diff --git a/+PlotID/Publish.m b/+PlotID/Publish.m
index 4c7b154c5b3a5aa96a45e981c822f04a8185fa50..da8a62cdeb949cb1cdc40a3499f275da7e1a5e6d 100644
--- a/+PlotID/Publish.m
+++ b/+PlotID/Publish.m
@@ -1,128 +1,135 @@
-function Publish(DataPaths, ID, figure, options)
-%Publishes saves plot, data and measuring script
-% Location sets the storage location. 'local' sets the storage location
-% to the current folder (an export folder will be created), 'server' is a
-% remote path, that is defined in the config file.
-% Two Methods are implemented 'individual' stores the data for
-% each plot while 'centralized' uses a data folder and uses reference links
-% to the original data (hdf5 only).
-
-arguments
- DataPaths
- ID (1,:) {mustBeNonzeroLengthText} % ID must be provided
- figure (1,:) {mustBeFigure} % Checks if figure is a figure object
- options.Location {mustBeMember(options.Location ,['local','server','CI-Test'])} = 'local' % storage path
- options.Method {mustBeMember(options.Method ,['individual','centralized'])} = 'individual'
- options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true
- options.CSV (1,1) {mustBeNumericOrLogical} = false
-end
-
-%catch multiple figures in fig
-if numel(figure) > 1
- figure = figure(1);
- msg = ['Publish is designed for handeling one figure at once' newline,...
- '- publishes uses only the first figure.' newline , ...
- 'Consider an external for loop for multi figure export as provided in example.m'];
- warning(msg);
-end
-
-switch options.Location
- case 'local'
- % use the script path as export path
- scriptPath = fileparts(DataPaths.script);
- storPath = fullfile(scriptPath,'export');
- case 'server' %from config File
- txt = fileread('config.json');
- config = jsondecode(txt);
- storPath = config.ServerPath;
- case 'CI-Test'
- storPath = fullfile(pwd,'CI_files','export');
-end
-folderName = char(ID);
-
-%% Create Data-Directory
-addpath(storPath); % ToDo necessary? -
-if isfolder(fullfile(storPath,folderName))
- error(['Folder ',folderName, ' exists - Plot was already published ']);
-elseif mkdir(fullfile(storPath,folderName))
-else
- error('Directory could not be created - check remote path and permissions');
-end
-
-disp('Publishing started');
-
-%% Create a Copy of the script and User functions(optional)
-PlotID.createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
-
-if options.CopyUserFCN
- [fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
- % plist contains the required MATLAB Toolboxes, maybe usefull in future
- fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
- fList = PlotID.removePltIdFiles(fList); % Do not copy files that are part of plot ID
- if ~isempty(fList)
- PlotID.createFileCopy(fList,folderName,storPath,ID,'userFcn');
- end
-end
-
-%% Research data handeling
-switch options.Method
- case 'centralized'
- % check if data folder exists
- if ~isfolder(fullfile(storPath,'data'))
- mkdir(fullfile(storPath,'data'));
- end
- %list all files
- fList = dir(fullfile(storPath,'data', '**\*.*')); %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)
- % check if identical file exists (status = 1)
- [~, 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
- if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
- PlotID.createLinkedHDF5(sourcePath,storPath,ID);
- end
- else % no identical file exists
- PlotID.createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
- end
- end
- case 'individual'
- % Create a copy of the research data
- PlotID.createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
-end
-%% Export the Plot
-try
- PlotName = [ID,'_plot']; % plotname
- RemotePath = fullfile(storPath ,folderName, PlotName);
- % Matlab figure
- savefig(figure,RemotePath);
- % the png should only be a preview
- exportgraphics(figure,[RemotePath,'.png'],'Resolution',300);
-catch
- warning('Plot export was not successful')
-end
-
-disp(['publishing of ', ID , ' done']);
-
-% CSV EXport
-if options.CSV
- T = table();
- T.research_Data = DataPaths.rdata'; T.PlotID(:) = {ID};
- T.Script_Name(:) = {[DataPaths.script,'.m']};
- T.Storage_Location(:) = {storPath};
- T.Date(:) = {datestr(now)};
- T = movevars(T,'PlotID','before',1);
- writetable(T, fullfile(storPath, 'overview_table.csv'),'WriteMode','append');
-end
-
-end %function
-
-function tf = mustBeFigure(h)
-%checks if input is a figure object
- tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');
-end
+function Publish(DataPaths, ID, figure, options)
+%Publishes saves plot, data and measuring script
+% Location sets the storage location. 'local' sets the storage location
+% to the current folder (an export folder will be created), 'server' is a
+% remote path, that is defined in the config file.
+% Two Methods are implemented 'individual' stores the data for
+% each plot while 'centralized' uses a data folder and uses reference links
+% to the original data (hdf5 only).
+% ParentFolder is the folder Name where the exported data is stored if an
+% path is used, PlotId will use this path a storagePath
+
+arguments
+ DataPaths
+ ID (1,:) {mustBeNonzeroLengthText} % ID must be provided
+ figure (1,:) {mustBeFigure} % Checks if figure is a figure object
+ options.Location {mustBeMember(options.Location ,['local','server','CI-Test'])} = 'local' % storage path
+ options.Method {mustBeMember(options.Method ,['individual','centraliced'])} = 'individual'
+ options.ParentFolder (1,:) {mustBeText} = 'export'
+ options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true
+ options.CSV (1,1) {mustBeNumericOrLogical} = false
+end
+
+%catch multiple figures in fig
+if numel(figure) > 1
+ figure = figure(1);
+ msg = ['Publish is designed for handeling one figure at once' newline,...
+ '- publishes uses only the first figure.' newline , ...
+ 'Consider an external for loop for multi figure export as provided in example.m'];
+ warning(msg);
+end
+
+switch options.Location
+ case 'local'
+ if contains(options.ParentFolder, {'/','\'})
+ storPath = options.ParentFolder;
+ else
+ % use the script path as export path
+ scriptPath = fileparts(DataPaths.script);
+ storPath = fullfile(scriptPath,options.ParentFolder);
+ end
+ case 'server' %from config File
+ txt = fileread('config.json');
+ config = jsondecode(txt);
+ storPath = config.ServerPath;
+ case 'CI-Test'
+ storPath = fullfile(pwd,'CI_files',options.ParentFolder);
+end
+folderName = char(ID);
+
+%% Create Data-Directory
+addpath(storPath); % ToDo necessary? -
+if isfolder(fullfile(storPath,folderName))
+ error(['Folder ',folderName, ' exists - Plot was already published ']);
+elseif mkdir(fullfile(storPath,folderName))
+else
+ error('Directory could not be created - check remote path and permissions');
+end
+
+disp('Publishing started');
+
+%% Create a Copy of the script and User functions(optional)
+PlotID.createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
+
+if options.CopyUserFCN
+ [fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
+ % plist contains the required MATLAB Toolboxes, maybe usefull in future
+ fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
+ fList = PlotID.removePltIdFiles(fList); % Do not copy files that are part of plot ID
+ if ~isempty(fList)
+ PlotID.createFileCopy(fList,folderName,storPath,ID,'userFcn');
+ end
+end
+
+%% Research data handeling
+switch options.Method
+ case 'centraliced'
+ % check if data folder exists
+ if ~isfolder(fullfile(storPath,'data'))
+ mkdir(fullfile(storPath,'data'));
+ end
+ %list all files
+ fList = dir(fullfile(storPath,'data', '**\*.*')); %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)
+ % check if identical file exists (status = 1)
+ [~, 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
+ if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
+ PlotID.createLinkedHDF5(sourcePath,storPath,ID);
+ end
+ else % no identical file exists
+ PlotID.createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
+ end
+ end
+ case 'individual'
+ % Create a copy of the research data
+ PlotID.createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
+end
+%% Export the Plot
+try
+ PlotName = [ID,'_plot']; % plotname
+ RemotePath = fullfile(storPath ,folderName, PlotName);
+ % Matlab figure
+ savefig(figure,RemotePath);
+ % the png should only be a preview
+ exportgraphics(figure,[RemotePath,'.png'],'Resolution',300);
+catch
+ warning('Plot export was not successful')
+end
+
+disp(['publishing of ', ID , ' done']);
+
+% CSV EXport
+if options.CSV
+ T = table();
+ T.research_Data = DataPaths.rdata'; T.PlotID(:) = {ID};
+ T.Script_Name(:) = {[DataPaths.script,'.m']};
+ T.Storage_Location(:) = {storPath};
+ T.Date(:) = {datestr(now)};
+ T = movevars(T,'PlotID','before',1);
+ writetable(T, fullfile(storPath, 'overview_table.csv'),'WriteMode','append');
+end
+
+end %function
+
+function tf = mustBeFigure(h)
+%checks if input is a figure object
+ tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');
+end
diff --git a/+PlotID/createFileCopy.m b/+PlotID/createFileCopy.m
index f8fb6f87ccb78dfbed207ca21cef2a2779a770d6..e10a1d9d3f9f9823ce9f788b90bce25a54537653 100644
--- a/+PlotID/createFileCopy.m
+++ b/+PlotID/createFileCopy.m
@@ -1,52 +1,54 @@
-function [] = 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
- disp(['start to copy ', type]);
-
- if ~iscell(filePaths)
- %fixes Issue if Filepath is a char and not a cell array
- filePaths = {filePaths};
- end
-
- try
- for i = 1:numel(filePaths)
- FileNameAndLocation = filePaths{i};
- [~,name,ext] = fileparts(filePaths{i}); % get the extension
-
- switch type
- case 'data'
- sufix = '_data';
- newfile = sprintf([ID, sufix, '_' , num2str(i) ,ext]);
- case 'dataCentral'
- %keep original name
- newfile = sprintf([name,ext]);
- case 'script'
- sufix = '_script';
- newfile = sprintf([ID, sufix ,ext]);
- case 'userFcn'
- %keep original name
- newfile = sprintf([name,ext]);
- otherwise
- error([type,' is not a valid type for createFileCopy'])
- end %switch
-
- % Write the file
- RemotePath = fullfile(storPath,folderName, newfile);
-
-% Check if remote file already exists
- count = 0;
- while isfile(RemotePath) && ismember(type,{'data','dataCentral'})
- % Add a Sufix number to new file name
- count = count + 1;
- [~,name,ext] = fileparts(RemotePath);
- RemotePath = fullfile(storPath,folderName,...
- [name,'_',num2str(count),ext]);
- end
- copyfile(FileNameAndLocation,RemotePath);
- end
- disp([type, ' sucessfully published']);
- catch
- warning([type,' export was not sucessful'])
- end %try
-end
-
+function [] = 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
+ disp(['start to copy ', type]);
+
+ if ~iscell(filePaths)
+ %fixes Issue if Filepath is a char and not a cell array
+ filePaths = {filePaths};
+ end
+
+ try
+ for i = 1:numel(filePaths)
+ FileNameAndLocation = filePaths{i};
+ [~,name,ext] = fileparts(filePaths{i}); % get the extension
+
+ switch type
+ case 'data'
+ sufix = '_data';
+ newfile = sprintf([ID, sufix, '_' , num2str(i) ,ext]);
+ case 'dataCentral'
+ %keep original name
+ newfile = sprintf([name,ext]);
+ case 'script'
+ sufix = '_script';
+ newfile = sprintf([ID, sufix ,ext]);
+ case 'userFcn'
+ %keep original name
+ newfile = sprintf([name,ext]);
+ otherwise
+ error([type,' is not a valid type for createFileCopy'])
+ end %switch
+
+ % Write the file
+ RemotePath = fullfile(storPath,folderName, newfile);
+
+% Check if remote file already exists
+ count = 0;
+ while isfile(RemotePath) && ismember(type,{'data','dataCentral'})
+ % Add a Sufix number to new file name
+ % TODO add more inteligent way then a simple sufix
+ count = count + 1;
+ [~,name,ext] = fileparts(RemotePath);
+ RemotePath = fullfile(storPath,folderName,...
+ [name,'_',num2str(count),ext]);
+ warning('Filename already exists in data folder');
+ end
+ copyfile(FileNameAndLocation,RemotePath);
+ end
+ disp([type, ' sucessfully published']);
+ catch
+ warning([type,' export was not sucessful'])
+ end %try
+end
+
diff --git a/+PlotID/createLinkedHDF5.m b/+PlotID/createLinkedHDF5.m
index ea59760ecec0219ac4a2ac07476f7c913ccc7c51..17ad29de36e5613975a17afaf4a0d3f9afadf731 100644
--- a/+PlotID/createLinkedHDF5.m
+++ b/+PlotID/createLinkedHDF5.m
@@ -5,6 +5,11 @@ function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
plist_id = 'H5P_DEFAULT';
+%catches error of wrong file type
+if iscell(SourceFile)
+ SourceFile = SourceFile{1};
+end
+
% try
fid = H5F.create(fullfile(TargetPath,ID,[ID,'_data.h5']));
%create External Link to Sourcefile in the Group linkToExternal
diff --git a/CI_files/default_test.m b/CI_files/default_test.m
index 3d1f20cf2420bac03b5f90a4ec7d1da38b21c49a..9f275accc9d660806a6208fa1c9bd4767d3ff090 100644
--- a/CI_files/default_test.m
+++ b/CI_files/default_test.m
@@ -61,7 +61,7 @@ try
delete CI_files/export/* CI_files/*.mat CI_files/*.h5
rmdir('CI_files/export','s');
result = true;
- clc;
+ clc; clear;
catch
result = false;
warning('simple_test failed');
diff --git a/example.m b/example.m
index 25707e6913a71fe0103cd78dc697cb1c01df19ab..86648e098ba9e3735bca16d0afe6768678fa0bfa 100644
--- a/example.m
+++ b/example.m
@@ -111,4 +111,4 @@ plot(x1,y1,'-r');
[fig2, ID] = PlotID.TagPlot(fig2,'ProjectID', ProjectID);
-PlotID.Publish(path, ID, fig2, 'Location', 'local','Method','centralized')
\ No newline at end of file
+PlotID.Publish(path, ID, fig2, 'Location', 'local','Method','centraliced')