Merge branch '838-deprecacy-information-for-data-overlay' into 'master'

Resolve "deprecacy information for data overlay"

Closes #838

See merge request !859

CHANGELOG

@@ -19,6 +19,9 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
     about type of database that identifies the target (#66)
   * Small improvement: redundant 'references' field in gene variants data 
     overlay is now deprecated (#850)
+  * Small improvement: information about deprecated columns in data overlay is 
+    visible in overlay list (#838)
+  * Small improvement: publication list is resizable (#740)
   * Bug fix: export to CellDesigner of reaction with two modifiers connected
     with boolean operator resulted was skipping some layout information
   * Bug fix: reaction in SBGNML file containing two products was improperly

commons/src/main/java/lcsb/mapviewer/common/UnitTestFailedWatcher.java

@@ -6,6 +6,8 @@ import org.junit.runner.Description;
 public class UnitTestFailedWatcher extends TestWatcher {
   @Override
   protected void failed(Throwable e, Description description) {
-    e.printStackTrace();
+    if (!(e instanceof AssertionError)) {
+      e.printStackTrace();
+    }
   }
 }

frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js

@@ -318,7 +318,17 @@ OverlayPanel.prototype.createOverlayRow = function (overlay, checked, disabled)
 OverlayPanel.prototype.overlayToDataRow = function (overlay, checked, disabled) {
   var result = [];
   result[0] = overlay.getOrder();
-  result[1] = overlay.getName();
+  if (overlay.getDeprecatedColumns() !== undefined && overlay.getDeprecatedColumns() !== null && overlay.getDeprecatedColumns().length > 0) {
+
+    result[1] = "<div title='This data overlay uses old deprecated column names: ";
+    for (var j = 0; j < overlay.getDeprecatedColumns().length; j++) {
+      result[1] += overlay.getDeprecatedColumns()[j] + ", ";
+    }
+    result[1] += " This format will be not supported in minerva 15 and higher. Please re-upload data set using new format.'>" +
+      "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:orange'></i>" + overlay.getName() + "</div>"
+  } else {
+    result[1] = overlay.getName();
+  }
 
   if (overlay.getInputDataAvailable()) {
     if (disabled) {
@@ -351,6 +361,7 @@ OverlayPanel.prototype.overlayToDataRow = function (overlay, checked, disabled)
         "</div>";
     }
   }
+  logger.debug(result);
   return result;
 };
 

frontend-js/src/main/js/map/data/DataOverlay.js

@@ -26,6 +26,7 @@ function DataOverlay(overlayId, name) {
     this.setImagesDirectory(object.images);
     this.setDescription(object.description);
     this.setCreator(object.creator);
+    this.setDeprecatedColumns(object.deprecatedColumns);
     this.setContent(object.content);
     this.setFilename(object.filename);
     this.setPublicOverlay(object.publicOverlay);
@@ -328,6 +329,22 @@ DataOverlay.prototype.setContent = function (content) {
   this._content = content;
 };
 
+/**
+ *
+ * @returns {string[]}
+ */
+DataOverlay.prototype.getDeprecatedColumns = function () {
+  return this._deprecatedColumns;
+};
+
+/**
+ *
+ * @param {string[]} deprecatedColumns
+ */
+DataOverlay.prototype.setDeprecatedColumns = function (deprecatedColumns) {
+  this._deprecatedColumns = deprecatedColumns;
+};
+
 /**
  *
  * @returns {number}
@@ -380,7 +397,7 @@ DataOverlay.prototype.setType = function (type) {
  *
  * @param {boolean} value
  */
-DataOverlay.prototype.setGoogleLicenseConsent = function(value) {
+DataOverlay.prototype.setGoogleLicenseConsent = function (value) {
   this._googleLicenseConsent = value;
 };
 
@@ -388,7 +405,7 @@ DataOverlay.prototype.setGoogleLicenseConsent = function(value) {
  *
  * @returns {boolean}
  */
-DataOverlay.prototype.isGoogleLicenseConsent = function() {
+DataOverlay.prototype.isGoogleLicenseConsent = function () {
   return this._googleLicenseConsent;
 };
 

persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java

@@ -254,7 +254,10 @@ public abstract class BaseDao<T> {
    * @return object width identifier given as parameter
    */
   @SuppressWarnings("unchecked")
-  public T getById(int id) {
+  public T getById(Integer id) {
+    if (id == null) {
+      return null;
+    }
     List<?> list = getSession()
         .createQuery(" from " + this.clazz.getSimpleName() + " where id=:id " + removableAndStatemant())
         .setParameter("id", id).list();

persist/src/main/java/lcsb/mapviewer/persist/dao/map/ModelDao.java

@@ -40,12 +40,6 @@ public class ModelDao extends BaseDao<ModelData> {
     super.delete(model);
   }
 
-  @Override
-  public ModelData getById(int id) {
-    ModelData result = super.getById(id);
-    return result;
-  }
-
   /**
    * Return the latest model for the project with a given project identifier.
    * 

rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java

@@ -14,6 +14,7 @@ import org.springframework.web.HttpMediaTypeNotSupportedException;
 import org.springframework.web.bind.MissingServletRequestParameterException;
 import org.springframework.web.bind.ServletRequestBindingException;
 import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.method.annotation.MethodArgumentTypeMismatchException;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.ObjectNode;
@@ -42,7 +43,7 @@ public abstract class BaseController {
         || e instanceof HttpMessageNotReadableException
         || e instanceof MissingServletRequestParameterException
         || e instanceof HttpMediaTypeNotSupportedException
-        || e instanceof IllegalArgumentException) {
+        || e instanceof MethodArgumentTypeMismatchException) {
       logger.error(e, e);
       return createErrorResponse("Query server error.", e.getMessage(), new HttpHeaders(), HttpStatus.BAD_REQUEST);
     } else if (e instanceof ServletRequestBindingException && e.getMessage().contains(Configuration.AUTH_TOKEN)) {

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -8,6 +8,7 @@ import javax.xml.transform.*;
 import javax.xml.transform.stream.StreamResult;
 import javax.xml.transform.stream.StreamSource;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -160,10 +161,9 @@ public abstract class BaseRestImpl {
    * @param modelId
    *          list of model identifiers separated by "," or '*' when all models
    *          should be returned
-   * @throws ObjectNotFoundException
-   *           thrown when data for given identifiers doesn't exist
+   * @throws QueryException 
    */
-  protected List<Model> getModels(String projectId, String modelId) throws ObjectNotFoundException {
+  protected List<Model> getModels(String projectId, String modelId) throws QueryException {
     Model model = modelService.getLastModelByProjectId(projectId);
     if (model == null) {
       throw new ObjectNotFoundException("Project with given id doesn't exist");
@@ -172,6 +172,10 @@ public abstract class BaseRestImpl {
 
     if (!modelId.equals("*")) {
       for (String str : modelId.split(",")) {
+        if (!StringUtils.isNumeric(str)) {
+          throw new QueryException("Invalid modelId: " + modelId);
+        }
+
         Model submodel = model.getSubmodelById(Integer.valueOf(str));
         if (submodel == null) {
           throw new ObjectNotFoundException("Model with given id doesn't exist");

rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java

@@ -36,13 +36,13 @@ public class FileController extends BaseController {
 
   @PostAuthorize("hasAuthority('IS_ADMIN') or returnObject['owner'] == authentication.name")
   @GetMapping(value = "/{id}")
-  public Map<String, Object> getFile(@PathVariable(value = "id") String id) throws ObjectNotFoundException {
+  public Map<String, Object> getFile(@PathVariable(value = "id") Integer id) throws ObjectNotFoundException {
     return fileRest.getFile(id);
   }
 
-  @PreAuthorize("@fileService.getById(#id)?.owner?.login == authentication.name")
+  @PreAuthorize("@fileService.getOwnerByFileId(#id)?.login == authentication.name")
   @PostMapping(value = "/{id}:uploadContent")
-  public Map<String, Object> uploadContent(@PathVariable(value = "id") String id, @RequestBody byte[] data)
+  public Map<String, Object> uploadContent(@PathVariable(value = "id") Integer id, @RequestBody byte[] data)
       throws ObjectNotFoundException {
     return fileRest.uploadContent(id, data);
   }

rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java

@@ -15,6 +15,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
+import lcsb.mapviewer.services.interfaces.IFileService;
 
 @Transactional
 @Service
@@ -22,9 +23,12 @@ public class FileRestImpl extends BaseRestImpl {
 
   private UploadedFileEntryDao uploadedFileEntryDao;
 
+  private IFileService fileService;
+
   @Autowired
-  public FileRestImpl(UploadedFileEntryDao uploadedFileEntryDao) {
+  public FileRestImpl(UploadedFileEntryDao uploadedFileEntryDao, IFileService fileService) {
     this.uploadedFileEntryDao = uploadedFileEntryDao;
+    this.fileService = fileService;
   }
 
   public Map<String, Object> createFile(String filename, String length, User user) {
@@ -35,15 +39,14 @@ public class FileRestImpl extends BaseRestImpl {
     entry.setOwner(user);
     uploadedFileEntryDao.add(entry);
     try {
-      return getFile(entry.getId() + "");
+      return getFile(entry.getId());
     } catch (ObjectNotFoundException e) {
       throw new InvalidStateException(e);
     }
   }
 
-  public Map<String, Object> getFile(String id) throws ObjectNotFoundException {
-    int fileId = Integer.valueOf(id);
-    UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
+  public Map<String, Object> getFile(Integer id) throws ObjectNotFoundException {
+    UploadedFileEntry fileEntry = fileService.getById(id);
     if (fileEntry == null) {
       throw new ObjectNotFoundException("Object not found");
     }
@@ -60,7 +63,7 @@ public class FileRestImpl extends BaseRestImpl {
     return result;
   }
 
-  public Map<String, Object> uploadContent(String id, byte[] data) throws ObjectNotFoundException {
+  public Map<String, Object> uploadContent(Integer id, byte[] data) throws ObjectNotFoundException {
     int fileId = Integer.valueOf(id);
     UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
     if (fileEntry == null) {

rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java

@@ -168,7 +168,12 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
 
   public List<Map<String, Object>> getReferenceGenomeVersions(String organismId, String type)
       throws QueryException {
-    ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+    ReferenceGenomeType genomeType = null;
+    try {
+      genomeType = ReferenceGenomeType.valueOf(type);
+    } catch (IllegalArgumentException e) {
+      throw new QueryException("Invalid type: " + type);
+    }
     MiriamData organism;
     if (organismId != null && !organismId.isEmpty()) {
       organism = new MiriamData(MiriamType.TAXONOMY, organismId);

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java

@@ -114,7 +114,7 @@ public class ProjectController extends BaseController {
 
   @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
   @GetMapping(value = "/{projectId}/statistics")
-  public Object getStatistics(@PathVariable(value = "projectId") String projectId) throws ObjectNotFoundException {
+  public Object getStatistics(@PathVariable(value = "projectId") String projectId) throws QueryException {
     return projectController.getStatistics(projectId);
   }
 

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java

@@ -195,7 +195,7 @@ public class ProjectRestImpl extends BaseRestImpl {
     return project.getInputData();
   }
 
-  public Map<String, Object> getStatistics(String projectId) throws ObjectNotFoundException {
+  public Map<String, Object> getStatistics(String projectId) throws QueryException {
     Map<String, Object> result = new TreeMap<>();
 
     Map<MiriamType, Integer> elementAnnotations = new TreeMap<>();
@@ -624,7 +624,7 @@ public class ProjectRestImpl extends BaseRestImpl {
     return null;
   }
 
-  public List<Map<String, Object>> getSubmapConnections(String projectId) throws ObjectNotFoundException {
+  public List<Map<String, Object>> getSubmapConnections(String projectId) throws QueryException {
     List<Map<String, Object>> result = new ArrayList<>();
     List<Model> models = getModels(projectId, "*");
     List<Element> elements = new ArrayList<>();

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java

@@ -4,6 +4,7 @@ import java.io.IOException;
 import java.util.List;
 import java.util.Map;
 
+import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -37,7 +38,7 @@ public class ModelController extends BaseController {
   @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
   @GetMapping(value = "/")
   public List<Map<String, Object>> getModels(@PathVariable(value = "projectId") String projectId)
-      throws ObjectNotFoundException {
+      throws QueryException {
     return modelController.getModels(projectId);
   }
 
@@ -45,7 +46,7 @@ public class ModelController extends BaseController {
   @GetMapping(value = "/{modelId:.+}")
   public Object getModel(
       @PathVariable(value = "modelId") String modelId,
-      @PathVariable(value = "projectId") String projectId) throws ObjectNotFoundException {
+      @PathVariable(value = "projectId") String projectId) throws QueryException {
     if (modelId.equals("*")) {
       return modelController.getModels(projectId);
     } else {

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java

 package lcsb.mapviewer.api.projects.models;
 
-import java.awt.*;
+import java.awt.Color;
 import java.awt.geom.*;
 import java.io.*;
 import java.util.*;
-import java.util.List;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -59,7 +59,7 @@ public class ModelRestImpl extends BaseRestImpl {
     this.layoutService = layoutService;
   }
 
-  public List<Map<String, Object>> getModels(String projectId) throws ObjectNotFoundException {
+  public List<Map<String, Object>> getModels(String projectId) throws QueryException {
     Project project = getProjectService().getProjectByProjectId(projectId);
     if (project == null) {
       throw new ObjectNotFoundException("Project with given id doesn't exist");
@@ -67,7 +67,10 @@ public class ModelRestImpl extends BaseRestImpl {
     return createData(project);
   }
 
-  public Map<String, Object> getModel(String projectId, String modelId) {
+  public Map<String, Object> getModel(String projectId, String modelId) throws QueryException {
+    if (!StringUtils.isNumeric(modelId)) {
+      throw new QueryException("Invalid modelId: " + modelId);
+    }
     Model model = getModelService().getLastModelByProjectId(projectId);
     Model submodel = model.getSubmodelById(modelId);
     if (submodel == null) {
@@ -95,7 +98,7 @@ public class ModelRestImpl extends BaseRestImpl {
     }
   }
 
-  private List<Map<String, Object>> createData(Project project) {
+  private List<Map<String, Object>> createData(Project project) throws QueryException {
     List<Map<String, Object>> result = new ArrayList<>();
     Model model = getModelService().getLastModelByProjectId(project.getProjectId());
     if (model != null) {

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java

@@ -36,7 +36,7 @@ public class ParametersRestImpl extends BaseRestImpl {
   }
 
   private Set<SbmlParameter> getParametersFromProject(String projectId, String modelId)
-      throws ObjectNotFoundException {
+      throws QueryException {
     List<Model> models = getModels(projectId, modelId);
     Set<SbmlParameter> parameters = new LinkedHashSet<>();
 
@@ -52,7 +52,7 @@ public class ParametersRestImpl extends BaseRestImpl {
   }
 
   private Set<SbmlParameter> getGlobalParametersFromProject(String projectId, String modelId)
-      throws ObjectNotFoundException {
+      throws QueryException {
     List<Model> models = getModels(projectId, modelId);
     Set<SbmlParameter> parameters = new LinkedHashSet<>();
 

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java

@@ -59,7 +59,7 @@ public class UnitsRestImpl extends BaseRestImpl {
     return result;
   }
 
-  public List<Map<String, Object>> getUnits(String projectId, String modelId) throws ObjectNotFoundException {
+  public List<Map<String, Object>> getUnits(String projectId, String modelId) throws QueryException {
     List<Map<String, Object>> result = new ArrayList<>();
     List<Model> models = getModels(projectId, modelId);
     for (Model model : models) {

rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java

@@ -53,18 +53,18 @@ public class OverlayController extends BaseController {
   @GetMapping(value = "/{overlayId}/")
   public Map<String, Object> getOverlayById(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId) throws QueryException {
+      @PathVariable(value = "overlayId") Integer overlayId) throws QueryException {
     return overlayRestImp.getOverlayById(projectId, overlayId);
   }
 
   @PreAuthorize("hasAuthority('IS_ADMIN')" +
       " or hasAuthority('IS_CURATOR') and hasAuthority('READ_PROJECT:' + #projectId)" +
       " or hasAuthority('READ_PROJECT:' + #projectId) and " +
-      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout)")
+      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout == true)")
   @GetMapping(value = "/{overlayId}/models/{modelId}/bioEntities/")
   public List<Map<String, Object>> getOverlayElements(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @RequestParam(value = "columns", defaultValue = "") String columns) throws QueryException {
     return overlayRestImp.getOverlayElements(projectId, Integer.valueOf(overlayId), columns);
   }
@@ -72,12 +72,12 @@ public class OverlayController extends BaseController {
   @PreAuthorize("hasAuthority('IS_ADMIN')" +
       " or hasAuthority('IS_CURATOR') and hasAuthority('READ_PROJECT:' + #projectId)" +
       " or hasAuthority('READ_PROJECT:' + #projectId) and " +
-      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout)")
+      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout == true)")
   @GetMapping(value = "/{overlayId}/models/{modelId}/bioEntities/reactions/{reactionId}/")
   public Map<String, Object> getFullReaction(
       @PathVariable(value = "projectId") String projectId,
       @PathVariable(value = "modelId") String modelId,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @PathVariable(value = "reactionId") String reactionId,
       @RequestParam(value = "columns", defaultValue = "") String columns)
       throws QueryException, NumberFormatException, ObjectNotFoundException {
@@ -88,12 +88,12 @@ public class OverlayController extends BaseController {
   @PreAuthorize("hasAuthority('IS_ADMIN')" +
       " or hasAuthority('IS_CURATOR') and hasAuthority('READ_PROJECT:' + #projectId)" +
       " or hasAuthority('READ_PROJECT:' + #projectId) and " +
-      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout)")
+      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout == true)")
   @GetMapping(value = "/{overlayId}/models/{modelId}/bioEntities/elements/{elementId}/")
   public Map<String, Object> getFullSpecies(
       @PathVariable(value = "projectId") String projectId,
       @PathVariable(value = "modelId") String modelId,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @PathVariable(value = "elementId") String reactionId,
       @RequestParam(value = "columns", defaultValue = "") String columns)
       throws QueryException, NumberFormatException, ObjectNotFoundException {
@@ -126,7 +126,7 @@ public class OverlayController extends BaseController {
   @DeleteMapping(value = "/{overlayId}")
   public Map<String, Object> removeOverlay(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId) throws QueryException, IOException {
+      @PathVariable(value = "overlayId") Integer overlayId) throws QueryException, IOException {
     return overlayRestImp.removeOverlay(projectId, overlayId);
   }
 
@@ -136,7 +136,7 @@ public class OverlayController extends BaseController {
   @PatchMapping(value = "/{overlayId}")
   public Map<String, Object> updateOverlay(
       @RequestBody String body,
-      @PathVariable(value = "overlayId") String overlayId,
+      @PathVariable(value = "overlayId") Integer overlayId,
       @PathVariable(value = "projectId") String projectId)
       throws QueryException, IOException {
     Map<String, Object> node = parseBody(body);
@@ -147,11 +147,11 @@ public class OverlayController extends BaseController {
   @PreAuthorize("hasAuthority('IS_ADMIN')" +
       " or hasAuthority('IS_CURATOR') and hasAuthority('READ_PROJECT:' + #projectId)" +
       " or hasAuthority('READ_PROJECT:' + #projectId) and " +
-      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout)")
+      "   (@layoutService.getLayoutById(#overlayId)?.creator?.login == authentication.name or @layoutService.getLayoutById(#overlayId)?.publicLayout == true)")
   @GetMapping(value = "/{overlayId}:downloadSource")
   public ResponseEntity<byte[]> getOverlaySource(
       @PathVariable(value = "projectId") String projectId,
-      @PathVariable(value = "overlayId") String overlayId)
+      @PathVariable(value = "overlayId") Integer overlayId)
       throws QueryException {
 
     FileEntry file = overlayRestImp.getOverlaySource(projectId, overlayId);

rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java

@@ -12,6 +12,7 @@ import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.*;
 import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.cache.FileEntry;
@@ -26,6 +27,8 @@ import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
 import lcsb.mapviewer.persist.dao.map.LayoutDao;
 import lcsb.mapviewer.services.interfaces.ILayoutService;
 import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
+import lcsb.mapviewer.services.utils.ColorSchemaReader;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
 
 @Transactional
 @Service
@@ -78,6 +81,8 @@ public class OverlayRestImpl extends BaseRestImpl {
     result.put("description", overlay.getDescription());
     result.put("publicOverlay", overlay.isPublicLayout());
     result.put("defaultOverlay", overlay.isDefaultOverlay());
+
+    result.put("deprecatedColumns", getDeprecatedColumns(overlay));
     result.put("googleLicenseConsent", overlay.isGoogleLicenseConsent());
     List<Map<String, Object>> images = new ArrayList<>();
     List<DataOverlayImageLayer> imageList = new ArrayList<>(overlay.getDataOverlayImageLayers());
@@ -97,6 +102,18 @@ public class OverlayRestImpl extends BaseRestImpl {
     return result;
   }
 
+  private List<String> getDeprecatedColumns(Layout overlay) {
+    try {
+      List<String> result = new ArrayList<>();
+      for (ColorSchemaColumn column : new ColorSchemaReader().getDeprecatedColumns(overlay)) {
+        result.add(column.name());
+      }
+      return result;
+    } catch (IOException | InvalidColorSchemaException e) {
+      throw new InvalidStateException(e);
+    }
+  }
+
   public List<Map<String, Object>> getOverlayElements(String projectId, int overlayId, String columns)
       throws QueryException {
 
@@ -130,28 +147,27 @@ public class OverlayRestImpl extends BaseRestImpl {
     return result;
   }
 
-  public Map<String, Object> getOverlayById(String projectId, String overlayId)
+  public Map<String, Object> getOverlayById(String projectId, Integer overlayId)
       throws QueryException {
     Model model = getModelService().getLastModelByProjectId(projectId);
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Layout overlay = layoutService.getLayoutById(Integer.valueOf(overlayId));
+    Layout overlay = layoutService.getLayoutById(overlayId);
     if (overlay == null) {
       throw new QueryException("Overlay with given id doesn't exist");
     }
     return overlayToMap(overlay);
   }
 
-  public FileEntry getOverlaySource(String projectId, String overlayId)
+  public FileEntry getOverlaySource(String projectId, Integer overlayId)
       throws QueryException {
     Model model = getModelService().getLastModelByProjectId(projectId);
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
     try {
-      int id = Integer.parseInt(overlayId);
-      Layout layout = layoutService.getLayoutById(id);
+      Layout layout = layoutService.getLayoutById(overlayId);
       if (layout == null) {
         throw new QueryException("Invalid overlay id");
       }
@@ -163,13 +179,12 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
   }
 
-  public Map<String, Object> updateOverlay(String overlayId, Map<String, Object> overlayData) throws QueryException {
+  public Map<String, Object> updateOverlay(Integer overlayId, Map<String, Object> overlayData) throws QueryException {
     if (overlayData == null) {
       throw new QueryException("overlay field cannot be undefined");
     }
     try {
-      int id = Integer.parseInt(overlayId);
-      Layout layout = layoutService.getLayoutById(id);
+      Layout layout = layoutService.getLayoutById(overlayId);
       if (layout == null) {
         throw new ObjectNotFoundException("overlay doesn't exist");
       }
@@ -215,15 +230,14 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
   }
 
-  public Map<String, Object> removeOverlay(String projectId, String overlayId)
+  public Map<String, Object> removeOverlay(String projectId, Integer overlayId)
       throws QueryException, IOException {
     Project project = getProjectService().getProjectByProjectId(projectId);
     if (project == null) {
       throw new ObjectNotFoundException("Project with given id doesn't exist");
     }