Database connectivity Issue

[Keith Jones]

Hi All,

I'm trying to move an installation of Dspace 5.3 to a new Centos 7
server. I've installed all the software required and have everything
running. I'm able to compile the Dspace software, which goes without a
problem. I test the database connection and it works fine. When I
deploy the xmlui into the webapps area of Tomcat, I'm getting the
following error:

SEVERE: Exception sending context destroyed event to listener instance
of class org.dspace.app.util.DS
paceContextListener
java.lang.IllegalStateException: The connection attempt failed.
at org.dspace.storage.rdbms.DatabaseManager.getDataSource(DatabaseManager.java:655)
at org.dspace.storage.rdbms.DatabaseManager.getConnection(DatabaseManager.java:629)
at org.dspace.core.Context.init(Context.java:121)
at org.dspace.core.Context.<init>(Context.java:95)
at org.dspace.app.util.AbstractDSpaceWebapp.deregister(AbstractDSpaceWebapp.java:97)
at org.dspace.app.util.DSpaceContextListener.contextDestroyed(DSpaceContextListener.java:146)
at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:5165)
at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5829)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:221)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:149)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1260)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:2002)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:
152)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
at org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:125)
at org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:30)
at org.postgresql.jdbc3g.AbstractJdbc3gConnection.<init>(AbstractJdbc3gConnection.java:22)
at org.postgresql.jdbc4.AbstractJdbc4Connection.<init>(AbstractJdbc4Connection.java:32)
at org.postgresql.jdbc4.Jdbc4Connection.<init>(Jdbc4Connection.java:24)
at org.postgresql.Driver.makeConnection(Driver.java:393)
at org.postgresql.Driver.connect(Driver.java:267)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at org.apache.commons.dbcp.DriverManagerConnectionFactory.createConnection(DriverManagerConnec
tionFactory.java:75)
at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java
:582)
at org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:974)
at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:106)
at org.dspace.storage.rdbms.DatabaseManager.initialize(DatabaseManager.java:1336)
at org.dspace.storage.rdbms.DatabaseManager.getDataSource(DatabaseManager.java:650)
... 19 more
Caused by: java.net.SocketException: Permission denied (connect failed)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at org.postgresql.core.PGStream.<init>(PGStream.java:62)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:
76)
... 35 more

Any help would be appreciated.

Thanks
Keith

[Ayuka Phanuel]

Confirm your database credentials (name, url, password, username) added to your local.cfg or dspace.cfg

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[Keith Jones]

Hi,
I checked the dspace.cfg file and the information is correct.

I've run this:

-bash-4.2$ ../bin/dspace database test

Attempting to connect to database using these configurations:
- URL: jdbc:postgresql://localhost:5432/dspace
- Driver: org.postgresql.Driver
- Username: dspace
- Password: [hidden]
- Schema:

Testing connection...
Connected successfully!

[Tony Brian Albers]

What does getenforce say? This might be SELinux doing its job ;)

Check /var/log/audit/audit.log for stuff related to tomcat/catalina,
pgsql etc.

Check the pgsql logs, they usually have some pointer as to where it
goes wrong. Also check the tomcat logs.

And an important thing:

The password stated in dspace.cfg or local.cfg must be entered as
follows:

db.password = un@b0mb3R?

make sure the spaces are there and be careful that your password
doesn't contain = or localized characters (german umlaut etc.)

also try to connect to pgsql directly from the CLI as the dspace user
like so:

[dspace@rigel config]$ psql -U dspace -W -d dspace
Password for user dspace: 
psql (9.5.14)
Type "help" for help.

dspace=>> \l
                                  List of databases
   Name    |  Owner   | Encoding |   Collate   |    Ctype    |   Access
privileges   
-----------+----------+----------+-------------+-------------+---------
--------------
 dspace    | dspace   | UTF8     | C           | C           | 
 postgres  | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | 
 template0 | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
=c/postgres          +
           |          |          |             |             |
postgres=CTc/postgres
 template1 | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
=c/postgres          +
           |          |          |             |             |
postgres=CTc/postgres
(4 rows)

dspace=>

HTH

/tony

--
Tony Albers - Systems Architect - IT Development
Royal Danish Library, Victor Albecks Vej 1, 8000 Aarhus C, Denmark
Tel: +45 2566 2383 - CVR/SE: 2898 8842 - EAN: 5798000792142

[Keith Jones]

Hi Thanks for the information:

I used the getenforce and the result says: Enforcing.

Checking the audit log gives me this error:

type=AVC msg=audit(1561555586.173:6325): avc: denied { name_connect
} for pid=15077 comm="java" des
t=5432 scontext=system_u:system_r:tomcat_t:s0
tcontext=system_u:object_r:postgresql_port_t:s0 tclass=t
cp_socket permissive=0
type=SYSCALL msg=audit(1561555586.173:6325): arch=c000003e syscall=42
success=no exit=-13 a0=35 a1=7f6
7977312f0 a2=1c a3=224 items=0 ppid=1 pid=15077 auid=4294967295 uid=53
gid=53 euid=53 suid=53 fsuid=53
egid=53 sgid=53 fsgid=53 tty=(none) ses=4294967295 comm="java"
exe="/usr/lib/jvm/java-1.8.0-openjdk-1
.8.0.212.b04-0.el7_6.x86_64/jre/bin/java"
subj=system_u:system_r:tomcat_t:s0 key=(null)

Running the CLI dspace database command gives me this result:
dspace databse test

Attempting to connect to database using these configurations:
- URL: jdbc:postgresql://localhost:5432/dspace
- Driver: org.postgresql.Driver
- Username: dspace
- Password: [hidden]
- Schema:

Testing connection...
Connected successfully!

Also when I run the command to connect to postgres, it runs fine as well:
As the dspace use I run the psql command, and get this:

psql (9.2.24)

Type "help" for help.

dspace=>

Run \l command and get this:

List of databases
Name | Owner | Encoding | Collate | Ctype | Access
privileges

-----------+----------+----------+------------+------------+-----------------------
dspace | dspace | UTF8 | en_US.utf8 | en_US.utf8 |
postgres | postgres | LATIN1 | en_US | en_US |
template0 | postgres | LATIN1 | en_US | en_US |
=c/postgres +
| | | | |
postgres=CTc/postgres
template1 | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
(4 rows)

I'm still not able to get the xmlui running.

Thanks
Keith