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Release 1.0.0
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‎CODE_OF_CONDUCT.md‎

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# Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and
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expression, level of experience, education, socio-economic status, nationality,
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personal appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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- Using welcoming and inclusive language
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- Being respectful of differing viewpoints and experiences
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- Gracefully accepting constructive criticism
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- Focusing on what is best for the community
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- Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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- The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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- Trolling, insulting/derogatory comments, and personal or political attacks
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- Public or private harassment
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- Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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- Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, or to ban temporarily or permanently any
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contributor for other behaviors that they deem inappropriate, threatening,
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offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the contacting the project lead or Sage Privacy Officer
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(privacyofficer@sagebase.org). The project team will review and investigate all
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complaints, and will respond in a way that it deems appropriate to the
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circumstances. The project team is obligated to maintain confidentiality with
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regard to the reporter of an incident. Further details of specific enforcement
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policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 1.4, available at
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https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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<!-- Links -->
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[homepage]: https://www.contributor-covenant.org

‎CONTRIBUTING.md‎

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## Contributing
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A big welcome and thank you for considering contributing to this project.
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This project is a community effort and lives off your contributions, be it in
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the form of bug reports, feature requests, discussions, or fixes and other
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code changes.
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Reading and following these guidelines will help us make the contribution
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process easy and effective for everyone involved. It also communicates that you
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agree to respect the time of the developers managing and developing these open
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source projects. In return, we will reciprocate that respect by addressing your
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issue, assessing changes, and helping you finalize your pull requests.
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## Quicklinks
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- [Code of Conduct](#code-of-conduct)
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- [Getting Started](#getting-started)
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- [Issues](#issues)
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- [Pull Requests](#pull-requests)
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- [Setup Development Environment](#setup-development-environment)
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- [HTML Preview](#html-preview)
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- [Testing](#testing)
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- [Release Procedure](#release-procedure)
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- [Getting Help](#getting-help)
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## Code of Conduct
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We take our open source community seriously and hold ourselves and other
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contributors to high standards of communication. By participating and
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contributing to this project, you agree to uphold our [Code of Conduct].
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## Getting Started
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Contributions are made to this repo via Issues and Pull Requests (PRs). A few
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general guidelines that cover both:
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- Search for existing Issues and PRs before creating your own.
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- We work hard to makes sure issues are handled in a timely manner but,
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depending on the impact, it could take a while to investigate the root cause.
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A friendly ping in the comment thread to the submitter or a contributor can
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help draw attention if your issue is blocking.
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### Issues
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Issues should be used to report problems with this project, request a new
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feature, or to discuss potential changes before a PR is created. When you
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create a new Issue, a template will be loaded that will guide you through
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collecting and providing the information we need to investigate.
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If you find an Issue that addresses the problem you're having, please add your
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own reproduction information to the existing issue rather than creating a new
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one. Adding a [reaction] can also help be indicating to our maintainers that a
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particular problem is affecting more than just the reporter.
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### Pull Requests
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PRs to our repositories are always welcome and can be a quick way to get your
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fix or improvement slated for the next release. In general, PRs should:
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- Only fix/add the functionality in question **OR** address wide-spread
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whitespace/style issues, not both.
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- Add unit or integration tests for fixed or changed functionality
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(if a test suite already exists).
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- Address a single concern in the least number of changed lines as possible.
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- Include documentation in the repo or on our [docs site].
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- Be accompanied by a complete Pull Request template (loaded automatically
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when a PR is created).
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For changes that address core functionality or would require breaking changes
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(e.g. a major release), it's best to open an Issue to discuss your proposal
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first. This is not required but can save time creating and reviewing changes.
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In general, we follow the [Forking Workflow]:
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1. Fork the repository to your own Github account
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2. Clone the project to your machine
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3. Create a branch locally with a succinct but descriptive name
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4. Commit changes to the branch
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5. Following any formatting and testing guidelines specific to this repo
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6. Push changes to your fork
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7. Open a PR in our repository and follow the PR template so that we can
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efficiently review the changes.
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We recommend that you add this repository as an [upstream remote] to your local
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git repository so that you can fetch the latest updates.
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On your local machine make sure you have the latest version of the `develop`
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branch from this upstream repository:
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git checkout develop
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git pull upstream develop
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### Setup Development Environment
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This project relies on Node tools and project-specific commands defined in
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[package.json] to streamline the development and testing. The command below will
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install the required development tools.
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npm ci
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### HTML Preview
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The command below builds and serves a preview of the HTML documentation of one
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of the APIs defined in this repository:
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npm run start --api=<name>
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where `<name>` is the name of one of the API folders included in
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[openapi/](openapi/) for which you want to see the HTML documentation. The HTML
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page will be available at http://localhost:8080.
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### Testing
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Before submitting a PR, please check that the content of the branch that you
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plan to submit passes with the tests defined for this project:
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npm run lint:all
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npm run validate --api=<name>
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where `<name>` is the name of the API folder in [openapi/](openapi/) that you
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want to test.
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## Release Procedure
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Maintainers are required to follow the procedure below when creating a new
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release.
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TBA
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## Getting Help
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Join us on the [NLP Sandbox Discord server] and post your question to the
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channel that best matches the topic of your request.
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<!-- Links -->
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[Code of Conduct]: https://github.com/auth0/open-source-template/blob/master/CODE-OF-CONDUCT.md
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[upstream remote]: https://help.github.com/en/articles/configuring-a-remote-for-a-fork
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[reaction]: https://github.blog/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/
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[docs site]: https://github.com/nlpsandbox/nlpsandbox-website-synapse
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[Forking Workflow]: https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow
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[package.json]: package.json
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[NLP Sandbox Discord server]: https://discord.gg/Zb4ymtF

‎README.md‎

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[![GitHub License](https://img.shields.io/github/license/nlpsandbox/nlpsandbox-schemas.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/nlpsandbox/nlpsandbox-schemas)
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[![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")
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## OpenAPI specifications
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OpenAPI specifications of the NLP Sandbox services
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List of APIs defined by the NLP Sandbox sorted by type and name in alphabetic
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order.
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## Overview
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| API | Type | Version |
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|---|---|---|
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| [Data Node](/openapi/data-node) | | 1.0.0 |
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| [Date Annotator](/openapi/date-annotator) | `nlpsandbox:date-annotator` | 1.0.0 |
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| [Person Name Annotator](/openapi/person-name-annotator) | `nlpsandbox:person-name-annotator` | 1.0.0 |
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| [Physical Address Annotator](/openapi/physical-address-annotator) | `nlpsandbox:physical-address-annotator` | 1.0.0 |
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| [PHI Deidentifier](/openapi/phi-deidentifier) | `nlpsandbox:phi-deidentifier` | 1.0.0 |
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This repository contains the OpenAPI specifications of the NLP tools and
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services defined by the NLP Sandbox. The NLP Tools that implement these
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specifications can have their performance benchmark on [nlpsandbox.io].
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## Web services
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## NLP Tools
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You can find below example implementations of the APIs defined by the NLP Sandbox.
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The OpenAPI specifications of the NLP Tools defined by the NLP Sandbox (and
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counting) are listed below. The OpenAPI specification available in JSON and YAML
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formats can be used to generate an NLP Tool "stub" using the [OpenAPI
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Generator]. For more information on how to develop an NLP Tool, please refer to
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the examples listed below. For more information on how to benchmark the
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performance of your tool, please visit [nlpsandbox.io].
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| GitHub repository | API |
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|---|---|
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| [nlpsandbox/data-node](https://github.com/nlpsandbox/data-node) | Data Node |
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| [nlpsandbox/date-annotator-example](https://github.com/nlpsandbox/date-annotator-example) | Date Annotator |
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| [nlpsandbox/person-name-annotator-example](https://github.com/nlpsandbox/person-name-annotator-example) | Person Name Annotator |
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| [nlpsandbox/physical-address-annotator-example](https://github.com/nlpsandbox/physical-address-annotator-example) | Physical Address Annotator |
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| [nlpsandbox/phi-deidentifier](https://github.com/nlpsandbox/phi-deidentifier) | PHI Deidentifier |
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API Name | Type | Version
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-----------------------------|-----------------------------------------|---
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[Date Annotator] | `nlpsandbox:date-annotator` | 1.0.0
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[Person Name Annotator] | `nlpsandbox:person-name-annotator` | 1.0.0
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[Physical Address Annotator] | `nlpsandbox:physical-address-annotator` | 1.0.0
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[PHI Deidentifier] | `nlpsandbox:phi-deidentifier` | 1.0.0
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## Development
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## Examples
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### Install
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These repositories provide the source code of examples for each NLP Tools
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defined by the NLP Sandbox. These repositories have a CI/CD workflow that
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automatically tests the tool, and build and publish a Docker image that can then
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be submitted as-is to the [nlpsandbox.io], if you wish to benchmark its
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performance -- just don't expect a high performance!
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1. Install [Node JS](https://nodejs.org/).
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2. Clone this repo and run `npm install` in the repo root.
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GitHub repository | Language
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------------------------------------------------|----------
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[nlpsandbox/date-annotator-example] | Python
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[nlpsandbox/date-annotator-example-java] | Java
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[nlpsandbox/person-name-annotator-example] | Python
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[nlpsandbox/physical-address-annotator-example] | Python
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[nlpsandbox/phi-deidentifier] | Python
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### Usage
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## Docker images
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Lint one OpenAPI specification, for example
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You can pull the images published by the NLP Sandbox from [Docker Hub].
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npm run lint:ibm --entrypoint=openapi/date-annotator/openapi.yaml
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npm run lint:ibm --entrypoint=openapi/person-name-annotator/openapi.yaml
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npm run lint:ibm --entrypoint=openapi/physical-address-annotator/openapi.yaml
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npm run lint:ibm --entrypoint=openapi/data-node/openapi.yaml
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npm run lint:ibm --entrypoint=openapi/phi-deidentifier/openapi.yaml
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## Contributing
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Build a bundled API file for one of the specifications:
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Thinking about contributing to this project? Get started by reading our
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[Contributor Guide](CONTRIBUTING.md).
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npm run build openapi/date-annotator/openapi.yaml
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npm run build openapi/person-name-annotator/openapi.yaml
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npm run build openapi/physical-address-annotator/openapi.yaml
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npm run build openapi/data-node/openapi.yaml
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npm run build openapi/phi-deidentifier/openapi.yaml
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## License
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You can then preview the OpenAPI docs in your browser: http://localhost:8080
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[Apache License 2.0]
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## Contribution guidelines
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<!-- Links -->
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TBA
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[nlpsandbox.io]: https://nlpsandbox.io
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[Date Annotator]: https://nlpsandbox.github.io/nlpsandbox-schemas/date-annotator/latest/docs/
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[Person Name Annotator]: https://nlpsandbox.github.io/nlpsandbox-schemas/person-name-annotator/latest/docs/
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[Physical Address Annotator]: https://nlpsandbox.github.io/nlpsandbox-schemas/physical-address-annotator/latest/docs/
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[PHI Deidentifier]: https://nlpsandbox.github.io/nlpsandbox-schemas/phi-deidentifier/latest/docs/
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- List paths in alphanumerical order
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- Add schemas and paths used in more than one API to `commons`
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[OpenAPI Generator]: https://github.com/OpenAPITools/openapi-generator
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## TODO
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[nlpsandbox/date-annotator-example]: https://github.com/nlpsandbox/date-annotator-example
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[nlpsandbox/date-annotator-example-java]: https://github.com/nlpsandbox/date-annotator-example-java
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[nlpsandbox/person-name-annotator-example]: https://github.com/nlpsandbox/person-name-annotator-example
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[nlpsandbox/physical-address-annotator-example]: https://github.com/nlpsandbox/physical-address-annotator-example
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[nlpsandbox/phi-deidentifier]: https://github.com/nlpsandbox/phi-deidentifier
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> "description": "Creates a new Annotation record. It is valid to create Annotation objects for the same source more than once since a unique ID is assigned to each record by this service.",
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[Docker Hub]: https://hub.docker.com/u/nlpsandbox
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<!-- Definitions -->
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[data_node_yaml]: https://nlpsandbox.github.io//nlpsandbox-schemas/data-node/develop/openapi.yaml
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[data_node_json]: https://nlpsandbox.github.io//nlpsandbox-schemas/data-node/develop/openapi.json
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[data_node_html]: https://nlpsandbox.github.io//nlpsandbox-schemas/data-node/develop/docs/index.html
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[Apache License 2.0]: https://github.com/nlpsandbox/date-annotator-example/blob/develop/LICENSE

‎openapi/commons/components/schemas/ResponsePageMetadata.yaml‎

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type: string
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format: uri
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totalResults:
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description: Total number of results in the result set
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description: The total number of results in the result set
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type: integer
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required:
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- links

‎openapi/data-node/openapi.yaml‎

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url: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/develop/LICENSE
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x-logo:
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url: https://nlpsandbox.github.io/nlpsandbox-schemas/logo.png
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description: >
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description: |
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# Overview
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The NLP Sandbox Data Node is a repository of data used to benchmark NLP
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Tools like the NLP Sandbox Date Annotator and Person Name Annotator. The
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resources that can be stored in this Data Node and the operations supported
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are listed below:
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Tools like the NLP Sandbox Date Annotator and Person Name Annotator.
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- Create and manage datasets
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- Create and manage FHIR stores
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- Store and retrieve FHIR patient profiles
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- Store and retrieve clinical notes
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The resources that can be stored in this Data Node and the operations
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supported are listed below:
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- Create and manage datasets - Create and manage FHIR stores
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- Store and retrieve FHIR patient profiles - Store and retrieve clinical
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notes
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- Create and manage annotation stores
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- Store and retrieve text annotations
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tags:

‎openapi/date-annotator/components/schemas/TextDateAnnotationRequest.yaml‎

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type: object
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description: An annotation request
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description: A request to annotate dates in a clinical note
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properties:
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note:
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$ref: ../../../commons/components/schemas/Note.yaml

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