htsworkflow/submission/test/test_daf.py

   1 from StringIO import StringIO
   2 import unittest
   3
   4 from htsworkflow.submission import daf
   5 from htsworkflow.util.rdfhelp import \
   6      dafTermOntology, \
   7      fromTypedNode, \
   8      rdfNS, \
   9      submissionLog, \
  10      submissionOntology, \
  11      get_model, \
  12      get_serializer
  13
  14 import RDF
  15
  16 test_daf = """# Lab and general info
  17 grant             Hardison
  18 lab               Caltech-m
  19 dataType          ChipSeq
  20 variables         cell, antibody,sex,age,strain,control
  21 compositeSuffix   CaltechHistone
  22 assembly          mm9
  23 dafVersion        2.0
  24 validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
  25
  26 # Track/view definition
  27 view             FastqRd1
  28 longLabelPrefix  Caltech Fastq Read 1
  29 type             fastq
  30 hasReplicates    yes
  31 required         no
  32
  33 view             Signal
  34 longLabelPrefix  Caltech Histone Signal
  35 type             bigWig
  36 hasReplicates    yes
  37 required         no
  38 """
  39
  40 class TestDAF(unittest.TestCase):
  41     def test_parse(self):
  42
  43         parsed = daf.fromstring(test_daf)
  44
  45         self.failUnlessEqual(parsed['assembly'], 'mm9')
  46         self.failUnlessEqual(parsed['grant'], 'Hardison')
  47         self.failUnlessEqual(len(parsed['variables']), 6)
  48         self.failUnlessEqual(len(parsed['views']), 2)
  49         self.failUnlessEqual(len(parsed['views']['FastqRd1']), 5)
  50         self.failUnlessEqual(len(parsed['views']['Signal']), 5)
  51         signal = parsed['views']['Signal']
  52         self.failUnlessEqual(signal['required'], False)
  53         self.failUnlessEqual(signal['longLabelPrefix'],
  54                              'Caltech Histone Signal')
  55
  56     def test_rdf(self):
  57
  58         parsed = daf.fromstring(test_daf)
  59         #mem = RDF.Storage(storage_name='hashes',
  60         #                  options_string='hash-type="memory"'),
  61         mem = RDF.MemoryStorage()
  62         model = RDF.Model(mem)
  63
  64         name = 'cursub'
  65         subNS = RDF.NS(str(submissionLog[name].uri))
  66         daf.add_to_model(model, parsed, name)
  67
  68         signal_view_node = RDF.Node(subNS['/view/Signal'].uri)
  69
  70         writer = get_serializer()
  71         turtle =  writer.serialize_model_to_string(model)
  72         self.failUnless(str(signal_view_node) in turtle)
  73
  74         statements = list(model.find_statements(
  75             RDF.Statement(
  76                 signal_view_node, None, None)))
  77         self.failUnlessEqual(len(statements), 6)
  78         name = model.get_target(signal_view_node, dafTermOntology['name'])
  79         self.failUnlessEqual(fromTypedNode(name), u'Signal')
  80
  81 def load_daf_mapper(name, extra_statements=None):
  82     """Load test model in
  83     """
  84     model = get_model()
  85     if extra_statements is not None:
  86         parser = RDF.Parser(name='turtle')
  87         parser.parse_string_into_model(model, extra_statements,
  88                                        'http://extra.extra')
  89
  90     test_daf_stream = StringIO(test_daf)
  91     mapper = daf.DAFMapper(name, daf_file = test_daf_stream, model=model)
  92     return mapper
  93
  94 def dump_model(model):
  95     writer = get_serializer()
  96     turtle =  writer.serialize_model_to_string(model)
  97     print turtle
  98
  99 class TestDAFMapper(unittest.TestCase):
 100     def test_create_mapper_add_pattern(self):
 101         name = 'testsub'
 102         mapper = load_daf_mapper(name)
 103         pattern = '.bam\Z(?ms)'
 104         mapper.add_pattern('Signal', pattern)
 105
 106         s = RDF.Statement(daf.get_view_namespace(name)['Signal'],
 107                           dafTermOntology['filename_re'],
 108                           None)
 109         search = list(mapper.model.find_statements(s))
 110         self.failUnlessEqual(len(search), 1)
 111         self.failUnlessEqual(str(search[0].subject),
 112                              str(submissionLog['testsub/view/Signal']))
 113         self.failUnlessEqual(str(search[0].predicate),
 114                              str(dafTermOntology['filename_re']))
 115         #self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
 116
 117     def test_find_one_view(self):
 118         extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
 119
 120 <%(submissionLog)s/testfind/view/Signal> dafTerm:filename_re ".*\\\\.bam" .
 121 <%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*_r1\\\\.fastq" .
 122 ''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog'}
 123
 124         daf_mapper = load_daf_mapper('testfind', extra_statements = extra)
 125
 126         view = daf_mapper.find_view('filename_r1.fastq')
 127         self.failUnlessEqual(str(view),
 128                              str(submissionLog['testfind/view/FastqRd1']))
 129
 130         #writer = get_serializer()
 131         #turtle =  writer.serialize_model_to_string(model)
 132         #print turtle
 133
 134     def test_find_overlapping_view(self):
 135         extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
 136
 137 <%(submissionLog)s/testfind/view/fastq> dafTerm:filename_re ".*\\\\.fastq" .
 138 <%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*_r1\\\\.fastq" .
 139 ''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog'}
 140
 141         daf_mapper = load_daf_mapper('testfind', extra_statements = extra)
 142
 143         self.failUnlessRaises(daf.ModelException,
 144                               daf_mapper.find_view,
 145                               'filename_r1.fastq')
 146
 147     def test_find_attributes(self):
 148         lib_id = '11204'
 149         lib_url = 'http://jumpgate.caltech.edu/library/%s' %(lib_id)
 150         extra = '''@prefix dafTerm: <http://jumpgate.caltech.edu/wiki/UcscDaf#> .
 151 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 152
 153 <%(submissionLog)s/testfind/view/Signal> dafTerm:filename_re ".*\\\\.bam" .
 154 <%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*\\\\.fastq" .
 155 <%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
 156 ''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog',
 157        'libraryOntology': 'http://jumpgate.caltech.edu/wiki/LibraryOntology#',
 158        'libUrl': lib_url}
 159
 160         daf_mapper = load_daf_mapper('testfind', extra)
 161         libNode = RDF.Node(RDF.Uri(lib_url))
 162         daf_mapper._add_library_details_to_model(libNode)
 163         gel_cut = daf_mapper._get_library_attribute(libNode, 'gel_cut')
 164         # make sure we can override attributes, the value in our
 165         # server is 500 for this library
 166         self.failUnlessEqual(gel_cut, 100)
 167
 168         species = daf_mapper._get_library_attribute(libNode, 'species')
 169         self.failUnlessEqual(species, "Homo sapiens")
 170
 171         daf_mapper.construct_file_attributes('/tmp/analysis1', libNode, 'filename.bam')
 172         source = daf_mapper.model.get_source(rdfNS['type'], submissionOntology['submission'])
 173         self.failUnlessEqual(str(source), "<http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1>")
 174         view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
 175         self.failUnlessEqual(str(view), "<http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1/Signal>")
 176
 177
 178     def test_library_url(self):
 179         daf_mapper = load_daf_mapper('urltest')
 180
 181         self.failUnlessEqual(daf_mapper.library_url,
 182                              'http://jumpgate.caltech.edu/library/')
 183         daf_mapper.library_url = 'http://google.com'
 184         self.failUnlessEqual(daf_mapper.library_url, 'http://google.com' )
 185
 186
 187 def suite():
 188     suite = unittest.makeSuite(TestDAF, 'test')
 189     suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))
 190     return suite
 191
 192 if __name__ == "__main__":
 193     unittest.main(defaultTest='suite')