chore: Remove knora-ontologies symlink (DEV-3236) (#3035)

build.sbt

@@ -207,7 +207,11 @@ lazy val webapi: Project = Project(id = "webapi", base = file("webapi"))
         contentOf("webapi/src/main/resources").toMap.mapValues("config/" + _)
     },
     // add 'config' directory to the classpath of the start script,
-    Universal / scriptClasspath := Seq("webapi/scripts", "knora-ontologies", "../config/") ++ scriptClasspath.value,
+    Universal / scriptClasspath := Seq(
+      "webapi/scripts",
+      "webapi/src/main/resources/knora-ontologies",
+      "../config/"
+    ) ++ scriptClasspath.value,
     // need this here, so that the Manifest inside the jars has the correct main class set.
     Compile / mainClass := Some("org.knora.webapi.Main"),
     // add dockerCommands used to create the image

docker-compose.yml

@@ -94,7 +94,6 @@ services:
     volumes:
       - /tmp:/tmp
       # Needed for local development when resetting the triplestore
-      - ./knora-ontologies:/opt/knora-ontologies
       - ./test_data:/opt/test_data
     networks:
       - knora-net

test_data/test_route/texts/README.md

@@ -21,7 +21,7 @@ Is the mapping used to translate html markup using the default mapping `Ontology
 - example text file: `StandardHTML`
 
 Note: that you can use this mapping to generate the default mapping that is distributed
-as `knora-ontologies/standoff-data.ttl`.  
+as `webapi/src/main/resources/knora-ontologies/standoff-data.ttl`.
 Please read the official documentation about Standoff Standard Mapping.
 
 Step to update standard mapping:
@@ -76,7 +76,7 @@ WHERE {
 }
 ```
 
-5. Find differences to update by hand (to avoid massive IRI update) the `knora-ontologies/standoff-data.ttl`, pay attention to namespaces (e.g. replace all `http://rdfh.ch/projects/0001/mappings/update-standard-mapping` by `http://rdfh.ch/standoff/mappings/StandardMapping`)!
+5. Find differences to update by hand (to avoid massive IRI update) the `webapi/src/main/resources/knora-ontologies/standoff-data.ttl`, pay attention to namespaces (e.g. replace all `http://rdfh.ch/projects/0001/mappings/update-standard-mapping` by `http://rdfh.ch/standoff/mappings/StandardMapping`)!
 6. Prepare an upgrade script of an existing Knora base
 
 ## HTML

webapi/scripts/fuseki-init-knora-test-minimal.sh

@@ -8,10 +8,10 @@ REPOSITORY="knora-test"
 
 # delete-repository // delete dos not work correctly. need to delete database manually.
 create-repository
-upload-graph ../../knora-ontologies/knora-admin.ttl http://www.knora.org/ontology/knora-admin
-upload-graph ../../knora-ontologies/knora-base.ttl http://www.knora.org/ontology/knora-base
-upload-graph ../../knora-ontologies/standoff-onto.ttl http://www.knora.org/ontology/standoff
-upload-graph ../../knora-ontologies/standoff-data.ttl http://www.knora.org/data/standoff
-upload-graph ../../knora-ontologies/salsah-gui.ttl http://www.knora.org/ontology/salsah-gui
+upload-graph ../../webapi/src/main/resources/knora-ontologies/knora-admin.ttl http://www.knora.org/ontology/knora-admin
+upload-graph ../../webapi/src/main/resources/knora-ontologies/knora-base.ttl http://www.knora.org/ontology/knora-base
+upload-graph ../../webapi/src/main/resources/knora-ontologies/standoff-onto.ttl http://www.knora.org/ontology/standoff
+upload-graph ../../webapi/src/main/resources/knora-ontologies/standoff-data.ttl http://www.knora.org/data/standoff
+upload-graph ../../webapi/src/main/resources/knora-ontologies/salsah-gui.ttl http://www.knora.org/ontology/salsah-gui
 upload-graph ../../test_data/project_data/admin-data-minimal.ttl http://www.knora.org/data/admin
 upload-graph ../../test_data/project_data/permissions-data-minimal.ttl http://www.knora.org/data/permissions

webapi/scripts/fuseki-init-knora-test.sh

@@ -8,11 +8,11 @@ REPOSITORY="knora-test"
 
 # delete-repository // delete dos not work correctly. need to delete database manually.
 create-repository
-upload-graph ../../knora-ontologies/knora-admin.ttl http://www.knora.org/ontology/knora-admin
-upload-graph ../../knora-ontologies/knora-base.ttl http://www.knora.org/ontology/knora-base
-upload-graph ../../knora-ontologies/standoff-onto.ttl http://www.knora.org/ontology/standoff
-upload-graph ../../knora-ontologies/standoff-data.ttl http://www.knora.org/data/standoff
-upload-graph ../../knora-ontologies/salsah-gui.ttl http://www.knora.org/ontology/salsah-gui
+upload-graph ../../webapi/src/main/resources/knora-ontologies/knora-admin.ttl http://www.knora.org/ontology/knora-admin
+upload-graph ../../webapi/src/main/resources/knora-ontologies/knora-base.ttl http://www.knora.org/ontology/knora-base
+upload-graph ../../webapi/src/main/resources/knora-ontologies/standoff-onto.ttl http://www.knora.org/ontology/standoff
+upload-graph ../../webapi/src/main/resources/knora-ontologies/standoff-data.ttl http://www.knora.org/data/standoff
+upload-graph ../../webapi/src/main/resources/knora-ontologies/salsah-gui.ttl http://www.knora.org/ontology/salsah-gui
 upload-graph ../../test_data/project_data/admin-data.ttl http://www.knora.org/data/admin
 upload-graph ../../test_data/project_data/permissions-data.ttl http://www.knora.org/data/permissions
 upload-graph ../../test_data/project_data/system-data.ttl http://www.knora.org/data/0000/SystemProject

webapi/src/main/scala/org/knora/webapi/store/triplestore/defaults/DefaultRdfData.scala

@@ -5,9 +5,11 @@
 
 package org.knora.webapi.store.triplestore.defaults
 
+import zio.Chunk
 import zio.NonEmptyChunk
 
 import org.knora.webapi.messages.store.triplestoremessages.RdfDataObject
+import org.knora.webapi.store.triplestore.upgrade.RepositoryUpdatePlan
 
 object DefaultRdfData {
 
@@ -18,27 +20,7 @@ object DefaultRdfData {
    * then a list of `RdfDataObject` instances containing the path and the name of the named graph
    * can be supplied to the `ResetTriplestoreContent` message.
    */
-  val data = NonEmptyChunk(
-    RdfDataObject(
-      path = "knora-ontologies/knora-admin.ttl",
-      name = "http://www.knora.org/ontology/knora-admin"
-    ),
-    RdfDataObject(
-      path = "knora-ontologies/knora-base.ttl",
-      name = "http://www.knora.org/ontology/knora-base"
-    ),
-    RdfDataObject(
-      path = "knora-ontologies/standoff-onto.ttl",
-      name = "http://www.knora.org/ontology/standoff"
-    ),
-    RdfDataObject(
-      path = "knora-ontologies/standoff-data.ttl",
-      name = "http://www.knora.org/data/standoff"
-    ),
-    RdfDataObject(
-      path = "knora-ontologies/salsah-gui.ttl",
-      name = "http://www.knora.org/ontology/salsah-gui"
-    ),
+  val data: NonEmptyChunk[RdfDataObject] = NonEmptyChunk(
     RdfDataObject(
       path = "test_data/project_data/admin-data.ttl",
       name = "http://www.knora.org/data/admin"
@@ -83,5 +65,5 @@ object DefaultRdfData {
       path = "test_data/project_ontologies/webern-onto.ttl",
       name = "http://www.knora.org/ontology/0806/webern"
     )
-  )
+  ) ++ Chunk(RepositoryUpdatePlan.builtInNamedGraphs.toSeq: _*)
 }

webapi/src/main/scala/org/knora/webapi/store/triplestore/impl/TriplestoreServiceLive.scala

@@ -42,6 +42,7 @@ import java.nio.file.Paths
 import java.nio.file.StandardCopyOption
 import java.time.temporal.ChronoUnit
 import java.util
+import scala.io.Source
 
 import dsp.errors.*
 import org.knora.webapi.*
@@ -224,21 +225,17 @@ case class TriplestoreServiceLive(
     rdfDataObjects: List[RdfDataObject],
     prependDefaults: Boolean
   ): Task[Unit] = {
-
     val calculateCompleteRdfDataObjectList: Task[NonEmptyChunk[RdfDataObject]] =
-      if (prependDefaults) { // prepend
-        if (rdfDataObjects.isEmpty) {
-          ZIO.succeed(DefaultRdfData.data)
-        } else {
-          // prepend default data objects like those of knora-base, knora-admin, etc.
-          ZIO.succeed(DefaultRdfData.data ++ NonEmptyChunk.fromIterable(rdfDataObjects.head, rdfDataObjects.tail))
-        }
-      } else { // don't prepend
-        if (rdfDataObjects.isEmpty) {
-          ZIO.fail(BadRequestException("Cannot insert list with empty data into triplestore."))
-        } else {
-          ZIO.succeed(NonEmptyChunk.fromIterable(rdfDataObjects.head, rdfDataObjects.tail))
-        }
+      if (prependDefaults) {
+        ZIO.succeed(DefaultRdfData.data.append(Chunk(rdfDataObjects: _*)))
+      } else {
+        NonEmptyChunk
+          .fromIterableOption(rdfDataObjects)
+          .fold[Task[NonEmptyChunk[RdfDataObject]]](
+            ZIO.fail(BadRequestException("Cannot insert list with empty data into triplestore."))
+          )(
+            ZIO.succeed(_)
+          )
       }
 
     for {
@@ -261,19 +258,13 @@ case class TriplestoreServiceLive(
                 uriBuilder
               }
 
+            rdfContents <- loadRdfObject(elem.path)
+
             httpPost <-
               ZIO.attemptBlocking {
-                val httpPost = new HttpPost(uriBuilder.build())
-                // Add the input file to the body of the request.
-                // here we need to tweak the base directory path from "webapi"
-                // to the parent folder where the files can be found
-                val inputFile = Paths.get("..", elem.path)
-                if (!Files.exists(inputFile)) {
-                  throw BadRequestException(s"File ${inputFile.toAbsolutePath} does not exist")
-                }
-                val fileEntity =
-                  new FileEntity(inputFile.toFile, ContentType.create(mimeTypeTextTurtle, "UTF-8"))
-                httpPost.setEntity(fileEntity)
+                val httpPost          = new HttpPost(uriBuilder.build())
+                val turtleContentType = ContentType.create(mimeTypeTextTurtle, "UTF-8")
+                httpPost.setEntity(new StringEntity(rdfContents, turtleContentType))
                 httpPost
               }
             responseHandler <- ZIO.attempt(returnInsertGraphDataResponse(graphName)(_))
@@ -284,6 +275,16 @@ case class TriplestoreServiceLive(
     } yield ()
   }
 
+  /**
+   * Load the RdfDataObject into some AbstractHttpEntity from either a relative ../$path or through a resource.
+   */
+  private def loadRdfObject(path: String): Task[String] = {
+    val relativeFileEntity   = ZIO.readFile(Paths.get("..", path))
+    val resourceStringEntity = ZIO.attemptBlocking(Source.fromResource(path).mkString)
+
+    relativeFileEntity.orElse(resourceStringEntity)
+  }
+
   /**
    * Checks the Fuseki triplestore if it is available and configured correctly. If it is not
    * configured, tries to automatically configure (initialize) the required dataset.

webapi/src/test/scala/org/knora/webapi/store/triplestore/api/TriplestoreServiceInMemory.scala

@@ -22,6 +22,7 @@ import zio.ZIO
 import zio.ZLayer
 import zio.macros.accessible
 
+import java.io.InputStream
 import java.nio.charset.StandardCharsets
 import java.nio.file.Path
 import java.nio.file.Paths
@@ -210,18 +211,23 @@ final case class TriplestoreServiceInMemory(datasetRef: Ref[Dataset], implicit v
     }
   }
 
-  private def insertRdfDataObject(elem: RdfDataObject): ZIO[Any, Throwable, Unit] = {
-    val inputFile = Paths.get("..", elem.path)
+  private def insertRdfDataObject(elem: RdfDataObject): ZIO[Any, Throwable, Unit] =
     ZIO.scoped {
       for {
         graphName <- checkGraphName(elem)
-        in        <- fileInputStream(inputFile)
+        in        <- loadRdfUrl(elem.path)
         ds        <- getDataSetWithTransaction(ReadWrite.WRITE)
         model      = ds.getNamedModel(graphName)
         _          = model.read(in, null, "TURTLE")
       } yield ()
     }
-  }
+
+  private def loadRdfUrl(path: String): ZIO[Any & Scope, Throwable, InputStream] =
+    ZIO
+      .attemptBlocking(
+        Option(getClass.getClassLoader.getResourceAsStream(path)).getOrElse(throw new Exception("can't find resource"))
+      )
+      .orElse(fileInputStream(Paths.get("..", path)))
 
   private def checkGraphName(elem: RdfDataObject): Task[String] =
     checkGraphName(elem.name)

webapi/src/test/scala/org/knora/webapi/store/triplestore/api/TriplestoreServiceInMemorySpec.scala

@@ -262,7 +262,7 @@ object TriplestoreServiceInMemorySpec extends ZIOSpecDefault {
             _ <- TriplestoreService.insertDataIntoTriplestore(
                    List(
                      RdfDataObject(
-                       path = "knora-ontologies/knora-base.ttl",
+                       path = "webapi/src/main/resources/knora-ontologies/knora-base.ttl",
                        name = "http://www.knora.org/ontology/knora-admin"
                      )
                    ),
@@ -283,7 +283,7 @@ object TriplestoreServiceInMemorySpec extends ZIOSpecDefault {
             _ <- TriplestoreService.insertDataIntoTriplestore(
                    List(
                      RdfDataObject(
-                       path = "knora-ontologies/knora-base.ttl",
+                       path = "webapi/src/main/resources/knora-ontologies/knora-base.ttl",
                        name = "http://www.knora.org/ontology/knora-base"
                      )
                    ),