Develop Reference

Unable to create directory path [/User/Desktop/db2/logs] for Neo4j store

I am trying to use a tool that, in two steps, analyzes code smells for android.
In the first step, the tool parses an apk and generates within a directory .db files that should then be converted to CSV files in the next step; however, whenever I try to run the second step, the console returns the following error:
java.io.IOException: Unable to create directory path [/User/Desktop/db2/logs] for Neo4j store.
I think it is a Neo4J configuration problem.
I am currently running the tool with the following Java configuration:
echo $JAVA_HOME
/home/User/openlogic-openjdk-11.0.15
update-alternatives --config java
* 0 /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 auto mode
To be safe, I also started Neo4J, which returned the following output
sudo systemctl status neo4j.service
neo4j.service - Neo4j Graph Database
Loaded: loaded (/lib/systemd/system/neo4j.service; enabled; vendor preset: enabled)
Active: active (running) since Wed 2022-07-06 20:11:04 CEST; 16min ago
Main PID: 1040 (java)
Tasks: 57 (limit: 18901)
Memory: 705.4M
CPU: 16.639s
CGroup: /system.slice/neo4j.service
└─1040 /usr/bin/java -cp "/var/lib/neo4j/plugins:/etc/neo4j:/usr/share/neo4j/lib/*:/var/lib/neo4j/plugins/*" -XX:+UseG1GC -XX:-OmitStackTraceInFastThrow -XX:+AlwaysPreTouch -XX:+UnlockExper>.
How can I solve this?

You posted this error:
java.io.IOException: Unable to create directory path [/User/Desktop/db2/logs] for Neo4j store.
From that error, it looks like:
Neo4j was installed at "/User/Desktop/db2"
The permissions for that directory do not have "write" permission
I tried to reproduce this locally using Neo4j Community 4.4.5, following the steps below.
I do see an IOException related to "logs", but it's slightly different from what you posted. Perhaps we're on different versions of Neo4j.
Open terminal into install directory: cd neo4j
Verify "neo4j" is stopped: ./bin/neo4j stop
Rename existing "logs" directory: mv logs logs.save
Remove write permission for the Neo4j install: chmod u-w .
Start neo4j in console mode: ./bin/neo4j console
Observe errors in console output
2022-07-08 03:28:38.081+0000 INFO Starting...
ERROR StatusLogger Unable to create file [****************************]/neo4j/logs/debug.log
java.io.IOException: Could not create directory [****************************]/neo4j/logs
...
To fix things, try:
Get a terminal into your Neo4j directory:
cd /User/Desktop/db2
Set write permissions for the entire directory tree:
chmod u+w -R .
Start neo4j in console mode:
./bin/neo4j console
If this works and you're able to run neo4j fine, it points to an issue with user permissions when running neo4j as a system service.
The best steps from there depend on the system, your access, how comfortable you are making changes, probably other things. An easy, brute-force hammer would be to manually create each directory you discover (such as "/User/Desktop/db2/logs") and grant premissions to all users (chmod ugo+w .), then try re-running the service, see what errors pop up. Repeat that until you're able to run the service without errors.

Use docker-machine create from java

I have an application that (I want to) uses Java to start and stop Docker containers. It seems that the way to do this is using docker-machine create, which works fine when I test from the command line.
However, when running using Commons-Exec from Java I get the error:
(aa4567c1-058f-46ae-9e97-56fb8b45211c) Creating SSH key...
Error creating machine: Error in driver during machine creation: /usr/local/bin/VBoxManage modifyvm aa4567c1-058f-46ae-9e97-56fb8b45211c --firmware bios --bioslogofadein off --bioslogofadeout off --bioslogodisplaytime 0 --biosbootmenu disabled --ostype Linux26_64 --cpus 1 --memory 1024 --acpi on --ioapic on --rtcuseutc on --natdnshostresolver1 off --natdnsproxy1 on --cpuhotplug off --pae on --hpet on --hwvirtex on --nestedpaging on --largepages on --vtxvpid on --accelerate3d off --boot1 dvd failed:
VBoxManage: error: Could not find a registered machine with UUID {aa4567c1-058f-46ae-9e97-56fb8b45211c}
VBoxManage: error: Details: code VBOX_E_OBJECT_NOT_FOUND (0x80bb0001), component VirtualBoxWrap, interface IVirtualBox, callee nsISupports
VBoxManage: error: Context: "FindMachine(Bstr(a->argv[0]).raw(), machine.asOutParam())" at line 500 of file VBoxManageModifyVM.cpp
I have set my VBOX_USER_HOME variable in an initializationScript that I'm using to start the machine:
export WORKERID=$1
export VBOX_USER_HOME=/Users/me/Library/VirtualBox
# create the machine
docker-machine create $WORKERID && \ # create the worker using docker-machine
eval $(docker-machine env $WORKERID) && \ # load the env of the newly created machine
docker run -d myimage
And I'm executing this from Java via the Commons Exec CommandLine class:
CommandLine cmdline = new CommandLine("/bin/sh");
cmdline.addArgument(initializeWorkerScript.getAbsolutePath());
cmdline.addArgument("test");
Executor executor = new DefaultExecutor();
If there is another library that can interface with docker-machine from Java I'm happy to use that, or to change out Commons Exec if that's the issue (though I don't understand why). The basic requirement is that I have some way to get docker-machine to create a machine using Java and then later to be able to use docker-machine to stop that machine.

As it turns out the example that I posted should work, the issue that I was having is that I was provisioning machines with a UUID name. That name contained dash (-) characters which apparently break VBoxManage. This might be because of some kind of path problem but I'm just speculating. When I changed my UUID to have dot (.) instead of dash it loaded and started the machine just fine.
I'm happy to remove this post if the moderators want, but will leave it up here in case people are looking for solutions to problems with docker-machine create naming issues.

CHECK_NRPE: Error - Could not complete SSL handshake (web)

I have a local Nagios Server and I'm trying to configure it to monitor my tomcat8 server with check_jvm, so I can control the memory and classes used by Java.
To do so I installed the check_nrpe plugin on the client, and configured it but I'm having an 'odd' error.
If I try to call the plugin on the client from my server, it answers correctly, even using check_jvm commands as parameter.
But when I configure it so nagios do the check on his own, the web browser returns a "CHECK_NRPE: Error - Could not complete SSL handshake" for that service specifically.
This is what I have:
From my nagios server
# /usr/local/nagios/libexec/check_nrpe -H <client.ip>
NRPE v2.12
# /usr/local/nagios/libexec/check_nrpe -H <client.ip> -c tomcat_heap
OK 799998504 |max=2101870592;;; commited=2101870592;;; used=799998504;;;
Where tomcat_heap is the name of a command defined in nrpe.cfg at the client in order to use the check_jvm plugin.
command[tomcat_heap]=sudo /usr/local/nagios/libexec/check_jvm -n org.apache.catalina.startup.Bootstrap -p heap -w 1700000000 -c 2000000000
Now, back again on my Nagios server, this is the service definition
define service{
use generic-service
host_name lin-des
service_description Tomcat heap
check_command check_nrpe!tomcat_heap
}
Now, this returns a 'CHECK_NRPE: Error - Could not complete SSL handshake' on the web app.
I've checked the allowed_hostson the nrpe.cfgfile, as well as on /etc/xinetd.d/nrpe, so it includes my nagios server IP.
I've also checked Selinux and Iptables configuration.
I've also checked that both my Nagios server, and the client share the same version of the ssl libraries.
Lastly, I've checked all the permissions on /usr/local/nagios/libexec on both the server and the client, so the user nagios have the ownership of them.
At this point, I ran out of ideas, and that's why I'm asking you. Any ideas on where the problem may be?

Found it.
It seems when I defined the check_nrpe command in the command.cfg, I made a mistake on the command line.
define command{
command_name check_nrpe
command_line $USER1$/check_nrpe -H $HOSTADDRESS$ -p 5656 -t 30 -c $ARG1$
}
As you can see, I defined the command to work on the port 5656 which isn't the port used by the nrpe service (it actually is 5666).
After fixing this error, everything runs properly.
I hope this helps to anyone with similar problems.

Error while starting GoldFish server: Ubuntu 13.10

I consulted here and here but could not get my problem solved.
When I type this on terminal /opt/glassfish4/glassfish/bin/asadmin start, I get the following result:
Remote server does not listen for requests on [localhost:4848]. Is the server up?
Unable to get remote commands.
Closest matching local command(s):
restart-domain
restart-local-instance
start-database
start-domain
start-local-instance
Command start failed.
Similarly, when I type this /opt/glassfish4/glassfish/bin/asadmin --port 5656 start-domain, I get
java.io.IOException: Couldn't get lock for /opt/glassfish4/glassfish/domains/domain1/logs/server.log
at java.util.logging.FileHandler.openFiles(FileHandler.java:389)
at java.util.logging.FileHandler.<init>(FileHandler.java:287)
at com.sun.enterprise.admin.launcher.GFLauncherLogger.addLogFileHandler(GFLauncherLogger.java:98)
at com.sun.enterprise.admin.launcher.GFLauncher.setup(GFLauncher.java:191)
at com.sun.enterprise.admin.servermgmt.cli.StartDomainCommand.createLauncher(StartDomainCommand.java:220)
at com.sun.enterprise.admin.servermgmt.cli.StartDomainCommand.executeCommand(StartDomainCommand.java:117)
at com.sun.enterprise.admin.cli.CLICommand.execute(CLICommand.java:321)
at com.sun.enterprise.admin.cli.AdminMain.executeCommand(AdminMain.java:360)
at com.sun.enterprise.admin.cli.AdminMain.doMain(AdminMain.java:298)
at org.glassfish.admin.cli.AsadminMain.main(AsadminMain.java:56)
Waiting for domain1 to start .Error starting domain domain1.
The server exited prematurely with exit code 1.
Before it died, it produced the following output:
Launching GlassFish on Felix platform
Exception in thread "main" java.lang.RuntimeException: the domain directory is not writable.
at com.sun.enterprise.glassfish.bootstrap.MainHelper.verifyDomainRoot(MainHelper.java:244)
at com.sun.enterprise.glassfish.bootstrap.MainHelper.findInstanceRoot(MainHelper.java:347)
at com.sun.enterprise.glassfish.bootstrap.GlassFishMain.main(GlassFishMain.java:78)
at com.sun.enterprise.glassfish.bootstrap.ASMain.main(ASMain.java:54)
Command start-domain failed.
I sense there is something problem in path /opt/glassfish4/glassfish/bin/asadmin. I am working on my first JSF web application and cannot run glassfish server. I am using Netbeans and ubuntu 13.10.
Can anyone show me the way?
Thank you!

The error messages
java.io.IOException: Couldn't get lock for
/opt/glassfish4/glassfish/domains/domain1/logs/server.log
and
Exception in thread "main" java.lang.RuntimeException: the domain
directory is not writable.
indicate that the user account you use to start the server doesn't have write permissions in your Glassfish domain folder.
To solve the problem either change the permissions or start the asadmin command with a user who has sufficient permissions.
If this doesn't solve the problem, there may be another process which has a lock on your server.log file, but I guess you would have noticed that. To make sure you can run
lsof /opt/glassfish4/glassfish/domains/domain1/logs/server.log
to see if any process is using the file.
See also:
Failed to start glassfish server because Couldn't get lock for /opt/glassfishv3/glassfish/domains/domain1/logs/server.log

RAD - JVM debug port is in use

I am using RAD 7.5.0 and the websphere server v6.1. When i start the server in debug mode, it displays a error message states that
'Starting WebSphere application server in localhost; has encountered a problem.
JVM debug port #### is in use.
What is the problem? How to resolve this?

i also frustrated many times because of this eroor.. Finally found out the solution
To resolve this problem you will need to do the following to all of your subsequent servers:
1.Start the server in 'normal' mode (i.e. non-debug mode).
2.Launch the Administrative console and log in.
3.Expand 'Servers', click on 'Application Servers', and then your server instance (typically 'server1').
4.On the 'Configuration' tab expand 'Java and Process Management' and then click on 'Process Definition'.
5.Under the 'Additional Properties' header, click on 'Java Virtual Machine'.
6.Scroll to the bottom of the page, locate the 'Debug Arguments' text field, and increment the 'address' property at the very end of the string so it will use a unique port value.
7.Save your changes, exit the administrative console, stop the server, and then start it in debug mode

It simply means that the debug port is currently in use. Do you have any other IBM products already running on that box? Does this happen when you start your server for the first time or for subsequent tries?
One suggestion would be to hunt down rogue hanging Java processes and kill them (in case you don't need them) to resolve this.

Open task manager in admin mode and run the following two commands.
1: netstat -ano | findstr :PORT_NUMBER
e.g.: netstat -ano | findstr 7781
2: taskkill /PID PID /F (PID will be the number that is shown e.g.: 32181)
e.g.: taskkill /PID 32181 /F