Add requests import and improve logging formatting #5

	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

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