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import.yaml
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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
merge:
runs-on: ubuntu-latest
needs:
- biotools
- openebench
- bioconda
- biii
- biocontainers
- galaxytool
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"
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"