Update project

.github/CONTRIBUTING.md

@@ -0,0 +1,135 @@
+# Contributing
+
+A big welcome and thank you for considering contributing to this project.
+
+This project is a community effort and lives off your contributions, be it in
+the form of bug reports, feature requests, discussions, or fixes and other
+code changes.
+
+Reading and following these guidelines will help us make the contribution
+process easy and effective for everyone involved. It also communicates that you
+agree to respect the time of the developers managing and developing these open
+source projects. In return, we will reciprocate that respect by addressing your
+issue, assessing changes, and helping you finalize your pull requests.
+
+## Quicklinks
+
+- [Code of Conduct](#code-of-conduct)
+- [Getting Started](#getting-started)
+  - [Issues](#issues)
+  - [Pull Requests](#pull-requests)
+  - [Setup Development Environment](#setup-development-environment)
+  - [Testing](#testing)
+- [Release Procedure](#release-procedure)
+- [Getting Help](#getting-help)
+
+## Code of Conduct
+
+We take our open source community seriously and hold ourselves and other
+contributors to high standards of communication. By participating and
+contributing to this project, you agree to uphold our [Code of Conduct].
+
+## Getting Started
+
+Contributions are made to this repo via Issues and Pull Requests (PRs). A few
+general guidelines that cover both:
+
+- Search for existing Issues and PRs before creating your own.
+- We work hard to makes sure issues are handled in a timely manner but,
+  depending on the impact, it could take a while to investigate the root cause.
+  A friendly ping in the comment thread to the submitter or a contributor can
+  help draw attention if your issue is blocking.
+
+### Issues
+
+Issues should be used to report problems with this project, request a new
+feature, or to discuss potential changes before a PR is created. When you
+create a new Issue, a template will be loaded that will guide you through
+collecting and providing the information we need to investigate.
+
+If you find an Issue that addresses the problem you're having, please add your
+own reproduction information to the existing issue rather than creating a new
+one. Adding a [reaction] can also help be indicating to our maintainers that a
+particular problem is affecting more than just the reporter.
+
+### Pull Requests
+
+PRs to our repositories are always welcome and can be a quick way to get your
+fix or improvement slated for the next release. In general, PRs should:
+
+- Only fix/add the functionality in question **OR** address wide-spread
+  whitespace/style issues, not both.
+- Add unit or integration tests for fixed or changed functionality
+  (if a test suite already exists).
+- Address a single concern in the least number of changed lines as possible.
+- Include documentation in the repo or on our [docs site].
+- Be accompanied by a complete Pull Request template (loaded automatically
+  when a PR is created).
+
+For changes that address core functionality or would require breaking changes
+(e.g. a major release), it's best to open an Issue to discuss your proposal
+first. This is not required but can save time creating and reviewing changes.
+
+In general, we follow the [Forking Workflow]:
+
+1. Fork the repository to your own Github account
+2. Clone the project to your machine
+3. Create a branch locally with a succinct but descriptive name
+4. Commit changes to the branch
+5. Following any formatting and testing guidelines specific to this repo
+6. Push changes to your fork
+7. Open a PR in our repository and follow the PR template so that we can
+   efficiently review the changes.
+
+We recommend that you add this repository as an [upstream remote] to your local
+git repository so that you can fetch the latest updates.
+
+On your local machine make sure you have the latest version of the `develop`
+branch from this upstream repository:
+
+    git checkout develop
+    git pull upstream develop
+
+### Setup Development Environment
+
+This project relies on Node tools and project-specific commands listed in the
+file [package.json] to streamline the development and testing of this project.
+The command below will install the required development tools.
+
+    npm ci
+
+### Testing
+
+Please add tests for new code. These might include unit tests (to test specific
+functionality of code that was added to support fixing the bug or feature),
+integration tests (to test that the feature is usable - e.g., it should have
+complete the expected behavior as reported in the feature request or bug
+report), or both.
+
+Before submitting a PR, please check that the content of the branch that you
+plan to submit passes with the tests defined for this project:
+
+    npm run lint
+    npm run test
+
+## Release Procedure
+
+Maintainers are required to follow the procedure below when creating a new
+release.
+
+TBA
+
+## Getting Help
+
+Join us on the [NLP Sandbox Discord server] and post your question to the
+channel that best matches the topic of your request.
+
+<!-- Links -->
+
+[Code of Conduct]: CODE_OF_CONDUCT.md
+[upstream remote]: https://help.github.com/en/articles/configuring-a-remote-for-a-fork
+[reaction]: https://github.blog/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/
+[docs site]: https://nlpsandbox.io
+[Forking Workflow]: https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow
+[package.json]: ../package.json
+[NLP Sandbox Discord server]: https://nlpsandbox.io/discord

.github/dependabot.yml

@@ -6,37 +6,27 @@ updates:
     schedule:
       interval: "monthly"
     target-branch: "main"
-    reviewers:
-      - "nlpsandbox/maintainers"
 
   - package-ecosystem: "docker"
     directory: "/client"
     schedule:
       interval: "monthly"
     target-branch: "main"
-    reviewers:
-      - "nlpsandbox/maintainers"
 
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "monthly"
     target-branch: "develop"
-    reviewers:
-      - "nlpsandbox/maintainers"
 
   - package-ecosystem: "npm"
     directory: "/"
     schedule:
       interval: "monthly"
     target-branch: "main"
-    reviewers:
-      - "nlpsandbox/maintainers"
 
   - package-ecosystem: "npm"
     directory: "/client"
     schedule:
       interval: "monthly"
     target-branch: "main"
-    reviewers:
-      - "nlpsandbox/maintainers"

.github/workflows/ci.yml

@@ -15,25 +15,10 @@ env:
   docker_repository: nlpsandbox/phi-deidentifier-app
 
 jobs:
-  build:
-    env:
-      working-directory: ./client
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Install modules
-      working-directory: ${{env.working-directory}}
-      run: npm ci
-    - name: Run ESLint
-      working-directory: ${{env.working-directory}}
-      run: npm run lint
-  docker:
-    # needs: [test]
+  configure:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Prepare
-      id: prep
+    - name: Create configuration
       run: |
         DOCKER_IMAGE=${{ env.docker_repository }}
         VERSION=noop
@@ -54,46 +39,87 @@ jobs:
         fi
         TAGS="${DOCKER_IMAGE}:${VERSION}"
         if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
-          MINOR=${VERSION%.*}
-          MAJOR=${MINOR%.*}
-          TAGS="$TAGS,${DOCKER_IMAGE}:${MINOR},${DOCKER_IMAGE}:${MAJOR},${DOCKER_IMAGE}:latest"
+          TAGS="$TAGS,${DOCKER_IMAGE}:latest"
           PUSH=true
-        # elif [ "${{ github.event_name }}" = "push" ]; then
-        #   TAGS="$TAGS,${DOCKER_IMAGE}:sha-${GITHUB_SHA::8}"
         fi
-        echo ::set-output name=version::${VERSION}
-        echo ::set-output name=tags::${TAGS}
-        echo ::set-output name=created::$(date -u +'%Y-%m-%dT%H:%M:%SZ')
-        echo ::set-output name=push::${PUSH}
+        printf "%s\n" \
+          "version=${VERSION}" \
+          "tags=${TAGS}" \
+          "created=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" \
+          "push=${PUSH}" | tee -a .github_env
+
+    - name: Upload .github_env
+      uses: actions/upload-artifact@v2
+      with:
+        name: GITHUB_ENV
+        path: .github_env
+
+  lint:
+    needs: [configure]
+    runs-on: ubuntu-latest
+    env:
+      working-directory: ./client
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Lint Dockerfiles
+      uses: docker://hadolint/hadolint:latest
+      with:
+        entrypoint: hadolint
+        args: client/Dockerfile
+
+    # - name: Validate docker-compose.yml
+    #   run: |
+    #     docker-compose -f docker-compose.yml config >/dev/null
+
+    - name: Install dependencies
+      working-directory: ${{env.working-directory}}
+      run: npm ci
+
+    - name: Run ESLint
+      working-directory: ${{env.working-directory}}
+      run: npm run lint
+
+  docker:
+    needs: [lint]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Download .github_env
+      uses: actions/download-artifact@v2
+      with:
+        name: GITHUB_ENV
+        path: .
+
+    - name: Restore $GITHUB_ENV
+      run: cat .github_env >> $GITHUB_ENV
+
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v1
+
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v1
-    - name: Login to DockerHub
-      if: steps.prep.outputs.push == 'true'
+
+    - name: Login to Docker Hub Registry
+      if: env.push == 'true'
       uses: docker/login-action@v1
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_PASSWORD }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
     - name: Build and push
       id: docker_build
       uses: docker/build-push-action@v2
       with:
         context: client
         file: client/Dockerfile
         platforms: linux/amd64
-        push: ${{ steps.prep.outputs.push }}
-        tags: ${{ steps.prep.outputs.tags }}
+        push: ${{ env.push }}
+        tags: ${{ env.tags }}
         labels: |
-          org.opencontainers.image.created=${{ steps.prep.outputs.created }}
+          org.opencontainers.image.created=${{ env.created }}
           org.opencontainers.image.source=${{ github.repositoryUrl }}
-          org.opencontainers.image.version=${{ steps.prep.outputs.version }}
+          org.opencontainers.image.version=${{ env.version }}
           org.opencontainers.image.revision=${{ github.sha }}
           org.opencontainers.image.licenses=${{ github.event.repository.license.name }}
-    - name: Push README to DockerHub
-      if: steps.prep.outputs.push == 'true'
-      uses: peter-evans/dockerhub-description@v2
-      with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_PASSWORD }}
-        repository: ${{ env.docker_repository }}

.github/workflows/lock.yml

@@ -1,4 +1,4 @@
-name: 'Lock Threads'
+name: Lock threads
 
 on:
   schedule:

client/Dockerfile

@@ -1,13 +1,17 @@
 # pull official node base image
 FROM node:16.2.0-alpine3.12 as build
+
 WORKDIR /app
 ENV PATH /app/node_modules/.bin:$PATH
 COPY package.json ./
 COPY package-lock.json ./
-RUN npm ci --silent
-RUN npm install [email protected] -g --silent
+
+# TODO Either copy file individually or use this line + .gitignore
 COPY . ./
-RUN npm run build
+
+RUN npm ci --silent \
+    && npm install [email protected] -g --silent \
+    && npm run build
 
 # production environment
 FROM nginx:1.21.0-alpine
@@ -19,8 +23,9 @@ WORKDIR /usr/share/nginx/html
 COPY env.sh .
 COPY env_vars .
 
-RUN apk add --no-cache bash
-RUN chmod +x env.sh
+# hadolint ignore=DL3018
+RUN apk add --no-cache bash \
+    && chmod +x env.sh
 
 EXPOSE 80
 CMD ["/bin/bash", "-c", "/usr/share/nginx/html/env.sh && nginx -g \"daemon off;\""]

docker-compose.yml

@@ -37,7 +37,7 @@ services:
       - nlpsandbox-internal
 
   phi-deidentifier:
-    image: nlpsandbox/phi-deidentifier:1.1.0
+    image: docker.synapse.org/syn22277123/phi-deidentifier-example:1.1.0
     container_name: phi-deidentifier
     restart: always
     environment:
@@ -57,13 +57,17 @@ services:
       - date-annotator
       - person-name-annotator
       - physical-address-annotator
+      - contact-annotator
+      - id-annotator
 
   phi-deidentifier-app:
     image: nlpsandbox/phi-deidentifier-app:1.1.0
     build:
       context: client
       dockerfile: Dockerfile
     container_name: phi-deidentifier-app
+    env_file:
+      - .env
     environment:
       - SERVER_PORT=${SERVER_PORT}
       - SERVER_PROTOCOL=${SERVER_PROTOCOL}
@@ -91,7 +95,7 @@ services:
       - nlpsandbox
       - nlpsandbox-internal
     ports:
-      - "80:80"
+      - "${SERVER_PORT}:80"
     depends_on:
       - phi-deidentifier-app