+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, \
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)
- #print turtle
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), 5)
-
+ 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()
class TestDAFMapper(unittest.TestCase):
def test_create_mapper_add_pattern(self):
name = 'testsub'
- test_daf_stream = StringIO(test_daf)
- mapper = daf.DAFMapper(name, daf_file=test_daf_stream)
+ mapper = load_daf_mapper(name)
pattern = '.bam\Z(?ms)'
mapper.add_pattern('Signal', pattern)
#self.failUnlessEqual(search[0].object.literal_value['string'], pattern)
def test_find_one_view(self):
- model = get_model()
-
- parser = RDF.Parser(name='turtle')
- parser.parse_string_into_model(model, '''
-@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+ 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'},
- 'http://blank')
- name = 'testfind'
- test_stream = StringIO(test_daf)
- daf_mapper = daf.DAFMapper(name, daf_file=test_stream, model=model)
+''' % {'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),
#print turtle
def test_find_overlapping_view(self):
- model = get_model()
-
- parser = RDF.Parser(name='turtle')
- parser.parse_string_into_model(model, '''
-@prefix dafTerm:<http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+ 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'},
- 'http://blank')
- name = 'testfind'
- test_stream = StringIO(test_daf)
- daf_mapper = daf.DAFMapper(name, daf_file=test_stream, model=model)
+''' % {'submissionLog': 'http://jumpgate.caltech.edu/wiki/SubmissionsLog'}
+
+ daf_mapper = load_daf_mapper('testfind', extra_statements = extra)
self.failUnlessRaises(daf.ModelException,
daf_mapper.find_view,
def test_find_attributes(self):
lib_id = '11204'
lib_url = 'http://jumpgate.caltech.edu/library/%s' %(lib_id)
- model = get_model()
-
- parser = RDF.Parser(name='turtle')
- parser.parse_string_into_model(model, '''
-@prefix dafTerm: <http://jumpgate.caltech.edu/wiki/UcscDaf#> .
+ 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" .
<%(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},
- 'http://blank')
- name = 'testfind'
- test_stream = StringIO(test_daf)
- daf_mapper = daf.DAFMapper(name, daf_file=test_stream, model=model)
+ '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')
species = daf_mapper._get_library_attribute(libNode, 'species')
self.failUnlessEqual(species, "Homo sapiens")
-
- daf_mapper.construct_file_attributes('/tmp/analysis1', libNode, 'filename.bam')
+
+ 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)
+
+ 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), "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1")
- view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
- self.failUnlessEqual(str(view.uri), "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/view/Signal")
+ 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():
suite = unittest.makeSuite(TestDAF, 'test')
suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))
projects / htsworkflow.git / blobdiff