From 78e2b5cc7793390fd9bbe06bc0f7cfed2919dd48 Mon Sep 17 00:00:00 2001
From: Jan Lemmer <jan.lemmer@fst.tu-darmstadt.de>
Date: Thu, 24 Feb 2022 10:00:56 +0100
Subject: [PATCH] Move code of the centralized method into an function Reasons:
Clearness, eliminate unwanted dependencies, improve readability
ID is also stored in dataObj so no need to pass it individually
---
+PlotID/@dataPath/dataPath.m | 3 +-
+PlotID/Publish.m | 52 +--------------------------
+PlotID/centralized.m | 68 +++++++++++++++++++++++++++++++++++
CHANGELOG.md | 5 ++-
Examples/PlotID_centralized.m | 10 +++++-
5 files changed, 84 insertions(+), 54 deletions(-)
create mode 100644 +PlotID/centralized.m
diff --git a/+PlotID/@dataPath/dataPath.m b/+PlotID/@dataPath/dataPath.m
index 67c3ede..bc4f395 100644
--- a/+PlotID/@dataPath/dataPath.m
+++ b/+PlotID/@dataPath/dataPath.m
@@ -6,7 +6,8 @@ classdef dataPath < handle
properties (SetAccess = protected)
DataPaths (1,:) cell % dataPaths
tmpPath % path to TMP files
- ID %ID
+ ID %PlotID
+ dataFolderName = 'data' %name for the data folder when using centralized
end
methods
diff --git a/+PlotID/Publish.m b/+PlotID/Publish.m
index 45e8a31..ddb9017 100644
--- a/+PlotID/Publish.m
+++ b/+PlotID/Publish.m
@@ -167,58 +167,8 @@ end
%% Research data handling
switch options.Method
case 'centralized'
- DataFolderName = 'data';
- warning(['Linked HDF5 can only be moved with their ',...
- 'respective master files in the ', DataFolderName, ' folder.']);
- % check if data folder exists
- if ~isfolder(fullfile(storPath,DataFolderName))
- mkdir(fullfile(storPath,DataFolderName));
- end
- % to get relative Paths
- currentPath = fullfile(storPath);
+ [status, msg] = PlotID.centralized(storPath, dataObj, folderName);
- %list all files
- fList = dir(fullfile(storPath,DataFolderName, ['**',filesep,'*.*']));
- %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(dataObj.DataPaths)
- % check if identical file exists (status = 1)
- [~, idx] = PlotID.fileCompare(dataObj.DataPaths{i},fList);
- % create Linked HDF5 files for identical files
- if any(idx)
- fList.path = fullfile(fList.folder,fList.name);
- sourcePath = fList{idx,'path'};
- if ~iscell(sourcePath)
- sourcePath = {sourcePath};
- end
- relativeSourcePath = strrep(sourcePath,currentPath,'');
-
- if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
- linkedHDFPath = fullfile(storPath,folderName);
- PlotID.createLinkedHDF5(relativeSourcePath{1,1},linkedHDFPath);
- end
- else % no identical file exists
- %Copy the file in data and create the links (if hdf5)
- [dataPath, status, msg] = PlotID.createFileCopy(dataObj.DataPaths{i},'data',storPath,ID,'dataCentral');
- pathToData = strrep(dataPath,currentPath,'');
- %WIP
- if contains(dataObj.DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
- % and create also linked files in the plot folder
- linkedHDFPath = fullfile(storPath,folderName);
- [status] = PlotID.createLinkedHDF5(pathToData,linkedHDFPath);
- end %if
- end %if
- % add do not move message
- doNotMove = ['do not move this folder without the ',...
- DataFolderName, ' folder'];
- fid = fopen(fullfile(storPath,folderName,[doNotMove,'.txt']),'w');
- fprintf(fid,doNotMove); fclose(fid);
- end %for
- clear DataFolderName doNotmove
case 'individual'
% Create a copy of the research data
[~, status, msg] = PlotID.createFileCopy(dataObj.DataPaths,folderName,storPath,ID, 'data');
diff --git a/+PlotID/centralized.m b/+PlotID/centralized.m
new file mode 100644
index 0000000..f5c92e7
--- /dev/null
+++ b/+PlotID/centralized.m
@@ -0,0 +1,68 @@
+function [status, msg] = centralized(storPath, dataObj, folderName)
+%centralized stores the research files in a centrelized folder. Linked
+%files are created for subsequent folders (HDF5 only).
+msg = '';
+warning(['Linked HDF5 can only be moved with their ',...
+ 'respective master files in the ', dataObj.dataFolderName, ' folder.']);
+
+% check if data folder exists
+if ~isfolder(fullfile(storPath,dataObj.dataFolderName))
+ mkdir(fullfile(storPath,dataObj.dataFolderName));
+end
+% to get relative Paths
+currentPath = fullfile(storPath);
+
+%list all files
+fList = dir(fullfile(storPath,dataObj.dataFolderName, ['**',filesep,'*.*']));
+%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(dataObj.DataPaths)
+ % check if identical file exists (status = 1)
+ [~, idx] = PlotID.fileCompare(dataObj.DataPaths{i},fList);
+ % create l inked HDF5 files for identical files
+ if any(idx)
+ fList.path = fullfile(fList.folder,fList.name);
+ sourcePath = fList{idx,'path'};
+ if ~iscell(sourcePath)
+ sourcePath = {sourcePath};
+ end
+ relativeSourcePath = strrep(sourcePath,currentPath,'');
+
+ if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
+ linkedHDFPath = fullfile(storPath,folderName);
+ [status] = PlotID.createLinkedHDF5(relativeSourcePath{1,1},linkedHDFPath);
+ end
+ else % no identical file exists
+ %Copy the file in data and create the links (if hdf5)
+ [dataPath, status, msg] = PlotID.createFileCopy(dataObj.DataPaths{i},...
+ 'data',storPath,dataObj.ID,'dataCentral');
+ pathToData = strrep(dataPath,currentPath,'');
+
+ if ~status
+ return; % an error orccured
+ end
+
+ %WIP
+ if contains(dataObj.DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
+ % and create also linked files in the plot folder
+ linkedHDFPath = fullfile(storPath,folderName);
+ [status] = PlotID.createLinkedHDF5(pathToData,linkedHDFPath);
+ else
+ warning(['You use the centralized method for non hdf files,',...
+ newline, 'Your research files are located in the ',...
+ DataFolederName , 'folder.']);
+ status = true;
+ end %if
+ end %if
+ % add do not move message
+ doNotMove = ['do not move this folder without the ',...
+ dataObj.dataFolderName, ' folder'];
+ fid = fopen(fullfile(storPath,folderName,[doNotMove,'.txt']),'w');
+ fprintf(fid,doNotMove); fclose(fid);
+end %for
+
+end
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b7deebb..4dab225 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,7 @@
-# V0.3
+# V1.0 RC1
- Add changelog
- Add support for file or function name as scriptPath
- Add support for passing Variables in publish
+- Move centralized method in fuction
+- Improve usability
+- Improve documentation
diff --git a/Examples/PlotID_centralized.m b/Examples/PlotID_centralized.m
index 33209f2..921917e 100644
--- a/Examples/PlotID_centralized.m
+++ b/Examples/PlotID_centralized.m
@@ -22,4 +22,12 @@ fig2 = figure;
plot(x.^2,y,'-r');
[fig2, ID] = PlotID.TagPlot(fig2);
-PlotID.Publish(datapath,scriptPath, fig2, 'Method','centralized')
\ No newline at end of file
+PlotID.Publish(datapath,scriptPath, fig2, 'Method','centralized')
+
+%% Note:
+% If you rerun this script PlotId will tell you that a identical named (but
+% not binary idetical) file exists in the data folder. This is intended,
+% due protect the user from overwritting non (binary) identical files. The
+% reason for this is that two hdf files with the same data are not idetical
+% when recreated (see line 11). Usually you would use an existing file
+% without changing it.
\ No newline at end of file
--
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