Use htsworkflow ontology to validate various RDF using components.

[htsworkflow.git] / encode_submission / test_encode_find.py

diff --git a/encode_submission/test_encode_find.py b/encode_submission/test_encode_find.py
index cb6216711bb078caf9e880522b8f2c383ddfdf85..05108955a4d31927b98d395b290ef986a3163d88 100644 (file)
--- a/encode_submission/test_encode_find.py
+++ b/encode_submission/test_encode_find.py
@@ -7,12 +7,19 @@ import RDF
 
 import encode_find
 from htsworkflow.submission.ucsc import submission_view_url
-from htsworkflow.util.rdfhelp import dump_model, get_model, fromTypedNode
+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):
+    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)
@@ -35,11 +42,10 @@ class TestEncodeFind(unittest.TestCase):
         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)
         object_date = fromTypedNode(dates[0].object)
         self.assertEqual(object_date, datetime(2011,12,7,15,23,0))
@@ -58,43 +64,54 @@ class TestEncodeFind(unittest.TestCase):
     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):
-        model = get_model()
+        ontology_size = len(self.model)
         parser = RDF.Parser(name='turtle')
-        parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+        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 .
+    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/')
-        self.failUnlessEqual(len(model), 5)
+        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(model, urn)
-        self.failUnlessEqual(len(model), 0)
+        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):
-        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#> .
+        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 .
@@ -104,14 +121,16 @@ _:bnode110110
     libns:has_lane <http://jumpgate.caltech.edu/lane/1232> ;
     libns:library_id "11011"@en ;
     libns:library_type "None"@en ;
-    a "libns:library"@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 .
@@ -120,22 +139,25 @@ _:bnode110110
     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"@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(model, urn)
+        encode_find.delete_library(self.model, urn)
         q = RDF.Statement(None, encode_find.libraryOntology['reads'], None)
-        stmts = list(model.find_statements(q))
+        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(model.find_statements(q))
+        stmts = list(self.model.find_statements(q))
         self.failUnlessEqual(len(stmts), 1)
         self.failUnlessEqual(fromTypedNode(stmts[0].object),
                              '12097')