:
         identifier:
@@ -246,7 +246,7 @@ components:
         text:
           description: The content of the clinical note
           type: string
-        noteType:
+        type:
           description: The note type (LOINC concept)
           type: string
         patientId:
@@ -258,17 +258,17 @@ components:
           type: string
       required:
       - identifier
-      - noteType
       - patientId
       - text
+      - type
       type: object
     TextDateAnnotationRequest:
       description: A request to annotate dates in a clinical note
       example:
         note:
           identifier: awesome-note
           text: On 12/26/2020, Ms. Chloe Price met with Dr. Prescott in Seattle.
-          noteType: loinc:LP29684-5
+          type: loinc:LP29684-5
           patientId: awesome-patient
       properties:
         note:
@@ -398,8 +398,8 @@ components:
         author: Awesome Team
         authorEmail: author@example.com
         url: https://example.com
-        toolType: nlpsandbox:date-annotator
-        toolApiVersion: 1.0.1
+        type: nlpsandbox:date-annotator
+        apiVersion: 1.0.2
       properties:
         name:
           description: The tool name
@@ -432,27 +432,27 @@ components:
           description: The URL to the homepage of the tool
           format: uri
           type: string
-        toolType:
+        type:
           description: The type of this tool
           example: nlpsandbox:date-annotator
           maxLength: 60
           minLength: 3
           pattern: ^[a-z0-9]+(?:-[a-z0-9]+)*(:)[a-z0-9]+(?:-[a-z0-9]+)*$
           type: string
-        toolApiVersion:
+        apiVersion:
           description: The version of the tool OpenAPI specification
           minLength: 1
           pattern: ^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$
           type: string
       required:
+      - apiVersion
       - author
       - authorEmail
       - description
       - license
       - name
       - repository
-      - toolApiVersion
-      - toolType
+      - type
       - url
       - version
       type: object
@@ -468,8 +468,8 @@ components:
           author: Awesome Team
           authorEmail: author@example.com
           url: https://example.com
-          toolType: nlpsandbox:date-annotator
-          toolApiVersion: 1.0.1
+          type: nlpsandbox:date-annotator
+          apiVersion: 1.0.2
         - name: awesome-nlp-tool
           version: 1.0.6
           license: apache-2.0
@@ -478,8 +478,8 @@ components:
           author: Awesome Team
           authorEmail: author@example.com
           url: https://example.com
-          toolType: nlpsandbox:date-annotator
-          toolApiVersion: 1.0.1
+          type: nlpsandbox:date-annotator
+          apiVersion: 1.0.2
       properties:
         toolDependencies:
           description: A list of tools

server/openapi_server/test/integration/test_text_date_annotation_controller.py

@@ -19,7 +19,7 @@ def test_create_text_date_annotations(self):
         text_date_annotation_request = {
             "note": {
                 "identifier": "awesome-note",
-                "noteType": "loinc:LP29684-5",
+                "type": "loinc:LP29684-5",
                 "patientId": "awesome-patient",
                 "text": "On 12/26/2020, Ms. Chloe Price met with Dr. Prescott."
             }