1 from contextlib import contextmanager
3 from StringIO import StringIO
6 from unittest2 import TestCase, TestSuite, defaultTestLoader
8 from htsworkflow.submission import daf, results
9 from htsworkflow.util.rdfhelp import \
18 from htsworkflow.submission.test import test_results
21 test_daf = """# Lab and general info
25 variables cell, antibody,sex,age,strain,control
26 compositeSuffix CaltechHistone
29 validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
31 # Track/view definition
33 longLabelPrefix Caltech Fastq Read 1
39 longLabelPrefix Caltech Histone Signal
45 test_daf_no_rep = """# Lab and general info
49 variables cell, antibody,sex,age,strain,control
50 compositeSuffix CaltechHistone
53 validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
55 # Track/view definition
57 longLabelPrefix Caltech Fastq Read 1
63 test_daf_extra = """# Lab and general info
67 variables cell,antibody,sex,age,strain
68 extraVariables controlId,treatment
69 compositeSuffix CaltechHistone
72 validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
74 # Track/view definition
76 longLabelPrefix Caltech Fastq Read 1
83 class TestDAF(TestCase):
86 parsed = daf.fromstring(test_daf)
88 self.failUnlessEqual(parsed['assembly'], 'mm9')
89 self.failUnlessEqual(parsed['grant'], 'Hardison')
90 self.failUnlessEqual(len(parsed['variables']), 6)
91 self.failUnlessEqual(len(parsed['views']), 2)
92 self.failUnlessEqual(len(parsed['views']['FastqRd1']), 5)
93 self.failUnlessEqual(len(parsed['views']['Signal']), 5)
94 signal = parsed['views']['Signal']
95 self.failUnlessEqual(signal['required'], False)
96 self.failUnlessEqual(signal['longLabelPrefix'],
97 'Caltech Histone Signal')
102 parsed = daf.fromstring(test_daf)
103 #mem = RDF.Storage(storage_name='hashes',
104 # options_string='hash-type="memory"'),
105 mem = RDF.MemoryStorage()
106 model = RDF.Model(mem)
109 subNS = RDF.NS(str(submissionLog[name].uri))
110 daf.add_to_model(model, parsed, submissionLog[name].uri)
112 signal_view_node = RDF.Node(subNS['/view/Signal'].uri)
114 writer = get_serializer()
115 turtle = writer.serialize_model_to_string(model)
117 self.failUnless(str(signal_view_node.uri) in turtle)
119 statements = list(model.find_statements(
121 signal_view_node, None, None)))
122 self.failUnlessEqual(len(statements), 6)
123 name = model.get_target(signal_view_node, dafTermOntology['name'])
124 self.failUnlessEqual(fromTypedNode(name), u'Signal')
126 def test_get_view_namespace_from_string(self):
127 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
128 target = RDF.NS(url + 'view/')
129 view_namespace = daf.get_view_namespace(url)
130 self.assertEqual(view_namespace[''], target[''])
132 def test_get_view_namespace_from_string_no_trailing_slash(self):
133 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub"
134 target = RDF.NS(url + '/view/')
135 view_namespace = daf.get_view_namespace(url)
136 self.assertEqual(view_namespace[''], target[''])
138 def test_get_view_namespace_from_uri_node(self):
139 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
140 node = RDF.Node(RDF.Uri(url))
141 target = RDF.NS(url + 'view/')
142 view_namespace = daf.get_view_namespace(node)
143 self.assertEqual(view_namespace[''], target[''])
146 def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
147 """Load test model in
153 if extra_statements is not None:
154 parser = RDF.Parser(name='turtle')
155 parser.parse_string_into_model(model, extra_statements,
158 test_daf_stream = StringIO(test_daf)
159 mapper = daf.UCSCSubmission(name, daf_file = test_daf_stream, model=model)
162 def dump_model(model):
163 writer = get_serializer()
164 turtle = writer.serialize_model_to_string(model)
168 class TestUCSCSubmission(TestCase):
170 test_results.generate_sample_results_tree(self)
173 # see things created by temp_results.generate_sample_results_tree
174 shutil.rmtree(self.tempdir)
176 def test_create_mapper_add_pattern(self):
178 mapper = load_daf_mapper(name)
179 pattern = '.bam\Z(?ms)'
180 mapper.add_pattern('Signal', pattern)
182 s = RDF.Statement(mapper.viewNS['Signal'],
183 dafTermOntology['filename_re'],
185 search = list(mapper.model.find_statements(s))
186 self.failUnlessEqual(len(search), 1)
187 self.failUnlessEqual(str(search[0].subject),
188 str(submissionLog['testsub/view/Signal']))
189 self.failUnlessEqual(str(search[0].predicate),
190 str(dafTermOntology['filename_re']))
191 #self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
194 def test_find_one_view(self):
196 extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
197 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/> .
199 thisView:Signal dafTerm:filename_re ".*\\\\.bam" .
200 thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
202 daf_mapper = load_daf_mapper(name, extra_statements = extra)
204 view = daf_mapper.find_view('filename_r1.fastq')
206 # dump_model(daf_mapper.model)
207 view_root = 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/'
208 view_root = view_root.format(name)
209 self.failUnlessEqual(str(view.uri),
210 '{0}{1}'.format(view_root,'FastqRd1'))
212 def test_find_overlapping_view(self):
214 extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
215 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/> .
217 thisView:fastq dafTerm:filename_re ".*\\\\.fastq" .
218 thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
220 daf_mapper = load_daf_mapper(name, extra_statements = extra)
222 self.failUnlessRaises(daf.ModelException,
223 daf_mapper.find_view,
226 def test_find_attributes(self):
228 lib_url = 'http://jumpgate.caltech.edu/library/%s/' %(lib_id)
229 extra = '''@prefix dafTerm: <http://jumpgate.caltech.edu/wiki/UcscDaf#> .
230 @prefix submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#> .
231 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/view/> .
232 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
234 thisView:Signal dafTerm:filename_re ".*\\\\.bam" ;
235 submissionOntology:view_name "Signal" .
236 thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
237 submissionOntology:view_name "FastqRd1" .
238 <%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
239 ''' % {'libraryOntology': 'http://jumpgate.caltech.edu/wiki/LibraryOntology#',
242 daf_mapper = load_daf_mapper('testfind', extra)
243 libNode = RDF.Node(RDF.Uri(lib_url))
244 daf_mapper._add_library_details_to_model(libNode)
245 gel_cut = daf_mapper._get_library_attribute(libNode, 'gel_cut')
246 # make sure we can override attributes, the value in our
247 # server is 500 for this library
248 self.failUnlessEqual(gel_cut, 100)
250 species = daf_mapper._get_library_attribute(libNode, 'species_name')
251 self.failUnlessEqual(species, "Homo sapiens")
253 with mktempdir('analysis') as analysis_dir:
254 path, analysis_name = os.path.split(analysis_dir)
255 with mktempfile('.bam', dir=analysis_dir) as filename:
256 daf_mapper.construct_track_attributes(analysis_dir,
260 #dump_model(daf_mapper.model)
262 sub_root = "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/"
263 submission_name = sub_root + analysis_name
264 source = daf_mapper.model.get_source(rdfNS['type'], submissionOntology['submission'])
265 self.failUnlessEqual(str(source.uri), submission_name)
267 view_name = submission_name + '/Signal'
268 view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
269 self.failUnlessEqual(str(view.uri), view_name)
272 def test_library_url(self):
273 daf_mapper = load_daf_mapper('urltest')
275 self.failUnlessEqual(daf_mapper.library_url,
276 'http://jumpgate.caltech.edu/library/')
277 daf_mapper.library_url = 'http://google.com'
278 self.failUnlessEqual(daf_mapper.library_url, 'http://google.com' )
280 def test_daf_with_replicate(self):
281 daf_mapper = load_daf_mapper('test_rep')
282 self.failUnlessEqual(daf_mapper.need_replicate(), True)
283 self.failUnless('replicate' in daf_mapper.get_daf_variables())
285 def test_daf_without_replicate(self):
286 daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_no_rep)
287 self.failUnlessEqual(daf_mapper.need_replicate(), False)
288 self.failUnless('replicate' not in daf_mapper.get_daf_variables())
290 def test_daf_with_extra(self):
291 daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_extra)
292 variables = daf_mapper.get_daf_variables()
293 self.assertEqual(len(variables), 11)
294 self.failUnless('treatment' in variables)
295 self.failUnless('controlId' in variables)
298 def test_link_daf(self):
300 submission = load_daf_mapper(name, test_daf=test_daf)
301 result_map = results.ResultMap()
302 result_dir = os.path.join(self.sourcedir,
303 test_results.S1_NAME)
304 result_map['1000'] = result_dir
306 submission.link_daf(result_map)
308 # make sure daf gets linked
309 created_daf = os.path.join(result_dir, name+'.daf')
310 self.failUnless(os.path.exists(created_daf))
311 stream = open(created_daf,'r')
312 daf_body = stream.read()
315 self.failUnlessEqual(test_daf, daf_body)
319 def mktempdir(prefix='tmp'):
320 d = tempfile.mkdtemp(prefix=prefix)
326 def mktempfile(suffix='', prefix='tmp', dir=None):
327 fd, pathname = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir)
334 suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCInfo))
337 if __name__ == "__main__":
338 from unittest2 import main
339 main(defaultTest='suite')