refactor(knora-admin): Remove unused Institution class and its properties (DEV-3365)

docs/02-dsp-ontologies/knora-base.md

@@ -39,8 +39,6 @@ In Knora, each item of data belongs to some particular project. Each project usi
 
 - `projectDescription` (1-n): A description of the project.
 
-- `belongsToInstitution` (0-1): The `kb:Institution` that the project belongs to.
-
 Ontologies and resources are associated with a project by means of the
 `kb:attachedToProject` property, as described in [Ontologies](#ontologies)
 and [Properties of Resource](#properties-of-resource)). Users are associated with a project by means of

docs/05-internals/design/domain/domain-entities-and-relations.md

@@ -97,12 +97,6 @@ erDiagram
 
 ```
 
-!!! danger "Unclear/Unexpected Stuff"
-
-    - User.phone?
-    - Institution? (name, description, website, phone, address, email)
-    - Project.belongsToInstitution?
-
 ### Overview V2
 
 ```mermaid

test_data/project_data/admin-data.ttl

@@ -83,7 +83,6 @@
                                                "collection"^^xsd:string ;
     knora-admin:projectRestrictedViewSize      "!512,512"^^xsd:string ;
     knora-admin:projectRestrictedViewWatermark "true"^^xsd:boolean;
-    knora-admin:belongsToInstitution           <http://rdfh.ch/institutions/dhlab-basel> ;
     knora-admin:status                         "true"^^xsd:boolean ;
     knora-admin:hasSelfJoinEnabled             "false"^^xsd:boolean .
 
@@ -141,11 +140,6 @@
     knora-admin:hasSelfJoinEnabled "false"^^xsd:boolean .
 
 
-<http://rdfh.ch/institutions/dhlab-basel>
-    rdf:type                    knora-admin:Institution ;
-    knora-admin:institutionName "Digital Humanities Lab, Basel" .
-
-
 ##########################################################
 #
 # INCUNABULA PROJECT / USERS / GROUPS

test_data/upgrade/pr1746.trig

@@ -24,8 +24,6 @@
 
                                 knora-admin:projectRestrictedViewSize "!512,512"^^xsd:string ;
 
-                                knora-admin:belongsToInstitution <http://rdfh.ch/institutions/dhlab-basel> ;
-
                                 knora-admin:status "true"^^xsd:boolean ;
 
                                 knora-admin:hasSelfJoinEnabled "false"^^xsd:boolean .

webapi/src/main/resources/knora-ontologies/knora-admin.ttl

@@ -27,16 +27,6 @@
 #################################################################
 
 
-###  http://www.knora.org/ontology/knora-admin#belongsToInstitution
-
-:belongsToInstitution
-    rdf:type                          owl:ObjectProperty ;
-    rdfs:subPropertyOf                knora-base:objectCannotBeMarkedAsDeleted ;
-    rdfs:comment                      "Indicates which Institution a project belongs to."@en ;
-    knora-base:subjectClassConstraint :knoraProject ;
-    knora-base:objectClassConstraint  :Institution .
-
-
 ###  http://www.knora.org/ontology/knora-admin#belongsToProject
 
 :belongsToProject
@@ -96,16 +86,6 @@
 #
 #################################################################
 
-
-###  http://www.knora.org/ontology/knora-admin#address
-
-:address
-    rdf:type                            owl:DatatypeProperty ;
-    rdfs:subPropertyOf                  knora-base:objectCannotBeMarkedAsDeleted ;
-    knora-base:objectDatatypeConstraint xsd:string ;
-    rdfs:comment                        "The address of a person or an institution"@en .
-
-
 ###  http://www.knora.org/ontology/knora-admin#groupName
 
 :groupName
@@ -139,37 +119,6 @@
     knora-base:objectDatatypeConstraint xsd:boolean .
 
 
-###  http://www.knora.org/ontology/knora-admin#institutionName
-
-:institutionName
-    rdf:type                            owl:DatatypeProperty ;
-    rdfs:subPropertyOf                  knora-base:objectCannotBeMarkedAsDeleted ;
-    rdfs:comment                        "The institutions's name."@en ;
-    rdfs:subPropertyOf                  <http://xmlns.com/foaf/0.1/name> ;
-    knora-base:subjectClassConstraint   :Institution ;
-    knora-base:objectDatatypeConstraint xsd:string .
-
-
-###  http://www.knora.org/ontology/knora-admin#institutionDescription
-
-:institutionDescription
-    rdf:type                            owl:DatatypeProperty ;
-    rdfs:subPropertyOf                  knora-base:objectCannotBeMarkedAsDeleted ;
-    rdfs:comment                        "A description of an institution."@en ;
-    knora-base:subjectClassConstraint   :Institution ;
-    knora-base:objectDatatypeConstraint xsd:string .
-
-
-###  http://www.knora.org/ontology/knora-admin#institutionWebsite
-
-:institutionWebsite
-    rdf:type                            owl:DatatypeProperty ;
-    rdfs:subPropertyOf                  knora-base:objectCannotBeMarkedAsDeleted ;
-    rdfs:comment                        "The URL of a web site."@en ;
-    knora-base:subjectClassConstraint   :Institution ;
-    knora-base:objectDatatypeConstraint xsd:anyURI .
-
-
 ###  http://www.knora.org/ontology/knora-admin#isActiveUser
 
 :isInSystemAdminGroup
@@ -209,16 +158,6 @@
     knora-base:subjectClassConstraint   :User ;
     knora-base:objectDatatypeConstraint xsd:string .
 
-
-###  http://www.knora.org/ontology/knora-admin#phone
-
-:phone
-    rdf:type                            owl:DatatypeProperty ;
-    rdfs:subPropertyOf                  knora-base:objectCannotBeMarkedAsDeleted ;
-    rdfs:comment                        "The phone number of a person, institution, etc."@en ;
-    knora-base:objectDatatypeConstraint xsd:string .
-
-
 ###  http://www.knora.org/ontology/knora-admin#preferredLanguage
 
 :preferredLanguage
@@ -345,33 +284,6 @@
 #
 #################################################################
 
-
-###  http://www.knora.org/ontology/knora-admin#Institution
-
-:Institution
-    rdf:type        owl:Class ;
-    rdfs:subClassOf foaf:Organization,
-                    [ rdf:type        owl:Restriction ;
-                      owl:onProperty  :institutionName ;
-                      owl:cardinality "1"^^xsd:nonNegativeInteger ],
-                    [ rdf:type           owl:Restriction ;
-                      owl:onProperty     :institutionDescription ;
-                      owl:maxCardinality "1"^^xsd:nonNegativeInteger ],
-                    [ rdf:type           owl:Restriction ;
-                      owl:onProperty     :institutionWebsite ;
-                      owl:minCardinality "0"^^xsd:nonNegativeInteger ],
-                    [ rdf:type           owl:Restriction ;
-                      owl:onProperty     :phone ;
-                      owl:minCardinality "0"^^xsd:nonNegativeInteger ],
-                    [ rdf:type           owl:Restriction ;
-                      owl:onProperty     :address ;
-                      owl:minCardinality "0"^^xsd:nonNegativeInteger ],
-                    [ rdf:type           owl:Restriction ;
-                      owl:onProperty     :email ;
-                      owl:minCardinality "0"^^xsd:nonNegativeInteger ] ;
-    rdfs:comment    "An institution that has data in Knora."@en .
-
-
 ###  http://www.knora.org/ontology/knora-admin#User
 
 :User
@@ -465,9 +377,6 @@
                     [ rdf:type           owl:Restriction ;
                       owl:onProperty     :projectRestrictedViewWatermark ;
                       owl:maxCardinality "1"^^xsd:nonNegativeInteger ],
-                    [ rdf:type           owl:Restriction ;
-                      owl:onProperty     :belongsToInstitution ;
-                      owl:maxCardinality "1"^^xsd:nonNegativeInteger ],
                     [ rdf:type        owl:Restriction ;
                       owl:onProperty  :status ;
                       owl:cardinality "1"^^xsd:nonNegativeInteger ],

webapi/src/main/resources/knora-ontologies/knora-base.ttl

@@ -19,7 +19,7 @@
     rdf:type           owl:Ontology ;
     rdfs:label         "The Knora base ontology"@en ;
     :attachedToProject knora-admin:SystemProject ;
-    :ontologyVersion   "knora-base v28" .
+    :ontologyVersion   "knora-base v29" .
 
 
 #################################################################

webapi/src/main/scala/org/knora/webapi/messages/OntologyConstants.scala

@@ -457,7 +457,6 @@ object OntologyConstants {
     val GivenName: IRI             = KnoraAdminPrefixExpansion + "givenName"
     val FamilyName: IRI            = KnoraAdminPrefixExpansion + "familyName"
     val Password: IRI              = KnoraAdminPrefixExpansion + "password"
-    val Address: IRI               = KnoraAdminPrefixExpansion + "address"
     val UsersActiveProject: IRI    = KnoraAdminPrefixExpansion + "currentproject"
     val PreferredLanguage: IRI     = KnoraAdminPrefixExpansion + "preferredLanguage"
     val IsInProject: IRI           = KnoraAdminPrefixExpansion + "isInProject"
@@ -478,7 +477,6 @@ object OntologyConstants {
     val ProjectLogo: IRI                    = KnoraAdminPrefixExpansion + "projectLogo"
     val ProjectRestrictedViewSize: IRI      = KnoraAdminPrefixExpansion + "projectRestrictedViewSize"
     val ProjectRestrictedViewWatermark: IRI = KnoraAdminPrefixExpansion + "projectRestrictedViewWatermark"
-    val BelongsToInstitution: IRI           = KnoraAdminPrefixExpansion + "belongsToInstitution"
     val HasSelfJoinEnabled: IRI             = KnoraAdminPrefixExpansion + "hasSelfJoinEnabled"
 
     /* Group */
@@ -504,13 +502,6 @@ object OntologyConstants {
       ProjectAdmin,
     )
 
-    /* Institution */
-    val Institution: IRI            = KnoraAdminPrefixExpansion + "Institution"
-    val InstitutionDescription: IRI = KnoraAdminPrefixExpansion + "institutionDescription"
-    val InstitutionName: IRI        = KnoraAdminPrefixExpansion + "institutionName"
-    val InstitutionWebsite: IRI     = KnoraAdminPrefixExpansion + "institutionWebsite"
-    val Phone: IRI                  = KnoraAdminPrefixExpansion + "phone"
-
     /* Permissions */
     val Permission: IRI                    = KnoraAdminPrefixExpansion + "Permission"
     val AdministrativePermission: IRI      = KnoraAdminPrefixExpansion + "AdministrativePermission"

webapi/src/main/scala/org/knora/webapi/package.scala

@@ -11,7 +11,7 @@ package object webapi {
    * The version of `knora-base` and of the other built-in ontologies that this version of Knora requires.
    * Must be the same as the object of `knora-base:ontologyVersion` in the `knora-base` ontology being used.
    */
-  val KnoraBaseVersion: String = "knora-base v28"
+  val KnoraBaseVersion: String = "knora-base v29"
 
   /**
    * `IRI` is a synonym for `String`, used to improve code readability.

webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/RepositoryUpdatePlan.scala

@@ -63,6 +63,7 @@
       PluginForKnoraBaseVersion(versionNumber = 26, plugin = new MigrateOnlyBuiltInGraphs), // PR 3003
       PluginForKnoraBaseVersion(versionNumber = 27, plugin = new MigrateOnlyBuiltInGraphs), // PR 3026
       PluginForKnoraBaseVersion(versionNumber = 28, plugin = new MigrateOnlyBuiltInGraphs), // PR 3038
+      PluginForKnoraBaseVersion(versionNumber = 29, plugin = new UpgradePluginPR3110()),
       // KEEP IT ON THE BOTTOM
       // From "versionNumber = 6" don't use prBasedVersionString!
     )

webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/RepositoryUpdater.scala

@@ -204,7 +204,7 @@
         graphs = pluginsForNeededUpdates
                    .map(_.plugin.graphsForMigration)
                    .reduce(_ merge _)
-        _ <- ZIO.logInfo("Downloading repository file...")
+        _ <- ZIO.logInfo(s"Downloading .$graphs repository file..")
         _ <- triplestoreService.downloadRepository(graphsBeforeMigrationFile, graphs)
 
         // Run the transformations to produce an output file.

webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/plugins/AbstractSparqlUpdatePlugin.scala

@@ -0,0 +1,35 @@
+/*
+ * Copyright © 2021 - 2024 Swiss National Data and Service Center for the Humanities and/or DaSCH Service Platform contributors.
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package org.knora.webapi.store.triplestore.upgrade.plugins
+
+import com.typesafe.scalalogging.Logger
+import org.apache.jena.query.Dataset
+import org.apache.jena.update.UpdateExecutionFactory
+import org.apache.jena.update.UpdateFactory
+import org.eclipse.rdf4j.sparqlbuilder.core.query.ModifyQuery
+
+import org.knora.webapi.messages.util.rdf.*
+import org.knora.webapi.store.triplestore.upgrade.UpgradePlugin
+
+abstract class AbstractSparqlUpdatePlugin extends UpgradePlugin {
+
+  private val log: Logger = Logger(this.getClass)
+
+  def getQueries: List[ModifyQuery]
+
+  override def transform(model: RdfModel): Unit = {
+    val dataset = model.asInstanceOf[JenaModel].getDataset
+    getQueries.foreach(execute(dataset, _))
+  }
+
+  private def execute(dataset: Dataset, query: ModifyQuery) = {
+    val queryString = query.getQueryString
+    log.info(s"Executing SPARQL update: $queryString")
+    val update = UpdateFactory.create(queryString)
+    val qExec  = UpdateExecutionFactory.create(update, dataset)
+    qExec.execute()
+  }
+}

webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/plugins/UpgradePluginPR3110.scala

@@ -0,0 +1,53 @@
+/*
+ * Copyright © 2021 - 2024 Swiss National Data and Service Center for the Humanities and/or DaSCH Service Platform contributors.
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package org.knora.webapi.store.triplestore.upgrade.plugins
+
+import org.eclipse.rdf4j.model.vocabulary.RDF
+import org.eclipse.rdf4j.sparqlbuilder.core.SparqlBuilder.`var` as variable
+import org.eclipse.rdf4j.sparqlbuilder.core.query.ModifyQuery
+import org.eclipse.rdf4j.sparqlbuilder.core.query.*
+import org.eclipse.rdf4j.sparqlbuilder.rdf.Rdf
+
+import org.knora.webapi.messages.OntologyConstants.KnoraAdmin.KnoraAdminPrefixExpansion
+import org.knora.webapi.slice.admin.AdminConstants
+import org.knora.webapi.slice.admin.repo.rdf.Vocabulary
+import org.knora.webapi.store.triplestore.upgrade.GraphsForMigration
+import org.knora.webapi.store.triplestore.upgrade.MigrateSpecificGraphs
+
+/**
+ * After removing `knora-admin:Institution` class and its properties from the knora-admin ontology this cleans up the DB.
+ * Removes all `knora-admin:Institution` classes from the `knora-admin` named graph.
+ */
+class UpgradePluginPR3110 extends AbstractSparqlUpdatePlugin {
+
+  override def graphsForMigration: GraphsForMigration =
+    MigrateSpecificGraphs.from(AdminConstants.adminDataNamedGraph)
+
+  private val removeAllInstitutions: ModifyQuery = {
+    val (s, p, o) = (variable("s"), variable("p"), variable("o"))
+    Queries
+      .MODIFY()
+      .prefix(Vocabulary.KnoraAdmin.NS, RDF.NS)
+      .delete(s.has(p, o))
+      .where(
+        s.isA(Rdf.iri(KnoraAdminPrefixExpansion, "Institution"))
+          .andHas(p, o)
+          .from(Vocabulary.NamedGraphs.knoraAdminIri),
+      )
+  }
+
+  private val removeAllBelongsToInstitutionTriples: ModifyQuery = {
+    val (s, o)               = (variable("s"), variable("o"))
+    val belongsToInstitution = Rdf.iri(KnoraAdminPrefixExpansion, "belongsToInstitution")
+    Queries
+      .MODIFY()
+      .prefix(Vocabulary.KnoraAdmin.NS, RDF.NS)
+      .delete(s.has(belongsToInstitution, o))
+      .where(s.has(belongsToInstitution, o).from(Vocabulary.NamedGraphs.knoraAdminIri))
+  }
+
+  override def getQueries: List[ModifyQuery] = List(removeAllInstitutions, removeAllBelongsToInstitutionTriples)
+}

webapi/src/test/scala/org/knora/webapi/slice/resourceinfo/domain/IriTestConstants.scala

@@ -67,7 +67,6 @@ object IriTestConstants {
 
     object Class {
       val AdministrativePermission: InternalIri = makeEntity(KnoraAdmin.Ontology, "AdministrativePermission")
-      val Institution: InternalIri              = makeEntity(KnoraAdmin.Ontology, "Institution")
       val Permission: InternalIri               = makeEntity(KnoraAdmin.Ontology, "Permission")
     }
   }