Merge general Fixes

Fixed a Bug that no linked hdfs were created in the first folder, remove some hard coding

+PlotID/Publish.m

@@ -76,15 +76,20 @@ end
 %% Research data handeling
 switch options.Method
     case 'centralized' 
+        DataFolderName = 'data';
         % check if data folder exists
-        if ~isfolder(fullfile(storPath,'data'))
-            mkdir(fullfile(storPath,'data'));
+        if ~isfolder(fullfile(storPath,DataFolderName))
+            mkdir(fullfile(storPath,DataFolderName));
         end
+        % to get relative Paths
+        currentPath = fullfile(storPath);
+        
         %list all files
-        fList = dir(fullfile(storPath,'data', '**\*.*'));  %get list of files and folders in any subfolder
+        fList = dir(fullfile(storPath,DataFolderName, '**\*.*'));
+        %get list of files and folders in any subfolder
         fList = fList(~[fList.isdir]);  %remove folders from list
         fList = struct2table(fList);
-        
+                
         % Check if the new plot is based on the original data-set    
             % copy the data(once)
         for i=1:numel(DataPaths.rdata)            
@@ -92,20 +97,26 @@ switch options.Method
             [~, idx] = PlotID.fileCompare(DataPaths.rdata{i},fList);
             % create Linked HDF5 files for identical files
             if any(idx)
-                sourcePath = fList{idx,'name'}; % If there are multiple copies already, this only picks the last entry
+                fList.path = fullfile(fList.folder,fList.name);
+                sourcePath = fList{idx,'path'};
+                relativeSourcePath = strrep(sourcePath,currentPath,'');
+                
+                %WIP relative PATh!!
                 if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
-                    PlotID.createLinkedHDF5(sourcePath{1,1},storPath,ID);
+                    PlotID.createLinkedHDF5(relativeSourcePath{1,1},storPath,ID);
                 end
             else % no identical file exists
-                %Copy the file in data 
-                PlotID.createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
+                %Copy the file in data and create the links (if hdf5)
+                [dataPath] = PlotID.createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
+                relativeDataPath = strrep(dataPath,currentPath,'');
                 %WIP
-%                 if contains(DataPaths.rdata{i},{'.h5','.hdf5'}) % Linking only for HDF5
-%                    % and create linked files in the plot folder 
-%                    PlotID.createLinkedHDF5(DataPaths.rdata{i},storPath,ID);
-%                 end  %if
+                if contains(DataPaths.rdata{i},{'.h5','.hdf5'}) % Linking only for HDF5
+                   % and create also linked files in the plot folder 
+                   PlotID.createLinkedHDF5(relativeDataPath,storPath,ID);
+                end  %if
             end %if
         end %for
+        clear DataFolderName 
     case 'individual'
         % Create a copy of the research data    
         PlotID.createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');