+class TestSubmission(TestCase):
+ def setUp(self):
+ generate_sample_results_tree(self)
+ self.model = get_model()
+
+ def tearDown(self):
+ shutil.rmtree(self.tempdir)
+
+ def test_create_submission(self):
+ model = get_model()
+ s = Submission('foo', self.model, 'http://localhost')
+ self.assertEqual(str(s.submissionSet),
+ "http://jumpgate.caltech.edu/wiki/SubmissionsLog/foo")
+ self.assertEqual(str(s.submissionSetNS['']),
+ str(RDF.NS(str(s.submissionSet) + '#')['']))
+ self.assertEqual(str(s.libraryNS['']),
+ str(RDF.NS('http://localhost/library/')['']))
+
+ def test_scan_submission_dirs(self):
+ turtle = get_turtle_header() + """
+@prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/> .
+thisView:Fastq ucscDaf:filename_re ".*[^12]\\.fastq\\.bz2$" ;
+ a geoSoft:raw ;
+ geoSoft:fileTypeLabel "fastq" ;
+ ucscDaf:output_type "read" .
+thisView:FastqRead1 ucscDaf:filename_re ".*r1\\.fastq\\.bz2$" ;
+ a geoSoft:raw ;
+ geoSoft:fileTypeLabel "fastq" ;
+ ucscDaf:output_type "read1" .
+thisView:FastqRead2 ucscDaf:filename_re ".*r2\\.fastq\\.bz2$" ;
+ a geoSoft:raw ;
+ geoSoft:fileTypeLabel "fastq" ;
+ ucscDaf:output_type "read2" .
+thisView:alignments ucscDaf:filename_re ".*\\.bam$" ;
+ a geoSoft:supplemental ;
+ geoSoft:fileTypeLabel "bam" ;
+ ucscDaf:output_type "alignments" .
+
+ """
+ map = ResultMap()
+ print self.tempdir
+ print os.listdir(self.tempdir)
+ map['1000'] = os.path.join(self.tempdir, S1_NAME)
+ map['2000'] = os.path.join(self.tempdir, S2_NAME)
+
+ s = Submission('foo', self.model, 'http://localhost')
+ mock = MockAddDetails(self.model, turtle)
+ mock.add_turtle(S1_TURTLE)
+ mock.add_turtle(S2_TURTLE)
+ s._add_library_details_to_model = mock
+ s.scan_submission_dirs(map)
+
+ nodes = list(s.analysis_nodes(map))
+ self.assertEqual(len(nodes), 2)
+ expected = set((
+ 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/foo#1000-sample',
+ 'http://jumpgate.caltech.edu/wiki/SubmissionsLog/foo#2000-sample',
+ ))
+ got = set((str(nodes[0]), str(nodes[1])))
+ self.assertEqual(expected, got)
+
+ def test_find_best_match(self):
+ turtle = get_turtle_header() + """
+@prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/> .
+thisView:Fastq ucscDaf:filename_re ".*[^12]\\.fastq\\.bz2$" ;
+ a geoSoft:raw ;
+ geoSoft:fileTypeLabel "fastq" ;
+ ucscDaf:output_type "read" .
+thisView:FastqRead1 ucscDaf:filename_re ".*r1\\.fastq\\.bz2$" ;
+ a geoSoft:raw ;
+ geoSoft:fileTypeLabel "fastq" ;
+ ucscDaf:output_type "read1" .
+thisView:FastqRead2 ucscDaf:filename_re ".*r2\\.fastq\\.bz2$" ;
+ a geoSoft:raw ;
+ geoSoft:fileTypeLabel "fastq" ;
+ ucscDaf:output_type "read2" .
+thisView:alignments ucscDaf:filename_re ".*\\.bam$" ;
+ a geoSoft:supplemental ;
+ geoSoft:fileTypeLabel "bam" ;
+ ucscDaf:output_type "alignments" .
+
+ """
+ load_string_into_model(self.model, 'turtle', turtle)
+ s = Submission('foo', self.model, 'http://localhost')
+ q = RDF.Statement(None, dafTermOntology['filename_re'], None)
+ view_map = s._get_filename_view_map()
+ self.assertEqual(len(view_map), 4)
+
+ fastq = s.find_best_match("asdf.fastq.bz2")
+ self.assertEqual(
+ str(fastq),
+ "http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/Fastq")
+
+ fastq = s.find_best_match("asdf.r2.fastq.bz2")
+ self.assertEqual(
+ str(fastq),
+ "http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/FastqRead2")
+