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_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_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_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_log_output():
image = {
"name": "bioboxes/crash-test-biobox",
"sha256":
"eaf1ab35314712db9d3fff0d265613629fe628ed9b058a9a4fe94424184f8c41",
"task": "exit-1-with-log",
"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'))
file_helper.assert_is_file(
fs.get_task_file_path(app, 'outputs/container_log/1d4dba8a3c'))
def test_copy_container_output_files_with_intermediates():
app = app_helper.setup_app_state('quast', 'intermediates')
input_files = {
'container_log': 'meta/log.txt',
'assembly_metrics': 'tmp/report.tsv'
}
output_files = ['assembly_metrics/63d2a18fa1', 'container_log/e0e8af3790']
fs.copy_container_output_files(app, input_files)
for f in output_files:
loc = fs.get_task_file_path(app, "outputs/" + f)
assert os.path.isfile(loc), "Output file should be copied: {}".format(
loc)
def collect_metrics(self, app):
import json, gzip
path = fs.get_task_file_path(
app, "outputs/container_runtime_metrics/metrics.json.gz")
if not os.path.isfile(path):
return {}
with gzip.open(path) as f:
raw_metrics = json.loads(f.read())
mapping_file = os.path.join('mappings',
self.metric_mapping_file(app) + '.yml')
mapping = yaml.safe_load(util.get_asset_file_contents(mapping_file))
return met.process_raw_metrics(app, raw_metrics, mapping)
def copy_output_files(app):
"""
Creates a list of source file paths and destination directory names. Copies each
the source file to destination directory.
"""
path = lambda x: os.path.abspath(fs.get_task_file_path(app, x))
output_files = {'container_log': path('meta/log.txt')}
if fs.biobox_yaml_exists(app):
tmp_files = funcy.walk_values(lambda x: path("tmp/" + x),
image_type(app).output_file_paths(app))
output_files = funcy.merge(output_files, tmp_files)
else:
msg = "No biobox.yaml file created, cannot find paths of any container generated files"
app['logger'].warn(msg)
fs.copy_container_output_files(app, output_files)
def test_copy_output_files():
app = app_helper.setup_app_state('sra', 'intermediates')
run.copy_output_files(app)
file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/container_log/e0e8af3790'))
file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/contig_fasta/de3d9f6d31'))
def test_output_file_paths():
app = app_helper.setup_app_state('sra', 'intermediates')
paths = task().output_file_paths(app)
for (_, f) in paths.items():
location = fs.get_task_file_path(app, "tmp/" + f)
nose.assert_true(os.path.isfile(location))
