Merge pull request #218 from srdc/prefix-management

Prefix management

tofhir-server/src/main/scala/io/tofhir/server/model/Project.scala

@@ -12,30 +12,23 @@ import io.tofhir.common.model.SchemaDefinition
  *
  * @param id                 Unique identifier for the project
  * @param name               Project name
- * @param url                Project url
  * @param description        Description of the project
+ * @param schemaUrlPrefix    Prefix (beginning) of the URLs to be used while creating schema definitions within this project.
+ * @param mappingUrlPrefix   Prefix (beginning) of the URLs to be used while creating mapping definitions within this project.
  * @param schemas            Schemas defined in this project
  * @param mappingContexts    Identifiers of the mapping contexts defined in this project
  * @param mappingJobs        Mapping jobs defined in this project
  */
 case class Project(id: String = UUID.randomUUID().toString,
                    name: String,
-                   url: String,
                    description: Option[String] = None,
+                   schemaUrlPrefix: Option[String] = None,
+                   mappingUrlPrefix: Option[String] = None,
                    schemas: Seq[SchemaDefinition] = Seq.empty,
                    mappings: Seq[FhirMapping] = Seq.empty,
                    mappingContexts: Seq[String] = Seq.empty,
                    mappingJobs: Seq[FhirMappingJob] = Seq.empty
                   ) {
-  /**
-   * Validates the fields of a project.
-   *
-   * @throws IllegalArgumentException when the project id is not a valid UUID
-   * */
-  def validate(): Unit = {
-    // throws IllegalArgumentException if the id is not a valid UUID
-    UUID.fromString(id)
-  }
 
   /**
    * Extracts the project metadata to be written to the metadata file.
@@ -47,8 +40,9 @@ case class Project(id: String = UUID.randomUUID().toString,
       List(
         "id" -> JString(this.id),
         "name" -> JString(this.name),
-        "url" -> JString(this.url),
         "description" -> JString(this.description.getOrElse("")),
+        "schemaUrlPrefix" -> JString(this.schemaUrlPrefix.getOrElse("")),
+        "mappingUrlPrefix" -> JString(this.mappingUrlPrefix.getOrElse("")),
         "schemas" -> JArray(
           List(
             this.schemas.map(_.getMetadata()): _*
@@ -79,4 +73,6 @@ case class Project(id: String = UUID.randomUUID().toString,
  * */
 object ProjectEditableFields {
   val DESCRIPTION = "description"
+  val SCHEMA_URL_PREFIX = "schemaUrlPrefix"
+  val MAPPING_URL_PREFIX = "mappingUrlPrefix"
 }

tofhir-server/src/main/scala/io/tofhir/server/repository/job/JobFolderRepository.scala

@@ -185,6 +185,7 @@ class JobFolderRepository(jobRepositoryFolderPath: String, projectFolderReposito
   private def initMap(jobRepositoryFolderPath: String): mutable.Map[String, mutable.Map[String, FhirMappingJob]] = {
     val map = mutable.Map.empty[String, mutable.Map[String, FhirMappingJob]]
     val jobRepositoryFolder = FileUtils.getPath(jobRepositoryFolderPath).toFile
+    logger.info(s"Initializing the Mapping Repository from path ${jobRepositoryFolder.getAbsolutePath}.")
     if (!jobRepositoryFolder.exists()) {
       jobRepositoryFolder.mkdirs()
     }

tofhir-server/src/main/scala/io/tofhir/server/repository/mapping/ProjectMappingFolderRepository.scala

@@ -228,7 +228,12 @@ class ProjectMappingFolderRepository(mappingRepositoryFolderPath: String, projec
             System.exit(1)
         }
       }
-      map.put(projectDirectory.getName, fhirMappingMap)
+      if(fhirMappingMap.isEmpty) {
+        // No processable schema files under projectDirectory
+        logger.warn(s"There are no processable mapping files under ${projectDirectory.getAbsolutePath}. Skipping ${projectDirectory.getName}.")
+      } else {
+        map.put(projectDirectory.getName, fhirMappingMap)
+      }
     }
     map
   }

tofhir-server/src/main/scala/io/tofhir/server/repository/project/IProjectRepository.scala

@@ -34,9 +34,9 @@ trait IProjectRepository {
   def getProject(id: String): Future[Option[Project]]
 
   /**
-   * Update the some fields of project in the repository.
+   * Update some fields of project in the repository.
    *
-   * @param id      id of the project
+   * @param id    id of the project
    * @param patch patch to be applied to the project
    * @return
    */

tofhir-server/src/main/scala/io/tofhir/server/repository/project/ProjectFolderRepository.scala

@@ -87,7 +87,7 @@ class ProjectFolderRepository(config: ToFhirEngineConfig) extends IProjectReposi
   }
 
   /**
-   * Update the some fields of project in the repository.
+   * Update some fields of the project in the repository.
    *
    * @param id    id of the project
    * @param patch patch to be applied to the project
@@ -100,8 +100,10 @@ class ProjectFolderRepository(config: ToFhirEngineConfig) extends IProjectReposi
         throw ResourceNotFound("Project does not exist.", s"Project $id not found")
 
       // update the editable fields of project with new values
-      val newDescription = (patch \ ProjectEditableFields.DESCRIPTION).extract[String]
-      val updatedProject = projects(id).copy(description = Some(newDescription))
+      val newDescription = (patch \ ProjectEditableFields.DESCRIPTION).extractOpt[String]
+      val newSchemaUrlPrefix = (patch \ ProjectEditableFields.SCHEMA_URL_PREFIX).extractOpt[String]
+      val newMappingUrlPrefix = (patch \ ProjectEditableFields.MAPPING_URL_PREFIX).extractOpt[String]
+      val updatedProject = projects(id).copy(description = newDescription, schemaUrlPrefix = newSchemaUrlPrefix, mappingUrlPrefix = newMappingUrlPrefix)
       projects.put(id, updatedProject)
 
       // update the projects metadata

tofhir-server/src/main/scala/io/tofhir/server/repository/schema/SchemaFolderRepository.scala

@@ -274,7 +274,12 @@ class SchemaFolderRepository(schemaRepositoryFolderPath: String, projectFolderRe
             System.exit(1)
         }
       }
-      schemaDefinitionMap.put(projectFolder.getName, projectSchemas)
+      if(projectSchemas.isEmpty) {
+        // No processable schema files under projectFolder
+        logger.warn(s"There are no processable schema files under ${projectFolder.getAbsolutePath}. Skipping ${projectFolder.getName}.")
+      } else {
+        schemaDefinitionMap.put(projectFolder.getName, projectSchemas)
+      }
     })
     schemaDefinitionMap
   }

tofhir-server/src/main/scala/io/tofhir/server/service/ProjectService.scala

@@ -33,15 +33,9 @@ class ProjectService(projectRepository: IProjectRepository,
    * Save project to the repository.
    *
    * @param project project to be saved
-   * @throws BadRequest when the given project is not valid
    * @return the created project
    */
   def createProject(project: Project): Future[Project] = {
-    try {
-      project.validate()
-    } catch {
-      case _: IllegalArgumentException => throw BadRequest("Invalid project content !", s"The given id ${project.id} is not a valid UUID.")
-    }
     projectRepository.createProject(project)
   }
 
@@ -56,7 +50,7 @@ class ProjectService(projectRepository: IProjectRepository,
   }
 
   /**
-   * Update the some fields of a project in the repository.
+   * Update some fields of a project in the repository.
    *
    * @param id      id of the project
    * @param project patch to be applied to the project
@@ -77,9 +71,9 @@ class ProjectService(projectRepository: IProjectRepository,
     // first delete the project from repository
     projectRepository.removeProject(id)
       // if project deletion is failed throw the error
-      .recover {case e: Throwable => throw e}
+      .recover { case e: Throwable => throw e }
       // else delete jobs, mappings, mapping contexts and schemas as well
-      .map(_=> {
+      .map(_ => {
         jobRepository.deleteProjectJobs(id)
         mappingRepository.deleteProjectMappings(id)
         mappingContextRepository.deleteProjectMappingContexts(id)
@@ -94,10 +88,20 @@ class ProjectService(projectRepository: IProjectRepository,
    * @throws BadRequest when the given patch is invalid
    */
   private def validateProjectPatch(patch: JObject): Unit = {
-    if (patch.obj.isEmpty || !patch.obj.forall {
-      case (ProjectEditableFields.DESCRIPTION, JString(_)) => true
-      case _ => false
-    })
+    // Define the allowed fields set from ProjectEditableFields
+    val allowedFields = Set(
+      ProjectEditableFields.DESCRIPTION,
+      ProjectEditableFields.SCHEMA_URL_PREFIX,
+      ProjectEditableFields.MAPPING_URL_PREFIX
+    )
+
+    // Extract the keys from the patch
+    val patchKeys = patch.obj.map(_._1).toSet
+
+    // Check for invalid fields
+    val invalidFields = patchKeys.diff(allowedFields)
+    if (invalidFields.nonEmpty) {
       throw BadRequest("Invalid Patch!", "Invalid project patch!")
+    }
   }
 }

tofhir-server/src/main/scala/io/tofhir/server/service/db/FolderDBInitializer.scala

@@ -41,9 +41,9 @@ class FolderDBInitializer(schemaFolderRepository: SchemaFolderRepository,
     val parsedProjects = if (file.exists()) {
       val projects: JArray = FileOperations.readFileIntoJson(file).asInstanceOf[JArray]
       val projectMap: Map[String, Project] = projects.arr.map(p => {
-        val project: Project = initProjectFromMetadata(p.asInstanceOf[JObject])
-        project.id -> project
-      })
+          val project: Project = initProjectFromMetadata(p.asInstanceOf[JObject])
+          project.id -> project
+        })
         .toMap
       collection.mutable.Map(projectMap.toSeq: _*)
     } else {
@@ -67,8 +67,9 @@ class FolderDBInitializer(schemaFolderRepository: SchemaFolderRepository,
   private def initProjectFromMetadata(projectMetadata: JObject): Project = {
     val id: String = (projectMetadata \ "id").extract[String]
     val name: String = (projectMetadata \ "name").extract[String]
-    val url: String = (projectMetadata \ "url").extract[String]
     val description: Option[String] = (projectMetadata \ "description").extractOpt[String]
+    val schemaUrlPrefix: Option[String] = (projectMetadata \ "schemaUrlPrefix").extractOpt[String]
+    val mappingUrlPrefix: Option[String] = (projectMetadata \ "mappingUrlPrefix").extractOpt[String]
     val mappingContexts: Seq[String] = (projectMetadata \ "mappingContexts").extract[Seq[String]]
     // resolve schemas via the schema repository
     val schemaFutures: Future[Seq[Option[SchemaDefinition]]] = Future.sequence(
@@ -109,7 +110,16 @@ class FolderDBInitializer(schemaFolderRepository: SchemaFolderRepository,
     )
     val jobs: Seq[FhirMappingJob] = Await.result[Seq[Option[FhirMappingJob]]](mappingJobFutures, 2 seconds).map(_.get)
 
-    Project(id, name, url, description, schemas, mappings, mappingContexts, jobs)
+    Project(id, name, description, schemaUrlPrefix, mappingUrlPrefix, schemas, mappings, mappingContexts, jobs)
+  }
+
+  private def dropLastPart(url: String): String = {
+    // Remove trailing slash if it exists, to handle cases where URL ends with "/"
+    val cleanedUrl = if (url.endsWith("/")) url.dropRight(1) else url
+    // Find the last slash and drop everything after it
+    val lastSlashIndex = cleanedUrl.lastIndexOf('/')
+    if (lastSlashIndex != -1) cleanedUrl.substring(0, lastSlashIndex + 1)
+    else url // Return original URL if no slashes found
   }
 
   /**
@@ -125,17 +135,19 @@ class FolderDBInitializer(schemaFolderRepository: SchemaFolderRepository,
     val schemas: mutable.Map[String, mutable.Map[String, SchemaDefinition]] = schemaFolderRepository.getCachedSchemas()
     schemas.foreach(projectIdAndSchemas => {
       val projectId: String = projectIdAndSchemas._1
+      val schemaUrl: String = projectIdAndSchemas._2.head._2.url
       // If there is no project create a new one. Use id as name as well
-      val project: Project = projects.getOrElse(projectId, Project(projectId, projectId, convertToUrl(projectId), None))
+      val project: Project = projects.getOrElse(projectId, Project(id = projectId, name = projectId, schemaUrlPrefix = Some(dropLastPart(schemaUrl))))
       projects.put(projectId, project.copy(schemas = projectIdAndSchemas._2.values.toSeq))
     })
 
     // Parse mappings
     val mappings: mutable.Map[String, mutable.Map[String, FhirMapping]] = mappingFolderRepository.getCachedMappings()
     mappings.foreach(projectIdAndMappings => {
       val projectId: String = projectIdAndMappings._1
+      val mappingUrl: String = projectIdAndMappings._2.head._2.url
       // If there is no project create a new one. Use id as name as well
-      val project: Project = projects.getOrElse(projectId, Project(projectId, projectId, convertToUrl(projectId), None))
+      val project: Project = projects.getOrElse(projectId, Project(id = projectId, name = projectId, mappingUrlPrefix = Some(dropLastPart(mappingUrl))))
       projects.put(projectId, project.copy(mappings = projectIdAndMappings._2.values.toSeq))
     })
 
@@ -144,7 +156,7 @@ class FolderDBInitializer(schemaFolderRepository: SchemaFolderRepository,
     jobs.foreach(projectIdAndMappingsJobs => {
       val projectId: String = projectIdAndMappingsJobs._1
       // If there is no project create a new one. Use id as name as well
-      val project: Project = projects.getOrElse(projectId, Project(projectId, projectId, convertToUrl(projectId), None))
+      val project: Project = projects.getOrElse(projectId, Project(id = projectId, name = projectId))
       projects.put(projectId, project.copy(mappingJobs = projectIdAndMappingsJobs._2.values.toSeq))
     })
 
@@ -153,21 +165,11 @@ class FolderDBInitializer(schemaFolderRepository: SchemaFolderRepository,
     mappingContexts.foreach(mappingContexts => {
       val projectId: String = mappingContexts._1
       // If there is no project create a new one. Use id as name as well
-      val project: Project = projects.getOrElse(projectId, Project(projectId, projectId, convertToUrl(projectId), None))
+      val project: Project = projects.getOrElse(projectId, Project(id = projectId, name = projectId))
       projects.put(projectId, project.copy(mappingContexts = mappingContexts._2))
     })
 
     projects
   }
 
-  /**
-   * Converts a project id to a url in a specific format.
-   * @param inputString
-   * @return
-   */
-  private def convertToUrl(inputString: String): String = {
-    val transformedString = inputString.replaceAll("\\s", "").toLowerCase
-    val url = s"https://www.$inputString.com"
-    url
-  }
 }

tofhir-server/src/test/scala/io/tofhir/server/BaseEndpointTest.scala

@@ -47,7 +47,7 @@ trait BaseEndpointTest extends AnyWordSpec with Matchers with ScalatestRouteTest
    * Creates a test project whose identifier is stored in [[projectId]].
    * */
   def createProject(id: Option[String] = None): Unit = {
-    val project1: Project = Project(id = id.getOrElse(UUID.randomUUID().toString), name = "example", url = "https://www.example.com", description = Some("example project"))
+    val project1: Project = Project(id = id.getOrElse(UUID.randomUUID().toString), name = "example", description = Some("example project"))
     // create a project
     Post(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}", HttpEntity(ContentTypes.`application/json`, writePretty(project1))) ~> route ~> check {
       status shouldEqual StatusCodes.Created

tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingExecutionEndpointTest.scala

@@ -370,8 +370,8 @@ class MappingExecutionEndpointTest extends BaseEndpointTest with OnFhirTestConta
       // run the job
       Post(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}/$projectId/${JobEndpoint.SEGMENT_JOB}/$jobId/${JobEndpoint.SEGMENT_RUN}", HttpEntity(ContentTypes.`application/json`, "")) ~> route ~> check {
         status shouldEqual StatusCodes.OK
-        // Mappings run asynchronously. Wait at most 30 seconds for mappings to complete.
-        val success = waitForCondition(30) {
+        // Mappings run asynchronously. Wait at most 45 seconds for mappings to complete.
+        val success = waitForCondition(45) {
           fsSinkFolder.listFiles.exists(_.getName.contains("results.csv")) && {
             // read the csv file created in the file system
             val csvFile: File = fsSinkFolder.listFiles.find(_.getName.contains("results.csv"))

tofhir-server/src/test/scala/io/tofhir/server/endpoint/ProjectEndpointTest.scala

@@ -5,7 +5,6 @@ import io.tofhir.common.model.Json4sSupport.formats
 import io.tofhir.common.model.SchemaDefinition
 import io.tofhir.engine.util.FileUtils
 import io.tofhir.server.BaseEndpointTest
-import io.tofhir.server.endpoint.{ProjectEndpoint, SchemaDefinitionEndpoint}
 import io.tofhir.server.model.{Project, ProjectEditableFields}
 import io.tofhir.server.util.TestUtil
 import org.json4s.JArray
@@ -14,9 +13,9 @@ import org.json4s.jackson.Serialization.writePretty
 
 class ProjectEndpointTest extends BaseEndpointTest {
   // first project to be created
-  val project1: Project = Project(name = "example", url = "https://www.example.com", description = Some("example project"))
+  val project1: Project = Project(name = "example", description = Some("example project"), schemaUrlPrefix = Some("https://example.com/StructureDefinition/"), mappingUrlPrefix = Some("https://example.com/mappings/"))
   // second project to be created
-  val project2: Project = Project(name = "second example", url = "https://www.secondexample.com", description = Some("second example project"))
+  val project2: Project = Project(name = "second example", description = Some("second example project"))
   // patch to be applied to the existing project
   val projectPatch: (String, String) = ProjectEditableFields.DESCRIPTION -> "updated description"
   // schema definition
@@ -66,7 +65,8 @@ class ProjectEndpointTest extends BaseEndpointTest {
         val project: Project = JsonMethods.parse(responseAs[String]).extract[Project]
         project.id shouldEqual project1.id
         project.name shouldEqual project1.name
-        project.url shouldEqual project1.url
+        project.schemaUrlPrefix shouldEqual project1.schemaUrlPrefix
+        project.mappingUrlPrefix shouldEqual project1.mappingUrlPrefix
       }
       // get a project with invalid id
       Get(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}/123123") ~> route ~> check {

tofhir-server/src/test/scala/io/tofhir/server/endpoint/ToFhirRejectionHandlerTest.scala

@@ -3,13 +3,12 @@ package io.tofhir.server.endpoint
 import akka.http.scaladsl.model.{ContentTypes, StatusCodes}
 import io.tofhir.engine.util.FhirMappingJobFormatter.formats
 import io.tofhir.server.BaseEndpointTest
-import io.tofhir.server.endpoint.ProjectEndpoint
 import io.tofhir.server.model.Project
 import org.json4s.jackson.Serialization.writePretty
 
 
 class ToFhirRejectionHandlerTest extends BaseEndpointTest {
-  val project1: Project = Project(name = "example", url = "https://www.example.com", description = Some("example project"))
+  val project1: Project = Project(name = "example", description = Some("example project"))
 
   "ToFhirRejectionHandler" should {
 
@@ -23,14 +22,14 @@ class ToFhirRejectionHandlerTest extends BaseEndpointTest {
     }
 
     "create an HTTP response with bad request status for content not complying with the data model" in {
-      // Send a POST request with a project without URL
-      val projectWithoutUrl = Map("name" -> "example3",
+      // Send a POST request with a project without name
+      val projectWithoutUrl = Map("url" -> "http://example3.com/example-project",
         "description" -> Some("example project"))
       Post(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}", akka.http.scaladsl.model.HttpEntity.apply(ContentTypes.`application/json`, writePretty(projectWithoutUrl))) ~> route ~> check {
         status shouldEqual StatusCodes.BadRequest
         val response = responseAs[String]
         response should include("Type: https://tofhir.io/errors/BadRequest")
-        response should include("Detail: No usable value for url")
+        response should include("Detail: No usable value for name")
       }
     }