import data #104
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| name: import data | |
| on: | |
| schedule: | |
| - cron: "0 0 * * 0" | |
| workflow_dispatch: | |
| jobs: | |
| biotools: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_hash: ${{ steps.commit-and-push-biotools.outputs.commit_hash }} | |
| steps: | |
| - name: checkout contents repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: delete previous import branch | |
| run: | | |
| branch_name="biotools-import-branch" | |
| # Check if the branch exists on the remote repository | |
| if git rev-parse --verify --quiet "origin/$branch_name"; then | |
| # The branch exists, so it can be safely deleted | |
| git push origin --delete "$branch_name" | |
| echo "Branch $branch_name has been deleted." | |
| else | |
| # The branch does not exist | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| - name: Create and checkout feature branch | |
| run: git checkout -b biotools-import-branch | |
| - name: import bio.tools data from server | |
| uses: research-software-ecosystem/utils/biotools-import@main | |
| with: | |
| repo-user: ${{ secrets.GITHUB_USER }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit and Push Changes | |
| id: commit-and-push-biotools | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: Tools Platform Ecosystem bot | |
| commit_user_email: tpe-bot@github.com | |
| commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com> | |
| commit_message: import bio.tools data on $(date) | |
| branch: biotools-import-branch | |
| create_branch: true | |
| openebench: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_hash: ${{ steps.commit-and-push-openebench.outputs.commit_hash }} | |
| steps: | |
| - name: checkout contents repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: delete previous import branch | |
| run: | | |
| branch_name="openebench-import-branch" | |
| # Check if the branch exists on the remote repository | |
| if git rev-parse --verify --quiet "origin/$branch_name"; then | |
| # The branch exists, so it can be safely deleted | |
| git push origin --delete "$branch_name" | |
| echo "Branch $branch_name has been deleted." | |
| else | |
| # The branch does not exist | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| - name: Create and checkout feature branch | |
| run: git checkout -b openebench-import-branch | |
| - name: import OpenEBench data from server | |
| uses: research-software-ecosystem/utils/openebench-import@main | |
| with: | |
| repo-user: ${{ secrets.GITHUB_USER }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit and Push Changes | |
| id: commit-and-push-openebench | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: Tools Platform Ecosystem bot | |
| commit_user_email: tpe-bot@github.com | |
| commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com> | |
| commit_message: import OpenEBench data on $(date) | |
| branch: openebench-import-branch | |
| create_branch: true | |
| bioconda: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_hash: ${{ steps.commit-and-push-bioconda.outputs.commit_hash }} | |
| steps: | |
| - name: checkout contents repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: delete previous import branch | |
| run: | | |
| branch_name="bioconda-import-branch" | |
| # Check if the branch exists on the remote repository | |
| if git rev-parse --verify --quiet "origin/$branch_name"; then | |
| # The branch exists, so it can be safely deleted | |
| git push origin --delete "$branch_name" | |
| echo "Branch $branch_name has been deleted." | |
| else | |
| # The branch does not exist | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| - name: Create and checkout feature branch | |
| run: git checkout -b bioconda-import-branch | |
| - name: import bioconda data from server | |
| uses: research-software-ecosystem/utils/bioconda-import@main | |
| with: | |
| repo-user: ${{ secrets.GITHUB_USER }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit and Push Changes | |
| id: commit-and-push-bioconda | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: Tools Platform Ecosystem bot | |
| commit_user_email: tpe-bot@github.com | |
| commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com> | |
| commit_message: import bioconda data on $(date) | |
| branch: bioconda-import-branch | |
| create_branch: true | |
| biii: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_hash: ${{ steps.commit-and-push-biii.outputs.commit_hash }} | |
| steps: | |
| - name: checkout contents repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: delete previous import branch | |
| run: | | |
| branch_name="biii-import-branch" | |
| # Check if the branch exists on the remote repository | |
| if git rev-parse --verify --quiet "origin/$branch_name"; then | |
| # The branch exists, so it can be safely deleted | |
| git push origin --delete "$branch_name" | |
| echo "Branch $branch_name has been deleted." | |
| else | |
| # The branch does not exist | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| - name: Create and checkout feature branch | |
| run: git checkout -b biii-import-branch | |
| - name: import biii data from server | |
| uses: research-software-ecosystem/utils/biii-import@main | |
| with: | |
| repo-user: ${{ secrets.GITHUB_USER }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit and Push Changes | |
| id: commit-and-push-biii | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: Tools Platform Ecosystem bot | |
| commit_user_email: tpe-bot@github.com | |
| commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com> | |
| branch: biii-import-branch | |
| create_branch: true | |
| biocontainers: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_hash: ${{ steps.commit-and-push-biocontainers.outputs.commit_hash }} | |
| steps: | |
| - name: checkout contents repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: delete previous import branch | |
| run: | | |
| branch_name="biocontainers-import-branch" | |
| # Check if the branch exists on the remote repository | |
| if git rev-parse --verify --quiet "origin/$branch_name"; then | |
| # The branch exists, so it can be safely deleted | |
| git push origin --delete "$branch_name" | |
| echo "Branch $branch_name has been deleted." | |
| else | |
| # The branch does not exist | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| - name: Create and checkout feature branch | |
| run: git checkout -b biocontainers-import-branch | |
| - name: import biocontainers data from server | |
| uses: research-software-ecosystem/utils/biocontainers-import@main | |
| with: | |
| repo-user: ${{ secrets.GITHUB_USER }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit and Push Changes | |
| id: commit-and-push-biocontainers | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: Tools Platform Ecosystem bot | |
| commit_user_email: tpe-bot@github.com | |
| commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com> | |
| commit_message: import biocontainers data on $(date) | |
| branch: biocontainers-import-branch | |
| create_branch: true | |
| galaxytool: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_hash: ${{ steps.commit-and-push-galaxytool.outputs.commit_hash }} | |
| steps: | |
| - name: checkout contents repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: delete previous import branch | |
| run: | | |
| branch_name="galaxytool-import-branch" | |
| # Check if the branch exists on the remote repository | |
| if git rev-parse --verify --quiet "origin/$branch_name"; then | |
| # The branch exists, so it can be safely deleted | |
| git push origin --delete "$branch_name" | |
| echo "Branch $branch_name has been deleted." | |
| else | |
| # The branch does not exist | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| - name: Create and checkout feature branch | |
| run: git checkout -b galaxytool-import-branch | |
| - name: import galaxy tool data from server | |
| uses: research-software-ecosystem/utils/galaxytool-import@main | |
| with: | |
| repo-user: ${{ secrets.GITHUB_USER }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit and Push Changes | |
| id: commit-and-push-galaxytool | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: Tools Platform Ecosystem bot | |
| commit_user_email: tpe-bot@github.com | |
| commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com> | |
| commit_message: import galaxy tools data on $(date) | |
| branch: galaxytool-import-branch | |
| create_branch: true | |
| debian-med: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_hash: ${{ steps.commit-and-push-debianmed.outputs.commit_hash }} | |
| steps: | |
| - name: checkout contents repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| - name: delete previous import branch | |
| run: | | |
| branch_name="debianmed-import-branch" | |
| # Check if the branch exists on the remote repository | |
| if git rev-parse --verify --quiet "origin/$branch_name"; then | |
| # The branch exists, so it can be safely deleted | |
| git push origin --delete "$branch_name" | |
| echo "Branch $branch_name has been deleted." | |
| else | |
| # The branch does not exist | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| - name: Create and checkout feature branch | |
| run: git checkout -b debianmed-import-branch | |
| - name: import Debian Med data | |
| uses: research-software-ecosystem/utils/debian-med-import@main | |
| with: | |
| repo-user: ${{ secrets.GITHUB_USER }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit and Push Changes | |
| id: commit-and-push-debianmed | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: Tools Platform Ecosystem bot | |
| commit_user_email: tpe-bot@github.com | |
| commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com> | |
| commit_message: import Debian Med tools data on $(date) | |
| branch: debianmed-import-branch | |
| create_branch: true | |
| merge: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - biotools | |
| - openebench | |
| - bioconda | |
| - biii | |
| - biocontainers | |
| - galaxytool | |
| - debian-med | |
| if: always() | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Merge feature branches | |
| run: | | |
| git config --local user.email "tpe-bot@github.com" | |
| git config --local user.name "Tools Platform Ecosystem bot" | |
| merge_branch_if_exists() { | |
| local branch_name="$1" | |
| # Check if the branch exists on the remote repository | |
| if git ls-remote --exit-code --heads origin "$branch_name" &>/dev/null; then | |
| # The branch exists on the remote, so it can be safely merged | |
| git fetch origin "$branch_name" | |
| git merge "origin/$branch_name" | |
| echo "Merged $branch_name into the current branch." | |
| else | |
| # The branch does not exist on the remote | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| } | |
| merge_branch_if_exists "biotools-import-branch" | |
| merge_branch_if_exists "openebench-import-branch" | |
| merge_branch_if_exists "bioconda-import-branch" | |
| merge_branch_if_exists "biii-import-branch" | |
| merge_branch_if_exists "biocontainers-import-branch" | |
| merge_branch_if_exists "galaxytool-import-branch" | |
| merge_branch_if_exists "debianmed-import-branch" | |
| git push origin master | |
| clean-branches: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - merge | |
| if: always() | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Delete feature branches | |
| run: | | |
| git config --local user.email "tpe-bot@github.com" | |
| git config --local user.name "Tools Platform Ecosystem bot" | |
| delete_branch_if_exists() { | |
| local branch_name="$1" | |
| # Check if the branch exists on the remote repository | |
| if git ls-remote --exit-code --heads origin "$branch_name" &>/dev/null; then | |
| # The branch exists on the remote, so it can be deleted | |
| git push origin --delete "$branch_name" | |
| echo "Deleted $branch_name into the current branch." | |
| else | |
| # The branch does not exist on the remote | |
| echo "Branch $branch_name does not exist on the remote repository." | |
| fi | |
| } | |
| delete_branch_if_exists "biotools-import-branch" | |
| delete_branch_if_exists "openebench-import-branch" | |
| delete_branch_if_exists "bioconda-import-branch" | |
| delete_branch_if_exists "biii-import-branch" | |
| delete_branch_if_exists "biocontainers-import-branch" | |
| delete_branch_if_exists "galaxytool-import-branch" | |
| delete_branch_if_exists "debianmed-import-branch" |