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Rename project to location annotator (#56)
* Update package.json * Update package-lock.json * Run npm generate:server:edge * Minor update * Fix typo in README * Bump schema and annotator version to 1.2.0
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| Original file line number | Diff line number | Diff line change |
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| @@ -1 +1 @@ | ||
| 1.1.2 | ||
| 1.2.0 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,10 +1,10 @@ | ||
| [](https://nlpsandbox.io) | ||
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| # NLP Sandbox Physical Address Annotator Example | ||
| # NLP Sandbox Location Annotator Example | ||
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| [](https://github.com/nlpsandbox/physical-address-annotator-example/releases) | ||
| [](https://github.com/nlpsandbox/physical-address-annotator-example/actions) | ||
| [](https://github.com/nlpsandbox/physical-address-annotator-example/blob/develop/LICENSE) | ||
| [](https://github.com/nlpsandbox/location-annotator-example/releases) | ||
| [](https://github.com/nlpsandbox/location-annotator-example/actions) | ||
| [](https://github.com/nlpsandbox/location-annotator-example/blob/develop/LICENSE) | ||
| [](https://www.synapse.org/#!Synapse:syn25830546 "Get the Docker image of this tool on NLPSandbox.io") | ||
| [](https://www.synapse.org/#!Synapse:syn22277123/wiki/609143 "View the performance of this tool on NLPSandbox.io") | ||
| [](https://nlpsandbox.io/discord "Realtime support / chat with the community and the team") | ||
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@@ -16,14 +16,14 @@ processing (NLP) tools on both public and private datasets. Academics, students, | |
| and industry professionals are invited to browse the available tasks and | ||
| participate by developing and submitting an NLP Sandbox tool. | ||
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| This repository provides an example implementation of the [NLP Sandbox Physical | ||
| Address Annotator API] written in Python-Flask. An NLP Sandbox physical address | ||
| annotator takes as input a clinical note (text) and outputs a list of predicted | ||
| physical address annotations found in the clinical note. Here physicall | ||
| addresses are identified using dictionaries. | ||
| This repository provides an example implementation of the [NLP Sandbox Location | ||
| Annotator API] written in Python-Flask. An NLP Sandbox location annotator takes | ||
| as input a clinical note (text) and outputs a list of predicted location | ||
| annotations found in the clinical note. Here locations are identified using | ||
| dictionaries. | ||
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| This tool is provided to NLP developers who develop in Python as a starting | ||
| point to package their own physical address annotator as an NLP Sandbox tool | ||
| point to package their own location annotator as an NLP Sandbox tool | ||
| (see section [Development](#Development)). This section also describes how to | ||
| generate a tool "stub" using [openapi-generator] for 50+ programming | ||
| languages-frameworks. This repository includes a GitHub CI/CD workflow that | ||
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@@ -62,9 +62,9 @@ performance! | |
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| ## Specification | ||
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| - NLP Sandbox schemas version: 1.1.2 | ||
| - NLP Sandbox tool version: 1.1.2 | ||
| - Docker image: [docker.synapse.org/syn22277123/physical-address-annotator-example] | ||
| - NLP Sandbox schemas version: 1.2.0 | ||
| - NLP Sandbox tool version: 1.2.0 | ||
| - Docker image: [docker.synapse.org/syn22277123/location-annotator-example] | ||
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| ## Requirements | ||
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@@ -76,7 +76,7 @@ performance! | |
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| ### Running with Docker | ||
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| The command below starts this NLP Sandbox physical address annotator locally. | ||
| The command below starts this NLP Sandbox location annotator locally. | ||
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| ```console | ||
| docker compose up --build | ||
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@@ -89,11 +89,11 @@ You can stop the container run with `Ctrl+C`, followed by `docker compose down`. | |
| Create a Conda environment. | ||
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| ```console | ||
| conda create --name physical-address-annotator python=3.9 | ||
| conda activate physical-address-annotator | ||
| conda create --name location-annotator python=3.9 | ||
| conda activate location-annotator | ||
| ``` | ||
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| Install and start this NLP Sandbox physical address annotator. | ||
| Install and start this NLP Sandbox location annotator. | ||
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| ```console | ||
| cd server && pip install -r requirements.txt | ||
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@@ -114,10 +114,10 @@ the tool using Docker (production) or Python (development). | |
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| ## Development | ||
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| This section describes how to develop your own NLP Sandbox physical address | ||
| This section describes how to develop your own NLP Sandbox location | ||
| annotator in Python-Flask and other programming languages-frameworks. This | ||
| example tool is also available in Java in the GitHub repository | ||
| [nlpsandbox/physical-address-annotator-example-java]. | ||
| [nlpsandbox/location-annotator-example-java]. | ||
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| ### Development requirements | ||
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@@ -177,9 +177,9 @@ disabling version updates]. | |
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| The development of new NLP Sandbox tools is streamlined by using the | ||
| [openapi-generator] to generate tool "stubs" for more than 50 programming | ||
| languages and frameworks. Here a physical address annotator stub refers to an | ||
| languages and frameworks. Here a location annotator stub refers to an | ||
| initial implementation that has been automatically generated by | ||
| [openapi-generator] from the [NLP Sandbox Physical Address Annotator API] | ||
| [openapi-generator] from the [NLP Sandbox Location Annotator API] | ||
| specification. | ||
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| Run the command below to get the list of languages-framework supported by the | ||
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@@ -189,23 +189,23 @@ Run the command below to get the list of languages-framework supported by the | |
| npx @openapitools/openapi-generator-cli list | ||
| ``` | ||
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| Generate the physical address annotator stub from an empty GitHub repository | ||
| Generate the location annotator stub from an empty GitHub repository | ||
| (here in Python-Flask): | ||
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| ```console | ||
| mkdir server | ||
| npx @openapitools/openapi-generator-cli generate \ | ||
| -g python-flask \ | ||
| -o server \ | ||
| -i https://nlpsandbox.github.io/nlpsandbox-schemas/physical-address-annotator/latest/openapi.json | ||
| -i https://nlpsandbox.github.io/nlpsandbox-schemas/location-annotator/latest/openapi.json | ||
| ``` | ||
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| where the option `-i` refers to the OpenAPI specification of the [NLP Sandbox | ||
| Physical Address Annotator API]. | ||
| Location Annotator API]. | ||
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| The URL is composed of different elements: | ||
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| - `physical-address-annotator` - The type of NLP Sandbox tool to generate. The | ||
| - `location-annotator` - The type of NLP Sandbox tool to generate. The | ||
| list of all the NLP Sandbox tool types available is defined in the [NLP | ||
| Sandbox schemas]. | ||
| - `latest` - The latest stable version of the [NLP Sandbox schemas]. This token | ||
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@@ -332,11 +332,11 @@ Thinking about contributing to this project? Get started by reading our | |
| <!-- Links --> | ||
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| [nlpsandbox.io]: https://www.synapse.org/nlpsandbox | ||
| [docker.synapse.org/syn22277123/physical-address-annotator-example]: https://www.synapse.org/#!Synapse:syn25828638 | ||
| [docker.synapse.org/syn22277123/location-annotator-example]: https://www.synapse.org/#!Synapse:syn25828638 | ||
| [Synapse.org]: https://synapse.org | ||
| [openapi-generator]: https://github.com/OpenAPITools/openapi-generator | ||
| [contribution guide]: .github/CONTRIBUTING.md | ||
| [Apache License 2.0]: https://github.com/nlpsandbox/physical-address-annotator-example/blob/main/LICENSE | ||
| [Apache License 2.0]: https://github.com/nlpsandbox/location-annotator-example/blob/main/LICENSE | ||
| [Docker Engine]: https://docs.docker.com/engine/install/ | ||
| [Node]: https://nodejs.org/en/ | ||
| [Java]: https://www.java.com/en/download/help/download_options.html | ||
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@@ -352,9 +352,9 @@ Thinking about contributing to this project? Get started by reading our | |
| [Enabling and disabling version updates]: https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/enabling-and-disabling-version-updates | ||
| [NLP Sandbox schemas]: https://github.com/nlpsandbox/nlpsandbox-schemas | ||
| [nlpsandbox/nlpsandbox-schemas]: https://github.com/nlpsandbox/nlpsandbox-schemas | ||
| [NLP Sandbox Physical Address Annotator API]: https://nlpsandbox.github.io/nlpsandbox-schemas/physical-address-annotator/latest/docs/ | ||
| [this GitHub template]: https://github.com/nlpsandbox/physical-address-annotator-example/generate | ||
| [nlpsandbox/physical-address-annotator-example-java]: https://github.com/nlpsandbox/physical-address-annotator-example-java | ||
| [NLP Sandbox Location Annotator API]: https://nlpsandbox.github.io/nlpsandbox-schemas/location-annotator/latest/docs/ | ||
| [this GitHub template]: https://github.com/nlpsandbox/location-annotator-example/generate | ||
| [nlpsandbox/location-annotator-example-java]: https://github.com/nlpsandbox/location-annotator-example-java | ||
| [Patient schema]: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/openapi/commons/components/schemas/Patient.yaml | ||
| [semantic versioning]: https://semver.org/ | ||
| [NLP Sandbox schemas CHANGELOG]: .github/CHANGELOG.md | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| from openapi_server.models.tool import Tool # noqa: E501 | ||
| from openapi_server.models.tool_dependencies import ToolDependencies # noqa: E501 | ||
| from openapi_server.models.tool_type import ToolType | ||
| from openapi_server.models.license import License | ||
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@@ -12,17 +13,17 @@ def get_tool(): # noqa: E501 | |
| :rtype: Tool | ||
| """ | ||
| tool = Tool( | ||
| name="physical-address-annotator-example", | ||
| version="1.1.2", | ||
| name="location-annotator-example", | ||
| version="1.2.0", | ||
| license=License.APACHE_2_0, | ||
| repository="github:nlpsandbox/physical-address-annotator-example", | ||
| description="Example implementation of the NLP Sandbox Physical " + | ||
| "Address Annotator", | ||
| repository="github:nlpsandbox/location-annotator-example", | ||
| description="Example implementation of the NLP Sandbox Location " + | ||
| "Annotator API", | ||
| author="NLP Sandbox Team", | ||
| author_email="[email protected]", | ||
| url="https://github.com/nlpsandbox/physical-address-annotator-example", | ||
| type="nlpsandbox:physical-address-annotator", | ||
| api_version="1.1.2" | ||
| url="https://github.com/nlpsandbox/location-annotator-example", | ||
| type=ToolType.LOCATION_ANNOTATOR, | ||
| api_version="1.2.0" | ||
| ) | ||
| return tool, 200 | ||
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