-import unittest
+from contextlib import contextmanager
+import logging
+import os
+from StringIO import StringIO
+import shutil
+import tempfile
+from unittest import TestCase, TestSuite, defaultTestLoader
-from htsworkflow.submission import daf
+from htsworkflow.submission import daf, results
+from htsworkflow.util.rdfhelp import \
+ dafTermOntology, \
+ fromTypedNode, \
+ rdfNS, \
+ submissionLog, \
+ submissionOntology, \
+ get_model, \
+ get_serializer
+
+from htsworkflow.submission.test import test_results
+import RDF
test_daf = """# Lab and general info
grant Hardison
lab Caltech-m
-dataType ChipSeq
+dataType ChipSeq
variables cell, antibody,sex,age,strain,control
compositeSuffix CaltechHistone
assembly mm9
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
required no
"""
-class TestDAF(unittest.TestCase):
+test_daf_no_rep = """# Lab and general info
+grant Hardison
+lab Caltech-m
+dataType ChipSeq
+variables cell, antibody,sex,age,strain,control
+compositeSuffix CaltechHistone
+assembly mm9
+dafVersion 2.0
+validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
+
+# Track/view definition
+view FastqRd1
+longLabelPrefix Caltech Fastq Read 1
+type fastq
+hasReplicates no
+required no
+"""
+
+test_daf_extra = """# Lab and general info
+grant Hardison
+lab Caltech-m
+dataType ChipSeq
+variables cell,antibody,sex,age,strain
+extraVariables controlId,treatment
+compositeSuffix CaltechHistone
+assembly mm9
+dafVersion 2.0
+validationSettings validateFiles.bam:mismatches=2,bamPercent=99.9;validateFiles.fastq:quick=1000
+
+# Track/view definition
+view FastqRd1
+longLabelPrefix Caltech Fastq Read 1
+type fastq
+hasReplicates no
+required no
+"""
+
+
+class TestDAF(TestCase):
def test_parse(self):
parsed = daf.fromstring(test_daf)
-
+
self.failUnlessEqual(parsed['assembly'], 'mm9')
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)
self.failUnlessEqual(signal['longLabelPrefix'],
'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)
-
- except ImportError, e:
- print "Skipped test_rdf"
+
+ 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, submissionLog[name].uri)
+
+ 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 test_get_view_namespace_from_string(self):
+ url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
+ target = RDF.NS(url + 'view/')
+ view_namespace = daf.get_view_namespace(url)
+ self.assertEqual(view_namespace[''], target[''])
+
+ def test_get_view_namespace_from_string_no_trailing_slash(self):
+ url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub"
+ target = RDF.NS(url + '/view/')
+ view_namespace = daf.get_view_namespace(url)
+ self.assertEqual(view_namespace[''], target[''])
+
+ def test_get_view_namespace_from_uri_node(self):
+ url = "http://jumpgate.caltech.edu/wiki/SubmissionLog/cursub/"
+ node = RDF.Node(RDF.Uri(url))
+ target = RDF.NS(url + 'view/')
+ view_namespace = daf.get_view_namespace(node)
+ self.assertEqual(view_namespace[''], target[''])
+
+
+def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
+ """Load test model in
+ """
+ model = get_model()
+ if ns is None:
+ ns="http://extra"
+
+ if extra_statements is not None:
+ parser = RDF.Parser(name='turtle')
+ parser.parse_string_into_model(model, extra_statements,
+ ns)
+
+ test_daf_stream = StringIO(test_daf)
+ mapper = daf.UCSCSubmission(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 TestUCSCSubmission(TestCase):
+ def setUp(self):
+ test_results.generate_sample_results_tree(self, 'daf_results')
+
+ def tearDown(self):
+ # see things created by temp_results.generate_sample_results_tree
+ shutil.rmtree(self.tempdir)
+
+ 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(mapper.viewNS['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):
+ name='testfind'
+ extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+@prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/> .
+
+thisView:Signal dafTerm:filename_re ".*\\\\.bam" .
+thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
+'''.format(name)
+ daf_mapper = load_daf_mapper(name, extra_statements = extra)
+
+ view = daf_mapper.find_view('filename_r1.fastq')
+
+ # dump_model(daf_mapper.model)
+ view_root = 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/'
+ view_root = view_root.format(name)
+ self.failUnlessEqual(str(view.uri),
+ '{0}{1}'.format(view_root,'FastqRd1'))
+
+ def test_find_overlapping_view(self):
+ name = 'testfind'
+ extra = '''@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+@prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/{0}/view/> .
+
+thisView:fastq dafTerm:filename_re ".*\\\\.fastq" .
+thisView:FastqRd1 dafTerm:filename_re ".*_r1\\\\.fastq" .
+'''.format(name)
+ daf_mapper = load_daf_mapper(name, 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 submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#> .
+@prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/view/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+thisView:Signal dafTerm:filename_re ".*\\\\.bam" ;
+ submissionOntology:view_name "Signal" .
+thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
+ submissionOntology:view_name "FastqRd1" .
+<%(libUrl)s> <%(libraryOntology)sgel_cut> "100"^^xsd:decimal .
+''' % {'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_name')
+ 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:
+ daf_mapper.construct_track_attributes(analysis_dir,
+ libNode,
+ filename)
+
+ #dump_model(daf_mapper.model)
+
+ 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' )
+
+ def test_daf_with_replicate(self):
+ daf_mapper = load_daf_mapper('test_rep')
+ self.failUnlessEqual(daf_mapper.need_replicate(), True)
+ self.failUnless('replicate' in daf_mapper.get_daf_variables())
+
+ def test_daf_without_replicate(self):
+ daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_no_rep)
+ self.failUnlessEqual(daf_mapper.need_replicate(), False)
+ self.failUnless('replicate' not in daf_mapper.get_daf_variables())
+
+ def test_daf_with_extra(self):
+ daf_mapper = load_daf_mapper('test_rep',test_daf=test_daf_extra)
+ variables = daf_mapper.get_daf_variables()
+ self.assertEqual(len(variables), 11)
+ self.failUnless('treatment' in variables)
+ self.failUnless('controlId' in variables)
+
+
+ def test_link_daf(self):
+ name = 'testsub'
+ submission = load_daf_mapper(name, test_daf=test_daf)
+ result_map = results.ResultMap()
+ result_dir = os.path.join(self.sourcedir,
+ test_results.S1_NAME)
+ result_map['1000'] = result_dir
+
+ submission.link_daf(result_map)
+
+ # make sure daf gets linked
+ created_daf = os.path.join(result_dir, name+'.daf')
+ self.failUnless(os.path.exists(created_daf))
+ stream = open(created_daf,'r')
+ daf_body = stream.read()
+ stream.close()
+
+ self.failUnlessEqual(test_daf, daf_body)
+
+
+@contextmanager
+def mktempdir(prefix='tmp'):
+ d = tempfile.mkdtemp(prefix=prefix)
+ yield d
+ shutil.rmtree(d)
+
+
+@contextmanager
+def mktempfile(suffix='', prefix='tmp', dir=None):
+ fd, pathname = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir)
+ yield pathname
+ os.close(fd)
+ os.unlink(pathname)
def suite():
- return unittest.makeSuite(TestDAF, 'test')
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestDAF))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestUCSCSubmission))
+ return suite
if __name__ == "__main__":
- unittest.main(defaultTest='suite')
+ logging.basicConfig(level=logging.DEBUG)
+ from unittest import main
+ main(defaultTest='suite')
projects / htsworkflow.git / blobdiff