Merge pull request #12 from Sage-Bionetworks/prepare-release

Prepare release

.github/workflows/ci.yml

@@ -5,9 +5,10 @@ on:
     - cron: '0 10 * * *' # everyday at 10am
   push:
     branches:
-      - '**'
+      - main
+      - develop
     tags:
-      - 'v*.*.*'
+      - '*.*.*'
   pull_request:
 
 jobs:
@@ -19,13 +20,19 @@ jobs:
       uses: docker://hadolint/hadolint:latest
       with:
         entrypoint: hadolint
-        args: src/server/Dockerfile
+        args: server/Dockerfile
+    - name: Check that packages in requirements.txt files are in asc order
+      run: |
+        sort -f --check server/requirements.txt
+        sort -f --check server/test-requirements.txt
 
   test:
     needs: [lint]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+    - name: Validate docker-compose.yml
+      run: docker-compose -f docker-compose.yml config >/dev/null
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
@@ -49,8 +56,10 @@ jobs:
       run: |
         DOCKER_IMAGE=nlpsandbox/date-annotator-example
         VERSION=noop
+        PUSH=false
         if [ "${{ github.event_name }}" = "schedule" ]; then
           VERSION=nightly
+          PUSH=true
         elif [[ $GITHUB_REF == refs/tags/* ]]; then
           VERSION=${GITHUB_REF#refs/tags/}
         elif [[ $GITHUB_REF == refs/heads/* ]]; then
@@ -62,22 +71,24 @@ jobs:
           VERSION=pr-${{ github.event.number }}
         fi
         TAGS="${DOCKER_IMAGE}:${VERSION}"
-        if [[ $VERSION =~ ^v[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
+        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"
+          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}
     - 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: github.event_name != 'pull_request'
+      if: ${{ steps.prep.outputs.push }}
       uses: docker/login-action@v1
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -86,14 +97,14 @@ jobs:
       id: docker_build
       uses: docker/build-push-action@v2
       with:
-        context: src/server
-        file: src/server/Dockerfile
-        platforms: linux/amd64,linux/arm64,linux/386
-        push: ${{ github.event_name != 'pull_request' }}
+        context: server
+        file: server/Dockerfile
+        platforms: linux/amd64
+        push: ${{ steps.prep.outputs.push }}
         tags: ${{ steps.prep.outputs.tags }}
-        # labels: |
-        #   org.opencontainers.image.created=${{ steps.prep.outputs.created }}
-        #   org.opencontainers.image.source=${{ github.repositoryUrl }}
-        #   org.opencontainers.image.version=${{ steps.prep.outputs.version }}
-        #   org.opencontainers.image.revision=${{ github.sha }}
-        #   org.opencontainers.image.licenses=${{ github.event.repository.license.name }}
+        labels: |
+          org.opencontainers.image.created=${{ steps.prep.outputs.created }}
+          org.opencontainers.image.source=${{ github.repositoryUrl }}
+          org.opencontainers.image.version=${{ steps.prep.outputs.version }}
+          org.opencontainers.image.revision=${{ github.sha }}
+          org.opencontainers.image.licenses=${{ github.event.repository.license.name }}

.gitignore

@@ -1,5 +1,3 @@
-# Dir for bundles
-dist
 node_modules
 .idea
-venv
+venv

README.md

@@ -1,13 +1,10 @@
 # nlp-sandbox-date-annotator-example
 
-[![GitHub Stars](https://img.shields.io/github/stars/data2health/nlp-sandbox-date-annotator-example.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/data2health/nlp-sandbox-date-annotator-example)
 [![Docker Pulls](https://img.shields.io/docker/pulls/nlpsandbox/date-annotator-example.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&label=pulls&logo=docker)](https://hub.docker.com/r/data2health/nlp-sandbox-date-annotator-example)
 [![GitHub CI](https://img.shields.io/github/workflow/status/data2health/nlp-sandbox-date-annotator-example/ci.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/data2health/nlp-sandbox-date-annotator-example)
 [![GitHub License](https://img.shields.io/github/license/data2health/nlp-sandbox-date-annotator-example.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/data2health/nlp-sandbox-date-annotator-example)
-<!-- [![GitHub Release](https://img.shields.io/github/release/data2health/nlp-sandbox-date-annotator-example.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/data2health/nlp-sandbox-date-annotator-example/releases) -->
-<!-- [![Docker Stars](https://img.shields.io/docker/stars/nlpsandbox/date-annotator-example.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&label=stars&logo=docker)](https://hub.docker.com/r/data2health/nlp-sandbox-date-annotator-example) -->
 
-An example implementation of the NLP Sandbox Date Annotator
+An example implementation of the NLP Sandbox Date Annotator.
 
 ## Development
 

docker-compose.yml

@@ -0,0 +1,11 @@
+version: "3.8"
+
+services:
+  date-annotator:
+    image: nlpsandbox/date-annotator-example:latest
+    build:
+      context: server
+      dockerfile: Dockerfile
+    container_name: date-annotator-example
+    ports:
+      - "8080:8080"

package.json

@@ -1,6 +1,6 @@
 {
     "name": "nlp-sandbox-date-annotator-example",
-    "version": "1.0.0-beta.1",
+    "version": "1.0.0",
     "license": "Apache-2.0",
     "repository": "github:data2health/nlp-sandbox-date-annotator-example",
     "devDependencies": {

server/Dockerfile

@@ -0,0 +1,45 @@
+FROM python:3.8.5-slim-buster
+
+ARG S6_VERSION
+ENV S6_VERSION=${S6_VERSION:-v2.1.0.0}
+ENV S6_BEHAVIOUR_IF_STAGE2_FAILS=2
+ENV PIP_NO_CACHE_DIR=off
+ENV APP_USER=app
+ENV APP_DIR=/opt/app
+
+# Safer bash scripts with 'set -euxo pipefail'
+SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]
+
+# Install dependencies
+# hadolint ignore=DL3008
+RUN apt-get update -qq -y \
+    && apt-get install --no-install-recommends -qq -y \
+        curl \
+        unzip \
+    && apt-get -y autoclean \
+    && apt-get -y autoremove \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up S6 init system
+RUN curl -fsSL https://github.com/just-containers/s6-overlay/releases/download/${S6_VERSION}/s6-overlay-amd64.tar.gz \
+        -o /tmp/s6-overlay.tar.gz \
+    && tar xzf /tmp/s6-overlay.tar.gz --directory / \
+    && rm -fr /tmp/s6-overlay.tar.gz
+
+# Add app user
+RUN useradd -m -s /bin/bash ${APP_USER} \
+    && echo "${APP_USER}:${APP_USER}" | chpasswd
+
+# Copy server files
+COPY . ${APP_DIR}
+RUN chown -R ${APP_USER}:${APP_USER} ${APP_DIR}
+
+# Install dependencies
+RUN pip install -r ${APP_DIR}/requirements.txt
+
+# Add s6 scripts
+COPY root /
+
+EXPOSE 8080
+
+ENTRYPOINT ["/init"]

server/requirements.txt

@@ -0,0 +1,4 @@
+connexion==2.7.0
+requests==2.24.0
+swagger-ui-bundle==0.0.8
+synapseclient==2.2.0

server/root/etc/cont-init.d/20-create-app-logfolder

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+mkdir -p /var/log/app
+chown nobody:nogroup /var/log/app

server/root/etc/services.d/app/finish

@@ -0,0 +1,5 @@
+#!/usr/bin/execlineb -S0
+
+# By default, services created in /etc/services.d will automatically restart.
+# Here we bring the container down if a service crashes.
+s6-svscanctl -t /var/run/s6/services

server/root/etc/services.d/app/run

@@ -0,0 +1,4 @@
+#!/usr/bin/with-contenv sh
+
+cd /opt/app
+s6-setuidgid app python -m openapi_server

server/test-requirements.txt

@@ -0,0 +1,4 @@
+Flask-Testing==0.8.0
+pytest-cov>=2.8.1
+pytest-randomly==3.4.1 # needed for python 2.7+3.4
+pytest~=6.1.1 # needed for python 2.7+3.4