htsworkflow/submission/test/test_submission.py

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