class TestDAF(TestCase):
def test_parse(self):
-
parsed = daf.fromstring(test_daf)
self.failUnlessEqual(parsed['assembly'], 'mm9')
self.failUnlessEqual(signal['longLabelPrefix'],
'Caltech Histone Signal')
-
def test_rdf(self):
parsed = daf.fromstring(test_daf)
"""
model = Graph()
if ns is None:
- ns="http://extra"
+ ns = "http://extra"
if extra_statements is not None:
model.parse(data=extra_statements, format='turtle', publicID=ns)
test_daf_stream = StringIO(test_daf)
- mapper = daf.UCSCSubmission(name, daf_file = test_daf_stream, model=model)
+ mapper = daf.UCSCSubmission(name, daf_file=test_daf_stream, model=model)
return mapper
thisView:Signal dafTerm:filename_re ".*\\\\.bam" .
thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
'''.format(name)
- daf_mapper = load_daf_mapper(name, extra_statements = extra)
+ daf_mapper = load_daf_mapper(name, extra_statements=extra)
view = daf_mapper.find_view('filename_r1.fastq')
view_root = 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/'
view_root = view_root.format(name)
self.failUnlessEqual(str(view),
- '{0}{1}'.format(view_root,'FastqRd1'))
+ '{0}{1}'.format(view_root, 'FastqRd1'))
def test_find_overlapping_view(self):
name = 'testfind'
thisView:fastq dafTerm:filename_re ".*\\\\.fastq" .
thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
'''.format(name)
- daf_mapper = load_daf_mapper(name, extra_statements = extra)
+ daf_mapper = load_daf_mapper(name, extra_statements=extra)
self.failUnlessRaises(daf.ModelException,
daf_mapper.find_view,
self.assertEqual(len(views), 1)
self.failUnlessEqual(str(views[0]), view_name)
-
def test_library_url(self):
daf_mapper = load_daf_mapper('urltest')
self.failUnlessEqual(daf_mapper.library_url,
'http://jumpgate.caltech.edu/library/')
daf_mapper.library_url = 'http://google.com'
- self.failUnlessEqual(daf_mapper.library_url, 'http://google.com' )
+ self.failUnlessEqual(daf_mapper.library_url, 'http://google.com')
def test_daf_with_replicate(self):
daf_mapper = load_daf_mapper('test_rep')
self.failUnless('replicate' in daf_mapper.get_daf_variables())
def test_daf_without_replicate(self):
- daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_no_rep)
+ daf_mapper = load_daf_mapper('test_rep', test_daf=test_daf_no_rep)
self.failUnlessEqual(daf_mapper.need_replicate(), False)
self.failUnless('replicate' not in daf_mapper.get_daf_variables())
def test_daf_with_extra(self):
- daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_extra)
+ daf_mapper = load_daf_mapper('test_rep', test_daf=test_daf_extra)
variables = daf_mapper.get_daf_variables()
self.assertEqual(len(variables), 11)
self.failUnless('treatment' in variables)
self.failUnless('controlId' in variables)
-
def test_link_daf(self):
name = 'testsub'
submission = load_daf_mapper(name, test_daf=test_daf)
# make sure daf gets linked
created_daf = os.path.join(result_dir, name+'.daf')
self.failUnless(os.path.exists(created_daf))
- stream = open(created_daf,'r')
+ stream = open(created_daf, 'r')
daf_body = stream.read()
stream.close()