Upon installation, the program creates a folder '~/.vanted' in the home directory, containing preferences, plugin storage and licence acceptance flags.

This is not XDG conform: The folder should be created as '$XDG_CONFIG_HOME/vanted' (and maybe even more differentiated as per specification).

installation

• Verify that $XDG_CONFIG_HOME is set on your Linux system
• Run the installer
• Discover the folder at '~/.vanted'
• Do not discover a folder at '$XDG_CONFIG_HOME/vanted'

Additionally, on specialty OSes like NixOS with nonstandard locations for things like /bin/chmod, the installer throws a failure error in that. Manually running the rest of the installer script's parts works fine to get the program running.

It is not possible to load a dataset for mapping (an Excel file) after a network has been exported as a website.

The problem is in org,OpenFileDialogService

openDialog is static and reused if it is not null.

However, in the method getDirectoryFromUser (line 184) the file selection mode is set to JFileChooser.DIRECTORIES_ONLY.

That causes a problem in the methods getFile and getFiles because the same instance of the JFileChooser is used.

The solution would be to set the file selection mode to JFileChooser.FILES_ONLY (the default value for Java 8 according to https://docs.oracle.com/javase/8/docs/api/javax/swing/JFileChooser.html).

Export a network as website
Try to load a dataset on the "Experiment" tab

The method getConnectedComponentsAsCopy from the GraphHelper class duplicates edges in the copy of the connected component.
I think it needs to keep track of edges which have already been added to the connected component.

1) Add the attached bsh script to your VANTED user profile.
Windows: c:/Users/<username>/AppData/Roaming/VANTED
Linux: /home/<username>/.vanted
MacOS: /Users/<username>/Library/Preferences/VANTED/
2) Run VANTED.
3) Run the script on the attached test.gml (probably adjust path separator if necessary).
It should create two files ./test/test_1.gml and ./test_2.gml (see also the attached files).
Both gml files should have two edges instead of one.

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=67&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=68&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=69&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=70&type=bug

The multilevel layout seems to take considerably more time than it should (Compare to stress minimization). It also shows idle times for the level layouts.

Originally reported on GitHub (by KK): https://github.com/LSI-UniKonstanz/vanted/issues/10

Sofern bereits auf einem Graphen der Multilevel Framework Algorithmus ausgeführt wurde, wird bei der ersten! Ausführung auf einem weiteren Graphen keinerlei Änderung vorgenommen.
Bei einer weiteren Ausführung, wird der Algorithmus jedoch korrekt ausgeführt und das Ergebnis auch graphisch richtig dargestellt.

1.) Ausführen des Multilevel Framework Algorithmus auf einem beliebigen Graphen
2.) Graph schließen und weiteren Graphen öffnen
3.) Algorithmus auf diesem neuen Graphen ausführen

Getestet mittels zufallsgenerierter Graphen.

Hi, I've been trying to use the flux map add-on recently on Vanted version 2.8.1. I come across the issue of java errors when loading the flux dataset (the example files offered from the website). I've tried on two windows 10 platforms and one LINUX platform. The same errors happen to all of the tested platforms. Could you help me have a check and solve the issue？Thanks in advance.

The errors are shown below:

generated with VANTED V2.01 at Thu Feb 16 11:00:58 CET 2012

Graph file processed: example-fluxmap.gml
Create view for file: C:\Users\huangl5\Downloads\example\example\example-fluxmap.gml
Exception in thread "Load Flux Dataset" java.lang.NoClassDefFoundError: org/jdom/Attribute
at de.ipk_gatersleben.ag_pbi.fluxmap.FluxExperimentDataLoader.getSampleData(FluxExperimentDataLoader.java:402)
at de.ipk_gatersleben.ag_pbi.fluxmap.FluxExperimentDataLoader.getSamples(FluxExperimentDataLoader.java:386)
at de.ipk_gatersleben.ag_pbi.fluxmap.FluxExperimentDataLoader.getExperimentDataFromFile(FluxExperimentDataLoader.java:152)
at de.ipk_gatersleben.ag_pbi.fluxmap.FluxExperimentDataLoader.getExperimentDataFromFileList(FluxExperimentDataLoader.java:86)
at de.ipk_gatersleben.ag_pbi.fluxmap.FluxExperimentDataLoader.process(FluxExperimentDataLoader.java:64)
at de.ipk_gatersleben.ag_pbi.datahandling.TemplateLoader$1.run(Unknown Source)
at de.ipk_gatersleben.ag_nw.graffiti.services.task.SimpleBackgroundTask.run(Unknown Source)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: java.lang.ClassNotFoundException: org.jdom.Attribute
at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:435)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:589)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 8 more

error

Test data:
Example data files of a simlated knockout in the glycolysis pathway (filled template, layouted glycolysis and glycolysis with mapped flux data).
https://kim25.wwwdns.kim.uni-konstanz.de/vanted/addons/fluxmap/download_installation_tutorial.html

Please use the newest current version of the FluxMap add-on, version 1.15. The problem was due to a library incompatibility, i.e. jdom.

Download/Update the FluxMap add-on using the built-in Add-on Manager. The add-on can also be downloaded from here: http://kim25.wwwdns.kim.uni-konstanz.de/vanted/addons/fluxmap/releases/v1.15/FluxMap.jar

Vanted V2.8.1.
Only few edges are actually displayed

open kegg pathway. example: bvg00360.

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=65&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=66&type=bug

Beim Laden von Daten taucht unzählige Fehlermeldungen auf, die vermutlich mit der Java-Version zusammenhängen. Auf meinem Laptop ist Java 9 und Java 12 installiert, die Library ist Java 9. Ein Team-Mitglied meiner Software Projekt Gruppe hatte zuerst Java 9 auf seinem Laptop installiert, auf welchem Vanted nicht lief. Als er Java 8 aktivierte lief es plötzlich. Inzwischen kann man jedoch nicht mehr Java 8 herunterladen.

Beim öffnen von Vanted (via StartVantedWithAddon) tauchen 5 Warnungen auf, aber kein Fehler. Beim Laden der Daten tauchen dann die unten im Screenshot aufgezeigten Fehlermeldungen auf. Die Daten werden zwar angezeigt aber nicht so gemappt wie vorgesehen. Der Code basiert auf dem gegebenen AddOn-Example und die hinzugefügten Zeilen Code von unserer Gruppe funktionieren soweit, denn der gleiche Code, der bei mir diesen Fehler wirft, läuft bei den anderen Mitgliedern. Zu erwähnen jedoch ist, dass diese alle mit Windows arbeiten.

Console:

Starting VANTED with Add-on Add-on-Example.xml for development...
Welcome! About to start the application...
2019-06-03 14:53:22 DEBUG Main:205 - installing max os x handlers
2019-06-03 14:53:22 DEBUG ScanForUpdate:131 - waiting for update scan until app has started
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.vanted.osx.OSXSupport (file:/Users/antonellabidlingmaier/Uni-IE/4.%20Semester/Software%20Projekt/newworkspace/vanted/target/classes/) to method com.apple.eawt.Application.getApplication()
WARNING: Please consider reporting this to the maintainers of org.vanted.osx.OSXSupport
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Trying to load Add-ons...
Add-on CentiLib-Vanted.jar processed
Add-ons loaded in 334ms

Hier werden die Daten geladen + Fehlermeldung:

Read file: /Users/antonellabidlingmaier/Uni-IE/4. Semester/Software Projekt/Testfiles/Daten_subfish_500/frame_2000.graphml
SAX Parser: org.apache.xerces.jaxp.SAXParserImpl
XML Reader: org.apache.xerces.jaxp.SAXParserImpl.JAXPSAXParser
Graph file processed: frame_2000.graphml
Create view for file: /Users/antonellabidlingmaier/Uni-IE/4. Semester/Software Projekt/Testfiles/Daten_subfish_500/frame_2000.graphml
org.graffiti.attributes.AttributeNotFoundException
at org.graffiti.attributes.AbstractCollectionAttribute.getAttribute(AbstractCollectionAttribute.java:124)
at org.graffiti.attributes.AbstractAttributable.getAttribute(AbstractAttributable.java:96)
at org.vanted.addons.exampleaddon.AddonTab.sessionChanged(AddonTab.java:172)
at org.graffiti.plugins.inspectors.defaults.Inspector.sessionChanged(Inspector.java:229)
at org.graffiti.editor.MainFrame.fireSessionChanged(MainFrame.java:1338)
at org.graffiti.editor.MainFrame.createInternalFrame(MainFrame.java:1155)
at org.graffiti.editor.MainFrame.showViewChooserDialog(MainFrame.java:2799)
at org.graffiti.editor.MainFrame.showViewChooserDialog(MainFrame.java:2732)
at org.graffiti.editor.MainFrame.showViewChooserDialog(MainFrame.java:2727)
at org.graffiti.editor.MainFrame$6$1.run(MainFrame.java:1556)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764)
at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:734)
at org.graffiti.editor.GlobalHotkeyManager.dispatchEvent(GlobalHotkeyManager.java:63)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
org.graffiti.attributes.AttributeNotFoundException
at org.graffiti.attributes.AbstractCollectionAttribute.getAttribute(AbstractCollectionAttribute.java:124)
at org.graffiti.attributes.AbstractAttributable.getAttribute(AbstractAttributable.java:96)
at org.vanted.addons.exampleaddon.AddonTab.sessionChanged(AddonTab.java:172)
at org.graffiti.plugins.inspectors.defaults.Inspector.sessionChanged(Inspector.java:229)
at org.graffiti.editor.MainFrame.fireSessionChanged(MainFrame.java:1338)
at org.graffiti.editor.MainFrame.setActiveSession(MainFrame.java:736)
at org.graffiti.editor.GraffitiInternalFrame$1.internalFrameActivated(GraffitiInternalFrame.java:176)
at java.desktop/javax.swing.JInternalFrame.fireInternalFrameEvent(JInternalFrame.java:1543)
at java.desktop/javax.swing.JInternalFrame.setSelected(JInternalFrame.java:1079)
at org.graffiti.editor.MainFrame$5.run(MainFrame.java:1235)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764)
at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:734)
at org.graffiti.editor.GlobalHotkeyManager.dispatchEvent(GlobalHotkeyManager.java:63)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=62&type=bug

This may be related to a similar issue resolved in 2.8.0. Which add-ons were running? E.g. having CentiLib with versions prior to 2.8.0 causes similar behaviour, while loading data.

To whom it may concern,

I recently read Vanted on the paper and started using VANTED 2.6.5 Java Web Start (64 bit). However, as the add-ons cannot be uploaded for the web start, I decided to use VANTED 2.6.5 for Windows. However, after I installed the latest Java runtime, I installed and ran Vanted. However, it does not run nor show the sign of errors. Due to no error message, I do not know what to do for the next.

Does anyone have the same issue or know how to solve this issue?

Thank you,

The issue may be due to Java version incompatibility. Make sure you have a Java version between Java 7 and Java 9.

To get a message, you could start it from the .cmdfile in its installation folder.

On trying to apply the layout algorithm, one see the following unsatisfied precondition:

The list of patterns is empty. Use tab "Tools" → "Search Subgraph" to create some.

However, this is nowhere to be found.

Resolved in Vanted 2.8.0

Hallo,

I am struggling with customizing graphs that can not be changed. Data input is values with replicates. I am trying to change axis via ATTRIBUTES>NODES>CHARTING by ticking RANGE AXIS CUSTOM MIN/MAX but that does not work, although other functions are OK.

I tried to use data without replicates (mean values) but with no succes. I tried to upload demo file but does not work. Only by loading examples I can use custom ranges

Any help is very appreciated
Thank you

Lukas Kucera

Thanks for reporting the issue! The feature is actually working, but its behaviour is not very clear. When you tick RANGE AXIS CUSTOM MIN/MAX, you also have to change the Min and Max values RANGE AXIS MAXIMUM and RANGE AXIS MINIMUM from the above input boxes. When you tick the box without changing the above values, the default min and max are taken, which are 0 and 1, and since the mapped data values are quite different, it looks like nothing happens.

The feature should be Improved for more clarity in a next version of Vanted by:

1. Synchronising the starting attribute min and max with chart min and max, so that when the custom axis checkbox is ticked, the chart remains unchanged, until new min and max attribute values are set.
2. Adding a tooltip to custom axis checkbox hinting the need to change the min and max attribute values.

The installer crashes, when there is a special character in the path, e.g. "!". The crash opens a dialog, which keeps re-occurring after it is closed.

Steps to reproduce:

1. Download Vanted 2.6.5.
2. Locate Vanted in a path with a special characters in the path tree.
3. Try to install Vanted 2.6.5.
4. Try to close the error pop-up dialog window.

Such paths also can influence other functions, such e.g. loading of add-ons.

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=63&type=bug

I am having difficulty drawing line graph using Vanted on my Time series data. I have used the template provided on the web and edited it to accommodate my data attributes. I can successfully import data and perform mapping, but I cannot change my graph layout to a line graph. Apparently "show line" function doesn't work!

I tried to download the SIB Enzyme Database and after it was finished the textbox was bugged, so the OK Button wasn't visibile anymore.
But I couldnt reproduce this neither in Vanted 2.6.4 nor in 2.6.3. Maybe just a bugged view from my system.

(Didn't work for me twice)

Open Vanted -> ? -> Database Status -> Download/Update

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=19&type=bug

I Have been able to reproduce it - it does indeed have strange behaviour.

If you are editing a graph it would be nice to have the possibility to undo (as well as redo) your changes more often. The current maximum of undoing (and redoing) your changes is five times and this seems quite few.

feature

The issue has been resolved and will arrive with version 2.6.6. Setting will be 20.

If you have a graph/network loaded and want to export attributes via the "Export" function and you choose to export every attribute in the list you either get an error (screenshot below) or nothing happens after confirming the selection.

export, nullpointerexception

File -> New -> Random Network -> Generate Erdos-Renyi random network -> OK
File -> Export -> Calculated Data -> Select all Attributes -> OK

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=4&type=bug

And the respective stacktrace:

java.lang.NullPointerException
at de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ExportDataTableAlgorithm$NodePair.hashCode(ExportDataTableAlgorithm.java:176)
at java.util.HashMap.hash(HashMap.java:338)
at java.util.HashMap.put(HashMap.java:611)
at java.util.HashSet.add(HashSet.java:219)
at de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ExportDataTableAlgorithm.execute(ExportDataTableAlgorithm.java:90)
at org.graffiti.editor.GravistoService.multiGraphExecution(GravistoService.java:682)
at org.graffiti.editor.GravistoService.runAlgorithm(GravistoService.java:554)
at org.graffiti.editor.GravistoService.runAlgorithm(GravistoService.java:476)
at org.graffiti.editor.actions.RunAlgorithm.actionPerformed(RunAlgorithm.java:123)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at org.graffiti.editor.GlobalHotkeyManager.dispatchEvent(GlobalHotkeyManager.java:65)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Being able to reproduce. The reason is that some of the attributes are not set, therefore - null. A proper highlighting, e.g. not being enabled, should not permit the user to select any null values to export.

There is generated Javadoc on the website, but this is for a previous version and should be updated.

documentation, links

Go to http://kim25.wwwdns.kim.uni-konstanz.de/vanted/javadoc/.

The Javadoc has been updated, see http://kim25.wwwdns.kim.uni-konstanz.de/vanted/javadoc/ with 2.6.5 SNAPSHOT.

If you open a network from the MetaCrop pathways and then change to the Network tab in Attributes, there is the possibility to show the network in the browser. Unfortunately the link leads to a non available resource (Error 404)

Edit_1: Doesn't work for the option in the Node tab either

links

1. Pathways -> MetaCrop -> Get list of pathways -> Open a random network
2. Change to Attributes Tab -> Network -> Show in Browser

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=21&type=bug

Fixed server-side.

When trying to use the Remove Connecting Nodes function on a random graph with one node selected, Vanted throws a NullPointerException

nullpointerexception

File -> New -> Random Network
Select one Node -> Nodes -> Remove Connecting Nodes -> OK

java.lang.NullPointerException
at de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.RemoveSelectedNodesPreserveEdgesAlgorithm.removeNodes(RemoveSelectedNodesPreserveEdgesAlgorithm.java:300)
at de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.RemoveSelectedNodesPreserveEdgesAlgorithm.removeNodesPreserveEdges(RemoveSelectedNodesPreserveEdgesAlgorithm.java:164)
at de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.RemoveSelectedNodesPreserveEdgesAlgorithm.execute(RemoveSelectedNodesPreserveEdgesAlgorithm.java:111)
at org.graffiti.editor.GravistoService.multiGraphExecution(GravistoService.java:684)
at org.graffiti.editor.GravistoService.runAlgorithm(GravistoService.java:556)
at org.graffiti.editor.GravistoService.runAlgorithm(GravistoService.java:478)
at org.graffiti.editor.actions.RunAlgorithm.actionPerformed(RunAlgorithm.java:123)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at org.graffiti.editor.GlobalHotkeyManager.dispatchEvent(GlobalHotkeyManager.java:65)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=33&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=34&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=35&type=bug

Fixed with commit f8278b5.

It is not possible to undo the 'remove connection nodes' command

• Select some nodes
• Click on Network -> Nodes -> Remove connection nodes
• Try to undo changes

I created a network with the demo.gml data from the tutorial. Then I tried to cut a node from the view, assuming it gets copied to the clipboard and removed from the view. After that I wanted to paste this perviously cutted node again via the "paste"-button. But instead of pasting this node it pasted a different random node in a random position on the view. Then I tried to undo this change via the "undo"-button. Now it pasted the previously cutted node again instead of removing the falsely pasted node.

(The following only occured while I used the demo.gml and input.xls from the tutorial)
After that I tried to redo this last change via the "redo"-button and an error message popped up. I clicked "ok" and tried to edit the view again with adding a new node. But the view stucked and it threw an error. Now I wanted to recreate the view, to be able to edit it again. Doing this just another error occured.

Steps to reproduce the cut and paste error:

1. Create random network
2. Cut a node -> Paste the elements from the clipboard -> Undo

Steps to reproduce the whole error:

1. Load Demo-Dataset input.xls
2. Load Pathway File demo.gml
3. Perform Data-Mapping
4. Cut a node -> Paste the elements from the clipboard -> Undo -> Redo (2 times) -> Error -> Ok -> Create new node -> Error -> Recreate View -> Error

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=55&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=56&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=57&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=58&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=59&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=60&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=61&type=bug

It would be nice to have some tool, that would automatically convert the loaded KEGG pathways into a nice layout. For example some algorithm that rearranges the nodes in a nice way when their size is changed. Also the letters for post transcriptional modification, like phosphorylation should not be directly on the arrows.

I tried to get a list of example files via the "Example" option in the "?"-tab. So I clicked on "Get list of example files" and then double clicked a directory assuming it gets opened then. Instead of just opening the directory it began to download all the example files in the directory I clicked on. When I tried to stop this instant download of all the files via the "stop"-button the button label changed to "wait" but nothing happend and it still downloaded all the files and opened a view for every file after finishing.

? -> Examples -> Get list of example files -> double click a random directory -> stop -> wait

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=31&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=32&type=bug

Menutabs/Icons like Undo and Redo are labeled with the german words: "Wiederherstellen" and "Rückgängig. As well as the view from a random network has the german labeled options "Schließen" "Maximieren" "Minimieren". And if you try to close the view and you'll get the warning message "Changes not saved" the options you get are also german labeled: "Ja" "Nein" "Abbrechen"

icons

Open a view -> Edit something -> hover above the redo undo icons as well as the view option icons in the right top corner -> Close -> Textbox appears

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=29&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=30&type=bug

This is expected and somewhat desired behaviour. Such text fragments depend on the current Locale and/or are taken from the Look And Feel defaults, which in turn again originate from the Locale.

The JPanel that accommodates the Workflow Tutorial has fixed size. Meaning resizing does not affect it. See image.

1. Go to "?" and choose "Workflow Tutorial"
2. Resize the dialog window

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=54&type=bug

Fixed with commit 658f947.

After creating a LEC1/AFL-B3 network and going through some menu options at some point the view stucked in a state where you couldn't manipulate the graph anymore. A recreation of the view was followed by an error.

rimas

RIMAS -> LEC1/AFL-B3 network -> Some unknown steps in the menu

It wasn't possible for me to reproduce this error

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=7&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=8&type=bug

Not being able to reproduce the issue.

When one accesses http://kim25.wwwdns.kim.uni-konstanz.de, the root address of the VANTED Website, excluding the /vanted/ sub-directory, s/he is welcomed by a default New Website Coming banner.

Should redirect to the default page http://kim25.wwwdns.kim.uni-konstanz.de/vanted/.

Go to this link.

Fixed server-side by adding the necessary rewrite rules in .htaccess directory-level file.

If you have an empty view and hover above the redo or undo icons a hintbox shows up with the text edit.redo and edit.undo whilst the other icons have a small textual description. Probably the hintbox contains the method name here. Btw. if there is a graph existing in the view the hintboxes have a correct textual description.

icons

Open Vanted -> Hover above the redo and undo icons and wait for the hintboxes to show up.

or

Open Vanted -> Edit -> Hover above the redo and undo icons and wait for the hintboxes to show up.

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=17&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=18&type=bug

Fixed with commit 97bc200.

This goes only for users of 2.6.3, switching to 2.6.4.

Although, links have been updated in the code-base itself, there are still saved in Java Preferences, stored in the Os-specific registries (under Linux ~/USER/.java/.userPrefs, under Windows the Windows registry) and polled from there. Thus, those from code get overridden, and defaulted to the old repository at immersive-analytics.infotech.monash.edu.

links, preferences

Pathways -> MetaCrop -> Get list of pathways -> Download any from the file tree

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=20&type=bug

Fixed with commit 55f4b00. Now we force preferences update only for version 2.4.6.

If you want to get a list of pathways from the MetaCrop tab, Vanted responses with an Error. Server returned HTTP response code: 403

error

Pathways -> MetaCrop -> Get list of pathways

Error Message:

Thread: AWT-EventQueue-0 sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) java.net.URL.openStream(Unknown Source) de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop.WebDirectoryFileListAccess.getWebDirectoryFileListItems(WebDirectoryFileListAccess.java:52) de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop.PathwayWebLinkTab$3.actionPerformed(PathwayWebLinkTab.java:190) javax.swing.AbstractButton.fireActionPerformed(Unknown Source) javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) javax.swing.DefaultButtonModel.setPressed(Unknown Source) javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) java.awt.Component.processMouseEvent(Unknown Source) javax.swing.JComponent.processMouseEvent(Unknown Source) java.awt.Component.processEvent(Unknown Source) java.awt.Container.processEvent(Unknown Source) java.awt.Component.dispatchEventImpl(Unknown Source) java.awt.Container.dispatchEventImpl(Unknown Source) java.awt.Component.dispatchEvent(Unknown Source) java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) java.awt.Container.dispatchEventImpl(Unknown Source) java.awt.Window.dispatchEventImpl(Unknown Source) java.awt.Component.dispatchEvent(Unknown Source) java.awt.EventQueue.dispatchEventImpl(Unknown Source) java.awt.EventQueue.access$500(Unknown Source) java.awt.EventQueue$3.run(Unknown Source) java.awt.EventQueue$3.run(Unknown Source) java.security.AccessController.doPrivileged(Native Method) java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.awt.EventQueue$4.run(Unknown Source) java.awt.EventQueue$4.run(Unknown Source) java.security.AccessController.doPrivileged(Native Method) java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.awt.EventQueue.dispatchEvent(Unknown Source) org.graffiti.editor.GlobalHotkeyManager.dispatchEvent(GlobalHotkeyManager.java:65) java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) java.awt.EventDispatchThread.pumpEvents(Unknown Source) java.awt.EventDispatchThread.pumpEvents(Unknown Source) java.awt.EventDispatchThread.run(Unknown Source)

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=16&type=bug

Fixed server-side.

If you open several graphs in different views and edit them without saving it and then use the function "Close all Windows" a warning message appears. If you choose to abort it still deletes some of the other views. If you try it again then sometimtes it also closes the view which you specifically stopped to close.

1. Create X graphes in different views -> Edit the graphs without saving
2. Window -> Close All Windows -> Abbrechen/Abort

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=9&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=10&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=11&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=12&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=13&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=14&type=bug

http://kim25.wwwdns.kim.uni-konstanz.de/vanted/mantis/file_download.php?file_id=15&type=bug

Reproduced.

Fixed with commit b418d98.

Following the steps to reproduce, you end up with on view containing a modified graph. Although visible, this is not active or could be enabled too, so that it could be worked on. Step 3 acts as a stimuli to unlock the effect, meaning other similar actions could lead to the same outcome.

1. Create and modify any graph
2. Repeat step 1. any number of times
3. Press the edit tool button on the left of the graph view field (Other actions could also trigger this bug!)
4. Choose Window Menu -> 'Close All Windows' menu item
5. For all but the last graphs press 'No'.
6. For the last press 'Cancel'
7. Try to access the edit tools. Those are disabled and remain so regardless of the course of subsequent actions taken.

Fixed with commit b418d98. Found, while fixing issue 0000010 ("Close all Windows" doesn't work properly).

For the website favicon has been used the VANTED Logo. This has been redesigned in a previous version, however, the one used for the website has not been up to date.

icons

Favicon updated with VANTED Logo as of VANTED version 2.6.3.