fix filename #18
Workflow file for this run
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| name: Check KEGG API for new records | |
| on: | |
| #schedule: | |
| # - cron: '0 0 1 * *' # Runs at midnight on the 1st of every month | |
| push: | |
| branches: | |
| - code-improvements | |
| jobs: | |
| check-api: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.x' | |
| - name: Get current date | |
| id: date | |
| run: | | |
| echo "BRANCH_DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: Check API for new records | |
| run: python kegg_pathways_completeness/bin/update_pathways_data/get_modules_list.py | |
| - name: Check if new_modules.txt exists | |
| id: check-file | |
| run: | | |
| if [[ -f "new_modules.txt" ]]; then | |
| echo "file_exists=true" >> $GITHUB_ENV | |
| else | |
| echo "file_exists=false" >> $GITHUB_ENV | |
| fi | |
| - name: Add new modules info into existing and sort | |
| if: env.file_exists == 'true' | |
| run: | | |
| cat kegg_pathways_completeness/pathways_data/all_pathways.txt pathways/all_pathways.txt | sort > kegg_pathways_completeness/pathways_data/all_pathways_sorted.txt | |
| mv kegg_pathways_completeness/pathways_data/all_pathways_sorted.txt kegg_pathways_completeness/pathways_data/all_pathways.txt | |
| cat kegg_pathways_completeness/pathways_data/all_pathways_class.txt pathways/all_pathways_class.txt | sort > kegg_pathways_completeness/pathways_data/all_pathways_class_sorted.txt | |
| mv kegg_pathways_completeness/pathways_data/all_pathways_class_sorted.txt kegg_pathways_completeness/pathways_data/all_pathways_class.txt | |
| cat kegg_pathways_completeness/pathways_data/all_pathways_names.txt pathways/all_pathways_names.txt | sort > kegg_pathways_completeness/pathways_data/all_pathways_names_sorted.txt | |
| mv kegg_pathways_completeness/pathways_data/all_pathways_names_sorted.txt kegg_pathways_completeness/pathways_data/all_pathways_names.txt | |
| - name: Regenerate graphs and move old to updates folder | |
| if: env.file_exists == 'true' | |
| run: | | |
| python3 kegg_pathways_completeness/bin/make_graphs/make_graphs.py -i kegg_pathways_completeness/pathways_data/all_pathways.txt | |
| mv kegg_pathways_completeness/graphs/graphs.pkl kegg_pathways_completeness/graphs/updates/graphs-{{ env.BRANCH_DATE }}.pkl | |
| mv graphs.pkl kegg_pathways_completeness/graphs/graphs.pkl | |
| - name: Generate plots for updates modules | |
| if: env.file_exists == 'true' | |
| run: | | |
| python3 kegg_pathways_completeness/bin/make_graphs/get_dot.py -g kegg_pathways_completeness/graphs/graphs.pkl -l kegg_pathways_completeness/pathways_data/all_pathways.txt | |
| python3 kegg_pathways_completeness/bin/make_graphs/plot.py -l kegg_pathways_completeness/pathways_data/all_pathways.txt | |
| mv png dots kegg_pathways_completeness/graphs/ | |
| - name: Count number of lines in all_pathways.txt | |
| if: env.file_exists == 'true' | |
| id: line_count | |
| run: | | |
| lines=$(wc -l < kegg_pathways_completeness/pathways_data/all_pathways.txt) | |
| echo "line_count=$lines" >> $GITHUB_ENV | |
| - name: Update README | |
| if: env.file_exists == 'true' | |
| run: | | |
| sed -i "s/The current version of this tool has .* KEGG modules (updated .*)./The current version of this tool has ${line_count} KEGG modules (updated ${BRANCH_DATE})./" README.md | |
| - name: Commit and push changes | |
| if: env.file_exists == 'true' | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| git config pull.rebase false | |
| git pull origin master --allow-unrelated-histories | |
| git checkout -b changes-${{ env.BRANCH_DATE }} | |
| git add kegg_pathways_completeness/pathways_data/all_pathways.txt | |
| git add kegg_pathways_completeness/pathways_data/all_pathways_class.txt | |
| git add kegg_pathways_completeness/pathways_data/all_pathways_name.txt | |
| git add kegg_pathways_completeness/graphs/dots | |
| git add kegg_pathways_completeness/graphs/png | |
| git add kegg_pathways_completeness/graphs/graphs.pkl | |
| git add README.md | |
| git commit -m "Add updated files" | |
| git push origin HEAD:changes-${{ env.BRANCH_DATE }} | |
| - name: Create Pull Request | |
| if: env.file_exists == 'true' | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: changes-${{ env.BRANCH_DATE }} | |
| base: master | |
| title: "Automated update of new modules" | |
| body: "This PR was created automatically by the GitHub Action." |