fix!: fix valueHasUri bad values and missing types (DEV-1036) (#2079)

* add plugin, test and test data

* add another case to fix

* fix filenames

* add logging & plugin to repo upgrade plan

* cleanup

* review changes

* fix knora-base version

* remove the standoff case

Author: mpro7

.gitignore

@@ -21,6 +21,7 @@ sipi/test
 /docs/architecture/.structurizr
 /docs/architecture/workspace.json
 
+
 **/target/
 *.aux
 *.bbl
@@ -35,15 +36,14 @@ sipi/test
 *.bak
 *.rdb
 .sbtrc
-.trig
+*.trig
 
 dependencies.txt
 /client-test-data.zip
 /sipi/images/082E/*
 /sipi/images/originals/082E/*
 sipi/images/1111/*
 sipi/images/originals/1111/*
-/dependencies.bzl
 
 .idea/
 .metals/

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 v20" .
+    :ontologyVersion   "knora-base v21" .
 
 
 #################################################################

test_data/upgrade/pr2079.trig

@@ -0,0 +1,15 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix knora-base: <http://www.knora.org/ontology/knora-base#> .
+
+# value with missing valueHasUri datatype
+<http://rdfh.ch/0103/fN89IUgvSSyMxJ7XWssP9w/values/Rl2rfjDlRBWeuRr-EgIgCw>
+    rdf:type                      knora-base:UriValue ;
+    knora-base:attachedToUser     <http://rdfh.ch/users/user-unil-valentina-ponzetto> ;
+    knora-base:hasPermissions     "CR knora-admin:ProjectAdmin|D knora-admin:Creator|M knora-admin:ProjectMember|V knora-admin:KnownUser,knora-admin:UnknownUser" ;
+    knora-base:isDeleted          false ;
+    knora-base:valueCreationDate  "2018-01-12T19:21:37.991+00:00"^^xsd:dateTime ;
+    knora-base:valueHasOrder      1 ;
+    knora-base:valueHasString     "https://viaf.org/viaf/2571146" ;
+    knora-base:valueHasUUID       "PYQ5mqH8TYOKCytMozecWw" ;
+    knora-base:valueHasUri        "https://viaf.org/viaf/2571146" .

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 v20"
+  val KnoraBaseVersion: String = "knora-base v21"
 
   /**
    * `IRI` is a synonym for `String`, used to improve code readability.

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

@@ -54,6 +54,11 @@ object RepositoryUpdatePlan {
         versionNumber = 20,
         plugin = new UpgradePluginPR2018(featureFactoryConfig, log),
         prBasedVersionString = Some("PR 2018")
+      ),
+      PluginForKnoraBaseVersion(
+        versionNumber = 21,
+        plugin = new UpgradePluginPR2079(featureFactoryConfig, log),
+        prBasedVersionString = Some("PR 2079")
       )
     )
 

webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/plugins/UpgradePluginPR2079.scala

@@ -0,0 +1,54 @@
+/*
+ * Copyright © 2021 - 2022 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.knora.webapi.feature.FeatureFactoryConfig
+import org.knora.webapi.messages.OntologyConstants
+import org.knora.webapi.messages.util.rdf._
+import org.knora.webapi.store.triplestore.upgrade.UpgradePlugin
+
+/**
+ * Transforms a repository for Knora PR 2079.
+ * Adds missing datatype ^^<http://www.w3.org/2001/XMLSchema#anyURI> and/or value to valueHasUri
+ */
+class UpgradePluginPR2079(featureFactoryConfig: FeatureFactoryConfig, log: Logger) extends UpgradePlugin {
+  private val nodeFactory: RdfNodeFactory = RdfFeatureFactory.getRdfNodeFactory(featureFactoryConfig)
+
+  override def transform(model: RdfModel): Unit = {
+    val statementsToRemove: collection.mutable.Set[Statement] = collection.mutable.Set.empty
+    val statementsToAdd: collection.mutable.Set[Statement]    = collection.mutable.Set.empty
+    val newObjectValue: String => DatatypeLiteral = (value: String) =>
+      nodeFactory.makeDatatypeLiteral(value, OntologyConstants.Xsd.Uri)
+
+    for (statement: Statement <- model) {
+      if (statement.pred.iri == OntologyConstants.KnoraBase.ValueHasUri) {
+        statement.obj match {
+          case literal: DatatypeLiteral =>
+            if (literal.datatype != OntologyConstants.Xsd.Uri) {
+              statementsToRemove += statement
+
+              statementsToAdd += nodeFactory.makeStatement(
+                subj = statement.subj,
+                pred = statement.pred,
+                obj = newObjectValue(literal.value),
+                context = statement.context
+              )
+
+              log.info(
+                s"Transformed valueHasIri: $literal to ${newObjectValue(literal.value)}."
+              )
+            }
+
+          case _ => ()
+        }
+      }
+    }
+
+    model.removeStatements(statementsToRemove.toSet)
+    model.addStatements(statementsToAdd.toSet)
+  }
+}

webapi/src/test/scala/org/knora/webapi/store/triplestore/upgrade/plugins/UpgradePluginPR2079Spec.scala

@@ -0,0 +1,50 @@
+/*
+ * Copyright © 2021 - 2022 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.LazyLogging
+import dsp.errors.AssertionException
+import org.knora.webapi.messages.OntologyConstants
+import org.knora.webapi.messages.util.rdf._
+
+class UpgradePluginPR2079Spec extends UpgradePluginSpec with LazyLogging {
+  private val nodeFactory: RdfNodeFactory = RdfFeatureFactory.getRdfNodeFactory(defaultFeatureFactoryConfig)
+
+  "Upgrade plugin PR2079" should {
+    "fix the missing valueHasUri datatype" in {
+      // Parse the input file.
+      val model: RdfModel = trigFileToModel("../test_data/upgrade/pr2079.trig")
+
+      // Use the plugin to transform the input.
+      val plugin = new UpgradePluginPR2079(defaultFeatureFactoryConfig, log)
+      plugin.transform(model)
+
+      // Check that the datatype was fixed.
+      val subj = nodeFactory.makeIriNode("http://rdfh.ch/0103/fN89IUgvSSyMxJ7XWssP9w/values/Rl2rfjDlRBWeuRr-EgIgCw")
+      val pred = nodeFactory.makeIriNode(OntologyConstants.KnoraBase.ValueHasUri)
+
+      model
+        .find(
+          subj = Some(subj),
+          pred = Some(pred),
+          obj = None
+        )
+        .toSet
+        .headOption match {
+        case Some(statement: Statement) =>
+          statement.obj match {
+            case datatypeLiteral: DatatypeLiteral =>
+              assert(datatypeLiteral.datatype == OntologyConstants.Xsd.Uri)
+
+            case other =>
+              throw AssertionException(s"Unexpected object for $pred: $other")
+          }
+
+        case None => throw AssertionException(s"No statement found with subject $subj and predicate $pred")
+      }
+    }
+  }
+}