fix!: transform valueHasUri values from node to string type (DEV-1047) (

#2094)

* add test data

* add plugin and test

* add plugin to Upgrade plan + increase knora-base version

* cleanup

.gitignore

@@ -36,7 +36,7 @@ sipi/test
 *.bak
 *.rdb
 .sbtrc
-**/*.trig
+/*.trig
 
 dependencies.txt
 /client-test-data.zip

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 v22" .
+    :ontologyVersion   "knora-base v23" .
 
 
 #################################################################

test_data/upgrade/pr2094.trig

@@ -0,0 +1,12 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix knora-base: <http://www.knora.org/ontology/knora-base#> .
+
+# bad valueHasUri value and missing datatype
+<http://rdfh.ch/0103/5LE8P57nROClWUxEPJhiug/values/fEbt5NzaSe6GnCqKoF4Nhg/standoff/2>
+    rdf:type                                knora-base:StandoffUriTag ;
+    knora-base:standoffTagHasEnd            50 ;
+    knora-base:standoffTagHasStart          20 ;
+    knora-base:standoffTagHasStartIndex     2 ;
+    knora-base:standoffTagHasStartParent     <http://rdfh.ch/0103/5LE8P57nROClWUxEPJhiug/values/fEbt5NzaSe6GnCqKoF4Nhg/standoff/1> ;
+    knora-base:standoffTagHasUUID           "dd2e785b-041e-4bcb-a77d-570efe8a068c" ;
+    knora-base:valueHasUri                  <http://www.maison-george-sand.fr/> .

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 v22"
+  val KnoraBaseVersion: String = "knora-base v23"
 
   /**
    * `IRI` is a synonym for `String`, used to improve code readability.

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

@@ -49,7 +49,8 @@ object RepositoryUpdatePlan {
       PluginForKnoraBaseVersion(versionNumber = 14, plugin = new NoopPlugin), // PR 1992
       PluginForKnoraBaseVersion(versionNumber = 20, plugin = new UpgradePluginPR2018(log)),
       PluginForKnoraBaseVersion(versionNumber = 21, plugin = new UpgradePluginPR2079(log)),
-      PluginForKnoraBaseVersion(versionNumber = 22, plugin = new UpgradePluginPR2081(log))
+      PluginForKnoraBaseVersion(versionNumber = 22, plugin = new UpgradePluginPR2081(log)),
+      PluginForKnoraBaseVersion(versionNumber = 23, plugin = new UpgradePluginPR2094(log))
       // KEEP IT ON THE BOTTOM
       // From "versionNumber = 6" don't use prBasedVersionString!
     )

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

@@ -38,7 +38,7 @@ class UpgradePluginPR2079(log: Logger) extends UpgradePlugin {
               )
 
               log.info(
-                s"Transformed valueHasIri: $literal to ${newObjectValue(literal.value)}."
+                s"Transformed valueHasUri: $literal to ${newObjectValue(literal.value)}."
               )
             }
 

webapi/src/main/scala/org/knora/webapi/store/triplestore/upgrade/plugins/UpgradePluginPR2094.scala

@@ -0,0 +1,52 @@
+/*
+ * 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.messages.OntologyConstants
+import org.knora.webapi.messages.util.rdf._
+import org.knora.webapi.store.triplestore.upgrade.UpgradePlugin
+
+/**
+ * Transforms a repository for Knora PR 2094.
+ * Transforms incorrect value of valueHasUri from node to string type adding also
+ * missing datatype ^^<http://www.w3.org/2001/XMLSchema#anyURI>
+ */
+class UpgradePluginPR2094(log: Logger) extends UpgradePlugin {
+  private val nodeFactory: RdfNodeFactory = RdfFeatureFactory.getRdfNodeFactory()
+
+  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 node: IriNode =>
+            statementsToRemove += statement
+
+            statementsToAdd += nodeFactory.makeStatement(
+              subj = statement.subj,
+              pred = statement.pred,
+              obj = newObjectValue(node.iri),
+              context = statement.context
+            )
+
+            log.info(
+              s"Transformed valueHasUri $node to ${newObjectValue(node.iri)}."
+            )
+
+          case _ => ()
+        }
+      }
+    }
+
+    model.removeStatements(statementsToRemove.toSet)
+    model.addStatements(statementsToAdd.toSet)
+  }
+}

webapi/src/test/scala/org/knora/webapi/store/triplestore/upgrade/plugins/UpgradePluginPR2094Spec.scala

@@ -0,0 +1,51 @@
+/*
+ * 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 UpgradePluginPR2094Spec extends UpgradePluginSpec with LazyLogging {
+  private val nodeFactory: RdfNodeFactory = RdfFeatureFactory.getRdfNodeFactory()
+
+  "Upgrade plugin PR2094" should {
+    "fix the missing valueHasUri datatype" in {
+      // Parse the input file.
+      val model: RdfModel = trigFileToModel("../test_data/upgrade/pr2094.trig")
+
+      // Use the plugin to transform the input.
+      val plugin = new UpgradePluginPR2094(log)
+      plugin.transform(model)
+
+      // Check that the datatype was fixed.
+      val subj =
+        nodeFactory.makeIriNode("http://rdfh.ch/0103/5LE8P57nROClWUxEPJhiug/values/fEbt5NzaSe6GnCqKoF4Nhg/standoff/2")
+      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")
+      }
+    }
+  }
+}