def test_make_control_report(self):
"""
Test that the report gets written proppa
"""
cmph5 = os.path.join(self.DATA_DIR, 'control_reads.cmp.h5')
csv = os.path.join(self.DATA_DIR, 'filtered_summary.csv')
make_control_report(cmph5, csv, 'foo.json', self._output_dir, 60,
False)
# deserialize report
s = None
with open(os.path.join(self._output_dir, 'foo.json'), 'r') as f:
s = json.load(f)
report = dict_to_report(s)
self.assertEqual(7, len(report.attributes))
for i in range(2):
pg = report.plotGroups[i]
self.assertFalse(os.path.isabs(pg.thumbnail))
self.assertTrue(
os.path.exists(os.path.join(self._output_dir, pg.thumbnail)))
p = pg.plots[0]
self.assertFalse(os.path.isabs(p.image))
self.assertTrue(
os.path.exists(os.path.join(self._output_dir, p.image)))
def test_make_control_report(self):
"""
Test that the report gets written proppa
"""
cmph5 = os.path.join(self.DATA_DIR, 'control_reads.cmp.h5')
csv = os.path.join(self.DATA_DIR, 'filtered_summary.csv')
make_control_report(cmph5, csv, 'foo.json',
self._output_dir, 60, False)
# deserialize report
s = None
with open(os.path.join(self._output_dir, 'foo.json'), 'r') as f:
s = json.load(f)
report = dict_to_report(s)
validate_report_complete(self, report)
self.assertEqual(7, len(report.attributes))
for i in range(2):
pg = report.plotGroups[i]
self.assertFalse(os.path.isabs(pg.thumbnail))
self.assertTrue(os.path.exists(
os.path.join(self._output_dir, pg.thumbnail)))
p = pg.plots[0]
self.assertFalse(os.path.isabs(p.image))
self.assertTrue(os.path.exists(
os.path.join(self._output_dir, p.image)))
def test_make_coverage_report_none_csv(self):
"""
csv cannot be null
"""
cmph5 = os.path.join(self.DATA_DIR, 'control_reads.cmp.h5')
with self.assertRaises(PbReportError):
make_control_report(cmph5, None, 'foo.json',
self._output_dir, '1', False)
def test_make_coverage_report_no_cmp_h5(self):
"""
cmp.h5 must exist
"""
csv = os.path.join(self.DATA_DIR, 'filtered_summary.csv')
with self.assertRaises(IOError):
make_control_report('foo', csv, 'foo.json',
self._output_dir, '1', False)
def test_make_coverage_report_none_cmp_h5(self):
"""
cmp.h5 cannot be null
"""
csv = os.path.join(self.DATA_DIR, 'filtered_summary.csv')
with self.assertRaises(PbReportError):
make_control_report(None, csv, 'foo.json',
self._output_dir, '1', False)
def test_make_coverage_report_no_csv(self):
"""
csv must exist
"""
cmph5 = os.path.join(self.DATA_DIR, 'control_reads.cmp.h5')
with self.assertRaises(IOError):
make_control_report(cmph5, 'foo', 'foo.json',
self._output_dir, '1', False)
def test_make_coverage_report_none_csv(self):
"""
csv cannot be null
"""
cmph5 = os.path.join(self.DATA_DIR, 'control_reads.cmp.h5')
with self.assertRaises(PbReportError):
make_control_report(cmph5, None, 'foo.json', self._output_dir, '1',
False)
def test_make_coverage_report_no_cmp_h5(self):
"""
cmp.h5 must exist
"""
csv = os.path.join(self.DATA_DIR, 'filtered_summary.csv')
with self.assertRaises(IOError):
make_control_report('foo', csv, 'foo.json', self._output_dir, '1',
False)
def test_make_coverage_report_none_cmp_h5(self):
"""
cmp.h5 cannot be null
"""
csv = os.path.join(self.DATA_DIR, 'filtered_summary.csv')
with self.assertRaises(PbReportError):
make_control_report(None, csv, 'foo.json', self._output_dir, '1',
False)
def test_make_coverage_report_no_csv(self):
"""
csv must exist
"""
cmph5 = os.path.join(self.DATA_DIR, 'control_reads.cmp.h5')
with self.assertRaises(IOError):
make_control_report(cmph5, 'foo', 'foo.json', self._output_dir,
'1', False)
def _create_control_report(self):
"""
Creates and returns a Control Report
"""
from pbreports.report.control import make_control_report
datadir = os.path.join(ROOT_DATA_DIR, 'control')
log.info('Creating Control report using datadir {d}'.format(d=datadir))
cmph5 = os.path.join(datadir, 'control_reads.cmp.h5')
csv = os.path.join(datadir, 'filtered_summary.csv')
report_json = 'control.json'
output_json = os.path.join(self._output_dir, report_json)
dpi = 60
dumpdata = False
make_control_report(cmph5, csv, report_json, self._output_dir, dpi,
dumpdata)
return self._deserialize_report(output_json)
def _create_control_report(self):
"""
Creates and returns a Control Report
"""
from pbreports.report.control import make_control_report
datadir = os.path.join(ROOT_DATA_DIR, 'control')
log.info('Creating Control report using datadir {d}'.format(d=datadir))
cmph5 = os.path.join(datadir, 'control_reads.cmp.h5')
csv = os.path.join(datadir, 'filtered_summary.csv')
report_json = 'control.json'
output_json = os.path.join(self._output_dir, report_json)
dpi = 60
dumpdata = False
make_control_report(
cmph5, csv, report_json, self._output_dir, dpi, dumpdata)
return self._deserialize_report(output_json)
def run_report(args):
return make_control_report(args.cntrCmpH5, args.csv,
args.report, args.output, args.dpi, args.dumpdata)
