htsworkflow/submission/test/test_submission.py

   1
   2 import os
   3 import shutil
   4 from unittest import TestCase, TestSuite, defaultTestLoader
   5
   6 from htsworkflow.util.rdfhelp import \
   7      dafTermOntology, \
   8      get_turtle_header, \
   9      load_string_into_model, \
  10      get_model
  11 from htsworkflow.submission.submission import list_submissions, Submission
  12 from htsworkflow.submission.results import ResultMap
  13 from .submission_test_common import  (
  14     generate_sample_results_tree,
  15     S1_NAME,
  16     S2_NAME,
  17     S1_TURTLE,
  18     S2_TURTLE,
  19     MockAddDetails,
  20 )
  21
  22 import RDF
  23 #import logging
  24 #logging.basicConfig(level=logging.DEBUG)
  25
  26 class TestSubmissionModule(TestCase):
  27     def test_empty_list_submission(self):
  28         model = get_model()
  29         self.assertEqual(len(list(list_submissions(model))), 0)
  30
  31     def test_one_submission(self):
  32         model = get_model()
  33         load_string_into_model(model, "turtle",
  34             """
  35             @prefix subns: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#> .
  36             @prefix test: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test#> .
  37
  38             <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test#>
  39                subns:has_submission test:lib1 ;
  40                subns:has_submission test:lib2.
  41             """)
  42         submissions = list(list_submissions(model))
  43         self.assertEqual(len(submissions), 1)
  44         self.assertEqual(submissions[0], "test")
  45
  46     def test_two_submission(self):
  47         model = get_model()
  48         load_string_into_model(model, "turtle",
  49             """
  50             @prefix subns: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#> .
  51             @prefix test: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test#> .
  52
  53             <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test1#>
  54                subns:has_submission test:lib1 .
  55             <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test2#>
  56                subns:has_submission test:lib2 .
  57             """)
  58         submissions = list(list_submissions(model))
  59         self.assertEqual(len(submissions), 2)
  60         truth = set(["test1", "test2"])
  61         testset = set()
  62         for name in submissions:
  63             testset.add(name)
  64         self.assertEqual(testset, truth)
  65
  66 class TestSubmission(TestCase):
  67     def setUp(self):
  68         generate_sample_results_tree(self, 'submission_test')
  69         self.model = get_model()
  70
  71     def tearDown(self):
  72         shutil.rmtree(self.tempdir)
  73
  74     def test_create_submission(self):
  75         s = Submission('foo', self.model, 'http://localhost')
  76         self.assertEqual(str(s.submissionSet),
  77                          "http://jumpgate.caltech.edu/wiki/SubmissionsLog/foo")
  78         self.assertEqual(str(s.submissionSetNS['']),
  79                          str(RDF.NS(str(s.submissionSet) + '#')['']))
  80         self.assertEqual(str(s.libraryNS['']),
  81                          str(RDF.NS('http://localhost/library/')['']))
  82
  83     def test_scan_submission_dirs(self):
  84         turtle = get_turtle_header() + """
  85 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/> .
  86 thisView:Fastq ucscDaf:filename_re ".*[^12]\\.fastq$" ;
  87                a geoSoft:raw ;
  88                geoSoft:fileTypeLabel "fastq" ;
  89                ucscDaf:output_type "read" .
  90 thisView:FastqRead1 ucscDaf:filename_re ".*r1\\.fastq$" ;
  91                a geoSoft:raw ;
  92                geoSoft:fileTypeLabel "fastq" ;
  93                ucscDaf:output_type "read1" .
  94 thisView:FastqRead2 ucscDaf:filename_re ".*r2\\.fastq$" ;
  95                a geoSoft:raw ;
  96                geoSoft:fileTypeLabel "fastq" ;
  97                ucscDaf:output_type "read2" .
  98 thisView:alignments ucscDaf:filename_re ".*\\.bam$" ;
  99                a geoSoft:supplemental ;
 100                geoSoft:fileTypeLabel "bam" ;
 101                ucscDaf:output_type "alignments" .
 102
 103         """
 104         map = ResultMap()
 105         map['1000'] = os.path.join(self.sourcedir, S1_NAME)
 106         map['2000'] = os.path.join(self.sourcedir, S2_NAME)
 107
 108         s = Submission('foo', self.model, 'http://localhost')
 109         mock = MockAddDetails(self.model, turtle)
 110         mock.add_turtle(S1_TURTLE)
 111         mock.add_turtle(S2_TURTLE)
 112         s._add_library_details_to_model =  mock
 113         s.scan_submission_dirs(map)
 114
 115         nodes = list(s.analysis_nodes(map))
 116         self.assertEqual(len(nodes), 2)
 117         expected = set((
 118             'http://jumpgate.caltech.edu/wiki/SubmissionsLog/foo#1000-sample',
 119             'http://jumpgate.caltech.edu/wiki/SubmissionsLog/foo#2000-sample',
 120         ))
 121         got = set((str(nodes[0]), str(nodes[1])))
 122         self.assertEqual(expected, got)
 123
 124     def test_find_best_match(self):
 125         turtle = get_turtle_header() + """
 126 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/> .
 127 thisView:Fastq ucscDaf:filename_re ".*[^12]\\.fastq\\.bz2$" ;
 128                a geoSoft:raw ;
 129                geoSoft:fileTypeLabel "fastq" ;
 130                ucscDaf:output_type "read" .
 131 thisView:FastqRead1 ucscDaf:filename_re ".*r1\\.fastq\\.bz2$" ;
 132                a geoSoft:raw ;
 133                geoSoft:fileTypeLabel "fastq" ;
 134                ucscDaf:output_type "read1" .
 135 thisView:FastqRead2 ucscDaf:filename_re ".*r2\\.fastq\\.bz2$" ;
 136                a geoSoft:raw ;
 137                geoSoft:fileTypeLabel "fastq" ;
 138                ucscDaf:output_type "read2" .
 139 thisView:alignments ucscDaf:filename_re ".*\\.bam$" ;
 140                a geoSoft:supplemental ;
 141                geoSoft:fileTypeLabel "bam" ;
 142                ucscDaf:output_type "alignments" .
 143
 144         """
 145         load_string_into_model(self.model, 'turtle', turtle)
 146         s = Submission('foo', self.model, 'http://localhost')
 147         q = RDF.Statement(None, dafTermOntology['filename_re'], None)
 148         view_map = s._get_filename_view_map()
 149         self.assertEqual(len(view_map), 4)
 150
 151         fastq = s.find_best_match("asdf.fastq.bz2")
 152         self.assertEqual(
 153             str(fastq),
 154             "http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/Fastq")
 155
 156         fastq = s.find_best_match("asdf.r2.fastq.bz2")
 157         self.assertEqual(
 158             str(fastq),
 159             "http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/FastqRead2")
 160
 161 def suite():
 162     suite = TestSuite()
 163     suite.addTests(
 164         defaultTestLoader.loadTestsFromTestCase(TestSubmissionModule))
 165     suite.addTests(
 166         defaultTestLoader.loadTestsFromTestCase(TestSubmission))
 167     return suite
 168
 169 if __name__ == "__main__":
 170     from unittest import main
 171     main(defaultTest='suite')