Hospital fixes #301
Workflow file for this run
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name: test_modules | |
on: | |
push: | |
branches: "**" | |
pull_request: | |
types: [opened, reopened, synchronize, closed] | |
branches: "**" | |
jobs: | |
test_map: | |
runs-on: ubuntu-latest | |
strategy: | |
max-parallel: 2 | |
matrix: | |
map_args: ["-d 'ENA' -f relecov_tools/schema/ena_schema.json", "-d 'GISAID' -f relecov_tools/schema/gisaid_schema.json"] | |
steps: | |
- name: Set up Python 3.9.16 | |
uses: actions/setup-python@v3 | |
with: | |
python-version: '3.9.16' | |
- name: Checkout code | |
uses: actions/checkout@v3 | |
with: | |
ref: ${{ github.event.pull_request.head.sha }} | |
fetch-depth: 0 | |
- name: Install package and dependencies | |
run: | | |
pip install -r requirements.txt | |
pip install . | |
- name: Run each module tests | |
run: | | |
relecov-tools map -j tests/data/map_validate/processed_metadata_lab_test.json -p relecov_tools/schema/relecov_schema.json ${{ matrix.map_args }} -o . | |
env: | |
OUTPUT_LOCATION: ${{ github.workspace }}/tests/ | |
- name: Upload output file | |
uses: actions/upload-artifact@v4 | |
with: | |
name: test-output | |
path: output.txt | |
test_all_modules: | |
runs-on: ubuntu-latest | |
strategy: | |
max-parallel: 3 | |
matrix: | |
modules: ["read-lab-metadata", "read-bioinfo-metadata", "validate"] | |
steps: | |
- name: Set up Python 3.9.16 | |
uses: actions/setup-python@v3 | |
with: | |
python-version: '3.9.16' | |
- name: Checkout code | |
uses: actions/checkout@v3 | |
with: | |
ref: ${{ github.event.pull_request.head.sha }} | |
fetch-depth: 0 | |
- name: Install package and dependencies | |
run: | | |
pip install -r requirements.txt | |
pip install . | |
- name: Run each module tests | |
run: | | |
if [ "${{ matrix.modules }}" == "read-lab-metadata" ]; then | |
relecov-tools read-lab-metadata -m tests/data/read_lab_metadata/metadata_lab_test.xlsx -s tests/data/read_lab_metadata/samples_data_test.json -o $OUTPUT_LOCATION | |
elif [ "${{ matrix.modules }}" == "validate" ]; then | |
relecov-tools validate -j tests/data/map_validate/processed_metadata_lab_test.json -s relecov_tools/schema/relecov_schema.json -m tests/data/map_validate/metadata_lab_test.xlsx -o $OUTPUT_LOCATION | |
fi | |
env: | |
OUTPUT_LOCATION: ${{ github.workspace }}/tests/ | |
- name: Upload output file | |
uses: actions/upload-artifact@v4 | |
with: | |
name: test-output | |
path: output.txt |