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.

Cloud Foundry java buildpack - java: command not found

New to cloud foundry, using the java buildpack to push a zip distribution of a java app. It detects the start script correctly, but when the start script gets to the point where it needs to start up the jvm, I get this error:
bash: java: command not found
Apparently 'java' is not on the shell's path during execution of the script, and I'm not finding a JAVA_HOME definition anywhere.
What is the path to use for starting java apps?
Where is it documented?
FALSE ALARM
Many thanks to #DanielMikusa for pointing out that JAVA_HOME is indeed set, even in the pretty old version of the buildpack that was in use. Nothing to see here.
EDIT #1
I've been able to find out that when the start script launches there is a jre located in $PWD/.buildpack-java/oracle_jre. But, this can't be what I'm expected to use to specify for the path of JAVA_HOME, can it? It seems like this location is entirely dependent on the java buildpack's current implementation. It seems like either the jre's bin folder should be in the start script's process' path or that there should be an environment variable or other configuration established prior to running the launch script so I can use that value for finding the java executable.
EDIT #2
Below is the output during the cf push operation:
PS E:\dev\hoobajoob\myproject\build\distributions> cf push -p .\my-service-1.0.0.zip my-service
Using manifest file E:\dev\hoobajoob\myproject\build\distributions\manifest.yml
Creating app my-service in org DEV / space dev as chefhoobajoob#github.com...
OK
Creating route my-service.cflab.dctmlabs.com...
OK
Binding my-service.cflab.dctmlabs.com to my-service...
OK
Uploading my-service...
Uploading app files from: C:\Users\hoobajoob\AppData\Local\Temp\unzipped-app384867239
Uploading 9.7M, 9390 files
Done uploading
OK
Starting app my-service in org DEV / space dev as chefhoobajoob#github.com...
Downloading oracle_buildpack_151...
Downloading binary_buildpack...
Downloading go_buildpack...
Downloading python_buildpack...
Downloading java-buildpack-offline-v3-19-2...
Downloaded java-buildpack-offline-v3-19-2
Downloading java-buildpack-offline-4-7...
...<more downloads>
Creating container
Successfully created container
Downloading app package...
Downloaded app package (53.1M)
Staging...
-----> Java Buildpack Version: v3.5.1 (offline) | https://github.com/cloudfoundry/java-buildpack.git#3abc3db
-----> Downloading Oracle JRE 1.8.0_112 from http://127.0.0.1/oracle-jre/trusty/x86_64/jre-8u112-linux-x64.tar.gz (found
in cache)
Expanding Oracle JRE to .java-buildpack/oracle_jre (2.3s)
-----> Downloading Open JDK Like Memory Calculator 2.0.1_RELEASE from https://download.run.pivotal.io/memory-calculator/
trusty/x86_64/memory-calculator-2.0.1_RELEASE.tar.gz (found in cache)
Memory Settings: -Xms2304M -XX:MetaspaceSize=314572K -Xss1M -Xmx2304M -XX:MaxMetaspaceSize=314572K
-----> Downloading Spring Auto Reconfiguration 1.10.0_RELEASE from https://download.run.pivotal.io/auto-reconfiguration/
auto-reconfiguration-1.10.0_RELEASE.jar (found in cache)
Exit status 0
Staging complete
Uploading droplet, build artifacts cache...
Uploading droplet...
Uploading build artifacts cache...
Uploaded build artifacts cache (108B)
Uploaded droplet (120.5M)
Uploading complete
Destroying container
Successfully destroyed container
0 of 1 instances running, 1 starting
0 of 1 instances running, 1 starting
0 of 1 instances running, 1 starting
0 of 1 instances running, 1 starting
0 of 1 instances running, 1 starting
0 of 1 instances running, 1 starting
0 of 1 instances running, 1 starting
0 of 1 instances running, 1 starting
1 of 1 instances running
App started
OK
App my-service was started using this command `CALCULATED_MEMORY=$($PWD/.java-buildpack/oracle_jre/bin/java-buildpack-memory-calculator-2.0.1_RELEASE -memorySizes=metaspace:64m.. -memoryWeights=heap:75,metaspace:10,native:10,stack:5 -memoryInitials=heap:100%,metaspace:100% -totMemory=$MEMORY_LIMIT) && JAVA_HOME=$PWD/.java-buildpack/oracle_jre JAVA_OPTS="-Djava.io.tmpdir=$TMPDIR -XX:OnOutOfMemoryError=$PWD/.java-buildpack/oracle_jre/bin/killjava.sh $CALCULATED_MEMORY" exec $PWD/my-service-1.0.0/bin/launch`

Writing up the comments above in case someone else comes across this question.
We reviewed the full output of staging and the start up command generated by the Java buildpack.
We could see from the start command generated by the Java buildpack that it is the start commands responsibility to set JAVA_HOME.
If you rely on the Java buildpack to create the start command for your dist-zip style applications, it will "do the right thing" and add the JAVA_HOME environment variable with the correct path to the start command.
If you need to create a custom start command, it is your responsibility to set JAVA_HOME correctly.
If you cf ssh into an application started by the Java buildpack, it is your responsibility to set JAVA_HOME.

CentOS Java application error with SELinux

I have a CentOS box hosting a Drupal 7 site. I've attempted to run a Java application called Tika on it, to index files using Apache Solr search.
I keep running into an issue only when SELinux is enabled:
extract using tika: OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00007f1ed9000000, 2555904, 1) failed; error='Permission denied' (errno=13)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 2555904 bytes for committing reserved memory.
# An error report file with more information is saved as:
# /tmp/jvm-2356/hs_error.log
This does not happen if I disable selinux. If I run the command from SSH, it works fine -- but not in browser. This is the command it is running:
java '-Dfile.encoding=UTF8' -cp '/var/www/drupal/sites/all/modules/contrib/apachesolr_attachments/tika' -jar '/var/www/drupal/sites/all/modules/contrib/apachesolr_attachments/tika/tika-app-1.11.jar' -t '/var/www/drupal/sites/all/modules/contrib/apachesolr_attachments/tests/test-tika.pdf'
Here is the log from SELinux at /var/log/audit/audit.log:
type=AVC msg=audit(1454636072.494:3351): avc: denied { execmem } for pid=11285 comm="java" scontext=unconfined_u:system_r:httpd_t:s0 tcontext=unconfined_u:system_r:httpd_t:s0 tclass=process
type=SYSCALL msg=audit(1454636072.494:3351): arch=c000003e syscall=9 success=no exit=-13 a0=7fdfe5000000 a1=270000 a2=7 a3=32 items=0 ppid=2377 pid=11285 auid=506 uid=48 gid=48 euid=48 suid=48 fsuid=48 egid=48 sgid=48 fsgid=48 tty=(none) ses=1 comm="java" exe="/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.95.x86_64/jre/bin/java" subj=unconfined_u:system_r:httpd_t:s0 key=(null)
Is there a way I can run this with SELinux enabled? I do not know the policy name of Tika (or should I use Java?) so I'm unsure where to go from here...

This worked for me...
I have tika at /var/apache-tika/tika-app-1.14.jar
setsebool -P httpd_execmem 1
chcon -t httpd_exec_t /var/apache-tika/tika-app-1.14.jar
Using the sealert tools (https://wiki.centos.org/HowTos/SELinux) helped track down the correct selinux type.

All of your context messages reference httpd_t, so I would run
/usr/sbin/getsebool -a | grep httpd
And experiment with enabling properties that show as off. It's been a while since I ran a database-backed website (Drupal, WordPress, etc.) on CentOS, but as I recall, these two were required to be enabled:
httpd_can_network_connect
httpd_can_network_connect_db
to enable a property with persistence, run
setsebool -P httpd_can_network_connect on
etc.

The booleans you're looking for are:
httpd_execmem
httpd_read_user_content
How to find:
audit2why -i /var/log/audit/audit.log will tell you this.
Part of package: policycoreutils-python-utils

specify port for standalone mode in PlayFrameWork 2.2.1

I have two apps developed in PlayFrameWork 2.2.1 named:
1. helloWorld_88
2. helloWorld_99
For helloWorld_88:
I want to build this app run (standalone) on port 88.
For helloWorld_99:
I want to build this app run (standalone) on port 99.
As I know, using "dist" task will help me to build a standalone version of apps but I don't know how to specify the port.
Can anybody advice step by step.
Thanks
Rado
Hi Rado, Thanks for your quick reply.
I have already try this before I post the question, but the port always 9000.
See bellow output from the command line (Windows)
E:\Deploy\helloworld_88\bin>helloworld_88 -Dhttp.port=88
Play server process ID is 2216
[info] play - Application started (Prod)
[info] play - Listening for HTTP on /0:0:0:0:0:0:0:0:9000
Any other idea
Thanks

I assume that you have built both applications using "play dist" command and that you run them using generated "bin/helloWorld_88" and "bin/helloWorld_99" script files on Linux. (for Windows these files are named "bin/helloWorld_88.bat" and "bin/helloWorld_99.bat")
Go to the "bin" folder and run:
helloWorld_88 -Dhttp.port=88
and then for the second application do:
helloWorld_88 -Dhttp.port=99

Automatically stop "tail -f catalina.out" when exception found or server is running

I have set up an automated deployment script (in shell script) for my web application.
It uses java, tomcat, maven and a postgres database.
The deployment script does this:
builds the deployable application from source repository
stops tomcat
applies database migration patches
deploys the war files in tomcat
starts tomcat (by invoking $TOMCAT_HOME/bin/startup.sh)
exits with a success message
It's all working and it's pretty neat - but it needs a little improvement.
You see, even though it exits with a success message, sometimes the deploy was not successful because the web application did not start correctly.
I would like to refactor steps 5 and 6 so that after bring up the tomcat server, the deployment script would "tail -f" in the catalina.out file, looking either for a "server started successfully" message or an exception stack trace.
The tail -f output up to that point should be part of the output of the deployment script, and step 6 would "exit 0" or "exit 1" accordingly.
I know that should be possible, if not in shell script, maybe with python.
The problem is I'm a java specialist - and by specialist I mean I suck at everything else :-)
Help please? :-)

Maybe something like this?
tmp=$(mktemp -t catalina.XXXXXXX) || exit 136
trap 'rm "$tmp"' 0
trap 'exit 255' 2 15
tail -n 200 catalina.out >"$tmp"
if grep -q error "$tmp"; then
cat "$tmp"
exit 1
fi
exit 0
On the other hand, if startup.sh were competently coded, you could just
if startup.sh; then
tail -f catalina.out
else
exit $?
fi
which can be shortened to
startup.sh || exit $?
tail -f catalina.out

As an alternative, you might want to take a look at the Apache Tomcat Manager application. It supports, amongst other things:
Deploying applications remotely, and from local paths
Listing currently deployed applications
Reloading existing applications
Starting an existing application
Stopping an existing application
Undeploying an existing application
The manager provides a web interface that can be called via curl, and which returns simple, parseable messages to indicate the status of the invoked command. Management functions can also be invoked via JMX, or Ant scripts. All in all, a very handy tool.

I ended up implementing a solution using Python's subprocess.Popen, as suggested by #snies.
Here's what it looks like:
waitForIt.py
#! /usr/bin/env python
import subprocess
import sys
def main(argv):
filename = argv[1]
match=argv[2]
p = subprocess.Popen(['tail', '-n', '0', '-f', filename], stdout=subprocess.PIPE)
while True :
line = p.stdout.readline()
print line ,
if match in line :
break
p.terminate()
if __name__ == "__main__":
main(sys.argv)
tailUntil.sh
#!/bin/bash
set -e
filename=$1
match=$2
thisdir=$(dirname $0)
python $thisdir/waitForIt.py "$filename" "$match"
and then
startTomcat.sh
${TOMCAT_HOME}/bin/startup.sh
logDeploy.sh "Agora vamos dar um tail no catalina.out..."
util_tailUntil.sh "$TOMCAT_HOME/logs/catalina.out" 'INFO: Server startup in '
It doesn't do what I originally intended (it still exits with return code 0 even when there is a stacktrace - but that could be changed with a little bit more of Python magic),
but all of tomcat's initialization log is part of the automated deploy out (and easily viewable on Jenkins' deploy job) -
so that's good enough.