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bio-borisbio-boris
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Merge pull request #439 from kbase/develop
D->Main
2 parents 9ecb3b3 + 1414ddf commit 9719893

19 files changed

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‎.github/workflows/build_feature_branch.yml‎

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‎.github/workflows/build_on_push.yaml‎

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‎.github/workflows/ee2-tests.yml‎

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name: Execution Engine 2 Test Suite
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on:
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[push, pull_request]
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[pull_request]
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jobs:
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build:
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cp test/env/test.travis.env test.env
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make test-coverage
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codecov
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‎.github/workflows/manual-build.yml‎

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---
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name: Manual Build & Push
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on:
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workflow_dispatch:
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jobs:
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build-push:
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uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
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with:
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name: '${{ github.event.repository.name }}-develop'
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tags: br-${{ github.ref_name }}
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secrets: inherit

‎.github/workflows/pr_build.yml‎

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---
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name: Pull Request Build, Tag, & Push
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on:
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pull_request:
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branches:
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- develop
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- main
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- master
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types:
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- opened
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- reopened
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- synchronize
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- merged
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jobs:
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build-develop-open:
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if: github.base_ref == 'develop' && github.event.pull_request.merged == false
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uses: kbase/.github/.github/workflows/reusable_build.yml@main
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secrets: inherit
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build-develop-merge:
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if: github.base_ref == 'develop' && github.event.pull_request.merged == true
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uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
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with:
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name: '${{ github.event.repository.name }}-develop'
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tags: pr-${{ github.event.number }},latest
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secrets: inherit
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build-main-open:
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if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == false
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uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
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with:
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name: '${{ github.event.repository.name }}'
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tags: pr-${{ github.event.number }}
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secrets: inherit
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build-main-merge:
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if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == true
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uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
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with:
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name: '${{ github.event.repository.name }}'
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tags: pr-${{ github.event.number }},latest-rc
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secrets: inherit
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trivy-scans:
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if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false
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uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main
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secrets: inherit

‎.github/workflows/prod_release.yml‎

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---
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name: Release - Build & Push Image
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on:
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release:
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branches:
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- main
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- master
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types: [ published ]
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jobs:
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check-source-branch:
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uses: kbase/.github/.github/workflows/reusable_validate-branch.yml@main
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with:
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build_branch: '${{ github.event.release.target_commitish }}'
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validate-release-tag:
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needs: check-source-branch
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uses: kbase/.github/.github/workflows/reusable_validate-release-tag.yml@main
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with:
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release_tag: '${{ github.event.release.tag_name }}'
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build-push:
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needs: validate-release-tag
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uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
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with:
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name: '${{ github.event.repository.name }}'
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tags: '${{ github.event.release.tag_name }},latest'
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secrets: inherit

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/ambv/black
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rev: 21.5b0
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rev: 22.1.0
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hooks:
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- id: black
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exclude: '.+Impl.py'
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- repo: https://gitlab.com/pycqa/flake8
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rev: ''
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rev: '3.9.2'
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hooks:
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- id: flake8

‎Dockerfile‎

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FROM quay.io/kbase/sdkbase2:python
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FROM kbase/sdkpython:3.8.0
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MAINTAINER KBase Developer
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RUN apt-get clean all && apt-get update --fix-missing -y
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RUN apt-get clean all && apt-get update --fix-missing -y && apt-get upgrade -y
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# -----------------------------------------
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# In this section, you can install any system dependencies required
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RUN apt-get install -y gcc wget vim htop tmpreaper
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RUN mkdir -p /etc/apt/sources.list.d
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# Install condor
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RUN curl -fsSL https://get.htcondor.org | /bin/bash -s -- --no-dry-run
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RUN DEBIAN_FRONTEND=noninteractive wget -qO - https://research.cs.wisc.edu/htcondor/debian/HTCondor-Release.gpg.key | apt-key add - \
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&& echo "deb http://research.cs.wisc.edu/htcondor/debian/8.8/stretch stretch contrib" >> /etc/apt/sources.list \
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&& echo "deb-src http://research.cs.wisc.edu/htcondor/debian/8.8/stretch stretch contrib" >> /etc/apt/sources.list \
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&& apt-get update -y \
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&& apt-get install -y condor
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# Install jars for testing purposes
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# Uncomment this if you want to run tests inside the ee2 container on MacOSX
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# RUN cd /opt && git clone https://github.com/kbase/jars && cd -
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# install jars
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# perhaps we should have test and prod dockerfiles to avoid jars and mongo installs in prod
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RUN cd /opt \
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&& git clone https://github.com/kbase/jars \
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&& cd -
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# Remove due to cve-2021-4104 issue in spin (log4j)
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RUN rm /opt/jars/lib/jars/dockerjava/docker-java-shaded-3.0.14.jar
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# Install DOCKERIZE
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RUN curl -o /tmp/dockerize.tgz https://raw.githubusercontent.com/kbase/dockerize/dist/dockerize-linux-amd64-v0.5.0.tar.gz && \
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cd /usr/bin && \
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tar xvzf /tmp/dockerize.tgz && \
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rm /tmp/dockerize.tgz
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# install mongodb
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WORKDIR /kb/module
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RUN make all
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# Remove Jars and old Conda for Trivy Scans and after compilation is done
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RUN rm -rf /sdk && rm -rf /opt
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RUN rm -rf /miniconda-latest/pkgs/conda-4.12.0-py39h06a4308_0/info/test/tests/data/env_metadata
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WORKDIR /kb/module/scripts
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RUN chmod +x download_runner.sh && ./download_runner.sh
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‎Pipfile‎

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toml = "==0.10.1"
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tqdm = "==4.42.1"
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typing-extensions = "==3.7.4.3"
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ujson = "==1.35"
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ujson = "==5.2.0"
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urllib3 = "==1.25.8"
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uvloop = "==0.12.2"
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websockets = "==6.0"

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