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whitespace fixes
author
Diane Trout
<diane@ghic.org>
Thu, 9 Mar 2017 23:49:06 +0000
(15:49 -0800)
committer
Diane Trout
<diane@ghic.org>
Thu, 9 Mar 2017 23:49:06 +0000
(15:49 -0800)
htsworkflow/submission/test/test_daf.py
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diff --git
a/htsworkflow/submission/test/test_daf.py
b/htsworkflow/submission/test/test_daf.py
index b992af95ea3bacfda98fa1570c57f769b519e893..e7d9e835e49af45bae9baa61635fd722cfbb66d5 100644
(file)
--- a/
htsworkflow/submission/test/test_daf.py
+++ b/
htsworkflow/submission/test/test_daf.py
@@
-82,7
+82,6
@@
required no
class TestDAF(TestCase):
def test_parse(self):
class TestDAF(TestCase):
def test_parse(self):
-
parsed = daf.fromstring(test_daf)
self.failUnlessEqual(parsed['assembly'], 'mm9')
parsed = daf.fromstring(test_daf)
self.failUnlessEqual(parsed['assembly'], 'mm9')
@@
-96,7
+95,6
@@
class TestDAF(TestCase):
self.failUnlessEqual(signal['longLabelPrefix'],
'Caltech Histone Signal')
self.failUnlessEqual(signal['longLabelPrefix'],
'Caltech Histone Signal')
-
def test_rdf(self):
parsed = daf.fromstring(test_daf)
def test_rdf(self):
parsed = daf.fromstring(test_daf)
@@
-143,13
+141,13
@@
def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
"""
model = Graph()
if ns is None:
"""
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)
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
return mapper
@@
-187,14
+185,14
@@
class TestUCSCSubmission(TestCase):
thisView:Signal dafTerm:filename_re ".*\\\\.bam" .
thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
'''.format(name)
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),
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'
def test_find_overlapping_view(self):
name = 'testfind'
@@
-204,7
+202,7
@@
thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
thisView:fastq dafTerm:filename_re ".*\\\\.fastq" .
thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
'''.format(name)
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.failUnlessRaises(daf.ModelException,
daf_mapper.find_view,
@@
-256,14
+254,13
@@
thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
self.assertEqual(len(views), 1)
self.failUnlessEqual(str(views[0]), view_name)
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'
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')
def test_daf_with_replicate(self):
daf_mapper = load_daf_mapper('test_rep')
@@
-271,19
+268,18
@@
thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
self.failUnless('replicate' in daf_mapper.get_daf_variables())
def test_daf_without_replicate(self):
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):
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)
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)
def test_link_daf(self):
name = 'testsub'
submission = load_daf_mapper(name, test_daf=test_daf)
@@
-297,7
+293,7
@@
thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
# make sure daf gets linked
created_daf = os.path.join(result_dir, name+'.daf')
self.failUnless(os.path.exists(created_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()
daf_body = stream.read()
stream.close()