Release 1.1.0 (#105)

* Run OpenAPI generator

* Update schemas (part 1/2)

* Update codebase (part 2/2)

* Add scripts to package.json

* Update schemas and tool versions

* Patch README

README.md

@@ -21,8 +21,8 @@ note.
 
 ### Specification
 
-- Date Annotator API version: 1.0.2
-- Tool version: 1.0.2
+- Date Annotator API version: 1.1.0
+- Tool version: 1.1.0
 - Docker image: [nlpsandbox/date-annotator-example]
 
 ## Model
@@ -53,13 +53,13 @@ You can stop the container run with `Ctrl+C`, followed by `docker-compose down`.
 
 We recommend using a Conda environment to install and run the Date Annotator.
 
-    conda create --name date-annotator python=3.9.1
+    conda create --name date-annotator python=3.9
     conda activate date-annotator
 
 Install and start the Date Annotator.
 
     cd server/
-    pip install -e .
+    pip install -r requirements.txt
     python -m openapi_server
 
 ### Accessing the UI

docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.8"
 
 services:
   date-annotator:
-    image: nlpsandbox/date-annotator-example:1.0.2
+    image: nlpsandbox/date-annotator-example:1.1.0
     build:
       context: server
       dockerfile: Dockerfile

package.json

@@ -7,6 +7,9 @@
         "generate:server:latest": "openapi-generator-cli generate -g python-flask -o server -i https://nlpsandbox.github.io/nlpsandbox-schemas/date-annotator/latest/openapi.json",
         "generate:server:edge": "openapi-generator-cli generate -g python-flask -o server -i https://nlpsandbox.github.io/nlpsandbox-schemas/date-annotator/edge/openapi.json",
         "lint": "cd server && flake8",
-        "test": "cd server && tox"
+        "test": "cd server && tox",
+        "install:dependencies": "npm ci && cd server && pip install -r requirements.txt",
+        "start:dev": "cd server && python -m openapi_server",
+        "start:prod": "docker-compose up --build"
     }
 }

server/openapi_server/__main__.py

@@ -15,7 +15,7 @@
 
 
 def main():
-    app.run(port=8080)
+    app.run(port=8080, debug=False)
 
 
 if __name__ == '__main__':

server/openapi_server/controllers/tool_controller.py

@@ -13,15 +13,15 @@ def get_tool():  # noqa: E501
     """
     tool = Tool(
         name="date-annotator-example",
-        version="1.0.2",
+        version="1.1.0",
         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",
         type="nlpsandbox:date-annotator",
-        api_version="1.0.2"
+        api_version="1.1.0"
     )
     return tool, 200
 
@@ -34,4 +34,4 @@ def get_tool_dependencies():  # noqa: E501
 
     :rtype: ToolDependencies
     """
-    return ToolDependencies(tool_dependencies=[]), 200
+    return ToolDependencies(tools=[]), 200

server/openapi_server/models/tool_dependencies.py

@@ -17,21 +17,21 @@ class ToolDependencies(Model):
     Do not edit the class manually.
     """
 
-    def __init__(self, tool_dependencies=None):  # noqa: E501
+    def __init__(self, tools=None):  # noqa: E501
         """ToolDependencies - a model defined in OpenAPI
 
-        :param tool_dependencies: The tool_dependencies of this ToolDependencies.  # noqa: E501
-        :type tool_dependencies: List[Tool]
+        :param tools: The tools of this ToolDependencies.  # noqa: E501
+        :type tools: List[Tool]
         """
         self.openapi_types = {
-            'tool_dependencies': List[Tool]
+            'tools': List[Tool]
         }
 
         self.attribute_map = {
-            'tool_dependencies': 'toolDependencies'
+            'tools': 'tools'
         }
 
-        self._tool_dependencies = tool_dependencies
+        self._tools = tools
 
     @classmethod
     def from_dict(cls, dikt) -> 'ToolDependencies':
@@ -45,26 +45,26 @@ def from_dict(cls, dikt) -> 'ToolDependencies':
         return util.deserialize_model(dikt, cls)
 
     @property
-    def tool_dependencies(self):
-        """Gets the tool_dependencies of this ToolDependencies.
+    def tools(self):
+        """Gets the tools of this ToolDependencies.
 
         A list of tools  # noqa: E501
 
-        :return: The tool_dependencies of this ToolDependencies.
+        :return: The tools of this ToolDependencies.
         :rtype: List[Tool]
         """
-        return self._tool_dependencies
+        return self._tools
 
-    @tool_dependencies.setter
-    def tool_dependencies(self, tool_dependencies):
-        """Sets the tool_dependencies of this ToolDependencies.
+    @tools.setter
+    def tools(self, tools):
+        """Sets the tools of this ToolDependencies.
 
         A list of tools  # noqa: E501
 
-        :param tool_dependencies: The tool_dependencies of this ToolDependencies.
-        :type tool_dependencies: List[Tool]
+        :param tools: The tools of this ToolDependencies.
+        :type tools: List[Tool]
         """
-        if tool_dependencies is None:
-            raise ValueError("Invalid value for `tool_dependencies`, must not be `None`")  # noqa: E501
+        if tools is None:
+            raise ValueError("Invalid value for `tools`, must not be `None`")  # noqa: E501
 
-        self._tool_dependencies = tool_dependencies
+        self._tools = tools

server/openapi_server/openapi/openapi.yaml

@@ -1,24 +1,25 @@
 openapi: 3.0.3
 info:
   contact:
-    email: thomas.schaffter@sagebionetworks.org
-    name: The NLP Sandbox Team
+    email: team@nlpsandbox.io
+    name: NLP Sandbox Team
     url: https://nlpsandbox.io
   description: |
     # Introduction
-    The Date Annotator is one of the first type of NLP Tools that can be benchmarked on [nlpsandbox.io](https://nlpsandbox.io). A Date Annotator takes as input a clinical note and outputs a list of predicted date annotations found in the clinical note. This OpenAPI document describes the specification of a Date Annotator. This specification includes the schemas of the input and output data, and the conditions that this annotator must meet if you want to benchmark its performance on [nlpsandbox.io](https://nlpsandbox.io).
+    A Date Annotator takes as input a clinical note and outputs a list of predicted date annotations found in the clinical note. This OpenAPI document describes the specification of a Date Annotator. This specification includes the schemas of the input and output data, and the conditions that this annotator must meet if you want to benchmark its performance on [nlpsandbox.io](https://nlpsandbox.io).
     # Getting Started
-    The GitHub repository [nlpsandbox/date-annotator-example](https://github.com/nlpsandbox/date-annotator-example) provides a simple example implementation of a Python-Flask Date Annotator. By the end of the tutorial available in this repository, you will have built a Docker image for a simple Date Annotator. You will then be able to submit this image to [nlpsandbox.io](https://nlpsandbox.io) to benchmark its performance.
+    The GitHub repository [nlpsandbox/date-annotator-example](https://github.com/nlpsandbox/date-annotator-example) provides a simple example implementation of a Python-Flask Date Annotator. By the end of the tutorial available in the README, you will have built a Docker image for a simple Date Annotator. You will then be able to submit this image to [nlpsandbox.io](https://nlpsandbox.io) to benchmark its performance.
     # Benchmarking Requirements
-    The following conditions must be met by your Date Annotator if you want to benchmark its performance on [nlpsandbox.io](https://nlpsandbox.io).
+    Your NLP Sandbox tool must meet the following conditions before evaluating its performance on [nlpsandbox.io](https://nlpsandbox.io).
     - The endpoint `/` must redirect to `/api/v1/tool`.
     - The endpoint `/ui` must redirect to the web interface (UI).
     - The output of this tool must be reproducible: a given input should always
       generate the same output.
 
-    - This tool must not attempt to connect to remote server for reproducibility,
-      robustness, and security reasons. When benchmarked on [nlpsandbox.io](https://nlpsandbox.io),
-      this tool will not be able to connect to remote servers.
+    - To ensure the results are reproducible and robust, and the data are
+      secured, this tool must not connect to any remote server. When benchmarked
+      on [nlpsandbox.io](https://nlpsandbox.io), this tool will not be able to
+      connect to remote servers.
 
     # Examples
     - [Date Annotator Example (Python)](https://github.com/nlpsandbox/date-annotator-example)
@@ -27,7 +28,7 @@ info:
     name: Apache 2.0
     url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE
   title: NLP Sandbox Date Annotator API
-  version: 1.0.2
+  version: 1.1.0
   x-logo:
     url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png
 servers:
@@ -399,7 +400,7 @@ components:
         authorEmail: author@example.com
         url: https://example.com
         type: nlpsandbox:date-annotator
-        apiVersion: 1.0.2
+        apiVersion: 1.1.0
       properties:
         name:
           description: The tool name
@@ -459,7 +460,7 @@ components:
     ToolDependencies:
       description: A list of tool dependencies
       example:
-        toolDependencies:
+        tools:
         - name: awesome-nlp-tool
           version: 1.0.6
           license: apache-2.0
@@ -469,7 +470,7 @@ components:
           authorEmail: author@example.com
           url: https://example.com
           type: nlpsandbox:date-annotator
-          apiVersion: 1.0.2
+          apiVersion: 1.1.0
         - name: awesome-nlp-tool
           version: 1.0.6
           license: apache-2.0
@@ -479,15 +480,15 @@ components:
           authorEmail: author@example.com
           url: https://example.com
           type: nlpsandbox:date-annotator
-          apiVersion: 1.0.2
+          apiVersion: 1.1.0
       properties:
-        toolDependencies:
+        tools:
           description: A list of tools
           items:
             $ref: '#/components/schemas/Tool'
           type: array
       required:
-      - toolDependencies
+      - tools
       type: object
     TextDateAnnotation_allOf:
       properties:

server/openapi_server/test/__init__.py

@@ -0,0 +1,16 @@
+import logging
+
+import connexion
+from flask_testing import TestCase
+
+from openapi_server.encoder import JSONEncoder
+
+
+class BaseTestCase(TestCase):
+
+    def create_app(self):
+        logging.getLogger('connexion.operation').setLevel('ERROR')
+        app = connexion.App(__name__, specification_dir='../openapi/')
+        app.app.json_encoder = JSONEncoder
+        app.add_api('openapi.yaml', pythonic_params=True)
+        return app.app

server/openapi_server/test/integration/test_health_check_controller.py → server/openapi_server/test/test_health_check_controller.py

@@ -3,7 +3,12 @@
 from __future__ import absolute_import
 import unittest
 
-from openapi_server.test.integration import BaseTestCase
+from flask import json
+from six import BytesIO
+
+from openapi_server.models.error import Error  # noqa: E501
+from openapi_server.models.health_check import HealthCheck  # noqa: E501
+from openapi_server.test import BaseTestCase
 
 
 class TestHealthCheckController(BaseTestCase):
@@ -14,7 +19,7 @@ def test_get_health_check(self):
 
         Get health check information
         """
-        headers = {
+        headers = { 
             'Accept': 'application/json',
         }
         response = self.client.open(

server/openapi_server/test/integration/test_text_date_annotation_controller.py → server/openapi_server/test/test_text_date_annotation_controller.py

@@ -4,8 +4,12 @@
 import unittest
 
 from flask import json
+from six import BytesIO
 
-from openapi_server.test.integration import BaseTestCase
+from openapi_server.models.error import Error  # noqa: E501
+from openapi_server.models.text_date_annotation_request import TextDateAnnotationRequest  # noqa: E501
+from openapi_server.models.text_date_annotation_response import TextDateAnnotationResponse  # noqa: E501
+from openapi_server.test import BaseTestCase
 
 
 class TestTextDateAnnotationController(BaseTestCase):
@@ -17,14 +21,14 @@ def test_create_text_date_annotations(self):
         Annotate dates in a clinical note
         """
         text_date_annotation_request = {
-            "note": {
-                "identifier": "awesome-note",
-                "type": "loinc:LP29684-5",
-                "patientId": "awesome-patient",
-                "text": "On 12/26/2020, Ms. Chloe Price met with Dr. Prescott."
-            }
-        }
-        headers = {
+  "note" : {
+    "identifier" : "awesome-note",
+    "text" : "On 12/26/2020, Ms. Chloe Price met with Dr. Prescott in Seattle.",
+    "type" : "loinc:LP29684-5",
+    "patientId" : "awesome-patient"
+  }
+}
+        headers = { 
             'Accept': 'application/json',
             'Content-Type': 'application/json',
         }

server/openapi_server/test/integration/test_tool_controller.py → server/openapi_server/test/test_tool_controller.py

@@ -3,7 +3,13 @@
 from __future__ import absolute_import
 import unittest
 
-from openapi_server.test.integration import BaseTestCase
+from flask import json
+from six import BytesIO
+
+from openapi_server.models.error import Error  # noqa: E501
+from openapi_server.models.tool import Tool  # noqa: E501
+from openapi_server.models.tool_dependencies import ToolDependencies  # noqa: E501
+from openapi_server.test import BaseTestCase
 
 
 class TestToolController(BaseTestCase):
@@ -14,7 +20,7 @@ def test_get_tool(self):
 
         Get tool information
         """
-        headers = {
+        headers = { 
             'Accept': 'application/json',
         }
         response = self.client.open(
@@ -29,7 +35,7 @@ def test_get_tool_dependencies(self):
 
         Get tool dependencies
         """
-        headers = {
+        headers = { 
             'Accept': 'application/json',
         }
         response = self.client.open(

server/setup.cfg

@@ -5,6 +5,7 @@ max-line-length: 80
 exclude =
     .*
     openapi_server/models/*.py
+    openapi_server/test/*.py
 
 [coverage:run]
 omit =