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bio-borisBoris Sadkhin
bio-boris
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Boris Sadkhin
committedJun 22, 2022
Initial Release
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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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- closed
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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/release-main.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

‎Dockerfile

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FROM ubuntu:20.04
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# Note that these labels need to be manually updated with the actual contents of the image
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LABEL maintainer="scanon@lbl.gov"
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LABEL us.kbase.ubuntu="20.04"
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LABEL us.kbase.python="3.8.4"
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LABEL us.kbase.sdk="1.0.18"
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LABEL us.kbase.python="3.9.12"
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LABEL us.kbase.sdk="1.2.1"
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LABEL us.kbase.sdkcommit="8def489f648a7ff5657d33ed05f41c60f4766e1b"
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# Fix KBase Catalog Registration Issue
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ENV PIP_PROGRESS_BAR=off
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# Install system dependencies
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RUN \
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apt-get -y update && \
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apt-get -y upgrade && \
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export DEBIAN_FRONTEND=noninteractive && \
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export TZ=Etc/UTC && \
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apt-get -y install gcc make curl git openjdk-8-jre
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apt-get -y install gcc make curl git openjdk-8-jre unzip htop
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# Copy in the SDK
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COPY --from=kbase/kb-sdk:20180808 /src /sdk
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COPY --from=kbase/kb-sdk:1.2.1 /src /sdk
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RUN sed -i 's|/src|/sdk|g' /sdk/bin/*
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# Install Conda version py39_4.12.0 and Python 3.9.12
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ENV CONDA_VERSION=py39_4.12.0
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ENV CONDA_INSTALL_DIR=/opt/conda/py39_4.12.0
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RUN \
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V=py38_4.10.3 && \
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curl -o conda.sh -s https://repo.anaconda.com/miniconda/Miniconda3-${V}-Linux-x86_64.sh && \
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sh ./conda.sh -b -p /opt/conda3 && \
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echo "Installing to ${CONDA_INSTALL_DIR}" && \
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curl -o conda.sh -s https://repo.anaconda.com/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh && \
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sh ./conda.sh -b -p ${CONDA_INSTALL_DIR} && \
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rm conda.sh
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ENV PATH=/opt/conda3/bin:$PATH:/sdk/bin
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# Add in some legacy modules
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# Install packages including mamba
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RUN \
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conda install -c conda-forge mamba
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ADD biokbase $CONDA_INSTALL_DIR/lib/biokbase
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ADD biokbase/user-env.sh /kb/deployment/user-env.sh
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ADD requirements.txt /tmp/requirements.txt
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ADD ./requirements.txt /tmp/
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RUN \
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pip install -r /tmp/requirements.txt
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ENV PATH=$CONDA_INSTALL_DIR/bin:/sdk/bin:$PATH
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run env
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# Add in some legacy modules
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ADD biokbase /opt/conda3/lib/python3.8/site-packages/biokbase
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# Configure Conda and Install Mamba
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RUN \
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conda config --add channels conda-forge && \
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conda config --set channel_priority strict && \
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conda install -y mamba=0.15.3
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#Install packages required for base image
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RUN \
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which pip && \
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pip install -r /tmp/requirements.txt

‎README.md

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# SDK Base Python Image
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This is a very minimal base python image for building KBase SDK apps.
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This is a very minimal base python image for building KBase SDK apps. It also contains a copy of the KBase SDK.
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## Contents
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* Ubuntu 20.04 base image
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* Dependencies packages: gcc make curl git openjdk-8-jre
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* Installation of the kb-sdk tool (1.0.18)
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* Python 3.8 via Conda
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* Installation of the kb-sdk tool (1.2.1)
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* Python 3.9.13 via Conda
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* Mamba for Conda package installation
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* A select set of python modules
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* A select set of python modules in the requirements.txt

‎biokbase/user-env.sh

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#!/usr/bin/env bash
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# In order to avoid `./scripts/entrypoint.sh: line 3: /kb/deployment/user-env.sh: No such file or directory`
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# This file is now here
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echo "user-env.sh is ignored"

‎requirements.txt

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requests
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coverage
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nose
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sphinx
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jsonrpcbase
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requests==2.27.1
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coverage==6.3.3
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nose==1.3.7
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sphinx==4.5.0
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jsonrpcbase==0.2.0
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pytest==7.1.1
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pytest-cov==3.0.0

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