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