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Commit 52518cdf authored by Lemmer, Jan's avatar Lemmer, Jan
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Revert "Merge branch 'dev/config' into 'master'" 

This reverts merge request !30
parent 804a1abc
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1 merge request!31Revert "Merge branch 'dev/config' into 'master'"
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+PlotID/@config/config.m deleted 100644 → 0
+ 0
− 78
View file @ 804a1abc
classdef config < handle
%CONFIG class handles methoths and attributes related to the config
%file
% Detailed explanation goes here
% handle class used for dynamicy property updates
properties (SetAccess = private)
mandatoryFields = {'Author', 'ProjectID'}
optionFields
end
properties (SetAccess = protected)
configData
configFileName
end
methods
function obj = config(configFileName)
%CONFIG Construct an instance of this class
% Detailed explanation goes here
obj.configFileName = configFileName;
try
txt = fileread(obj.configFileName);
obj.configData = jsondecode(txt);
assert(checkConfig(obj));
catch
msg = ['no valid config File with the filename ',...
obj.configFileName, ' found.' newline,...
'Please enter the required information manually'];
disp(msg);
obj.configData = obj.wizard('initilise');
m = input('Do you want to save the config, Y/N [Y]:','s');
if ismember(m,{'Y','y'})
obj.writeConfig(fullfile(pwd));
end
end%try
end
function outputArg = checkConfig(obj)
%checkConfig validates the config file
% 1. Check if mandatory Fields are set
check = isfield(obj.configData,obj.mandatoryFields);
outputArg = all(check);
end
function writeConfig(obj,path)
%writeConfig writes the config file to path
% TODo;
fid = fopen(fullfile(path,obj.configFileName),'w');
txt = jsonencode(obj.configData,'PrettyPrint',true);
%fprintf does not write paths correctly !!!
fwrite(fid,txt);
fclose(fid);
end
function configData = addPublishOptions(obj,mode)
%writeConfig writes the config file to path
% TODo;
obj.configData.options = obj.plotID_options(mode);
end
function outputArg = method1(obj,inputArg)
%METHOD1 Summary of this method goes here
% Detailed explanation goes here
outputArg = obj.Property1 + inputArg;
end
end
methods (Static)
configStruct = wizard(mode)
optionStruct = plotID_options(input)
end
end
+PlotID/@config/plotID_options.m deleted 100644 → 0
+ 0
− 28
View file @ 804a1abc
function [options] = plotID_options(input)
%PLOTID_OPTIONS Summary of this function goes here
% Detailed explanation goes here
options = struct();
switch input
case 'default' %same as Arguments Block
options.Location = 'local'; % storage path
options.Method = 'individual';
options.ParentFolder = 'export';
options.ConfigFileName = 'config.json';%individual config names possible
options.CopyUserFCN = true;
options.CSV = false;
options.ShowMessages = true;
options.ForcePublish = false; %publish anyway
case 'debug'
options.Location = 'local'; % storage path
options.Method = 'individual';
options.ParentFolder = 'export';
options.ConfigFileName = 'config.json';%individual config names possible
options.CopyUserFCN = true;
options.CSV = true;
options.ShowMessages = true;
options.ForcePublish = true; %publish anyway
end
end
+PlotID/@config/wizard.m deleted 100644 → 0
+ 0
− 39
View file @ 804a1abc
function config = wizard(mode)
%wizard creates config files depending on the selected mode
% initilise ask only for the input that is neccessary to run plotID
config = struct();
switch mode
case 'initilise'
config.Author = inputRequired('your Name');
config.ProjectID = inputRequired('your Project Number');
msg = ['Do you want to add a remote path?' newline,...
'Otherwise your files will be stored locally.' newline,...
'You can add this later by rerunning the initilisation.'];
disp(msg);
m = input('Do you want add a remothe path, Y/N [Y]:','s');
if ismember(m,{'Y','y'})
config.ServerPath = uigetdir();
end
otherwise
error('wizard mode undefined in CLASS config');
end %switch
end
function usrTxt = inputRequired(msg)
%Input Dialog that repeats if left empty
inputRequired = true;
while inputRequired
prompt = ['Please enter ', msg , ':'];
inpt = input(prompt,'s');
if isempty(inpt)
disp('Input must not be empty!');
else
usrTxt = inpt;
inputRequired = false;
end
end
end
\ No newline at end of file
+PlotID/@userDLG/userDLG.m deleted 100644 → 0
+ 0
− 80
View file @ 804a1abc
classdef userDLG
%userDLG the userDLG Class is responsible for the user dialog
% error handeling, user messages and warnings will be provided from
% this class, depending on the user options and error type.
% This reduces messaging overhead and code length in PlotID.Publish()
properties
configError = false
scriptPublished = false
rdFilesPublished = false
figurePublished = false
msg = ''
end
properties (SetAccess = protected)
success = false
showMessages {mustBeNumericOrLogical}
forcePublish {mustBeNumericOrLogical}
ID %plotID
end
methods
function obj = userDLG(ID,options)
%CATCHERROR Construct an instance of this class
if isempty(ID)
ID = '';
end
obj.ID = ID;
obj.showMessages = options.ShowMessages;
obj.forcePublish = options.ForcePublish;
end
function output = get.success(obj)
% checks if all publish operations are true
obj.success = all([obj.scriptPublished; obj.rdFilesPublished;...
obj.figurePublished]);
output = obj.success;
end
function obj = set.msg(obj,message)
%setmsg Summary of this method goes here
% Detailed explanation goes here
obj.msg = message;
end
function [] = userMSG(obj,message)
%userMSG user message without priority
% MSG will only be displaye if ShowMessages is true
if obj.showMessages
disp(message);
end
end
function [] = error(obj,message)
%error handles critical errors
% critical errors will always result in a matlab error
%ToDO: Add function(s) before termination
error(message);
end
function [] = softError(obj,message)
%softError handles soft errors
% soft errors can be changed to warning if ForcePublish is
% selected by the user
if obj.forcePublish
warning(message);
else
error(message);
end
end
function outputArg = method1(obj,inputArg)
%METHOD1 Summary of this method goes here
% Detailed explanation goes here
outputArg = obj.Property1 + inputArg;
end
end
end
+PlotID/Publish.m
+ 64
− 150
View file @ 52518cdf
function Publish(DataPaths,scriptPath, figure, options)
%%Publish(DataPaths,scriptPath, ID, figure, options) saves plot, data and measuring script
%
% DataPaths contains the path(s) to the research data, for multiple files
% use a cell array
% scriptPath contains the path to the script, this can be provided with
% the simple call of scriptPath = [mfilename('fullpath'),'.m'], note that
% the extension is mandatory
%
% Options:
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.
......@@ -18,31 +10,14 @@ function Publish(DataPaths,scriptPath, figure, options)
% path is used, PlotId will use this path a storagePath
arguments
DataPaths {mustBeDataPath} % location of the data-file(s)
scriptPath (1,:) {mustBeFile} % location of the matlab script
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','manual','CI-Test'})} = 'local' % storage path
options.Method {mustBeMember(options.Method ,{'individual','centralized'})} = 'individual'
options.ParentFolder (1,:) {mustBeText} = 'export'
options.ConfigFileName (1,:) {mustBeText} = 'config.json' %individual config names possible
options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true
options.CSV (1,1) {mustBeNumericOrLogical} = false
options.ShowMessages(1,1) {mustBeNumericOrLogical} = true
options.ForcePublish (1,1) {mustBeNumericOrLogical} = false %publish anyway
end
%% argument validation
%catch string and non cell inputs in DataPaths
if ~iscell(DataPaths)
DataPaths = {DataPaths}; %Cell array
end
for i=1:numel(DataPaths)
if isstring(DataPaths{i})
% strings will cause problems
DataPaths{i} = char(DataPaths{i});
end
end
%catch multiple figures in fig
......@@ -54,31 +29,18 @@ if numel(figure) > 1
warning(msg);
end
%get ID from Figure
ID = figure.Tag;
if isempty(ID)
% no ID found, User dialog for Folder name
ID = inputdlg(['No ID defined- ' newline,...
'Please enter a folder name to continue:'],'Please enter a folder name');
ID = ID{1};
msg = ['No ID found - consider to use the TagPlot function before ',...
'you publish ', newline, 'your files will be stored in ' , ID];
warning(msg);
end
%% read config file
% there is only one config Object (handleClass)
configObj = PlotID.config(options.ConfigFileName);
if isfield(configObj.configData, 'options')
% is working but prune to user errors
options = configObj.configData.options;
try
txt = fileread('config.json');
config = jsondecode(txt);
configError = false;
catch
msg = ['Error while reading the config file' newline,...
' publishing on server not possible'];
warning(msg);
configError = true;
end
% Error and MSG handeling
dlgObj = PlotID.userDLG(ID,options);
%% storage location
switch options.Location
case 'local'
......@@ -86,43 +48,35 @@ switch options.Location
storPath = options.ParentFolder;
else
% use the script path as export path
scriptLocation = fileparts(scriptPath);
storPath = fullfile(scriptLocation,options.ParentFolder);
scriptPath = fileparts(DataPaths.script);
storPath = fullfile(scriptPath,options.ParentFolder);
end
case 'server' %from config File
if dlgObj.configError
msg = ['Error while reading the config file' newline,...
' publishing on server not possible'];
dlgObj.error(msg);
end
storPath = config.ServerPath;
case 'manual' %UI
storPath = uigetdir();
case 'CI-Test'
storPath = fullfile(pwd,'CI_files',options.ParentFolder);
end
folderName = char(ID);
folderName = ['.',char(ID)]; %hidden folder
%% Create data directory
%% Create Data-Directory
if isfolder(fullfile(storPath,folderName))
dlgObj.error(['Folder ',folderName, ' exists - Plot was already published ']);
error(['Folder ',folderName, ' exists - Plot was already published ']);
elseif mkdir(fullfile(storPath,folderName))
else
dlgObj.error('Directory could not be created - check remote path and permissions');
error('Directory could not be created - check remote path and permissions');
end
disp(['publishing of ', ID, ' started']);
%% Create a copy of the script and user functions(optional)
%% Create a Copy of the script and user functions(optional)
% script
[~, status, msg] = PlotID.createFileCopy({scriptPath},folderName,storPath,ID, 'script');
dlgObj.scriptPublished =status;
dlgObj.userMSG(msg);
PlotID.createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
% user functions
[fList,pList] = matlab.codetools.requiredFilesAndProducts(scriptPath);
[fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
if options.CopyUserFCN
fList = fList(~ismember(fList,scriptPath)); % rmv script from list
fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
fList = fList(~contains(fList,'config.json')); % rmv config.json from list
fList = PlotID.removePltIdFiles(fList); % Do not copy files that are part of plot ID
if ~isempty(fList)
......@@ -142,16 +96,16 @@ switch options.Method
currentPath = fullfile(storPath);
%list all files
fList = dir(fullfile(storPath,DataFolderName, ['**',filesep,'*.*']));
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)
for i=1:numel(DataPaths.rdata)
% check if identical file exists (status = 1)
[~, idx] = PlotID.fileCompare(DataPaths{i},fList);
[~, idx] = PlotID.fileCompare(DataPaths.rdata{i},fList);
% create Linked HDF5 files for identical files
if any(idx)
fList.path = fullfile(fList.folder,fList.name);
......@@ -159,48 +113,46 @@ switch options.Method
relativeSourcePath = strrep(sourcePath,currentPath,'');
if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
linkedHDFPath = fullfile(storPath,folderName);
PlotID.createLinkedHDF5(relativeSourcePath{1,1},linkedHDFPath);
PlotID.createLinkedHDF5(relativeSourcePath{1,1},storPath,ID);
end
else % no identical file exists
%Copy the file in data and create the links (if hdf5)
[dataPath, status, msg] = PlotID.createFileCopy(DataPaths{i},'data',storPath,ID,'dataCentral');
pathToData = strrep(dataPath,currentPath,'');
[dataPath] = PlotID.createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
relativeDataPath = strrep(dataPath,currentPath,'');
%WIP
if contains(DataPaths{i},{'.h5','.hdf5'}) % Linking only for HDF5
if contains(DataPaths.rdata{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);
PlotID.createLinkedHDF5(relativeDataPath,storPath,ID);
end %if
end %if
end %for
clear DataFolderName
case 'individual'
% Create a copy of the research data
[~, status, msg] = PlotID.createFileCopy(DataPaths,folderName,storPath,ID, 'data');
PlotID.createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
end
%temporary:
dlgObj.rdFilesPublished = status;
dlgObj.userMSG(msg);
%% Write Config File
exportPath = fullfile(storPath,folderName);
configObj.writeConfig(exportPath);
% add further Metadata
meta =struct();
if ~configError %config File must exist
% copy config file
configPath = PlotID.createFileCopy('config.json',folderName,...
storPath,ID, 'data');
else
configPath = fullfile(storPath,folderName,'config.json');
config = struct();
if ispc
meta.author = getenv('USERNAME');
config.author = getenv('USERNAME');
end
meta.ProjectID = ID;
meta.CreationDate = datestr(now);
meta.MatlabVersion = version;
meta.ToolboxVersions = pList;
% write meta
metaPath = fullfile(storPath,folderName,'plotID_data.json');
fid = fopen(char(metaPath),'w');
txt = jsonencode(meta,'PrettyPrint',true);
end
% add further Metadata
config.ProjectID = ID;
config.CreationDate = datestr(now);
config.MatlabVersion = version;
config.ToolboxVersions = pList;
%write config
fid = fopen(char(configPath),'w');
txt = jsonencode(config,'PrettyPrint',true);
fprintf(fid,txt);
fclose(fid);
......@@ -213,64 +165,26 @@ try
savefig(figure,RemotePath);
% the png should only be a preview
exportgraphics(figure,[RemotePath,'.png'],'Resolution',300);
dlgObj.figurePublished = true;
catch
dlgObj.softError('Plot export was not successful');
warning('Plot export was not successful')
end
disp(['publishing of ', ID , ' done']);
% CSV EXport
if options.CSV
T = table();
T.research_Data = DataPaths'; T.PlotID(:) = {ID};
T.Script_Name(:) = {scriptPath};
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
%% final renaming and error/warning handeling
% if no error orcurred or if force publish is activated, rename the hidden
% folder to a non hidden one, otherwise delete it.
if dlgObj.success || options.ForcePublish
oldPath = fullfile(storPath,folderName);
newPath = strrep(oldPath,'.',''); %remov dot
status = movefile(oldPath,newPath); %rename directory
else
% error from userDlg class!
end
if status
disp(['publishing of ', ID , ' done']); %always displayed onsucess
else % publish was not sucessfull!
%replace with error from userDLG Class
dlgObj.error(['publishing of ', ID , ' failed'])
end
end %function
%% Argument Validation Functions
function tf = mustBeFigure(h)
%checks if input is a figure object
tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');
end
function mustBeDataPath(DataPaths)
%checks if input is a valid DataPath object
if ~iscell(DataPaths)
DataPaths = {DataPaths};
end
tf = zeros(1,numel(DataPaths));
for i=1:numel(DataPaths)
tf(i) = ~isfile(DataPaths{i});
end
if any(tf)
eidType = 'mustBeDataPath:notaValidFilePath';
msgType = 'DataPaths must contain file-path(s)';
throwAsCaller(MException(eidType,msgType))
end
end
+PlotID/TagPlot.m
+ 28
− 32
View file @ 52518cdf
......@@ -15,41 +15,42 @@ arguments
figs (1,:) {mustBeFigure}
options.ProjectID (1,:) {mustBeText}= ''
options.Fontsize (1,1) {mustBeInteger} = 8
options.Color (1,3) {mustBeNonnegative} = 0.65*[1 1 1] % grey
options.Location (1,:) {mustBeText} = 'east'
options.DistanceToAxis {mustBeReal} = .01 % relative distance
options.Position (1,2) {mustBeVector} = [1,0.4] % default for east
options.Rotation (1,1) {mustBeReal} = NaN
options.ConfigFileName (1,:) {mustBeText} = 'config.json'
options.Rotation (1,1) {mustBeInteger} = 0
end
if isempty(options.ProjectID)
configObj = PlotID.config(options.ConfigFileName);
configData = configObj.configData;
options.ProjectID = configData.ProjectID;
try
txt = fileread('config.json');
config = jsondecode(txt);
catch
config =struct;
config.ProjectID = '';
warning("No ProjectID was definded and no config.json could be found");
end
if ~isempty(config.ProjectID)
options.ProjectID = config.ProjectID;
else
warning('no project options.ProjectID defined')
end
end
switch options.Location
case 'north'
y = 1 - options.DistanceToAxis
options.Position = [0.4,y];
Rotation = 0;
options.Position = [0.4,0.95];
options.Rotation = 0;
case 'east'
x = 1 - options.DistanceToAxis;
options.Position = [x,0.4];
Rotation = 90;
options.Position = [1,0.4];
options.Rotation = 90;
case 'south'
y = 0 + options.DistanceToAxis;
options.Position = [0.4,y];
Rotation = 0;
options.Position = [0.4,.02];
options.Rotation = 0;
case 'west'
x = 0 + options.DistanceToAxis;
options.Position = [x,0.4];
Rotation = 90;
case 'southeast'
y = 0 + options.DistanceToAxis;
options.Position = [0.8, y];
Rotation = 0;
options.Position = [.05,0.4];
options.Rotation = 90;
case 'custom'
% Check if Position is valid
if ~all(0 <= options.Position & options.Position <= 1)
......@@ -61,10 +62,6 @@ switch options.Location
options.Location = 'east'; options.Position = [1,0.4];
end
if ~isnan(options.Rotation)
Rotation = options.Rotation;
end
IDs = cell(numel(figs),1);
for n = 1:numel(figs)
......@@ -75,11 +72,10 @@ for n = 1:numel(figs)
ylim =get(axes,'YLim');
xlim =get(axes,'XLim');
%ID
position = [options.Position(1), options.Position(2)];
position = [options.Position(1)*xlim(2), options.Position(2)*ylim(2)];
text(axes,position(1),position(2), IDs{n},'Fontsize',options.Fontsize,...
'Rotation',Rotation, 'VerticalAlignment','bottom','Color',...
options.Color,'BackgroundColor','w', 'Units', 'normalized');
'Rotation',options.Rotation, 'VerticalAlignment','bottom','Color',...
0.65*[1 1 1],'BackgroundColor','w');
set(figs(n),'Tag', IDs{n});
end
......
+PlotID/createFileCopy.m
+ 2
− 4
View file @ 52518cdf
function [storagePaths, status, msg] = 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
......@@ -68,10 +68,8 @@ try
copyfile(FileNameAndLocation,RemotePath);
storagePaths{i} = RemotePath;
end
status = true;
msg =([type, ' successfully published']);
disp([type, ' sucessfully published']);
catch
status = false;
warning([type,' export was not sucessful'])
if exist('errorMSG')
error(errorMSG);
......
+PlotID/createLinkedHDF5.m
+ 5
− 5
View file @ 52518cdf
function [status] = createLinkedHDF5(SourceFile,TargetPath)
function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
%createLinkedHDF5 creates a HDF file that references the Sourcefile
% TargetPath is the storage location, ID the foldername
% Status returns true if the function was sucessfull
......@@ -16,12 +16,12 @@ end
%old
%fid = H5F.create(fullfile(TargetPath,ID,[ID,'_data.h5']));
fid = H5F.create(fullfile(TargetPath,[filename,ext]));
fid = H5F.create(fullfile(TargetPath,ID,[filename,ext]));
%create External Link to Sourcefile in the Group linkToExternal
H5L.create_external(['..',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
%H5L.create_external(['..',filesep,'data',filesep,SourceFile],'/',fid, SourceFile ,plist_id,plist_id); %original
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,[filename,ext]),' created']);
disp([fullfile(TargetPath,ID,[filename,ext]),' created']);
status = 1;
% catch
% warning('No linked HDF file was created');
......
+PlotID/initilise.m deleted 100644 → 0
+ 0
− 7
View file @ 804a1abc
function [status] = initilise()
%INITILISE Initilisation for first time úsage
end
+PlotID/removePltIdFiles.m
+ 7
− 14
View file @ 52518cdf
function [fListClean] = removePltIdFiles(fList)
%removePltIdFiles removes functions that are part of PlotID out of flist
% Detailed explanation goes here
%addpath('..\fcn_core');
[~,names,ext] = fileparts(fList);
names = strcat(names, ext); % add ext for comparison
% Get a list of all .m files that are part of Plot id
packageContent = what('PlotID');
% packageContent.classes has no extensions
PltID_classlist = packageContent.classes;
PltID_flist = struct2table(dir('+PlotID')); %get list of files
[~,~,PltID_flist.ext(:)] = fileparts(PltID_flist.name(:)); % add ext column
% Class Methods need to be listed in an additional function
Class_flist = cell(1,numel(packageContent.classes)); %preallocate
for i=1:numel(packageContent.classes)
temp = what(['PlotID',filesep,'@',PltID_classlist{i}]);
Class_flist{i} = temp.m;
end
PltID_flist = PltID_flist(strcmp(PltID_flist.ext,'.m'),:);
Class_flist = vertcat(Class_flist{:});
% all plotID .m files:
PltID_flist = [packageContent.m; Class_flist];
% Comparison and filter
fListClean = fList(~ismember(names,PltID_flist));
fListClean = fList(~ismember(names,PltID_flist.name));
end
.gitignore
+ 0
− 1
View file @ 52518cdf
......@@ -37,7 +37,6 @@ testdata_2.h5
testdata2.h5
test_data.mat
export/*
unused*/*
# Octave session info
octave-workspace
......
.gitlab-ci.yml
+ 2
− 12
View file @ 52518cdf
......@@ -5,16 +5,6 @@ Test Code:
stage: Run
tags:
- matlab
- bash
script:
- cd ./CI_files
- chmod +x ./runner_linux.sh
- ./runner_linux.sh
- cat ./log.txt
artifacts:
paths:
- ./CI_files/log.txt
- ./CI_files/matlab_log.txt
when: always
expire_in: 1 week
- ./CI_files/runtest.ps1
- cat log2.txt
CITATION.cff deleted 100644 → 0
+ 0
− 18
View file @ 804a1abc
cff-version: 1.2.0
title: >-
plotID a toolkit for connecting research data and
figures
message: >-
developed at the Chair of Fluid System, Techische
Universität Darmstadt within the framework of the NFDI4Ing consortium Funded by the German Research Foundation (DFG) - project number 442146713
type: software
authors:
- given-names: Jan
family-names: Lemmer
email: jan.lemmer@fst.tu-darmstadt.de
affiliation: 'Chair of Fluid Systems, TU Darmstadt'
orcid: 'https://orcid.org/0000-0002-0638-1567'
- given-names: Martin
family-names: Hock
email: martin.hock@fst.tu-darmstadt.de
affiliation: 'Chair of Fluid Systems, TU Darmstadt'
CI_files/default_test.m
+ 45
− 99
View file @ 52518cdf
function [result] = default_test()
%default_test() This is a simple test if Plot ID works for the default settings
%UNTITLED2 This is a simple test if Plot ID works for the default settings
% Detailed explanation goes here
clear; clc; close all;
% set path
% starting path of gitlab runner is in CI_files
if contains(pwd,'CI_files')
cd .. % move one directory up
end
addpath('CI_files');
% clean up, if previous run failed
try
delete(['CI_files' filesep 'export' filesep '*']);
delete(['CI_files' filesep '*.mat']);
delete(['CI_files' filesep '*.h5']);
rmdir(['CI_files' filesep 'export'],'s');
delete CI_files/export/* CI_files/*.mat CI_files/*.h5
rmdir('CI_files/export','s');
end
% initialise
numberOfTests = 2;
testResults = zeros(numberOfTests,1);
%start log
fid = fopen(fullfile('CI_files','log.txt'),'w');
txt = ['default test started ' newline];
fprintf(fid,txt);
% create Config for CI-Tests
fid1 = fopen(fullfile('CI_files','CI_config.json'),'w');
configData.Author = 'CI-Test'; configData.ProjectID = 'CI-001';
txt = jsonencode(configData,'PrettyPrint',true);
%fprintf does not write paths correctly !!!
fwrite(fid1,txt);
fclose(fid1);
try
ProjectID = 'Test01';
%% Data
% some random data
x = linspace(0,7);
y = rand(1,100)+2;
dataset1 = fullfile('CI_files','test_data.mat');
save(dataset1,'x','y');
dataset1 = 'test_data.mat';
save('CI_files/test_data.mat','x','y');
% some data as .h5
x1 = linspace(0,2*pi);
y1 = sin(x1)+2;
% define file path & name
fpath = fullfile("CI_files","testdata2.h5");
dataset2 = fullfile('CI_files','testdata2.h5');
fpath = "CI_files/testdata_2.h5";
dataset2 = 'testdata_2.h5';
% create hdf5 file and dataset > write data to hdf5 file / dataset
h5create(fpath, "/x1", size(x1), "Datatype", class(x1))
......@@ -65,62 +37,36 @@ try
plot(x,y,'-k');
hold on
plot(x1,y1,'-r');
msg = 'simple_test succeed stage 1';
catch
testResults(1) = 1; %test fails
msg = 'simple_test failed in Stage 1';
warning(msg);
end
fprintf(fid,[msg newline]);
%% Tag the plot
try
[figs, ID] = PlotID.TagPlot(fig,'ConfigFileName', 'CI_config.json');
[figs, ID] = PlotID.TagPlot(fig,'ProjectID', ProjectID);
%% call a dummy function
%a=1;
%a = example_fcn(a);
a=1;
a = example_fcn(a);
%% publishing
% The functions needs the file location, the location of the data and the
% figure
script = [mfilename('fullpath'),'.m']; % filename of the m.script
path.script = mfilename('fullpath'); % filename of the m.script
% file name of the data
rdata = {dataset1,dataset2} ; % don't forget the extension
path.rdata = {dataset1,dataset2} ; % don't forget the extension
PlotID.Publish(rdata,script, figs, 'Location', 'CI-Test',...
'ConfigFileName', 'CI_config.json');
PlotID.Publish(path, ID, figs, 'Location', 'CI-Test')
result = true;
msg = 'simple_test succeed Stage 2';
catch
testResults(2) = 1; %fail
msg = 'simple_test failed in Stage 2';
warning(msg);
end
fprintf(fid,[msg newline]); %log
%% Test result
if any(testResults)
result = 1; %fail
warning('test failed');
else
result = 0; % pass
disp('test succeed');
end
% clean up
delete CI_files/export/* CI_files/*.mat CI_files/*.h5
rmdir('CI_files/export','s');
fclose(fid);
clear; clc;
% final clean up
try
delete(['CI_files' filesep 'export' filesep '*']);
delete(['CI_files' filesep '*.mat']);
delete(['CI_files' filesep '*.h5']);
rmdir(['CI_files' filesep 'export'],'s');
delete(fullfile('CI_files','CI_config.json'));
catch
result = false;
warning('simple_test failed');
end
end
......
CI_files/fail_runner.m deleted 100644 → 0
+ 0
− 8
View file @ 804a1abc
function [retVal] = fail_runner()
%RUNNER_TESTING testing function to test, if the runner is set up properly
retVal = 1; % test should fail !
fid = fopen(fullfile('log.txt'),'w');
txt = ['This is a test, Errorstate: ', num2str(retVal)];
fprintf(fid,txt);
fclose(fid);
end
CI_files/pass_runner.m deleted 100644 → 0
+ 0
− 8
View file @ 804a1abc
function [retVal] = pass_runner()
%pass_runner testing function to test, if the runner is set up properly
retVal = 0; % test should succeed !
fid = fopen(fullfile('log.txt'),'w');
txt = ['This is a test, Errorstate: ', num2str(retVal)];
fprintf(fid,txt);
fclose(fid);
end
CI_files/runner_linux.sh deleted 100644 → 0
+ 0
− 15
View file @ 804a1abc
#!/bin/bash
#matlab -r "disp(['Current folder: ' pwd])"
matlab $@ -nodisplay -nodesktop -nosplash -logfile matlab_log.txt -r "default_test;exit(ans);"
exitstatus=$?
if [[ $exitstatus -eq '0' ]]
then
echo "matlab succeed. Exitstatus: $exitstatus"
exit $exitstatus
else
echo "matlab failed. Exitstatus: $exitstatus"
exit $exitstatus
fi
CI_files/runner_test.m 0 → 100644
+ 7
− 0
View file @ 52518cdf
function [result] = runner_test()
%RUNNER_TEST testing function to test, if the runner is set up properly
result = true;
exit(result);
end
CI_files/runtest.ps1 deleted 100644 → 0
+ 0
− 17
View file @ 804a1abc
# runtest.ps1
$LOGFILE='CI_log.txt'
$wd = pwd;
$LOGFILE = $("$wd" + "\" + "$LOGFILE")
$CIfolder = "$wd" + "\" + "CI_files\"
# $MFILE='"C:\git\NFDI4ing\plot_ID_matlab\CI_files\runner_test.m"'
$arguments = "-nodesktop", "-nosplash","-minimize","-wait","-sd", "$wd", "-logfile", "$LOGFILE","-batch","CI_files\test_runner_STFS.m"
$Returnvalue = & 'C:\Program Files\MATLAB\R2021b\bin\matlab.exe' $arguments
#$CODE = $?
# Returnvalue doesnt get anything useful from matlab
# Write-Output($Returnvalue)
Write-Output(Get-Content($LOGFILE))
exit $CODE
Initialisation.m deleted 100644 → 0
+ 0
− 29
View file @ 804a1abc
%% This is the PlotID Initialisation file
% Please run this script before using PlotID
%% Step 1: Add plotID location to you MATLAB path
% This is necessary to use PlotID in your personal MATLAB Scripts
addpath(pwd);
savepath;
%% Section 2 Config File
% To make things easy, you should use the config file. The following wizard
% will help you create one:
writeConfig = true;
% Ask User if current config should be overwritten
if isfile('config.json')
m = input('Do you want to overwrite the current config file, Y/N [Y]:','s');
writeConfig = ismember(m,{'Y','y'});
end
if writeConfig
config = PlotID.config.wizard('initilise');
fid = fopen('config.json','w');
txt = jsonencode(config,'PrettyPrint',true);
fwrite(fid,txt);
fclose(fid);
end
%%
disp('Initialisition done.')
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