✨ Add column renaming support for saved csv content

tofhir-server/src/main/scala/io/tofhir/server/endpoint/CodeSystemEndpoint.scala

@@ -12,6 +12,7 @@ import io.tofhir.server.endpoint.TerminologyServiceManagerEndpoint._
 import io.tofhir.common.model.Json4sSupport._
 import io.tofhir.server.service.terminology.CodeSystemService
 import io.tofhir.server.repository.terminology.codesystem.ICodeSystemRepository
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 class CodeSystemEndpoint(codeSystemRepository: ICodeSystemRepository) extends LazyLogging {
 
@@ -92,7 +93,7 @@ class CodeSystemEndpoint(codeSystemRepository: ICodeSystemRepository) extends La
    */
   private def updateCodeSystemHeaderRoute(terminologyId: String, codeSystemId: String): Route = {
     post {
-      entity(as[Seq[String]]) { headers =>
+      entity(as[Seq[CsvHeader]]) { headers =>
         complete {
           service.updateCodeSystemHeader(terminologyId, codeSystemId, headers) map { _ =>
             StatusCodes.OK

tofhir-server/src/main/scala/io/tofhir/server/endpoint/ConceptMapEndpoint.scala

@@ -12,6 +12,7 @@ import io.tofhir.server.endpoint.TerminologyServiceManagerEndpoint._
 import io.tofhir.common.model.Json4sSupport._
 import io.tofhir.server.service.terminology.ConceptMapService
 import io.tofhir.server.repository.terminology.conceptmap.IConceptMapRepository
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 class ConceptMapEndpoint(conceptMapRepository: IConceptMapRepository) extends LazyLogging {
 
@@ -92,7 +93,7 @@ class ConceptMapEndpoint(conceptMapRepository: IConceptMapRepository) extends La
    */
   private def updateConceptMapHeaderRoute(terminologyId: String, conceptMapId: String): Route = {
     post {
-      entity(as[Seq[String]]) { headers =>
+      entity(as[Seq[CsvHeader]]) { headers =>
         complete {
           service.updateConceptMapHeader(terminologyId, conceptMapId, headers) map { _ =>
             StatusCodes.OK

tofhir-server/src/main/scala/io/tofhir/server/endpoint/MappingContextEndpoint.scala

@@ -11,6 +11,7 @@ import io.tofhir.server.endpoint.MappingContextEndpoint.{ATTACHMENT, SEGMENT_CON
 import io.tofhir.common.model.Json4sSupport._
 import io.tofhir.server.repository.mappingContext.IMappingContextRepository
 import io.tofhir.server.service.MappingContextService
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 class MappingContextEndpoint(mappingContextRepository: IMappingContextRepository) extends LazyLogging {
 
@@ -108,7 +109,7 @@ class MappingContextEndpoint(mappingContextRepository: IMappingContextRepository
    */
   private def updateMappingContextHeaderRoute(projectId: String, id: String): Route = {
     post {
-      entity(as[Seq[String]]) { headers =>
+      entity(as[Seq[CsvHeader]]) { headers =>
         complete {
           service.updateMappingContextHeader(projectId, id, headers) map { _ =>
             StatusCodes.OK

tofhir-server/src/main/scala/io/tofhir/server/repository/mappingContext/IMappingContextRepository.scala

@@ -2,6 +2,7 @@ package io.tofhir.server.repository.mappingContext
 
 import akka.stream.scaladsl.Source
 import akka.util.ByteString
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 import scala.concurrent.Future
 
@@ -48,7 +49,7 @@ trait IMappingContextRepository {
    * @param headers mapping context headers
    * @return
    */
-  def updateMappingContextHeader(projectId: String, id: String, headers: Seq[String]): Future[Unit]
+  def updateMappingContextHeader(projectId: String, id: String, headers: Seq[CsvHeader]): Future[Unit]
 
   /**
    * Save the mapping context content to the repository

tofhir-server/src/main/scala/io/tofhir/server/repository/mappingContext/MappingContextFolderRepository.scala

@@ -9,7 +9,7 @@ import io.tofhir.server.common.model.{AlreadyExists, ResourceNotFound}
 import io.tofhir.server.model._
 import io.tofhir.server.repository.project.ProjectFolderRepository
 import io.tofhir.server.util.CsvUtil
-
+import io.tofhir.server.util.CsvUtil.CsvHeader
 import java.io.File
 import scala.collection.mutable
 import scala.concurrent.Future
@@ -114,7 +114,7 @@ class MappingContextFolderRepository(mappingContextRepositoryFolderPath: String,
    * @param headers mapping context headers
    * @return
    */
-  def updateMappingContextHeader(projectId: String, id: String, headers: Seq[String]): Future[Unit] = {
+  def updateMappingContextHeader(projectId: String, id: String, headers: Seq[CsvHeader]): Future[Unit] = {
     if (!mappingContextExists(projectId, id)) {
       throw ResourceNotFound("Mapping context does not exists.", s"A mapping context with id $id does not exists in the mapping context repository at ${FileUtils.getPath(mappingContextRepositoryFolderPath).toAbsolutePath.toString}")
     }

tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/codesystem/CodeSystemRepository.scala

@@ -9,6 +9,7 @@ import io.tofhir.server.common.model.{AlreadyExists, BadRequest, ResourceNotFoun
 import io.tofhir.server.model.TerminologySystem.TerminologyCodeSystem
 import io.tofhir.server.model._
 import io.tofhir.server.repository.terminology.TerminologySystemFolderRepository.getTerminologySystemsJsonPath
+import io.tofhir.server.util.CsvUtil.CsvHeader
 import io.tofhir.server.util.{CsvUtil, FileOperations}
 import org.json4s.jackson.Serialization.writePretty
 
@@ -166,7 +167,7 @@ class CodeSystemRepository(terminologySystemFolderPath: String) extends ICodeSys
    * @param headers new headers to update
    * @return
    */
-  def updateCodeSystemHeader(terminologyId: String, codeSystemId: String, headers: Seq[String]): Future[Unit] = {
+  def updateCodeSystemHeader(terminologyId: String, codeSystemId: String, headers: Seq[CsvHeader]): Future[Unit] = {
     val codeSystem = findCodeSystemById(terminologyId, codeSystemId)
     // get file and update headers
     val codeSystemFile = FileUtils.getPath(terminologySystemFolderPath, terminologyId, codeSystem.id).toFile

tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/codesystem/ICodeSystemRepository.scala

@@ -3,6 +3,7 @@ package io.tofhir.server.repository.terminology.codesystem
 import akka.stream.scaladsl.Source
 import akka.util.ByteString
 import io.tofhir.server.model.TerminologySystem.TerminologyCodeSystem
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 import scala.concurrent.Future
 
@@ -53,7 +54,7 @@ trait ICodeSystemRepository {
   * @param headers new headers to update
   * @return
   */
-  def updateCodeSystemHeader(terminologyId: String, codeSystemId: String, headers: Seq[String]): Future[Unit]
+  def updateCodeSystemHeader(terminologyId: String, codeSystemId: String, headers: Seq[CsvHeader]): Future[Unit]
 
   /**
    * Retrieve and save the content of a code system csv file within a terminology

tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/conceptmap/ConceptMapRepository.scala

@@ -10,6 +10,7 @@ import io.tofhir.server.common.model.{AlreadyExists, BadRequest, InternalError,
 import io.tofhir.server.model.TerminologySystem.TerminologyConceptMap
 import io.tofhir.server.model._
 import io.tofhir.server.repository.terminology.TerminologySystemFolderRepository.getTerminologySystemsJsonPath
+import io.tofhir.server.util.CsvUtil.CsvHeader
 import io.tofhir.server.util.{CsvUtil, FileOperations}
 import org.json4s.jackson.Serialization.writePretty
 
@@ -168,7 +169,7 @@ class ConceptMapRepository(terminologySystemFolderPath: String) extends IConcept
    * @param headers new headers to update
    * @return
    */
-  def updateConceptMapHeader(terminologyId: String, conceptMapId: String, headers: Seq[String]): Future[Unit] = {
+  def updateConceptMapHeader(terminologyId: String, conceptMapId: String, headers: Seq[CsvHeader]): Future[Unit] = {
     val conceptMap = findConceptMapById(terminologyId, conceptMapId)
     // get file and update headers
     val conceptMapFile = FileUtils.getPath(terminologySystemFolderPath, terminologyId, conceptMap.id).toFile

tofhir-server/src/main/scala/io/tofhir/server/repository/terminology/conceptmap/IConceptMapRepository.scala

@@ -3,6 +3,7 @@ package io.tofhir.server.repository.terminology.conceptmap
 import akka.stream.scaladsl.Source
 import akka.util.ByteString
 import io.tofhir.server.model.TerminologySystem.TerminologyConceptMap
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 import scala.concurrent.Future
 
@@ -53,7 +54,7 @@ trait IConceptMapRepository {
    * @param headers new headers to update
    * @return
    */
-  def updateConceptMapHeader(terminologyId: String, conceptMapId: String, headers: Seq[String]): Future[Unit]
+  def updateConceptMapHeader(terminologyId: String, conceptMapId: String, headers: Seq[CsvHeader]): Future[Unit]
 
   /**
    * Retrieve and save the content of a concept map csv file within a terminology

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

@@ -4,6 +4,7 @@ import akka.stream.scaladsl.Source
 import akka.util.ByteString
 import com.typesafe.scalalogging.LazyLogging
 import io.tofhir.server.repository.mappingContext.IMappingContextRepository
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 import scala.concurrent.Future
 
@@ -49,7 +50,7 @@ class MappingContextService(mappingContextRepository: IMappingContextRepository)
   * @param headers mapping context headers
   * @return
   */
-  def updateMappingContextHeader(projectId: String, id: String, headers: Seq[String]): Future[Unit] = {
+  def updateMappingContextHeader(projectId: String, id: String, headers: Seq[CsvHeader]): Future[Unit] = {
     mappingContextRepository.updateMappingContextHeader(projectId, id, headers)
   }
 

tofhir-server/src/main/scala/io/tofhir/server/service/terminology/CodeSystemService.scala

@@ -5,6 +5,7 @@ import akka.util.ByteString
 import com.typesafe.scalalogging.LazyLogging
 import io.tofhir.server.model.TerminologySystem.TerminologyCodeSystem
 import io.tofhir.server.repository.terminology.codesystem.ICodeSystemRepository
+import io.tofhir.server.util.CsvUtil.CsvHeader
 
 import scala.concurrent.Future
 
@@ -67,7 +68,7 @@ class CodeSystemService(codeSystemRepository: ICodeSystemRepository) extends Laz
    * @param headers new headers to update
    * @return
    */
-  def updateCodeSystemHeader(terminologyId: String, codeSystemId: String, headers: Seq[String]): Future[Unit] = {
+  def updateCodeSystemHeader(terminologyId: String, codeSystemId: String, headers: Seq[CsvHeader]): Future[Unit] = {
     codeSystemRepository.updateCodeSystemHeader(terminologyId, codeSystemId, headers)
   }
 

tofhir-server/src/main/scala/io/tofhir/server/service/terminology/ConceptMapService.scala

@@ -5,7 +5,7 @@ import akka.util.ByteString
 import com.typesafe.scalalogging.LazyLogging
 import io.tofhir.server.model.TerminologySystem.TerminologyConceptMap
 import io.tofhir.server.repository.terminology.conceptmap.IConceptMapRepository
-
+import io.tofhir.server.util.CsvUtil.CsvHeader
 import scala.concurrent.Future
 
 class ConceptMapService(conceptMapRepository: IConceptMapRepository) extends LazyLogging {
@@ -67,7 +67,7 @@ class ConceptMapService(conceptMapRepository: IConceptMapRepository) extends Laz
    * @param headers new headers to update
    * @return
    */
-  def updateConceptMapHeader(terminologyId: String, conceptMapId: String, headers: Seq[String]): Future[Unit] = {
+  def updateConceptMapHeader(terminologyId: String, conceptMapId: String, headers: Seq[CsvHeader]): Future[Unit] = {
     conceptMapRepository.updateConceptMapHeader(terminologyId, conceptMapId, headers)
   }
 

tofhir-server/src/main/scala/io/tofhir/server/util/CsvUtil.scala

@@ -50,14 +50,15 @@ object CsvUtil {
   /**
    * Overwrite headers string to the first line of the CSV file
    * Adjust the rows to match the new headers if necessary e.g.
+   * - if a column name is changed, change headers of the rows with new name
    * - if a column removed, remove the column from the rows
    * - if a new column name recognized, add the column to the rows with a default value (<column_name>)
    * - order of the columns are preserved according to the newHHeaders
    * @param file CSV file
    * @param newHeaders Headers to write to the file
    * @return
    */
-  def writeCsvHeaders(file: File, newHeaders: Seq[String]): Future[Unit] = {
+  def writeCsvHeaders(file: File, newHeaders: Seq[CsvHeader]): Future[Unit] = {
     // Used external CSV Parser library to handle double quotes in the CSV file
     val parser = new CSVParserBuilder().withSeparator(',').withQuoteChar('"').build()
 
@@ -79,34 +80,43 @@ object CsvUtil {
         }
       }
 
+
     // here an example existingContent looks like:
     // [
-    //   [ "header1" -> "value1", "header2" -> "value2" ],
-    //   [ "header1" -> "value3", "header2" -> "value4" ]
+    //   [ "header1" -> "value1", "header2" -> "value2", "header3" -> "value3" ],
+    //   [ "header1" -> "value4", "header2" -> "value5", "header3" -> "value6" ]
     // ]
     //
     // an example newHeaders looks like:
-    // [ "header2", "header3" ]
+    // [ "header2", "headerChanged", "header4" ]
+    // "header1" is deleted,
+    // "header3" changed to "headerChanged"
+    // "header4" is added
     existingContentFuture.map { existingContent =>
+
       // Create a new list of lists where each list is a row and the first element in the tuples is the header
-      val updatedContent = existingContent.map { row => // iterate each row
+      var updatedContent = existingContent.map { row => // iterate each row
         newHeaders.map { header => // iterate each new header
-          // if the header already exists, use its value (header2 -> value2)
-          // otherwise, use a default value (header3 -> <header3>)
-          header -> row.find(_._1 == header).map(_._2).getOrElse(s"<$header>")
+          // If name (field) is different than the previously saved name, update the header of tuples
+          val key = if (header.field != header.savedName) header.field else header.savedName
+          // if the header already exists or header name is changed, use its value (header2 -> value2, headerChanged -> value3)
+          // otherwise, use a default value (header4 -> <header4>)
+          key -> row.find(_._1 == header.savedName).map(_._2).getOrElse(s"<${header.field}>")
         }
       }
 
       // here an example updatedContent looks like:
       // [
-      //   [ "header2" -> "value2", "header3" -> "<header3>" ],
-      //   [ "header2" -> "value4", "header3" -> "<header3>" ]
+      //   [ "header2" -> "value2", "headerChanged" -> "value3" ,"header4" -> "<header4>" ],
+      //   [ "header2" -> "value5", "headerChanged" -> "value6" ,"header4" -> "<header4>" ]
       // ]
 
+      // Extract the new names from CsvHeader array
+      val newHeaderNames = newHeaders.map(_.field)
       // create a header line by joining the new headers with a comma
       // create row content by using the second element of the tuple and joining them with a comma
       // finally merge the header and row content with a comma
-      val csvContent = (newHeaders.mkString(",") +: updatedContent.map(_.map(x => s"\"${x._2}\"").mkString(","))).map(ByteString(_))
+      val csvContent = (newHeaderNames.mkString(",") +: updatedContent.map(_.map(x => s"\"${x._2}\"").mkString(","))).map(ByteString(_))
       // Write the updated CSV content back to the file
       Source(csvContent).intersperse(ByteString("\n"))
         .runWith(FileIO.toPath(file.toPath, Set(StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING)))
@@ -206,4 +216,11 @@ object CsvUtil {
 
   }
 
+  /**
+   * Represents a CSV header with a new name and a previously saved name.
+   * @param field The current name of the header.
+   * @param savedName The previously saved name of the header, used for column name change without data loss
+   * If a new header is desired to be created, saved name may be any placeholder
+   */
+  case class CsvHeader(field: String, savedName: String)
 }