encode_submission/test_encode_find.py

   1 #!/usr/bin/env python
   2 from datetime import datetime
   3 import os
   4 import unittest
   5
   6 import RDF
   7
   8 import encode_find
   9 from htsworkflow.submission.ucsc import submission_view_url
  10 from htsworkflow.util.rdfhelp import dump_model, get_model, fromTypedNode
  11
  12 SOURCE_PATH = os.path.split(os.path.abspath(__file__))[0]
  13 print SOURCE_PATH
  14
  15 class TestEncodeFind(unittest.TestCase):
  16     def test_create_status_node_with_uri(self):
  17         subURL = submission_view_url('5136')
  18         submissionUri = RDF.Uri(subURL)
  19         timestamp = '2011-12-19T12:42:53.048956'
  20         manualUri = subURL + '/' + timestamp
  21         nodeUri = encode_find.create_status_node(submissionUri, timestamp)
  22         self.assertEqual(str(nodeUri.uri), manualUri)
  23
  24     def test_create_status_node_with_str(self):
  25         subURL = submission_view_url('5136')
  26         timestamp = '2011-12-19T12:42:53.048956'
  27         manualUri = subURL + '/' + timestamp
  28         nodeUri = encode_find.create_status_node(subURL, timestamp)
  29         self.assertEqual(str(nodeUri.uri), manualUri)
  30
  31     def test_parse_submission_page(self):
  32         timestamp = '2011-12-19T12:42:53.048956'
  33         subURL = submission_view_url('5136')
  34         subNode = encode_find.create_status_node(subURL, timestamp)
  35         test_file = os.path.join(SOURCE_PATH, 'testdata', '5136SubDetail.html')
  36         from lxml.html import parse
  37         tree = parse(test_file)
  38         model = get_model()
  39         dates = encode_find.get_creation_dates(model, subNode)
  40         self.assertEqual(len(dates), 0)
  41         encode_find.parse_submission_page(model, tree, subNode)
  42         dates = encode_find.get_creation_dates(model, subNode)
  43         self.assertEqual(len(dates), 1)
  44         object_date = fromTypedNode(dates[0].object)
  45         self.assertEqual(object_date, datetime(2011,12,7,15,23,0))
  46
  47     def test_delete_simple_lane(self):
  48         model = get_model()
  49         parser = RDF.Parser(name='turtle')
  50         parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
  51 @prefix : <http://www.w3.org/1999/xhtml> .
  52 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  53 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  54 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
  55
  56 <http://jumpgate.caltech.edu/lane/1232>
  57     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
  58     libns:total_unique_locations 5789938 .
  59
  60 ''', 'http://jumpgate.caltech.edu/library/')
  61         urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
  62         encode_find.delete_lane(model, urn)
  63         self.failUnlessEqual(len(model), 0)
  64
  65     def test_delete_lane_with_mapping(self):
  66         model = get_model()
  67         parser = RDF.Parser(name='turtle')
  68         parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
  69 @prefix : <http://www.w3.org/1999/xhtml> .
  70 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  71 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  72 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
  73
  74 <http://jumpgate.caltech.edu/lane/1232>
  75     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
  76     libns:has_mappings _:bnode110110 ;
  77     libns:total_unique_locations 5789938 .
  78
  79 _:bnode110110
  80     libns:mapped_to "newcontam_UK.fa"@en ;
  81     libns:reads 42473 .
  82 ''', 'http://jumpgate.caltech.edu/library/')
  83         self.failUnlessEqual(len(model), 5)
  84         urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
  85         encode_find.delete_lane(model, urn)
  86         self.failUnlessEqual(len(model), 0)
  87
  88     def test_delete_library(self):
  89         model = get_model()
  90         parser = RDF.Parser(name='turtle')
  91         parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
  92 @prefix : <http://www.w3.org/1999/xhtml> .
  93 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
  94 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
  95 @prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
  96
  97 <http://jumpgate.caltech.edu/lane/1232>
  98     libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
  99     libns:has_mappings _:bnode110110 ;
 100     libns:total_unique_locations 5789938 .
 101
 102 <http://jumpgate.caltech.edu/library/11011/>
 103     libns:affiliation "ENCODE"@en, "ENCODE_Tier1"@en, "Georgi Marinov"@en ;
 104     libns:has_lane <http://jumpgate.caltech.edu/lane/1232> ;
 105     libns:library_id "11011"@en ;
 106     libns:library_type "None"@en ;
 107     a "libns:library"@en ;
 108     <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> .
 109
 110 _:bnode110110
 111     libns:mapped_to "newcontam_UK.fa"@en ;
 112     libns:reads 42473 .
 113
 114 <http://jumpgate.caltech.edu/lane/1903>
 115     libns:flowcell <http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> ;
 116     libns:has_mappings _:bnode120970 ;
 117     libns:total_unique_locations 39172114 .
 118
 119 <http://jumpgate.caltech.edu/library/12097/>
 120     libns:has_lane <http://jumpgate.caltech.edu/lane/1903> ;
 121     libns:library_id "12097"@en ;
 122     libns:library_type "Paired End (non-multiplexed)"@en ;
 123     a "libns:library"@en .
 124
 125 _:bnode120970
 126     libns:mapped_to "newcontam_UK.fa"@en ;
 127     libns:reads 64 .
 128 ''', 'http://jumpgate.caltech.edu/library')
 129         urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/library/11011/'))
 130         encode_find.delete_library(model, urn)
 131         q = RDF.Statement(None, encode_find.libraryOntology['reads'], None)
 132         stmts = list(model.find_statements(q))
 133         self.failUnlessEqual(len(stmts), 1)
 134         self.failUnlessEqual(fromTypedNode(stmts[0].object),
 135                              64)
 136
 137         q = RDF.Statement(None, encode_find.libraryOntology['library_id'], None)
 138         stmts = list(model.find_statements(q))
 139         self.failUnlessEqual(len(stmts), 1)
 140         self.failUnlessEqual(fromTypedNode(stmts[0].object),
 141                              '12097')
 142
 143 def suite():
 144     return unittest.makeSuite(TestEncodeFind, "test")
 145
 146 if __name__ == "__main__":
 147     unittest.main(defaultTest="suite")