1. Collect files for data release monthly #47
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| name: 1. Collect files for data release monthly | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "30 06 10 * *" | |
| jobs: | |
| collect-files: | |
| runs-on: ubuntu-latest | |
| name: Collect data release files | |
| env: | |
| RELDATE: $(date +"%Y%m%d") | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| persist-credentials: false | |
| token: ${{ secrets.PICOPAT2 }} | |
| path: wikipathways-data-release | |
| fetch-depth: 0 | |
| ref: main | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install jq | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y jq | |
| - name: Checkout Assets | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: wikipathways/wikipathways-assets | |
| path: wikipathways-assets | |
| fetch-depth: 0 | |
| ref: main | |
| - name: Make data release folders | |
| run: | | |
| mkdir -p "wikipathways-data-release/${{ env.RELDATE }}/gpml" | |
| mkdir -p "wikipathways-data-release/${{ env.RELDATE }}/svg" | |
| mkdir -p "wikipathways-data-release/${{ env.RELDATE }}/gmt" | |
| mkdir -p "wikipathways-data-release/${{ env.RELDATE }}/rdf" | |
| - name: Collect GPML, SVG, TSV and INFO files | |
| run: | | |
| OPINDEX=$(curl -s https://www.wikipathways.org/org-pathway-index.json | jq -c '.') | |
| for ORGANISM in $(echo $OPINDEX | jq -r '.organisms[] | @base64'); do | |
| ORGANISM_JSON=$(echo ${ORGANISM} | base64 --decode) | |
| LATIN=$(echo ${ORGANISM_JSON} | jq -r '.latin') | |
| echo "${LATIN}" | |
| TWO_LETTER_CODE=$(echo ${ORGANISM_JSON} | jq -r '.["two-letter-code"]') | |
| GPML_FOLDER="wikipathways-${{ env.RELDATE }}-gpml-${LATIN}" | |
| mkdir -p "wikipathways-data-release/${{ env.RELDATE }}/gpml/${GPML_FOLDER}" | |
| SVG_FOLDER="wikipathways-${{ env.RELDATE }}-svg-${LATIN}" | |
| mkdir -p "wikipathways-data-release/${{ env.RELDATE }}/svg/${SVG_FOLDER}" | |
| GMT_FOLDER="wikipathways-${{ env.RELDATE }}-gmt-${LATIN}" | |
| mkdir -p "wikipathways-data-release/${{ env.RELDATE }}/gmt/${GMT_FOLDER}" | |
| for PATHWAY in $(echo ${ORGANISM_JSON} | jq -r '.pathways[] | @base64'); do | |
| PATHWAY_JSON=$(echo ${PATHWAY} | base64 --decode) | |
| TITLE=$(echo ${PATHWAY_JSON} | jq -r '.title') | |
| WPID=$(echo ${PATHWAY_JSON} | jq -r '.wpid') | |
| echo "${WPID}" | |
| LAST_EDITED=$(echo ${PATHWAY_JSON} | jq -r '.["last-edited"]') | |
| GPML_FILE="${TWO_LETTER_CODE}_${TITLE}_${WPID}_${LAST_EDITED}.gpml" | |
| cp wikipathways-assets/pathways/${WPID}/${WPID}.gpml "wikipathways-data-release/${{ env.RELDATE }}/gpml/${GPML_FOLDER}/${GPML_FILE}" | |
| SVG_FILE="${TWO_LETTER_CODE}_${TITLE}_${WPID}_${LAST_EDITED}.svg" | |
| cp wikipathways-assets/pathways/${WPID}/${WPID}.svg "wikipathways-data-release/${{ env.RELDATE }}/svg/${SVG_FOLDER}/${SVG_FILE}" | |
| TSV_FILE="${WPID}.tsv" | |
| cp wikipathways-assets/pathways/${WPID}/${WPID}-datanodes.tsv "wikipathways-data-release/${{ env.RELDATE }}/gmt/${GMT_FOLDER}/${TSV_FILE}" | |
| INFO_FILE="wikipathways-data-release/${{ env.RELDATE }}/gmt/${GMT_FOLDER}/${WPID}.info" | |
| TITLE_GMT=$(echo ${TITLE} | sed 's/[^a-zA-Z0-9]\+/_/g') | |
| echo "title: ${TITLE_GMT}" > "${INFO_FILE}" | |
| echo "version: WikiPathways_${{ env.RELDATE }}" >> "${INFO_FILE}" | |
| echo "wpid: ${WPID}" >> "${INFO_FILE}" | |
| LATIN_GMT=$(echo ${LATIN} | sed 's/_\+/ /g') | |
| echo "latin: ${LATIN_GMT}" >> "${INFO_FILE}" | |
| echo "url: https://www.wikipathways.org/instance/${WPID}" >> "${INFO_FILE}" | |
| done | |
| echo "zip gpml" | |
| zip -j wikipathways-data-release/${{ env.RELDATE }}/gpml/${GPML_FOLDER}.zip wikipathways-data-release/${{ env.RELDATE }}/gpml/${GPML_FOLDER}/* | |
| echo "zip svg" | |
| zip -j wikipathways-data-release/${{ env.RELDATE }}/svg/${SVG_FOLDER}.zip wikipathways-data-release/${{ env.RELDATE }}/svg/${SVG_FOLDER}/* | |
| done | |
| - name: Install R packages | |
| run: | | |
| sudo apt-get install libcurl4-openssl-dev | |
| Rscript -e 'install.packages(c("tidyr","dplyr","magrittr","yaml","WikidataQueryServiceR","remotes"))' | |
| - name: Install rWikiPathways | |
| run: | | |
| remotes::install_cran("BiocManager") | |
| BiocManager::install("rWikiPathways", ask = FALSE) | |
| shell: Rscript {0} | |
| - name: Generate GMT files from TSV and temporary INFO | |
| run: | | |
| cp wikipathways-data-release/make-gmts.R wikipathways-data-release/${{ env.RELDATE }}/gmt/. | |
| cd wikipathways-data-release/${{ env.RELDATE }}/gmt | |
| Rscript -e "source('make-gmts.R')" | |
| cd ../../.. | |
| - name: Checkout Jekyll | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: wikipathways/wikipathways.github.io | |
| path: wikipathways.github.io | |
| fetch-depth: 0 | |
| ref: main | |
| - name: Generate Authors RDF | |
| if: true | |
| run: | | |
| Rscript -e "source('wikipathways-data-release/make-authors-rdf.R')" | |
| ls -l | |
| mv wikipathways-${{ env.RELDATE }}-rdf-authors.zip wikipathways-data-release/${{ env.RELDATE }}/rdf/. | |
| - name: Collect RDF and TTL files | |
| if: false | |
| run: | | |
| wget -O wikipathways-data-release/${{ env.RELDATE }}/rdf/wikipathways-${{ env.RELDATE }}-rdf-gpml.zip https://jenkins.bigcat.unimaas.nl/job/WikiPathways%20RDF%20-%20Monthly/lastSuccessfulBuild/artifact/WP2RDF/output/wikipathways-rdf-gpml.zip | |
| wget -O wikipathways-data-release/${{ env.RELDATE }}/rdf/wikipathways-${{ env.RELDATE }}-rdf-wp.zip https://jenkins.bigcat.unimaas.nl/job/WikiPathways%20RDF%20-%20Monthly/lastSuccessfulBuild/artifact/WP2RDF/output/wikipathways-rdf-wp.zip | |
| wget -O wikipathways-data-release/${{ env.RELDATE }}/rdf/wikipathways-${{ env.RELDATE }}-rdf-void.ttl https://jenkins.bigcat.unimaas.nl/job/WikiPathways%20RDF%20-%20Monthly/lastSuccessfulBuild/artifact/WP2RDF/output/void_for_data.wp.org.ttl | |
| - name: Replace current | |
| run: | | |
| rm -rf wikipathways-data-release/current | |
| mkdir wikipathways-data-release/current | |
| cp -R wikipathways-data-release/${{ env.RELDATE }}/* wikipathways-data-release/current/. | |
| - name: Commit new files and remove oldest | |
| run: | | |
| git config --global user.name 'GitHub Action' | |
| git config --global user.email '[email protected]' | |
| cd wikipathways-data-release | |
| git add */*.{zip,gmt,ttl} | |
| RETIRE=$(ls -d * | grep -o '[0-9]\{8\}' | sort -n | head -1) | |
| git rm -r ${RETIRE} | |
| if git diff --exit-code --staged; then | |
| echo "No changes" | |
| else | |
| git commit -m 'New release of data files' | |
| fi | |
| - name: Push as user | |
| uses: ad-m/github-push-action@master | |
| with: | |
| directory: wikipathways-data-release | |
| github_token: ${{ secrets.PICOPAT2}} |