JAVA_HOME variable not defined correctly
William Chaney
The JAVA_HOME environment variable is not defined correctly
This environment variable is needed to run this program
NB: JAVA_HOME should point to a JDK not a JRE
this is the path for JAVA_HOME
/usr/lib/jvm/java-1.7.0-openjdk-amd64
this is the which java result
/usr/lib/jvm/java-1.7.0-openjdk-amd64/bin/java
this is the type java result
java is /usr/lib/jvm/java-1.7.0-openjdk-amd64/bin/java
this is the java -version
java version "1.7.0_51"
OpenJDK Runtime Environment (IcedTea 2.4.6) (7u51-2.4.6-1ubuntu4)
OpenJDK 64-Bit Server VM (build 24.51-b03, mixed mode)
if their is anything else you need for this darn thing to work tell me.
Herrick, Rick
Are you getting those values from the setup.sh script output? Right as you run that script, it should output something like:
Using XDAT Installation: /data/tip/home/xnat_builder_1_6dev
Using JAVA_HOME: /usr/lib/jvm/java-1.7.0
Verify Java Version (with java -version)
java version "1.7.0_45"
Java(TM) SE Runtime Environment (build 1.7.0_45-b18)
Java HotSpot(TM) 64-Bit Server VM (build 24.45-b08, mixed mode)
That would indicate exactly what the script is getting when invoked, which may differ from what you’re seeing running from the command line.
If you see the same thing there, then the only other thing I could guess would be issues with the OpenJDK version of Java 1.7. If you’re on Ubuntu, it’s easy enough to install the Oracle 1.7 JDK:
http://www.webupd8.org/2012/01/install-oracle-java-jdk-7-in-ubuntu-via.html
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
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William Chaney
maven.appserver.home = TOMCAT_HOME
xdat.project.name=xnat
xdat.project.template=xnat
xdat.project.db.name=
xdat.project.db.driver=org.postgresql.Driver
xdat.project.db.connection.string=jdbc:postgresql://localhost/xnat
xdat.project.db.user=postgres
xdat.project.db.password=xxxxxxx
and when I run the setup.sh script it now gives me this error
Using XDAT Installation: /home/liam/Downloads/xnat
Using JAVA_HOME: /usr/lib/jvm/java-7-oracle
Verify Java Version (with java -version)
Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
Executing /home/liam/Downloads/xnat/plugin-resources/maven-1.0.2/bin/maven xdat:setup
__ __
| \/ |__ _Apache__ ___
| |\/| / _` \ V / -_) ' \ ~ intelligent projects ~
|_| |_\__,_|\_/\___|_||_| v. 1.0.2
build:start:
xdat:setup:
[echo] HOME: /home/liam/Downloads/xnat
Unable to connected to 'jdbc:postgresql://localhost/xnat'
Please resolve the PostgreSQL issue (specified below).
BUILD FAILED
File...... /home/liam/Downloads/xnat/maven.xml
Element... ant:TestDB
Line...... 1427
Column.... 183
Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
Total time: 1 seconds
Finished at: Fri Jul 25 13:10:05 CDT 2014
Herrick, Rick
[xnatdev@xnat-dev02 xnat]$ createuser -U postgres xnat
Shall the new role be a superuser? (y/n) n
Shall the new role be allowed to create databases? (y/n) y
Shall the new role be allowed to create more new roles? (y/n) n
[xnatdev@xnat-dev02 xnat]$ createdb -U xnat xnat
Then you may need to modify your pg_hba.conf configuration to set the authentication method for the xnat user. If you search this group, there were a few conversations recently about how to set that up.
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
(314) 827-4250
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] on behalf of William Chaney [william...@gmail.com]
Sent: Friday, July 25, 2014 1:49 PM
To: xnat_di...@googlegroups.com
Subject: [XNAT Discussion] Re: JAVA_HOME variable not defined correctly
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William Chaney
On Friday, July 25, 2014 10:50:30 AM UTC-5, William Chaney wrote:
William Chaney
Using XDAT Installation: /home/liam/Downloads/xnat
Using JAVA_HOME: /usr/lib/jvm/java-7-oracle
Verify Java Version (with java -version)
java version "1.7.0_65"
Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
Executing /home/liam/Downloads/xnat/plugin-resources/maven-1.0.2/bin/maven xdat:setup
__ __
| \/ |__ _Apache__ ___
| |\/| / _` \ V / -_) ' \ ~ intelligent projects ~
|_| |_\__,_|\_/\___|_||_| v. 1.0.2
build:start:
xdat:setup:
[echo] HOME: /home/liam/Downloads/xnat
Unable to connected to 'jdbc:postgresql://localhost/xnat'
Please resolve the PostgreSQL issue (specified below).
BUILD FAILED
File...... /home/liam/Downloads/xnat/maven.xml
Element... ant:TestDB
Column.... 183
FATAL: role "postgres" does not exist
Total time: 1 seconds
Finished at: Mon Jul 28 14:42:44 CDT 2014
and I matched my pg_hba.conf file to this example
# TYPE DATABASE USER CIDR-ADDRESS METHOD
local all all trust
# The same using local loopback TCP/IP connections.
#
# TYPE DATABASE USER CIDR-ADDRESS METHOD
host all all 127.0.0.1/32 trust
# The same as the last line but using a separate netmask column
#
# TYPE DATABASE USER IP-ADDRESS IP-MASK METHOD
host all all 127.0.0.1 255.255.255.255 trust
# Allow any user from any host with IP address 192.168.93.x to connect
# to database "postgres" as the same user name that ident reports for
# the connection (typically the Unix user name).
#
# TYPE DATABASE USER CIDR-ADDRESS METHOD
host postgres all 192.168.93.0/24 ident sameuser
# Allow a user from host 192.168.12.10 to connect to database
# "postgres" if the user's password is correctly supplied.
#
# TYPE DATABASE USER CIDR-ADDRESS METHOD
host postgres all 192.168.12.10/32 md5
# In the absence of preceding "host" lines, these two lines will
# reject all connection from 192.168.54.1 (since that entry will be
# matched first), but allow Kerberos 5 connections from anywhere else
# on the Internet. The zero mask means that no bits of the host IP
# address are considered so it matches any host.
#
# TYPE DATABASE USER CIDR-ADDRESS METHOD
host all all 192.168.54.1/32 reject
host all all 0.0.0.0/0 krb5
# Allow users from 192.168.x.x hosts to connect to any database, if
# they pass the ident check. If, for example, ident says the user is
# "bryanh" and he requests to connect as PostgreSQL user "guest1", the
# connection is allowed if there is an entry in pg_ident.conf for map
# "omicron" that says "bryanh" is allowed to connect as "guest1".
#
# TYPE DATABASE USER CIDR-ADDRESS METHOD
host all all 192.168.0.0/16 ident omicron
# If these are the only three lines for local connections, they will
# allow local users to connect only to their own databases (databases
# with the same name as their database user name) except for administrators
# and members of role "support", who can connect to all databases. The file
# $PGDATA/admins contains a list of names of administrators. Passwords
# are required in all cases.
#
# TYPE DATABASE USER CIDR-ADDRESS METHOD
local sameuser all md5
local all @admins md5
local all +support md5
# The last two lines above can be combined into a single line:
local all @admins,+support md5
# The database column can also use lists and file names:
local db1,db2,@demodbs all md5
On Friday, July 25, 2014 10:50:30 AM UTC-5, William Chaney wrote:
Herrick, Rick
Are you able to log into PostgreSQL through psql? This is really not an XNAT issue, but is an issue with how the PostgreSQL server is configured. You need to make sure you can connect to that before XNAT itself can connect. Like I said previously, I’d also suggest not using the postgres user for that purpose, but creating a specific xnat user and creating a config in your pg_hba.conf for that user.
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com]
On Behalf Of William Chaney
Sent: Monday, July 28, 2014 3:04 PM
To: xnat_di...@googlegroups.com
Subject: [XNAT Discussion] Re: JAVA_HOME variable not defined correctly
it is now giving me a new problem this is the text
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William Chaney
On Friday, July 25, 2014 10:50:30 AM UTC-5, William Chaney wrote:
Herrick, Rick
That’s something you’re going to need to get figured out. There’s clearly some kind of connection issue with your database. You should be able to add a user (e.g. xnat), modify the pg_hba.conf to allow that user to connect from the localhost without a password, restart postgres, and then connect with that user.
You can find out more about the pg_hba.conf here: http://www.postgresql.org/docs/9.2/static/auth-pg-hba-conf.html
You’ll want to add something like this:
host xnat xnat 127.0.0.1/32 trust
local xnat xnat trust
That says that on hosts starting with 127.0.0 (i.e. anything that is normally construed as localhost), the xnat user is trusted on the xnat database, so you can’t fail on login. The second line says that the same thing goes for user xnat on database xnat on the localhost (which can be different from 127.0.0.* depending on whether the connection uses the loopback network interface).
I think you don’t need to add the xnat role before doing that, but you want to do that anyway just in case.
But however you do it, you need to be able to connect to the database reliably as a prerequisite to getting XNAT to work.
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com]
On Behalf Of William Chaney
Sent: Wednesday, July 30, 2014 10:44 AM
To: xnat_di...@googlegroups.com
Subject: [XNAT Discussion] Re: JAVA_HOME variable not defined correctly
I could not connect through psql through anyone else but postgres whenever I try to sign in to another postgres user it says their is no password entry for them I have several times gone in through users to circumvent this problem: MyUser > Root > postgres and for some reason postgres does not like my password.
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