encode_submission/test_encode_find.py

   1 #!/usr/bin/env python
   2 from __future__ import absolute_import
   3
   4 from datetime import datetime
   5 import os
   6 from unittest import TestCase
   7
   8 from rdflib import ConjunctiveGraph, URIRef
   9
  10 import keyring.backend
  11
  12 class MockKeyring(keyring.backend.KeyringBackend):
  13     priority = 1
  14     def set_password(self, servicename, username, password):
  15         pass
  16
  17     def get_password(self, servicename, username):
  18         return "example"
  19
  20     def delete_password(self, servicename, username, password):
  21         pass
  22
  23 import keyring
  24 keyring.set_keyring(MockKeyring())
  25
  26 from . import encode_find
  27 from htsworkflow.submission.ucsc import submission_view_url
  28 from htsworkflow.util.rdfhelp import add_default_schemas, \
  29      dump_model
  30 from htsworkflow.util.rdfinfer import Infer
  31
  32 SOURCE_PATH = os.path.split(os.path.abspath(__file__))[0]
  33
  34 class TestEncodeFind(TestCase):
  35     def setUp(self):
  36         self.model = ConjunctiveGraph()
  37         add_default_schemas(self.model)
  38         self.inference = Infer(self.model)
  39
  40     def test_create_status_node_with_uri(self):
  41         subURL = submission_view_url('5136')
  42         submissionUri = URIRef(subURL)
  43         timestamp = '2011-12-19T12:42:53.048956'
  44         manualUri = subURL + '/' + timestamp
  45         nodeUri = encode_find.create_status_node(submissionUri, timestamp)
  46         self.assertEqual(str(nodeUri), manualUri)
  47
  48     def test_create_status_node_with_str(self):
  49         subURL = submission_view_url('5136')
  50         timestamp = '2011-12-19T12:42:53.048956'
  51         manualUri = subURL + '/' + timestamp
  52         nodeUri = encode_find.create_status_node(subURL, timestamp)
  53         self.assertEqual(str(nodeUri), manualUri)
  54
  55     def test_parse_submission_page(self):
  56         timestamp = '2011-12-19T12:42:53.048956'
  57         subURL = submission_view_url('5136')
  58         subNode = encode_find.create_status_node(subURL, timestamp)
  59         test_file = os.path.join(SOURCE_PATH, 'testdata', '5136SubDetail.html')
  60         from lxml.html import parse
  61         tree = parse(test_file)
  62         dates = encode_find.get_creation_dates(self.model, subNode)
  63         self.assertEqual(len(dates), 0)
  64         encode_find.parse_submission_page(self.model, tree, subNode)
  65         dates = encode_find.get_creation_dates(self.model, subNode)
  66         self.assertEqual(len(dates), 1)
  67         object_date = dates[0][2].toPython()
  68         self.assertEqual(object_date, datetime(2011,12,7,15,23,0))
  69
  70     def test_delete_simple_lane(self):
  71         model = ConjunctiveGraph()
  72         lane_1232_ttl ='''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
  73 @prefix : <http://www.w3.org/1999/xhtml> .
  74 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  75 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  76 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
  77
  78 <http://jumpgate.caltech.edu/lane/1232>
  79     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
  80     libns:total_unique_locations 5789938 .
  81
  82 '''
  83         model.parse(data=lane_1232_ttl, format='turtle', publicID='http://jumpgate.caltech.edu/library/')
  84         errmsgs = list(self.inference.run_validation())
  85         self.assertEqual(len(errmsgs), 0)
  86         urn = URIRef('http://jumpgate.caltech.edu/lane/1232')
  87         encode_find.delete_lane(model, urn)
  88         self.failUnlessEqual(len(model), 0)
  89
  90     def test_delete_lane_with_mapping(self):
  91         ontology_size = len(self.model)
  92         lane_1232_ttl = '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
  93 @prefix : <http://www.w3.org/1999/xhtml> .
  94 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  95 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  96 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
  97
  98 <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
  99 <http://jumpgate.caltech.edu/lane/1232>
 100     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
 101     libns:has_mappings _:bnode110110 ;
 102     libns:total_unique_locations 5789938 ;
 103     a libns:IlluminaLane .
 104
 105 _:bnode110110
 106     a libns:MappedCount ;
 107     libns:mapped_to "newcontam_UK.fa"@en ;
 108     libns:reads 42473 .
 109 '''
 110         self.model.parse(data=lane_1232_ttl, format='turtle', publicID='http://jumpgate.caltech.edu/library/')
 111         errmsgs = list(self.inference.run_validation())
 112         self.assertEqual(len(errmsgs), 0)
 113         self.failUnlessEqual(len(self.model), 8 + ontology_size)
 114         urn = URIRef('http://jumpgate.caltech.edu/lane/1232')
 115         encode_find.delete_lane(self.model, urn)
 116         self.failUnlessEqual(len(self.model), 1 + ontology_size)
 117         # the flowcell triple wasn't deleted.
 118
 119     def test_delete_library(self):
 120         ttl = '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 121 @prefix : <http://www.w3.org/1999/xhtml> .
 122 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 123 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 124 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
 125
 126 <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
 127 <http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> a libns:IlluminaFlowcell .
 128
 129 <http://jumpgate.caltech.edu/lane/1232>
 130     a libns:IlluminaLane ;
 131     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
 132     libns:has_mappings _:bnode110110 ;
 133     libns:total_unique_locations 5789938 .
 134
 135 <http://jumpgate.caltech.edu/library/11011/>
 136     libns:affiliation "ENCODE"@en, "ENCODE_Tier1"@en, "Georgi Marinov"@en ;
 137     libns:has_lane <http://jumpgate.caltech.edu/lane/1232> ;
 138     libns:library_id "11011"@en ;
 139     libns:library_type "None"@en ;
 140     a libns:Library ;
 141     <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> .
 142
 143 _:bnode110110
 144     a libns:MappedCount ;
 145     libns:mapped_to "newcontam_UK.fa"@en ;
 146     libns:reads 42473 .
 147
 148 <http://jumpgate.caltech.edu/lane/1903>
 149     a libns:IlluminaLane ;
 150     libns:flowcell <http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> ;
 151     libns:has_mappings _:bnode120970 ;
 152     libns:total_unique_locations 39172114 .
 153
 154 <http://jumpgate.caltech.edu/library/12097/>
 155     libns:has_lane <http://jumpgate.caltech.edu/lane/1903> ;
 156     libns:library_id "12097"@en ;
 157     libns:library_type "Paired End (non-multiplexed)"@en ;
 158     a libns:Library .
 159
 160 _:bnode120970
 161     a libns:MappedCount ;
 162     libns:mapped_to "newcontam_UK.fa"@en ;
 163     libns:reads 64 .
 164 '''
 165         self.model.parse(data=ttl, format='turtle', publicID='http://jumpgate.caltech.edu/library')
 166         errmsgs = list(self.inference.run_validation())
 167         self.assertEqual(len(errmsgs), 0)
 168         urn = URIRef('http://jumpgate.caltech.edu/library/11011/')
 169         encode_find.delete_library(self.model, urn)
 170         q = (None, encode_find.libraryOntology['reads'], None)
 171         stmts = list(self.model.triples(q))
 172         self.failUnlessEqual(len(stmts), 1)
 173         self.failUnlessEqual(stmts[0][2].toPython(), 64)
 174
 175         q = (None, encode_find.libraryOntology['library_id'], None)
 176         stmts = list(self.model.triples(q))
 177         self.failUnlessEqual(len(stmts), 1)
 178         self.failUnlessEqual(stmts[0][2].toPython(), '12097')
 179
 180 def suite():
 181     from unittest import TestSuite, defaultTestLoader
 182     suite = TestSuite()
 183     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind))
 184     return suite
 185
 186 if __name__ == "__main__":
 187     from unittest import main
 188     main()