def test_get_runObj_miseq(self):
"""Return MiSeq run object."""
miseq_run = os.path.join(self.tmp_dir, '141124_ST-MISEQ1_01_AFCIDXX')
os.mkdir(miseq_run)
shutil.copy('data/runParameters_miseq.xml', os.path.join(miseq_run, 'runParameters.xml'))
got_miseq_run = an.get_runObj(miseq_run)
self.assertEqual(got_miseq_run.sequencer_type, 'MiSeq')
def test_get_runObj_novaseq(self):
"""Return NovaSeq run object."""
novaseq_run = os.path.join(self.tmp_dir, '141124_ST-NOVASEQ1_01_AFCIDXX')
os.mkdir(novaseq_run)
shutil.copy('data/runParameters_novaseq.xml', os.path.join(novaseq_run, 'RunParameters.xml'))
got_novaseq_run = an.get_runObj(novaseq_run)
self.assertEqual(got_novaseq_run.sequencer_type, 'NovaSeq')
def test__upload_to_statusdb(self, mock_statusdb):
"""Upload to statusdb."""
run = os.path.join(self.tmp_dir, '141124_ST-NOINDEX1_01_AFCIDYX')
os.mkdir(run)
shutil.copy('data/runParameters_minimal.xml', os.path.join(run, 'runParameters.xml'))
demux_dir = os.path.join(run, 'Demultiplexing', 'Stats')
os.makedirs(demux_dir)
shutil.copy('data/DemuxSummaryF1L1.txt', demux_dir)
reports_dir = os.path.join(run, 'Demultiplexing', 'Reports', 'html', 'FCIDYX', 'all', 'all', 'all')
os.makedirs(reports_dir)
shutil.copy('data/laneBarcode.html', (reports_dir))
shutil.copy('data/lane.html', (reports_dir))
noindex_run = an.get_runObj(run)
an._upload_to_statusdb(noindex_run)
mock_statusdb.update_doc.assert_called_once()
def test_get_runObj_hiseqx(self):
"""Return HiSeqX run object."""
got_run = an.get_runObj(self.completed)
self.assertEqual(got_run.sequencer_type, 'HiSeqX')