encode_submission/test_encode_find.py

   1 #!/usr/bin/env python
   2 from datetime import datetime
   3 import os
   4 from unittest import TestCase
   5
   6 import RDF
   7
   8 import encode_find
   9 from htsworkflow.submission.ucsc import submission_view_url
  10 from htsworkflow.util.rdfhelp import add_default_schemas, \
  11      dump_model, get_model, fromTypedNode
  12 from htsworkflow.util.rdfinfer import Infer
  13
  14 SOURCE_PATH = os.path.split(os.path.abspath(__file__))[0]
  15
  16 class TestEncodeFind(TestCase):
  17     def setUp(self):
  18         self.model = get_model()
  19         add_default_schemas(self.model)
  20         self.inference = Infer(self.model)
  21
  22     def test_create_status_node_with_uri(self):
  23         subURL = submission_view_url('5136')
  24         submissionUri = RDF.Uri(subURL)
  25         timestamp = '2011-12-19T12:42:53.048956'
  26         manualUri = subURL + '/' + timestamp
  27         nodeUri = encode_find.create_status_node(submissionUri, timestamp)
  28         self.assertEqual(str(nodeUri.uri), manualUri)
  29
  30     def test_create_status_node_with_str(self):
  31         subURL = submission_view_url('5136')
  32         timestamp = '2011-12-19T12:42:53.048956'
  33         manualUri = subURL + '/' + timestamp
  34         nodeUri = encode_find.create_status_node(subURL, timestamp)
  35         self.assertEqual(str(nodeUri.uri), manualUri)
  36
  37     def test_parse_submission_page(self):
  38         timestamp = '2011-12-19T12:42:53.048956'
  39         subURL = submission_view_url('5136')
  40         subNode = encode_find.create_status_node(subURL, timestamp)
  41         test_file = os.path.join(SOURCE_PATH, 'testdata', '5136SubDetail.html')
  42         from lxml.html import parse
  43         tree = parse(test_file)
  44         dates = encode_find.get_creation_dates(self.model, subNode)
  45         self.assertEqual(len(dates), 0)
  46         encode_find.parse_submission_page(self.model, tree, subNode)
  47         dates = encode_find.get_creation_dates(self.model, subNode)
  48         self.assertEqual(len(dates), 1)
  49         object_date = fromTypedNode(dates[0].object)
  50         self.assertEqual(object_date, datetime(2011,12,7,15,23,0))
  51
  52     def test_delete_simple_lane(self):
  53         model = get_model()
  54         parser = RDF.Parser(name='turtle')
  55         parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
  56 @prefix : <http://www.w3.org/1999/xhtml> .
  57 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  58 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  59 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
  60
  61 <http://jumpgate.caltech.edu/lane/1232>
  62     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
  63     libns:total_unique_locations 5789938 .
  64
  65 ''', 'http://jumpgate.caltech.edu/library/')
  66         errmsgs = list(self.inference.run_validation())
  67         self.assertEqual(len(errmsgs), 0)
  68         urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
  69         encode_find.delete_lane(model, urn)
  70         self.failUnlessEqual(len(model), 0)
  71
  72     def test_delete_lane_with_mapping(self):
  73         ontology_size = len(self.model)
  74         parser = RDF.Parser(name='turtle')
  75         parser.parse_string_into_model(self.model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
  76 @prefix : <http://www.w3.org/1999/xhtml> .
  77 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  78 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  79 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
  80
  81 <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
  82 <http://jumpgate.caltech.edu/lane/1232>
  83     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
  84     libns:has_mappings _:bnode110110 ;
  85     libns:total_unique_locations 5789938 ;
  86     a libns:IlluminaLane .
  87
  88 _:bnode110110
  89     a libns:MappedCount ;
  90     libns:mapped_to "newcontam_UK.fa"@en ;
  91     libns:reads 42473 .
  92 ''', 'http://jumpgate.caltech.edu/library/')
  93         errmsgs = list(self.inference.run_validation())
  94         self.assertEqual(len(errmsgs), 0)
  95         self.failUnlessEqual(len(self.model), 8 + ontology_size)
  96         urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
  97         encode_find.delete_lane(self.model, urn)
  98         self.failUnlessEqual(len(self.model), 1 + ontology_size)
  99         # the flowcell triple wasn't deleted.
 100
 101     def test_delete_library(self):
 102         parser = RDF.Parser(name='turtle')
 103         parser.parse_string_into_model(self.model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 104 @prefix : <http://www.w3.org/1999/xhtml> .
 105 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 106 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 107 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
 108
 109 <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
 110 <http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> a libns:IlluminaFlowcell .
 111
 112 <http://jumpgate.caltech.edu/lane/1232>
 113     a libns:IlluminaLane ;
 114     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
 115     libns:has_mappings _:bnode110110 ;
 116     libns:total_unique_locations 5789938 .
 117
 118 <http://jumpgate.caltech.edu/library/11011/>
 119     libns:affiliation "ENCODE"@en, "ENCODE_Tier1"@en, "Georgi Marinov"@en ;
 120     libns:has_lane <http://jumpgate.caltech.edu/lane/1232> ;
 121     libns:library_id "11011"@en ;
 122     libns:library_type "None"@en ;
 123     a libns:Library ;
 124     <http://www.w3.org/1999/xhtml/vocab#stylesheet> <http://jumpgate.caltech.edu/static/css/app.css>, <http://jumpgate.caltech.edu/static/css/data-browse-index.css> .
 125
 126 _:bnode110110
 127     a libns:MappedCount ;
 128     libns:mapped_to "newcontam_UK.fa"@en ;
 129     libns:reads 42473 .
 130
 131 <http://jumpgate.caltech.edu/lane/1903>
 132     a libns:IlluminaLane ;
 133     libns:flowcell <http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> ;
 134     libns:has_mappings _:bnode120970 ;
 135     libns:total_unique_locations 39172114 .
 136
 137 <http://jumpgate.caltech.edu/library/12097/>
 138     libns:has_lane <http://jumpgate.caltech.edu/lane/1903> ;
 139     libns:library_id "12097"@en ;
 140     libns:library_type "Paired End (non-multiplexed)"@en ;
 141     a libns:Library .
 142
 143 _:bnode120970
 144     a libns:MappedCount ;
 145     libns:mapped_to "newcontam_UK.fa"@en ;
 146     libns:reads 64 .
 147 ''', 'http://jumpgate.caltech.edu/library')
 148         errmsgs = list(self.inference.run_validation())
 149         self.assertEqual(len(errmsgs), 0)
 150         urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/library/11011/'))
 151         encode_find.delete_library(self.model, urn)
 152         q = RDF.Statement(None, encode_find.libraryOntology['reads'], None)
 153         stmts = list(self.model.find_statements(q))
 154         self.failUnlessEqual(len(stmts), 1)
 155         self.failUnlessEqual(fromTypedNode(stmts[0].object),
 156                              64)
 157
 158         q = RDF.Statement(None, encode_find.libraryOntology['library_id'], None)
 159         stmts = list(self.model.find_statements(q))
 160         self.failUnlessEqual(len(stmts), 1)
 161         self.failUnlessEqual(fromTypedNode(stmts[0].object),
 162                              '12097')
 163
 164 def suite():
 165     from unittest import TestSuite, defaultTestLoader
 166     suite = TestSuite()
 167     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind))
 168     return suite
 169
 170
 171 if __name__ == "__main__":
 172     from unittest import main
 173     main()