Fixed test 2. #3245
Workflow file for this run
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--- | |
name: TraceBase Tests | |
"on": [push, workflow_dispatch] | |
# Set permissions for GITHUB_TOKEN | |
# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs | |
permissions: read-all | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
services: | |
postgres: | |
image: postgres:13.4 | |
env: | |
POSTGRES_USER: postgres | |
POSTGRES_PASSWORD: postgres | |
POSTGRES_DB: tracebase | |
ports: | |
- 5432:5432 | |
# needed because the postgres container does not provide a healthcheck | |
options: >- | |
--health-cmd pg_isready --health-interval 10s | |
--health-timeout 5s --health-retries 5 | |
env: | |
DATABASE_NAME: tracebase | |
DATABASE_USER: postgres | |
DATABASE_PASSWORD: postgres | |
DATABASE_HOST: 127.0.0.1 | |
DATABASE_PORT: 5432 | |
DEBUG: true | |
CACHES: TEST_CACHES | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Set up Python 3.9 | |
uses: actions/setup-python@v1 | |
with: | |
python-version: 3.9 | |
- name: psycopg2 prerequisites | |
run: | | |
sudo apt-get update | |
sudo apt-get install python3-dev libpq-dev | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip wheel | |
pip install -r requirements.txt | |
- name: Check makemigrations are complete | |
run: python manage.py makemigrations --check --dry-run | |
- name: Run migrations | |
run: python manage.py migrate | |
- name: Make the cache table | |
run: python manage.py createcachetable | |
- name: Run tests | |
run: python manage.py test | |
- name: Load lcmethod fixtures | |
run: | | |
python manage.py loaddata \ | |
"DataRepo/fixtures/lc_methods.yaml" | |
- name: Load initial tissue records | |
run: | | |
python manage.py legacy_load_study \ | |
"DataRepo/data/tests/tissues/loading.yaml" | |
- name: Load example compounds | |
run: | | |
python manage.py load_compounds \ | |
--infile \ | |
"DataRepo/data/tests/compounds/consolidated_tracebase_compound_list.tsv" | |
- name: Load example sample table | |
run: | | |
python manage.py legacy_load_samples \ | |
"DataRepo/data/tests/small_obob2/obob_animal_sample_table.tsv" |