def test_quast_complete_run_through(): app = app_helper.setup_app_state('quast', 'execute') image_helper.execute_image(app) file_helper.assert_is_file( fs.get_task_file_path(app, 'outputs/assembly_metrics/684281f282')) file_helper.assert_is_file( fs.get_task_file_path(app, 'outputs/container_log/86bbc499b0'))
def test_complete_run_through(): app = app_helper.setup_app_state('sra', 'inputs') image_helper.execute_image(app) file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/contig_fasta/01eb7cec61')) file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/container_runtime_metrics/metrics.json.gz')) file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/container_log/1099992390'))
def test_gaet_complete_run_through(): app = app_helper.setup_app_state('gaet', 'execute') image_helper.execute_image(app) file_helper.assert_is_file( fs.get_task_file_path(app, 'outputs/assembly_metrics/d70c163200')) file_helper.assert_is_file( fs.get_task_file_path(app, 'outputs/container_log/1661337965'))
def test_execution_with_empty_contig_file(): app = app_helper.setup_app_state('quast', 'execute') input_contigs = fs.get_task_file_path(app, "inputs/contig_fasta/de3d9f6d31.fa") open(input_contigs, "w").truncate() image_helper.execute_image(app) file_helper.assert_is_empty_directory( fs.get_task_file_path(app, 'outputs/assembly_metrics/')) file_helper.assert_is_empty_directory( fs.get_task_file_path(app, 'outputs/container_log/'))
def test_failing_image_with_no_outputs(): image = { "name": "bioboxes/crash-test-biobox", "sha256": "eaf1ab35314712db9d3fff0d265613629fe628ed9b058a9a4fe94424184f8c41", "task": "exit-1", "type": "short_read_assembler" } app = app_helper.setup_app_state('sra', 'inputs') app["task"]["image"] = image app_helper.rewrite_app_task(app) image_helper.execute_image(app) file_helper.assert_is_file( fs.get_task_file_path( app, 'outputs/container_runtime_metrics/metrics.json.gz'))