Develop -> Master

.github/dependabot.yml

@@ -0,0 +1,23 @@
+version: 2
+updates:
+
+  # Docker
+  - package-ecosystem: docker
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 25
+
+  # Python
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 25
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 25

.github/workflows/codeql.yml

@@ -0,0 +1,38 @@
+name: "CodeQL"
+
+on:
+  pull_request:
+    types:
+    - opened
+    - reopened
+    - synchronize
+    - ready_for_review
+  push:
+    # run workflow when merging to main or develop
+    branches:
+      - main
+      - master
+      - develop
+
+jobs:
+  CodeQL-Build:
+    # CodeQL runs on ubuntu-latest, windows-latest, and macos-latest
+    runs-on: ubuntu-latest
+
+    permissions:
+      # required for all workflows
+      security-events: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        # Override language selection by uncommenting this and choosing your languages
+        with:
+          languages: python
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3

.github/workflows/docker-publish.yml

@@ -0,0 +1,57 @@
+name: Docker
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "main", "master", "develop" ]
+    # Publish semver tags as releases.
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+-*'
+  pull_request:
+    branches: [ "main", "master", "develop" ]
+  release:
+    types: [published]
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/test.yaml

@@ -0,0 +1,100 @@
+name: ID Mapping Service test
+
+on:
+  pull_request:
+    types:
+    - opened
+    - reopened
+    - synchronize
+    - ready_for_review
+  push:
+    # run workflow when merging to main or develop
+    branches:
+      - main
+      - master
+      - develop
+
+jobs:
+  id_mapping_service_container_tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out GitHub repo
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9.19"
+
+      - name: Install dependencies and set up test config
+        shell: bash
+        run: |
+          # set up python dependencies
+          pip install pytest requests
+
+          # set up deploy.cfg
+          cp -n deploy.cfg.example deploy.cfg
+          sed -i "s#^mongo-host.*#mongo-host=mongo#" deploy.cfg
+          sed -i "s#^mongo-db.*#mongo-db=idmapping#" deploy.cfg
+
+      - name: Run tests
+        shell: bash
+        run: |
+          sh container_test/run_tests.sh
+
+  id_mapping_service_tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - python: '3.9.19'
+            mongo: 'mongodb-linux-x86_64-3.6.23'
+            wired_tiger: 'false'
+          - python: '3.9.19'
+            mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
+            wired_tiger: 'true'
+
+    steps:
+    - name: Check out GitHub repo
+      uses: actions/checkout@v4
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{matrix.python}}
+
+    - name: Install dependencies and set up test config
+      shell: bash
+      run: |
+
+        # install python libraries
+        python -m pip install --upgrade pip
+        pip install pipenv
+        pipenv sync --system --dev
+
+        # set up mongo
+        cd ..
+        wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz
+        tar xfz ${{matrix.mongo}}.tgz
+        export MONGOD=`pwd`/${{matrix.mongo}}/bin/mongod
+        cd -
+
+        # set up test config
+        cp -n test.cfg.example test.cfg
+        sed -i "s#^test.temp.dir =.*#test.temp.dir=temp_test_dir#" test.cfg
+        sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg
+        sed -i "s#^test.mongo.wired_tiger.*#test.mongo.wired_tiger=${{matrix.wired_tiger}}#" test.cfg
+
+    - name: Run tests
+      shell: bash
+      run: |
+        HOMEDIR=`pwd`
+        PYTHONPATH=$HOMEDIR/src:$PYTHONPATH
+        make test
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: true

Dockerfile

@@ -1,6 +1,6 @@
 FROM kbase/kb_jre:latest as dockerize
 
-FROM python:3.6-alpine
+FROM python:3.9.19-alpine
 
 # These ARGs values are passed in via the docker build command
 ARG BUILD_DATE
@@ -10,13 +10,16 @@ ARG BRANCH=develop
 RUN apk add gcc linux-headers libc-dev make git
 COPY --from=dockerize /kb/deployment/bin/dockerize /usr/bin/
 
-ADD requirements.txt /tmp/
-
-RUN pip install -r /tmp/requirements.txt
+# install pipenv
+RUN pip install --upgrade pip && \
+    pip install pipenv
 
+WORKDIR /kb
 ADD . /kb
 
-RUN cd /kb && make
+# install deps
+RUN pipenv sync --system
+RUN make
 
 # The BUILD_DATE value seem to bust the docker cache when the timestamp changes, move to
 # the end
@@ -27,7 +30,6 @@ LABEL org.label-schema.build-date=$BUILD_DATE \
       us.kbase.vcs-branch=$BRANCH \
       maintainer="Steve Chan [email protected]"
 
-WORKDIR /kb/
 ENV KB_DEPLOYMENT_CONFIG=/kb/deploy.cfg
 ENV PYTHONPATH=$PYTHONPATH:/kb/src
 

Makefile

@@ -19,7 +19,7 @@ test: all
 	flake8 src
 	mypy src
 	IDMAP_TEST_FILE=$(TEST_CFG) pytest --verbose src --cov src/jgikbase/idmapping
-	bandit --recursive src --exclude src/jgikbase/test
+	bandit --configfile bandit.yaml --recursive src --exclude src/jgikbase/test
 
 # Only test the MongoDB related code.
 test-mongo:

Pipfile

@@ -0,0 +1,28 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+cacheout = "==0.10.2"
+flask = "==2.0.0"
+gevent = "==24.2.1"
+gunicorn = "==22.0.0"
+pymongo = "==4.7.2"
+requests = "==2.20.0"
+types-requests = "==2.25.0"
+werkzeug = "==2.0.3"
+
+[dev-packages]
+bandit = "==1.7.9"
+coverage = "==7.5.3"
+flake8 = "==7.1.0"
+mypy = "==1.10.0"
+pytest-cov = "==2.5.1"
+requests-mock = "==1.5.2"
+semver = "==2.8.1"
+sphinx = "==1.7.4"
+sphinx-autodoc-typehints = "==1.3.0"
+
+[requires]
+python_version = "3.9"