Early 0.7beta bugs fixed

[mbastian]

Five bugfixes were just deployed to updates

Chaining Dynamic Filter - https://bugs.launchpad.net/gephi/+bug/654018
Statistics report not refreshed after a new execution - https://bugs.launchpad.net/gephi/+bug/654036
Labels are not hidden on Preview - https://bugs.launchpad.net/gephi/+bug/654006
Data Lab: number columns not sorted by value - https://bugs.launchpad.net/gephi/+bug/653640
NullPointerException on saving project - https://bugs.launchpad.net/gephi/+bug/622154

[ajegga]

I have also noticed that when I try to open the old project files (alpha version) and try to preview them, it is throwing up an error. Below is the stack trace. I am also unable to export the pdf. The pdf file is created but it is blank.

java.lang.IllegalArgumentException: negative width
at java.awt.BasicStroke.<init>(Unknown Source)
at java.awt.BasicStroke.<init>(Unknown Source)
at processing.core.PGraphicsJava2D.strokeImpl(PGraphicsJava2D.java:1417)
at processing.core.PGraphicsJava2D.strokeWeight(PGraphicsJava2D.java:1398)
at processing.core.PApplet.strokeWeight(PApplet.java:7757)
at org.gephi.desktop.preview.ProcessingPreview.renderEdge(ProcessingPreview.java:370)
at org.gephi.desktop.preview.ProcessingPreview.renderGraphUndirectedEdges(ProcessingPreview.java:252)
at org.gephi.desktop.preview.ProcessingPreview.renderGraphEdges(ProcessingPreview.java:225)
at org.gephi.desktop.preview.ProcessingPreview.renderGraph(ProcessingPreview.java:210)
at org.gephi.desktop.preview.ProcessingPreview.draw(ProcessingPreview.java:88)
at processing.core.PApplet.handleDraw(PApplet.java:1425)
at processing.core.PApplet.run(PApplet.java:1327)
[catch] at java.lang.Thread.run(Unknown Source)

[mbastian]

Are your edge weight negative?

And could you tell me if you tired with or without the "rescale weight" option in Preview?

Thanks

[ajegga]

As far as I know there are negative values for the edge weights. And the "rescale weight" option is unchecked. I tried with checked in too but getting the same error. I tried it several other networks too (created using the 0.7 alpha version) and they all throw the same error. If I use the alpha version (another computer) instead, everything works fine.

Thanks
Anil

[ajegga]

You are right. Seems like it is related to the negative weights for the edges. I changed them all to 1 and that seems to have done the trick Everything now works perfect!

Thanks
Anil

[aplume]

I just installed 0.7 beta and when trying to open existing .gexf files that opened fine in alpha, they come in with loads of errors and the edges are not imported.
Can I roll back to an alpha release? I can't find anywhere to download this on the site.
Any help much appreciated!
P.S. My networks have negative edge weights.

[mbastian]

Can you please post here a sample of your GEXF file? Negative weights are normally fully supported and shouldn't generate any errors.

[aplume]

Thanks! For example:

Code: Select all

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.1draft" version="1.1">
<meta lastmodifieddate="2009-03-20">
<creator>Gexf.net</creator>
<description>First test of manually encoded data</description>
</meta>
<graph mode="static" defaultedgetype="directed">
<nodes>
<node id="Algeria" label="Algeria"/>
<node id="Angola" label="Angola"/>
<node id="Benin" label="Benin"/>
<node id="Botswana" label="Botswana"/>
<node id="Burkina Faso" label="Burkina Faso"/>
<node id="Burundi" label="Burundi"/>
<node id="Cameroon" label="Cameroon"/>
<node id="Central African Republic" label="Central African Republic"/>
<node id="Chad" label="Chad"/>
<node id="Congo" label="Congo"/>
<node id="Congo, the Democratic Republic of the" label="Congo, the Democratic Republic of the"/>
<node id="Côte d'Ivoire" label="Côte d'Ivoire"/>
<node id="Djibouti" label="Djibouti"/>
<node id="Egypt" label="Egypt"/>
<node id="Equatorial Guinea" label="Equatorial Guinea"/>
<node id="Eritrea" label="Eritrea"/>
<node id="Ethiopia" label="Ethiopia"/>
<node id="Gabon" label="Gabon"/>
<node id="Gambia" label="Gambia"/>
<node id="Ghana" label="Ghana"/>
<node id="Guinea" label="Guinea"/>
<node id="Guinea-Bissau" label="Guinea-Bissau"/>
<node id="Kenya" label="Kenya"/>
<node id="Lesotho" label="Lesotho"/>
<node id="Libya" label="Libya"/>
<node id="Madagascar" label="Madagascar"/>
<node id="Malawi" label="Malawi"/>
<node id="Mali" label="Mali"/>
<node id="Mauritania" label="Mauritania"/>
<node id="Mauritius" label="Mauritius"/>
<node id="Morocco" label="Morocco"/>
<node id="Mozambique" label="Mozambique"/>
<node id="Namibia" label="Namibia"/>
<node id="Niger" label="Niger"/>
<node id="Nigeria" label="Nigeria"/>
<node id="Reunion" label="Reunion"/>
<node id="Rwanda" label="Rwanda"/>
<node id="Senegal" label="Senegal"/>
<node id="Seychelles" label="Seychelles"/>
<node id="Sierra Leone" label="Sierra Leone"/>
<node id="South Africa" label="South Africa"/>
<node id="Sudan" label="Sudan"/>
<node id="Swaziland" label="Swaziland"/>
<node id="Tanzania" label="Tanzania"/>
<node id="Togo" label="Togo"/>
<node id="Tunisia" label="Tunisia"/>
<node id="Uganda" label="Uganda"/>
<node id="Zambia" label="Zambia"/>
<node id="Zimbabwe" label="Zimbabwe"/>
</nodes>
<edges>
<edge id="0" source="Algeria" target="Algeria" weight="1"/>
<edge id="0" source="Algeria" target="Morocco" weight="0.01094159"/>
<edge id="0" source="Algeria" target="Tunisia" weight="0.01063338"/>
<edge id="0" source="Algeria" target="Egypt" weight="0.005701957"/>
<edge id="0" source="Angola" target="Angola" weight="1"/>
<edge id="0" source="Benin" target="Benin" weight="1"/>
<edge id="0" source="Benin" target="Cameroon" weight="0.06139154"/>
<edge id="0" source="Benin" target="Nigeria" weight="0.06002729"/>
<edge id="0" source="Benin" target="Burkina Faso" weight="0.053206"/>
<edge id="0" source="Benin" target="Ghana" weight="0.04638472"/>
<edge id="0" source="Benin" target="South Africa" weight="0.04092769"/>
<edge id="0" source="Benin" target="Senegal" weight="0.03956344"/>
<edge id="0" source="Benin" target="Togo" weight="0.03956344"/>
<edge id="0" source="Benin" target="Côte d'Ivoire" weight="0.03410641"/>
<edge id="0" source="Botswana" target="Botswana" weight="1"/>
<edge id="0" source="Botswana" target="South Africa" weight="0.128031"/>
<edge id="0" source="Botswana" target="Nigeria" weight="0.03588749"/>
<edge id="0" source="Botswana" target="Cameroon" weight="0.0271581"/>
<edge id="0" source="Burkina Faso" target="Burkina Faso" weight="1"/>
<edge id="0" source="Burkina Faso" target="Senegal" weight="0.06843718"/>
<edge id="0" source="Burkina Faso" target="Côte d'Ivoire" weight="0.05107252"/>
<edge id="0" source="Burkina Faso" target="Mali" weight="0.04085802"/>
<edge id="0" source="Burkina Faso" target="Benin" weight="0.03983657"/>
<edge id="0" source="Burkina Faso" target="Cameroon" weight="0.03881512"/>
<edge id="0" source="Burkina Faso" target="Togo" weight="0.03881512"/>
<edge id="0" source="Burkina Faso" target="Kenya" weight="0.03370786"/>
<edge id="0" source="Burkina Faso" target="Ghana" weight="0.02962206"/>
<edge id="0" source="Burkina Faso" target="Niger" weight="0.02553626"/>
<edge id="0" source="Burundi" target="Burundi" weight="1"/>
<edge id="0" source="Cameroon" target="Cameroon" weight="1"/>
<edge id="0" source="Cameroon" target="Nigeria" weight="0.03397651"/>
<edge id="0" source="Cameroon" target="South Africa" weight="0.03187919"/>
<edge id="0" source="Cameroon" target="Senegal" weight="0.01971477"/>
<edge id="0" source="Cameroon" target="Benin" weight="0.01887584"/>
<edge id="0" source="Cameroon" target="Kenya" weight="0.01719799"/>
<edge id="0" source="Cameroon" target="Congo" weight="0.01635906"/>
<edge id="0" source="Cameroon" target="Burkina Faso" weight="0.0159396"/>
<edge id="0" source="Cameroon" target="Gabon" weight="0.01510067"/>
<edge id="0" source="Cameroon" target="Côte d'Ivoire" weight="0.01384228"/>
<edge id="0" source="Cameroon" target="Botswana" weight="0.01174497"/>
<edge id="0" source="Cameroon" target="Ghana" weight="0.01090604"/>
<edge id="0" source="Cameroon" target="Uganda" weight="0.01048658"/>
<edge id="0" source="Central African Republic" target="Central African Republic" weight="1"/>
<edge id="0" source="Chad" target="Chad" weight="1"/>
<edge id="0" source="Congo" target="Congo" weight="1"/>
<edge id="0" source="Congo" target="Cameroon" weight="0.06543624"/>
<edge id="0" source="Congo" target="Kenya" weight="0.04194631"/>
<edge id="0" source="Congo, the Democratic Republic of the" target="Congo, the Democratic Republic of the" weight="1"/>
<edge id="0" source="Côte d'Ivoire" target="Côte d'Ivoire" weight="1"/>
<edge id="0" source="Côte d'Ivoire" target="Burkina Faso" weight="0.05197505"/>
<edge id="0" source="Côte d'Ivoire" target="Cameroon" weight="0.03430353"/>
<edge id="0" source="Côte d'Ivoire" target="Senegal" weight="0.02702703"/>
<edge id="0" source="Côte d'Ivoire" target="Benin" weight="0.02598753"/>
<edge id="0" source="Djibouti" target="Djibouti" weight="1"/>
<edge id="0" source="Egypt" target="Egypt" weight="1"/>
<edge id="0" source="Egypt" target="South Africa" weight="0.003153535"/>
<edge id="0" source="Egypt" target="Libya" weight="0.002212181"/>
<edge id="0" source="Egypt" target="Tunisia" weight="0.001882707"/>
<edge id="0" source="Egypt" target="Algeria" weight="0.001741504"/>
<edge id="0" source="Egypt" target="Morocco" weight="0.001270827"/>
<edge id="0" source="Egypt" target="Sudan" weight="0.001176692"/>
<edge id="0" source="Equatorial Guinea" target="Equatorial Guinea" weight="1"/>
<edge id="0" source="Eritrea" target="Eritrea" weight="1"/>
<edge id="0" source="Ethiopia" target="Ethiopia" weight="1"/>
<edge id="0" source="Ethiopia" target="South Africa" weight="0.06198347"/>
<edge id="0" source="Ethiopia" target="Kenya" weight="0.0348944"/>
<edge id="0" source="Ethiopia" target="Tanzania" weight="0.0137741"/>
<edge id="0" source="Ethiopia" target="Uganda" weight="0.01285583"/>
<edge id="0" source="Ethiopia" target="Ghana" weight="0.01193756"/>
<edge id="0" source="Gabon" target="Gabon" weight="1"/>
<edge id="0" source="Gabon" target="Cameroon" weight="0.08200455"/>
<edge id="0" source="Gabon" target="South Africa" weight="0.06150342"/>
<edge id="0" source="Gambia" target="Gambia" weight="1"/>
<edge id="0" source="Ghana" target="Ghana" weight="1"/>
<edge id="0" source="Ghana" target="Nigeria" weight="0.03544883"/>
<edge id="0" source="Ghana" target="South Africa" weight="0.03259005"/>
<edge id="0" source="Ghana" target="Kenya" weight="0.0268725"/>
<edge id="0" source="Ghana" target="Benin" weight="0.01943968"/>
<edge id="0" source="Ghana" target="Burkina Faso" weight="0.0165809"/>
<edge id="0" source="Ghana" target="Tanzania" weight="0.01600915"/>
<edge id="0" source="Ghana" target="Cameroon" weight="0.01486564"/>
<edge id="0" source="Ghana" target="Ethiopia" weight="0.01486564"/>
<edge id="0" source="Guinea" target="Guinea" weight="1"/>
<edge id="0" source="Guinea-Bissau" target="Guinea-Bissau" weight="1"/>
<edge id="0" source="Kenya" target="Kenya" weight="1"/>
<edge id="0" source="Kenya" target="South Africa" weight="0.05370733"/>
<edge id="0" source="Kenya" target="Uganda" weight="0.0400087"/>
<edge id="0" source="Kenya" target="Tanzania" weight="0.0332681"/>
<edge id="0" source="Kenya" target="Ethiopia" weight="0.01652533"/>
<edge id="0" source="Kenya" target="Nigeria" weight="0.01456838"/>
<edge id="0" source="Kenya" target="Zimbabwe" weight="0.01348119"/>
<edge id="0" source="Kenya" target="Ghana" weight="0.01021961"/>
<edge id="0" source="Kenya" target="Cameroon" weight="0.008914982"/>
<edge id="0" source="Kenya" target="Sudan" weight="0.007827789"/>
<edge id="0" source="Kenya" target="Malawi" weight="0.007392912"/>
<edge id="0" source="Kenya" target="Zambia" weight="0.007392912"/>
<edge id="0" source="Kenya" target="Burkina Faso" weight="0.007175473"/>
<edge id="0" source="Kenya" target="Senegal" weight="0.006958034"/>
<edge id="0" source="Kenya" target="Mali" weight="0.005870841"/>
<edge id="0" source="Kenya" target="Congo" weight="0.005435965"/>
<edge id="0" source="Lesotho" target="Lesotho" weight="1"/>
<edge id="0" source="Lesotho" target="South Africa" weight="0.4175824"/>
<edge id="0" source="Libya" target="Libya" weight="1"/>
<edge id="0" source="Libya" target="Egypt" weight="0.08529945"/>
<edge id="0" source="Madagascar" target="Madagascar" weight="1"/>
<edge id="0" source="Madagascar" target="South Africa" weight="0.04654443"/>
<edge id="0" source="Madagascar" target="Senegal" weight="0.03808181"/>
<edge id="0" source="Malawi" target="Malawi" weight="1"/>
<edge id="0" source="Malawi" target="South Africa" weight="0.1063373"/>
<edge id="0" source="Malawi" target="Zambia" weight="0.0622986"/>
<edge id="0" source="Malawi" target="Tanzania" weight="0.04726101"/>
<edge id="0" source="Malawi" target="Zimbabwe" weight="0.04189044"/>
<edge id="0" source="Malawi" target="Kenya" weight="0.03651987"/>
<edge id="0" source="Malawi" target="Uganda" weight="0.03007519"/>
<edge id="0" source="Mali" target="Mali" weight="1"/>
<edge id="0" source="Mali" target="Burkina Faso" weight="0.078125"/>
<edge id="0" source="Mali" target="Senegal" weight="0.06640625"/>
<edge id="0" source="Mali" target="Kenya" weight="0.05273438"/>
<edge id="0" source="Mali" target="Niger" weight="0.05273438"/>
<edge id="0" source="Mauritania" target="Mauritania" weight="1"/>
<edge id="0" source="Mauritania" target="Tunisia" weight="0.2403846"/>
<edge id="0" source="Mauritius" target="Mauritius" weight="1"/>
<edge id="0" source="Morocco" target="Morocco" weight="1"/>
<edge id="0" source="Morocco" target="Tunisia" weight="0.01504683"/>
<edge id="0" source="Morocco" target="Algeria" weight="0.01090127"/>
<edge id="0" source="Morocco" target="Egypt" weight="0.004145555"/>
<edge id="0" source="Mozambique" target="Mozambique" weight="1"/>
<edge id="0" source="Mozambique" target="South Africa" weight="0.1492891"/>
<edge id="0" source="Namibia" target="Namibia" weight="1"/>
<edge id="0" source="Namibia" target="South Africa" weight="0.4474273"/>
<edge id="0" source="Niger" target="Niger" weight="1"/>
<edge id="0" source="Niger" target="Senegal" weight="0.1151079"/>
<edge id="0" source="Niger" target="Mali" weight="0.0971223"/>
<edge id="0" source="Niger" target="Burkina Faso" weight="0.08992806"/>
<edge id="0" source="Nigeria" target="Nigeria" weight="1"/>
<edge id="0" source="Nigeria" target="South Africa" weight="0.02719496"/>
<edge id="0" source="Nigeria" target="Cameroon" weight="0.007294012"/>
<edge id="0" source="Nigeria" target="Kenya" weight="0.006033318"/>
<edge id="0" source="Nigeria" target="Ghana" weight="0.005583071"/>
<edge id="0" source="Nigeria" target="Benin" weight="0.003962179"/>
<edge id="0" source="Nigeria" target="Botswana" weight="0.003331833"/>
<edge id="0" source="Nigeria" target="Tanzania" weight="0.003241783"/>
<edge id="0" source="Nigeria" target="Uganda" weight="0.003151733"/>
<edge id="0" source="Reunion" target="Reunion" weight="1"/>
<edge id="0" source="Rwanda" target="Rwanda" weight="1"/>
<edge id="0" source="Senegal" target="Senegal" weight="1"/>
<edge id="0" source="Senegal" target="Burkina Faso" weight="0.0505279"/>
<edge id="0" source="Senegal" target="Cameroon" weight="0.03544495"/>
<edge id="0" source="Senegal" target="Mali" weight="0.02564103"/>
<edge id="0" source="Senegal" target="Kenya" weight="0.02413273"/>
<edge id="0" source="Senegal" target="Niger" weight="0.02413273"/>
<edge id="0" source="Senegal" target="Benin" weight="0.02187029"/>
<edge id="0" source="Senegal" target="Madagascar" weight="0.02036199"/>
<edge id="0" source="Senegal" target="South Africa" weight="0.02036199"/>
<edge id="0" source="Senegal" target="Côte d'Ivoire" weight="0.01960784"/>
<edge id="0" source="Seychelles" target="Seychelles" weight="1"/>
<edge id="0" source="Sierra Leone" target="Sierra Leone" weight="1"/>
<edge id="0" source="South Africa" target="South Africa" weight="1"/>
<edge id="0" source="South Africa" target="Nigeria" weight="0.009639015"/>
<edge id="0" source="South Africa" target="Kenya" weight="0.007883566"/>
<edge id="0" source="South Africa" target="Zimbabwe" weight="0.007787814"/>
<edge id="0" source="South Africa" target="Namibia" weight="0.006383454"/>
<edge id="0" source="South Africa" target="Uganda" weight="0.004500335"/>
<edge id="0" source="South Africa" target="Ethiopia" weight="0.004308831"/>
<edge id="0" source="South Africa" target="Botswana" weight="0.00421308"/>
<edge id="0" source="South Africa" target="Tanzania" weight="0.003925824"/>
<edge id="0" source="South Africa" target="Malawi" weight="0.00315981"/>
<edge id="0" source="South Africa" target="Cameroon" weight="0.002425713"/>
<edge id="0" source="South Africa" target="Zambia" weight="0.002329961"/>
<edge id="0" source="South Africa" target="Egypt" weight="0.002138457"/>
<edge id="0" source="South Africa" target="Mozambique" weight="0.002010788"/>
<edge id="0" source="South Africa" target="Ghana" weight="0.001819284"/>
<edge id="0" source="South Africa" target="Lesotho" weight="0.001212856"/>
<edge id="0" source="South Africa" target="Madagascar" weight="0.00105327"/>
<edge id="0" source="South Africa" target="Swaziland" weight="0.0009894354"/>
<edge id="0" source="South Africa" target="Benin" weight="0.0009575181"/>
<edge id="0" source="South Africa" target="Sudan" weight="0.0008936836"/>
<edge id="0" source="South Africa" target="Gabon" weight="0.0008617663"/>
<edge id="0" source="South Africa" target="Senegal" weight="0.0008617663"/>
<edge id="0" source="Sudan" target="Sudan" weight="1"/>
<edge id="0" source="Sudan" target="Kenya" weight="0.03821656"/>
<edge id="0" source="Sudan" target="South Africa" weight="0.02972399"/>
<edge id="0" source="Sudan" target="Egypt" weight="0.02653928"/>
<edge id="0" source="Swaziland" target="Swaziland" weight="1"/>
<edge id="0" source="Swaziland" target="South Africa" weight="0.2246377"/>
<edge id="0" source="Tanzania" target="Tanzania" weight="1"/>
<edge id="0" source="Tanzania" target="Kenya" weight="0.06423174"/>
<edge id="0" source="Tanzania" target="South Africa" weight="0.05163728"/>
<edge id="0" source="Tanzania" target="Uganda" weight="0.04156171"/>
<edge id="0" source="Tanzania" target="Malawi" weight="0.01847187"/>
<edge id="0" source="Tanzania" target="Nigeria" weight="0.01511335"/>
<edge id="0" source="Tanzania" target="Ethiopia" weight="0.01259446"/>
<edge id="0" source="Tanzania" target="Zimbabwe" weight="0.01217464"/>
<edge id="0" source="Tanzania" target="Ghana" weight="0.01175483"/>
<edge id="0" source="Tanzania" target="Zambia" weight="0.01049538"/>
<edge id="0" source="Togo" target="Togo" weight="1"/>
<edge id="0" source="Togo" target="Burkina Faso" weight="0.1589958"/>
<edge id="0" source="Togo" target="Benin" weight="0.1213389"/>
<edge id="0" source="Tunisia" target="Tunisia" weight="1"/>
<edge id="0" source="Tunisia" target="Morocco" weight="0.009858163"/>
<edge id="0" source="Tunisia" target="Algeria" weight="0.006940952"/>
<edge id="0" source="Tunisia" target="Egypt" weight="0.00402374"/>
<edge id="0" source="Tunisia" target="Mauritania" weight="0.002514838"/>
<edge id="0" source="Uganda" target="Uganda" weight="1"/>
<edge id="0" source="Uganda" target="Kenya" weight="0.08927705"/>
<edge id="0" source="Uganda" target="South Africa" weight="0.06841339"/>
<edge id="0" source="Uganda" target="Tanzania" weight="0.04803494"/>
<edge id="0" source="Uganda" target="Zimbabwe" weight="0.02183406"/>
<edge id="0" source="Uganda" target="Nigeria" weight="0.01698205"/>
<edge id="0" source="Uganda" target="Ethiopia" weight="0.01358564"/>
<edge id="0" source="Uganda" target="Malawi" weight="0.01358564"/>
<edge id="0" source="Uganda" target="Cameroon" weight="0.01213003"/>
<edge id="0" source="Zambia" target="Zambia" weight="1"/>
<edge id="0" source="Zambia" target="South Africa" weight="0.1028169"/>
<edge id="0" source="Zambia" target="Malawi" weight="0.08169014"/>
<edge id="0" source="Zambia" target="Zimbabwe" weight="0.05352113"/>
<edge id="0" source="Zambia" target="Kenya" weight="0.04788733"/>
<edge id="0" source="Zambia" target="Tanzania" weight="0.03521127"/>
<edge id="0" source="Zimbabwe" target="Zimbabwe" weight="1"/>
<edge id="0" source="Zimbabwe" target="South Africa" weight="0.194113"/>
<edge id="0" source="Zimbabwe" target="Kenya" weight="0.04932379"/>
<edge id="0" source="Zimbabwe" target="Uganda" weight="0.03579952"/>
<edge id="0" source="Zimbabwe" target="Malawi" weight="0.03102625"/>
<edge id="0" source="Zimbabwe" target="Zambia" weight="0.03023071"/>
<edge id="0" source="Zimbabwe" target="Tanzania" weight="0.0230708"/>
</edges>
</graph>
</gexf>

Much appreciated for any help you can offer!

[mbastian]

Your edges have all the same id, this is not correct.

Simply remove all

Code: Select all

id="0"

in your file. The source and target is enough for edges.

[aplume]

That did the job - thank you so much!
Andrew