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import unittest
import json
import logging
from pbcommand.models.report import Report
from pbcommand.pb_io import load_report_from_json
_SERIALIZED_JSON_DIR = 'example-reports'
from base_utils import get_data_file_from_subdir
log = logging.getLogger(__name__)
def _to_report(name):
file_name = get_data_file_from_subdir(_SERIALIZED_JSON_DIR, name)
log.info("loading json report from {f}".format(f=file_name))
r = load_report_from_json(file_name)
return r
class TestReportModel(unittest.TestCase):
def test_from_simple_dict(self):
r = Report.from_simple_dict("pbcommand_test", {"n_reads": 50},
"pbcommand")
json_dict = json.loads(r.to_json())
self.assertEqual(json_dict['attributes'], [
{
"id": "pbcommand_test.pbcommand_n_reads",
"name": "n_reads",
"value": 50
},
])
def test_merge(self):
r = Report.merge([
Report.from_simple_dict("pbcommand_test",
{"n_reads": 50, "n_zmws": 10},
"pbcommand"),
Report.from_simple_dict("pbcommand_test",
{"n_reads": 250, "n_zmws": 50},
"pbcommand")])
attr = {a.id: a.value for a in r.attributes}
self.assertEqual(attr['pbcommand_n_reads'], 300)
self.assertEqual(attr['pbcommand_n_zmws'], 60)
def test_merge_tables(self):
names = ['laa_report1.json', 'laa_report2.json']
r = Report.merge([_to_report(names[0]), _to_report(names[1])])
table = r.tables[0]
self.assertEqual(len(table.columns), 7)
self.assertEqual(
[col.header for col in table.columns],
['BarcodeName', 'FastaName', 'CoarseCluster', 'Phase',
'TotalCoverage', 'SequenceLength', 'PredictedAccuracy'])
for col in table.columns:
self.assertEqual(len(col.values), 4)
if col.header == 'BarcodeName':
self.assertEqual(
col.values,
['Barcode1', 'Barcode2', 'Barcode4', 'Barcode3'])
elif col.header == 'FastaName':
self.assertEqual(
col.values,
['BarcodeFasta1', 'BarcodeFasta2', 'BarcodeFasta4',
'BarcodeFasta3'])
else:
self.assertEqual(col.values, [1, 2, 4, 3])
if __name__ == "__main__":
unittest.main()
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