Merge remote-tracking branch 'origin/main' into feature_docker_k8s

# Conflicts:
#	.github/workflows/starter.yaml

.pylintrc

@@ -3,6 +3,7 @@ disable=C0111, broad-except, cyclic-import, duplicate-code
 good-names=f,i,j,k,ex,Run,_,e,js,bc,id,rv,ip,to  # default is i,j,k,ex,Run,_
 ignore=openatlas.wsgi
 min-public-methods=0
+--disable=W cidoc_rtfs_parser
 
 [FORMAT]
 max-line-length=79

README.md

@@ -42,8 +42,10 @@ Please refer to our [contributing guidelines](CONTRIBUTING.md)
 ([bernhard.koschicek-krombholz@oeaw.ac.at](mailto:bernhard.koschicek-krombholz@oeaw.ac.at))
 - **Nina Richards** - Bioarchaeological Expertise
 ([nina.richards@oeaw.ac.at](mailto:nina.richards@oeaw.ac.at))
-- **Andreas Olschnögger** - Frontend Development
+- **Moritz Großfurtner** - Frontend Development
 ([moritz.großfurtner@oeaw.ac.at](mailto:moritz.großfurtner@oeaw.ac.at)
+- **Olivia Reichl** - Frontend Development
+([Olivia.Reichl@oeaw.ac.at](mailto:Olivia.Reichl@oeaw.ac.at)
 - **Jan Belik** - Logo Design and Design Consulting
 ([buero@janbelik.com](mailto:buero@janbelik.com))
 

config/database_versions.py

@@ -1,5 +1,8 @@
 # Used for automatic database upgrades and database version checks
 DATABASE_VERSIONS = [
+    '7.16.0',
+    '7.15.0',
+    '7.14.0',
     '7.13.0',
     '7.11.0',
     '7.10.0',

config/default.py

@@ -3,11 +3,16 @@
 
 from config.database_versions import DATABASE_VERSIONS
 
-VERSION = '7.14.0'
+VERSION = '7.16.1'
 DATABASE_VERSION = DATABASE_VERSIONS[0]
 DEMO_MODE = False  # If activated some options are disabled, login is prefilled
 
-LANGUAGES = {'ca': 'Català', 'de': 'Deutsch', 'en': 'English', 'es': 'Español'}
+LANGUAGES = {
+    'ca': 'Català',
+    'de': 'Deutsch',
+    'en': 'English',
+    'es': 'Español',
+    'fr': 'Français'}
 DEBUG = False
 
 DATABASE_NAME = 'openatlas'
@@ -70,6 +75,8 @@
     'geojson-v2': 'application/json'}
 API_FORMATS = RDF_FORMATS | JSON_FORMATS
 
+API_PROXY = ''
+
 LOGICAL_OPERATOR: list[str] = ['and', 'or']
 STR_CATEGORIES: list[str] = [
     "entityName", "entityDescription", "entityAliases", "entityCidocClass",
@@ -79,17 +86,18 @@
     "entityID", "typeID", "typeIDWithSubs", "relationToID"]
 SET_CATEGORIES: list[str] = ["valueTypeID"]
 VALID_CATEGORIES: list[str] = [
-    *STR_CATEGORIES, *INT_CATEGORIES, *SET_CATEGORIES]
+    *STR_CATEGORIES,
+    *INT_CATEGORIES,
+    *SET_CATEGORIES]
 COMPARE_OPERATORS: list[str] = [
     'equal', 'notEqual', 'greaterThan', 'lesserThan', 'greaterThanEqual',
     'lesserThanEqual', 'like']
 
 # Used to connect to ACDH-CH ARCHE systems
-ARCHE = {
-    'id': None,
-    'collection_ids': None,
-    'base_url': None,
-    'thumbnail_url': 'https://arche-thumbnails.acdh.oeaw.ac.at/'}
+ARCHE = {'id': None, 'url': None}
+
+# Used to connect to password protected Vocabs systems
+VOCABS_PASS = ''
 
 # Table options
 TABLE_ROWS = {10: '10', 25: '25', 50: '50', 100: '100'}

install/3_data_web.sql

@@ -15,7 +15,7 @@ INSERT INTO web.user (username, password, active, email, group_id) VALUES (
   (SELECT id FROM web.group WHERE name = 'admin'));
 
 INSERT INTO web.settings (name, value) VALUES
-  ('database_version', '7.13.0'),
+  ('database_version', '7.16.0'),
   ('api_public', ''),
   ('default_language', 'en'),
   ('table_rows', '25'),
@@ -45,4 +45,7 @@ INSERT INTO web.settings (name, value) VALUES
   ('profile_image_width', '200'),
   ('random_password_length', '16'),
   ('reset_confirm_hours', '24'),
-  ('site_name', 'OpenAtlas');
+  ('site_name', 'OpenAtlas'),
+  ('vocabs_base_url', 'https://vocabs.acdh.oeaw.ac.at/'),
+  ('vocabs_endpoint', 'rest/v1/'),
+  ('vocabs_user', '');

install/crm/cidoc_rtfs_parser.py

@@ -1,15 +1,33 @@
+# pylint: disable=C,R
+#
 # This script is for developing purposes and not needed to install OpenAtlas.
 #
 # CIDOC CRM is used as basis for the underlying data model of OpenAtlas.
-# Currently we are using CIDOC CRM 7.7.1 (October 2021) from
-# http://www.cidoc-crm.org/versions-of-the-cidoc-crm
+# Currently, we are using CIDOC CRM 7.1.2 (June 2022):
+# https://cidoc-crm.org/rdfs/7.1.2/CIDOC_CRM_v7.1.2.rdf
 #
 # The script parses the rdfs file and imports it to a PostgreSQL database.
-# Installation of needed package: # apt-get install python3-rdflib
+# Installation of needed package:
+# apt-get install python3-rdflib
+#
+# Create a database named cidoc
+# $ createdb cidoc -O openatlas
+# $ psql cidoc -c "CREATE EXTENSION postgis; CREATE EXTENSION unaccent;"
+# $ cd install
+# $ cat 1_structure.sql 2_data_model.sql | psql -d cidoc -f -
+#
+# Execute the script in install/crm:
+# $ python3 cidoc_rtfs_parser.py
+#
+# Table data can than be extracted to be joined in an upgrade SQL with e.g.
+# pg_dump --column-inserts --data-only --rows-per-insert=1000 --table=model.cidoc_class cidoc > class.sql
+#
+# Following has to be added manually to the upgrade SQL
+# UPDATE model.property_i18n set text_inverse = 'ist erster Ort von' WHERE property_code = 'OA8' AND language_code = 'de';
+# UPDATE model.property_i18n set text_inverse = 'is first appearance of' WHERE property_code = 'OA8' AND language_code = 'en';
+# UPDATE model.property_i18n set text_inverse = 'ist letzter Ort von' WHERE property_code = 'OA9' AND language_code = 'de';
+# UPDATE model.property_i18n set text_inverse = 'is last appearance of' WHERE property_code = 'OA9' AND language_code = 'en';
 #
-# Once run table data can be extracted with e.g.
-# pg_dump --column-inserts --data-only --rows-per-insert=1000
-# --table=model.cidoc_class cidoc > class.sql
 
 import time
 from typing import Dict, List, Optional
@@ -18,12 +36,12 @@
 from rdflib import URIRef
 from rdflib.graph import Graph
 
-FILENAME = 'CIDOC_CRM_v7.1.1.rdfs'
+FILENAME = 'CIDOC_CRM_v7.1.2.rdf'
 CRM_URL = 'http://www.cidoc-crm.org/cidoc-crm/'
 
 EXCLUDE_PROPERTIES = [
     'P3', 'P57', 'P79', 'P80', 'P81', 'P81a', 'P81b', 'P82', 'P82a', 'P82b',
-    'P90', 'P90a', 'P90b', 'P171', 'P172', 'P190', 'P168']
+    'P90', 'P90a', 'P90b', 'P168', 'P169', 'P170', 'P171', 'P172', 'P190']
 
 DATABASE_NAME = 'cidoc'
 DATABASE_USER = 'openatlas'
@@ -42,7 +60,6 @@ def connect() -> psycopg2.connect:
 
 
 class Item:
-
     domain_code: str
     range_code: str
 
@@ -161,28 +178,30 @@ def import_cidoc() -> None:
         'de': 'hat Beziehung zu'}
     properties['OA8'] = Item(
         'OA8',
-        ' begins in',
+        'begins in',
         "OA8 is used to link the beginning of a persistent item's (E77) life "
         "span (or time of usage) with a certain place. E.g to document the "
         "birthplace of a person. E77 Persistent Item linked with a E53 Place: "
         "E77 (Persistent Item) - P92i (was brought into existence by) - E63 "
         "(Beginning of Existence) - P7 (took place at) - E53 (Place) Example: "
         "[Albert Einstein (E21)] was brought into existence by [Birth of "
         "Albert Einstein (E12)] took place at [Ulm (E53)]")
+    properties['OA8'].name_inverse = 'is first appearance of'
     properties['OA8'].domain_code = 'E77'
     properties['OA8'].range_code = 'E53'
     properties['OA8'].label = {'en': 'begins in', 'de': 'beginnt in'}
 
     properties['OA9'] = Item(
         'OA9',
-        ' begins in',
+        'ends in',
         "OA9 is used to link the end of a persistent item's (E77) life span "
         "(or time of usage) with a certain place. E.g to document a person's "
         "place of death. E77 Persistent Item linked with a E53 Place: E77 "
         "(Persistent Item) - P93i (was taken out of existence by) - E64 "
         "(End of Existence) - P7 (took place at) - E53 (Place) Example: "
         "[Albert Einstein (E21)] was taken out of by [Death of Albert "
         "Einstein (E12)] took place at [Princeton (E53)]")
+    properties['OA9'].name_inverse = 'is last appearance of'
     properties['OA9'].domain_code = 'E77'
     properties['OA9'].range_code = 'E53'
     properties['OA9'].label = {'en': 'ends in', 'de': 'endet in'}
@@ -192,31 +211,6 @@ def import_cidoc() -> None:
     cursor.execute("""
         BEGIN;
 
-        UPDATE model.entity SET (cidoc_class_code, openatlas_class_name) = 
-            ('E41', 'appellation') WHERE cidoc_class_code = 'E82';
-        UPDATE model.link SET property_code = 'P1' 
-            WHERE property_code = 'P131';
-        DELETE FROM model.openatlas_class WHERE cidoc_class_code = 'E82';
-        ALTER TABLE model.cidoc_class DROP COLUMN IF EXISTS created, 
-            DROP COLUMN IF EXISTS modified;
-        ALTER TABLE model.cidoc_class_inheritance 
-            DROP COLUMN IF EXISTS created, DROP COLUMN IF EXISTS modified;
-        ALTER TABLE model.cidoc_class_i18n DROP COLUMN IF EXISTS created, 
-            DROP COLUMN IF EXISTS modified;
-        ALTER TABLE model.property DROP COLUMN IF EXISTS created, 
-            DROP COLUMN IF EXISTS modified;
-        ALTER TABLE model.property_inheritance DROP COLUMN IF EXISTS created, 
-            DROP COLUMN IF EXISTS modified;
-        ALTER TABLE model.property_i18n DROP COLUMN IF EXISTS created, 
-            DROP COLUMN IF EXISTS modified;
-        DROP TRIGGER IF EXISTS update_modified ON model.cidoc_class;
-        DROP TRIGGER IF EXISTS update_modified 
-            ON model.cidoc_class_inheritance;
-        DROP TRIGGER IF EXISTS update_modified ON model.cidoc_class_i18n;
-        DROP TRIGGER IF EXISTS update_modified ON model.property;
-        DROP TRIGGER IF EXISTS update_modified ON model.property_inheritance;
-        DROP TRIGGER IF EXISTS update_modified ON model.property_i18n;
-
         ALTER TABLE model.entity 
             DROP CONSTRAINT IF EXISTS entity_class_code_fkey;
         ALTER TABLE model.entity 
@@ -246,9 +240,12 @@ def import_cidoc() -> None:
                 reference_system_openatlas_class_openatlas_class_name_fkey;
 
         TRUNCATE 
-            model.cidoc_class_inheritance, model.cidoc_class_i18n, 
-            model.cidoc_class, model.property_inheritance, 
-            model.property_i18n, model.property;
+            model.cidoc_class_inheritance,
+            model.cidoc_class_i18n,
+            model.cidoc_class,
+            model.property_inheritance,
+            model.property_i18n,
+            model.property;
 
         ALTER SEQUENCE model.cidoc_class_id_seq RESTART;
         ALTER SEQUENCE model.cidoc_class_inheritance_id_seq RESTART;
@@ -259,6 +256,7 @@ def import_cidoc() -> None:
 
     # Classes
     for code, class_ in classes.items():
+        print(code)
         sql = """
             INSERT INTO model.cidoc_class (code, name, comment)
             VALUES (%(code)s, %(name)s, %(comment)s);"""
@@ -268,13 +266,14 @@ def import_cidoc() -> None:
             'comment': class_.comment})
     for code, class_ in classes.items():
         for sub_code_of in class_.sub_class_of:
-            sql = """
-                INSERT INTO model.cidoc_class_inheritance 
-                    (super_code, sub_code)
-                VALUES (%(super_code)s, %(sub_code)s);"""
-            cursor.execute(sql, {
-                'super_code': sub_code_of,
-                'sub_code': class_.code})
+            if sub_code_of != class_.code:  # Prevent circular relations
+                sql = """
+                    INSERT INTO model.cidoc_class_inheritance
+                        (super_code, sub_code)
+                    VALUES (%(super_code)s, %(sub_code)s);"""
+                cursor.execute(sql, {
+                    'super_code': sub_code_of,
+                    'sub_code': class_.code})
         for language, label in class_.label.items():
             sql = """
                 INSERT INTO model.cidoc_class_i18n
@@ -398,7 +397,7 @@ def import_cidoc() -> None:
             ON UPDATE CASCADE ON DELETE CASCADE;
         """)
     cursor.execute("COMMIT")
-    print('Execution time: ' + str(int(time.time() - start)) + ' seconds')
+    print(f'Execution time: {int(time.time() - start)} seconds')
 
 
 import_cidoc()