Merge branch 'refs/heads/develop' into feature/femcare-import

Author: BernhardKoschicek

config/default.py

@@ -5,7 +5,7 @@
 
 from config.database_versions import DATABASE_VERSIONS
 
-VERSION = '9.0.0'
+VERSION = '9.1.0'
 DATABASE_VERSION = DATABASE_VERSIONS[0]
 DEMO_MODE = False  # If activated some options are disabled, login is prefilled
 DEBUG = False

config/model/README.md

@@ -1,67 +1,72 @@
 # Model configuration
-In **config/model** are the configuration files which are responsible for
-model relations, display, forms and similar. The main motivation for this
-approach is to speed up development and make it easier to understand the
-system.
+
+Within the OpenAtlas source code configuration files, which determine model
+relations, display, forms and the like, can be found in **config/model**.
+The main motivation for this approach is to speed up development and make
+it easier to understand the system.
 
 Changes can be made to test different setups, but we strongly advice against
 implementing changes for productive environments because:
 
-* There may be conflicts with future OpenAtlas versions, especially because
-this approach is relatively new and will be subject to changes.
+* There may be conflicts with future OpenAtlas versions, as this approach is
+relatively new and will be subject to changes.
 * Currently, there are no check or validation functions for the configuration
-* Even if changes appear to work, they might cause unwanted
-side effects in the application, API or presentation sites.
+* Even if changes appear to work, they might cause unwanted side effects in
+the application, API or presentation sites.
 
-A better approach would be to test needed changes and then tell us about
-it. In case we implement suggested changes, it would mitigate the
-issues mentioned above.
+A better approach would be to test needed changes and then tell us about it.
+In case we implement suggested changes, it would mitigate the issues mentioned
+above.
 
 # Functionality
-With changes in the config files it is possible to:
-* Add, change or remove entity classes and their relations
-* Determine modes of linking, e.g. if relations are edited directly at an
-entity form or via tabs
+
+Changes in the config files allow you to:
+
+* Add, change, or remove entity classes and their relations
 * Change display details like labels and the order of shown items, e.g. tabs
 
 # Limitations
-* It is not possible to add new classes via the config alone. This would also
-require database adaptions.
-* Although it is possible to define none CIDOC conform relations they will fail
-because of additional checks in the user interface.
+
+* It is not possible to add new classes via the config alone, as this requires
+database adaptations. * Non-CIDOC-conformant relations can be defined in the
+file, but they will fail because of additional user-interface checks.
 
 # File structure
+
 * **class_groups.py** - configuration for grouping classes, e.g. person and
 group will be displayed together in "actor" sections at overviews
 * **model.py** - used for class instantiation
 * **classes** folder - detailed configuration of individual OpenAtlas classes
 
-# Class configuration structure
+# **Class configuration structure**
+
 Description of the structure for classes used in the classes directory.
+
 * **label** - optional (default = class name)
 * **attributes**
   * **values**: name, alias, dates, location, description
   * **options**: label, required, annotated (only for description)
 * **relations** - the order affects display of entity views and forms
   * **label** - optional (default = relation name)
   * **classes** - a list of related OpenAtlas classes
-  * **property** - the CIDOC property used to link them
+  * **property** - the CIDOC property used to link classes
   * **inverse** - link direction (default = False)
-  * **required** - if possible to remove (default = False)
+  * **required** - if link is required (default = False)
   * **multiple** - if multiple connections are possible (default = False)
   * **mode**
     * **direct** - editable at the entity form
     * **tab** - editable via tabs (default)
-  * **add_dynamic** - if types can be added dynamically (default = False)
+  * **add_dynamic** - determines if types can be added dynamically
+    (default = False)
   * **type** - special case to add a type to the link, e.g. involvement
   * **additional_fields** - special cases to add link information
     * **dates**
     * **description**
     * **page** - like description, used for references
   * **tooltip** - shown in entity form if mode is direct
   * **tab** - display options if shown via tabs
-    * **columns** - columns shown for related entities,
-      optional (default = standard columns)
+    * **columns** - columns shown for related entities, optional
+      (default = standard columns)
     * **buttons**
       * **link** - link to existing entities
       * **insert** - insert a new entity and link automatically
@@ -80,13 +85,13 @@ Description of the structure for classes used in the classes directory.
     * **insert_continue_human_remains** - continue with entering human remains
   * **additional_tabs**
     * **note** - possibility to add notes
-    * **person_place** - special function to show event places at an actor
-    * **place_person** - special function to show actors of events at a place
+    * **person_place** - show event places at an actor view
+    * **place_person** - show involved actors of events at a place view
   * **additional_information** - labels can be set optionally
     * **file_size** - used for files
     * **file_extension** - used for files
-    * **type_information** - show additional infor for types, e.g. the id for
-      imports and if selectable
+    * **type_information** - show additional information for types, e.g. the id
+      for imports and if selectable
   * **network_color** - color of entities in the backend network visualisation
 * **extra**
   * **reference_system** - possibility to configure to add external reference

openatlas/__init__.py

@@ -52,7 +52,7 @@ def get_locale() -> str:
 def before_request() -> Response | None:
     from openatlas.models.cidoc import cidoc_classes, cidoc_properties
     from openatlas.models.entity import Entity
-    from openatlas.models.settings import Settings
+    from openatlas.models.settings import get_settings
 
     if request.path.startswith('/static'):
         return None  # Avoid overheads if not using Apache with static alias
@@ -61,7 +61,7 @@ def before_request() -> Response | None:
     g.db = open_connection(app.config)
     g.db.autocommit = True
     g.cursor = g.db.cursor(cursor_factory=extras.DictCursor)
-    g.settings = Settings.get_settings()
+    g.settings = get_settings()
 
     if request.path.startswith('/display'):
         return None  # Avoid overheads for file display

openatlas/api/endpoints/content.py

@@ -113,7 +113,7 @@ def get() -> tuple[Resource, int] | Response:
         if parser == 'yaml':
             data = yaml.dump(data)
         response = make_response(data)
-        response.headers["Content-Disposition"] = \
-            f"attachment; filename=openapi.{parser}"
-        response.headers["Content-Type"] = f"application/{parser}"
+        response.headers['Content-Disposition'] = \
+            f'attachment; filename=openapi.{parser}'
+        response.headers['Content-Type'] = f'application/{parser}'
         return response

openatlas/api/endpoints/endpoint.py

@@ -27,7 +27,7 @@
     replace_empty_list_values_in_dict_with_none)
 from openatlas.display.table import entity_table
 from openatlas.models.entity import Entity, Link
-from openatlas.models.gis import Gis
+from openatlas.models.gis import get_centroids_by_entities, get_gis_by_entities
 
 
 class Endpoint:
@@ -58,11 +58,10 @@ def get_links_for_entities(self) -> None:
         for link_ in self.link_parser_check(inverse=True):
             self.entities_with_links[
                 link_.range.id]['links_inverse'].append(link_)
-        for id_, geom in Gis.get_by_entities(self.entities).items():
+        for id_, geom in get_gis_by_entities(self.entities).items():
             self.entities_with_links[id_]['geometry'].extend(geom)
         if self.parser.centroid:
-            for id_, geom in \
-                    Gis.get_centroids_by_entities(self.entities).items():
+            for id_, geom in get_centroids_by_entities(self.entities).items():
                 self.entities_with_links[id_]['geometry'].extend(geom)
 
     def get_pagination(self) -> None:
@@ -264,8 +263,7 @@ def get_entities_formatted(self) -> None:
                 self.formated_entities = [
                     self.get_linked_places_entity(_id)
                     for _id in self.entities_with_links]
-            case _ if self.parser.format \
-                      in app.config['RDF_FORMATS']:  # pragma: no cover
+            case _ if self.parser.format in app.config['RDF_FORMATS']:
                 license_links = get_license_ids_with_links()
                 parsed_context = parse_loud_context()
                 self.generator_entities = (
@@ -352,7 +350,7 @@ def get_linked_places_entity(self, _id: int) -> dict[str, Any]:
         links = self.entities_with_links[_id]['links']
         links_inverse = self.entities_with_links[_id]['links_inverse']
         geometry = self.entities_with_links[_id]['geometry']
-        crm = f"crm:{entity.cidoc_class.code} {entity.cidoc_class.i18n['en']}"
+        crm = f'crm:{entity.cidoc_class.code} {entity.cidoc_class.i18n['en']}'
         feature = {
             '@id': url_for('api.entity', id_=entity.id, _external=True),
             'type': 'Feature',

openatlas/api/endpoints/file.py

@@ -15,8 +15,8 @@
 from openatlas.api.resources.parser import files, image
 from openatlas.api.resources.resolve_endpoints import download
 from openatlas.api.resources.templates import licensed_file_template
-from openatlas.api.resources.util import get_iiif_manifest_and_path, \
-    get_license_name
+from openatlas.api.resources.util import (
+    get_iiif_manifest_and_path, get_license_name)
 from openatlas.database.overlay import get_by_object
 from openatlas.display.util import (
     check_iiif_activation, check_iiif_file_exist, get_file_path)
@@ -42,7 +42,7 @@ def get(filename: str) -> Response:
         size = None
         if parser['image_size']:
             size = app.config['IMAGE_SIZE'][parser['image_size']]
-        filepath = get_file_path(entity, size)
+        filepath = get_file_path(entity.id, size)
         if not filepath:
             raise DisplayFileNotFoundError
         return send_file(filepath, as_attachment=bool(parser['download']))
@@ -60,7 +60,7 @@ def get() -> Response | tuple[Any, int]:
         for entity in entities:
             if not (license_ := get_license_name(entity)):
                 continue
-            if not (path := get_file_path(entity)):
+            if not (path := get_file_path(entity.id)):
                 continue
             iiif_manifest = ''
             if check_iiif_activation() and check_iiif_file_exist(entity.id):
@@ -118,10 +118,11 @@ def get() -> Response:
     def get_file_dict(
             entity: Entity,
             overlay: Optional[Overlay] = None) -> dict[str, Any]:
-        path = get_file_path(entity.id)
+        url = 'N/A'
         mime_type = None
-        if path:
-            mime_type, _ = mimetypes.guess_type(path)  # pragma: no cover
+        if path := get_file_path(entity.id):
+            url = url_for('api.display', filename=path.stem, _external=True)
+            mime_type, _ = mimetypes.guess_type(path)
         data = {
             'id': entity.id,
             'title': entity.name,
@@ -130,10 +131,7 @@ def get_file_dict(
             'licenseHolder': entity.license_holder,
             'publicShareable': entity.public,
             'mimetype': mime_type,
-            'url': url_for(
-                'api.display',
-                filename=path.stem,
-                _external=True) if path else 'N/A'}
+            'url': url}
         data.update(get_iiif_manifest_and_path(entity.id))
         if overlay:
             data.update({'overlay': overlay.bounding_box})

openatlas/api/endpoints/iiif.py

@@ -152,7 +152,7 @@ def build_annotation(
         if annotation.entity_id:
             entity = ApiEntity.get_by_id(annotation.entity_id)
             url = get_url(entity.id, parser.url)
-            entity_link = f"<a href={url} target=_blank>{entity.name}</a>"
+            entity_link = f'<a href={url} target=_blank>{entity.name}</a>'
         return {
             "@id": url_for(
                 'api.iiif_annotation',
@@ -296,13 +296,13 @@ def get_metadata(entity: Entity) -> dict[str, Any]:
             and not check_iiif_file_exist(entity.id):
         raise DisplayFileNotFoundError
     ext = '.tiff' if g.settings['iiif_conversion'] else entity.get_file_ext()
-    image_url = f"{g.settings['iiif_url']}{entity.id}{ext}"
+    image_url = f'{g.settings['iiif_url']}{entity.id}{ext}'
 
     try:
         resp = requests.get(f"{image_url}/info.json", timeout=30)
         resp.raise_for_status()
-    except Exception as exc:  # pragma: no cover
-        raise IIIFMetadataNotFound(image_url) from exc
+    except Exception as e:  # pragma: no cover
+        raise IIIFMetadataNotFound(image_url) from e
 
     return {'entity': entity, 'img_url': image_url, 'img_api': resp.json()}
 

openatlas/api/external/arche.py

@@ -27,7 +27,7 @@ def is_arche_likeable_uri(uri: str) -> bool:
     for rule in g.arche_uri_rules:
         if search(rule['match'], uri):
             return True
-    return False  # pragma: no cover
+    return False
 
 
 def is_valid_url(url: str) -> bool:
@@ -56,12 +56,9 @@ def create_uri(value: str | list[str]) -> list[URIRef]:
     return [create_single_uri(value)]
 
 
-def ensure_person_exist(
-        graph: Graph,
-        names: str | list[str]) -> None:
+def ensure_person_exist(graph: Graph, names: str | list[str]) -> None:
     names = names if isinstance(names, list) else [names]
     for name in names:
-
         if not name or is_valid_url(name):
             continue  # pragma: no cover
         uri = create_single_uri(name)
@@ -117,13 +114,11 @@ def ensure_entity_exist(
 
 def transliterate_url(url: str) -> str:
     parsed = urlparse(url)
-    path = parsed.path
-    ascii_path = unidecode(path)
-    ascii_path = ascii_path.replace(' ', '_')
+    ascii_path = unidecode(parsed.path)
     return urlunparse((
         parsed.scheme,
         parsed.netloc,
-        ascii_path,
+        ascii_path.replace(' ', '_'),
         parsed.params,
         parsed.query,
         parsed.fragment))

openatlas/api/external/arche_class.py

@@ -40,14 +40,13 @@ def construct(
             publications: list[tuple[Entity, str]],
             license_: str) -> 'ArcheFileMetadata':
         metadata = app.config['ARCHE_METADATA']
-        part_of = "https://id.acdh.oeaw.ac.at/" \
-                  f"{metadata['topCollection'].replace(' ', '_')}"
-        titles = [(entity.name, 'und')]
+        part_of = 'https://id.acdh.oeaw.ac.at/' \
+            f'{metadata['topCollection'].replace(' ', '_')}'
         file_info = (g.files[entity.id].suffix[1:], g.files[entity.id].name)
         obj = cls(
-            uri=f"{part_of}/{type_name.replace(' ', '_')}/"
-                f"{file_info[0]}/{file_info[1]}",
-            titles=titles)
+            uri=f'{part_of}/{type_name.replace(' ', '_')}/'
+                f'{file_info[0]}/{file_info[1]}',
+            titles=[(entity.name, 'und')])
         obj.depositors = metadata['depositor']
         obj.language = metadata['language']
         obj.license = license_

openatlas/api/external/gnd.py

@@ -8,11 +8,10 @@
 
 
 def fetch_gnd(id_: str) -> dict[str, Any]:
-    url = f'{g.gnd.resolver_url}{id_}.json'
     info: dict[str, str] = {}
     try:
         data = requests.get(
-            url,
+            f'{g.gnd.resolver_url}{id_}.json',
             proxies=app.config['PROXIES'],
             timeout=10).json()
     except Exception:  # pragma: no cover