Export BugSigDB #13089
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| on: | |
| schedule: | |
| - cron: "55 * * * *" # UTC Time | |
| workflow_dispatch: | |
| name: Export BugSigDB | |
| jobs: | |
| export-bugsigdb: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:RELEASE_3_19 | |
| steps: | |
| - name: Checkout BugSigDBExports | |
| uses: actions/checkout@v3 | |
| with: | |
| path: BugSigDBExports | |
| - name: Install BugSigDBExports dependencies | |
| run: | | |
| Rscript -e "install.packages(c('rvest', 'readr', 'plyr', 'BiocFileCache', 'R.utils'))" | |
| - name: Install bugsigdbr | |
| run: | | |
| Rscript -e "BiocManager::install('bugsigdbr')" | |
| - name: Setup git config | |
| run: | | |
| cd $GITHUB_WORKSPACE/BugSigDBExports # Because we need to be in a repository | |
| git config user.name "GitHub Actions Bot" | |
| git config user.email "[email protected]" | |
| - name: Export BugSigDB | |
| run: | | |
| BUGSIGDB_TIMESTAMP="$(date -u +%Y-%m-%d_%H:%M_UTC)" | |
| echo "BUGSIGDB_TIMESTAMP=$BUGSIGDB_TIMESTAMP" >> $GITHUB_ENV | |
| echo $BUGSIGDB_TIMESTAMP | |
| Rscript $GITHUB_WORKSPACE/BugSigDBExports/inst/scripts/dump_release.R $BUGSIGDB_TIMESTAMP $GITHUB_WORKSPACE/BugSigDBExports | |
| mv *csv $GITHUB_WORKSPACE/BugSigDBExports | |
| timeout-minutes: 10 | |
| - name: Track file growth | |
| run: | | |
| library(R.utils) | |
| github_workspace <- Sys.getenv("GITHUB_WORKSPACE") | |
| setwd(file.path(github_workspace, "BugSigDBExports")) | |
| bugsigdb_timestamp <- Sys.getenv("BUGSIGDB_TIMESTAMP") | |
| number_of_lines <- c("timestamp" = bugsigdb_timestamp) | |
| files <- sort(list.files(pattern=".(csv|gmt)")) | |
| files <- files[files != "file_size.csv"] | |
| for (a_file in files) { | |
| number_of_lines[a_file] <- countLines(a_file)[1] | |
| } | |
| write.table(as.matrix(t(number_of_lines)), | |
| "file_size.csv", | |
| append = TRUE, | |
| col.names = FALSE, | |
| row.names = FALSE) | |
| shell: Rscript {0} | |
| - name: Commit Exports | |
| run: | | |
| cd $GITHUB_WORKSPACE/BugSigDBExports | |
| for export in `find . -type f -iname \*.gmt -o -iname \*.csv` | |
| do | |
| export=$(echo $export | sed 's/\.\///g') | |
| git_diff=$(git diff --numstat $export | sed -e 's/\t//g') | |
| if [ "$git_diff" = "11$export" -o "$git_diff" = "" ]; then | |
| echo "No changes to commit for $export" | |
| else | |
| echo "Add changes for $export" | |
| git add $export | |
| fi | |
| done | |
| echo "Check if any file contents have added to the index" | |
| has_updates=$(git diff --cached --shortstat) | |
| if [ -n "$has_updates" ]; then | |
| git add file_size.csv | |
| git commit -m "Hourly export update" | |
| git push origin devel | |
| else | |
| echo "No content changes to commit" | |
| fi |