from contextlib import contextmanager
+import logging
import os
from StringIO import StringIO
import shutil
import tempfile
-import unittest
+from unittest import TestCase, TestSuite, defaultTestLoader
-from htsworkflow.submission import daf
+from htsworkflow.submission import daf, results
from htsworkflow.util.rdfhelp import \
dafTermOntology, \
fromTypedNode, \
get_model, \
get_serializer
+from htsworkflow.submission.test import test_results
import RDF
test_daf = """# Lab and general info
grant Hardison
lab Caltech-m
-dataType ChipSeq
+dataType ChipSeq
variables cell, antibody,sex,age,strain,control
compositeSuffix CaltechHistone
assembly mm9
test_daf_no_rep = """# Lab and general info
grant Hardison
lab Caltech-m
-dataType ChipSeq
+dataType ChipSeq
variables cell, antibody,sex,age,strain,control
compositeSuffix CaltechHistone
assembly mm9
required no
"""
-class TestDAF(unittest.TestCase):
+test_daf_extra = """# Lab and general info
+grant Hardison
+lab Caltech-m
+dataType ChipSeq
+variables cell,antibody,sex,age,strain
+extraVariables controlId,treatment
+compositeSuffix CaltechHistone
+assembly mm9
+dafVersion 2.0
+validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
+
+# Track/view definition
+view FastqRd1
+longLabelPrefix Caltech Fastq Read 1
+type fastq
+hasReplicates no
+required no
+"""
+
+
+class TestDAF(TestCase):
def test_parse(self):
parsed = daf.fromstring(test_daf)
-
+
self.failUnlessEqual(parsed['assembly'], 'mm9')
self.failUnlessEqual(parsed['grant'], 'Hardison')
self.failUnlessEqual(len(parsed['variables']), 6)
self.failUnlessEqual(signal['longLabelPrefix'],
'Caltech Histone Signal')
+
def test_rdf(self):
parsed = daf.fromstring(test_daf)
name = 'cursub'
subNS = RDF.NS(str(submissionLog[name].uri))
- daf.add_to_model(model, parsed, name)
+ daf.add_to_model(model, parsed, submissionLog[name].uri)
signal_view_node = RDF.Node(subNS['/view/Signal'].uri)
name = model.get_target(signal_view_node, dafTermOntology['name'])
self.failUnlessEqual(fromTypedNode(name), u'Signal')
+ def test_get_view_namespace_from_string(self):
+ url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
+ target = RDF.NS(url + 'view/')
+ view_namespace = daf.get_view_namespace(url)
+ self.assertEqual(view_namespace[''], target[''])
+
+ def test_get_view_namespace_from_string_no_trailing_slash(self):
+ url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub"
+ target = RDF.NS(url + '/view/')
+ view_namespace = daf.get_view_namespace(url)
+ self.assertEqual(view_namespace[''], target[''])
+
+ def test_get_view_namespace_from_uri_node(self):
+ url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
+ node = RDF.Node(RDF.Uri(url))
+ target = RDF.NS(url + 'view/')
+ view_namespace = daf.get_view_namespace(node)
+ self.assertEqual(view_namespace[''], target[''])
+
+
def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
"""Load test model in
"""
model = get_model()
if ns is None:
ns="http://extra"
-
+
if extra_statements is not None:
parser = RDF.Parser(name='turtle')
parser.parse_string_into_model(model, extra_statements,
ns)
-
+
test_daf_stream = StringIO(test_daf)
- mapper = daf.DAFMapper(name, daf_file = test_daf_stream, model=model)
+ mapper = daf.UCSCSubmission(name, daf_file = test_daf_stream, model=model)
return mapper
def dump_model(model):
writer = get_serializer()
turtle = writer.serialize_model_to_string(model)
print turtle
-
-class TestDAFMapper(unittest.TestCase):
+
+
+class TestUCSCSubmission(TestCase):
+ def setUp(self):
+ test_results.generate_sample_results_tree(self, 'daf_results')
+
+ def tearDown(self):
+ # see things created by temp_results.generate_sample_results_tree
+ shutil.rmtree(self.tempdir)
+
def test_create_mapper_add_pattern(self):
name = 'testsub'
mapper = load_daf_mapper(name)
pattern = '.bam\Z(?ms)'
mapper.add_pattern('Signal', pattern)
- s = RDF.Statement(daf.get_view_namespace(name)['Signal'],
+ s = RDF.Statement(mapper.viewNS['Signal'],
dafTermOntology['filename_re'],
None)
search = list(mapper.model.find_statements(s))
str(dafTermOntology['filename_re']))
#self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
-
+
def test_find_one_view(self):
name='testfind'
extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
daf_mapper = load_daf_mapper(name, extra_statements = extra)
view = daf_mapper.find_view('filename_r1.fastq')
-
+
# dump_model(daf_mapper.model)
view_root = 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/'
view_root = view_root.format(name)
- self.failUnlessEqual(str(view)[1:-1],
+ self.failUnlessEqual(str(view.uri),
'{0}{1}'.format(view_root,'FastqRd1'))
def test_find_overlapping_view(self):
submissionOntology:view_name "Signal" .
thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
submissionOntology:view_name "FastqRd1" .
-<%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
+<%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
''' % {'libraryOntology': 'http://jumpgate.caltech.edu/wiki/LibraryOntology#',
'libUrl': lib_url}
# server is 500 for this library
self.failUnlessEqual(gel_cut, 100)
- species = daf_mapper._get_library_attribute(libNode, 'species')
+ species = daf_mapper._get_library_attribute(libNode, 'species_name')
self.failUnlessEqual(species, "Homo sapiens")
with mktempdir('analysis') as analysis_dir:
path, analysis_name = os.path.split(analysis_dir)
with mktempfile('.bam', dir=analysis_dir) as filename:
- print 'dir', os.listdir(analysis_dir)
- daf_mapper.construct_file_attributes(analysis_dir,
- libNode,
- filename)
-
+ daf_mapper.construct_track_attributes(analysis_dir,
+ libNode,
+ filename)
+
#dump_model(daf_mapper.model)
-
+
sub_root = "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/"
submission_name = sub_root + analysis_name
source = daf_mapper.model.get_source(rdfNS['type'], submissionOntology['submission'])
view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
self.failUnlessEqual(str(view.uri), view_name)
-
+
def test_library_url(self):
daf_mapper = load_daf_mapper('urltest')
daf_mapper = load_daf_mapper('test_rep')
self.failUnlessEqual(daf_mapper.need_replicate(), True)
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)
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)
+ 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)
+ result_map = results.ResultMap()
+ result_dir = os.path.join(self.sourcedir,
+ test_results.S1_NAME)
+ result_map['1000'] = result_dir
+
+ submission.link_daf(result_map)
+
+ # 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')
+ daf_body = stream.read()
+ stream.close()
+
+ self.failUnlessEqual(test_daf, daf_body)
+
+
@contextmanager
def mktempdir(prefix='tmp'):
d = tempfile.mkdtemp(prefix=prefix)
- print "made", d
yield d
shutil.rmtree(d)
- print "unmade", d
+
@contextmanager
def mktempfile(suffix='', prefix='tmp', dir=None):
fd, pathname = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir)
yield pathname
- print "made", pathname
os.close(fd)
os.unlink(pathname)
- print "unmade", pathname
-
def suite():
- suite = unittest.makeSuite(TestDAF, 'test')
- suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestDAF))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCSubmission))
return suite
if __name__ == "__main__":
- unittest.main(defaultTest='suite')
+ logging.basicConfig(level=logging.DEBUG)
+ from unittest import main
+ main(defaultTest='suite')
projects / htsworkflow.git / blobdiff