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
  73         self.failUnless(str(signal_view_node.uri) in turtle)
  74
  75         statements = list(model.find_statements(
  76             RDF.Statement(
  77                 signal_view_node, None, None)))
  78         self.failUnlessEqual(len(statements), 6)
  79         name = model.get_target(signal_view_node, dafTermOntology['name'])
  80         self.failUnlessEqual(fromTypedNode(name), u'Signal')
  81
  82 def load_daf_mapper(name, extra_statements=None):
  83     """Load test model in
  84     """
  85     model = get_model()
  86     if extra_statements is not None:
  87         parser = RDF.Parser(name='turtle')
  88         parser.parse_string_into_model(model, extra_statements,
  89                                        'http://extra.extra')
  90
  91     test_daf_stream = StringIO(test_daf)
  92     mapper = daf.DAFMapper(name, daf_file = test_daf_stream, model=model)
  93     return mapper
  94
  95 def dump_model(model):
  96     writer = get_serializer()
  97     turtle =  writer.serialize_model_to_string(model)
  98     print turtle
  99
 100 class TestDAFMapper(unittest.TestCase):
 101     def test_create_mapper_add_pattern(self):
 102         name = 'testsub'
 103         mapper = load_daf_mapper(name)
 104         pattern = '.bam\Z(?ms)'
 105         mapper.add_pattern('Signal', pattern)
 106
 107         s = RDF.Statement(daf.get_view_namespace(name)['Signal'],
 108                           dafTermOntology['filename_re'],
 109                           None)
 110         search = list(mapper.model.find_statements(s))
 111         self.failUnlessEqual(len(search), 1)
 112         self.failUnlessEqual(str(search[0].subject),
 113                              str(submissionLog['testsub/view/Signal']))
 114         self.failUnlessEqual(str(search[0].predicate),
 115                              str(dafTermOntology['filename_re']))
 116         #self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
 117
 118     def test_find_one_view(self):
 119         extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
 120
 121 <%(submissionLog)s/testfind/view/Signal> dafTerm:filename_re ".*\\\\.bam" .
 122 <%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*_r1\\\\.fastq" .
 123 ''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog'}
 124
 125         daf_mapper = load_daf_mapper('testfind', extra_statements = extra)
 126
 127         view = daf_mapper.find_view('filename_r1.fastq')
 128         self.failUnlessEqual(str(view),
 129                              str(submissionLog['testfind/view/FastqRd1']))
 130
 131         #writer = get_serializer()
 132         #turtle =  writer.serialize_model_to_string(model)
 133         #print turtle
 134
 135     def test_find_overlapping_view(self):
 136         extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
 137
 138 <%(submissionLog)s/testfind/view/fastq> dafTerm:filename_re ".*\\\\.fastq" .
 139 <%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*_r1\\\\.fastq" .
 140 ''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog'}
 141
 142         daf_mapper = load_daf_mapper('testfind', extra_statements = extra)
 143
 144         self.failUnlessRaises(daf.ModelException,
 145                               daf_mapper.find_view,
 146                               'filename_r1.fastq')
 147
 148     def test_find_attributes(self):
 149         lib_id = '11204'
 150         lib_url = 'http://jumpgate.caltech.edu/library/%s' %(lib_id)
 151         extra = '''@prefix dafTerm: <http://jumpgate.caltech.edu/wiki/UcscDaf#> .
 152 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 153
 154 <%(submissionLog)s/testfind/view/Signal> dafTerm:filename_re ".*\\\\.bam" .
 155 <%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*\\\\.fastq" .
 156 <%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
 157 ''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog',
 158        'libraryOntology': 'http://jumpgate.caltech.edu/wiki/LibraryOntology#',
 159        'libUrl': lib_url}
 160
 161         daf_mapper = load_daf_mapper('testfind', extra)
 162         libNode = RDF.Node(RDF.Uri(lib_url))
 163         daf_mapper._add_library_details_to_model(libNode)
 164         gel_cut = daf_mapper._get_library_attribute(libNode, 'gel_cut')
 165         # make sure we can override attributes, the value in our
 166         # server is 500 for this library
 167         self.failUnlessEqual(gel_cut, 100)
 168
 169         species = daf_mapper._get_library_attribute(libNode, 'species')
 170         self.failUnlessEqual(species, "Homo sapiens")
 171
 172         daf_mapper.construct_file_attributes('/tmp/analysis1', libNode, 'filename.bam')
 173         source = daf_mapper.model.get_source(rdfNS['type'], submissionOntology['submission'])
 174         self.failUnlessEqual(str(source.uri), "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1")
 175         view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
 176         self.failUnlessEqual(str(view.uri), "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1/Signal")
 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 def suite():
 187     suite = unittest.makeSuite(TestDAF, 'test')
 188     suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))
 189     return suite
 190
 191 if __name__ == "__main__":
 192     unittest.main(defaultTest='suite')