Stardag Tinkerpop Gremlin-server setup fails

bart....@gmail.com

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Jun 23, 2016, 5:45:11 AM6/23/16

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Hi All,

I am trying to implemente the gremlin-server for stardog graph traversal: http://docs.stardog.com/#_stardog_gremlin_server

Unfortunately I stumbled upon an error I can't seem to fix. When I start the gremlin-server I get:

[WARN] GraphManager - Graph [graph] configured at [conf/stardoggraph-imi1.properties] could not be instantiated and will not be available in Gremlin Server.  GraphFactory message: GraphFactory could not find [org.apache.tinkerpop.gremlin.stardog.structure.StardogGraph] - Ensure that the jar is in the classpath
java.lang.RuntimeException: GraphFactory could not find [org.apache.tinkerpop.gremlin.stardog.structure.StardogGraph] - Ensure that the jar is in the classpath
        at org.apache.tinkerpop.gremlin.structure.util.GraphFactory.open(GraphFactory.java:63)
        at org.apache.tinkerpop.gremlin.structure.util.GraphFactory.open(GraphFactory.java:104)
        at org.apache.tinkerpop.gremlin.server.GraphManager.lambda$new$28(GraphManager.java:50)
        at java.util.LinkedHashMap$LinkedEntrySet.forEach(Unknown Source)
        at org.apache.tinkerpop.gremlin.server.GraphManager.<init>(GraphManager.java:48)
        at org.apache.tinkerpop.gremlin.server.util.ServerGremlinExecutor.<init>(ServerGremlinExecutor.java:94)
        at org.apache.tinkerpop.gremlin.server.GremlinServer.<init>(GremlinServer.java:89)
        at org.apache.tinkerpop.gremlin.server.GremlinServer.main(GremlinServer.java:301)

I checked and I think all the jars are in the ext/stardog-gremlin/plugin folder.

Any help regarding the issue would be very appriciated!

Thx.

Zachary Whitley

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Jun 23, 2016, 6:31:29 AM6/23/16

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I checked and I think all the jars are in the ext/stardog-gremlin/plugin folderAny help regarding the issue would be very appriciated!

Thx--

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What version of Stardog? Is ext/stardog-gremlin/plugin in the gremlin-server folder? What version of tinkerpop? SD 4.1.1 requires 3.0.2-incubating. (Check carefully because the latest TP release happens to be 3.2.0). Can the user read everything in ext? Did you check the plugins folder to make sure all the jars are there?

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bart....@gmail.com

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Jun 23, 2016, 7:09:28 AM6/23/16

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The stardog version is 4.1.1 apache-gremlin-server version is 3.0.2-incubating.

Jars in the ext/stardog-gremlin/plugin folder are visible in the attached screenshot.

What do you mean with "can the user read everything in ext"? I start the server as root and all the jars are owned by root.

Do you know where the StardagGraph class should normally be located? I tried searching the stardog-gremlin-4.1.1.jar but I could only find com.complexible.stardog.gremlin.structure.StardogGraph

This is not the one mentioned in the manual and it also doesn't work. But if I set the path to com.complexible.... I get a different error. Which indicates that gremlin does find the jars I copied.

Op donderdag 23 juni 2016 12:31:29 UTC+2 schreef Zachary Whitley:

bart....@gmail.com

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Jun 23, 2016, 7:10:25 AM6/23/16

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Sorry forgot the screenshot...

Op donderdag 23 juni 2016 13:09:28 UTC+2 schreef bart....@gmail.com:

Capture.PNG

Zachary Whitley

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Jun 23, 2016, 7:19:26 AM6/23/16

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Can you send your conf/gremlin-server.yaml file?

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<Capture.PNG>

bart....@gmail.com

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Jun 23, 2016, 7:25:10 AM6/23/16

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Also attahced is my stardoggraph-graphname.properties which configures my stardog named graph.

Op donderdag 23 juni 2016 13:19:26 UTC+2 schreef Zachary Whitley:

gremlin-server.yaml

stardoggraph-imi1.properties

Zachary Whitley

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Jun 23, 2016, 9:27:20 AM6/23/16

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It looks like there might be a problem with your stardoggraph-imi1.properties

You don't appear to have connection, user, password, or named_graph set. I would have assumed that you changed it because you didn't want to share your password but I'm not sure why you'd change named_graph or connection so I'm wondering what you have these values actually set to.

You also appear to have the stardog properties prefixed with gremlin.*

gremlin.graph=org.apache.tinkerpop.gremlin.stardog.structure.StardogGraph
gremlin.stardog.connection=URL
gremlin.stardog.user=USER
gremlin.stardog.password=PASSWORD
gremlin.stardog.named_graph=GRAPH_NAME
gremlin.stardog.reasoning_enabled=false

should be

gremlin.graph=org.apache.tinkerpop.gremlin.stardog.structure.StardogGraph
stardog.connection=snarl://localhost:5820/mygraph
stardog.user=admin
stardog.password=admin
stardog.named_graph=tag:stardog:api:graph:default
stardog.reasoning_enabled=false

Pavel Klinov

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Jun 24, 2016, 7:20:56 AM6/24/16

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Bart,

You're correct that the graph class name in the documentation is wrong; the right configuration line is gremlin.graph=com.complexible.stardog.gremlin.structure.StardogGraph. We'll fix the docs.

What error do you get if you change it to the above? It might be due to the issues in your property file which Zach identified.

I've just repeated the steps in the manual and the Gremlin server started as expected:

[INFO] GraphManager - Graph [graph] was successfully configured via [conf/stardog-graph.properties].

Best,

Pavel

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bart....@gmail.com

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Jun 27, 2016, 3:38:44 AM6/27/16

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Hi,

With both changes (the StardogGraph class and the gremlin.* removed it works now.

Thanks!

Op vrijdag 24 juni 2016 13:20:56 UTC+2 schreef Pavel Klinov:

bart....@gmail.com

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Jun 27, 2016, 5:45:22 AM6/27/16

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I have just one more question:

If I now want to create a restful server, I would run ./bin/gremlin-server.sh ./conf/gremlin-server-rest-modern.yaml but this gives me an error:

[ERROR] GremlinServer - Gremlin Server Error

groovy.lang.MissingMethodException: No signature of method: static org.apache.tinkerpop.gremlin.tinkergraph.structure.TinkerFactory.generateClassic() is applicable for argument types: (com.complexible.stardog.gremlin.structure.StardogGraph) values: [stardoggraph[http://ekol.jnj.com/IMI1]]

Possible solutions: generateClassic(org.apache.tinkerpop.gremlin.tinkergraph.structure.TinkerGraph), createClassic()

at groovy.lang.MetaClassImpl.invokeStaticMissingMethod(MetaClassImpl.java:1495)

at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1481)

at org.codehaus.groovy.runtime.callsite.StaticMetaClassSite.call(StaticMetaClassSite.java:50)

at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:110)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:122)

at Script1$_run_closure1.doCall(Script1.groovy:28)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

at java.lang.reflect.Method.invoke(Unknown Source)

at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)

at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)

at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:292)

at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016)

at groovy.lang.Closure.call(Closure.java:423)

at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:50)

at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:103)

at com.sun.proxy.$Proxy10.onStartUp(Unknown Source)

at org.apache.tinkerpop.gremlin.server.GremlinServer.lambda$start$2(GremlinServer.java:136)

at java.util.ArrayList.forEach(Unknown Source)

at org.apache.tinkerpop.gremlin.server.GremlinServer.start(GremlinServer.java:133)

at org.apache.tinkerpop.gremlin.server.GremlinServer.main(GremlinServer.java:302)

[ERROR] GremlinServer - Gremlin Server was unable to start and will now begin shutdown: No signature of method: static org.apache.tinkerpop.gremlin.tinkergraph.structure.TinkerFactory.generateClassic() is applicable for argument types: (com.complexible.stardog.gremlin.structure.StardogGraph) values: [stardoggraph[http://ekol.jnj.com/IMI1]]

Possible solutions: generateClassic(org.apache.tinkerpop.gremlin.tinkergraph.structure.TinkerGraph), createClassic()

Any idea as to why this happens?

Kind regards,

Bart Praats

Op donderdag 23 juni 2016 11:45:11 UTC+2 schreef bart....@gmail.com:

Pavel Klinov

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Jun 27, 2016, 6:48:25 AM6/27/16

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I suspect the problem here is the clash between the Stardog TinkerPop plugin configuration and the TinkerGraph plugin which both bind the gramlin.graph variable (but to different class names). Note that the create-modern.groovy script, which is specified in conf/gremlin-server-rest-modern.yaml, explicitly calls the TinkerGraph factory.

Best,

Pavel

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bart....@gmail.com

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Jun 27, 2016, 7:08:22 AM6/27/16

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I just disabled the - tinkerpop.tinkergraph plugin but I still get an exception (a different one now).

But maybe I should tell you what I want to achieve first. I want to run the GremlinServer on a Stardog instance on my server, in order to be able to connect with a Gremlin console.

The console I want to use is the one used on http://gremlinbin.com/site/index

I would like a similar UI and I found this library: https://github.com/PommeVerte/gremlin-console-js

But first I have to get the GrmlinServer working. I'm not sure if I need a rest server or a websocket for this, and I still need to figure out how to get the web UI working.

So back to the error:

[ERROR] GremlinServer - Gremlin Server Error

groovy.lang.MissingPropertyException: No such property: TinkerFactory for class: Script1

at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:51)

at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:49)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:304)

at Script1$_run_closure1.doCall(Script1.groovy:28)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

at java.lang.reflect.Method.invoke(Unknown Source)

at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)

at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)

at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:292)

at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016)

at groovy.lang.Closure.call(Closure.java:423)

at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:50)

at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:103)

at com.sun.proxy.$Proxy10.onStartUp(Unknown Source)

at org.apache.tinkerpop.gremlin.server.GremlinServer.lambda$start$2(GremlinServer.java:136)

at java.util.ArrayList.forEach(Unknown Source)

at org.apache.tinkerpop.gremlin.server.GremlinServer.start(GremlinServer.java:133)

at org.apache.tinkerpop.gremlin.server.GremlinServer.main(GremlinServer.java:302)

[ERROR] GremlinServer - Gremlin Server was unable to start and will now begin shutdown: No such property: TinkerFactory for class: Script1

Thank you for all your help!

Op donderdag 23 juni 2016 11:45:11 UTC+2 schreef bart....@gmail.com:

Hi All,

Pavel Klinov

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Jun 27, 2016, 7:55:07 AM6/27/16

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Let me be a bit more precise: you got Gremlin Server working with Stardog. What doesn't work is loading a graph (the Modern example graph) in a particular TinkerGraph-specific way. As far as I can see at the moment this example is just not meant to work with arbitrary TinkerPop plugins.

First, you can't disable the TinkerGraph plugin and still use TinkerFactory in generate-modern.groovy. TinkerFactory is a part of TinkerGraph.

Second, even if you keep the TinkerGraph plugin enabled but don't bind gremlin.graph to TinkerGraph (i.e. remove the graph: conf/tinkergraph-empty.properties line), the script will still fail because TinkerFactory.generateClassic(..) method expects a TinkerGraph and not the generic TP Graph interface, which StardogGraph implements (see [1]).

Frankly, I don't really know why it's done like that you should just load your graph data in a generic way, then it should work with Stardog too.

Cheers,

Pavel

[1] https://github.com/apache/tinkerpop/blob/master/tinkergraph-gremlin/src/main/java/org/apache/tinkerpop/gremlin/tinkergraph/structure/TinkerFactory.java

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bart....@gmail.com

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Jun 28, 2016, 3:45:00 AM6/28/16

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Thank you for your response but I am still a little in the dark here...

What do you mean with loading the graph data in a generic way? Not use Tinkerpop?

The ultimate goal here is to be able to traverse the remote stardog graph with a user friendly UI. The first thing I stumbled upon was to use the tinkerpop gremlin server in combination with the web UI as shown on http://gremlinbin.com/site/index

Sorry for my limited knowledge about this topic, but I onky started working with stardog 2 week ago...

Op donderdag 23 juni 2016 11:45:11 UTC+2 schreef bart....@gmail.com:

Hi All,

Pavel Klinov

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Jun 28, 2016, 4:34:55 AM6/28/16

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On Tue, Jun 28, 2016 at 9:45 AM, <bart....@gmail.com> wrote:

Thank you for your response but I am still a little in the dark here...

What do you mean with loading the graph data in a generic way? Not use Tinkerpop?

I mean loading through the generic TinkerPop interfaces without referring to any particular implementations, like TinkerGraph.

Here're the steps:

1) create a copy of gremlin-rest-modern.yaml and get rid of the TinkerGraph plugin. It's of no use since we're going to use the Stardog plugin. The graphs and plugins sections should look like:

graphs: {

graph: conf/stardog-graph.properties

}

plugins:

- complexible.stardog

2) copy and edit generate-modern.groovy to get rid of TinkerFactory.generateClassic(graph). Again, we can't load property graph data into Stardog using some other TinkerPop plugin. Instead a generic way, as indicated in our docs [1], would be this:

graph.io(graphml()).readGraph('data/tinkerpop-modern.xml')

Now save the files, start the Stardog server, and then start Gremlin Server with gremlin-rest-modern.yaml (or whatever you renamed it to). You should see the following:

[INFO] Logger$info - Loading 'modern' graph data.

[INFO] AbstractChannelizer - Configured application/vnd.gremlin-v1.0+json with org.apache.tinkerpop.gremlin.driver.ser.GraphSONMessageSerializerGremlinV1d0

[INFO] AbstractChannelizer - Configured application/json with org.apache.tinkerpop.gremlin.driver.ser.GraphSONMessageSerializerV1d0

[INFO] GremlinServer$1 - Gremlin Server configured with worker thread pool of 1, gremlin pool of 8 and boss thread pool of 1.

[INFO] GremlinServer$1 - Channel started at port 8182.

Finally, to verify that the graph has been loaded successfully, you can post Gremlin queries to the Gremlin Server, which will ultimately be answered by Stardog:

> curl -X POST -d "{\"gremlin\":\"g.V().out().values('name')\", \"language\":\"gremlin-groovy\"}" http://localhost:8182

This should output something like:

{"requestId":"92c0cdbe-64fe-4e23-a71a-f178aeac9451","status":{"message":"","code":200,"attributes":{}},"result":{"data":["vadas","josh","lop","lop","lop","ripple"],"meta":{}}}

If this works, any UI which just posts Gremlin queries must work too.

The ultimate goal here is to be able to traverse the remote stardog graph with a user friendly UI. The first thing I stumbled upon was to use the tinkerpop gremlin server in combination with the web UI as shown on http://gremlinbin.com/site/index

Sorry for my limited knowledge about this topic, but I onky started working with stardog 2 week ago...

No worries, we'll improve our documentation on Gremlin Server to clarify this sort of things.

Cheers,

Pavel

[1] http://docs.stardog.com/#_example_2

Op donderdag 23 juni 2016 11:45:11 UTC+2 schreef bart....@gmail.com:

Hi All,

I am trying to implemente the gremlin-server for stardog graph traversal: http://docs.stardog.com/#_stardog_gremlin_server

Unfortunately I stumbled upon an error I can't seem to fix. When I start the gremlin-server I get:

[WARN] GraphManager - Graph [graph] configured at [conf/stardoggraph-imi1.properties] could not be instantiated and will not be available in Gremlin Server.  GraphFactory message: GraphFactory could not find [org.apache.tinkerpop.gremlin.stardog.structure.StardogGraph] - Ensure that the jar is in the classpath
java.lang.RuntimeException: GraphFactory could not find [org.apache.tinkerpop.gremlin.stardog.structure.StardogGraph] - Ensure that the jar is in the classpath
        at org.apache.tinkerpop.gremlin.structure.util.GraphFactory.open(GraphFactory.java:63)
        at org.apache.tinkerpop.gremlin.structure.util.GraphFactory.open(GraphFactory.java:104)
        at org.apache.tinkerpop.gremlin.server.GraphManager.lambda$new$28(GraphManager.java:50)
        at java.util.LinkedHashMap$LinkedEntrySet.forEach(Unknown Source)
        at org.apache.tinkerpop.gremlin.server.GraphManager.<init>(GraphManager.java:48)
        at org.apache.tinkerpop.gremlin.server.util.ServerGremlinExecutor.<init>(ServerGremlinExecutor.java:94)
        at org.apache.tinkerpop.gremlin.server.GremlinServer.<init>(GremlinServer.java:89)
        at org.apache.tinkerpop.gremlin.server.GremlinServer.main(GremlinServer.java:301)

I checked and I think all the jars are in the ext/stardog-gremlin/plugin folder.

Any help regarding the issue would be very appriciated!

Thx.

--

bart....@gmail.com

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Jun 28, 2016, 5:16:47 AM6/28/16

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Thank you! This is very clear.

Now I did what you said:

I start the server with the following command: ./bin/gremlin-server.sh ./conf/stardog-gremlin-rest-modern.yaml

My conf file is attached as well as my stardog-graph file and my .groovy script. I am trying all of this on a RedHat Linux server.

I get the following error now:

[INFO] Logger$info - Loading 'modern' graph data.

[ERROR] AbstractStardogTransaction - Error opening a Stardog connection

com.complexible.stardog.server.StardogConnectionException: Channel closed before response from server

at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:66)

at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:34)

at com.complexible.stardog.protocols.snarl.client.SNARLDriver.connect(SNARLDriver.java:130)

at com.complexible.stardog.api.DriverManager.getConnection(DriverManager.java:74)

at com.complexible.stardog.api.ConnectionConfiguration.connect(ConnectionConfiguration.java:126)

at com.complexible.stardog.gremlin.structure.tx.AbstractStardogTransaction.connection(AbstractStardogTransaction.java:73)

at com.complexible.stardog.gremlin.structure.tx.DefaultStardogTransaction.connection(DefaultStardogTransaction.java:22)

at com.complexible.stardog.gremlin.structure.tx.DefaultStardogTransaction.doOpen(DefaultStardogTransaction.java:35)

at org.apache.tinkerpop.gremlin.structure.util.AbstractTransaction.open(AbstractTransaction.java:87)

at org.apache.tinkerpop.gremlin.structure.Transaction$READ_WRITE_BEHAVIOR$1.accept(Transaction.java:209)

at org.apache.tinkerpop.gremlin.structure.Transaction$READ_WRITE_BEHAVIOR$1.accept(Transaction.java:206)

at org.apache.tinkerpop.gremlin.structure.util.AbstractTransaction.readWrite(AbstractTransaction.java:126)

at com.complexible.stardog.gremlin.structure.StardogGraph.addVertexWithProperties(StardogGraph.java:572)

at com.complexible.stardog.gremlin.structure.StardogGraph.addVertex(StardogGraph.java:558)

at org.apache.tinkerpop.gremlin.structure.io.graphml.GraphMLReader.findOrCreate(GraphMLReader.java:298)

at org.apache.tinkerpop.gremlin.structure.io.graphml.GraphMLReader.readGraph(GraphMLReader.java:166)

at org.apache.tinkerpop.gremlin.structure.io.graphml.GraphMLIo.readGraph(GraphMLIo.java:86)

at org.apache.tinkerpop.gremlin.structure.io.Io$readGraph.call(Unknown Source)

at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:110)

at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:122)

at Script1$_run_closure1.doCall(Script1.groovy:28)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

at java.lang.reflect.Method.invoke(Unknown Source)

at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)

at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)

at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:292)

at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016)

at groovy.lang.Closure.call(Closure.java:423)

at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:50)

at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:103)

at com.sun.proxy.$Proxy10.onStartUp(Unknown Source)

at org.apache.tinkerpop.gremlin.server.GremlinServer.lambda$start$2(GremlinServer.java:136)

at java.util.ArrayList.forEach(Unknown Source)

at org.apache.tinkerpop.gremlin.server.GremlinServer.start(GremlinServer.java:133)

at org.apache.tinkerpop.gremlin.server.GremlinServer.main(GremlinServer.java:302)

Caused by: java.net.ConnectException: Channel closed before response from server

at com.complexible.common.protocols.client.rpc.DefaultRPCClient.get(DefaultRPCClient.java:284)

at com.complexible.common.protocols.client.rpc.DefaultRPCClient.execute(DefaultRPCClient.java:254)

at com.complexible.stardog.protocols.snarl.client.AbstractSNARLClient.connect(AbstractSNARLClient.java:98)

at com.complexible.stardog.protocols.snarl.client.AbstractSNARLClient.connect(AbstractSNARLClient.java:60)

at com.complexible.stardog.protocols.snarl.client.SNARLDriver.connect(SNARLDriver.java:114)

... 35 more

[ERROR] GremlinServer - Gremlin Server Error

com.complexible.stardog.gremlin.structure.RuntimeStardogException: Error trying to begin Transaction

at com.complexible.stardog.gremlin.structure.tx.AbstractStardogTransaction.connection(AbstractStardogTransaction.java:81)