Merge pull request #912 from OnroerendErfgoed/develop

2.1.1

CHANGES.rst

@@ -1,3 +1,11 @@
+2.1.1 (01-08-2023)
+------------------
+
+- ConceptVisitLog has an integer concept_id in the ConceptVisitLog class #906
+- skosprovider route /expand does not work #903
+- Manual ID text box not writable #902
+
+
 2.1.0 (22-07-2023)
 ------------------
 

CITATION.cff

@@ -88,5 +88,5 @@ keywords:
   - vocabulary
   - python
 license: GPL-3.0
-version: 2.1.0
+version: 2.1.1
 date-released: '2024-06-20'

atramhasis/__init__.py

@@ -34,6 +34,8 @@ def includeme(config):
     for key, value in DEFAULT_SETTINGS.items():
         if key not in settings:
             settings[key] = value
+    # Regexes in path params clash with this validation.
+    settings["pyramid_openapi3.enable_endpoint_validation"] = False
     configure_session(config)
     config.include('pyramid_jinja2')
     config.include('pyramid_tm')
@@ -44,9 +46,10 @@ def includeme(config):
     config.include('pyramid_rewrite')
     config.include("pyramid_openapi3")
     config.include('atramhasis.routes')
+    # pyramid_skosprovider must be included after the atramhasis routes
+    # because it contains a regex in the path which consumes a lot of routes.
     config.include('pyramid_skosprovider')
     config.include('atramhasis.cache')
-    config.scan('pyramid_skosprovider')
 
     config.add_translation_dirs('atramhasis:locale/')
 

atramhasis/alembic/versions/29306f749043_alter_conceptvisitlog_concept_id_to_.py

@@ -0,0 +1,30 @@
+"""alter ConceptVisitLog concept_id to string
+
+Revision ID: 29306f749043
+Revises: b2a7d7614973
+Create Date: 2024-07-30 09:12:37.521748
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '29306f749043'
+down_revision = 'b2a7d7614973'
+
+
+def upgrade():
+    with op.batch_alter_table('concept_visit_log') as batch_op:
+        batch_op.alter_column('concept_id', type_=sa.String, existing_type=sa.Integer)
+
+
+def downgrade():
+    # Drop concept_visit_log which have non-integer concept_id
+    op.execute(
+        "DELETE FROM concept_visit_log "
+        "WHERE cast(cast(concept_id AS INTEGER) AS TEXT) != concept_id"
+    )
+    with op.batch_alter_table('concept_visit_log') as batch_op:
+        batch_op.alter_column('concept_id', type_=sa.Integer, existing_type=sa.String)

atramhasis/data/models.py

@@ -39,7 +39,7 @@ class ConceptschemeVisitLog(Base):
 class ConceptVisitLog(Base):
     __tablename__ = 'concept_visit_log'
     id = Column(Integer, primary_key=True, autoincrement=True)
-    concept_id = Column(Integer, nullable=False)
+    concept_id = Column(String, nullable=False)
     conceptscheme_id = Column(String(25), nullable=False)
     visited_at = Column(DateTime, default=func.now(), nullable=False)
     origin = Column(String(25), nullable=False)

atramhasis/openapi.yaml

@@ -2,7 +2,7 @@ openapi: 3.0.3
 
 info:
   title: Atramhasis API
-  version: 2.1.0
+  version: 2.1.1
 
 servers:
   - url: '/'
@@ -142,7 +142,7 @@ paths:
           description: The identifier for a certain concept or collection.
           required: true
           schema:
-            type: integer
+            type: string
       responses:
         200:
           description: The concept was found in the conceptscheme.
@@ -172,7 +172,7 @@ paths:
           description: The identifier for a certain concept or collection.
           required: true
           schema:
-            type: integer
+            type: string
       requestBody:
         required: true
         description: Data to create concept or collection
@@ -222,7 +222,7 @@ paths:
           description: The identifier for a certain concept or collection.
           required: true
           schema:
-            type: integer
+            type: string
 
       responses:
         200:
@@ -692,7 +692,7 @@ paths:
           description: The identifier for a certain concept or collection.
           required: true
           schema:
-            type: integer
+            type: string
         - name: language
           in: query
           description: Returns the label with the corresponding language-tag if present.
@@ -748,7 +748,7 @@ paths:
           description: The identifier for a certain concept or collection.
           required: true
           schema:
-            type: integer
+            type: string
       responses:
         200:
           description: The concept/collection was found in the conceptscheme.
@@ -900,7 +900,7 @@ components:
       type: object
       properties:
         id:
-          type: integer
+          type: string
     Label:
       type: object
       properties:
@@ -952,7 +952,7 @@ components:
       type: object
       properties:
         id:
-          type: integer
+          type: string
         type:
           type: string
         labels:
@@ -990,7 +990,7 @@ components:
         - type: object
           properties:
             id:
-              type: integer
+              type: string
             uri:
               type: string
     ConceptTree:

atramhasis/rdf.py

@@ -76,12 +76,12 @@ def _add_provider(graph, provider, dataseturi, request):
     graph.add((dataseturi, VOID.subset, pd))
     graph.add((pd, DCTERMS.identifier, Literal(pid)))
     graph.add((pd, VOID.rootResource, URIRef(provider.concept_scheme.uri)))
-    graph.add((pd, FOAF.homepage, URIRef(request.route_url('conceptscheme', scheme_id=pid))))
+    graph.add((pd, FOAF.homepage, URIRef(request.route_url('skosprovider.conceptscheme', scheme_id=pid))))
     _add_labels(graph, provider.concept_scheme, pd)
     _add_metadataset(graph, pd, metadataset)
     fmap = [
-        ('rdf', FORMATS.RDF_XML, 'atramhasis.rdf_full_export_ext'),
-        ('ttl', FORMATS.Turtle, 'atramhasis.rdf_full_export_turtle_ext')
+        ('rdf', FORMATS.RDF_XML, 'skosprovider.conceptscheme.cs.rdf'),
+        ('ttl', FORMATS.Turtle, 'skosprovider.conceptscheme.cs.ttl')
     ]
     for f in fmap:
         graph.add((pd, VOID.feature, f[1]))

atramhasis/routes.py

@@ -27,38 +27,22 @@ def includeme(config):
     config.add_static_view('static', 'static', cache_max_age=3600)
     config.add_route("sitemap", "/sitemap_index.xml")
 
+    # APIs with extensions instead of accept headers
     config.add_route('atramhasis.rdf_void_turtle_ext', pattern='/void.ttl', accept='text/turtle')
-    config.add_route('atramhasis.rdf_full_export_ext', pattern='/conceptschemes/{scheme_id}/c.rdf')
-    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_conceptscheme_jsonld_ext', pattern='/conceptschemes/{scheme_id}.jsonld')
-    config.add_route('atramhasis.rdf_individual_jsonld_ext', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}.jsonld')
+    # The routes below extend the existing skosprovider routes with extensions
+    config.add_route('skosprovider.conceptscheme.cs.rdf', pattern='/conceptschemes/{scheme_id}/c.rdf')
+    config.add_route('skosprovider.conceptscheme.cs.ttl', pattern='/conceptschemes/{scheme_id}/c.ttl')
+    config.add_route('skosprovider.conceptscheme.rdf', pattern='/conceptschemes/{scheme_id}.rdf')
+    config.add_route('skosprovider.conceptscheme.ttl', pattern='/conceptschemes/{scheme_id}.ttl')
+    config.add_route('skosprovider.conceptscheme.csv', pattern='/conceptschemes/{scheme_id}/c.csv')
+    config.add_route('skosprovider.c.rdf', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}.rdf')
+    config.add_route('skosprovider.c.ttl', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}.ttl')
 
-    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',
-                     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')
+    # tree
     config.add_route('scheme_tree_html', pattern='/conceptschemes/{scheme_id}/tree', accept='text/html')
     config.add_route('scheme_tree', pattern='/conceptschemes/{scheme_id}/tree', accept='application/json')
 
-    config.add_route('search_result_export', pattern='/conceptschemes/{scheme_id}/c.csv')
-    config.add_route('atramhasis.edit_conceptscheme', pattern='/conceptschemes/{scheme_id}',
-                     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:.*}',
-                     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:.*}',
-                     accept='application/json', request_method="PUT")
-    config.add_route('atramhasis.delete_concept', pattern='/conceptschemes/{scheme_id}/c/{c_id:.*}',
-                     accept='application/json', request_method="DELETE")
+    # language
     config.add_route('atramhasis.list_languages', pattern='/languages', accept='application/json',
                      request_method="GET")
     config.add_route('atramhasis.get_language', pattern='/languages/{l_id}', accept='application/json',
@@ -68,33 +52,16 @@ def includeme(config):
     config.add_route('atramhasis.delete_language', pattern='/languages/{l_id}', accept='application/json',
                      request_method="DELETE")
     config.add_route('locale', '/locale')
-    config.add_route('labeltypes', '/labeltypes', accept='application/json', request_method="GET")
-    config.add_route('notetypes', '/notetypes', accept='application/json', request_method="GET")
 
+    # admin
     config.add_route('admin', '/admin')
     config.add_route('scheme_tree_invalidate', pattern='/admin/tree/invalidate/{scheme_id}', accept='application/json')
     config.add_route('tree_invalidate', pattern='/admin/tree/invalidate', accept='application/json')
 
-    config.add_route('atramhasis.rdf_full_export_turtle', pattern='/conceptschemes/{scheme_id}/c', accept='text/turtle')
-    config.add_route('atramhasis.rdf_full_export_turtle_x', pattern='/conceptschemes/{scheme_id}/c',
-                     accept='application/x-turtle')
-    config.add_route('atramhasis.rdf_full_export', pattern='/conceptschemes/{scheme_id}/c',
-                     accept='application/rdf+xml')
-    config.add_route('atramhasis.rdf_conceptscheme_export', pattern='/conceptschemes/{scheme_id}',
-                     accept='application/rdf+xml')
-    config.add_route('atramhasis.rdf_conceptscheme_export_turtle', pattern='/conceptschemes/{scheme_id}',
-                     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:.*}',
-                     accept='application/rdf+xml')
-    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:.*}',
-                     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:.*}',
-                     accept='application/ld+json')
+    # providers
     config.add_route('atramhasis.providers', pattern='/providers')
     config.add_route('atramhasis.provider', pattern='/providers/{id}')
+
+    # other
+    config.add_route('labeltypes', '/labeltypes', accept='application/json', request_method="GET")
+    config.add_route('notetypes', '/notetypes', accept='application/json', request_method="GET")

atramhasis/static/admin/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "atramhasis",
-	"version": "2.1.0",
+	"version": "2.1.1",
 	"description": "Node packages for building Atramhasis.",
 	"repository": {
 		"type": "git",

atramhasis/static/admin/src/app/ui/dialogs/ManageProvidersDialog.js

@@ -349,8 +349,18 @@ define([
             'sticky': false,
             'channel': 'info'
           });
-          this._reset(true);
-          this.parentNode.refresh_conceptschemes();
+          // Update the provider lists with the new data
+          this.providerController.loadProviders().then(lang.hitch(this, function() {
+            this._reset(true);
+            this.parentNode.refresh_conceptschemes();
+          }), lang.hitch(this, function (error) {
+            var message = this._parseError(error);
+            topic.publish('dGrowl', message, {
+              'title': 'Error updating provider list',
+              'sticky': true,
+              'channel': 'error'
+            });
+          }));
         }),
         lang.hitch(this, function (error) {
           var message = this._parseError(error);
@@ -372,7 +382,17 @@ define([
             'sticky': false,
             'channel': 'info'
           });
-          this._reset();
+          // Update the provider lists with the updated data
+          this.providerController.loadProviders().then(lang.hitch(this, function() {
+            this._reset();
+          }), lang.hitch(this, function (error) {
+            var message = this._parseError(error);
+            topic.publish('dGrowl', message, {
+              'title': 'Error updating provider list',
+              'sticky': true,
+              'channel': 'error'
+            });
+          }));
         }),
         lang.hitch(this, function (error) {
           var message = this._parseError(error);

atramhasis/static/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "atramhasis",
-	"version": "2.1.0",
+	"version": "2.1.1",
 	"description": "Node packages for public part of Atramhasis.",
 	"repository": {
 		"type": "git",

atramhasis/templates/concept.jinja2

@@ -2,7 +2,7 @@
 {% block head %}
   {{ super() }}
   <meta name="og:type" content="website" />
-  <meta name="og:url" content="{{ request.route_url('concept', scheme_id=scheme_id, c_id=concept.concept_id) }}" />
+  <meta name="og:url" content="{{ request.route_url('skosprovider.c', scheme_id=scheme_id, c_id=concept.concept_id) }}" />
   <meta name="og:title" content="{{ concept.label(locale).label|safe }}" />
   {% if concept.notes|length > 0 %}
     <meta name="og:description" content="{{ concept.notes[0]|safe }}" />
@@ -13,7 +13,7 @@
   {% if concept.notes|length > 0 %}
     <meta name="twitter:description" content="{{ concept.notes[0]|safe }}" />
   {% endif %}
-  <link rel="canonical" href="{{ request.route_url('concept', scheme_id=scheme_id, c_id=concept.concept_id) }}" />
+  <link rel="canonical" href="{{ request.route_url('skosprovider.c', scheme_id=scheme_id, c_id=concept.concept_id) }}" />
 {% endblock %}
 {% block html_title %}{{ concept.label(locale).label|title }}{% endblock %}
 
@@ -31,9 +31,9 @@
       <div class="clearfix">
         <ul class="downloadtop right">
           <li>DOWNLOAD</li>
-          <li><a href="{{ request.route_path('atramhasis.rdf_individual_export_ext', scheme_id=scheme_id, c_id=concept.concept_id) }}">RDF/XML</a></li>
-          <li><a href="{{ request.route_path('atramhasis.rdf_individual_jsonld_ext', scheme_id=scheme_id, c_id=concept.concept_id) }}">JSON-LD</a></li>
-          <li><a href="{{ request.route_path('atramhasis.rdf_individual_export_turtle_ext', scheme_id=scheme_id, c_id=concept.concept_id) }}">N3/Turtle</a></li>
+          <li><a href="{{ request.route_path('skosprovider.c.rdf', scheme_id=scheme_id, c_id=concept.concept_id) }}">RDF/XML</a></li>
+          <li><a href="{{ request.route_path('skosprovider.c.jsonld', scheme_id=scheme_id, c_id=concept.concept_id) }}">JSON-LD</a></li>
+          <li><a href="{{ request.route_path('skosprovider.c.ttl', scheme_id=scheme_id, c_id=concept.concept_id) }}">N3/Turtle</a></li>
         </ul>
       </div>
       {% if concept %}
@@ -53,7 +53,7 @@
               <dd class="word-wrap-element"><a href="{{ concept.uri }}">{{ concept.uri }}</a></dd>
             {% endif %}
             <dt>schema</dt>
-            <dd><a href="{{ request.route_path('conceptscheme', scheme_id=scheme_id) }}">{{ get_conceptscheme_label(concept.conceptscheme, request.locale_name) }}</a></dd>
+            <dd><a href="{{ request.route_path('skosprovider.conceptscheme', scheme_id=scheme_id) }}">{{ get_conceptscheme_label(concept.conceptscheme, request.locale_name) }}</a></dd>
             {% if concept.labels %}
               {{ print_labels(concept.labels) }}
             {% endif %}