def test_get_input_scaffold(self):
# basic test. includes group stuff.
# Something, somewhere, isn't mocking the specmanager right.
# This forces it to work.
biokbase.narrative.jobs.specmanager.SpecManager().reload()
scaffold = get_input_scaffold("kb_trimmomatic/run_trimmomatic")
scaffold_standard = {
"adapter_clip": [
{
"adapterFa": None,
"palindrome_clip_threshold": None,
"seed_mismatches": None,
"simple_clip_threshold": None,
}
],
"crop_length": None,
"head_crop_length": None,
"input_reads_ref": None,
"leading_min_quality": None,
"min_length": None,
"output_reads_name": None,
"sliding_window": {
"sliding_window_min_quality": None,
"sliding_window_size": None,
},
"trailing_min_quality": None,
"translate_to_phred33": None,
}
self.assertEqual(scaffold_standard, scaffold)
def test_get_input_scaffold(self):
# basic test. includes group stuff.
# Something, somewhere, isn't mocking the specmanager right.
# This forces it to work.
biokbase.narrative.jobs.specmanager.SpecManager().reload()
scaffold = get_input_scaffold("kb_trimmomatic/run_trimmomatic")
scaffold_standard = {
'adapter_clip': [{
'adapterFa': None,
'palindrome_clip_threshold': None,
'seed_mismatches': None,
'simple_clip_threshold': None
}],
'crop_length': None,
'head_crop_length': None,
'input_reads_ref': None,
'leading_min_quality': None,
'min_length': None,
'output_reads_name': None,
'sliding_window': {
'sliding_window_min_quality': None,
'sliding_window_size': None
},
'trailing_min_quality': None,
'translate_to_phred33': None
}
self.assertEqual(scaffold_standard, scaffold)
def test_get_input_scaffold_defaults(self):
# Do standard, group params, lists, etc.
biokbase.narrative.jobs.specmanager.SpecManager().reload()
scaffold = get_input_scaffold(
"kb_trimmomatic/run_trimmomatic", use_defaults=True
)
scaffold_standard = {
"adapter_clip": [
{
"adapterFa": None,
"palindrome_clip_threshold": "30",
"seed_mismatches": "2",
"simple_clip_threshold": "10",
}
],
"crop_length": None,
"head_crop_length": "0",
"input_reads_ref": None,
"leading_min_quality": "3",
"min_length": "36",
"output_reads_name": None,
"sliding_window": {
"sliding_window_min_quality": "15",
"sliding_window_size": "4",
},
"trailing_min_quality": "3",
"translate_to_phred33": "1",
}
self.assertEqual(scaffold_standard, scaffold)
def test_get_input_scaffold_defaults(self):
# Do standard, group params, lists, etc.
biokbase.narrative.jobs.specmanager.SpecManager().reload()
scaffold = get_input_scaffold("kb_trimmomatic/run_trimmomatic", use_defaults=True)
scaffold_standard = {
'adapter_clip': [{
'adapterFa': None,
'palindrome_clip_threshold': '30',
'seed_mismatches': '2',
'simple_clip_threshold': '10'
}],
'crop_length': None,
'head_crop_length': '0',
'input_reads_ref': None,
'leading_min_quality': '3',
'min_length': '36',
'output_reads_name': None,
'sliding_window': {
'sliding_window_min_quality': '15',
'sliding_window_size': '4'
},
'trailing_min_quality': '3',
'translate_to_phred33': '1'
}
self.assertEqual(scaffold_standard, scaffold)
def test_get_input_scaffold(self):
# basic test. includes group stuff.
# Something, somewhere, isn't mocking the specmanager right.
# This forces it to work.
biokbase.narrative.jobs.specmanager.SpecManager().reload()
scaffold = get_input_scaffold("kb_trimmomatic/run_trimmomatic")
scaffold_standard = {
u'adapter_clip': [{
u'adapterFa': None,
u'palindrome_clip_threshold': None,
u'seed_mismatches': None,
u'simple_clip_threshold': None
}],
u'crop_length': None,
u'head_crop_length': None,
u'input_reads_ref': None,
u'leading_min_quality': None,
u'min_length': None,
u'output_reads_name': None,
u'sliding_window': {
u'sliding_window_min_quality': None,
u'sliding_window_size': None
},
u'trailing_min_quality': None,
u'translate_to_phred33': None
}
self.assertEqual(scaffold_standard, scaffold)
def test_get_input_scaffold_defaults(self):
# Do standard, group params, lists, etc.
biokbase.narrative.jobs.specmanager.SpecManager().reload()
scaffold = get_input_scaffold("kb_trimmomatic/run_trimmomatic", use_defaults=True)
scaffold_standard = {
u'adapter_clip': [{
u'adapterFa': None,
u'palindrome_clip_threshold': u'30',
u'seed_mismatches': u'2',
u'simple_clip_threshold': u'10'
}],
u'crop_length': None,
u'head_crop_length': u'0',
u'input_reads_ref': None,
u'leading_min_quality': u'3',
u'min_length': u'36',
u'output_reads_name': None,
u'sliding_window': {
u'sliding_window_min_quality': u'15',
u'sliding_window_size': u'4'
},
u'trailing_min_quality': u'3',
u'translate_to_phred33': u'1'
}
self.assertEqual(scaffold_standard, scaffold)
def test_get_input_scaffold_bad_tag(self):
with self.assertRaises(ValueError) as e:
get_input_scaffold("foo", tag="bar")
self.assertIn(
"Can't find tag bar - allowed tags are release, beta, dev", str(e.exception)
)
def test_get_input_scaffold_bad_id(self):
with self.assertRaises(ValueError) as e:
get_input_scaffold("foo")
self.assertIn('Unknown app id "foo" tagged as "release"', str(e.exception))
def test_get_input_scaffold_bad_tag(self):
with self.assertRaises(ValueError) as e:
get_input_scaffold("foo", tag="bar")
self.assertIn("Can't find tag bar - allowed tags are release, beta, dev", str(e.exception))
def test_get_input_scaffold_bad_id(self):
with self.assertRaises(ValueError) as e:
get_input_scaffold('foo')
self.assertIn('Unknown app id "foo" tagged as "release"', str(e.exception))
