Hi Pablo,
Is the database installed on the same machine as the webserver. Check the db
url here:
--------------db.url = jdbc:mysql://localhost/base2
Put the correct url and then the port number MYSQL is listening to. In most
cases it is: 3306.
Hope this helps.
Regards,
Dominic
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Pablo Lemos
Ochandio
Sent: 20 March 2006 12:15
To: basedb-users@lists.sourceforge.net
Subject: Re: [base] A problem with intidb in BASE2.0RC1
Hi dominic!!
My base.config is:
# $Id: base.config.in,v 1.2 2004/11/30 12:48:41 nicklas Exp $
#
# BioArray Software Environment (BASE) - http://base.thep.lu.se/
# Copyright (C) 2002-2004 Lao Saal, Carl Troein,
# Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
#
# This file is part of BASE.
#
# BASE is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# BASE is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330,
# Boston, MA 02111-1307, USA.
# ----------------------------------------
# =======================
# Database driver section
# =======================
# -----
# MySQL
# -----
db.dialect = org.hibernate.dialect.MySQLInnoDBDialect
db.driver = com.mysql.jdbc.Driver
db.url = jdbc:mysql://localhost/base2
db.dynamic.catalog = base2dynamic
db.queries = /mysql-queries.xml
export.max.items = 20000
# --------
# Postgres
# --------
#db.dialect = org.hibernate.dialect.PostgreSQLDialect
#db.driver = org.postgresql.Driver
#db.url = jdbc:postgresql:base2
#db.dynamic.catalog = base2
#db.dynamic.schema = dynamic
#db.queries = /postgres-queries.xml
#export.max.items = 0
# -------------
# Common to all
# -------------
db.username = base2user
db.password = password
db.extended-properties = /extended-properties.xml
db.raw-data-types = /raw-data-types.xml
db.batch-size = 50
# ======================
# Authentication section
# ======================
# ----------------
# POP3 mail server
# ----------------
#auth.driver = net.sf.basedb.core.authentication.POP3Authenticator
#auth.init = mail.example.com
#auth.synchronize = 0
#auth.cachepasswords = 0
#auth.daystocache = 0
# ==========================
# Internal job queue section
# ==========================
# If the internal job queue should be enabled or not
jobqueue.internal.enabled = true
#jobqueue.internal.maxthreadpriority = 4
# Number of seconds between checks to the job queue
jobqueue.internal.checkinterval = 30
# NOTE! A quick job may use threads from any of the "slower" pools
# if there is place for another thread
# Number of threads to reserved for jobs that takes < 1 minute to execute
jobqueue.internal.shortest.threads = 1
#jobqueue.internal.shortest.threadpriority = 4
# Number of threads to reserved for jobs that takes < 10 minutes to execute
jobqueue.internal.short.threads = 1
#jobqueue.internal.short.threadpriority = 4
# Number of threads to reserved for jobs that takes < 1 hour to execute
jobqueue.internal.medium.threads = 2
#jobqueue.internal.medium.threadpriority = 3
# Number of threads to reserved for jobs that takes > 1 hour to execute
jobqueue.internal.long.threads = 4
#jobqueue.internal.medium.threadpriority = 3
# =========================
# Secondary storage section
# =========================
# The classname of the driver; leave empty to disable secondary storage
# secondary.storage.driver = net.sf.basedb.core.InternalStorageController
# Initialisation options to the seconday storage controller
# The internal implementation wants a path to the secondary directory
# secondary.storage.init = /usr/local/base2/secondary
# The interval (in seconds) between checks for new files to move
# secondary.storage.interval = 3600
# ===============
# General section
# ===============
# The path to the directory where uploaded files are stored
userfiles = /usr/local/base/files
# Number of minutes to keep permission information for the logged
# in user in memory before it is reloaded from the database.
permission.timeout = 10
# Number of minutes to keep SessionControl object in the cache
# after the last use
cache.timeout = 20
i have tryed to not change any of the settings to check if the initbd
work. I create a base2user as the documentation say...
I dont know if the problem are to connect to MySQL server or privileges
of the user. My base2user have privileges to: create, update, delete,
drop, alter, insert
Thanks
dominic oyeniran escribió:
Hi
I reckon its something to do with the database setup parameters in your
base
config file. Can u check it again or post it here and I can have a look at
it?
Regards,
Dominic
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Pablo Lemos
Ochandio
Sent: 20 March 2006 10:57
To: basedb-users@lists.sourceforge.net
Subject: [base] A problem with intidb in BASE2.0RC1
Hi!!
Im not sure if this is the right way to communicate a problem with the
installation of BASE2.0RC1 but im desesperate.
Im the Sysadmin of Instituto Valenciano de Investigaciones Agrarias
(IVIA) at Spain. The Genomic Departament request to me if i can to
install the BASE2 package at the Web server. Im trying to install it but
when i launch the initdb script it crash at give the next message error:
[EMAIL PROTECTED] bin]# ./initdb.sh netsensor
[0%] Building
database....................................................................
.11:30:35,173
WARN BasicResourcePool:1222 -
[EMAIL PROTECTED] --
Acquisition Attempt Failed!!! Clearing pending acquires. While trying to
acquire a needed new resource, we failed to succeed more than the
maximum number of allowed acquisition attempts (30).
.11:30:36,147 WARN BasicResourcePool:1222 -
[EMAIL PROTECTED] --
Acquisition Attempt Failed!!! Clearing pending acquires. While trying to
acquire a needed new resource, we failed to succeed more than the
maximum number of allowed acquisition attempts (30).
........................................................11:31:33,739
WARN BasicResourcePool:1222 -
[EMAIL PROTECTED] --
Acquisition Attempt Failed!!! Clearing pending acquires. While trying to
acquire a needed new resource, we failed to succeed more than the
maximum number of allowed acquisition attempts (30).
[30%] Building database failed: Cannot open connection
net.sf.basedb.core.BaseException: Cannot open connection
at
net.sf.basedb.core.HibernateUtil.newSession(HibernateUtil.java:760)
at
net.sf.basedb.core.HibernateUtil.isEmptyDatabase(HibernateUtil.java:439)
at
net.sf.basedb.core.HibernateUtil.createStaticTables(HibernateUtil.java:403)
at net.sf.basedb.core.Install.createTables(Install.java:108)
at net.sf.basedb.install.InitDB.main(InitDB.java:57)
Caused by: org.hibernate.exception.GenericJDBCException: Cannot open
connection
at
org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLSta
teConverter.java:91)
at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79)
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java
:43)
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java
:29)
at
org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:3
63)
at
org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:12
2)
at
org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.ja
va:40)
at $Proxy0.setTransactionIsolation(Unknown Source)
at
net.sf.basedb.core.HibernateUtil.newSession(HibernateUtil.java:755)
... 4 more
Caused by: java.sql.SQLException: Connections could not be acquired from
the underlying database!
at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:104)
at
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C
3P0PooledConnectionPool.java:236)
at
com.mchange.v2.c3p0.PoolBackedDataSource.getConnection(PoolBackedDataSource.
java:94)
at
org.hibernate.connection.C3P0ConnectionProvider.getConnection(C3P0Connection
Provider.java:35)
at
org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:3
60)
... 8 more
Caused by: com.mchange.v2.resourcepool.CannotAcquireResourceException: A
ResourcePool could not acquire a resource from its primary factory or
source.
at
com.mchange.v2.resourcepool.BasicResourcePool.awaitAcquire(BasicResourcePool
.java:970)
at
com.mchange.v2.resourcepool.BasicResourcePool.checkoutResource(BasicResource
Pool.java:208)
at
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C
3P0PooledConnectionPool.java:232)
... 11 more
I have tested all the steps in the documentation since the initdb
script. (I test MySQL database (ok), apache installation (ok), java
installation and home variable (ok), ant installation (ok) and BASE
configuration (ok)).
Please, Can you help me?
PS: I create a user base2user by the following way:
GRANT ALL ON base2.* TO 'base2user'@'%' IDENTIFIED BY 'password';
GRANT ALL ON base2dynamic.* TO 'base2user'@'%';
with the wildcard '%' i can to connect to the MySQL server in different
machine with command:
mysql -h<IP_MACHINE_REMOTE> -ubase2user -p
Thanks a lot
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that extends applications into web and mobile media. Attend the live webcast
and join the prime developer group breaking into this new coding territory!
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