1 from contextlib import contextmanager
4 from six.moves import StringIO
7 from unittest import TestCase, TestSuite, defaultTestLoader
9 from rdflib import Graph, Namespace, URIRef
10 from rdflib.namespace import RDF
12 from htsworkflow.submission import daf, results
13 from htsworkflow.util.rdfns import (
19 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)
106 subNS = Namespace(str(submissionLog[name]))
107 daf.add_to_model(model, parsed, submissionLog[name])
109 signal_view_node = subNS['/view/Signal']
111 turtle = str(model.serialize(format='turtle'))
113 self.failUnless(str(signal_view_node) in turtle)
115 statements = list(model.triples((signal_view_node, None, None)))
116 self.failUnlessEqual(len(statements), 6)
117 names = list(model.objects(signal_view_node, dafTermOntology['name']))
118 self.assertEqual(len(names), 1)
119 self.failUnlessEqual(names[0].toPython(), u'Signal')
121 def test_get_view_namespace_from_string(self):
122 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
123 target = Namespace(url + 'view/')
124 view_namespace = daf.get_view_namespace(url)
125 self.assertEqual(view_namespace[''], target[''])
127 def test_get_view_namespace_from_string_no_trailing_slash(self):
128 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub"
129 target = Namespace(url + '/view/')
130 view_namespace = daf.get_view_namespace(url)
131 self.assertEqual(view_namespace[''], target[''])
133 def test_get_view_namespace_from_uri_node(self):
134 url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
136 target = Namespace(url + 'view/')
137 view_namespace = daf.get_view_namespace(node)
138 self.assertEqual(view_namespace[''], target[''])
141 def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
142 """Load test model in
148 if extra_statements is not None:
149 model.parse(data=extra_statements, format='turtle', publicID=ns)
151 test_daf_stream = StringIO(test_daf)
152 mapper = daf.UCSCSubmission(name, daf_file = test_daf_stream, model=model)
156 class TestUCSCSubmission(TestCase):
158 test_results.generate_sample_results_tree(self, 'daf_results')
161 # see things created by temp_results.generate_sample_results_tree
162 shutil.rmtree(self.tempdir)
164 def test_create_mapper_add_pattern(self):
166 mapper = load_daf_mapper(name)
167 pattern = '.bam\Z(?ms)'
168 mapper.add_pattern('Signal', pattern)
170 s = (mapper.viewNS['Signal'],
171 dafTermOntology['filename_re'],
173 search = list(mapper.model.triples(s))
174 self.failUnlessEqual(len(search), 1)
175 self.failUnlessEqual(str(search[0][0]),
176 str(submissionLog['testsub/view/Signal']))
177 self.failUnlessEqual(str(search[0][1]),
178 str(dafTermOntology['filename_re']))
179 #self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
182 def test_find_one_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:Signal dafTerm:filename_re ".*\\\\.bam" .
188 thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
190 daf_mapper = load_daf_mapper(name, extra_statements = extra)
192 view = daf_mapper.find_view('filename_r1.fastq')
194 view_root = 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/'
195 view_root = view_root.format(name)
196 self.failUnlessEqual(str(view),
197 '{0}{1}'.format(view_root,'FastqRd1'))
199 def test_find_overlapping_view(self):
201 extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
202 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/> .
204 thisView:fastq dafTerm:filename_re ".*\\\\.fastq" .
205 thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
207 daf_mapper = load_daf_mapper(name, extra_statements = extra)
209 self.failUnlessRaises(daf.ModelException,
210 daf_mapper.find_view,
213 def test_find_attributes(self):
215 lib_url = 'http://jumpgate.caltech.edu/library/%s/' %(lib_id)
216 extra = '''@prefix dafTerm: <http://jumpgate.caltech.edu/wiki/UcscDaf#> .
217 @prefix submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#> .
218 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/view/> .
219 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
221 thisView:Signal dafTerm:filename_re ".*\\\\.bam" ;
222 submissionOntology:view_name "Signal" .
223 thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
224 submissionOntology:view_name "FastqRd1" .
225 <%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
226 ''' % {'libraryOntology': 'http://jumpgate.caltech.edu/wiki/LibraryOntology#',
229 daf_mapper = load_daf_mapper('testfind', extra)
230 libNode = URIRef(lib_url)
231 daf_mapper._add_library_details_to_model(libNode)
232 gel_cut = daf_mapper._get_library_attribute(libNode, 'gel_cut')
233 # make sure we can override attributes, the value in our
234 # server is 500 for this library
235 self.failUnlessEqual(gel_cut, 100)
237 species = daf_mapper._get_library_attribute(libNode, 'species_name')
238 self.failUnlessEqual(species, "Homo sapiens")
240 with mktempdir('analysis') as analysis_dir:
241 path, analysis_name = os.path.split(analysis_dir)
242 with mktempfile('.bam', dir=analysis_dir) as filename:
243 daf_mapper.construct_track_attributes(analysis_dir,
247 sub_root = "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/"
248 submission_name = sub_root + analysis_name
249 sources = list(daf_mapper.model.subjects(RDF['type'], submissionOntology['submission']))
250 self.assertEqual(len(sources), 1)
252 self.failUnlessEqual(str(source), submission_name)
254 view_name = submission_name + '/Signal'
255 views = list(daf_mapper.model.objects(source, submissionOntology['has_view']))
256 self.assertEqual(len(views), 1)
257 self.failUnlessEqual(str(views[0]), view_name)
260 def test_library_url(self):
261 daf_mapper = load_daf_mapper('urltest')
263 self.failUnlessEqual(daf_mapper.library_url,
264 'http://jumpgate.caltech.edu/library/')
265 daf_mapper.library_url = 'http://google.com'
266 self.failUnlessEqual(daf_mapper.library_url, 'http://google.com' )
268 def test_daf_with_replicate(self):
269 daf_mapper = load_daf_mapper('test_rep')
270 self.failUnlessEqual(daf_mapper.need_replicate(), True)
271 self.failUnless('replicate' in daf_mapper.get_daf_variables())
273 def test_daf_without_replicate(self):
274 daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_no_rep)
275 self.failUnlessEqual(daf_mapper.need_replicate(), False)
276 self.failUnless('replicate' not in daf_mapper.get_daf_variables())
278 def test_daf_with_extra(self):
279 daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_extra)
280 variables = daf_mapper.get_daf_variables()
282 self.assertEqual(len(variables), 11)
283 self.failUnless('treatment' in variables)
284 self.failUnless('controlId' in variables)
287 def test_link_daf(self):
289 submission = load_daf_mapper(name, test_daf=test_daf)
290 result_map = results.ResultMap()
291 result_dir = os.path.join(self.sourcedir,
292 test_results.S1_NAME)
293 result_map['1000'] = result_dir
295 submission.link_daf(result_map)
297 # make sure daf gets linked
298 created_daf = os.path.join(result_dir, name+'.daf')
299 self.failUnless(os.path.exists(created_daf))
300 stream = open(created_daf,'r')
301 daf_body = stream.read()
304 self.failUnlessEqual(test_daf, daf_body)
308 def mktempdir(prefix='tmp'):
309 d = tempfile.mkdtemp(prefix=prefix)
315 def mktempfile(suffix='', prefix='tmp', dir=None):
316 fd, pathname = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir)
323 suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestDAF))
324 suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCSubmission))
327 if __name__ == "__main__":
328 logging.basicConfig(level=logging.DEBUG)
329 from unittest import main
330 main(defaultTest='suite')