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From: wei yuan [mailto:yuanwei2@hotmail.com]
Sent: Wednesday, August 11, 2010 3:27 PM
To: Forbes, Megan
Subject: cspace installation error at nuxeo start up
Dear Megan,
I got this error when I started nuxeo:
Caused by: com.hp.hpl.jena.shared.JenaException: The database appears to
be unformatted or corrupted and
an attempt to automatically format the database has failed
at
com.hp.hpl.jena.db.impl.DriverRDB.getSystemSpecializedGraph(DriverRDB.ja
va:311)
at
com.hp.hpl.jena.db.impl.DriverRDB.getDefaultModelProperties(DriverRDB.ja
va:835)
at
com.hp.hpl.jena.db.DBConnection.getDefaultModelProperties(DBConnection.j
ava:195)
at
com.hp.hpl.jena.db.impl.GraphRDBMaker.consGraph(GraphRDBMaker.java:123)
at
com.hp.hpl.jena.db.impl.GraphRDBMaker.createGraph(GraphRDBMaker.java:107
)
at
com.hp.hpl.jena.rdf.model.impl.ModelMakerImpl.createModel(ModelMakerImpl
.java:47)
at
com.hp.hpl.jena.rdf.model.impl.ModelMakerImpl.createModel(ModelMakerImpl
.java:50)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.openGraph(JenaGraph.java
:280)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.openGraph(JenaGraph.java
:181)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.size(JenaGraph.java:820)
... 17 more
Though I ant create_db many times, it seems this error would not go
away. Your help is greatly appreciated. If such messages should not go
to you, could you please direct me to the person who I should contact.
thanks,
Mary
Dear Team,
I got this error when I started nuxeo:
Caused by: com.hp.hpl.jena.shared.JenaException: The
database appears to be unformatted or corrupted and
an attempt to automatically format the database has failed
at
com.hp.hpl.jena.db.impl.DriverRDB.getSystemSpecializedGraph(DriverRDB.java:311)
at
com.hp.hpl.jena.db.impl.DriverRDB.getDefaultModelProperties(DriverRDB.java:835)
at
com.hp.hpl.jena.db.DBConnection.getDefaultModelProperties(DBConnection.java:195)
at
com.hp.hpl.jena.db.impl.GraphRDBMaker.consGraph(GraphRDBMaker.java:123)
at
com.hp.hpl.jena.db.impl.GraphRDBMaker.createGraph(GraphRDBMaker.java:107)
at
com.hp.hpl.jena.rdf.model.impl.ModelMakerImpl.createModel(ModelMakerImpl.java:47)
at
com.hp.hpl.jena.rdf.model.impl.ModelMakerImpl.createModel(ModelMakerImpl.java:50)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.openGraph(JenaGraph.java:280)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.openGraph(JenaGraph.java:181)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.size(JenaGraph.java:820)
... 17
more
Though I ant create_db many times, it seems this error
would not go away. Your help is greatly appreciated. If such
messages should not go to you, could you please direct me to the person who I
should contact.
thanks,
Mary
Mary (Wei Yuan) wrote:
I got this error when I started nuxeo:
Caused by: com.hp.hpl.jena.shared.JenaException: The database
appears to be unformatted or corrupted and
an attempt to automatically format the database has failed ...
Though I ant create_db many times, it seems this error would not go
away. Your help is greatly appreciated. If such messages should
not go to you, could you please direct me to the person who I should
contact.
This response is from a quick Google search, noting with some
caution that I don't understand this issue in depth and haven't tried
the procedure described below first-hand, and thus this response may
contain errors:
Nuxeo uses Jena - an open source Java framework for building
Semantic Web applications, to store concept relationships to
documents, and the like:
http://doc.nuxeo.org/5.3/books/nuxeo-book/html/relation-service.html
The tables that Jena uses can be stored in any number of back-end
databases: MySQL, PostgreSQL, Derby, etc.
You can find an article on what to do if the Jena tables gets corrupted here:
"What are the preferred backends for Jena, what to do in case of corruption?"
http://www.nuxeo.org/xwiki/bin/view/FAQ/JenaBackend.
It appears the fix is to find the database Nuxeo is using to store
its Jena tables, and drop all those tables. Nuxeo will later
re-create them as needed.
To do this, in the abstract:
-
Stop both the cspace and default (Nuxeo) JBoss servers.
This is important, since the changes you'll be making below
should take place when Nuxeo is not running. -
Identify which database system Nuxeo is using to
store the Jena tables. -
Go into that database and drop each Jena table.
In my copy of the CollectionSpace system, the file
$JBOSS_HOME/server/default/deploy/nuxeo.ear/config/sql.properties
contained a line identifying which database system it's using to
store the Jena tables; e.g.
org.nuxeo.ecm.sql.jena.databaseType=MySQL
There could be other configuration file(s) that also indicate this,
but this is a start - it means there's a chance there might be Jena
tables stored in MySQL.
The next step, if so, would be to go into a MySQL client, as a user
with the administrative rights to drop tables, and look for and drop
the Jena tables. For instance, in the command-line MySQL table:
mysql> use nuxeo;
mysql> show tables like 'jena%';
If this shows a number of tables whose names begin with 'jena',
then you can do this (in the abstract):
mysql> drop table yyy
For "yyy" in the above example, you would substitute the name of a
specific table, beginning with 'jena', such as 'jena_prefix' or
'jena_g1t0_reif'.
Repeat the 'drop table' command for each jena table displayed by
the "show tables like ..." command, until all are gone.
As a more convenient alternative - I haven't tried this - you might
even be able to do this, to delete all of these tables in a single
command:
mysql> drop tables like 'jena%';
Regarding 'ant create_db': that task should drop and re-create the
'nuxeo' database in MySQL, which presumably would resolve that issue,
as well, and perhaps be simpler and quicker than the steps above.
The drawback of using 'ant create_db', rather than the steps above,
would be that any data in both the 'nuxeo' and 'cspace' databases
would be wiped out; so the approach above - deleting just the Jena
tables - is safer - and the only reasonable way to do this if you
have existing data you wish to preserve.
Two possibilities for why ant create_db might not be 'fixing' the
Jena table corruption issue:
-
The MySQL database user under which this task is being run doesn't
exist, doesn't have sufficient privileges; or the task isn't being
run from the right point in the service layer source code tree.To check on this:
a. Change to the services/trunk directory (and not
one level further down in the source tree, at
services/trunk/services, where running ant create_db
won't drop the Nuxeo table).b. Verify that the settings of the DB_USER and DB_PASSWORD
environment variables in your command shell are for
a database user with the privileges to drop tables.c. Run 'ant create_db' in verbose mode and look for any
errors; e.g.ant create_db -verbose
-
Nuxeo might be storing its Jena tables in a database other
than MySQL.As described above, you can check the Jena database type in:
$JBOSS_HOME/server/default/deploy/nuxeo.ear/config/sql.properties
Good luck! Thanks for reporting this issue, and please feel free
to report what you observe, and any solution, to this list.
Aron Roberts Information Services and Technology . Warren Hall, 2195 Hearst
University of California, Berkeley, CA 94720-4876 USA
aron@socrates.berkeley.edu . +1 510-642-5974 . fax 510-643-5385
http://purl.org/net/aron
Mary,
When you get a chance, please attach and send the following 3 log files from
the 'default' JBoss domain -this is the domain in which Nuxeo is launched.
.\jboss-4.2.3.GA\server\default\log\server.log
.\jboss-4.2.3.GA\server\default\log\nuxeo-error.log
.\jboss-4.2.3.GA\server\default\log\boot.log
This might help us diagnose the problem more easily.
Thanks,
Richard Millet
CollectionSpace Services
From: talk-bounces@lists.collectionspace.org
[mailto:talk-bounces@lists.collectionspace.org] On Behalf Of wei yuan
Sent: Wednesday, August 11, 2010 12:52 PM
To: talk@lists.collectionspace.org
Subject: [Talk] cspace db error at nuxeo start up
Dear Team,
I got this error when I started nuxeo:
Caused by: com.hp.hpl.jena.shared.JenaException: The database appears to be
unformatted or corrupted and
an attempt to automatically format the database has failed
at
com.hp.hpl.jena.db.impl.DriverRDB.getSystemSpecializedGraph(DriverRDB.java:3
11)
at
com.hp.hpl.jena.db.impl.DriverRDB.getDefaultModelProperties(DriverRDB.java:8
35)
at
com.hp.hpl.jena.db.DBConnection.getDefaultModelProperties(DBConnection.java:
195)
at
com.hp.hpl.jena.db.impl.GraphRDBMaker.consGraph(GraphRDBMaker.java:123)
at
com.hp.hpl.jena.db.impl.GraphRDBMaker.createGraph(GraphRDBMaker.java:107)
at
com.hp.hpl.jena.rdf.model.impl.ModelMakerImpl.createModel(ModelMakerImpl.jav
a:47)
at
com.hp.hpl.jena.rdf.model.impl.ModelMakerImpl.createModel(ModelMakerImpl.jav
a:50)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.openGraph(JenaGraph.java:280
)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.openGraph(JenaGraph.java:181
)
at
org.nuxeo.ecm.platform.relations.jena.JenaGraph.size(JenaGraph.java:820)
... 17 more
Though I ant create_db many times, it seems this error would not go away.
Your help is greatly appreciated. If such messages should not go to you,
could you please direct me to the person who I should contact.
thanks,
Mary