Release 1.0.1 (#34)

* Update README and package.json

* Re-generate tool for API version 1.0.1

* Update API and tool version in Tool object

README.md

@@ -5,7 +5,6 @@
 [![GitHub License](https://img.shields.io/github/license/nlpsandbox/physical-address-annotator-example.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/nlpsandbox/physical-address-annotator-example/blob/develop/LICENSE)
 [![Docker Pulls](https://img.shields.io/docker/pulls/nlpsandbox/physical-address-annotator-example.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&label=pulls&logo=docker)](https://hub.docker.com/r/nlpsandbox/physical-address-annotator-example)
 [![Discord](https://img.shields.io/discord/770484164393828373.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&label=Discord&logo=discord)](https://discord.gg/Zb4ymtF "Realtime support / chat with the community and the team")
-[![nlpsandbox.io](https://img.shields.io/badge/OpenAPI-nlpsandbox.io-blue?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=data:image/svg%2bxml;base64,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&label=)](https://www.nlpsandbox.io/tools/physical-address-annotator/leaderboards "View the performance of this NLP Tool on nlpsandbox.io")
 
 Example implementation of the [NLP Sandbox Physical Address Annotator]
 
@@ -19,8 +18,8 @@ physical address annotations found in the clinical note.
 
 ### Specification
 
-- Physical Address Annotator API version: 1.0.0
-- Tool version: 1.0.0
+- Physical Address Annotator API version: 1.0.1
+- Tool version: 1.0.1
 - Docker image: [nlpsandbox/physical-address-annotator-example]
 
 ## Model

docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.8"
 
 services:
   physical-address-annotator:
-    image: nlpsandbox/physical-address-annotator-example:1.0.0
+    image: nlpsandbox/physical-address-annotator-example: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/physical-address-annotator/latest/openapi.json",
         "lint": "cd server && flake8",
         "test": "cd server && tox"
     }

server/openapi_server/controllers/tool_controller.py

@@ -13,7 +13,7 @@ def get_tool():  # noqa: E501
     """
     tool = Tool(
         name="physical-address-annotator-example",
-        version="1.0.0",
+        version="1.0.1",
         license=License.APACHE_2_0,
         repository="github:nlpsandbox/physical-address-annotator-example",
         description="Example implementation of the NLP Sandbox Physical " +
@@ -22,7 +22,7 @@ def get_tool():  # noqa: E501
         author_email="[email protected]",
         url="https://github.com/nlpsandbox/physical-address-annotator-example",
         tool_type="nlpsandbox:physical-address-annotator",
-        tool_api_version="1.0.0"
+        tool_api_version="1.0.1"
     )
     return tool, 200
 

server/openapi_server/models/license.py

@@ -52,6 +52,7 @@ class License(Model):
     NCSA = "ncsa"
     UNLICENSE = "unlicense"
     ZLIB = "zlib"
+    NONE = "none"
     def __init__(self):  # noqa: E501
         """License - a model defined in OpenAPI
 

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_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

@@ -5,19 +5,28 @@ info:
     name: The NLP Sandbox Team
     url: https://nlpsandbox.io
   description: |
-    # Overview
+    # Introduction
+    The Physical Address Annotator is one of the first type of NLP Tools that can be benchmarked on [nlpsandbox.io](https://nlpsandbox.io). A Physical Address Annotator takes as input a clinical note and outputs a list of predicted physical address annotations found in the clinical note. This OpenAPI document describes the specification of a Physical Address 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/physical-address-annotator-example](https://github.com/nlpsandbox/physical-address-annotator-example) provides a simple example implementation of a Python-Flask Physical Address Annotator. By the end of the tutorial available in this repository, you will have built a Docker image for a simple Physical Address 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 Physical Address Annotator if you want to benchmark 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 NLP tool detects references of physical addresses in the clinical note
-    given as input and returns a list of physical address annotations.
+    - 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.
 
     # Examples
-
-    - [NLP Sandbox Physical Address Annotator (Python)](https://github.com/nlpsandbox/physical-address-annotator-example)
+    - [Physical Address Annotator Example (Python)](https://github.com/nlpsandbox/physical-address-annotator-example)
   license:
     name: Apache 2.0
     url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE
   title: NLP Sandbox Physical Address Annotator API
-  version: 1.0.0
+  version: 1.0.1
   x-logo:
     url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png
 servers:
@@ -290,6 +299,7 @@ components:
           minimum: 0
           type: number
       required:
+      - confidence
       - length
       - start
       - text
@@ -366,6 +376,7 @@ components:
       - ncsa
       - unlicense
       - zlib
+      - none
       example: apache-2.0
       type: string
     ToolType:
@@ -387,7 +398,7 @@ components:
         authorEmail: [email protected]
         url: https://example.com
         toolType: nlpsandbox:date-annotator
-        toolApiVersion: 1.0.0
+        toolApiVersion: 1.0.1
       properties:
         name:
           description: The tool name
@@ -457,7 +468,7 @@ components:
           authorEmail: [email protected]
           url: https://example.com
           toolType: nlpsandbox:date-annotator
-          toolApiVersion: 1.0.0
+          toolApiVersion: 1.0.1
         - name: awesome-nlp-tool
           version: 1.0.6
           license: apache-2.0
@@ -467,7 +478,7 @@ components:
           authorEmail: [email protected]
           url: https://example.com
           toolType: nlpsandbox:date-annotator
-          toolApiVersion: 1.0.0
+          toolApiVersion: 1.0.1
       properties:
         toolDependencies:
           description: A list of tools