Merge pull request #424 from kbase/develop

D->M

.flake8

@@ -9,4 +9,6 @@ exclude =
  execution_engine2Impl.py,
  lib/installed_clients/,
  lib/execution_engine2/execution_engine2Impl.py,
+ lib/execution_engine2/authclient.py,
+ lib/biokbase/log.py,
  *Impl.py

.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@v2
+      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@v1
+      # 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@v1
+
+    # 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@v1

.github/pull_request_template.md

@@ -9,20 +9,20 @@
 
 # Testing Instructions
 * Details for how to test the PR: 
-- [ ] Tests pass in travis and locally 
+- [ ] Tests pass in Github Actions and locally 
 - [ ] Changes available by spinning up a local test suite and doing X
 
 # Dev Checklist:
 
-- [ ] My code follows the guidelines at https://sites.google.com/truss.works/kbasetruss/development
+- [ ] My code follows the guidelines at https://sites.google.com/truss.works/kbasetruss/data-upload-project/development
 - [ ] I have performed a self-review of my own code
 - [ ] I have commented my code, particularly in hard-to-understand areas
 - [ ] I have made corresponding changes to the documentation
 - [ ] My changes generate no new warnings
 - [ ] I have added tests that prove my fix is effective or that my feature works
 - [ ] New and existing unit tests pass locally with my changes
 - [ ] Any dependent changes have been merged and published in downstream modules
-- [ ] I have run Black and Flake8 on changed Python Code manually or with git precommit (and the travis build passes)
+- [ ] I have run Black and Flake8 on changed Python Code manually or with git precommit (and the Github Actions build passes)
 
 # Updating Version and Release Notes (if applicable)
 

.github/workflows/build_feature_branch.yml

@@ -0,0 +1,26 @@
+name: Build Feature Branches
+
+on:  [pull_request]
+
+jobs:
+  main:
+    runs-on: ubuntu-20.04
+    steps:
+      -       
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_TOKEN }}
+      -
+        name: Build and push this feature branch
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: ghcr.io/${{ github.repository }}:${{ github.head_ref }}
+
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/build_on_push.yaml

@@ -0,0 +1,31 @@
+name: Build Main/Develop Branches on push
+
+on:
+  push:
+    branches: 
+      - main
+      - master
+      - develop
+
+jobs:
+  main:
+    runs-on: ubuntu-20.04
+    steps:
+      -       
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_TOKEN }}
+      -
+        name: Build and push the main branch
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: ghcr.io/${{ github.repository }}:${ GITHUB_REF##*/ }
+
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/ee2-tests.yml

@@ -22,15 +22,18 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.8
-    - name: Install dependencies
+    - name: Lint with flake8 and black
       run: |
         python -m pip install --upgrade pip
         pip install flake8 black pytest
-        if [ -f requirements.txt ]; then pip install -r requirements-dev.txt; fi
-    - name: Lint with flake8 and black
-      run: |
         flake8 ./lib ./test
         black --check ./lib ./test
+    - name: Install dependencies
+      run: |
+        if [ -f requirements.txt ]; then pip install -r requirements-dev.txt; fi
+        cd /opt
+        git clone https://github.com/kbase/jars
+        cd -
     - name: Build Docker Image
       run: |
         docker build . -t execution_engine2:test
@@ -39,4 +42,5 @@ jobs:
         docker-compose up -d
         cp test/env/test.travis.env test.env
         make test-coverage
+        codecov
 

.gitignore

@@ -15,3 +15,5 @@ sdk.cfg
 .pytest_cache
 lib/execution_engine2/execution_engine2Impl.py.bak*
 
+coverage.xml
+test_temp_can_delete

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/ambv/black
-    rev: 20.8b1
+    rev: 21.5b0
     hooks:
     - id: black
       exclude: '.+Impl.py'

Dockerfile

@@ -1,4 +1,4 @@
-FROM kbase/sdkbase2:python
+FROM quay.io/kbase/sdkbase2:python
 MAINTAINER KBase Developer
 
 RUN apt-get clean all && apt-get update --fix-missing -y
@@ -18,6 +18,12 @@ RUN DEBIAN_FRONTEND=noninteractive wget -qO - https://research.cs.wisc.edu/htcon
     && apt-get update -y \
     && apt-get install -y condor
 
+# install jars
+# perhaps we should have test and prod dockerfiles to avoid jars and mongo installs in prod
+RUN cd /opt \
+    && git clone https://github.com/kbase/jars \
+    && cd -
+
 # install mongodb
 RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 2930ADAE8CAF5059EE73BB4B58712A2291FA4AD5 \
     && echo "deb http://repo.mongodb.org/apt/debian stretch/mongodb-org/3.6 main" | tee /etc/apt/sources.list.d/mongodb-org-3.6.list  \
@@ -37,12 +43,14 @@ RUN echo "mongodb-org hold" | dpkg --set-selections \
 RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh \
 && bash ~/miniconda.sh -b -p /miniconda-latest
 
+# Setup Cron
+COPY ./bin/ee2_cronjobs /etc/cron.d/ee2_cronjobs
+
 # Need to change startup scripts to match this in MAKEFILE
 ENV PATH=/miniconda-latest/bin:$PATH
 RUN pip install --upgrade pip && python -V
-
-
 COPY ./requirements.txt /kb/module/requirements.txt
+
 RUN pip install -r /kb/module/requirements.txt
 RUN adduser --disabled-password --gecos '' -shell /bin/bash kbase
 # -----------------------------------------
@@ -57,7 +65,10 @@ WORKDIR /kb/module/scripts
 RUN chmod +x download_runner.sh && ./download_runner.sh
 
 WORKDIR /kb/module/
+
+# Set deploy.cfg location
 ENV KB_DEPLOYMENT_CONFIG=/kb/module/deploy.cfg
+ENV PATH=/kb/module:$PATH
 
 ENTRYPOINT [ "./scripts/entrypoint.sh" ]
 CMD [ ]

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;
+}

Makefile

@@ -21,6 +21,10 @@ compile:
 		--pysrvname $(SERVICE_CAPS).$(SERVICE_CAPS)Server \
 		--pyimplname $(SERVICE_CAPS).$(SERVICE_CAPS)Impl;
 
+	kb-sdk compile $(SPEC_FILE) \
+		--out . \
+		--html \
+
 build:
 	chmod +x $(SCRIPTS_DIR)/entrypoint.sh