Server not starting Server_Stub not found Unmarshall

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seldont
Posts: 11
Joined: 14 Jun 2016, 10:58

I am looking at Essential for the first time and having problems with the server.

This is running on Linux Mint 13 with:
Java v1.8.0_91
Protege v3.5
Tomcat v9.0.0.M4
MySql v5.5
Essential Meta Model v5.0.5

run_protege.sh works without any problems; however no matter what I set CODEBASE_URL to (in run_protege_server.sh) I get ClassNotFound Server_Stub errors e.g.

Code: Select all

Listening for transport dt_socket at address: 8000
Protege server is starting...
Protege 3.5 Build 663, JVM 1.8.0_91-b14, memory=506M, Linux, encoding=UTF-8, language=en, country=GB
Server port = 0, registry port = 1099, compressed stream
Using metaproject from: file:/data/EAM/Repository/metaproject.pprj
WARNING: Missing project at /data/EAM/Repository/annotation_essentail_baseline_v505.pprj -- Server.getAvailableProjectNames()
Loading project Essential AM Repository from file:/data/EAM/Repository/essential_baseline_v505.pprj
Loaded 5000 instances: essential_baseline_v2.0_ProjectKB_Class8354
Loaded 6000 instances: essential_baseline_v1.2_ProjectKB_Class19475
Loaded 7000 instances: essential_baseline_v1.2_ProjectKB_Class21038
Loaded 8000 instances: essential_baseline_v1_ProjectKB_Instance_21209
Set type on 5000 instances: essential_baseline_v1_ProjectKB_Instance_21370
Loaded 9000 instances: essential_baseline_v1_ProjectKB_Instance_24172
Set type on 6000 instances: essential_baseline_v1_ProjectKB_Instance_24569
Loaded 10000 instances: essential_baseline_v1_ProjectKB_Instance_30352
Set type on 7000 instances: essential_baseline_v1_ProjectKB_Instance_31204
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Set type on 8000 instances: essential_baseline_v1_ProjectKB_Instance_35088
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Set type on 9000 instances: essential_baseline_v1_ProjectKB_Instance_42430
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Set type on 10000 instances: essential_baseline_v1_ProjectKB_Instance_47102
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Set type on 11000 instances: essential_baseline_v1_ProjectKB_Instance_53909
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Loaded 20000 instances: essential_baseline_v1_ProjectKB_Instance_8047
Set type on 15000 instances: essential_baseline_v1_ProjectKB_Instance_8347
Loaded 21000 instances: essential_baseline_v2.0_ProjectKB_Class10622
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Set type on 34000 instances: essential_baseline_v3.0.2_ProjectKB_Class4048
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Loaded 41000 instances: essential_baseline_v3.0.4_ProjectKB_Class7455
Set type on 35000 instances: essential_baseline_v3.0.3_ProjectKB_Class2100
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Set type on 36000 instances: essential_baseline_v3.0.4_ProjectKB_Class10173
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Set type on 37000 instances: essential_baseline_v3.0.4_ProjectKB_Class12608
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Set type on 38000 instances: essential_baseline_v3.0.4_ProjectKB_Class13631
Loaded 46000 instances: essential_baseline_v3.0.4_ProjectKB_Class16021
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Set type on 39000 instances: essential_baseline_v3.0.4_ProjectKB_Class14660
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Loaded 49000 instances: essential_baseline_v3.0.4_ProjectKB_Class2021
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Loaded 54000 instances: essential_baseline_v3.0.4_ProjectKB_Class7765
Set type on 43000 instances: essential_baseline_v3.0.4_ProjectKB_Class8964
Loaded 55000 instances: essential_baseline_v3.0.4_ProjectKB_Class9241
Loaded 56000 instances: essential_baseline_v3.0.6_ProjectKB_Class19835
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Set type on 52000 instances: essential_baseline_v3.5_ProjectKB_Class10527
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Set type on 53000 instances: essential_baseline_v3.5_ProjectKB_Class11548
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Loaded 69000 instances: essential_baseline_v3.5_ProjectKB_Class2778
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Set type on 67000 instances: essential_baseline_v4.0_ProjectKB_Class32494
Set type on 68000 instances: essential_baseline_v4.3.1_ProjectKB_Class2140
Loaded 80000 instances: essential_baseline_v4.3.1_ProjectKB_Class2219
Set type on 69000 instances: essential_baseline_v4.3.1_ProjectKB_Class3180
Loaded 81000 instances: essential_baseline_v4.3.1_ProjectKB_Class3251
Set type on 70000 instances: essential_baseline_v4.3.1_ProjectKB_Class4192
Loaded 82000 instances: essential_baseline_v4.3.1_ProjectKB_Class4425
Set type on 71000 instances: essential_baseline_v4.3.1_ProjectKB_Class5210
Loaded 83000 instances: essential_baseline_v4.3.1_ProjectKB_Class5472
Set type on 72000 instances: essential_baseline_v505_ProjectKB_Class4208
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Loaded 84000 instances: essential_baseline_v505_ProjectKB_Class5312
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Set type on 78000 instances: essential_baseline_v5_ProjectKB_Class1984
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Set type on 81000 instances: essential_baseline_v5_ProjectKB_Class4855
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Set type on 82000 instances: essential_baseline_v5_ProjectKB_Class5868
Loaded 92000 instances: essential_baseline_v5_ProjectKB_Class6041
Loaded 93000 instances: essential_prj_AA_v1.5_ProjectKB_Instance_1518
Set type on 83000 instances: essential_prj_CC_v1.0_ProjectKB_Instance_31590
Loaded 94000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_141859
Set type on 84000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_142055
Loaded 95000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_192360
Set type on 85000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_30013
Set type on 86000 instances: viewer3_dev_12032012_ProjectKB_Class12536
Loaded 96000 instances: viewer3_dev_12032012_ProjectKB_Class12751
Set type on 87000 instances: viewer3_dev_12032012_ProjectKB_Class14080
Loaded 97000 instances: viewer3_dev_12032012_ProjectKB_Class18727
Set type on 88000 instances: viewer3_devrep_14032012_003_ProjectKB_Class72202
Loading project plugins for project Essential AM Repository
SEVERE: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: 
	java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: 
	java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
	at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:421)
	at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:272)
	at sun.rmi.transport.Transport$1.run(Transport.java:200)
	at sun.rmi.transport.Transport$1.run(Transport.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
	at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
	at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:276)
	at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:253)
	at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:379)
	at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
	at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
	at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
	at edu.stanford.smi.protege.server.Server.main(Unknown Source)
Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: 
	java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
	at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source)
	at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:411)
	at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:272)
	at sun.rmi.transport.Transport$1.run(Transport.java:200)
	at sun.rmi.transport.Transport$1.run(Transport.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
	at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.rmi.server.LoaderHandler$Loader.loadClass(LoaderHandler.java:1207)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:348)
	at sun.rmi.server.LoaderHandler.loadClassForName(LoaderHandler.java:1221)
	at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:453)
	at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:186)
	at java.rmi.server.RMIClassLoader$2.loadClass(RMIClassLoader.java:637)
	at java.rmi.server.RMIClassLoader.loadClass(RMIClassLoader.java:264)
	at sun.rmi.server.MarshalInputStream.resolveClass(MarshalInputStream.java:219)
	at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1620)
	at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1521)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1781)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
	at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
	... 15 more
 -- Server.bindName()
SEVERE: server startup failed -- java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: 
	java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: 
	java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
	at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:421)
	at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:272)
	at sun.rmi.transport.Transport$1.run(Transport.java:200)
	at sun.rmi.transport.Transport$1.run(Transport.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
	at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
	at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:276)
	at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:253)
	at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:379)
	at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
	at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
	at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
	at edu.stanford.smi.protege.server.Server.main(Unknown Source)
Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is: 
	java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
	at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source)
	at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:411)
	at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:272)
	at sun.rmi.transport.Transport$1.run(Transport.java:200)
	at sun.rmi.transport.Transport$1.run(Transport.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
	at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.rmi.server.LoaderHandler$Loader.loadClass(LoaderHandler.java:1207)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:348)
	at sun.rmi.server.LoaderHandler.loadClassForName(LoaderHandler.java:1221)
	at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:453)
	at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:186)
	at java.rmi.server.RMIClassLoader$2.loadClass(RMIClassLoader.java:637)
	at java.rmi.server.RMIClassLoader.loadClass(RMIClassLoader.java:264)
	at sun.rmi.server.MarshalInputStream.resolveClass(MarshalInputStream.java:219)
	at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1620)
	at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1521)
	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1781)
	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
	at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
	... 15 more


I tried putting the full path to the jar files in the CLASSPATH which didn't make any difference.

I have tried the suggestion from an earlier post of copying the protege.jar into tomcat - but I still get the same error - CAN ANYONE HELP?

The relevant part of run_protege_server.sh currently contains the following:

Code: Select all

CLASSPATH=protege.jar:looks.jar:driver.jar
MAINCLASS=edu.stanford.smi.protege.server.Server


# ------------------- JVM Options -------------------
MAX_MEMORY=-Xmx500M
HEADLESS=-Djava.awt.headless=true
#CODEBASE_URL=file:/data/Protege_3.5/protege.jar
CODEBASE_URL=http://localhost:8080/essential_viewer/protege.jar
CODEBASE=-Djava.rmi.server.codebase=$CODEBASE_URL
HOSTNAME_PARAM=-Djava.rmi.server.hostname=`hostname`
TX="-Dtransaction.level=READ_COMMITTED"
LOG4J_OPT="-Dlog4j.configuration=file:log4j.xml"

User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Thanks for posting.

As you’ve described, this seems to be a variant of the CODEBASE_URL setting issue.

I’m going to start with a bit of a silly question. I assume that the CODEBASE_URL that you’ve specified in your run_protege_server.sh does actual point at the copy of protege.jar - that is, you’ve copied protege.jar into the root of your Essential Viewer web application, running on the default Tomcat port and that Tomcat is running?

Assuming that this is all set up, it is worth checking the useCodebaseOnly option for starting the RMI Registry in the run_protege_server.sh script.

Code: Select all

rmiregistry -J-Djava.rmi.server.useCodebaseOnly=false
Apparently, in recent versions of Java (as yours is) the default value of java.rmi.server.useCodebaseOnly was changed to true and others have found that setting this to false has resolved the ClassNotFound Exception

From what you’ve said, it sounds like you are using all the default ports for the server and the RMI Registry. Note that if you have changed any of these, you will need to pick up those changes in run_protege_server.bat

This thread Multi user install problems, ClassNotFoundException steps through the ‘useCodebaseOnly=false’ setting and RMI Registry ports and if any of the above do not get the server starting, are definitely worth a look. Also in this thread is a link to the detailed Protege configuration options for handling this issue, running under Java 7 rather than Java 6 (which you’ve tackled with the use of file:// for the URL of the protege.jar), working through firewalls etc.

I did also notice that the MAX_MEMORY setting that you’ve quoted is a bit low. I recommend that you set this to 2048M as this will avoid any issues loading the repositories.

Let us know whether these suggestions get your server started properly.

Jonathan
Essential Project Team
seldont
Posts: 11
Joined: 14 Jun 2016, 10:58

Thanks for the help

Adding -J-Djava.rmi.server.useCodebaseOnly=false to rmiregistry call got rid of the errors (Still have some warnings to sort out) and need to add some memory to the VM.

The startup now looks like this:

Code: Select all

Protege server is starting...
Protege 3.5 Build 663, JVM 1.8.0_91-b14, memory=506M, Linux, encoding=UTF-8, language=en, country=GB
Server port = 0, registry port = 1099, compressed stream
Using metaproject from: file:/data/EAM/Repository/metaproject.pprj
WARNING: Missing project at /data/EAM/Repository/annotation_essentail_baseline_v505.pprj -- Server.getAvailableProjectNames()
Loading project Essential AM Repository from file:/data/EAM/Repository/essential_baseline_v505.pprj
Loaded 5000 instances: essential_baseline_v2.0_ProjectKB_Class8354
Loaded 6000 instances: essential_baseline_v1.2_ProjectKB_Class19475
Loaded 7000 instances: essential_baseline_v1.2_ProjectKB_Class21038
:
:
Set type on 84000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_142055
Loaded 95000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_192360
Set type on 85000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_30013
Set type on 86000 instances: viewer3_dev_12032012_ProjectKB_Class12536
Loaded 96000 instances: viewer3_dev_12032012_ProjectKB_Class12751
Set type on 87000 instances: viewer3_dev_12032012_ProjectKB_Class14080
Loaded 97000 instances: viewer3_dev_12032012_ProjectKB_Class18727
Set type on 88000 instances: viewer3_devrep_14032012_003_ProjectKB_Class72202
Loading project plugins for project Essential AM Repository
Could not set up class specific logging
Exception configuring logger
Could not set logger level
Warning: IO exception getting logger. access denied ("java.util.PropertyPermission" "protege.properties.in.user.home" "read")
Protege server ready to accept connections...
mdpremkumar
Posts: 26
Joined: 17 Apr 2017, 09:06

Hi,

Below is a link which provides details about RMI enhancements (available from JDK 7 update 21)
http://docs.oracle.com/javase/7/docs/te ... nts-7.html

After upgrade to JRE version 8, I was also facing RMI issues and was not able to load server projects. As mentioned in this post, set useCodebaseOnly to false and that solved the issues.

As per the best practices, that option is not a recommended one since it may allow execution of untrusted code.

The recommended approach is to share same code base for RMI server/client/RMI registry daemon.

I tried these adjustments in run_protege_server.bat and it is working fine.

The command which starts rmiregistry daemon should be something like below.

start /D%JDKBIN% /min rmiregistry.exe -J-Djava.rmi.server.codebase=%CODEBASE_URL%

The same codebase should also be shared when calling JAVA exe using the command like argument -Djava.rmi.server.codebase=%CODEBASE_URL% (It has been done already in the batch file).

Thanks.
Prem
francesca.di.tosto
Posts: 2
Joined: 29 Aug 2019, 13:56

Hi,
can anyone help me because i have the same problem!

I have the following information in the .bat file:
set JDKBIN="C:\Program Files (x86)\Java\jre1.8.0_221\bin"

rem Note that a space character in the following path must be replaced with '%%20' in
rem a batch file. If you are typing directly on the command line, a space must be
rem replaced with '%%20'.

set CODEBASE_URL=file:/c:/program%%20files/Protege_3.5/protege.jar
rem "http://localhost:8080/essential_viewer_62/protege.jar"
rem C:\Program Files (x86)\Protege_3.5

rem start /D%JDKBIN% /min rmiregistry.exe -J-Djava.rmi.server.useCodebaseOnly=false
start /D%JDKBIN% /min rmiregistry.exe -J-Djava.rmi.server.codebase=%CODEBASE_URL%

rem set VM_OPTS=-Djava.rmi.server.useCodebaseOnly=true

set CLASSPATH=protege.jar;looks.jar;unicode_panel.jar;driver.jar;driver0.jar;driver1.jar
set MAINCLASS=edu.stanford.smi.protege.server.Server
set METAPROJECT=examples\server\metaproject.pprj

set MAX_MEMORY=-Xmx500M
set HEADLESS=-Djava.awt.headless=true
set CODEBASE=-Djava.rmi.server.codebase=%CODEBASE_URL%
set LOG4J_OPT=-Dlog4j.configuration=file:log4j.xml
set PORTOPTS=-Dprotege.rmi.server.port=5200 -Dprotege.rmi.registry.port=1099
rem RMI_REG_PORT=1099
rem RMI_SERV_PORT=5200

rem --- Optional arguments; uncomment if necessary ---
rem set HOSTNAME=-Djava.rmi.server.hostname=localhost
rem set "PORTOPTS=-Dprotege.rmi.server.port=5200 -Dprotege.rmi.registry.port=5100"
rem TX=-Dtransaction.level=READ_COMMITTED
rem "DEBUG_OPT=-Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n"

set OPTIONS=%MAX_MEMORY% %CODEBASE% %HEADLESS% %LOG4J_OPT% %HOSTNAME% %PORTOPTS% %TX% %DEBUG_OPT%

rem ------------------- Cmd Options -------------------
rem If you want automatic saving of the project,
rem setup the number of seconds in SAVE_INTERVAL_VALUE
rem set SAVE_INTERVAL=-saveIntervalSec=120
rem ------------------- Cmd Options -------------------


%JDKBIN%\java %OPTIONS% -cp %CLASSPATH% %MAINCLASS% %SAVE_INTERVAL% %METAPROJECT%

Thanks in advance!
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

I think you're almost there.

You will need to change the lines:

Code: Select all

set CODEBASE_URL=file:/c:/program%%20files/Protege_3.5/protege.jar
rem "http://localhost:8080/essential_viewer_62/protege.jar"
to

Code: Select all

rem set CODEBASE_URL=file:/c:/program%%20files/Protege_3.5/protege.jar
set CODEBASE_URL="http://localhost:8080/essential_viewer_62/protege.jar"
There's an issue with Java 1.7+ that means the codebase URL doesn't work with a file.
Make sure that you copy the file

Code: Select all

protege.jar
into the root of your Viewer so that the above URL is valid.

Jonathan
Essential Project Team
dleirman
Posts: 5
Joined: 23 Dec 2019, 15:25

I get following error

SEVERE: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub

Where is the root folder of the viewer to copy the protege.jar to ?

Is this under C:\Program Files\apache-tomcat-8.5.43\webapps\<viewer> ?
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Hi,
Where is the root folder of the viewer to copy the protege.jar to ?

Is this under C:\Program Files\apache-tomcat-8.5.43\webapps\<viewer> ?
You can copy the protege.jar file to any viewer web application that you have - and you only need to do this once. If you have multiple viewer versions in your Tomcat, you do NOT need to copy protege.jar to each new Viewer web application. Once is enough.

So, assuming that you have a copy of Essential Viewer deployed in your Tomcat that is running on port 8080, as "essential_viewer_68.war", this will expand to a folder when Tomcat deploys it, "essential_viewer_68". If you copy your protege.jar into this folder:

Code: Select all

C:\Program Files\apache-tomcat-8.5.43\webapps\essential_viewer_68
then your setting in run_protege_server.bat will be:

Code: Select all

set CODEBASE_URL="http://localhost:8080/essential_viewer_68/protege.jar"
Jonathan
Essential Project Team
dleirman
Posts: 5
Joined: 23 Dec 2019, 15:25

Hi Jonathan

Thanks for your info however I still get error msg when running "run_protege_server.bat" as administrator

"Loading class `com.mysql.jdbc.Driver'. This is deprecated. The new driver class is `com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary.
Loading project plugins for project Essential AM Repository
SEVERE: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub"


What else could be wrong ?

-----------------------------------------------------------------------------------------------------------------------------------------------
"run_protege_server.bat" looks like :

set JDKBIN="C:\Program Files\Java\jre1.8.0_231\bin"

rem Note that a space character in the following path must be replaced with '%%20' in
rem a batch file. If you are typing directly on the command line, a space must be
rem replaced with '%20'.

rem set CODEBASE_URL=file:/c:/program%%20files/protege_3.5/protege.jar
rem NEW set CODEBASE_URL="http://localhost:8080/essential_viewer_68/protege.jar"
set CODEBASE_URL="http://localhost:8080/EA_Infrabel_DEV/protege.jar"

rem start /D%JDKBIN% /min rmiregistry.exe
rem start /D%JDKBIN% /min rmiregistry.exe -J-Djava.rmi.server.useCodebaseOnly=false
start /D%JDKBIN% /min rmiregistry.exe -J-Djava.rmi.server.codebase=%CODEBASE_URL%

set CLASSPATH=protege.jar;looks.jar;unicode_panel.jar;driver.jar;driver0.jar;driver1.jar
set MAINCLASS=edu.stanford.smi.protege.server.Server
set METAPROJECT="examples\server\metaproject.pprj"

set MAX_MEMORY=-Xmx2048m
set HEADLESS=-Djava.awt.headless=true
set CODEBASE=-Djava.rmi.server.codebase=%CODEBASE_URL%
set LOG4J_OPT=-Dlog4j.configuration=file:log4j.xml
set PORTOPTS=-Dprotege.rmi.server.port=5200 -Dprotege.rmi.registry.port=1099

rem --- Optional arguments; uncomment if necessary ---
rem set HOSTNAME=-Djava.rmi.server.hostname=localhost
rem set "PORTOPTS=-Dprotege.rmi.server.port=5200 -Dprotege.rmi.registry.port=5100"
rem TX=-Dtransaction.level=READ_COMMITTED
rem "DEBUG_OPT=-Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n"

set OPTIONS=%MAX_MEMORY% %CODEBASE% %HEADLESS% %LOG4J_OPT% %HOSTNAME% %PORTOPTS% %TX% %DEBUG_OPT%

rem ------------------- Cmd Options -------------------
rem If you want automatic saving of the project,
rem setup the number of seconds in SAVE_INTERVAL_VALUE
rem set SAVE_INTERVAL=-saveIntervalSec=120
rem ------------------- Cmd Options -------------------


%JDKBIN%\java %OPTIONS% -cp %CLASSPATH% %MAINCLASS% %SAVE_INTERVAL% %METAPROJECT%

pause

-----------------------------------------------------------------------------------------------------------------------------------------------
dleirman
Posts: 5
Joined: 23 Dec 2019, 15:25

Hi

Thanks for your help however the intervention did not helped :

I still got error message :

Loaded 177000 instances: viewer3_devrep_14032012_003_ProjectKB_Class12320
Loading class `com.mysql.jdbc.Driver'. This is deprecated. The new driver class is `com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary.
Loading project plugins for project Essential AM Repository
SEVERE: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub


In annex run_protege_server.bat

set JDKBIN="C:\Program Files\Java\jre1.8.0_231\bin"

rem Note that a space character in the following path must be replaced with '%%20' in
rem a batch file. If you are typing directly on the command line, a space must be
rem replaced with '%20'.

rem set CODEBASE_URL=file:/c:/program%%20files/protege_3.5/protege.jar
rem NEW set CODEBASE_URL="http://localhost:8080/essential_viewer_68/protege.jar"
set CODEBASE_URL="http://localhost:8080/EA_Infrabel_DEV/protege.jar"

rem start /D%JDKBIN% /min rmiregistry.exe
rem start /D%JDKBIN% /min rmiregistry.exe -J-Djava.rmi.server.useCodebaseOnly=false
start /D%JDKBIN% /min rmiregistry.exe -J-Djava.rmi.server.codebase=%CODEBASE_URL%

set CLASSPATH=protege.jar;looks.jar;unicode_panel.jar;driver.jar;driver0.jar;driver1.jar
set MAINCLASS=edu.stanford.smi.protege.server.Server
set METAPROJECT="examples\server\metaproject.pprj"

set MAX_MEMORY=-Xmx2048m
set HEADLESS=-Djava.awt.headless=true
set CODEBASE=-Djava.rmi.server.codebase=%CODEBASE_URL%
set LOG4J_OPT=-Dlog4j.configuration=file:log4j.xml
set PORTOPTS=-Dprotege.rmi.server.port=5200 -Dprotege.rmi.registry.port=1099

rem --- Optional arguments; uncomment if necessary ---
rem set HOSTNAME=-Djava.rmi.server.hostname=localhost
rem set "PORTOPTS=-Dprotege.rmi.server.port=5200 -Dprotege.rmi.registry.port=5100"
rem TX=-Dtransaction.level=READ_COMMITTED
rem "DEBUG_OPT=-Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n"

set OPTIONS=%MAX_MEMORY% %CODEBASE% %HEADLESS% %LOG4J_OPT% %HOSTNAME% %PORTOPTS% %TX% %DEBUG_OPT%

rem ------------------- Cmd Options -------------------
rem If you want automatic saving of the project,
rem setup the number of seconds in SAVE_INTERVAL_VALUE
rem set SAVE_INTERVAL=-saveIntervalSec=120
rem ------------------- Cmd Options -------------------


%JDKBIN%\java %OPTIONS% -cp %CLASSPATH% %MAINCLASS% %SAVE_INTERVAL% %METAPROJECT%

pause

What could be wrong ?

Thanks for your help
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Thanks for posting back.

That you are seeing the message:
Loaded 177000 instances: viewer3_devrep_14032012_003_ProjectKB_Class12320
is good. That is Protege loading instances from your repository.

I assume that you are using MySQL as the "back end" for Protege server. Can you confirm this?
Which version of MySQL are you using?
Are you using the correct JDBC driver for that version?
Note, that we currently only support MySQL v5.5, v5.6, v5.7 and for 5.6 and 5.7 you need to make a small adjustment to the Protege configuration. This small adjustment should have been done by the installer, which adds a couple of lines - specifically about MySQL into the "protege.properties" file.

I suspect from the error message that you're seeing that the JDBC driver or the MySQL version might be newer than the v5.7 I mentioned above. However, before replacing all the stuff that you have in place, you could try the following:
  • Open your Protege project for your repository
  • File->Convert Project to Format and select Protege Database
  • Update the JDBC Driver Class Name to: com.mysql.cj.jdbc.Driver
  • Press OK
This will change the JDBC driver that Protege is attempting to use.
Note that we have not tried this ourselves and currently only support using MySQL 5.5, 5.6 and 5.7

Jonathan
Essential Project Team
dleirman
Posts: 5
Joined: 23 Dec 2019, 15:25

Hi,

Indeed MySQL version installed is 8.0.18. The correct JDBC driver is installed under protege folder = mysql-connector-java-8.0.18.jar and renamed to driver.jar.

I assume will need to desinstall MySQL server 8.0 and install MySQL server 5.7.28.

Kind Regards

Dirk
dleirman
Posts: 5
Joined: 23 Dec 2019, 15:25

In the meantime I desinstalled 8.0 and installed MySQL server 5.7.28

However I get following errors :

2020-03-23T18:19:01.584528Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2020-03-23T18:19:01.584631Z 0 [Note] --secure-file-priv is set to NULL. Operations related to importing and exporting data are disabled
2020-03-23T18:19:01.585080Z 0 [Note] mysqld (mysqld 5.7.28) starting as process 4236 ...
2020-03-23T18:19:01.594442Z 0 [Note] InnoDB: Mutexes and rw_locks use Windows interlocked functions
2020-03-23T18:19:01.594815Z 0 [Note] InnoDB: Uses event mutexes
2020-03-23T18:19:01.595073Z 0 [Note] InnoDB: _mm_lfence() and _mm_sfence() are used for memory barrier
2020-03-23T18:19:01.595329Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2020-03-23T18:19:01.595971Z 0 [Note] InnoDB: Number of pools: 1
2020-03-23T18:19:01.596362Z 0 [Note] InnoDB: Not using CPU crc32 instructions
2020-03-23T18:19:01.600083Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2020-03-23T18:19:01.612145Z 0 [Note] InnoDB: Completed initialization of buffer pool
2020-03-23T18:19:01.667274Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2020-03-23T18:19:01.705841Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2020-03-23T18:19:01.707010Z 0 [Note] InnoDB: Setting file '.\ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2020-03-23T18:19:01.742053Z 0 [Note] InnoDB: File '.\ibtmp1' size is now 12 MB.
2020-03-23T18:19:01.756799Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2020-03-23T18:19:01.758105Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2020-03-23T18:19:01.760591Z 0 [Note] InnoDB: Waiting for purge to start
2020-03-23T18:19:01.826447Z 0 [Note] InnoDB: 5.7.28 started; log sequence number 1210518
2020-03-23T18:19:01.827655Z 0 [Note] Plugin 'FEDERATED' is disabled.
mysqld: 2020-03-23T18:19:01.830724Z 0 [Note] InnoDB: Loading buffer pool(s) from C:\Program Files\MySQL\MySQL Server 5.7\data\ib_buffer_pool
Table 'mysql.plugin' doesn't exist
2020-03-23T18:19:01.833243Z 0 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2020-03-23T18:19:01.835473Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2020-03-23T18:19:01.837873Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
2020-03-23T18:19:01.838378Z 0 [Note] Skipping generation of SSL certificates as certificate files are present in data directory.
2020-03-23T18:19:01.840270Z 0 [Warning] CA certificate ca.pem is self signed.
2020-03-23T18:19:01.841242Z 0 [Note] Skipping generation of RSA key pair as key files are present in data directory.
2020-03-23T18:19:01.849009Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2020-03-23T18:19:01.851136Z 0 [Note] InnoDB: Buffer pool(s) load completed at 200323 19:19:01
2020-03-23T18:19:01.851849Z 0 [Note] IPv6 is available.
2020-03-23T18:19:01.854054Z 0 [Note] - '::' resolves to '::';
2020-03-23T18:19:01.854838Z 0 [Note] Server socket created on IP: '::'.
2020-03-23T18:19:01.856927Z 0 [Warning] Failed to open optimizer cost constant tables

2020-03-23T18:19:01.857978Z 0 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist
2020-03-23T18:19:01.861520Z 0 [ERROR] Fatal error: Failed to initialize ACL/grant/time zones structures or failed to remove temporary table files.
2020-03-23T18:19:01.867602Z 0 [ERROR] Aborting

Could someone help me out
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Hi,

I wonder if there are some remnants of the MySQL 8.0 left in the default permanent storage on your filesystem (e.g. the down-grade from v8 to v5.7 hasn't worked properly), or is this a completely fresh install?

This is a MySQL issue and I think the key line in the trace that you've sent is:

Code: Select all

Table 'mysql.plugin' doesn't exist
2020-03-23T18:19:01.833243Z 0 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2020-03-23T18:19:01.835473Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
Looking at this, if you haven't already run "mysql_upgrade" as suggested on the 2nd line, then that might be worth doing first. However, if MySQL is still confused between your old MySQL 8 installation and your new MySQL 5.8 install, resolve that first by completely de-installing MySQL 8 and removing all its data files as it is likely that MySQL 8 will use the same directories as MySQL 5.7 to store its data and configuration.

Jonathan
Essential Project Team
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