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'))