barcode update #704
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| name: barcode update | |
| on: | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: '30 0 * * *' | |
| jobs: | |
| testsuite: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@main | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: update | |
| shell: bash -l {0} | |
| run: | | |
| wget https://raw.githubusercontent.com/andersen-lab/Freyja/main/freyja/data/lineage_mutations.json -O lineage_mutations.json | |
| wget https://raw.githubusercontent.com/andersen-lab/Freyja/main/freyja/data/usher_barcodes.feather -O usher_barcodes.feather | |
| wget https://raw.githubusercontent.com/andersen-lab/Freyja/main/freyja/data/curated_lineages.json -O curated_lineages.json | |
| wget https://raw.githubusercontent.com/andersen-lab/Freyja/main/freyja/data/lineages.yml -O lineages.yml | |
| - name: update history if output is different | |
| run: | | |
| echo "running git diff, committing if different" | |
| if [[($(git status usher_barcodes.feather --porcelain | wc -c) -ne 0)]]; then | |
| echo "changes were made, updating barcodes" | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| timestamp=$(date +"%m_%d_%Y-%H-%M") | |
| cp usher_barcodes.feather history_barcodes/usher_barcodes${timestamp}.feather | |
| cp curated_lineages.json history_metadata/curated_lineages${timestamp}.json | |
| cp lineages.yml history_lineage_hierarchy/lineages${timestamp}.yml | |
| # if [[($(git status lineage_mutations.json --porcelain | wc -c) -ne 0)]]; then | |
| # git diff -U0 lineage_mutations.json | grep '^[+-]' | grep -Ev '^(--- a/|\+\+\+ b/)' > history_barcode_diffs/barcode_diff${timestamp}.txt | |
| # git add history_barcode_diffs/barcode_diff${timestamp}.txt | |
| # fi | |
| git add usher_barcodes.feather | |
| pip install pandas pyarrow | |
| python update_csv.py | |
| git add usher_barcodes.csv | |
| git add curated_lineages.json | |
| git add lineages.yml | |
| git add lineage_mutations.json | |
| git add history_barcodes/usher_barcodes${timestamp}.feather | |
| git add history_metadata/curated_lineages${timestamp}.json | |
| git add history_lineage_hierarchy/lineages${timestamp}.yml | |
| git commit -m "updating historic data" | |
| git push origin main | |
| else | |
| echo "no changes were made, doing nothing." | |
| fi; |