Hi Kjell,
Thanks for your quick answer.
But your proposition doesn't solve my problem. I think that the old
version of the driver is also not in the classpath as you suggest.
I rename my new version like the old one :
"mysql-connector-java-3.0.15-ga-bin.jar" but I always get this message :
dirname= /var/BASE_production/data/mageml/0/1/experiment1
stage= all
dtdpath= /usr/local/BASE_production/misc/MAGE-ML.dtd
Failed to load current driver.
java.sql.SQLException: Access denied for user 'base'@'localhost.localdomain'
(using password: YES)
I check the permissions on this file. It seems ok.
And when I take a look on the file magemlExporter.php I can see the good
name of the driver. Should I modify something in this file ?
Can it be a problem with my base user ? I "GRANT" this user again, but
nothing change.
Thanks a lot for your answer.
Cheers,
Audrey
Hi Audrey,
The BASE MAGE-ML export coding is no ongoing for full steam, so soon
the code below givinmg you trouble should be obsolete. But I'll try to
giv you a couple of hints to help you by.
Audrey Bihouee wrote:
Hi,
Sine I changed my server, I get a java error when I try to export my
data in MAGE-ML.
This is my message :
dirname= /var/BASE_production/data/mageml/0/1/experiment1
stage= all
dtdpath= /usr/local/BASE_production/misc/MAGE-ML.dtd
Failed to load current driver.
java.sql.SQLException: Invalid authorization specification message
from server: "Access denied for user 'base'@'localhost.localdomain'
(using password: YES)"
q=
java.lang.NullPointerException
at BASEutils.getStatement(BASEutils.java:141)
at Experiment_BASE.fromBASE(Experiment_BASE.java:40)
at
Experiment_package_BASE.getExperiment(Experiment_package_BASE.java:47)
at exportMAGEML.retrive(exportMAGEML.java:125)
at exportMAGEML.main(exportMAGEML.java:76)
created mageobjects
writeMAGEML
repair
java.lang.NullPointerException
at BASEutils.quickfix1(BASEutils.java:1076)
at BASEutils.repairMAGEML(BASEutils.java:1035)
at exportMAGEML.main(exportMAGEML.java:78)
validate
error: Attribute "identifier" is required and must be specified for
element type "MAGE-ML".
org.xml.sax.SAXParseException: Attribute "identifier" is required and
must be specified for element type "MAGE-ML".
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:151)
at BASEutils.validate(BASEutils.java:1137)
at exportMAGEML.main(exportMAGEML.java:79)
My version of Mysql is : 4.1.12 and I have
mysql-connector-java-3.0.15-ga-bin.jar in BASEpath/include/java
The first error (failed to load driver) seem to be causing the rest.
See below.
When I try to update my mysql-connector to 3.1.12-bin.jar I get this
message :
dirname= /var/BASE_production/data/mageml/0/1/experiment1
stage= all
dtdpath= /usr/local/BASE_production/misc/MAGE-ML.dtd
Failed to load current driver.
java.lang.ClassNotFoundException: org.gjt.mm.mysql.Driver
This is because your new driver jar is not explicitly in the classpath
of the jvm (set in a script before starting the java code). A quick
hack for now would be to rename your new driver to the same name as
the old driver jar (and keep a copy of the old one around of course).
Good look!
Kjell ;^)
--
*************************
Audrey Bihouee
Plate-forme transcriptome - OUEST-genopole
INSERM U533 - IFR 26
1 Rue Gaston Veil- BP 53508
44 035 NANTES
FRANCE
Tel : (33) 2 40 41 29 86
Fax : (33) 2 40 41 29 50
http://cardioserve.nantes.inserm.fr/ptf-puce
*************************
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