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database-update.yml
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name: Build-database
on:
push:
branches:
- '**'
paths:
- ./data/
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
jobs:
# Placeholder
# build-bmd:
# #if: github.actor != 'github-actions[bot]'
# runs-on: ubuntu-20.04
# environment: build
# steps:
# - name: Checkout Repo
# uses: actions/checkout@v3
# - name: Download artifacts from previous drug gen
# uses: actions/download-artifact@v3
# - name: Pull sample image
# run: docker pull sgosline/srp-bmd
# - name: Run bmd python command
# run: |
# docker run -v $PWD:/tmp sgosline/srp-bmd
# - name: List files cwd
# run: ls -la
build-samples:
#if: github.actor != 'github-actions[bot]'
runs-on: ubuntu-20.04
steps:
- name: Checkout Repo
uses: actions/checkout@v3
- name: Download artifacts from previous drug gen
uses: actions/download-artifact@v3
- name: Pull sample image
run: docker pull sgosline/srp-samplechem
- name: Run sample-chem python command
run: |
docker run -v $PWD:/tmp sgosline/srp-samplechem
- name: List files cwd
run: ls -la
- name: move files
run: |
mkdir samp-files
mv *csv samp-files
- name: upload artifacts
uses: actions/upload-artifact@v2
with:
name: samp-files
path: samp-files
build-expo:
#if: github.actor != 'github-actions[bot]'
runs-on: ubuntu-20.04
steps:
- name: Checkout Repo
uses: actions/checkout@v3
- name: Download artifacts from previous drug gen
uses: actions/download-artifact@v3
- name: Pull sample image
run: docker pull sgosline/srp-exposome
- name: Run sample-chem python command
run: |
docker run -v $PWD:/tmp sgosline/srp-exposome
- name: List files cwd
run: ls -la
- name: Copy files to artifact
run: |
mkdir expo-files
mv *.csv expo-files
- name: upload artifact
uses: actions/upload-artifact@v2
with:
name: expo-files
path: expo-files
build-expr:
#if: github.actor != 'github-actions[bot]'
runs-on: ubuntu-20.04
needs: build-samples
steps:
- name: Checkout Repo
uses: actions/checkout@v3
- name: Download artifacts from sample generation
uses: actions/download-artifact@v3
with:
name: samp-files
path: samp-files
- name: Pull sample image
run: docker pull sgosline/srp-zfexp
- name: move chemical list to tmp
run: mv samp-files/chemicals.csv .
- name: Run zfexp python command
run: |
docker run -v $PWD:/tmp sgosline/srp-zfexp
- name: List files cwd
run: ls -la
- name: Copy files to artifact
run: |
mkdir expr-files
mv *csv expr-files
- name: upload artifact
uses: actions/upload-artifact@v2
with:
name: expr-files
path: expr-files
artifact-test:
needs: [build-samples,build-expo,build-expr]
runs-on: ubuntu-20.04
steps:
- name: Checkout Repo
uses: actions/checkout@v2
- name: Download artifacts from expression
uses: actions/download-artifact@v2
with:
name: expr-files
- name: Downlod artifacts from exposome
uses: actions/download-artifact@v2
with:
name: expo-files
- name: Downlod artifacts from samples
uses: actions/download-artifact@v2
with:
name: samp-files
- name: List files cwd
run: ls -la *
- name: Moves files to single directory
run: |
mkdir srpAnalytics
mv *csv srpAnalytics
gzip -cvf srpAnalytics/* srpAnalytics.gz
- name: Pushes to figshare
uses: figshare/[email protected]
with:
FIGSHARE_TOKEN: ${{ secrets.FIGSHARE_TOKEN }}
FIGSHARE_ENDPOINT: 'https://api.figshare.com/v2'
# FIGSHARE_ARTICLE_ID:
FIGSHARE_PROJECT_ID: 177459
DATA_DIR: 'srpAnalytics'
#zipfiles push to figshare