def test_process_raw_metrics_with_no_path():
app.mock_app()
metrics = {"metric": "1"}
mapping = [{"key": "metric"}]
nose.assert_equal(
met.process_raw_metrics(app.mock_app(), metrics, mapping),
{"metric": 1})
def test_process_raw_metrics_with_only_path():
app.mock_app()
metrics = {"old_name": 1}
mapping = [{"key": "new_name", "path": "old_name"}]
nose.assert_equal(
met.process_raw_metrics(app.mock_app(), metrics, mapping),
{"new_name": 1})
def test_process_raw_metrics_with_unmappable_value():
metrics = {"old_name": "unmappable_value"}
mapping = [{
"key": "new_name",
"path": "old_name",
"lift": ["parse_quast_value"]
}]
parsed = met.process_raw_metrics(app.mock_app(), metrics, mapping)
nose.assert_equal(parsed, {})
def collect_metrics(self, app):
path = fs.get_task_path_file_without_name(app,
'outputs/assembly_metrics')
with open(path, 'r') as f:
raw_metrics = list(csv.reader(f, delimiter='\t'))
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, dict(raw_metrics), mapping)
def test_process_raw_metrics_with_lift():
metrics = {"old_name": "-"}
mapping = [{
"key": "new_name",
"path": "old_name",
"lift": ["parse_quast_value"]
}]
parsed = met.process_raw_metrics(app.mock_app(), metrics, mapping)
nose.assert_equal(parsed, {"new_name": 0.0})
nose.assert_is_instance(parsed["new_name"], float)
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 test_process_raw_metrics_with_optional_missing_value():
metrics = {}
mapping = [{"key": "new_name", "path": "old_name", "optional": True}]
nose.assert_equal(
met.process_raw_metrics(app.mock_app(), metrics, mapping),
{"new_name": 0.0})
