#!/usr/bin/env python
+from datetime import datetime
import os
-import unittest
+from unittest import TestCase
import RDF
import encode_find
from htsworkflow.submission.ucsc import submission_view_url
-from htsworkflow.util.rdfhelp import dump_model, get_model
+from htsworkflow.util.rdfhelp import add_default_schemas, \
+ dump_model, get_model, fromTypedNode
+from htsworkflow.util.rdfinfer import Infer
SOURCE_PATH = os.path.split(os.path.abspath(__file__))[0]
-print SOURCE_PATH
-class TestEncodeFind(unittest.TestCase):
+class TestEncodeFind(TestCase):
+ def setUp(self):
+ self.model = get_model()
+ add_default_schemas(self.model)
+ self.inference = Infer(self.model)
+
def test_create_status_node_with_uri(self):
subURL = submission_view_url('5136')
submissionUri = RDF.Uri(subURL)
test_file = os.path.join(SOURCE_PATH, 'testdata', '5136SubDetail.html')
from lxml.html import parse
tree = parse(test_file)
- model = get_model()
- dates = encode_find.get_creation_dates(model, subNode)
+ dates = encode_find.get_creation_dates(self.model, subNode)
self.assertEqual(len(dates), 0)
- encode_find.parse_submission_page(model, tree, subNode)
- dates = encode_find.get_creation_dates(model, subNode)
+ encode_find.parse_submission_page(self.model, tree, subNode)
+ dates = encode_find.get_creation_dates(self.model, subNode)
self.assertEqual(len(dates), 1)
- self.assertEqual(str(dates[0].object), '2011-12-07T15:23:00')
+ object_date = fromTypedNode(dates[0].object)
+ self.assertEqual(object_date, datetime(2011,12,7,15,23,0))
+
+ def test_delete_simple_lane(self):
+ model = get_model()
+ parser = RDF.Parser(name='turtle')
+ parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix : <http://www.w3.org/1999/xhtml> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
+
+<http://jumpgate.caltech.edu/lane/1232>
+ libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
+ libns:total_unique_locations 5789938 .
+
+''', 'http://jumpgate.caltech.edu/library/')
+ errmsgs = list(self.inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
+ urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
+ encode_find.delete_lane(model, urn)
+ self.failUnlessEqual(len(model), 0)
+
+ def test_delete_lane_with_mapping(self):
+ ontology_size = len(self.model)
+ parser = RDF.Parser(name='turtle')
+ parser.parse_string_into_model(self.model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix : <http://www.w3.org/1999/xhtml> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
+
+<http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
+<http://jumpgate.caltech.edu/lane/1232>
+ libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
+ libns:has_mappings _:bnode110110 ;
+ libns:total_unique_locations 5789938 ;
+ a libns:IlluminaLane .
+
+_:bnode110110
+ a libns:MappedCount ;
+ libns:mapped_to "newcontam_UK.fa"@en ;
+ libns:reads 42473 .
+''', 'http://jumpgate.caltech.edu/library/')
+ errmsgs = list(self.inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
+ self.failUnlessEqual(len(self.model), 8 + ontology_size)
+ urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
+ encode_find.delete_lane(self.model, urn)
+ self.failUnlessEqual(len(self.model), 1 + ontology_size)
+ # the flowcell triple wasn't deleted.
+
+ def test_delete_library(self):
+ parser = RDF.Parser(name='turtle')
+ parser.parse_string_into_model(self.model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix : <http://www.w3.org/1999/xhtml> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
+
+<http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
+<http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> a libns:IlluminaFlowcell .
+
+<http://jumpgate.caltech.edu/lane/1232>
+ a libns:IlluminaLane ;
+ libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
+ libns:has_mappings _:bnode110110 ;
+ libns:total_unique_locations 5789938 .
+
+<http://jumpgate.caltech.edu/library/11011/>
+ libns:affiliation "ENCODE"@en, "ENCODE_Tier1"@en, "Georgi Marinov"@en ;
+ libns:has_lane <http://jumpgate.caltech.edu/lane/1232> ;
+ libns:library_id "11011"@en ;
+ libns:library_type "None"@en ;
+ a libns:Library ;
+ <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> .
+
+_:bnode110110
+ a libns:MappedCount ;
+ libns:mapped_to "newcontam_UK.fa"@en ;
+ libns:reads 42473 .
+
+<http://jumpgate.caltech.edu/lane/1903>
+ a libns:IlluminaLane ;
+ libns:flowcell <http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> ;
+ libns:has_mappings _:bnode120970 ;
+ libns:total_unique_locations 39172114 .
+
+<http://jumpgate.caltech.edu/library/12097/>
+ libns:has_lane <http://jumpgate.caltech.edu/lane/1903> ;
+ libns:library_id "12097"@en ;
+ libns:library_type "Paired End (non-multiplexed)"@en ;
+ a libns:Library .
+
+_:bnode120970
+ a libns:MappedCount ;
+ libns:mapped_to "newcontam_UK.fa"@en ;
+ libns:reads 64 .
+''', 'http://jumpgate.caltech.edu/library')
+ errmsgs = list(self.inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
+ urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/library/11011/'))
+ encode_find.delete_library(self.model, urn)
+ q = RDF.Statement(None, encode_find.libraryOntology['reads'], None)
+ stmts = list(self.model.find_statements(q))
+ self.failUnlessEqual(len(stmts), 1)
+ self.failUnlessEqual(fromTypedNode(stmts[0].object),
+ 64)
+
+ q = RDF.Statement(None, encode_find.libraryOntology['library_id'], None)
+ stmts = list(self.model.find_statements(q))
+ self.failUnlessEqual(len(stmts), 1)
+ self.failUnlessEqual(fromTypedNode(stmts[0].object),
+ '12097')
def suite():
- return unittest.makeSuite(TestEncodeFind, "test")
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestEncodeFind))
+ return suite
+
if __name__ == "__main__":
- unittest.main(defaultTest="suite")
+ from unittest import main
+ main()
projects / htsworkflow.git / blobdiff