+from contextlib import contextmanager
+import os
+from StringIO import StringIO
+import shutil
+import tempfile
import unittest
from htsworkflow.submission import daf
+from htsworkflow.util.rdfhelp import \
+ dafTermOntology, \
+ fromTypedNode, \
+ rdfNS, \
+ submissionLog, \
+ submissionOntology, \
+ get_model, \
+ get_serializer
+
+import RDF
test_daf = """# Lab and general info
grant Hardison
validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
# Track/view definition
-view Peaks
-longLabelPrefix Caltech Histone Peaks
-type narrowPeak
+view FastqRd1
+longLabelPrefix Caltech Fastq Read 1
+type fastq
hasReplicates yes
required no
self.failUnlessEqual(parsed['grant'], 'Hardison')
self.failUnlessEqual(len(parsed['variables']), 6)
self.failUnlessEqual(len(parsed['views']), 2)
- self.failUnlessEqual(len(parsed['views']['Peaks']), 5)
+ self.failUnlessEqual(len(parsed['views']['FastqRd1']), 5)
self.failUnlessEqual(len(parsed['views']['Signal']), 5)
signal = parsed['views']['Signal']
self.failUnlessEqual(signal['required'], False)
'Caltech Histone Signal')
def test_rdf(self):
- try:
- import RDF
-
- parsed = daf.fromstring(test_daf)
- #mem = RDF.Storage(storage_name='hashes',
- # options_string='hash-type="memory"'),
- mem = RDF.MemoryStorage()
- model = RDF.Model(mem)
-
- daf.add_to_model(model, parsed)
- writer = RDF.Serializer(name='turtle')
- print writer.serialize_model_to_string(model)
+ parsed = daf.fromstring(test_daf)
+ #mem = RDF.Storage(storage_name='hashes',
+ # options_string='hash-type="memory"'),
+ mem = RDF.MemoryStorage()
+ model = RDF.Model(mem)
+
+ name = 'cursub'
+ subNS = RDF.NS(str(submissionLog[name].uri))
+ daf.add_to_model(model, parsed, name)
+
+ signal_view_node = RDF.Node(subNS['/view/Signal'].uri)
+
+ writer = get_serializer()
+ turtle = writer.serialize_model_to_string(model)
+
+ self.failUnless(str(signal_view_node.uri) in turtle)
+
+ statements = list(model.find_statements(
+ RDF.Statement(
+ signal_view_node, None, None)))
+ self.failUnlessEqual(len(statements), 6)
+ name = model.get_target(signal_view_node, dafTermOntology['name'])
+ self.failUnlessEqual(fromTypedNode(name), u'Signal')
+
+def load_daf_mapper(name, extra_statements=None):
+ """Load test model in
+ """
+ model = get_model()
+ if extra_statements is not None:
+ parser = RDF.Parser(name='turtle')
+ parser.parse_string_into_model(model, extra_statements,
+ 'http://extra.extra')
+
+ test_daf_stream = StringIO(test_daf)
+ mapper = daf.DAFMapper(name, daf_file = test_daf_stream, model=model)
+ return mapper
+
+def dump_model(model):
+ writer = get_serializer()
+ turtle = writer.serialize_model_to_string(model)
+ print turtle
+
+class TestDAFMapper(unittest.TestCase):
+ def test_create_mapper_add_pattern(self):
+ name = 'testsub'
+ mapper = load_daf_mapper(name)
+ pattern = '.bam\Z(?ms)'
+ mapper.add_pattern('Signal', pattern)
+
+ s = RDF.Statement(daf.get_view_namespace(name)['Signal'],
+ dafTermOntology['filename_re'],
+ None)
+ search = list(mapper.model.find_statements(s))
+ self.failUnlessEqual(len(search), 1)
+ self.failUnlessEqual(str(search[0].subject),
+ str(submissionLog['testsub/view/Signal']))
+ self.failUnlessEqual(str(search[0].predicate),
+ str(dafTermOntology['filename_re']))
+ #self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
+
+ def test_find_one_view(self):
+ extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+
+<%(submissionLog)s/testfind/view/Signal> dafTerm:filename_re ".*\\\\.bam" .
+<%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*_r1\\\\.fastq" .
+''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog'}
+
+ daf_mapper = load_daf_mapper('testfind', extra_statements = extra)
+
+ view = daf_mapper.find_view('filename_r1.fastq')
+ self.failUnlessEqual(str(view),
+ str(submissionLog['testfind/view/FastqRd1']))
+
+ #writer = get_serializer()
+ #turtle = writer.serialize_model_to_string(model)
+ #print turtle
+
+ def test_find_overlapping_view(self):
+ extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+
+<%(submissionLog)s/testfind/view/fastq> dafTerm:filename_re ".*\\\\.fastq" .
+<%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*_r1\\\\.fastq" .
+''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog'}
+
+ daf_mapper = load_daf_mapper('testfind', extra_statements = extra)
+
+ self.failUnlessRaises(daf.ModelException,
+ daf_mapper.find_view,
+ 'filename_r1.fastq')
+
+ def test_find_attributes(self):
+ lib_id = '11204'
+ lib_url = 'http://jumpgate.caltech.edu/library/%s/' %(lib_id)
+ extra = '''@prefix dafTerm: <http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<%(submissionLog)s/testfind/view/Signal> dafTerm:filename_re ".*\\\\.bam" .
+<%(submissionLog)s/testfind/view/FastqRd1> dafTerm:filename_re ".*\\\\.fastq" .
+<%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
+''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog',
+ 'libraryOntology': 'http://jumpgate.caltech.edu/wiki/LibraryOntology#',
+ 'libUrl': lib_url}
+
+ daf_mapper = load_daf_mapper('testfind', extra)
+ libNode = RDF.Node(RDF.Uri(lib_url))
+ daf_mapper._add_library_details_to_model(libNode)
+ gel_cut = daf_mapper._get_library_attribute(libNode, 'gel_cut')
+ # make sure we can override attributes, the value in our
+ # server is 500 for this library
+ self.failUnlessEqual(gel_cut, 100)
+
+ species = daf_mapper._get_library_attribute(libNode, 'species')
+ self.failUnlessEqual(species, "Homo sapiens")
+
+ with mktempdir('analysis') as analysis_dir:
+ path, analysis_name = os.path.split(analysis_dir)
+ with mktempfile('.bam', dir=analysis_dir) as filename:
+ print 'dir', os.listdir(analysis_dir)
+ daf_mapper.construct_file_attributes(analysis_dir,
+ libNode,
+ filename)
- except ImportError, e:
- print "Skipped test_rdf"
+ sub_root = "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/"
+ submission_name = sub_root + analysis_name
+ source = daf_mapper.model.get_source(rdfNS['type'], submissionOntology['submission'])
+
+ self.failUnlessEqual(str(source.uri), submission_name)
+
+ view_name = submission_name + '/Signal'
+ view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
+ self.failUnlessEqual(str(view.uri), view_name)
+
+ def test_library_url(self):
+ daf_mapper = load_daf_mapper('urltest')
+
+ self.failUnlessEqual(daf_mapper.library_url,
+ 'http://jumpgate.caltech.edu/library/')
+ daf_mapper.library_url = 'http://google.com'
+ self.failUnlessEqual(daf_mapper.library_url, 'http://google.com' )
+
+@contextmanager
+def mktempdir(prefix='tmp'):
+ d = tempfile.mkdtemp(prefix=prefix)
+ print "made", d
+ yield d
+ shutil.rmtree(d)
+ print "unmade", d
+@contextmanager
+def mktempfile(suffix='', prefix='tmp', dir=None):
+ fd, pathname = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir)
+ yield pathname
+ print "made", pathname
+ os.close(fd)
+ os.unlink(pathname)
+ print "unmade", pathname
+
def suite():
- return unittest.makeSuite(TestDAF, 'test')
+ suite = unittest.makeSuite(TestDAF, 'test')
+ suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))
+ return suite
if __name__ == "__main__":
unittest.main(defaultTest='suite')
projects / htsworkflow.git / blobdiff