Bugfix/810 concept id as uri (#811)

* Add testfile to import with non-numeric ids. Refs #810

* Fix routing of concept_id with slashes. Add tests for rdf downloads. Refs #810

atramhasis/routes.py

@@ -32,14 +32,14 @@ def includeme(config):
     config.add_route('atramhasis.rdf_full_export_turtle_ext', pattern='/conceptschemes/{scheme_id}/c.ttl')
     config.add_route('atramhasis.rdf_conceptscheme_export_ext', pattern='/conceptschemes/{scheme_id}.rdf')
     config.add_route('atramhasis.rdf_conceptscheme_export_turtle_ext', pattern='/conceptschemes/{scheme_id}.ttl')
-    config.add_route('atramhasis.rdf_individual_export_ext', pattern='/conceptschemes/{scheme_id}/c/{c_id}.rdf')
-    config.add_route('atramhasis.rdf_individual_export_turtle_ext', pattern='/conceptschemes/{scheme_id}/c/{c_id}.ttl')
+    config.add_route('atramhasis.rdf_individual_export_ext', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}.rdf')
+    config.add_route('atramhasis.rdf_individual_export_turtle_ext', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}.ttl')
     config.add_route('atramhasis.rdf_conceptscheme_jsonld_ext', pattern='/conceptschemes/{scheme_id}.jsonld')
-    config.add_route('atramhasis.rdf_individual_jsonld_ext', pattern='/conceptschemes/{scheme_id}/c/{c_id}.jsonld')
+    config.add_route('atramhasis.rdf_individual_jsonld_ext', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}.jsonld')
 
     config.add_route('conceptschemes', pattern='/conceptschemes', accept='text/html', request_method="GET")
     config.add_route('conceptscheme', pattern='/conceptschemes/{scheme_id}', accept='text/html', request_method="GET")
-    config.add_route('concept', pattern='/conceptschemes/{scheme_id}/c/{c_id}', accept='text/html',
+    config.add_route('concept', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}', accept='text/html',
                      request_method="GET")
     config.add_route('search_result', pattern='/conceptschemes/{scheme_id}/c', accept='text/html')
     config.add_route('scheme_root', pattern='/conceptschemes/{scheme_id}/c/', accept='text/html')
@@ -51,13 +51,13 @@ def includeme(config):
                      accept='application/json', request_method='PUT')
     config.add_route('atramhasis.get_conceptscheme', pattern='/conceptschemes/{scheme_id}', accept='application/json')
     config.add_route('atramhasis.get_conceptschemes', pattern='/conceptschemes', accept='application/json')
-    config.add_route('atramhasis.get_concept', pattern='/conceptschemes/{scheme_id}/c/{c_id}',
+    config.add_route('atramhasis.get_concept', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
                      accept='application/json', request_method="GET")
     config.add_route('atramhasis.add_concept', pattern='/conceptschemes/{scheme_id}/c', accept='application/json',
                      request_method="POST")
-    config.add_route('atramhasis.edit_concept', pattern='/conceptschemes/{scheme_id}/c/{c_id}',
+    config.add_route('atramhasis.edit_concept', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
                      accept='application/json', request_method="PUT")
-    config.add_route('atramhasis.delete_concept', pattern='/conceptschemes/{scheme_id}/c/{c_id}',
+    config.add_route('atramhasis.delete_concept', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
                      accept='application/json', request_method="DELETE")
     config.add_route('atramhasis.list_languages', pattern='/languages', accept='application/json',
                      request_method="GET")
@@ -86,15 +86,15 @@ def includeme(config):
                      accept='text/turtle')
     config.add_route('atramhasis.rdf_conceptscheme_export_turtle_x', pattern='/conceptschemes/{scheme_id}',
                      accept='application/x-turtle')
-    config.add_route('atramhasis.rdf_individual_export', pattern='/conceptschemes/{scheme_id}/c/{c_id}',
+    config.add_route('atramhasis.rdf_individual_export', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
                      accept='application/rdf+xml')
-    config.add_route('atramhasis.rdf_individual_export_turtle', pattern='/conceptschemes/{scheme_id}/c/{c_id}',
+    config.add_route('atramhasis.rdf_individual_export_turtle', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
                      accept='text/turtle')
-    config.add_route('atramhasis.rdf_individual_export_turtle_x', pattern='/conceptschemes/{scheme_id}/c/{c_id}',
+    config.add_route('atramhasis.rdf_individual_export_turtle_x', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
                      accept='application/x-turtle')
     config.add_route('atramhasis.rdf_conceptscheme_jsonld', pattern='/conceptschemes/{scheme_id}',
                      accept='application/ld+json')
-    config.add_route('atramhasis.rdf_individual_jsonld', pattern='/conceptschemes/{scheme_id}/c/{c_id}',
+    config.add_route('atramhasis.rdf_individual_jsonld', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
                      accept='application/ld+json')
     config.add_route('atramhasis.providers', pattern='/providers')
     config.add_route('atramhasis.provider', pattern='/providers/{id}')

atramhasis/views/rdf.py

@@ -49,7 +49,7 @@ def __init__(self, request):
             raise ConceptSchemeNotFoundException(self.scheme_id)   # pragma: no cover
         if 'c_id' in self.request.matchdict.keys():
             self.c_id = self.request.matchdict['c_id']
-            if not self.c_id.isdigit() or not self.provider.get_by_id(int(self.c_id)):
+            if not self.provider.get_by_id(self.c_id):
                 raise ConceptNotFoundException(self.c_id)
 
     @audit

tests/__init__.py

@@ -109,6 +109,13 @@ def fill_db():
                          'labels': [
                              {'type': 'prefLabel', 'language': 'nl', 'label': 'label'}
                          ],
+                     },
+                     {
+                         'id': 'http://id.manual.org/manual/68',
+                         'uri': 'http://id.manual.org/manual/68',
+                         'labels': [
+                             {'type': 'prefLabel', 'language': 'nl', 'label': 'handmatig'}
+                         ],
                      }]
                 ),
                 ConceptScheme(id=10, uri='urn:x-vioe:manual'),

tests/data/bluebirds.ttl

@@ -0,0 +1,47 @@
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<http://id.bluebirds.org/bird> a skos:Concept ;
+    skos:inScheme <http://id.bluebirds.org> ;
+    skos:narrower <http://id.bluebirds.org/parrot> ;
+    skos:narrower <http://id.bluebirds.org/579A439C-1A7A-476A-92C3-8A74ABD6B3DB> ;
+    skos:prefLabel "Bird"@en,
+        "Vogel"@nl .
+
+<http://id.bluebirds.org/parrot> a skos:Concept ;
+    dcterms:identifier "parrot" ;
+    skos:inScheme <http://id.bluebirds.org> ;
+    skos:narrower <http://id.bluebirds.org/norwegianblue> ;
+    skos:prefLabel "Parrot"@en,
+        "Papegaai"@nl .
+
+<http://id.bluebirds.org/norwegianblue> a skos:Concept ;
+    dcterms:identifier "norwegianblue" ;
+    skos:inScheme <http://id.bluebirds.org> ;
+    skos:broader <http://id.bluebirds.org/parrot> ;
+    skos:relatedMatch <http://id.slugs.org/slug> ;
+    skos:prefLabel "Norwegian Blue"@en,
+        "Noorse Blauwe"@nl .
+
+<http://id.bluebirds.org/579A439C-1A7A-476A-92C3-8A74ABD6B3DB> a skos:Concept ;
+    dcterms:identifier "579A439C-1A7A-476A-92C3-8A74ABD6B3DB" ;
+    skos:inScheme <http://id.bluebirds.org> ;
+    skos:narrower <http://id.bluebirds.org/blauwereiger> ;
+    skos:prefLabel "Heron"@en, 
+	"Héron"@fr,
+        "Reiger"@nl .
+
+<http://id.bluebirds.org/blauwereiger> a skos:Concept ;
+    dcterms:identifier "blauwereiger" ;
+    skos:inScheme <http://id.bluebirds.org> ;
+    skos:prefLabel "Grey heron"@en,
+	"Héron cendré"@fr,
+        "Blauwe reiger"@nl, 
+	"Ardea cinerea"@la .
+
+<http://id.bluebirds.org> a skos:ConceptScheme ;
+    dcterms:identifier "BLUEBIRDS" ;
+    skos:hasTopConcept <http://id.bluebirds.org/bird> ;
+    skos:prefLabel "Blue birds"@en,
+        "Blauwe vogels"@nl .

tests/test_functional.py

@@ -852,6 +852,26 @@ def test_rdf_individual_turtle_ext(self):
         self.assertEqual('200 OK', ttl_response.status)
         self.assertEqual('text/turtle', ttl_response.content_type)
 
+    def test_rdf_individual_jsonld_ext_manual(self):
+        res = self.testapp.get('/conceptschemes/manual-ids/c/manual-1.jsonld')
+        self.assertEqual('200 OK', res.status)
+        self.assertEqual('application/ld+json', res.content_type)
+
+    def test_rdf_individual_xml_ext_manual(self):
+        rdf_response = self.testapp.get('/conceptschemes/manual-ids/c/manual-2.rdf')
+        self.assertEqual('200 OK', rdf_response.status)
+        self.assertEqual('application/rdf+xml', rdf_response.content_type)
+
+    def test_rdf_individual_turtle_manual(self):
+        ttl_response = self.testapp.get('/conceptschemes/manual-ids/c/manual-1.ttl')
+        self.assertEqual('200 OK', ttl_response.status)
+        self.assertEqual('text/turtle', ttl_response.content_type)
+
+    def test_rdf_individual_turtle_manual_uri(self):
+        ttl_response = self.testapp.get('/conceptschemes/manual-ids/c/http://id.manual.org/manual/68.ttl')
+        self.assertEqual('200 OK', ttl_response.status)
+        self.assertEqual('text/turtle', ttl_response.content_type)
+
     def test_rdf_individual_not_found(self):
         res = self.testapp.get('/conceptschemes/TREES/c/test.ttl', headers={'Accept': 'text/turtle'}, status=404,
                                expect_errors=True)

tests/test_import_scripts.py

@@ -17,6 +17,7 @@
 
 test_data_rdf = os.path.join(TEST_DIR, 'data', 'trees.rdf')
 test_data_ttl = os.path.join(TEST_DIR, 'data', 'trees.ttl')
+test_data_ttl_string_id = os.path.join(TEST_DIR, 'data', 'bluebirds.ttl')
 test_data_json = os.path.join(TEST_DIR, 'data', 'trees.json')
 test_data_csv = os.path.join(TEST_DIR, 'data', 'menu.csv')
 
@@ -84,6 +85,21 @@ def _check_menu(self, uri_pattern=None):
         self.assertIn('Mornay', eb.notes[0].note)
         self.assertEqual('note', eb.notes[0].type)
 
+    def _check_parrots(self, conceptscheme_label):
+        sql_prov = SQLAlchemyProvider({'id': 'PARROTS', 'conceptscheme_id': 1}, self.session)
+
+        bird = sql_prov.get_by_id('http://id.parrots.org/bird')
+        assert sql_prov.get_by_uri('http://id.parrots.org/bird') == \
+                sql_prov.get_by_id('http://id.parrots.org/bird')
+        parrot = sql_prov.get_by_id('parrot')
+        assert parrot 
+        assert not sql_prov.get_by_id('bird')
+        blue = sql_prov.get_by_id('norwegianblue')
+        assert blue in parrot.narrower
+        reiger = sql_prov.get_by_id('579A439C-1A7A-476A-92C3-8A74ABD6B3DB')
+        blauwereiger = sql_prov.get_by_id('blauwereiger')
+        assert blauwereiger in reiger.narrower
+
     def test_import_rdf(self):
         sys.argv = ['import_file', '--from', test_data_rdf, '--to', SETTINGS['sqlalchemy.url']]
         import_file.main(sys.argv)
@@ -96,6 +112,11 @@ def test_import_ttl(self):
         tests.db_filled = True
         self._check_trees('Different types of trees')
 
+    def test_import_ttl_string_id(self):
+        sys.argv = ['import_file', '--from', test_data_ttl_string_id, '--to', SETTINGS['sqlalchemy.url']]
+        import_file.main(sys.argv)
+        tests.db_filled = True
+
     def test_import_json(self):
         sys.argv = ['import_file', '--from', test_data_json,
                     '--to', SETTINGS['sqlalchemy.url'],