D->M

.gitattributes

@@ -0,0 +1,12 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# Linux start script should use lf
+/gradlew        text eol=lf
+
+# These are Windows script files and should use crlf
+*.bat           text eol=crlf
+
+# Binary files should be left untouched
+*.jar           binary
+

.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 +1,26 @@
+version: 2
+updates:
+
+  # Docker base image updates
+  - package-ecosystem: docker
+    directory: "/"
+    schedule:
+      interval: monthly
+      time: "11:00"
+    open-pull-requests-limit: 25
+
+  # Python (pip) dependencies
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: monthly
+      time: "11:00"
+    open-pull-requests-limit: 25
+
+  # GitHub Actions dependencies
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows"
+    schedule:
+      interval: monthly
+      time: "11:00"
+    open-pull-requests-limit: 25

.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

.gitignore

@@ -0,0 +1,7 @@
+/bin/
+
+# Ignore Gradle project-specific cache directory
+.gradle
+
+# Ignore Gradle build output directory
+build

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" \

KIDLspec.css

@@ -0,0 +1,65 @@
+html, body {
+	height: 100%;
+}
+html {
+	display: table;
+	margin: auto;
+}
+body {
+	background-color: white;
+	color: #000;
+	font-family: Menlo, Monaco, Consolas, "Courier New", monospace;
+	font-weight: normal;
+	font-size: 12px;
+	margin: 0;
+	padding: 20px;
+	display: table-cell;
+	vertical-align: middle;
+}
+span.space {
+	display: inline-block;
+	width: 7px;
+}
+span.tab {
+	display: inline-block;
+	width: 30px;
+}
+span.keyword {
+	font-weight: bold;
+	color: #008;
+}
+span.name {
+	color: #000; !important
+}
+span.deprecated {
+	text-decoration: line-through;
+}
+span.annotation {
+	color: #303030;
+}
+span.primitive {
+	font-weight: bold;
+	color: #066;
+}
+div.body {
+	background-color: #ffffff;
+	color: #3e4349;
+	padding: 0 30px;
+}
+div.comment {
+	color: #A0A0A0;
+}
+a {
+	color: #004b6b;
+	text-decoration: none;
+}
+a:hover {
+	color: #6d4100;
+	text-decoration: underline;
+}
+:target {
+	background-color: #ffa;
+}
+div.body p, div.body dd, div.body li {
+	line-height: 1.4em;
+}