Add GitHub Action for Testing BLAST DB Updates on EC2

Configured workflow to test updating BLAST databases on EC2 instances. This includes setting up Python, mocking BLAST installation, and running the update script in test mode. Secrets are managed through GitHub Actions, and logs are uploaded for review.

.github/workflows/test_update_blast_db.yml

@@ -0,0 +1,59 @@
+name: Test Update BLAST DB on EC2
+
+on:
+ push:
+ branches: [ main, automation ]
+ workflow_dispatch:
+
+jobs:
+ update-blast-db:
+ runs-on: ubuntu-latest # This is compatible with act
+ steps:
+ - uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+
+ - name: Check working directory
+ run: |
+ echo "Current working directory: $(pwd)"
+ ls -la
+
+ - name: Set up Python
+ run: |
+ python3 -m pip install --upgrade pip
+ pip3 install poetry
+
+ - name: Install Poetry dependencies
+ run: |
+ poetry config virtualenvs.create false
+ poetry install --no-interaction --no-root
+
+ - name: Mock BLAST installation
+ run: |
+ echo "Mocking BLAST installation for testing"
+ mkdir -p $HOME/bin
+ echo -e '#!/bin/bash\necho "Mock blastn $@"' > $HOME/bin/blastn
+ chmod +x $HOME/bin/blastn
+ export PATH=$HOME/bin:$PATH
+
+ - name: Run BLAST DB update script (Test Mode)
+ env:
+ GITHUB_WEBHOOK_SECRET: ${{ secrets.GITHUB_WEBHOOK_SECRET }}
+ SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }}
+ AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+ AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+ run: |
+ echo "Running in test mode - mocking database update"
+ python3 src/create_blast_db.py \
+ --config_yaml config/blast_config.yaml \
+ --environment dev \
+ --update-slack \
+ --sync-s3 \
+ --dry-run
+
+ - name: Upload logs
+ uses: actions/upload-artifact@v3
+ if: always()
+ with:
+ name: blast-db-logs
+ path: logs/blast_db_creation.log