Re: [Neo4j] Gephi Neo4j plugin update
Hi, about the lazy loading, I just summarize some questions I see most important to solve until we start. 1.) So if I get it right, first after you choose starting node and set depth, this will be loaded, but just nodes with lower or equals depth from starting node? 2.) Others should be loaded dynamically after you click on any leaf including the same depth? 3.) Should the previous starting node stay as starting node, or should it be changed to the actively clicked one? 4.) Should there be an option to remove/unload loaded nodes+relationships? For example after clicking on existing non leaf node? Other technical questions: 1.) Neo4j 1.2 is still in development mode, right? I noticed performance improvements, integration of indexing and bug fixes. Is it really stable enough to include it into Gephi? 2.) From the changelog it seems like there are no API incompatible changes, is this true? 3.) I noticed that you switched to Lucene based on Java 5. I think it will be needed to change the version of Lucene library in Gephi too, right? 4.) Can you provide us any server with working remote Neo4j database in order to test the remote functionality? (During the development time I also noticed, that the exception handling during remote connection is not solved very well = Neo4j just throws instances of RuntimeException and not any more specified exception; this could be improved in version 1.2. what do you think?) thanks for responses... Martin 2010/11/27 Peter Neubauer peter.neuba...@neotechnology.com: Well done Martin and Mathieu! For the next step with lazy loading, let's talk about that, as there is a lot of interest around visualization of graphs over neo4j around. Some other interesting features that I could see (the first being the lazy loading): - lazy (live) loading of underlying data - programmatic invocation and saving of preferences, so Gephi can be used as a visualization module from other apps or from command line - different views, like Map, Charts (there are already tables of the current view, let's build on them) and maybe gauges etc. Great to see this evolving, I am sure it will improve Gephi to think about these, and we are happy to contribute with user feedback and input. Great work done by the Gephi team! Cheers, /peter neubauer GTalk: neubauer.peter Skype peter.neubauer Phone +46 704 106975 LinkedIn http://www.linkedin.com/in/neubauer Twitter http://twitter.com/peterneubauer http://www.neo4j.org - Your high performance graph database. http://www.thoughtmade.com - Scandinavia's coolest Bring-a-Thing party. On Sat, Nov 27, 2010 at 1:28 AM, Martin Skurla buja...@gmail.com wrote: Hi to all Neo4j guys, after longer time caused by starting school and starting work on my master thesis, Gephi team is happy to announce pre-release Neo4j plugin. With great help from Mathieu Bastian (Geophi development leader) we were able to fix some problems, make the NetBeans platform integration better and lower the memory consumption. The plugin now consist of 4 plugin in attachment. You can download Gephi 7 Beta and install all the attached plugins and give as response about what do you think about it. Peter mentioned some notes about lazy loading which seems like good idea and as soon as we specify the details the plugin can be improved. If you have any problems or further ideas, just contact me or Mathieu. Cheers, Martin Skurla ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
Re: [Neo4j] GSoC work result, Featuring Gephi Neo4j
) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [catch] at java.lang.Thread.run(Thread.java:619) On 8/14/2010 2:04 AM, Martin Skurla wrote: Hi Andreas, this is strange because yesterday I just download the source codes from Bazaar to be sure they work and they compile without problems. Do you use latest version of NetBeans? I mean NetBeans 6.9. The reason is because whole Gephi was ported to the 6.9 version and there are some changes in core modules and we changed appropriate dependencies too, so you have to have the newest version. If problems will remain even when you use 6.9 version, you can post the error message and we will solve it. Distribution other than from sources is not a very good idea as I am fixing last bugs these days, so every new branch version is more stable with less bugs. //Martin 2010/8/14 Andreas Guentherandreas.guent...@web.de: Martin, This is fantastic! I checked out the branch you point but when trying to build the build.xml file I am getting missing Netbeans dependency failures. Is there an easy way for me to use this cool extension without having to build it? Thanks, -Andreas On 8/11/2010 12:25 PM, Martin Skurla wrote: Hi all, My name is Martin Škurla and this summer I was working on GSoC project called Adding support for Neo4j in Gephi. I would like to introduce to all of you an article summarizing all implemented features including these under the hood, pictures of dialogs, common use cases and future plans. Very important part of the article is a Questionnaire which is a very valuable source of informations for further Gephi Neo4j cooperation. Thanks for any response. The article can be found here: http://gephi.org/2010/gsoc-2010-mid-term-adding-support-for-neo4j-in-gephi/ Thanks, Martin Škurla ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
Re: [Neo4j] GSoC work result, Featuring Gephi Neo4j
Hi Andreas, I just tried to download the database but you provide unvalid link, I cannot connect to it. Can you please provide valid link? Cheers, Martin 2010/8/14 Martin Skurla buja...@gmail.com: Hi Andreas, first problem is something with NetBeans and its Threads. In fact the Project API usage will be a little bit rewritten, because there are some minor problems and this maybe will fix this problem too. Second problems occurs during parsing and from the stack trace it seems like there is either new type in Neo4j or bug in my code, which is very strange because all possible Neo4j types were imported from testing database without problems. I will know more after debug. Anyway, thanks for response, I will try to solve them as soon as possible. Thanks, Martin 2010/8/14 Andreas Guenther andreas.guent...@web.de: Thanks for the reply. I actually ended up installing Netbeans and started it from within the IDE. When trying to perform a whole import of some Neo stores with all default values in the Gephi dialogs I am getting the following exception traces. Any ideas what I am doing wrong? BTW, I am able to open both stores with Neoclipse without any issues. [Test Import 1] Neo store used: svn.neo4j.org:\components\kernel\trunk\target\neodb Import type: whole import Exception: java.lang.IllegalStateException (See details below) [Test Import 2] Neo store used: Custom data from a Neo 1.0 store Import type: whole import Exception: java.lang.NullPointerException (See details below) -Andreas java.lang.IllegalStateException: Problem in some module which uses Window System: Window System API is required to be called from AWT thread only, see http://core.netbeans.org/proposals/threading/ at org.netbeans.core.windows.WindowManagerImpl.warnIfNotInEDT(WindowManagerImpl.java:1520) at org.netbeans.core.windows.WindowManagerImpl.findTopComponent(WindowManagerImpl.java:253) at org.gephi.desktop.preview.PreviewTopComponent.findInstance(PreviewTopComponent.java:282) at org.gephi.desktop.preview.PreviewUIController$1.disable(PreviewUIController.java:69) at org.gephi.project.impl.ProjectControllerImpl.fireWorkspaceEvent(ProjectControllerImpl.java:296) at org.gephi.project.impl.ProjectControllerImpl.closeCurrentProject(ProjectControllerImpl.java:116) at org.gephi.project.impl.ProjectControllerImpl.newProject(ProjectControllerImpl.java:77) at org.gephi.neo4j.impl.Neo4jImporterImpl.createNewProject(Neo4jImporterImpl.java:188) at org.gephi.neo4j.impl.Neo4jImporterImpl.importGraph(Neo4jImporterImpl.java:135) at org.gephi.neo4j.impl.Neo4jImporterImpl.doImport(Neo4jImporterImpl.java:123) at org.gephi.neo4j.impl.Neo4jImporterImpl.importDatabase(Neo4jImporterImpl.java:117) at org.gephi.neo4j.impl.Neo4jImporterImpl.importDatabase(Neo4jImporterImpl.java:61) at org.gephi.desktop.neo4j.Neo4jMenuAction$1$1.run(Neo4jMenuAction.java:100) at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:228) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [catch] at java.lang.Thread.run(Thread.java:619) java.lang.NullPointerException at org.gephi.data.attributes.AttributeFactoryImpl.newValue(AttributeFactoryImpl.java:45) at org.gephi.data.attributes.AttributeRowImpl.setValue(AttributeRowImpl.java:97) at org.gephi.data.attributes.AttributeRowImpl.setValue(AttributeRowImpl.java:80) at org.gephi.neo4j.impl.GraphModelConvertor.fillGephiEdgeDataWithNeoRelationshipData(GraphModelConvertor.java:139) at org.gephi.neo4j.impl.GraphModelConvertor.createGephiEdge(GraphModelConvertor.java:123) at org.gephi.neo4j.impl.Neo4jImporterImpl.processRelationship(Neo4jImporterImpl.java:183) at org.gephi.neo4j.impl.Neo4jImporterImpl.importRelationships(Neo4jImporterImpl.java:178) at org.gephi.neo4j.impl.Neo4jImporterImpl.importGraph(Neo4jImporterImpl.java:144) at org.gephi.neo4j.impl.Neo4jImporterImpl.doImport(Neo4jImporterImpl.java:123) at org.gephi.neo4j.impl.Neo4jImporterImpl.importDatabase(Neo4jImporterImpl.java:117) at org.gephi.neo4j.impl.Neo4jImporterImpl.importDatabase(Neo4jImporterImpl.java:61) at org.gephi.desktop.neo4j.Neo4jMenuAction$1$1.run(Neo4jMenuAction.java:100
Re: [Neo4j] GSoC work result, Featuring Gephi Neo4j
OK, thanks //Martin 2010/8/14 Andreas Guenther andreas.guent...@web.de: The database will be created when you build the neo kernel module using Maven. I can send my local version to your personal email address if you want me to. -Andreas On 8/14/2010 1:09 PM, Martin Skurla wrote: Hi Andreas, I just tried to download the database but you provide unvalid link, I cannot connect to it. Can you please provide valid link? Cheers, Martin 2010/8/14 Martin Skurlabuja...@gmail.com: Hi Andreas, first problem is something with NetBeans and its Threads. In fact the Project API usage will be a little bit rewritten, because there are some minor problems and this maybe will fix this problem too. Second problems occurs during parsing and from the stack trace it seems like there is either new type in Neo4j or bug in my code, which is very strange because all possible Neo4j types were imported from testing database without problems. I will know more after debug. Anyway, thanks for response, I will try to solve them as soon as possible. Thanks, Martin 2010/8/14 Andreas Guentherandreas.guent...@web.de: Thanks for the reply. I actually ended up installing Netbeans and started it from within the IDE. When trying to perform a whole import of some Neo stores with all default values in the Gephi dialogs I am getting the following exception traces. Any ideas what I am doing wrong? BTW, I am able to open both stores with Neoclipse without any issues. [Test Import 1] Neo store used: svn.neo4j.org:\components\kernel\trunk\target\neodb Import type: whole import Exception: java.lang.IllegalStateException (See details below) [Test Import 2] Neo store used: Custom data from a Neo 1.0 store Import type: whole import Exception: java.lang.NullPointerException (See details below) -Andreas java.lang.IllegalStateException: Problem in some module which uses Window System: Window System API is required to be called from AWT thread only, see http://core.netbeans.org/proposals/threading/ at org.netbeans.core.windows.WindowManagerImpl.warnIfNotInEDT(WindowManagerImpl.java:1520) at org.netbeans.core.windows.WindowManagerImpl.findTopComponent(WindowManagerImpl.java:253) at org.gephi.desktop.preview.PreviewTopComponent.findInstance(PreviewTopComponent.java:282) at org.gephi.desktop.preview.PreviewUIController$1.disable(PreviewUIController.java:69) at org.gephi.project.impl.ProjectControllerImpl.fireWorkspaceEvent(ProjectControllerImpl.java:296) at org.gephi.project.impl.ProjectControllerImpl.closeCurrentProject(ProjectControllerImpl.java:116) at org.gephi.project.impl.ProjectControllerImpl.newProject(ProjectControllerImpl.java:77) at org.gephi.neo4j.impl.Neo4jImporterImpl.createNewProject(Neo4jImporterImpl.java:188) at org.gephi.neo4j.impl.Neo4jImporterImpl.importGraph(Neo4jImporterImpl.java:135) at org.gephi.neo4j.impl.Neo4jImporterImpl.doImport(Neo4jImporterImpl.java:123) at org.gephi.neo4j.impl.Neo4jImporterImpl.importDatabase(Neo4jImporterImpl.java:117) at org.gephi.neo4j.impl.Neo4jImporterImpl.importDatabase(Neo4jImporterImpl.java:61) at org.gephi.desktop.neo4j.Neo4jMenuAction$1$1.run(Neo4jMenuAction.java:100) at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:228) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [catch] at java.lang.Thread.run(Thread.java:619) java.lang.NullPointerException at org.gephi.data.attributes.AttributeFactoryImpl.newValue(AttributeFactoryImpl.java:45) at org.gephi.data.attributes.AttributeRowImpl.setValue(AttributeRowImpl.java:97) at org.gephi.data.attributes.AttributeRowImpl.setValue(AttributeRowImpl.java:80) at org.gephi.neo4j.impl.GraphModelConvertor.fillGephiEdgeDataWithNeoRelationshipData(GraphModelConvertor.java:139) at org.gephi.neo4j.impl.GraphModelConvertor.createGephiEdge(GraphModelConvertor.java:123) at org.gephi.neo4j.impl.Neo4jImporterImpl.processRelationship(Neo4jImporterImpl.java:183) at org.gephi.neo4j.impl.Neo4jImporterImpl.importRelationships(Neo4jImporterImpl.java:178) at org.gephi.neo4j.impl.Neo4jImporterImpl.importGraph(Neo4jImporterImpl.java:144) at org.gephi.neo4j.impl.Neo4jImporterImpl.doImport(Neo4jImporterImpl.java:123
Re: [Neo4j] GSoC work result, Featuring Gephi Neo4j
Hi Peter, maybe my mistake that I do not describe plans and current problems more. The code will be merged in version 0.8, currently 0.7 is developed. I think the 0.8 version will be released this year. Yes, I plan to contribute through the year too. Plans for GSoC are just fix some minor bugs, because this is the last week of GSoC. After the GSoC we have to add support for manipulation with nodes/relationships and properties directly from the Gephi and all the action will be delegated directly to the database. This is developed partially but there must be some changes under the hood and the GUI also do not support it, where in 0.8 another student work on Data Laboratory project which will extend currently node/edge/attribute manipulation in huge way. Also an important response is the questionnaire where we will focus on features that users think usable with priority. About the outstanding bugs, there are mainly smaller ones. Menu icons approve you to debug or export graph even if no graph is imported, one problem with color restoration and one guy from this mailing list send me his database where not all nodes/relationships are imported. These problems should be solved until end of week, I will see how huge changes will be needed and what will I catch until end of week, because on Sunday/Monday there is official dead line and no more code could be added as part of GSoC. Thanks, Martin Škurla 2010/8/12 Peter Neubauer peter.neuba...@neotechnology.com: Great work Martin, thanks for putting in the effort! Do you have a list of outstanding issues somewhere for others to contribute, and what is your plan forward regarding this project? Do you plan to continue to develop within the Gephi community? Also, will the code be merged into the main Gephi distribution? Cheers, /peter neubauer COO and Sales, Neo Technology GTalk: neubauer.peter Skype peter.neubauer Phone +46 704 106975 LinkedIn http://www.linkedin.com/in/neubauer Twitter http://twitter.com/peterneubauer http://www.neo4j.org - Your high performance graph database. http://www.thoughtmade.com - Scandinavia's coolest Bring-a-Thing party. 2010/8/11 Martin Skurla buja...@gmail.com: Hi all, My name is Martin Škurla and this summer I was working on GSoC project called Adding support for Neo4j in Gephi. I would like to introduce to all of you an article summarizing all implemented features including these under the hood, pictures of dialogs, common use cases and future plans. Very important part of the article is a Questionnaire which is a very valuable source of informations for further Gephi Neo4j cooperation. Thanks for any response. The article can be found here: http://gephi.org/2010/gsoc-2010-mid-term-adding-support-for-neo4j-in-gephi/ Thanks, Martin Škurla ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
[Neo4j] GSoC work result, Featuring Gephi Neo4j
Hi all, My name is Martin Škurla and this summer I was working on GSoC project called Adding support for Neo4j in Gephi. I would like to introduce to all of you an article summarizing all implemented features including these under the hood, pictures of dialogs, common use cases and future plans. Very important part of the article is a Questionnaire which is a very valuable source of informations for further Gephi Neo4j cooperation. Thanks for any response. The article can be found here: http://gephi.org/2010/gsoc-2010-mid-term-adding-support-for-neo4j-in-gephi/ Thanks, Martin Škurla ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
Re: [Neo4j] Best way to visualize?
Hi Jeff, I am the student working on Neo4j support in Gephi. You are right that there are many cases where it can cause problems especially not treated all situations and exception throwing, but this make no sense to patch it until we get all features we want, because I have done many rewrites so far and there will be maybe some other needed. If you have certain list of problems, Gephi community will be very happy if you can fill them as bugs in Gephi bug tracker or just describe them. I am especially interested in problems you find with Neo4j support in Gephi and which nodes are not added, maybe you just fill wrong filtering options or it could be also a bug. The fact is that the GSoC students work will be included in 0.8 version, so there is a lot of time where we can fix problems and introduce more features. Also a GSoC midterm article will be finished early including quiz/questionnaire where you can express your opinions on many features and also suggest new ones. There is also a project called Gephi toolkit where you can use the Gephi APIs in your Java applications without NetBeans GUI. Anyway, any response will be great. See you. Martin Skurla 2010/8/5 Jeff Klann jkl...@iupui.edu: Hi all, there have been snippets of discussion on this but not a full answer. I'm looking for the best way to quickly pull up part of my graph to visualize. Optimally I'd like to visualize programmatically - e.g., write a little code that would throw up some subset of nodes and edges on the screen in a nicely laid-out way. The tools I've found: * Neoclipse: Seems super-slow and I can't look up a node either in an index or by ID, which makes it basically unusable for me. The search function, whatever it does, just runs and runs. * iGraph: Looks like a cool tool, but I can't figure out a way to interact with it in the JVM. Couldn't even figure out how to install it in Jython. * Gephi: Way too buggy. Looks like it will be cool eventually. The alpha version with the half-finished Neo4J import didn't get all my edges properly, and even after that most things worked erratically. The output looks awesome, though. * Cytoscape: Actually the best thing I've come across, though a little heavyweight for just throwing some stuff on the screen and I haven't learned the API well enough to get it to interact directly with my Neo4J code. It wasn't too hard to export part of my graph to XGMML via the Cytoscape API and then import it into the Cytoscape GUI, though it does seem an unnecessary extra step. So can anyone help with: - Neoclipse, can I look up a node by index value or at least by ID? - iGraph, how to integrate with the JVM? - Cytoscape, how can I tighten my integration (rather than through XGMML)? - Is there a tool I've missed? Thanks! Jeff Klann ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
Re: [Neo4j] Best way to visualize?
And I forget, many features will be mentioned in the quiz about their usefulness, so we can remove some of them and add some new ones. That is also the reason why not all cases are treated, because it is possible I will remove some parts of code and because of new features, some refactorings or rewrites will be needed. 2010/8/5 Martin Skurla buja...@gmail.com: Hi Jeff, I am the student working on Neo4j support in Gephi. You are right that there are many cases where it can cause problems especially not treated all situations and exception throwing, but this make no sense to patch it until we get all features we want, because I have done many rewrites so far and there will be maybe some other needed. If you have certain list of problems, Gephi community will be very happy if you can fill them as bugs in Gephi bug tracker or just describe them. I am especially interested in problems you find with Neo4j support in Gephi and which nodes are not added, maybe you just fill wrong filtering options or it could be also a bug. The fact is that the GSoC students work will be included in 0.8 version, so there is a lot of time where we can fix problems and introduce more features. Also a GSoC midterm article will be finished early including quiz/questionnaire where you can express your opinions on many features and also suggest new ones. There is also a project called Gephi toolkit where you can use the Gephi APIs in your Java applications without NetBeans GUI. Anyway, any response will be great. See you. Martin Skurla 2010/8/5 Jeff Klann jkl...@iupui.edu: Hi all, there have been snippets of discussion on this but not a full answer. I'm looking for the best way to quickly pull up part of my graph to visualize. Optimally I'd like to visualize programmatically - e.g., write a little code that would throw up some subset of nodes and edges on the screen in a nicely laid-out way. The tools I've found: * Neoclipse: Seems super-slow and I can't look up a node either in an index or by ID, which makes it basically unusable for me. The search function, whatever it does, just runs and runs. * iGraph: Looks like a cool tool, but I can't figure out a way to interact with it in the JVM. Couldn't even figure out how to install it in Jython. * Gephi: Way too buggy. Looks like it will be cool eventually. The alpha version with the half-finished Neo4J import didn't get all my edges properly, and even after that most things worked erratically. The output looks awesome, though. * Cytoscape: Actually the best thing I've come across, though a little heavyweight for just throwing some stuff on the screen and I haven't learned the API well enough to get it to interact directly with my Neo4J code. It wasn't too hard to export part of my graph to XGMML via the Cytoscape API and then import it into the Cytoscape GUI, though it does seem an unnecessary extra step. So can anyone help with: - Neoclipse, can I look up a node by index value or at least by ID? - iGraph, how to integrate with the JVM? - Cytoscape, how can I tighten my integration (rather than through XGMML)? - Is there a tool I've missed? Thanks! Jeff Klann ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
Re: [Neo4j] Best way to visualize?
Hi Jeff, about the problem, it looks like very general case. Can you publish your database data that I can debug the code and find bug? About the importing speed, there are more places where it could be improved, but this seems strange. Second thing will be implemented in the next version of Gephi toolkit. You will be able to programatically import Neo4j database (local or remote) and make any manipulation as export to other formats, applying layouts and much much more. Export from any loaded graph including many graph formats will be available too. Most of the code is working right now, some refactorings and bug fixing is needed. //Martin Skurla 2010/8/5 Jeff Klann jkl...@iupui.edu: Thanks, yeah Gephi looks promising but I felt it's a bit too alpha for me at this point. I will try to give feedback on the general eccentricities I ran into in the Gephi board and try it again in awhile. In import into Neo4J, I did a traversal import where I asked for outgoing edges of type 'item' and either direction of type 'tmprel' from a node I call the 'order root'. The 'order root' has 7500 outgoing edges to vertices representing 'items' , and then those vertices have about 55k edges interconnecting them, currently of type 'tmprel'. The Gephi Neo4j plugin grabbed all the vertices correctly but only about 5000 edges. If I did depth 2, it was pretty fast but more of the edges were 'item' type. If I did depth 'end of graph' it took awhile and more of the edges were 'tmprel'. Come to think of it, maybe it somehow stops retrieving edges once it stops finding new nodes? Hope that helps your development efforts. One feature request which might be covered by the Gephi toolkit - it'd be nice to do a Neo4j import save to a gephi file without running the whole program (i.e. command-line or code), just because Gephi uses OpenGL which doesn't seem to work over remote X. So then I could download the Gephi files and analyze them on my computer at home. Thanks, Jeff Klann On Thu, Aug 5, 2010 at 3:28 PM, Martin Skurla buja...@gmail.com wrote: Hi Jeff, I am the student working on Neo4j support in Gephi. You are right that there are many cases where it can cause problems especially not treated all situations and exception throwing, but this make no sense to patch it until we get all features we want, because I have done many rewrites so far and there will be maybe some other needed. If you have certain list of problems, Gephi community will be very happy if you can fill them as bugs in Gephi bug tracker or just describe them. I am especially interested in problems you find with Neo4j support in Gephi and which nodes are not added, maybe you just fill wrong filtering options or it could be also a bug. The fact is that the GSoC students work will be included in 0.8 version, so there is a lot of time where we can fix problems and introduce more features. Also a GSoC midterm article will be finished early including quiz/questionnaire where you can express your opinions on many features and also suggest new ones. There is also a project called Gephi toolkit where you can use the Gephi APIs in your Java applications without NetBeans GUI. Anyway, any response will be great. See you. Martin Skurla 2010/8/5 Jeff Klann jkl...@iupui.edu: Hi all, there have been snippets of discussion on this but not a full answer. I'm looking for the best way to quickly pull up part of my graph to visualize. Optimally I'd like to visualize programmatically - e.g., write a little code that would throw up some subset of nodes and edges on the screen in a nicely laid-out way. The tools I've found: * Neoclipse: Seems super-slow and I can't look up a node either in an index or by ID, which makes it basically unusable for me. The search function, whatever it does, just runs and runs. * iGraph: Looks like a cool tool, but I can't figure out a way to interact with it in the JVM. Couldn't even figure out how to install it in Jython. * Gephi: Way too buggy. Looks like it will be cool eventually. The alpha version with the half-finished Neo4J import didn't get all my edges properly, and even after that most things worked erratically. The output looks awesome, though. * Cytoscape: Actually the best thing I've come across, though a little heavyweight for just throwing some stuff on the screen and I haven't learned the API well enough to get it to interact directly with my Neo4J code. It wasn't too hard to export part of my graph to XGMML via the Cytoscape API and then import it into the Cytoscape GUI, though it does seem an unnecessary extra step. So can anyone help with: - Neoclipse, can I look up a node by index value or at least by ID? - iGraph, how to integrate with the JVM? - Cytoscape, how can I tighten my integration (rather than through XGMML)? - Is there a tool I've missed? Thanks! Jeff Klann
Re: [Neo4j] feature request for the GUI
Hi to all, I am a GSoC (Google Summer of Code) student working on adding support for Neo4j in Gephi. I appreciate you to look at Gephi as a very nice visualization tool. This week I will also finish the article summarizing what have I done and what is needed to do. In fact Gephi has much more visualization abilities that Neoclipse. I will also write some quiz/questionnaire about some possible features which may be implemented but I am not sure if they will be useful for Neo4j users. So if you can reply to the article, or fill in the quiz/questionnaire it will be very helpful for me. In fact the project now supports importing Neo4j database and exporting, importing with many options how to filter the imput. All the traversal work is done in trunk version of Neo4j, so the new traversal is used. you can get it at bzr branch lp:~bujacik/gephi/support-for-neo4j any advice or request are welcome //Martin Skurla 2010/7/20 Anders Nawroth and...@neotechnology.com: Hi! Thanks for your input. I'm working on a new version of neoclipse and hope to commit my changes soon. Just waiting for my code base to get reasonably consistent :-) The biggest change is that neoclipse will handle threads in a correct manner, that is, there will only be exactly one transaction running meaning that different views should always be reading the same data. (which isn't the case in older versions - it's just hard to discover this bug!) - open and close buttons: add buttons to make eclipse close the database Already done. (in upcoming version) - save configuration: the configuration of which edge types to follow should be saved, preferably in the database directory, where I can find and adapt it Actually interesting idea. Maybe we should have a neoclipse directory in the db directory, where we can put configuration, icons etc. - reload button: first close,then open; so that if the database directory is deleted and replaced, the new database is opened instead of the old one Not sure it's a good idea to remove the files of a running db instance! I'd rather go for stop + start (open + close) actions to be used in such a case. When connecting to a running db instance in read-only mode I see the use for some kind of refresh action to get the latest data and throw away what's been cached by the GUI. - export function: save as image, SVG or dot file Would be nice, I think there's support for such (only bitmap formats) in the underlying graph viewer somehow. Maybe someone can dig into that. There's a dot export utility here: https://svn.neo4j.org/laboratory/components/neo-graphviz/ which could be integrated into neoclipse. Does anyone else have suggestions for the gui? Well, here's some: https://trac.neo4j.org/query?status=assignedstatus=newstatus=reopenedcomponent=neoclipse And neoclipse should start using neo4j kernel 1.1 as soon as it's released. PS: I would implement the suggestions myself, but I'm not very experienced with eclipse development I think most of the Eclispe stuff needed is in place, so it's just plain java coding :-) There's quite a lot of utilities in the code base to deal with icons, actions etc. /anders ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
Re: [Neo4j] feature request for the GUI
Peter, about editing support = this is true. I firstly focused on core abilities like importing and exporting including filtering abilities. The fact is that another student is working on Data Laboratory, so the place where it will be possible to change data. We are also thinking about setting values and this must be solved, but we have to recognize how Neo4j behaves, because the actual values are not stored in memory, but are delegating at demand so you just cannot set the value directly, because it is node/relationship id in fact. There is very simple delegating mechanism behind that. about performance = this is the thing which will be solved at the end. In fact last week I rewrite the importing and exporting, because results does not return unconnected nodes. I test it with graph about 3000 nodes and 8000 edges and it works quite performant. On the other side export after the rewrite is brutal slow, I will have to figure out why. Performance optimizations will be done at the end, because there will be maybe some features that will cause to rewrite some core parts as previous week. If you tried the filtering abilities too, this can also cause the performance problem, because previous week it was just doing the parsing for every node which is now cachced. about surf nodes = sorry I don't get the point. Surf nodes are all nodes except leafs? If you would like to do that, this is currently not possible, but can be simply added as option to API and GUI. Same with start node, currently there is no way how to express the fact we would like to include it or not. I just forget about the option. And this will be added as checkbox in gui and in API too. In the case of any other questions, advices, requests, just write... //Martin Skurla 2010/7/20 Peter Neubauer peter.neuba...@neotechnology.com: Martin, On Tue, Jul 20, 2010 at 1:06 PM, Martin Skurla I am a GSoC (Google Summer of Code) student working on adding support for Neo4j in Gephi. I appreciate you to look at Gephi as a very nice visualization tool. This week I will also finish the article summarizing what have I done and what is needed to do. In fact Gephi has much more visualization abilities that Neoclipse. I will also write some quiz/questionnaire about some possible features which may be implemented but I am not sure if they will be useful for Neo4j users. So if you can reply to the article, or fill in the quiz/questionnaire it will be very helpful for me. Great Martin. I tried out your branch last week - worked partly for a small graph. Good work! It seems there is some editing support still missing, but I will be happy to test and provide more if you can provide more background on how to use Neo4j and Gephi in a good way. In fact the project now supports importing Neo4j database and exporting, importing with many options how to filter the imput. All the traversal work is done in trunk version of Neo4j, so the new traversal is used. Great. Would be awesome if you could maybe provide a short video tutorial on useing Neo4j in Gephi, and post your weekly progress to this list? Also, hav you tried to open big graphs with Gephi? I recently tried to open the Neo4j db generated by the test of http://github.com/neo4j/neo4j-spatial (run mvn clean test), but things slowed down to a trickle. Not sure if what the limit is for Gephi, and how to open/surf nodes with a depth-1 environment in scope in Gephi ... Cheers, /peter ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user ___ Neo4j mailing list User@lists.neo4j.org https://lists.neo4j.org/mailman/listinfo/user
