Merge e5df5ce into e51581a

atramhasis/alembic/versions/88214d86a9d1_concept_id_is_string.py

@@ -16,8 +16,12 @@
 
 
 def upgrade():
-    op.alter_column('concept', 'concept_id', _type=sa.String)
+    with op.batch_alter_table('concept') as batch_op:
+        batch_op.alter_column('concept_id', type_=sa.String, existing_type=sa.Integer)
 
 
 def downgrade():
-    op.alter_column('concept', 'concept_id', _type=sa.Integer)
+    # Drop concepts which have non-integer concept_id
+    op.execute("DELETE FROM concept WHERE cast(cast(concept_id AS INTEGER) AS TEXT) != concept_id")
+    with op.batch_alter_table('concept') as batch_op:
+        batch_op.alter_column('concept_id', existing_type=sa.String, type_=sa.Integer)

atramhasis/data/datamanagers.py

@@ -5,11 +5,11 @@
 :versionadded: 0.4.1
 """
 import uuid
-
 from datetime import date
 from datetime import datetime
 
 import dateutil.relativedelta
+import sqlalchemy as sa
 from skosprovider_sqlalchemy.models import Collection
 from skosprovider_sqlalchemy.models import Concept
 from skosprovider_sqlalchemy.models import ConceptScheme
@@ -221,7 +221,7 @@ def get_all_label_types(self):
     def get_next_cid(self, conceptscheme_id, id_generation_strategy):
         if id_generation_strategy == IDGenerationStrategy.NUMERIC:
             max_id = self.session.execute(
-               select(func.max(Thing.concept_id))
+               select(func.max(sa.cast(Thing.concept_id, sa.Integer)))
                .filter_by(conceptscheme_id=conceptscheme_id)
             ).scalar_one()
             return max_id + 1 if max_id else 1

atramhasis/scripts/import_file.py

@@ -226,7 +226,7 @@ def provider_to_db(provider, conceptscheme, session):
     import provider data into the database
     """
     session.add(conceptscheme)
-    import_provider(provider, conceptscheme, session)
+    import_provider(provider, session, conceptscheme)
     session.commit()
 
 

atramhasis/scripts/initializedb.py

@@ -37,6 +37,7 @@ def main(argv=sys.argv):
     db_session = sessionmaker(bind=engine)()
     import_provider(
         trees,
+        db_session,
         ConceptScheme(
             id=1,
             uri='urn:x-skosprovider:trees',
@@ -45,10 +46,10 @@ def main(argv=sys.argv):
                 Label('Different types of trees', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         geo,
+        db_session,
         ConceptScheme(
             id=2,
             uri='urn:x-skosprovider:geo',
@@ -57,10 +58,10 @@ def main(argv=sys.argv):
                 Label('Geography', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         styles_and_cultures,
+        db_session,
         ConceptScheme(
             id=3,
             uri='https://id.erfgoed.net/thesauri/stijlen_en_culturen',
@@ -69,10 +70,10 @@ def main(argv=sys.argv):
                 Label('Styles and Cultures', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         materials,
+        db_session,
         ConceptScheme(
             id=4,
             uri='https://id.erfgoed.net/thesauri/materialen',
@@ -81,10 +82,10 @@ def main(argv=sys.argv):
                 Label('Materials', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         eventtypes,
+        db_session,
         ConceptScheme(
             id=5,
             uri='https://id.erfgoed.net/thesauri/gebeurtenistypes',
@@ -93,10 +94,10 @@ def main(argv=sys.argv):
                 Label('Event types', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         heritagetypes,
+        db_session,
         ConceptScheme(
             id=6,
             uri='https://id.erfgoed.net/thesauri/erfgoedtypes',
@@ -105,10 +106,10 @@ def main(argv=sys.argv):
                 Label('Heritage types', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         periods,
+        db_session,
         ConceptScheme(
             id=7,
             uri='https://id.erfgoed.net/thesauri/dateringen',
@@ -117,10 +118,10 @@ def main(argv=sys.argv):
                 Label('Periods', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         species,
+        db_session,
         ConceptScheme(
             id=8,
             uri='https://id.erfgoed.net/thesauri/soorten',
@@ -129,10 +130,10 @@ def main(argv=sys.argv):
                 Label('Species', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     import_provider(
         bluebirds,
+        db_session,
         ConceptScheme(
             id=9,
             uri='https://id.bluebirds.org',
@@ -141,7 +142,6 @@ def main(argv=sys.argv):
                 Label('Blue birds', 'prefLabel', 'en')
             ]
         ),
-        db_session
     )
     db_session.commit()
     db_session.close()

requirements.txt

@@ -7,7 +7,7 @@ openapi-spec-validator==0.4.0  # https://github.com/p1c2u/openapi-core/issues/44
 
 # skosprovider
 skosprovider==1.2.0
-skosprovider_sqlalchemy==2.0.1
+skosprovider_sqlalchemy==2.1.1
 pyramid_skosprovider==1.2.0
 skosprovider_rdf==1.3.0
 skosprovider_getty==1.1.0

setup.py

@@ -48,7 +48,7 @@ def run(self):
     'transaction',
     'zope.sqlalchemy',
     'skosprovider',
-    'skosprovider_sqlalchemy>=2.0.1',
+    'skosprovider_sqlalchemy>=2.1.1',
     'skosprovider_rdf',
     'skosprovider_getty',
     'pyramid_skosprovider',

tests/__init__.py

@@ -9,6 +9,7 @@
 from skosprovider.registry import Registry
 from skosprovider.skos import ConceptScheme
 from skosprovider.uri import UriPatternGenerator
+from skosprovider_sqlalchemy.models import Concept
 from skosprovider_sqlalchemy.providers import SQLAlchemyProvider
 from skosprovider_sqlalchemy.utils import import_provider
 from sqlalchemy import engine_from_config
@@ -77,14 +78,14 @@ def fill_db():
         from skosprovider_sqlalchemy.models import ConceptScheme
         with db_session() as session:
             import_provider(trees,
-                            ConceptScheme(id=1, uri='urn:x-skosprovider:trees'),
-                            session)
+                            session,
+                            ConceptScheme(id=1, uri='urn:x-skosprovider:trees'))
             import_provider(material_data.materials,
-                            ConceptScheme(id=4, uri='urn:x-vioe:materials'),
-                            session)
+                            session,
+                            ConceptScheme(id=4, uri='urn:x-vioe:materials'))
             import_provider(data.geo,
-                            ConceptScheme(id=2, uri='urn:x-vioe:geography'),
-                            session)
+                            session,
+                            ConceptScheme(id=2, uri='urn:x-vioe:geography'))
             import_provider(
                 DictionaryProvider(
                     {'id': 'MISSING_LABEL', 'default_language': 'nl'},
@@ -97,8 +98,9 @@ def fill_db():
                          ],
                      }]
                 ),
-                ConceptScheme(id=9, uri='urn:x-vioe:test'),
-                session)
+                session,
+                ConceptScheme(id=9, uri='urn:x-vioe:test')
+            )
             import_provider(
                 DictionaryProvider(
                     {'id': 'manual-ids', 'default_language': 'nl'},
@@ -118,8 +120,8 @@ def fill_db():
                          ],
                      }]
                 ),
-                ConceptScheme(id=10, uri='urn:x-vioe:manual'),
                 session,
+                ConceptScheme(id=10, uri='urn:x-vioe:manual'),
             )
             session.add(ConceptScheme(id=3, uri='urn:x-vioe:styles'))
             for scheme_id in (5, 6, 7, 8):

tests/test_functional.py

@@ -204,7 +204,7 @@ def test_get_concept(self):
         self.assertEqual('200 OK', res.status)
         self.assertIn('application/json', res.headers['Content-Type'])
         self.assertIsNotNone(res.json['id'])
-        self.assertEqual(res.json['id'], 1)
+        self.assertEqual(res.json['id'], '1')
         self.assertEqual(res.json['type'], 'concept')
         self.assertIn('sortLabel', [label['type'] for label in res.json['labels']])
 
@@ -351,11 +351,14 @@ def test_edit_concept_not_found(self):
         self.assertIn('application/json', res.headers['Content-Type'])
 
     def test_delete_concept(self):
-        new_id = 1
-        res = self.testapp.delete('/conceptschemes/TREES/c/' + str(new_id), headers=self._get_default_headers())
+        new_id = '1'
+        res = self.testapp.delete(f'/conceptschemes/TREES/c/{new_id}', headers=self._get_default_headers())
         self.assertEqual('200 OK', res.status)
         self.assertIsNotNone(res.json['id'])
         self.assertEqual(new_id, res.json['id'])
+        from skosprovider_sqlalchemy.models import Concept
+        concepten = self.session.query(Concept).all()
+        print()
 
     def test_delete_concept_not_found(self):
         res = self.testapp.delete('/conceptschemes/TREES/c/7895', headers=self._get_default_headers(),
@@ -697,7 +700,7 @@ def test_match_filter(self):
         self.assertEqual(
             [
                 {
-                    'id': 1,
+                    'id': '1',
                     'uri': 'urn:x-skosprovider:trees/1',
                     'type': 'concept',
                     'label': 'De Lariks',

tests/test_import_scripts.py

@@ -47,8 +47,8 @@ def _check_trees(self, conceptscheme_label):
         self.assertEqual(conceptscheme_label, sql_prov.concept_scheme.label('en').label)
         obj_1 = [item for item in dump if item['uri'] == 'http://id.trees.org/2'][0]
         self.assertEqual(obj_1['broader'], [])
-        self.assertEqual(obj_1['id'], 2)
-        self.assertEqual(obj_1['member_of'], [3])
+        self.assertEqual(obj_1['id'], '2')
+        self.assertEqual(obj_1['member_of'], ['3'])
         self.assertEqual(obj_1['narrower'], [])
         label_en = [label for label in obj_1['labels'] if label['language'] == 'en'][0]
         self.assertDictEqual(label_en, {'label': 'The Chestnut', 'language': 'en', 'type': 'prefLabel'})
@@ -66,20 +66,20 @@ def _check_menu(self, uri_pattern=None):
         self.assertEqual(11, len(sql_prov.get_all()))
         eb = sql_prov.get_by_id(1)
         self.assertIsInstance(eb, Concept)
-        self.assertEqual(1, eb.id)
+        self.assertEqual('1', eb.id)
         self.assertEqual(uri_pattern % '1', eb.uri)
         self.assertEqual('Egg and Bacon', eb.label().label)
         self.assertEqual('prefLabel', eb.label().type)
         self.assertEqual([], eb.notes)
         eb = sql_prov.get_by_uri(uri_pattern % '3')
         self.assertIsInstance(eb, Concept)
-        self.assertEqual(3, eb.id)
+        self.assertEqual('3', eb.id)
         self.assertEqual(uri_pattern % '3', eb.uri)
         spam = sql_prov.find({'label': 'Spam'})
         self.assertEqual(8, len(spam))
         eb = sql_prov.get_by_id(11)
         self.assertIsInstance(eb, Concept)
-        self.assertEqual(11, eb.id)
+        self.assertEqual('11', eb.id)
         self.assertEqual('Lobster Thermidor', eb.label().label)
         self.assertIsInstance(eb.notes[0], Note)
         self.assertIn('Mornay', eb.notes[0].note)