D->M

.github/codeql.yml

@@ -0,0 +1,52 @@
+name: "Code scanning - action"
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 19 * * 0'
+
+jobs:
+  CodeQL-Build:
+
+    # CodeQL runs on ubuntu-latest and windows-latest
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        # We must fetch at least the immediate parents so that if this is
+        # a pull request then we can checkout the head.
+        fetch-depth: 2
+
+    # If this run was triggered by a pull request event, then checkout
+    # the head of the pull request instead of the merge commit.
+    - run: git checkout HEAD^2
+      if: ${{ github.event_name == 'pull_request' }}
+
+    # 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: go, javascript, csharp, python, cpp, java
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3

.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+- package-ecosystem: docker
+  directory: "/"
+  schedule:
+    interval: weekly
+    time: '11:00'
+  open-pull-requests-limit: 10
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: weekly
+    time: '11:00'
+  open-pull-requests-limit: 10

.github/workflows/test.yml

@@ -0,0 +1,90 @@
+name: KBase Catalog 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:
+  catalog_tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - python-version: '3.9.19'
+            mongo-version: '3.6'
+          - python-version: '3.9.19'
+            mongo-version: '7.0.4'
+    services:
+      mongo:
+        image: mongo:${{matrix.mongo-version}}
+        ports:
+            - 27017:27017
+        options: --name mongo${{matrix.mongo-version}}
+
+    env:
+      KBASE_CI_TOKEN: ${{ secrets.KBASE_CI_TOKEN }}
+      # This env var is also used in the catalog test docker compose file for starting NMS
+      ADMIN_USER: ${{ secrets.KBASE_BOT_USER_CI }}
+
+    steps:
+      - name: Repo checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{matrix.python-version}}
+
+      - name: Install dependencies and set up test config
+        shell: bash
+
+        run: |
+
+          # test mongo connection
+          curl http://localhost:27017
+          returncode=$?
+          if [ $returncode != 0 ]; then exit $returncode; fi
+
+          # set HOMEDIR
+          export HOMEDIR=`pwd`
+
+          # move to parent dir to install binaries etc
+          cd ..
+
+          # setup kb-sdk
+          mkdir -p $(pwd)/bin
+          docker run ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 genscript > $(pwd)/bin/kb-sdk
+          chmod 755 $(pwd)/bin/kb-sdk
+          export PATH=$(pwd)/bin:$PATH
+
+          # install catalog dependencies
+          cd $HOMEDIR
+          python -m pip install --upgrade pip
+          pip install pipenv
+          pipenv sync --system --dev
+
+          # setup test config
+          cp -n test/test.cfg.example test/test.cfg
+          sed -i "s#^nms-admin-token.*#nms-admin-token=$KBASE_CI_TOKEN#" test/test.cfg
+          sed -i "s#^method-spec-admin-users.*#method-spec-admin-users=$ADMIN_USER#" test/test.cfg
+
+      - name: Run tests
+        shell: bash
+        run: make test
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

Dockerfile

@@ -1,25 +1,43 @@
-FROM kbase/sdkbase2:python AS build
+FROM python:3.9.19 AS build
 
+# The rsync installation is required for the Makefile
+RUN apt-get update && apt-get install -y rsync
+RUN mkdir -p /kb/deployment/lib/biokbase
 
 COPY . /tmp/catalog
 RUN cd /tmp/catalog && make deploy-service deploy-server-control-scripts
 
-FROM kbase/sdkbase2:python
+FROM python:3.9.19
 # These ARGs values are passed in via the docker build command
 ARG BUILD_DATE
 ARG VCS_REF
 ARG BRANCH
 
+RUN apt-get update && apt-get install -y wget
+
+# install dockerize
+WORKDIR /opt
+RUN wget -q https://github.com/kbase/dockerize/raw/master/dockerize-linux-amd64-v0.6.1.tar.gz \
+    && tar xvzf dockerize-linux-amd64-v0.6.1.tar.gz \
+    && rm dockerize-linux-amd64-v0.6.1.tar.gz
+RUN mkdir -p /kb/deployment/bin/
+RUN ln -s /opt/dockerize /kb/deployment/bin/dockerize
+
 ENV KB_DEPLOYMENT_CONFIG "/kb/deployment/conf/deploy.cfg"
 
 COPY --from=build /kb/deployment/lib/biokbase /kb/deployment/lib/biokbase
 COPY --from=build /kb/deployment/services /kb/deployment/services
 COPY --from=build /tmp/catalog/deployment/conf /kb/deployment/conf
 
-SHELL ["/bin/bash", "-c"]
-COPY requirements.txt requirements.txt
-RUN source activate root && \
-    pip install -r requirements.txt
+WORKDIR /tmp/catalog
+
+# install pipenv
+RUN pip install --upgrade pip && \
+    pip install pipenv
+
+# install deps
+COPY Pipfile* ./
+RUN pipenv sync --system
 
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.vcs-url="https://github.com/kbase/catalog.git" \

Makefile

@@ -27,11 +27,6 @@ LIB_DIR = lib
 
 PATH := kb_sdk/bin:$(PATH)
 
-default: init
-
-init:
-	git submodule init
-	git submodule update
 
 compile-kb-module:
 	kb-sdk compile $(SPEC_FILE) \
@@ -102,10 +97,6 @@ setup-tests:
 	mkdir -p $(TESTLIB)/biokbase
 	mkdir -p $(TESTDIR)/nms
 	rsync -av lib/biokbase/* $(TESTLIB)/biokbase/. --exclude *.bak-*
-	rsync -av kbapi_common/lib/biokbase/* $(TESTLIB)/biokbase/.
-	cd narrative_method_store; make; make build-classpath-list;
-#	rsync -av narrative_method_store/lib/biokbase/* $(TESTLIB)/biokbase/.
-
 
 
 test: setup-tests

Pipfile

@@ -0,0 +1,18 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+docker = "==7.1.0"
+jsonrpcbase = "==0.2.0"
+pymongo = "==4.7.2"
+pyyaml = "==6.0.2"
+semantic-version = "==2.10.0"
+uwsgi = "==2.0.22"
+
+[dev-packages]
+coverage = "==7.6.1"
+
+[requires]
+python_version = "3.9.19"