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IDProjectCategoryView StatusLast Update
0000057VANTED 2.8.0[VANTED] Add-onpublic2021-07-09 17:59
ReporterJoyeeAssigned Todimitar.garkov 
PriorityhighSeveritymajorReproducibilityalways
Status resolvedResolutionfixed 
PlatformPCOSWindowsOS Version10
Product Version[VANTED] 2.8.0 
Target VersionFixed in Version[VANTED] 2.7.0 
Summary0000057: Unable to load flux dataset
Description

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

Steps To Reproduce

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

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dimitar.garkov

dimitar.garkov

2021-07-09 17:56

developer   ~0000785

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.

dimitar.garkov

dimitar.garkov

2021-07-09 17:59

developer   ~0000786

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

Issue History

Date Modified Username Field Change
2021-06-16 00:18 Joyee New Issue
2021-06-16 00:18 Joyee Tag Attached: error
2021-07-09 17:56 dimitar.garkov Note Added: 0000785
2021-07-09 17:59 dimitar.garkov Assigned To => dimitar.garkov
2021-07-09 17:59 dimitar.garkov Status new => resolved
2021-07-09 17:59 dimitar.garkov Resolution open => fixed
2021-07-09 17:59 dimitar.garkov Fixed in Version => 2.7.0
2021-07-09 17:59 dimitar.garkov Note Added: 0000786