def test_make_loading_report_with_sts_xml(self):
"""
Test the content of the loading report generated from a sts.xml
"""
sts_xml = data.getStats(0)
rpt = make_loading_report(sts_xml)
d = json.loads(rpt.to_json())
t = d["tables"][0]
c0 = t["columns"][0]
c1 = t["columns"][1]
c2 = t["columns"][2]
c3 = t["columns"][3]
c4 = t["columns"][4]
self.assertEqual("Collection Context", c0["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "collection_context", c0["id"])
self.assertEqual("NA", c0["values"][0])
self.assertEqual("Productive ZMWs", c1["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productive_zmws", c1["id"])
self.assertEqual(2876, c1["values"][0])
self.assertEqual("Productivity 0 (%)", c2["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productivity_0", c2["id"])
self.assertAlmostEqual(54.798, c2["values"][0], delta=0.0003)
self.assertEqual("Productivity 1 (%)", c3["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productivity_1", c3["id"])
self.assertAlmostEqual(31.328, c3["values"][0], delta=0.0003)
self.assertEqual("Productivity 2 (%)", c4["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productivity_2", c4["id"])
self.assertAlmostEqual(13.873, c4["values"][0], delta=0.0003)
def test_make_loading_report_with_dataset(self):
"""
Test the content of the loading report generated from a dataset
"""
sts_xml = data.getXmlWithStats()
rpt = make_loading_report(sts_xml)
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
c2 = t['columns'][2]
c3 = t['columns'][3]
c4 = t['columns'][4]
self.assertEqual('Collection Context', c0['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'collection_context', c0['id'])
self.assertEqual('Combined', c0['values'][0])
# Turn these back on when a context is inserted in the testdataset:
#self.assertEqual('dummy1', c0['values'][1])
#self.assertEqual('dummy2', c0['values'][2])
self.assertEqual('NA', c0['values'][1])
self.assertEqual('NA', c0['values'][2])
self.assertEqual('Productive ZMWs', c1['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productive_zmws', c1['id'])
self.assertEqual(153168, c1['values'][0])
self.assertEqual(2876, c1['values'][1])
self.assertEqual(150292, c1['values'][2])
self.assertEqual('Productivity 0 (%)',
c2['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_0',
c2['id'])
self.assertAlmostEqual(78.985, c2['values'][0], delta=.0003)
self.assertAlmostEqual(54.798, c2['values'][1], delta=.0003)
self.assertAlmostEqual(79.447, c2['values'][2], delta=.0003)
self.assertEqual('Productivity 1 (%)',
c3['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_1',
c3['id'])
self.assertAlmostEqual(16.402, c3['values'][0], delta=.0003)
self.assertAlmostEqual(31.328, c3['values'][1], delta=.0003)
self.assertAlmostEqual(16.117, c3['values'][2], delta=.0003)
self.assertEqual('Productivity 2 (%)',
c4['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_2',
c4['id'])
self.assertAlmostEqual(4.613, c4['values'][0], delta=.0003)
self.assertAlmostEqual(13.873, c4['values'][1], delta=.0003)
self.assertAlmostEqual(4.436, c4['values'][2], delta=.0003)
def test_make_loading_report_with_dataset(self):
"""
Test the content of the loading report generated from a dataset
"""
sts_xml = data.getXmlWithStats()
rpt = make_loading_report(sts_xml)
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
c2 = t['columns'][2]
c3 = t['columns'][3]
c4 = t['columns'][4]
self.assertEqual('Collection Context', c0['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'collection_context', c0['id'])
self.assertEqual('Combined', c0['values'][0])
# Turn these back on when a context is inserted in the testdataset:
#self.assertEqual('dummy1', c0['values'][1])
#self.assertEqual('dummy2', c0['values'][2])
self.assertEqual('NA', c0['values'][1])
self.assertEqual('NA', c0['values'][2])
self.assertEqual('Productive ZMWs', c1['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productive_zmws', c1['id'])
self.assertEqual(153168, c1['values'][0])
self.assertEqual(2876, c1['values'][1])
self.assertEqual(150292, c1['values'][2])
self.assertEqual('Productivity 0 (%)', c2['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_0', c2['id'])
self.assertAlmostEqual(78.985, c2['values'][0], delta=.0003)
self.assertAlmostEqual(54.798, c2['values'][1], delta=.0003)
self.assertAlmostEqual(79.447, c2['values'][2], delta=.0003)
self.assertEqual('Productivity 1 (%)', c3['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_1', c3['id'])
self.assertAlmostEqual(16.402, c3['values'][0], delta=.0003)
self.assertAlmostEqual(31.328, c3['values'][1], delta=.0003)
self.assertAlmostEqual(16.117, c3['values'][2], delta=.0003)
self.assertEqual('Productivity 2 (%)', c4['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_2', c4['id'])
self.assertAlmostEqual(4.613, c4['values'][0], delta=.0003)
self.assertAlmostEqual(13.873, c4['values'][1], delta=.0003)
self.assertAlmostEqual(4.436, c4['values'][2], delta=.0003)
def test_make_loading_report_with_sts_xml(self):
"""
Test the content of the loading report generated from a sts.xml
"""
try:
log.info(
TestXMLstatsRpts.test_make_loading_report_with_sts_xml.__doc__)
sts_xml = data.getStats(0)
rpt = make_loading_report(sts_xml)
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
c2 = t['columns'][2]
c3 = t['columns'][3]
c4 = t['columns'][4]
self.assertEqual('Collection Context', c0['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'collection_context', c0['id'])
self.assertEqual('NA', c0['values'][0])
self.assertEqual('Productive ZMWs', c1['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productive_zmws', c1['id'])
self.assertEqual(2876, c1['values'][0])
self.assertEqual('Productivity 0 (%)',
c2['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_0',
c2['id'])
self.assertAlmostEqual(54.80, c2['values'][0], delta=.0003)
self.assertEqual('Productivity 1 (%)',
c3['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_1',
c3['id'])
self.assertAlmostEqual(31.33, c3['values'][0], delta=.0003)
self.assertEqual('Productivity 2 (%)',
c4['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_2',
c4['id'])
self.assertAlmostEqual(13.87, c4['values'][0], delta=.0003)
except:
log.error(traceback.format_exc())
raise
def test_make_loading_report_with_dataset(self):
"""
Test the content of the loading report generated from a dataset
"""
sts_xml = data.getXmlWithStats()
rpt = make_loading_report(sts_xml)
d = json.loads(rpt.to_json())
t = d["tables"][0]
c0 = t["columns"][0]
c1 = t["columns"][1]
c2 = t["columns"][2]
c3 = t["columns"][3]
c4 = t["columns"][4]
self.assertEqual("Collection Context", c0["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "collection_context", c0["id"])
self.assertEqual("Combined", c0["values"][0])
# Turn these back on when a context is inserted in the testdataset:
# self.assertEqual('dummy1', c0['values'][1])
# self.assertEqual('dummy2', c0['values'][2])
self.assertEqual("NA", c0["values"][1])
self.assertEqual("NA", c0["values"][2])
self.assertEqual("Productive ZMWs", c1["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productive_zmws", c1["id"])
self.assertEqual(153168, c1["values"][0])
self.assertEqual(2876, c1["values"][1])
self.assertEqual(150292, c1["values"][2])
self.assertEqual("Productivity 0 (%)", c2["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productivity_0", c2["id"])
self.assertAlmostEqual(78.985, c2["values"][0], delta=0.0003)
self.assertAlmostEqual(54.798, c2["values"][1], delta=0.0003)
self.assertAlmostEqual(79.447, c2["values"][2], delta=0.0003)
self.assertEqual("Productivity 1 (%)", c3["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productivity_1", c3["id"])
self.assertAlmostEqual(16.402, c3["values"][0], delta=0.0003)
self.assertAlmostEqual(31.328, c3["values"][1], delta=0.0003)
self.assertAlmostEqual(16.117, c3["values"][2], delta=0.0003)
self.assertEqual("Productivity 2 (%)", c4["header"])
self.assertEqual("loading_xml_report.loading_xml_table." "productivity_2", c4["id"])
self.assertAlmostEqual(4.613, c4["values"][0], delta=0.0003)
self.assertAlmostEqual(13.873, c4["values"][1], delta=0.0003)
self.assertAlmostEqual(4.436, c4["values"][2], delta=0.0003)
validate_report_complete(self, rpt)
def test_make_loading_report_with_sts_xml(self):
"""
Test the content of the loading report generated from a sts.xml
"""
sts_xml = data.getStats(0)
rpt = make_loading_report(sts_xml)
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
c2 = t['columns'][2]
c3 = t['columns'][3]
c4 = t['columns'][4]
self.assertEqual('Collection Context', c0['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'collection_context', c0['id'])
self.assertEqual('NA', c0['values'][0])
self.assertEqual('Productive ZMWs', c1['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productive_zmws', c1['id'])
self.assertEqual(2876, c1['values'][0])
self.assertEqual('Productivity 0 (%)',
c2['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_0',
c2['id'])
self.assertAlmostEqual(54.798, c2['values'][0], delta=.0003)
self.assertEqual('Productivity 1 (%)',
c3['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_1',
c3['id'])
self.assertAlmostEqual(31.328, c3['values'][0], delta=.0003)
self.assertEqual('Productivity 2 (%)',
c4['header'])
self.assertEqual('loading_xml_report.loading_xml_table.'
'productivity_2',
c4['id'])
self.assertAlmostEqual(13.873, c4['values'][0], delta=.0003)
def test_make_loading_report_with_sts_xml(self):
"""
Test the content of the loading report generated from a sts.xml
"""
sts_xml = data.getStats(0)
rpt = make_loading_report(sts_xml)
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
c2 = t['columns'][2]
c3 = t['columns'][3]
c4 = t['columns'][4]
self.assertEqual('Collection Context', c0['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'collection_context', c0['id'])
self.assertEqual('NA', c0['values'][0])
self.assertEqual('Productive ZMWs', c1['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productive_zmws', c1['id'])
self.assertEqual(2876, c1['values'][0])
self.assertEqual('Productivity 0 (%)', c2['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_0', c2['id'])
self.assertAlmostEqual(54.798, c2['values'][0], delta=.0003)
self.assertEqual('Productivity 1 (%)', c3['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_1', c3['id'])
self.assertAlmostEqual(31.328, c3['values'][0], delta=.0003)
self.assertEqual('Productivity 2 (%)', c4['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_2', c4['id'])
self.assertAlmostEqual(13.873, c4['values'][0], delta=.0003)
def _test_ioerror():
make_loading_report("foo")
def _test_ioerror():
make_loading_report('foo')
def test_make_loading_report_with_merged_dataset(self):
"""
Test the content of the loading report generated from a dataset with
multiple sub-datasets
"""
ss = get_merged_subreadset()
rpt = make_loading_report(ss, self.get_output_dir())
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
c2 = t['columns'][2]
c3 = t['columns'][3]
c4 = t['columns'][4]
c5 = t['columns'][5]
c6 = t['columns'][6]
c7 = t['columns'][7]
self.assertEqual('Collection Context', c0['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'collection_context', c0['id'])
self.assertEqual('Combined', c0['values'][0])
# Turn these back on when a context is inserted in the testdataset:
#self.assertEqual('dummy1', c0['values'][1])
#self.assertEqual('dummy2', c0['values'][2])
self.assertEqual('m54086_160831_230338', c0['values'][1])
self.assertEqual('m54099_160830_232701', c0['values'][2])
self.assertEqual('Productive ZMWs', c1['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productive_zmws', c1['id'])
self.assertEqual(2073466, c1['values'][0])
self.assertEqual(1036722, c1['values'][1])
self.assertEqual(1036744, c1['values'][2])
self.assertEqual('Productivity 0', c2['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_0_n', c2['id'])
self.assertEqual(1325603, c2['values'][0])
self.assertEqual(853636, c2['values'][1])
self.assertEqual(471967, c2['values'][2])
self.assertEqual('(%)', c3['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_0_pct', c3['id'])
self.assertAlmostEqual(63.932, c3['values'][0], delta=.0003)
self.assertAlmostEqual(82.340, c3['values'][1], delta=.0003)
self.assertAlmostEqual(45.524, c3['values'][2], delta=.0003)
self.assertEqual('Productivity 1', c4['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_1_n', c4['id'])
self.assertEqual(743972, c4['values'][0])
self.assertEqual(180176, c4['values'][1])
self.assertEqual(563796, c4['values'][2])
self.assertEqual('(%)', c5['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_1_pct', c5['id'])
self.assertAlmostEqual(35.881, c5['values'][0], delta=.0003)
self.assertAlmostEqual(17.379, c5['values'][1], delta=.0003)
self.assertAlmostEqual(54.381, c5['values'][2], delta=.0003)
self.assertEqual('Productivity 2', c6['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_2_n', c6['id'])
self.assertEqual(3891, c6['values'][0])
self.assertEqual(2910, c6['values'][1])
self.assertEqual(981, c6['values'][2])
self.assertEqual('(%)', c7['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_2_pct', c7['id'])
self.assertAlmostEqual(0.188, c7['values'][0], delta=.0003)
self.assertAlmostEqual(0.281, c7['values'][1], delta=.0003)
self.assertAlmostEqual(0.095, c7['values'][2], delta=.0003)
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(),
'raw_read_length_plot.png')))
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(),
'raw_read_length_plot_thumb.png')))
validate_report_complete(self, rpt)
def test_make_loading_report_with_dataset(self):
"""
Test the content of the loading report generated from a simple
SubreadSet
"""
sts_xml = pbtestdata.get_file("subreads-sequel")
rpt = make_loading_report(sts_xml, self.get_output_dir())
d = json.loads(rpt.to_json())
t = d['tables'][0]
c0 = t['columns'][0]
c1 = t['columns'][1]
c2 = t['columns'][2]
c3 = t['columns'][3]
c4 = t['columns'][4]
c5 = t['columns'][5]
c6 = t['columns'][6]
c7 = t['columns'][7]
c8 = t['columns'][8]
self.assertEqual('Collection Context', c0['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'collection_context', c0['id'])
self.assertEqual('m54006_160504_020705', c0['values'][0])
self.assertEqual('Productive ZMWs', c1['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productive_zmws', c1['id'])
self.assertEqual(1035426, c1['values'][0])
self.assertEqual('Productivity 0', c2['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_0_n', c2['id'])
self.assertEqual(631530, c2['values'][0])
self.assertEqual('(%)', c3['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_0_pct', c3['id'])
self.assertAlmostEqual(60.992, c3['values'][0], delta=.0003)
self.assertEqual('Productivity 1', c4['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_1_n', c4['id'])
self.assertEqual(394658, c4['values'][0])
self.assertEqual('(%)', c5['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_1_pct', c5['id'])
self.assertAlmostEqual(38.116, c5['values'][0], delta=.0003)
self.assertEqual('Productivity 2', c6['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_2_n', c6['id'])
self.assertEqual(9238, c6['values'][0])
self.assertEqual('(%)', c7['header'])
self.assertEqual(
'loading_xml_report.loading_xml_table.'
'productivity_2_pct', c7['id'])
self.assertAlmostEqual(0.892, c7['values'][0], delta=.0003)
self.assertEqual(c8['values'][0], "Workflow_Magbead.py")
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(),
'raw_read_length_plot.png')))
self.assertTrue(
os.path.exists(
os.path.join(self.get_output_dir(),
'raw_read_length_plot_thumb.png')))
validate_report_complete(self, rpt)
def _test_ioerror():
make_loading_report('foo', self.get_output_dir())
def _test_ioerror():
make_loading_report('foo')
