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neo4j-graph-analytics / ml-models

Machine Learning Procedures and Functions for Neo4j
https://github.com/neo4j-graph-analytics/ml-models/releases/tag/1.0.0
Apache License 2.0
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DeepGL: Could not initialize class org.nd4j.linalg.factory.Nd4j #16

Open xaviermerino opened 5 years ago

xaviermerino commented 5 years ago

Hello! I am trying to run the example in: https://tbgraph.wordpress.com/2018/10/17/feature-extraction-on-a-peer-to-peer-network-with-deepgl-embedding-and-neo4j/

This example uses the Gnutella dataset.

At some point, the DeepGL algorithm is called:

CALL embedding.deepgl("Host","CONNECTION", { nodeFeatures: ['pagerank'], iterations: 2 })

But it returns the following error:

Neo.ClientError.Procedure.ProcedureCallFailed: Failed to invoke procedure embedding.deepgl: Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.nd4j.linalg.factory.Nd4j

I have tried putting the .jar inside the plugins folder, also, manually compiled the source and tried that. But something is not right.

@meltzerpete is there something that I am missing here?

Thanks for the help 👍

meltzerpete commented 5 years ago

@xaviermerino can you post the details about what versions of ml-models/neo4j you are using?

xaviermerino commented 5 years ago

@meltzerpete I am using Neo4j 3.5.2. And the ml-models version is 1.0.3 taken from https://github.com/neo4j-graph-analytics/ml-models/releases/tag/1.0.3

I am also running on Mac OS Mojave (10.14)

In the logs, the only warnings that I get are these:

log4j:WARN No appenders could be found for logger (org.apache.hadoop.metrics2.lib.MutableMetricsFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-7296183e-d7d0-44b4-b2a1-2b10f8f70328/installation-3.5.2/lib/slf4j-nop-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-7296183e-d7d0-44b4-b2a1-2b10f8f70328/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.helpers.NOPLoggerFactory]

After I import the Gnutella nodes and create all the relationships, I try to run DeepGL.

CALL embedding.deepgl("Host","CONNECTION", {
nodeFeatures: ['pagerank'],
iterations: 2
})

DeepGL says that you need Apache Commons Math. If I don't have commons-math3-3.6.1.jar in the plugins directory, then I get the following error:

Neo.ClientError.Procedure.ProcedureCallFailed: Failed to invoke procedure `embedding.deepgl`: Caused by: java.lang.UnsatisfiedLinkError: no openblas in java.library.path

(I don't know if this is related, but I do have openblas installed. I installed it via Homebrew and it is located in /usr/local/Cellar/openblas/0.3.7)

But if I do have commons-math3-3.6.1.jar in the plugins directory, then I get the following error:

Neo.ClientError.Procedure.ProcedureCallFailed: Failed to invoke procedure `embedding.deepgl`: Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.nd4j.linalg.factory.Nd4j

Do you have any idea of what could be going on? Seems to me like it might be a dependency issue. I just have no clue which dependency.

It is also worth noting that I had to disable the tests when compiling by source because otherwise it would fail.

Thank you so much for your time :)

BLuchterhand commented 5 years ago

Hey @xaviermerino and @meltzerpete it looks like I'm getting same issue. I'm getting the same errors word for word; I'm also on MacOS Mojave. Our environments look like they may be very similar; you didn't happen to find a solution to this issue yet, I assume? I'll keep doing my own troubleshooting and I'll keep you posted should I find anything. I'd greatly appreciate an update to this if you find anything!

meltzerpete commented 5 years ago

@xaviermerino @BLuchterhand I will check out the versions you have listed and take a look later today, but in the mean time do you have any other JARs in the plugins folder aside from the ml-models? The commons-math JAR should already beincluded in the ml-models JAR as far as I'm aware. The error could be the result of a dependency clash with another JAR also containing a different version.

xaviermerino commented 5 years ago

@meltzerpete The only other plugins in that directory are:

Xaviers-MBP-189:plugins xaviermerino$ ls
README.txt          
graphAlgorithms-3.5.9.0.jar
apoc-3.5.0.4.jar        
graphQL-3.5.0.4.jar
commons-math3-3.6.1.jar

Thanks for looking into it!

meltzerpete commented 5 years ago

I have tried the versions you have (although couldn't find graphAlgorithms-3.5.9.0 so used 3.5.4.0) and I can't reproduce the error. I don't have a mac though so running on ubuntu.

You should not require commons-math3 separately since it is included as a compile time dependency and should be contained within the ml-models JAR.

My first thoughts would be that you could try removing all other JARs leaving only the ml-models and graphAlgorithms ones and try that. Otherwise, looking at the 'pom.xml' it seems the dependency on graphAlgorithms is for version 3.4.7.0, so you could try using that JAR instead of the one you have, although that may not work with the database version you are using so you may also need to swap that to 3.4.11 which is also listed in the pom.

Beyond this I'm not really sure of what the problem could be. There may be some further information in the debug log (logs/debug.log) so if you could copy the output of that log from the time of database startup to the time of DeepGL: Could not initialize class org.nd4j.linalg.factory.Nd4j error and paste it here that might reveal something.

xaviermerino commented 5 years ago

@meltzerpete Here is the last bit of logs/debug.log. Most of those lines have the form of Failed to load: <insert_something> from .../neo4j-ml-models-1.0.3.jar

2019-10-09 15:23:31.487+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.metrics.MetricsServlet$TagsMetricsPair` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/util/ajax/JSON$Convertible
2019-10-09 15:23:31.522+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.fs.s3.MigrationTool$UnversionedStore` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/jets3t/service/S3ServiceException
2019-10-09 15:23:31.526+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.fs.s3.MigrationTool` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/jets3t/service/S3ServiceException
2019-10-09 15:23:31.527+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.fs.s3.Jets3tFileSystemStore` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/jets3t/service/S3ServiceException
2019-10-09 15:23:31.622+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.fs.s3native.Jets3tNativeFileSystemStore` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/jets3t/service/ServiceException
2019-10-09 15:23:31.630+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.fs.MD5MD5CRC32FileChecksum` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:32.032+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.ha.SshFenceByTcpPort` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/jcraft/jsch/Logger
2019-10-09 15:23:32.038+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.ha.SshFenceByTcpPort$LogAdapter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/jcraft/jsch/Logger
2019-10-09 15:23:32.049+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.http.HttpServer$1` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/security/SslSocketConnector
2019-10-09 15:23:32.049+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.http.AdminAuthorizedServlet` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/servlet/DefaultServlet
2019-10-09 15:23:32.050+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.http.HttpServer2$ListenerInfo` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/Connector
2019-10-09 15:23:32.052+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.http.HttpServer2` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/util/MultiException
2019-10-09 15:23:32.054+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.http.HttpServer` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/Connector
2019-10-09 15:23:32.058+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.http.HttpServer2$Builder` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/Connector
2019-10-09 15:23:32.061+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.http.HttpRequestLog` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/RequestLog
2019-10-09 15:23:32.145+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.record.compiler.ant.RccTask` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/tools/ant/Task
2019-10-09 15:23:32.569+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.logging.impl.AvalonLogger` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/avalon/framework/logger/Logger
2019-10-09 15:23:32.570+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.logging.impl.LogKitLogger` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/log/Logger
2019-10-09 15:23:32.695+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.log4j.net.JMSAppender` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/jms/JMSException
2019-10-09 15:23:32.696+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.log4j.net.JMSSink` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/jms/MessageListener
2019-10-09 15:23:32.696+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.log4j.net.SMTPAppender$1` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/mail/Authenticator
2019-10-09 15:23:32.698+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.log4j.net.SMTPAppender` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/mail/MessagingException
2019-10-09 15:23:32.709+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.log4j.or.jms.MessageRenderer` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/jms/JMSException
2019-10-09 15:23:32.861+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.configuration.tree.xpath.ConfigurationNodeIteratorAttribute` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/commons/jxpath/ri/model/NodeIterator
2019-10-09 15:23:32.862+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.configuration.tree.xpath.ConfigurationNodeIteratorBase` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/commons/jxpath/ri/model/NodeIterator
2019-10-09 15:23:32.863+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.configuration.tree.xpath.ConfigurationNodeIteratorChildren` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/commons/jxpath/ri/model/NodeIterator
2019-10-09 15:23:32.864+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.configuration.tree.xpath.ConfigurationNodePointer` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/commons/jxpath/ri/model/NodePointer
2019-10-09 15:23:32.864+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.configuration.tree.xpath.ConfigurationNodePointerFactory` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/commons/jxpath/ri/model/NodePointerFactory
2019-10-09 15:23:32.866+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.commons.configuration.tree.xpath.XPathExpressionEngine` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/commons/jxpath/ri/model/NodePointerFactory
2019-10-09 15:23:33.430+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.xerial.snappy.SnappyBundleActivator` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/osgi/framework/BundleActivator
2019-10-09 15:23:34.053+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.zookeeper.JLineZNodeCompletor` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: jline/Completor
2019-10-09 15:23:34.527+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.dfsclusterhealth_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.597+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.corrupt_005freplicas_005fxml_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.609+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.DfsServlet` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:34.649+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.NamenodeJspHelper$HealthJsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/servlet/jsp/JspWriter
2019-10-09 15:23:34.657+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.ClusterJspHelper$DecommissionStatus` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:34.686+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.NamenodeJspHelper` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/servlet/jsp/JspWriter
2019-10-09 15:23:34.696+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.NamenodeJspHelper$XMLCorruptBlockInfo` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:34.790+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.ClusterJspHelper` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:34.808+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.ClusterJspHelper$ClusterStatus` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:34.863+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.status_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.891+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.block_005finfo_005fxml_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.903+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.NamenodeJspHelper$XMLBlockInfo` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:34.907+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.corrupt_005ffiles_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.911+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.dfsnodelist_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.958+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.NameNodeHttpServer` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/servlet/Context
2019-10-09 15:23:34.969+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.dfshealth_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.970+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.nn_005fbrowsedfscontent_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:34.981+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.ListPathsServlet` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/znerd/xmlenc/XMLOutputter
2019-10-09 15:23:34.989+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.NamenodeJspHelper$NodeListJsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/servlet/jsp/JspWriter
2019-10-09 15:23:35.019+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.namenode.decommission_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:35.050+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.common.JspHelper` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/servlet/jsp/JspWriter
2019-10-09 15:23:35.059+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.journalservice.journalstatus_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:35.183+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.datanode.browseDirectory_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:35.185+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.datanode.DatanodeJspHelper` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/servlet/jsp/JspWriter
2019-10-09 15:23:35.193+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.datanode.tail_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:35.198+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.datanode.SecureDataNodeStarter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/commons/daemon/Daemon
2019-10-09 15:23:35.208+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.datanode.dataNodeHome_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:35.221+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.datanode.browseBlock_jsp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/jasper/runtime/JspSourceDependent
2019-10-09 15:23:35.265+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.hdfs.server.datanode.SecureDataNodeStarter$SecureResources` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/mortbay/jetty/Connector
2019-10-09 15:23:36.959+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.mapreduce.v2.app.webapp.AMWebApp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/servlet/ServletModule
2019-10-09 15:23:36.972+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.mapreduce.v2.app.webapp.JAXBContextResolver` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/sun/jersey/api/json/JSONJAXBContext
2019-10-09 15:23:36.995+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.mapreduce.v2.app.client.MRClientService` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/servlet/ServletModule
2019-10-09 15:23:37.432+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.sun.jersey.client.osgi.Activator` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/osgi/framework/BundleActivator
2019-10-09 15:23:38.646+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.YarnJacksonJaxbJsonProvider` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/codehaus/jackson/xc/JaxbAnnotationIntrospector
2019-10-09 15:23:38.647+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.WebApp` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/servlet/ServletModule
2019-10-09 15:23:38.649+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.View` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/Injector
2019-10-09 15:23:38.652+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.Dispatcher` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/servlet/ServletModule
2019-10-09 15:23:38.853+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.WebApps$Builder` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/servlet/ServletModule
2019-10-09 15:23:38.857+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.WebApps$Builder$2` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/AbstractModule
2019-10-09 15:23:38.862+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.WebApps$Builder$1` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/servlet/ServletModule
2019-10-09 15:23:38.864+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.webapp.Controller` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/google/inject/Injector
2019-10-09 15:23:38.905+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.apache.hadoop.yarn.util.timeline.TimelineUtils` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/codehaus/jackson/xc/JaxbAnnotationIntrospector
2019-10-09 15:23:39.001+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.sun.jersey.core.impl.provider.entity.MimeMultipartProvider` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: javax/mail/MessagingException
2019-10-09 15:23:39.032+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.sun.jersey.core.osgi.Activator` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/osgi/framework/BundleActivator
2019-10-09 15:23:39.043+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.sun.jersey.core.reflection.ReflectionHelper` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/osgi/framework/SynchronousBundleListener
2019-10-09 15:23:39.197+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.converters.reflection.CGLIBEnhancedConverter$ReverseEngineeredCallbackFilter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: net/sf/cglib/proxy/CallbackFilter
2019-10-09 15:23:39.198+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.converters.reflection.CGLIBEnhancedConverter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: net/sf/cglib/proxy/CallbackFilter
2019-10-09 15:23:39.253+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.BEAStaxDriver` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/bea/xml/stream/XMLOutputFactoryBase
2019-10-09 15:23:39.272+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.Dom4JDriver` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/dom4j/DocumentException
2019-10-09 15:23:39.273+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.WstxDriver` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: com/ctc/wstx/stax/WstxOutputFactory
2019-10-09 15:23:39.275+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.Dom4JWriter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/dom4j/Branch
2019-10-09 15:23:39.276+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.XomWriter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: nu/xom/Node
2019-10-09 15:23:39.281+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.XomDriver` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: nu/xom/ParsingException
2019-10-09 15:23:39.284+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.JDomWriter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/jdom/Content
2019-10-09 15:23:39.289+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.Dom4JXmlWriter` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/dom4j/Element
2019-10-09 15:23:39.293+0000 WARN [o.n.k.i.p.Procedures] Failed to load `com.thoughtworks.xstream.io.xml.JDomDriver` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/jdom/JDOMException
2019-10-09 15:23:41.512+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.bytedeco.javacpp.tools.BuildMojo` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/apache/maven/plugin/AbstractMojo
2019-10-09 15:23:43.811+0000 WARN [o.n.k.i.p.Procedures] Failed to load `org.nd4j.shade.jackson.dataformat.xml.jaxb.XmlJaxbAnnotationIntrospector` from plugin jar `/Users/xaviermerino/Library/Application%20Support/Neo4j%20Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/plugins/neo4j-ml-models-1.0.3.jar`: org/nd4j/shade/jackson/module/jaxb/JaxbAnnotationIntrospector
2019-10-09 15:23:45.386+0000 INFO [o.n.m.MetricsExtension] Sending metrics to CSV file at /Users/xaviermerino/Library/Application Support/Neo4j Desktop/Application/neo4jDatabases/database-5f75cbd8-243c-4a08-967c-2be17afae530/installation-3.5.2/metrics
2019-10-09 15:23:45.575+0000 INFO [o.n.b.BoltServer] Bolt server loaded
2019-10-09 15:23:45.711+0000 INFO [o.n.b.BoltServer] Bolt enabled on 127.0.0.1:7687.
2019-10-09 15:23:47.477+0000 INFO [o.n.i.d.DiagnosticsManager] --- SERVER STARTED START ---
2019-10-09 15:23:47.638+0000 INFO [o.n.m.s.s.ServerMetrics] Server thread metrics have been registered successfully
2019-10-09 15:23:48.681+0000 INFO [o.n.i.d.DiagnosticsManager] --- SERVER STARTED END ---

Also, this might be of interest. Before, I was disabling the tests to be able to get the source packaged. I decided to pay some attention to the tests and the DeepGL tests fail. Take a look:

Running embedding.DeepGLIntegrationTest
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.neo4j.io.pagecache.impl.SingleFilePageSwapper (file:/Users/xaviermerino/.m2/repository/org/neo4j/neo4j-io/3.4.11/neo4j-io-3.4.11.jar) to field sun.nio.ch.FileChannelImpl.positionLock
WARNING: Please consider reporting this to the maintainers of org.neo4j.io.pagecache.impl.SingleFilePageSwapper
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
result.next() = {features=[rbf_in_neighbourhood( sum_both_neighbourhood( OUT_DEGREE)), sum_out_neighbourhood( sum_out_neighbourhood( hadamard_out_neighbourhood( IN_DEGREE))), rbf_in_neighbourhood( sum_out_neighbourhood( BOTH_DEGREE)), rbf_in_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE))), sum_both_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE))), rbf_in_neighbourhood( sum_out_neighbourhood( OUT_DEGREE)), l1Norm_both_neighbourhood( rbf_both_neighbourhood( OUT_DEGREE)), rbf_in_neighbourhood( hadamard_out_neighbourhood( diffuse( rbf_out_neighbourhood( IN_DEGREE)))), sum_both_neighbourhood( rbf_in_neighbourhood( OUT_DEGREE)), l1Norm_both_neighbourhood( diffuse( sum_in_neighbourhood( OUT_DEGREE))), diffuse( mean_out_neighbourhood( rbf_both_neighbourhood( OUT_DEGREE))), rbf_both_neighbourhood( sum_out_neighbourhood( IN_DEGREE)), sum_both_neighbourhood( OUT_DEGREE), rbf_in_neighbourhood( hadamard_both_neighbourhood( rbf_both_neighbourhood( IN_DEGREE))), rbf_in_neighbourhood( sum_both_neighbourhood( BOTH_DEGREE)), l1Norm_both_neighbourhood( sum_out_neighbourhood( IN_DEGREE)), sum_in_neighbourhood( sum_out_neighbourhood( BOTH_DEGREE)), rbf_in_neighbourhood( rbf_both_neighbourhood( sum_out_neighbourhood( IN_DEGREE))), l1Norm_both_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE))), rbf_in_neighbourhood( rbf_both_neighbourhood( sum_both_neighbourhood( OUT_DEGREE))), diffuse( sum_in_neighbourhood( OUT_DEGREE)), rbf_both_neighbourhood( IN_DEGREE), sum_in_neighbourhood( BOTH_DEGREE), rbf_both_neighbourhood( OUT_DEGREE), l1Norm_both_neighbourhood( OUT_DEGREE), rbf_in_neighbourhood( OUT_DEGREE), diffuse( rbf_out_neighbourhood( IN_DEGREE)), rbf_both_neighbourhood( diffuse( rbf_out_neighbourhood( IN_DEGREE))), diffuse( sum_out_neighbourhood( IN_DEGREE)), mean_both_neighbourhood( sum_out_neighbourhood( sum_out_neighbourhood( BOTH_DEGREE))), BOTH_DEGREE, rbf_in_neighbourhood( diffuse( rbf_out_neighbourhood( IN_DEGREE))), sum_both_neighbourhood( BOTH_DEGREE), l1Norm_both_neighbourhood( rbf_both_neighbourhood( sum_out_neighbourhood( IN_DEGREE))), l1Norm_both_neighbourhood( rbf_both_neighbourhood( sum_both_neighbourhood( OUT_DEGREE))), l1Norm_both_neighbourhood( rbf_in_neighbourhood( OUT_DEGREE)), l1Norm_in_neighbourhood( sum_in_neighbourhood( BOTH_DEGREE)), diffuse( sum_out_neighbourhood( BOTH_DEGREE)), sum_out_neighbourhood( l1Norm_both_neighbourhood( OUT_DEGREE)), sum_out_neighbourhood( IN_DEGREE), sum_out_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE))), hadamard_out_neighbourhood( IN_DEGREE), sum_in_neighbourhood( rbf_out_neighbourhood( BOTH_DEGREE)), sum_out_neighbourhood( sum_out_neighbourhood( BOTH_DEGREE)), sum_out_neighbourhood( hadamard_out_neighbourhood( IN_DEGREE)), mean_both_neighbourhood( rbf_in_neighbourhood( OUT_DEGREE)), rbf_in_neighbourhood( sum_out_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE)))), sum_out_neighbourhood( BOTH_DEGREE), sum_out_neighbourhood( sum_out_neighbourhood( sum_out_neighbourhood( IN_DEGREE))), sum_out_neighbourhood( sum_out_neighbourhood( OUT_DEGREE)), sum_out_neighbourhood( sum_out_neighbourhood( IN_DEGREE)), rbf_out_neighbourhood( BOTH_DEGREE), l1Norm_both_neighbourhood( l1Norm_both_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE)))), rbf_out_neighbourhood( rbf_in_neighbourhood( OUT_DEGREE)), sum_out_neighbourhood( diffuse( rbf_out_neighbourhood( IN_DEGREE))), hadamard_out_neighbourhood( sum_both_neighbourhood( BOTH_DEGREE)), sum_out_neighbourhood( sum_out_neighbourhood( sum_out_neighbourhood( BOTH_DEGREE))), l1Norm_in_neighbourhood( sum_out_neighbourhood( sum_out_neighbourhood( IN_DEGREE))), l1Norm_in_neighbourhood( hadamard_out_neighbourhood( sum_both_neighbourhood( BOTH_DEGREE))), rbf_out_neighbourhood( sum_both_neighbourhood( BOTH_DEGREE)), rbf_in_neighbourhood( rbf_in_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE)))), sum_out_neighbourhood( rbf_in_neighbourhood( sum_in_neighbourhood( BOTH_DEGREE))), sum_out_neighbourhood( rbf_in_neighbourhood( OUT_DEGREE)), hadamard_both_neighbourhood( rbf_both_neighbourhood( IN_DEGREE)), rbf_both_neighbourhood( sum_both_neighbourhood( OUT_DEGREE)), sum_out_neighbourhood( rbf_out_neighbourhood( BOTH_DEGREE)), rbf_both_neighbourhood( sum_both_neighbourhood( BOTH_DEGREE)), rbf_in_neighbourhood( rbf_in_neighbourhood( sum_out_neighbourhood( BOTH_DEGREE))), rbf_in_neighbourhood( sum_out_neighbourhood( diffuse( rbf_out_neighbourhood( IN_DEGREE)))), sum_out_neighbourhood( OUT_DEGREE), rbf_both_neighbourhood( mean_both_neighbourhood( rbf_in_neighbourhood( OUT_DEGREE))), rbf_both_neighbourhood( sum_out_neighbourhood( sum_out_neighbourhood( IN_DEGREE))), OUT_DEGREE, rbf_both_neighbourhood( hadamard_both_neighbourhood( rbf_both_neighbourhood( IN_DEGREE))), rbf_both_neighbourhood( rbf_both_neighbourhood( sum_out_neighbourhood( IN_DEGREE))), hadamard_out_neighbourhood( diffuse( sum_out_neighbourhood( BOTH_DEGREE))), IN_DEGREE, hadamard_out_neighbourhood( diffuse( rbf_out_neighbourhood( IN_DEGREE))), max_both_neighbourhood( rbf_out_neighbourhood( BOTH_DEGREE)), rbf_in_neighbourhood( sum_in_neighbourhood( BOTH_DEGREE))], nodes=7, loadMillis=42, writeProperty=embedding, writeMillis=12, computeMillis=1573, embeddingSize=80, numberOfLayers=4}
result.next() = {nodeId=0, embedding=[0.0, 1.0, 0.0]}
result.next() = {nodeId=1, embedding=[0.0, 0.0, 1.0]}
result.next() = {nodeId=2, embedding=[0.0, 1.0, 1.0]}
result.next() = {nodeId=3, embedding=[0.0, 2.0, 2.0]}
result.next() = {nodeId=4, embedding=[1.0, 0.0, 0.0]}
result.next() = {nodeId=5, embedding=[1.0, 0.0, 0.0]}
result.next() = {nodeId=6, embedding=[2.0, 0.0, 0.0]}
summary = {features=[IN_DEGREE, diffuse( sum_out_neighbourhood( BOTH_DEGREE))], nodes=7, loadMillis=2, writeProperty=foo, writeMillis=2, computeMillis=81, embeddingSize=2, numberOfLayers=2}
embeddings = [0.0, 2.0]
embeddings = [0.0, 0.0]
embeddings = [0.0, 1.0]
embeddings = [0.0, 0.0]
embeddings = [1.0, 0.0]
embeddings = [1.0, 0.0]
embeddings = [2.0, 1.0]
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.451 sec
Running embedding.PruningTest
Embedding:
[[    1.0000,    2.0000,    3.0000,    9.0000], 
 [    2.0000,    3.0000,    4.0000,    9.0000], 
 [    3.0000,    4.0000,    5.0000,    8.0000]]
Features:
[IN_DEGREE, OUT_DEGREE, BOTH_DEGREE, MEAN_BOTH_NEIGHBOURHOOD]
0 -> 0
2 -> 1
4 -> 2
10 -> 0
12 -> 1
14 -> 2
16 -> 1
columns = 
[[         0,    1.0000,         0], 
 [    1.0000,         0,         0], 
 [    1.0000,    1.0000,         0], 
 [    2.0000,    2.0000,         0], 
 [         0,         0,    1.0000], 
 [         0,         0,    1.0000], 
 [         0,         0,    2.0000]]
2019-10-09 15:53:21.542+0000 INFO  [main] pruning 100% Feature Pruning: Creating features graph
2019-10-09 15:53:21.544+0000 INFO  [main] pruning 100% Creating IdMap - 7 nodes
2019-10-09 15:53:21.544+0000 INFO  [main] pruning 100% Created IdMap
2019-10-09 15:53:21.545+0000 INFO  [main] pruning 100% Allocation: 0 Bytes
2019-10-09 15:53:21.545+0000 INFO  [main] pruning 100% Allocation: 192 Bytes
2019-10-09 15:53:21.545+0000 INFO  [main] pruning 100% Size of combined embedding: [3, 7]
2019-10-09 15:53:21.545+0000 INFO  [main] pruning 100% Number of prev features: 3
2019-10-09 15:53:21.545+0000 INFO  [main] pruning 100% Creating AdjacencyMatrix
2019-10-09 15:53:21.545+0000 INFO  [main] pruning 100% Adding columns to array
2019-10-09 15:53:21.546+0000 INFO  [main] pruning 100% Added columns to array
2019-10-09 15:53:21.546+0000 INFO  [main] pruning 100% Populating adjacency matrix 2
2019-10-09 15:53:21.547+0000 INFO  [main] pruning 100% Populated adjacency matrix (new): 1 ms
2019-10-09 15:53:21.547+0000 INFO  [main] pruning 100% Created Adjacency Matrix
2019-10-09 15:53:21.547+0000 INFO  [main] pruning 100% Feature Pruning: Created features graph
2019-10-09 15:53:21.547+0000 INFO  [main] pruning 100% Feature Pruning: Finding features to keep
2019-10-09 15:53:21.548+0000 INFO  [main] pruning 100% Feature Pruning: Found features to keep
2019-10-09 15:53:21.548+0000 INFO  [main] pruning 100% Feature Pruning: Pruning embeddings
2019-10-09 15:53:21.548+0000 INFO  [main] pruning 100% Feature Pruning: Pruned embeddings
scores = 
[[    1.0000,         0,         0,         0], 
 [         0,    1.0000,    0.2500,    0.2500], 
 [         0,    0.2500,    1.0000,    0.7500], 
 [         0,    0.2500,    0.7500,    1.0000]]
adjacency matrix with self-loops = 
[[    1.0000,         0,         0,         0], 
 [         0,    1.0000,         0,         0], 
 [         0,         0,    1.0000,    1.0000], 
 [         0,         0,    1.0000,    1.0000]]
adjacency matrix with self loops removed = 
[[         0,         0,         0,         0], 
 [         0,         0,         0,         0], 
 [         0,         0,         0,    1.0000], 
 [         0,         0,    1.0000,         0]]
Tests run: 7, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec <<< FAILURE!
shouldOnlyKeepFeaturesThatAddSomethingUnique(embedding.PruningTest)  Time elapsed: 0.001 sec  <<< FAILURE!
java.lang.AssertionError: expected:<[9.0000, 
 9.0000, 
 8.0000]> but was:<[[    1.0000,    2.0000,    3.0000,    9.0000], 
 [    2.0000,    3.0000,    4.0000,    9.0000], 
 [    3.0000,    4.0000,    5.0000,    8.0000]]>
    at org.junit.Assert.fail(Assert.java:88)
    at org.junit.Assert.failNotEquals(Assert.java:834)
    at org.junit.Assert.assertEquals(Assert.java:118)
    at org.junit.Assert.assertEquals(Assert.java:144)
    at embedding.PruningTest.shouldOnlyKeepFeaturesThatAddSomethingUnique(PruningTest.java:246)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
    at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
    at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
    at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
    at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
    at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
    at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
    at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)

pruneEmbeddingsAndFeatures(embedding.PruningTest)  Time elapsed: 0.001 sec  <<< FAILURE!
arrays first differed at element [3]; expected:<MEAN_OUT_NEIGHBOURHOOD> but was:<MEAN_BOTH_NEIGHBOURHOOD>
    at org.junit.internal.ComparisonCriteria.arrayEquals(ComparisonCriteria.java:55)
    at org.junit.Assert.internalArrayEquals(Assert.java:532)
    at org.junit.Assert.assertArrayEquals(Assert.java:283)
    at org.junit.Assert.assertArrayEquals(Assert.java:298)
    at embedding.PruningTest.pruneEmbeddingsAndFeatures(PruningTest.java:208)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
    at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
    at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
    at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
    at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
    at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
    at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
    at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)
Caused by: java.lang.AssertionError: expected:<MEAN_OUT_NEIGHBOURHOOD> but was:<MEAN_BOTH_NEIGHBOURHOOD>
    at org.junit.Assert.fail(Assert.java:88)
    at org.junit.Assert.failNotEquals(Assert.java:834)
    at org.junit.Assert.assertEquals(Assert.java:118)
    at org.junit.Assert.assertEquals(Assert.java:144)
    at org.junit.internal.ExactComparisonCriteria.assertElementsEqual(ExactComparisonCriteria.java:8)
    at org.junit.internal.ComparisonCriteria.arrayEquals(ComparisonCriteria.java:53)
    ... 33 more

In the end, it summarizes:

Failed tests:   shouldOnlyKeepFeaturesThatAddSomethingUnique(embedding.PruningTest): expected:<[9.0000, (..)
  pruneEmbeddingsAndFeatures(embedding.PruningTest): arrays first differed at element [3]; expected:<MEAN_OUT_NEIGHBOURHOOD> but was:<MEAN_BOTH_NEIGHBOURHOOD>

Do you think this might be related @meltzerpete?

meltzerpete commented 5 years ago

@xaviermerino I think the failed tests in this case is unrelated, as the error in the tests would not cause the failed dependency error you are getting. I think the code and tests may have changed somewhat since I worked on this, so without looking into the code I couldn't say what the cause of these failures are.

As for the debug log, this looks rather curious.. assuming this is the log when you have all of the JARs you listed above in the plugins folder, do you get the same when only the graphAlgorithms and ml-models JARs are in there?

xaviermerino commented 5 years ago

@meltzerpete I really don't know what's going on. I was using Neo4j Desktop to install this and I decided to use the Community Server 3.5.11 instead to give it a try.

My neo4j.conf file has the following entries:

dbms.security.procedures.unrestricted=apoc.*,algo.*,regression.*, embedding.*
dbms.security.procedures.whitelist=algo.*,apoc.*,regression.*, embedding.*

Then, you can find the following plugins in $NEO4J_HOME/plugins:

README.txt          
graph-algorithms-3.5.11.0.jar
apoc-3.5.0.5-all.jar        
neo4j-ml-models-1.0.3.jar

In theory, this should work and all the dependencies should be within neo4j-ml-models-1.0.3.jar. Now, I wonder if it has something to do with other dependencies that are not listed inside ml-models. In issue #9, @mneedham said that you need to have the graph-algorithms installed in order to run the embedding procedures.

But with my new environment, I don't even see the deepGL procedures. It does not matter whether I package it or download the prepackaged jar. I do get to see the regression procedures. I also see the deepWalk ones. However, if I try to run them, I get: 

Neo.ClientError.Procedure.ProcedureCallFailed: Failed to invoke procedure `embedding.deepWalk.stream`: Caused by: java.lang.NoSuchMethodError: org.neo4j.graphalgo.core.GraphLoader.withoutNodeProperties()Lorg/neo4j/graphalgo/core/GraphLoader;

If you check the DeepWalkProc.java you'll then see that it attempts to import that:

import org.neo4j.graphalgo.api.Graph;
import org.neo4j.graphalgo.api.GraphFactory;
import org.neo4j.graphalgo.core.GraphLoader;

I went to take a look at another file, this time DeepGL.java and found this:

import org.neo4j.graphalgo.core.heavyweight.HeavyGraph;
import org.neo4j.graphalgo.core.utils.ParallelUtil;
import org.neo4j.graphalgo.core.utils.ProgressLogger;

Now, checking at the release notes from Graph Algorithms 3.5.11 it says:

Heavy Graph has been removed from the library: In the algorithm API, using graph:'heavy' will default to a Huge graph, and and the default in memory graph representation for algorithms has been moved to heavy. All algorithms work with Heavy graph; the only visible change to users may be slight differences in scoring calculations for algorithms like pageRank (due to using double type precision).

@mneedham Do you think the changes could have broken ml-models? If so, which is the version that you recommend using? In essence, I am trying to do something similar to your tutorial.

I see in the pom.xml file the following:

<neo4j.version>3.4.11</neo4j.version>
<neo4j.graphalgos.version>3.4.7.0</neo4j.graphalgos.version>
...
...
        <dependency>
            <groupId>org.neo4j</groupId>
            <artifactId>neo4j</artifactId>
            <version>${neo4j.version}</version>
            <scope>provided</scope>
        </dependency>

        <dependency>
            <groupId>org.neo4j</groupId>
            <artifactId>graph-algorithms-algo</artifactId>
            <version>${neo4j.graphalgos.version}</version>
            <scope>provided</scope>
        </dependency>

I don't know if issues #14 #10 #9 might be related to this. Everyone seems to be having the same problems. Which makes me wonder what @tomasonjo did to get it working in #7.

@meltzerpete @mneedham Sorry to be taking too much of your time. I just don't know where I'm going wrong.

meltzerpete commented 5 years ago

@xaviermerino I'm afraid I have not been following the changes to graphAlgorithms or ml-models so I'm really not sure about any breaking changes that may or may not have been made.. @mneedham would be the best to comment on this.

As for the pom, the <scope>provided</scope> line in the graph-algorithms-algo dependency means that the JAR is expected to be provided externally at runtime, so not included in the ml-models JAR. This is why you need the graph algos also installed. But the version it is expecting according to this pom is 3.4.7.0, not the version you have installed. Whether or not it could still work with this newer version I'm not sure. Sorry I can't be of more help on this matter. The best I can offer is to say try and match the exact version of the neo4j (3.4.11) (you can select this when you create a new database), match the version of the graph algo JAR listed in the pom (3.4.7.0), put it in the plugins folder, and remove all other JARs . You can get previous version of the graph algos JAR here.

xaviermerino commented 5 years ago

@meltzerpete @mneedham I followed your advice and downloaded an earlier version of Neo4j. Could not download the 3.4.11 community server (I can't seem to find it) but I ended up with 3.4.16. I ended up using version 3.4.7 of the graph algorithms library as you suggested.

And I am still having the same problem.

Neo.ClientError.Procedure.ProcedureCallFailed: Failed to invoke procedure `embedding.deepgl.stream`: Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.nd4j.linalg.factory.Nd4j

I am out of ideas.

@meltzerpete Do you know if there is another implementation of DeepGL? I tried searching GitHub but yours seems to be the only one so far. I'm trying to compare it with RandomWalk and Node2Vec but I can't seem to find another implementation.

Infoto commented 4 years ago

Hi guys, I had the exact same problem as you. I am also on MacOS Mojave and finally managed to get it going using the following versions:

Neo4j 3.4.7 Graph Algorithms 3.4.7.0 No APOC (I get the error when apoc jar is in the plugins folder) ML models 1.0.2 (1.0.3 does not work for me)

I've also added dbms.security.procedures.unrestricted=algo.*,embedding.* to the neo4j.conf.