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Unable to access neo4j 2.01 version db
I'm running Gephi 0.8.2-Beta together with the "Neo4j Graph Database support" plugin updated on March 3, 2014. I've used the BatchImporter to generate a neo4j-database but when I tried to open it from Gephi, I get an org.neo4j.graphdb.NotInTransactionException. The generated db opens up without any problems in neo4j and can be browsed from the web-admin.
I also tried to open the sample test database created by the 2.01 installer and get exactly the same exception.
Is this a known problem or have I missed something here?
Same problem here when I try a traversal import. If I try a full import I get an empty dialogbox.
Setup:
- Windows 8 - 64 bits
- Neo4j 2.0.1 Community (zip file)
- Gephi 0.8.2 beta (201210100934)
- Neo4j Graph db plugin 2.0.1
- Jvm Java(TM) SE Runtime Environment 1.7.0_40-b43
Some logs if it can help:
SEVERE [global]
org.neo4j.graphdb.NotInTransactionException
at org.neo4j.kernel.impl.persistence.PersistenceManager.getCurrentTransaction(PersistenceManager.java:284)
at org.neo4j.kernel.impl.core.ThreadToStatementContextBridge.assertInTransaction(ThreadToStatementContextBridge.java:79)
at org.neo4j.tooling.GlobalGraphOperations.assertInTransaction(GlobalGraphOperations.java:237)
at org.neo4j.tooling.GlobalGraphOperations.getAllRelationshipTypes(GlobalGraphOperations.java:124)
at org.neo4j.kernel.InternalAbstractGraphDatabase.getRelationshipTypes(InternalAbstractGraphDatabase.java:997)
at org.gephi.desktop.neo4j.ui.util.Neo4jUtils.relationshipTypeNames(Neo4jUtils.java:59)
at org.gephi.desktop.neo4j.ui.TraversalImportPanel.initComponents(TraversalImportPanel.java:191)
at org.gephi.desktop.neo4j.ui.TraversalImportPanel.
msg Caused: java.lang.IllegalAccessException: Class org.netbeans.modules.settings.convertors.XMLPropertiesConvertor can not access a member of class org.gephi.desktop.hierarchy.HierarchyTopComponent with modifiers "private" at sun.reflect.Reflection.ensureMemberAccess(Reflection.java:109) at java.lang.Class.newInstance(Class.java:368) at org.netbeans.modules.settings.convertors.XMLPropertiesConvertor.defaultInstanceCreate(XMLPropertiesConvertor.java:227) Caused: java.io.IOException: Cannot create instance of org.gephi.desktop.hierarchy.HierarchyTopComponent at org.netbeans.modules.settings.convertors.XMLPropertiesConvertor.defaultInstanceCreate(XMLPropertiesConvertor.java:229) at org.netbeans.modules.settings.convertors.XMLPropertiesConvertor.read(XMLPropertiesConvertor.java:98) at org.netbeans.modules.settings.InstanceProvider$InstanceCookieImpl.instanceCreate(InstanceProvider.java:310) [catch] at org.netbeans.core.windows.persistence.PersistenceManager.getTopComponentPersistentForID(PersistenceManager.java:571) at org.netbeans.core.windows.persistence.PersistenceManager.getTopComponentForID(PersistenceManager.java:681) at org.netbeans.core.windows.PersistenceHandler.getTopComponentForID(PersistenceHandler.java:489) at org.netbeans.core.windows.WindowManagerImpl.getTopComponentForID(WindowManagerImpl.java:933) at org.netbeans.core.windows.model.TopComponentSubModel.getTopComponent(TopComponentSubModel.java:378) at org.netbeans.core.windows.model.TopComponentSubModel.getTopComponents(TopComponentSubModel.java:90) at org.netbeans.core.windows.model.DefaultModeModel.getTopComponents(DefaultModeModel.java:356) at org.netbeans.core.windows.model.DefaultModel.getModeTopComponents(DefaultModel.java:944) at org.netbeans.core.windows.Central.getModeTopComponents(Central.java:1553) at org.netbeans.core.windows.ModeImpl.getTopComponents(ModeImpl.java:220) at org.netbeans.core.windows.model.DefaultModel.isModePermanent(DefaultModel.java:874) at org.netbeans.core.windows.Central.isModePermanent(Central.java:1532) at org.netbeans.core.windows.ModeImpl.isPermanent(ModeImpl.java:422) at org.netbeans.core.windows.PersistenceHandler.getConfigFromMode(PersistenceHandler.java:741) at org.netbeans.core.windows.PersistenceHandler.getConfig(PersistenceHandler.java:637) at org.netbeans.core.windows.PersistenceHandler.save(PersistenceHandler.java:322) at org.netbeans.core.windows.WindowSystemImpl.save(WindowSystemImpl.java:93) at org.netbeans.core.NbLifecycleManager$ExitActions.run(NbLifecycleManager.java:143) at org.netbeans.core.startup.ModuleSystem$2.run(ModuleSystem.java:317) at org.netbeans.ModuleManager.shutDown(ModuleManager.java:1939) at org.netbeans.core.startup.ModuleSystem.shutDown(ModuleSystem.java:322) at org.netbeans.core.NbLifecycleManager.doExit(NbLifecycleManager.java:179) at org.netbeans.core.NbLifecycleManager.access$000(NbLifecycleManager.java:75) at org.netbeans.core.NbLifecycleManager$ExitActions.run(NbLifecycleManager.java:135) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:703) at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) ALL [null]: org.netbeans.modules.settings.InstanceProvider@1c370f59[org.openide.loaders.InstanceDataObject@7f959392[MultiFileObject@55f8effc[Windows2Local-overview/Components/HierarchyTopComponent.settings]], MultiFileObject@2900a603[xml/lookups/org_gephi_desktop_hierarchy/Hierarchy.instance]]
same here...moreover in my case the db gets "corrupted" and I am not able to load it anymore with neo4j browser: Component 'org.neo4j.kernel.impl.transaction.XaDataSourceManager@47998b44' was successfully initialized, but failed to start. Please see attached cause exception.: Component 'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource@687e7a74' was successfully initialized, but failed to start. Please see attached cause exception.: 'neostore' has a store version number that we cannot upgrade from. Expected 'NeoStore v0.A.0' but file is version 'NeoStore v0.A.2'.
Same here, I can't even start my Neo4j database anymore! How do I fix this?
avr. 19, 2014 1:03:30 PM org.neo4j.server.logging.Logger log
Infos: Setting startup timeout to: 120000ms based on -1
avr. 19, 2014 1:03:31 PM org.neo4j.server.logging.Logger log
Grave:
org.neo4j.server.ServerStartupException: Starting Neo4j Server failed: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /usr/local/Cellar/neo4j/2.0.1/libexec/data/graph.db
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:218)
at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:87)
at org.neo4j.server.Bootstrapper.main(Bootstrapper.java:50)
Caused by: java.lang.RuntimeException: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /usr/local/Cellar/neo4j/2.0.1/libexec/data/graph.db
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:330)
at org.neo4j.kernel.EmbeddedGraphDatabase.
avr. 19, 2014 1:03:31 PM org.neo4j.server.logging.Logger log Grave: Failed to start Neo Server on port [7474]
I'm not sure if the corruption of the neo4j databases is fixed as well, at least the traversal import dialog pops up.
I am having the same problem, I commented here: https://forum.gephi.org/viewtopic.php?f=4&t=3495&p=10588#p10588
It seems this could be a problem of the early 2.0 Milestones.
https://groups.google.com/forum/#!topic/neo4j/PkHfgFlvfS0 maybe says this has been there up until M06. I'll try to update neo4j and seem if it helps.
I couldn't just change the libraries in the wrapper module. How could I easily update them to 2.1.2?
Currently, there are a number of open issues, some of them closely related:
- Eaten exceptions (might be caused by locked neo4jstore or neo4j version >2.1.0), (#44, fixed with pull request #45)
- NotInTransactionException for TraversalImport (#40, fixed with pull request)
- Missing support for current neo4j 2.1.2 (fixed with pull request #48)
- Finally, Node Labels (introduced with Neo4j2) are not yet supported, neither their import (#46, fixed with pull request #47), nor using them as import filter (I'm currently working on it)
Oh cool! Great, so you have been working to fix that, thanks!
So If I want to test that locally I would have to merge these 4 branches of yours?
- hbruch:neo4j-plugin-issue-44
- hbruch:neo4j-plugin-#40
- hbruch:neo4j-plugin-2.1.2
- hbruch:neo4j-plugin-issue-46
I sucessfully merged those branches and it seems to work. The only problems I have are:
- the node labels are somehow not normal fields - thus I can't use them for partitioning (which is obviously very useful) and they dont get saved
- saving to a gephi file seems to produce a broken file, exporting to graphml is fine
@LaurentMT I have encountered the same problem with you. Have you solved it?
I've also run into this issue. Has there been any progress or has anyone found a work around?
File -> Neo4j Database -> Full Import
Finder opens (on Mac OS X Yosemite)
Even though the filter in Finder is set to "All Files". I see no files even though there are files.
Confused, unable to import Neo4j database. It would be much easier if we could give connection parameters to the Neo4j database like localhost:7474 and then using the Neo4j REST API if Gephi could fetch the data.
same problem trying to import neo4j datbase into gephi, popup window with warning sign and no text on it.
indeed it would be better if it could read and update a database from a remote server. Might take more time but could be more useful for (turn-based) collaboration too
@birbilis: I specifically need the plugin to read from disk, because for some applications the sheer amount of data makes it necessary to avoid any bottlenecks (as a remote interface often is). Of course it would be neat if the option to access remote servers would be added, but the direct input should remain.
@mboeing3: Sigma.js library (on github) has code to import/export neo4j data via Cypher. Maybe could adapt implementation from there into the same or separate plugin.
BTW, with latest Neo4j and Gephi the import doesn't seem to work, shows that empty warning dialog
