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PathwayCommons / chibe

Pathway visualization and analysis tool for Pathway Commons and other BioPAX data
Eclipse Public License 1.0
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reaction2gene.txt not found #68

Closed marieBvr closed 5 years ago

marieBvr commented 6 years ago

Hi,

I cloned chibe project from git repository. I followed the Setup Guide to compile. When I run the query / PathwayCommons (in BioPAX) / Find enriched Pathway I get the error :

java.io.FileNotFoundException: /home/mlefebvre/Documents/Lib/chibe/portal-cache/pathway2gene.txt (Aucun fichier ou dossier de ce type)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at java.io.FileReader.<init>(FileReader.java:72)
    at org.gvt.action.EnrichedPathwaysAction.getPathways(EnrichedPathwaysAction.java:146)
    at org.gvt.action.EnrichedPathwaysAction.run(EnrichedPathwaysAction.java:40)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
    at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
    at org.eclipse.jface.window.Window.open(Window.java:787)
    at org.gvt.ChisioMain.main(ChisioMain.java:199)
java.lang.NullPointerException
    at org.gvt.action.EnrichedPathwaysAction.run(EnrichedPathwaysAction.java:45)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
    at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
    at org.eclipse.jface.window.Window.open(Window.java:787)
    at org.gvt.ChisioMain.main(ChisioMain.java:199)
java.io.FileNotFoundException: /home/mlefebvre/Documents/Lib/chibe/portal-cache/reaction2gene.txt (Aucun fichier ou dossier de ce type)
(...)

Any idea how to solve this ?

Thanks Marie

ozgunbabur commented 6 years ago

Hi Marie, yes, those features are not up-to-date with the latest version of Pathway Commons. I am on it and will notify you when fixed.

On Mon, Oct 23, 2017 at 7:44 AM, marieBvr notifications@github.com wrote:

Hi,

I cloned chibe project from git repository. I followed the Setup Guide to compile. When I run the query / PathwayCommons (in BioPAX) / Find enriched Pathway I get the error :

java.io.FileNotFoundException: /home/mlefebvre/Documents/Lib/chibe/portal-cache/pathway2gene.txt (Aucun fichier ou dossier de ce type) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138) at java.io.FileReader.(FileReader.java:72) at org.gvt.action.EnrichedPathwaysAction.getPathways(EnrichedPathwaysAction.java:146) at org.gvt.action.EnrichedPathwaysAction.run(EnrichedPathwaysAction.java:40) at org.eclipse.jface.action.Action.runWithEvent(Action.java:996) at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538) at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488) at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400) at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source) at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source) at org.eclipse.jface.window.Window.runEventLoop(Window.java:809) at org.eclipse.jface.window.Window.open(Window.java:787) at org.gvt.ChisioMain.main(ChisioMain.java:199) java.lang.NullPointerException at org.gvt.action.EnrichedPathwaysAction.run(EnrichedPathwaysAction.java:45) at org.eclipse.jface.action.Action.runWithEvent(Action.java:996) at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538) at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488) at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400) at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source) at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source) at org.eclipse.jface.window.Window.runEventLoop(Window.java:809) at org.eclipse.jface.window.Window.open(Window.java:787) at org.gvt.ChisioMain.main(ChisioMain.java:199) java.io.FileNotFoundException: /home/mlefebvre/Documents/Lib/chibe/portal-cache/reaction2gene.txt (Aucun fichier ou dossier de ce type) (...)

Any idea how to solve this ?

Thanks Marie

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/chibe/issues/68, or mute the thread https://github.com/notifications/unsubscribe-auth/ABUCC1qfX47enLka7nGSuMoipMprrEZqks5svKY4gaJpZM4QC9on .

ozgunbabur commented 6 years ago

Marie, it should be fixed now. You need to update the project. But before testing it, you also need to find and remove the file "chibe-conf.txt". It will be recreated when ChiBE runs. It can either be in your project folder, or under ".chibe" folder under your home folder.

On Mon, Oct 23, 2017 at 10:28 AM, Özgün Babur ozgunbabur@gmail.com wrote:

Hi Marie, yes, those features are not up-to-date with the latest version of Pathway Commons. I am on it and will notify you when fixed.

On Mon, Oct 23, 2017 at 7:44 AM, marieBvr notifications@github.com wrote:

Hi,

I cloned chibe project from git repository. I followed the Setup Guide to compile. When I run the query / PathwayCommons (in BioPAX) / Find enriched Pathway I get the error :

java.io.FileNotFoundException: /home/mlefebvre/Documents/Lib/chibe/portal-cache/pathway2gene.txt (Aucun fichier ou dossier de ce type) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138) at java.io.FileReader.(FileReader.java:72) at org.gvt.action.EnrichedPathwaysAction.getPathways(EnrichedPathwaysAction.java:146) at org.gvt.action.EnrichedPathwaysAction.run(EnrichedPathwaysAction.java:40) at org.eclipse.jface.action.Action.runWithEvent(Action.java:996) at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538) at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488) at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400) at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source) at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source) at org.eclipse.jface.window.Window.runEventLoop(Window.java:809) at org.eclipse.jface.window.Window.open(Window.java:787) at org.gvt.ChisioMain.main(ChisioMain.java:199) java.lang.NullPointerException at org.gvt.action.EnrichedPathwaysAction.run(EnrichedPathwaysAction.java:45) at org.eclipse.jface.action.Action.runWithEvent(Action.java:996) at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538) at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488) at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400) at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source) at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source) at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source) at org.eclipse.jface.window.Window.runEventLoop(Window.java:809) at org.eclipse.jface.window.Window.open(Window.java:787) at org.gvt.ChisioMain.main(ChisioMain.java:199) java.io.FileNotFoundException: /home/mlefebvre/Documents/Lib/chibe/portal-cache/reaction2gene.txt (Aucun fichier ou dossier de ce type) (...)

Any idea how to solve this ?

Thanks Marie

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/chibe/issues/68, or mute the thread https://github.com/notifications/unsubscribe-auth/ABUCC1qfX47enLka7nGSuMoipMprrEZqks5svKY4gaJpZM4QC9on .

marieBvr commented 6 years ago

I followed your instructions and it worked ! Thanks