Set tmp_dir: true for bismark tools
#996
Workflow file for this run
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| name: Check tool destinations and job configuration | |
| # # Controls when the action will run. Triggers the workflow on push or pull request | |
| # # events but only for the master branch | |
| on: | |
| pull_request: | |
| branches: [ master ] | |
| paths: | |
| - templates/galaxy/config/galaxy_job_conf.yml.j2 | |
| - files/galaxy/dynamic_job_rules/production/total_perspective_vortex/* # check | |
| # # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "build" | |
| build: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 # number of commits to fetch. 0 indicates all history for all branches and tags | |
| # Set up python environment | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| # Install python dependencies for check_files script | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install total-perspective-vortex==$TPV_VERSION pyyaml galaxy-app==23.1.4 galaxy-auth==23.1.4 galaxy-config==23.1.4 galaxy-data==23.1.4 galaxy-files==23.1.4 galaxy-job-execution==23.1.4 galaxy-job-metrics==23.1.4 galaxy-navigation==23.1.4 galaxy-objectstore==23.1.4 galaxy-tool-util==23.1.4 galaxy-tours==23.1.4 galaxy-util==23.1.4 galaxy-web-framework==23.1.4 galaxy-web-stack==23.1.4 | |
| env: | |
| TPV_VERSION: '2.3.2' | |
| - name: Check TPV files and job conf | |
| env: | |
| SETTING: github | |
| shell: python | |
| run: | | |
| """This code uses ansible to template out the jinja templates for tpv configs and job config, | |
| then runs the tpv linter on the resultant files.""" | |
| import re | |
| import subprocess | |
| import os | |
| import shutil | |
| working_dir = '.github/workflows/check_tpv_config' | |
| hosts_file = os.path.join(working_dir, 'hosts') | |
| playbook_file = os.path.join(working_dir, 'template_playbook.yml') | |
| files_dir = os.path.join(working_dir, 'files') | |
| templates_dir = os.path.join(working_dir, 'templates') | |
| os.mkdir(files_dir) | |
| os.mkdir(templates_dir) | |
| tpv_dir = 'files/galaxy/dynamic_job_rules/production/total_perspective_vortex' | |
| tpv_config_files = [os.path.join(tpv_dir, f) for f in os.listdir(tpv_dir)] | |
| job_conf_template = 'templates/galaxy/config/galaxy_job_conf.yml.j2' | |
| tpv_files = [] | |
| replace_patterns = ['\{\{\s?vault_\w+\s?\}\}', '\{\{\s?hostname\s?\}\}'] | |
| with open('.vault_pass.txt', 'w') as password_file: | |
| password_file.write('FalsePassword') | |
| def template_file(fname): | |
| output_fname = fname.replace(templates_dir, files_dir).replace('.j2', '') | |
| extra_vars = f'src={fname.replace(templates_dir+"/", "")} dest={os.path.realpath(output_fname)}' | |
| ansible_command = f'ansible-playbook -i {hosts_file} {playbook_file} --extra-vars \'{extra_vars}\'' | |
| try: | |
| subprocess.check_output(ansible_command, shell=True) | |
| except subprocess.CalledProcessError as e: | |
| print(e.output) | |
| raise Exception('Failed to template {os.path.basename(fname)}') | |
| return output_fname | |
| def sanitize_text(fname): | |
| """Replaces any references to vault variables with a constant string as the | |
| vault is not decrypted during tests""" | |
| with open(fname) as handle: | |
| text = handle.read() | |
| for rp in replace_patterns: | |
| text = re.sub(rp, 'text_replaced', text) | |
| with open(fname, 'w') as handle: | |
| handle.write(text) | |
| for t in tpv_config_files + [job_conf_template]: | |
| if t.endswith('.yml'): | |
| test_fname = os.path.join(files_dir, os.path.basename(t)) | |
| shutil.copy(t, test_fname) | |
| tpv_files.append(test_fname) | |
| elif t.endswith('.yml.j2'): | |
| test_fname = os.path.join(templates_dir, os.path.basename(t)) | |
| shutil.copy(t, test_fname) | |
| sanitize_text(test_fname) | |
| templated_file = template_file(test_fname) | |
| if 'tpv_dir' in t: | |
| tpv_files.append(templated_file) | |
| for t in tpv_files: | |
| subprocess.check_output(f'tpv lint {t}', shell=True) |