running slim version of test while working on git commit of visualiza… #151
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - builder_branch_JJ | |
| jobs: | |
| # build-hcmi-samples: | |
| # if: github.actor != 'github-actions[bot]' | |
| # runs-on: ubuntu-20.04 | |
| # environment: build | |
| # steps: | |
| # #Add upload artifact from CPTAC Samples | |
| # - name: Checkout HCMI | |
| # uses: actions/checkout@v2 | |
| # - name: Build HCMI Image | |
| # run: docker build -t hcmi-samples-builder -f build/docker/Dockerfile.hcmi.samples . | |
| # - name: Run HCMI Container | |
| # run: docker run --name hcmi-samples-container hcmi-samples-builder | |
| # - name: Copy file from HCMI Samples Container | |
| # run: | | |
| # mkdir hcmi-samples | |
| # for file in hcmi_samples.csv; do | |
| # docker cp hcmi-samples-container:/usr/src/app/$file hcmi-samples/$file | |
| # done | |
| # - name: Get HCMI container logs | |
| # run: docker logs hcmi-samples-container | |
| # # - name: dummy hcmi | |
| # # run: | | |
| # # mkdir hcmi-files | |
| # # echo "This is some sample text." > hcmi-files/d.txt | |
| # # echo "Another line of text." > hcmi-files/c.gz | |
| # - name: Upload artifacts for HCMI | |
| # uses: actions/upload-artifact@v2 | |
| # with: | |
| # name: hcmi-samples | |
| # path: hcmi-samples | |
| # build-hcmi: | |
| # if: github.actor != 'github-actions[bot]' | |
| # needs: [build-hcmi-samples] | |
| # runs-on: ubuntu-20.04 | |
| # environment: build | |
| # steps: | |
| # - name: Checkout HCMI | |
| # uses: actions/checkout@v2 | |
| # - name: Download artifacts from HCMI | |
| # uses: actions/download-artifact@v2 | |
| # with: | |
| # name: hcmi-samples | |
| # - name: List files cwd | |
| # run: ls -lah | |
| # - name: Build HCMI Image | |
| # run: docker build -t hcmi-builder -f build/docker/Dockerfile.hcmi . | |
| # - name: Run HCMI Container | |
| # run: docker run --name hcmi-container hcmi-builder | |
| # - name: Copy files from HCMI Container | |
| # run: | | |
| # mkdir hcmi-files | |
| # for file in hcmi_samples.csv hcmi_transcriptomics.csv hcmi_copy_number.csv hcmi_mutations.csv; do | |
| # docker cp hcmi-container:/usr/src/app/$file hcmi-files/$file | |
| # done | |
| # - name: Get HCMI container logs | |
| # run: docker logs hcmi-container | |
| # # - name: dummy hcmi | |
| # # run: | | |
| # # mkdir hcmi-files | |
| # # echo "This is some sample text." > hcmi-files/d.txt | |
| # # echo "Another line of text." > hcmi-files/c.gz | |
| # - name: Upload artifacts for HCMI | |
| # uses: actions/upload-artifact@v2 | |
| # with: | |
| # name: hcmi-files | |
| # path: hcmi-files | |
| # build-beataml: | |
| # if: github.actor != 'github-actions[bot]' | |
| # runs-on: ubuntu-20.04 | |
| # environment: build | |
| # steps: | |
| # - name: Checkout code BeatAML | |
| # uses: actions/checkout@v2 | |
| # - name: Build BeatAML Image | |
| # run: docker build -t beataml-builder -f build/docker/Dockerfile.beataml . | |
| # - name: Run BeatAML Container | |
| # run: docker run --name beataml-container -e SYNAPSE_TOKEN=${{ secrets.SYNAPSE_TOKEN_SECRET }} beataml-builder | |
| # - name: Copy files from BeatAML Container | |
| # run: | | |
| # mkdir beataml-files | |
| # for file in beataml_samples.csv beataml_transcriptomics.csv beataml_proteomics.csv beataml_mutations.csv beataml_drugs.tsv beataml_experiments.csv; do | |
| # docker cp beataml-container:/usr/src/app/$file beataml-files/$file | |
| # done | |
| # - name: Get BeatAML container logs | |
| # run: docker logs beataml-container | |
| # - name: Upload artifact for BeatAML | |
| # uses: actions/upload-artifact@v2 | |
| # with: | |
| # name: beataml-files | |
| # path: beataml-files | |
| data-visualization: | |
| if: github.actor != 'github-actions[bot]' | |
| # needs: [build-hcmi, build-beataml] | |
| environment: build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install R packages | |
| run: | | |
| R -e "install.packages('RColorBrewer', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| R -e "install.packages('circlize', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| R -e "install.packages('dplyr', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| R -e "install.packages('readr', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| R -e "install.packages('tools', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| R -e "install.packages('ggplot2', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| R -e "install.packages('reshape2', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| R -e "install.packages('ComplexUpset', dependencies=TRUE, repos='http://cran.rstudio.com/')" | |
| - name: checkout repo content | |
| uses: actions/checkout@v2 | |
| # - name: Download artifacts from HCMI | |
| # uses: actions/download-artifact@v2 | |
| # with: | |
| # name: hcmi-files | |
| # - name: Download artifacts from BeatAML | |
| # uses: actions/download-artifact@v2 | |
| # with: | |
| # name: beataml-files | |
| - name: Install coderdata and skip build steps | |
| run: pip install coderdata | |
| # - name: Download cptac data from coder data | |
| # run: coderdata download --prefix cptac | |
| # - name: Download cell_line data from coder data | |
| # run: coderdata download --prefix cell_line | |
| - name: Download all data from coder data | |
| run: coderdata download | |
| - name: Create all-files directory | |
| run: mkdir all-files | |
| - name: List files cwd | |
| run: ls -lah | |
| - name: List files dataSummary dir | |
| run: ls -lah dataSummary | |
| - name: Run Visualization01 | |
| if: success() || failure() | |
| run: Rscript dataSummary/visualization01.R | |
| # - name: Run Visualization02 | |
| # if: success() || failure() | |
| # run: Rscript dataSummary/visualization02.R | |
| - name: setup data-vis dir | |
| if: success() || failure() | |
| run: | | |
| mkdir -p data-vis | |
| rsync -av --remove-source-files --include='*.png' --include='*.pdf' --include='*table.csv' --exclude='*' . data-vis/ | |
| - name: Upload artifacts | |
| if: success() || failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: data-vis | |
| path: data-vis | |
| data-visualization-save-to-docs: | |
| if: github.actor != 'github-actions[bot]' | |
| needs: [data-visualization] | |
| environment: build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Download artifacts from data-vis | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: data-vis | |
| - name: List files cwd | |
| run: ls -lah | |
| - name: List files .. | |
| run: ls -lah .. | |
| - name: List files all | |
| run: ls -lah * | |
| - name: Move files to docs directory | |
| run: | | |
| mkdir -p data-vis | |
| rsync -av --remove-source-files --include='*.png' --include='*.pdf' --include='*table.csv' --exclude='*' . docs/ | |
| - name: List files in docs after moving | |
| run: ls -lah docs | |
| - name: List files in local after moving | |
| run: ls -lah | |
| - name: Setup Git config | |
| run: | | |
| git config user.name "jjacobson95" | |
| git config user.email "[email protected]" | |
| - name: Commit and push changes | |
| run: | | |
| git pull | |
| git add -f docs/* | |
| git status | |
| git commit -m "Add data visualization artifacts to docs" | |
| git push | |
| # upload-to-figshare: | |
| # if: github.actor != 'github-actions[bot]' | |
| # # needs: [build-hcmi, build-beataml] | |
| # environment: build | |
| # runs-on: ubuntu-20.04 | |
| # steps: | |
| # - name: checkout repo content | |
| # uses: actions/checkout@v2 | |
| # - name: Download artifacts from HCMI | |
| # uses: actions/download-artifact@v2 | |
| # with: | |
| # name: hcmi-files | |
| # - name: Download artifacts from BeatAML | |
| # uses: actions/download-artifact@v2 | |
| # with: | |
| # name: beataml-files | |
| # - name: Create all-files directory | |
| # run: mkdir all-files | |
| # - name: List files cwd | |
| # run: ls -lah | |
| # - name: Move files to all-files | |
| # run: | | |
| # rsync -av --remove-source-files --include='*.csv' --include='*.tsv' --include='*.gz' --exclude='*' . all-files/ | |
| # - name: gzip all files in all-files | |
| # run: gzip all-files/* | |
| # - name: gunzip all samples files in all-files | |
| # run: gunzip all-files/*samples* | |
| # - name: List files in all-files | |
| # run: ls -lah all-files/ | |
| # - name: Upload to Figshare | |
| # # This can be updated to trigger with tag releases. | |
| # # run: python scripts/push_to_figshare.py --directory all-files --title "CODERData${{ github.event.release.tag_name }}" --token ${{ secrets.FIGSHARE_TOKEN_SECRET }} -p False | |
| # #This is a short term alternative. Links to branch. Not as pretty but okay for now. | |
| # #To do: Extract version number from setup.py and run there. This can occur after merge with package dev branch. | |
| # run: python scripts/push_to_figshare.py --directory all-files --title "CODERData${{ github.ref }}" --token ${{ secrets.FIGSHARE_TOKEN_SECRET }} --project_id 189342 --publish | |
| # - name: List files in all-files | |
| # run: ls -lah all-files/ | |
| # - name: Setup Git config | |
| # run: | | |
| # git config user.name "jjacobson95" | |
| # git config user.email "[email protected]" | |
| # - name: Commit and push changes | |
| # run: | | |
| # mv figshare_latest.yml docs | |
| # git pull | |
| # git add docs | |
| # git commit -m "Add figshare stats to docs" | |
| # git push |