Gephi and subgraph visualizations

Suriya Narayani

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Jul 2, 2020, 8:17:14 PM7/2/20

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Hi,

I'm able to connect to Gephi from gremlin and visualize the whole graph. But how can we execute gremlin queries and view the resultant graph in gephi ? I created a subgraph but I don't see anything on gephi after submitting it ,

Example :

gremlin> subgraph = g.E().has('type','xc')

gremlin> :plugin use tinkerpop.gephi

==>tinkerpop.gephi activated

gremlin> :remote connect tinkerpop.gephi workspace1 <ip> <port>

==>Connection to Gephi - http://<ip>:<port>/workspace1 with stepDelay:1000, startRGBColor:[0.0, 1.0, 0.5], colorToFade:g, colorFadeRate:0.7, startSize:10.0,sizeDecrementRate:0.33

gremlin> :> subgraph

==>false

Thanks

Suriya

Stephen Mallette

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Jul 6, 2020, 7:04:55 AM7/6/20

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This:

subgraph = g.E().has('type','xc')

does not create a subgraph. That returns the list of edges that have the property "type" with a value of "xc". To be even more explicit, it actually constructs a Traversal object that gets that list and assigns it to "subgraph" and then the Gremlin Console evaluates "subgraph" sees it is a Traversal object and automatically iterates it for you.

Please see the subgraph() step for more information on how to actually get a subgraph:

https://tinkerpop.apache.org/docs/current/reference/#subgraph-step

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Suriya Narayani

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Jul 6, 2020, 8:56:10 PM7/6/20

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Stephen,

I followed the steps on the documentation to create subgraph,

gremlin> :remote connect tinkerpop.gephi workspace1 <ip> <port>

==>Connection to Gephi - http://<ip>:<port>/workspace1 with stepDelay:1000, startRGBColor:[0.0, 1.0, 0.5], colorToFade:g, colorFadeRate:0.7, startSize:10.0,sizeDecrementRate:0.33

gremlin> subgraph = g.E().hasLabel('xc').subgraph('subGraph').cap('subGraph').next()

20:44:58 WARN org.janusgraph.graphdb.transaction.StandardJanusGraphTx - Query requires iterating over all vertices [(~label = xc)]. For better performance, use indexes

==>tinkergraph[vertices:40 edges:20]

gremlin> :> subgraph

==>tinkergraph[vertices:40 edges:20]

==>false

But still I don't see the resultant subgraph on Gephi. Please let me know if I'm missing something.

On Monday, July 6, 2020 at 4:04:55 AM UTC-7, Stephen Mallette wrote:

This:

subgraph = g.E().has('type','xc')

does not create a subgraph. That returns the list of edges that have the property "type" with a value of "xc". To be even more explicit, it actually constructs a Traversal object that gets that list and assigns it to "subgraph" and then the Gremlin Console evaluates "subgraph" sees it is a Traversal object and automatically iterates it for you.

Please see the subgraph() step for more information on how to actually get a subgraph:

https://tinkerpop.apache.org/docs/current/reference/#subgraph-step

On Thu, Jul 2, 2020 at 8:17 PM Suriya Narayani <suriya.ja...@gmail.com> wrote:

Hi,

I'm able to connect to Gephi from gremlin and visualize the whole graph. But how can we execute gremlin queries and view the resultant graph in gephi ? I created a subgraph but I don't see anything on gephi after submitting it ,
Example :
gremlin> subgraph = g.E().has('type','xc')
gremlin> :plugin use tinkerpop.gephi
==>tinkerpop.gephi activated
gremlin> :remote connect tinkerpop.gephi workspace1 <ip> <port>
==>Connection to Gephi - http://<ip>:<port>/workspace1 with stepDelay:1000, startRGBColor:[0.0, 1.0, 0.5], colorToFade:g, colorFadeRate:0.7, startSize:10.0,sizeDecrementRate:0.33
gremlin> :> subgraph
==>false

Thanks
Suriya

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Stephen Mallette

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Jul 7, 2020, 7:02:40 AM7/7/20

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What version of Gephi and Streaming Plugin are you using? This feature was last validated for Gephi 0.9.1 and Graph Streaming plugin 1.0.3.

I've not personally tried this functionality in a long time so it's possible something has broken in the integration. Has anyone tried this more recently to success or tried newer versions (i.e. Gephi 0.9.2 has been out for a while now)?

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Message has been deleted

Suriya Narayani

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Jul 7, 2020, 7:35:57 PM7/7/20

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Stephen,

I'm using Gephi 0.9.2 and Graph Streaming Plugin 1.0.3.

I also noticed an exception in gephi log -messages.log while submitting the subgraph :

gremlin>subgraph=g.E().hasLabel('contains').subgraph('subgraph').cap('subgraph').next()

gremlin> :> subgraph

==>tinkergraph[vertices:3786 edges:3775]

INFO [null]: Last record repeated 2 more times.

WARNING [org.gephi.streaming.api.GraphUpdaterEventHandler]: Edge added event ignored for edge 2gpp1-zqg8-3ifp-238k8: Target node 3510296 not found

INFO [org.gephi.streaming.api.GraphUpdaterEventHandler]: Unknown type org.gephi.streaming.impl.json.parser.JSONArray

java.lang.IllegalArgumentException: Unknown type org.gephi.streaming.impl.json.parser.JSONArray

at org.gephi.graph.impl.TableImpl.checkSupportedTypes(TableImpl.java:181)

at org.gephi.graph.impl.TableImpl.addColumn(TableImpl.java:59)

at org.gephi.graph.impl.TableImpl.addColumn(TableImpl.java:43)

at org.gephi.streaming.api.GraphUpdaterEventHandler.addNodeAttribute(GraphUpdaterEventHandler.java:343)

at org.gephi.streaming.api.GraphUpdaterEventHandler.nodeAdded(GraphUpdaterEventHandler.java:292)

at org.gephi.streaming.api.GraphUpdaterEventHandler.doHandleGraphEvent(GraphUpdaterEventHandler.java:156)

[catch] at org.gephi.streaming.api.GraphUpdaterEventHandler.handleGraphEvent(GraphUpdaterEventHandler.java:134)

at org.gephi.streaming.api.CompositeGraphEventHandler.handleGraphEvent(CompositeGraphEventHandler.java:95)

at org.gephi.streaming.impl.json.JSONStreamReader.parse(JSONStreamReader.java:336)

at org.gephi.streaming.impl.json.JSONStreamReader.parse(JSONStreamReader.java:220)

at org.gephi.streaming.impl.json.JSONStreamReader.processStream(JSONStreamReader.java:134)

at org.gephi.streaming.server.impl.ServerOperationExecutor.executeUpdateGraph(ServerOperationExecutor.java:219)

at org.gephi.streaming.server.impl.ServerControllerImpl.handle(ServerControllerImpl.java:230)

at org.gephi.streaming.server.impl.jetty.StreamingServerImpl$ContextContainer.service(StreamingServerImpl.java:307)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)

at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)

at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)

at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)

at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)

at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)

at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)

at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)

at org.eclipse.jetty.server.Server.handle(Server.java:370)

at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)

at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982)

at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043)

at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)

at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)

at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)

at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)

at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)

at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)

at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)

at java.lang.Thread.run(Thread.java:748)

WARNING [org.gephi.streaming.api.GraphUpdaterEventHandler]: Edge added event ignored for edge 2fled-zdt4-3ifp-14h1k: Target node 1888328 not found