1 from contextlib import contextmanager
3 from StringIO import StringIO
8 from htsworkflow.submission import daf
9 from htsworkflow.util.rdfhelp import \
20 test_daf = """# Lab and general info
24 variables cell, antibody,sex,age,strain,control
25 compositeSuffix CaltechHistone
28 validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
30 # Track/view definition
32 longLabelPrefix Caltech Fastq Read 1
38 longLabelPrefix Caltech Histone Signal
44 test_daf_no_rep = """# Lab and general info
48 variables cell, antibody,sex,age,strain,control
49 compositeSuffix CaltechHistone
52 validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
54 # Track/view definition
56 longLabelPrefix Caltech Fastq Read 1
62 class TestDAF(unittest.TestCase):
65 parsed = daf.fromstring(test_daf)
67 self.failUnlessEqual(parsed['assembly'], 'mm9')
68 self.failUnlessEqual(parsed['grant'], 'Hardison')
69 self.failUnlessEqual(len(parsed['variables']), 6)
70 self.failUnlessEqual(len(parsed['views']), 2)
71 self.failUnlessEqual(len(parsed['views']['FastqRd1']), 5)
72 self.failUnlessEqual(len(parsed['views']['Signal']), 5)
73 signal = parsed['views']['Signal']
74 self.failUnlessEqual(signal['required'], False)
75 self.failUnlessEqual(signal['longLabelPrefix'],
76 'Caltech Histone Signal')
80 parsed = daf.fromstring(test_daf)
81 #mem = RDF.Storage(storage_name='hashes',
82 # options_string='hash-type="memory"'),
83 mem = RDF.MemoryStorage()
84 model = RDF.Model(mem)
87 subNS = RDF.NS(str(submissionLog[name].uri))
88 daf.add_to_model(model, parsed, submissionLog[name].uri)
90 signal_view_node = RDF.Node(subNS['/view/Signal'].uri)
92 writer = get_serializer()
93 turtle = writer.serialize_model_to_string(model)
95 self.failUnless(str(signal_view_node.uri) in turtle)
97 statements = list(model.find_statements(
99 signal_view_node, None, None)))
100 self.failUnlessEqual(len(statements), 6)
101 name = model.get_target(signal_view_node, dafTermOntology['name'])
102 self.failUnlessEqual(fromTypedNode(name), u'Signal')
104 def test_get_view_namespace_from_string(self):
105 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
106 target = RDF.NS(url + 'view/')
107 view_namespace = daf.get_view_namespace(url)
108 self.assertEqual(view_namespace[''], target[''])
110 def test_get_view_namespace_from_string_no_trailing_slash(self):
111 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub"
112 target = RDF.NS(url + '/view/')
113 view_namespace = daf.get_view_namespace(url)
114 self.assertEqual(view_namespace[''], target[''])
116 def test_get_view_namespace_from_uri_node(self):
117 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
118 node = RDF.Node(RDF.Uri(url))
119 target = RDF.NS(url + 'view/')
120 view_namespace = daf.get_view_namespace(node)
121 self.assertEqual(view_namespace[''], target[''])
124 def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
125 """Load test model in
131 if extra_statements is not None:
132 parser = RDF.Parser(name='turtle')
133 parser.parse_string_into_model(model, extra_statements,
136 test_daf_stream = StringIO(test_daf)
137 mapper = daf.DAFMapper(name, daf_file = test_daf_stream, model=model)
140 def dump_model(model):
141 writer = get_serializer()
142 turtle = writer.serialize_model_to_string(model)
145 class TestDAFMapper(unittest.TestCase):
146 def test_create_mapper_add_pattern(self):
148 mapper = load_daf_mapper(name)
149 pattern = '.bam\Z(?ms)'
150 mapper.add_pattern('Signal', pattern)
152 s = RDF.Statement(mapper.viewNS['Signal'],
153 dafTermOntology['filename_re'],
155 search = list(mapper.model.find_statements(s))
156 self.failUnlessEqual(len(search), 1)
157 self.failUnlessEqual(str(search[0].subject),
158 str(submissionLog['testsub/view/Signal']))
159 self.failUnlessEqual(str(search[0].predicate),
160 str(dafTermOntology['filename_re']))
161 #self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
164 def test_find_one_view(self):
166 extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
167 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/> .
169 thisView:Signal dafTerm:filename_re ".*\\\\.bam" .
170 thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
172 daf_mapper = load_daf_mapper(name, extra_statements = extra)
174 view = daf_mapper.find_view('filename_r1.fastq')
176 # dump_model(daf_mapper.model)
177 view_root = 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/'
178 view_root = view_root.format(name)
179 self.failUnlessEqual(str(view)[1:-1],
180 '{0}{1}'.format(view_root,'FastqRd1'))
182 def test_find_overlapping_view(self):
184 extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
185 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/> .
187 thisView:fastq dafTerm:filename_re ".*\\\\.fastq" .
188 thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
190 daf_mapper = load_daf_mapper(name, extra_statements = extra)
192 self.failUnlessRaises(daf.ModelException,
193 daf_mapper.find_view,
196 def test_find_attributes(self):
198 lib_url = 'http://jumpgate.caltech.edu/library/%s/' %(lib_id)
199 extra = '''@prefix dafTerm: <http://jumpgate.caltech.edu/wiki/UcscDaf#> .
200 @prefix submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#> .
201 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/view/> .
202 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
204 thisView:Signal dafTerm:filename_re ".*\\\\.bam" ;
205 submissionOntology:view_name "Signal" .
206 thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
207 submissionOntology:view_name "FastqRd1" .
208 <%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
209 ''' % {'libraryOntology': 'http://jumpgate.caltech.edu/wiki/LibraryOntology#',
212 daf_mapper = load_daf_mapper('testfind', extra)
213 libNode = RDF.Node(RDF.Uri(lib_url))
214 daf_mapper._add_library_details_to_model(libNode)
215 gel_cut = daf_mapper._get_library_attribute(libNode, 'gel_cut')
216 # make sure we can override attributes, the value in our
217 # server is 500 for this library
218 self.failUnlessEqual(gel_cut, 100)
220 species = daf_mapper._get_library_attribute(libNode, 'species')
221 self.failUnlessEqual(species, "Homo sapiens")
223 with mktempdir('analysis') as analysis_dir:
224 path, analysis_name = os.path.split(analysis_dir)
225 with mktempfile('.bam', dir=analysis_dir) as filename:
226 daf_mapper.construct_track_attributes(analysis_dir,
230 #dump_model(daf_mapper.model)
232 sub_root = "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/"
233 submission_name = sub_root + analysis_name
234 source = daf_mapper.model.get_source(rdfNS['type'], submissionOntology['submission'])
235 self.failUnlessEqual(str(source.uri), submission_name)
237 view_name = submission_name + '/Signal'
238 view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
239 self.failUnlessEqual(str(view.uri), view_name)
242 def test_library_url(self):
243 daf_mapper = load_daf_mapper('urltest')
245 self.failUnlessEqual(daf_mapper.library_url,
246 'http://jumpgate.caltech.edu/library/')
247 daf_mapper.library_url = 'http://google.com'
248 self.failUnlessEqual(daf_mapper.library_url, 'http://google.com' )
250 def test_daf_with_replicate(self):
251 daf_mapper = load_daf_mapper('test_rep')
252 self.failUnlessEqual(daf_mapper.need_replicate(), True)
253 self.failUnless('replicate' in daf_mapper.get_daf_variables())
255 def test_daf_without_replicate(self):
256 daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_no_rep)
257 self.failUnlessEqual(daf_mapper.need_replicate(), False)
258 self.failUnless('replicate' not in daf_mapper.get_daf_variables())
261 def mktempdir(prefix='tmp'):
262 d = tempfile.mkdtemp(prefix=prefix)
269 def mktempfile(suffix='', prefix='tmp', dir=None):
270 fd, pathname = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir)
272 print "made", pathname
275 print "unmade", pathname
279 suite = unittest.makeSuite(TestDAF, 'test')
280 suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))
283 if __name__ == "__main__":
284 unittest.main(defaultTest='suite')