Merge branch 'dev/generalFixes' into 'development'

Merge general Fixes

See merge request fst-tuda/projects/nfdi4ing/projects/plot_identifier!7

+PlotID/Publish.m

@@ -76,12 +76,17 @@ 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);
                 
@@ -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');

+PlotID/createFileCopy.m

-function [] = createFileCopy(filePaths,folderName,storPath,ID,type)
+function [storagePaths] = createFileCopy(filePaths,folderName,storPath,ID,type)
 % Creates a copy of the files (can be used for multiple paths in a cell array)
 % folderName is the name of the exporting folder
+% returns the storage paths were files were stored
     disp(['start to copy ', type]);  
     
     if ~iscell(filePaths)
@@ -9,6 +10,7 @@ function [] = createFileCopy(filePaths,folderName,storPath,ID,type)
     end
         
     try 
+        storagePaths = cell(numel(filePaths,1));
         for i = 1:numel(filePaths)
             FileNameAndLocation = filePaths{i};
             [~,name,ext] = fileparts(filePaths{i}); % get the extension
@@ -52,6 +54,7 @@ function [] = createFileCopy(filePaths,folderName,storPath,ID,type)
                 warning('Filename already exists in data folder');
             end
             copyfile(FileNameAndLocation,RemotePath);
+            storagePaths{i} = RemotePath; 
         end
         disp([type, ' sucessfully published']);
     catch

+PlotID/createLinkedHDF5.m

@@ -18,7 +18,8 @@ end
     
     fid = H5F.create(fullfile(TargetPath,ID,[filename,ext]));
     %create External Link to Sourcefile in the Group linkToExternal
-    H5L.create_external(['..\data\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
+    H5L.create_external(['..\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
+    %H5L.create_external(['..\data\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id); %original
     H5F.close(fid);
     disp([fullfile(TargetPath,ID,[filename,ext]),' created']);
     status = 1;

CI_files/default_test.m

@@ -56,12 +56,14 @@ try
     path.rdata =  {dataset1,dataset2} ; % don't forget the extension
 
     PlotID.Publish(path, ID, figs, 'Location', 'CI-Test')
+    result = true;
     
     % clean up 
     delete CI_files/export/* CI_files/*.mat CI_files/*.h5 
     rmdir('CI_files/export','s'); 
-    result = true;
-    clc; clear;
+    
+    clear; clc;
+     
 catch
     result = false;
     warning('simple_test failed');