Add column renaming support for saved csv content

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

@@ -10,6 +10,7 @@ import io.tofhir.server.common.model.{ResourceNotFound, ToFhirRestCall}
 import io.tofhir.server.endpoint.CodeSystemEndpoint.SEGMENT_CODE_SYSTEMS
 import io.tofhir.server.endpoint.TerminologyServiceManagerEndpoint._
 import io.tofhir.common.model.Json4sSupport._
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.service.terminology.CodeSystemService
 import io.tofhir.server.repository.terminology.codesystem.ICodeSystemRepository
 
@@ -73,26 +74,37 @@ class CodeSystemEndpoint(codeSystemRepository: ICodeSystemRepository) extends La
   }
 
   /**
-   * Route to update code system csv headers
-   * Headers are passed as a list of strings and overwrite the existing headers in the first line of the CSV file
-   * Compare existing columns names are new names and adjust the rows to match the new headers if necessary
+   * Route to update code system CSV headers.
+   *
+   * Headers are passed as a list of `CsvHeader` objects, where each `CsvHeader` contains both the `currentName` (new header name) and `previousName` (the previously saved header name).
+   * The existing headers in the first line of the CSV file are overwritten with the new headers provided. The rows are adjusted to match the new headers if necessary.
    *
    * e.g. 1:
-   * Existing headers in a CSV: "header1", "header2" --> New headers: "header1", "header2", "header3"
-   * Rows belonging to the header1 and header2 are preserved and only header3 is added with a default value for each row (<header3>)
+   * Existing headers in a CSV:
+   *  - CsvHeader(currentName = "header1", previousName = "header1")
+   *  - CsvHeader(currentName = "header2", previousName = "header2")
+   * New headers:
+   * - CsvHeader(currentName = "header1", previousName = "header1")
+   * - CsvHeader(currentName = "headerChanged", previousName = "header2")
+   * - CsvHeader(currentName = "header3", previousName = "header3")
+   * Rows under "header1" are preserved, rows belonging to "header2" are moved to "headerChanged", and "header3" is added with a default value for each row (`<header3>`).
    *
    * e.g. 2:
-   * Existing headers in a CSV: "header1", "header2" --> New headers: "header2", "header3"
-   * Rows belonging to the header1 are removed, header2 is preserved and shifted to the first column with its values
-   * and header3 is added as second column with a default value for each row (<header3>)
+   * Existing headers in a CSV:
+   * - CsvHeader(currentName = "header1", previousName = "header1")
+   * - CsvHeader(currentName = "header2", previousName = "header2")
+   * New headers:
+   * - CsvHeader(currentName = "header2", previousName = "header2")
+   * - CsvHeader(currentName = "header3", previousName = "header3")
+   * Rows under "header1" are removed, rows under "header2" are preserved and shifted to the first column, and "header3" is added as the second column with a default value for each row (`<header3>`).
    *
    * @param terminologyId terminology id
    * @param codeSystemId code system id
    * @return
    */
   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

@@ -10,6 +10,7 @@ import io.tofhir.server.common.model.{ResourceNotFound, ToFhirRestCall}
 import io.tofhir.server.endpoint.ConceptMapEndpoint.SEGMENT_CONCEPT_MAPS
 import io.tofhir.server.endpoint.TerminologyServiceManagerEndpoint._
 import io.tofhir.common.model.Json4sSupport._
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.service.terminology.ConceptMapService
 import io.tofhir.server.repository.terminology.conceptmap.IConceptMapRepository
 
@@ -75,24 +76,36 @@ class ConceptMapEndpoint(conceptMapRepository: IConceptMapRepository) extends La
   /**
    * Route to update concept map csv header
    *
-   * Headers are passed as a list of strings and overwrite the existing headers in the first line of the CSV file
-   * Compare existing columns names are new names and adjust the rows to match the new headers if necessary
+   * Headers are passed as a list of `CsvHeader` objects and overwrite the existing headers in the first line of the CSV file.
+   * The `CsvHeader` class represents each header with both its current name and previously saved name.
+   * The rows are adjusted to match the new headers if necessary.
    *
    * e.g. 1:
-   * Existing headers in a CSV: "header1", "header2" --> New headers: "header1", "header2", "header3"
-   * Rows belonging to the header1 and header2 are preserved and only header3 is added with a default value for each row (<header3>)
+   * Existing headers in a CSV:
+   *  - CsvHeader(currentName = "header1", previousName = "header1")
+   *  - CsvHeader(currentName = "header2", previousName = "header2")
+   * New headers:
+   * - CsvHeader(currentName = "header1", previousName = "header1")
+   * - CsvHeader(currentName = "headerChanged", previousName = "header2")
+   * - CsvHeader(currentName = "header3", previousName = "header3")
+   * Rows under "header1" are preserved, rows belonging to "header2" are moved to "headerChanged", and "header3" is added with a default value for each row (`<header3>`).
    *
    * e.g. 2:
-   * Existing headers in a CSV: "header1", "header2" --> New headers: "header2", "header3"
-   * Rows belonging to the header1 are removed, header2 is preserved and shifted to the first column with its values
-   * and header3 is added as second column with a default value for each row (<header3>)
+   * Existing headers in a CSV:
+   * - CsvHeader(currentName = "header1", previousName = "header1")
+   * - CsvHeader(currentName = "header2", previousName = "header2")
+   * New headers:
+   * - CsvHeader(currentName = "header2", previousName = "header2")
+   * - CsvHeader(currentName = "header3", previousName = "header3")
+   * Rows under "header1" are removed, rows under "header2" are preserved and shifted to the first column, and "header3" is added as the second column with a default value for each row (`<header3>`).
+   *
    * @param terminologyId terminology id
    * @param conceptMapId concept map id
    * @return
    */
   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

@@ -9,6 +9,7 @@ import io.tofhir.engine.Execution.actorSystem.dispatcher
 import io.tofhir.server.common.model.ToFhirRestCall
 import io.tofhir.server.endpoint.MappingContextEndpoint.{ATTACHMENT, SEGMENT_CONTENT, SEGMENT_CONTEXTS, SEGMENT_FILE, SEGMENT_HEADER}
 import io.tofhir.common.model.Json4sSupport._
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.repository.mappingContext.IMappingContextRepository
 import io.tofhir.server.service.MappingContextService
 
@@ -91,24 +92,36 @@ class MappingContextEndpoint(mappingContextRepository: IMappingContextRepository
   /**
    * Route to update the mapping context CSV headers
    *
-   * Headers are passed as a list of strings and overwrite the existing headers in the first line of the CSV file
-   * Compare existing columns names are new names and adjust the rows to match the new headers if necessary
+   * Headers are passed as a list of `CsvHeader` objects and overwrite the existing headers in the first line of the CSV file.
+   * The `CsvHeader` class represents each header with both its current name and previously saved name.
+   * The rows are adjusted to match the new headers if necessary.
    *
    * e.g. 1:
-   * Existing headers in a CSV: "header1", "header2" --> New headers: "header1", "header2", "header3"
-   * Rows belonging to the header1 and header2 are preserved and only header3 is added with a default value for each row (<header3>)
+   * Existing headers in a CSV:
+   *  - CsvHeader(currentName = "header1", previousName = "header1")
+   *  - CsvHeader(currentName = "header2", previousName = "header2")
+   * New headers:
+   * - CsvHeader(currentName = "header1", previousName = "header1")
+   * - CsvHeader(currentName = "headerChanged", previousName = "header2")
+   * - CsvHeader(currentName = "header3", previousName = "header3")
+   * Rows under "header1" are preserved, rows belonging to "header2" are moved to "headerChanged", and "header3" is added with a default value for each row (`<header3>`).
    *
    * e.g. 2:
-   * Existing headers in a CSV: "header1", "header2" --> New headers: "header2", "header3"
-   * Rows belonging to the header1 are removed, header2 is preserved and shifted to the first column with its values
-   * and header3 is added as second column with a default value for each row (<header3>)
+   * Existing headers in a CSV:
+   * - CsvHeader(currentName = "header1", previousName = "header1")
+   * - CsvHeader(currentName = "header2", previousName = "header2")
+   * New headers:
+   * - CsvHeader(currentName = "header2", previousName = "header2")
+   * - CsvHeader(currentName = "header3", previousName = "header3")
+   * Rows under "header1" are removed, rows under "header2" are preserved and shifted to the first column, and "header3" is added as the second column with a default value for each row (`<header3>`).
+   *
    * @param projectId project id
    * @param id mapping context id
    * @return
    */
   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/model/csv/CsvHeader.scala

@@ -0,0 +1,9 @@
+package io.tofhir.server.model.csv
+
+/**
+ * Represents a CSV header with a new name and a previously saved name.
+ * @param currentName The current name of the header.
+ * @param previousName 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(currentName: String, previousName: String)

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.model.csv.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

@@ -7,6 +7,7 @@ import io.tofhir.engine.Execution.actorSystem.dispatcher
 import io.tofhir.engine.util.FileUtils
 import io.tofhir.server.common.model.{AlreadyExists, ResourceNotFound}
 import io.tofhir.server.model._
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.repository.project.ProjectFolderRepository
 import io.tofhir.server.util.CsvUtil
 
@@ -114,7 +115,7 @@ 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

@@ -8,6 +8,7 @@ import io.tofhir.engine.util.FileUtils
 import io.tofhir.server.common.model.{AlreadyExists, BadRequest, ResourceNotFound}
 import io.tofhir.server.model.TerminologySystem.TerminologyCodeSystem
 import io.tofhir.server.model._
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.repository.terminology.TerminologySystemFolderRepository.getTerminologySystemsJsonPath
 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.model.csv.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

@@ -9,6 +9,7 @@ import io.tofhir.engine.util.FileUtils
 import io.tofhir.server.common.model.{AlreadyExists, BadRequest, InternalError, ResourceNotFound}
 import io.tofhir.server.model.TerminologySystem.TerminologyConceptMap
 import io.tofhir.server.model._
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.repository.terminology.TerminologySystemFolderRepository.getTerminologySystemsJsonPath
 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.model.csv.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

@@ -3,6 +3,7 @@ package io.tofhir.server.service
 import akka.stream.scaladsl.Source
 import akka.util.ByteString
 import com.typesafe.scalalogging.LazyLogging
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.repository.mappingContext.IMappingContextRepository
 
 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

@@ -4,6 +4,7 @@ import akka.stream.scaladsl.Source
 import akka.util.ByteString
 import com.typesafe.scalalogging.LazyLogging
 import io.tofhir.server.model.TerminologySystem.TerminologyCodeSystem
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.repository.terminology.codesystem.ICodeSystemRepository
 
 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

@@ -4,6 +4,7 @@ import akka.stream.scaladsl.Source
 import akka.util.ByteString
 import com.typesafe.scalalogging.LazyLogging
 import io.tofhir.server.model.TerminologySystem.TerminologyConceptMap
+import io.tofhir.server.model.csv.CsvHeader
 import io.tofhir.server.repository.terminology.conceptmap.IConceptMapRepository
 
 import scala.concurrent.Future
@@ -67,7 +68,7 @@ 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)
   }