update problem
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David...@schering.de
Apr 29, 2005, 9:42:11 AM4/29/05
to cpat...@googlegroups.com
Hello,
because of another application requiring mysql version 4 I updated my mysql
to 4.1.10.
Now there are some problems with cpath.
I took the latest snapshot.
Creating the database with cpath.sql works fine (After removing a
duplicate primary key from table import).
Resetting it with resetDb also works.
But tomcat gives me this error message:
########################################
INFO: validateJarFile(/usr/local/apache/jakarta-tomcat-5.5.9
/webapps/cpath/WEB-INF/lib/servlet.jar) - jar not loaded. See Servlet Spec
2.3,
section 9.7.2. Offending class: javax/servlet/Servlet.class
########################################
And probably as result of this, the web pages can't connet to the database.
Updating the database with the latest Intact (2005-04-01) data also failed:
> ./admin.pl -u tomcat -p kitty -x -f ../dbData/Intact/human_small.xml
validate
Validating XML File: /usr1/CPath/bin/../dbData/Intact/human_small.xml
XML File is Invalid.
Error #0: cvc-elt.1: Cannot find the declaration of element 'entrySet'.
[Line: 2, Column: 199
Total Time: 521779 ms
Any ideas ?
Thanks,
David.
because of another application requiring mysql version 4 I updated my mysql
to 4.1.10.
Now there are some problems with cpath.
I took the latest snapshot.
Creating the database with cpath.sql works fine (After removing a
duplicate primary key from table import).
Resetting it with resetDb also works.
But tomcat gives me this error message:
########################################
INFO: validateJarFile(/usr/local/apache/jakarta-tomcat-5.5.9
/webapps/cpath/WEB-INF/lib/servlet.jar) - jar not loaded. See Servlet Spec
2.3,
section 9.7.2. Offending class: javax/servlet/Servlet.class
########################################
And probably as result of this, the web pages can't connet to the database.
Updating the database with the latest Intact (2005-04-01) data also failed:
> ./admin.pl -u tomcat -p kitty -x -f ../dbData/Intact/human_small.xml
validate
Validating XML File: /usr1/CPath/bin/../dbData/Intact/human_small.xml
XML File is Invalid.
Error #0: cvc-elt.1: Cannot find the declaration of element 'entrySet'.
[Line: 2, Column: 199
Total Time: 521779 ms
Any ideas ?
Thanks,
David.
iain keddie
Apr 29, 2005, 10:39:38 AM4/29/05
to cpat...@googlegroups.com
David,
I have also tried using the latest version of mysql, but unfortunately I didn't have enough time to iron out the creases. (See my earlier post)
I can however tell you that the jar not loading, should not affect it. Tomcat has it's own version of the servlet code so it ignores any web application requesting to load the servlet.jar again. I too have this error on my system and everything works fine for me.
The error you have on loading data, looks like a schema validation issue. I have previously had a similar issue because of my company firewall. The xml contains the location of the schema, which is on another website. The xml validator tries to collect the schema from a remote site, but get stopped by the firewall; as the validator cannot find a schema it deems everything invalid and fails on the first tag "entrySet".
I am using the previous stable release 0.3.2 which doesn't have this problem.
Looking at the current source code on the developer site, it looks like cPath may be able to use a local schema, so I think Ethan/Gary could probably shed some more light on a solution?
Regards
I have also tried using the latest version of mysql, but unfortunately I didn't have enough time to iron out the creases. (See my earlier post)
I can however tell you that the jar not loading, should not affect it. Tomcat has it's own version of the servlet code so it ignores any web application requesting to load the servlet.jar again. I too have this error on my system and everything works fine for me.
The error you have on loading data, looks like a schema validation issue. I have previously had a similar issue because of my company firewall. The xml contains the location of the schema, which is on another website. The xml validator tries to collect the schema from a remote site, but get stopped by the firewall; as the validator cannot find a schema it deems everything invalid and fails on the first tag "entrySet".
I am using the previous stable release 0.3.2 which doesn't have this problem.
Looking at the current source code on the developer site, it looks like cPath may be able to use a local schema, so I think Ethan/Gary could probably shed some more light on a solution?
Regards
Ethan Cerami
Apr 29, 2005, 11:04:06 AM4/29/05
to cpat...@googlegroups.com
David,
I think there are probably a few issues going on here:
1) It looks like you are using tomcat 5.5.9. Since 5.5.9 uses Java
1.5, and 1.5 is not yet available on the Mac, I can't replicate the
problem. We do all of our testing/deployment using Tomcat 4, but this
morning, I was able to install cPath using Tomcat 5.029, and it worked fine.
So, my first suggestion is to try Tomcat 4 or 5.029, and see if that
fixes the first problem.
2) On the data validation, I am not sure. It could be a firewall
issue, as Iain suggests. Do you think this could be it? If so, you
could try replacing the schema location in the xml file with an absolute
path to the local copy of PSI-MI, e.g. ..cpath/testData/psi_mi/MIF.xsd.
Perhaps it's easiest if you emailed me a copy of human_small.xml, and I
will try to load it here, and email back with any progress I make.
Ethan
--
Ethan Cerami
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org
Email: cer...@cbio.mskcc.org
Direct phone: (646) 735-8082
I think there are probably a few issues going on here:
1) It looks like you are using tomcat 5.5.9. Since 5.5.9 uses Java
1.5, and 1.5 is not yet available on the Mac, I can't replicate the
problem. We do all of our testing/deployment using Tomcat 4, but this
morning, I was able to install cPath using Tomcat 5.029, and it worked fine.
So, my first suggestion is to try Tomcat 4 or 5.029, and see if that
fixes the first problem.
2) On the data validation, I am not sure. It could be a firewall
issue, as Iain suggests. Do you think this could be it? If so, you
could try replacing the schema location in the xml file with an absolute
path to the local copy of PSI-MI, e.g. ..cpath/testData/psi_mi/MIF.xsd.
Perhaps it's easiest if you emailed me a copy of human_small.xml, and I
will try to load it here, and email back with any progress I make.
Ethan
Ethan Cerami
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org
Email: cer...@cbio.mskcc.org
Direct phone: (646) 735-8082
David...@schering.de
Apr 29, 2005, 11:39:24 AM4/29/05
to cpat...@googlegroups.com
Hello,
as Iain suggested, it was a firewall issue.
With a local copy of MIF.xsd the validation is OK.
But now I still have a database problem with mysql4.
When importing I only get:
> ./admin.pl -u tomcat -p kitty -f ../dbData/Intact/human.xml import
Importing File: /usr1/CPath/bin/../dbData/Intact/human.xml
Validating XML File: /usr1/CPath/bin/../dbData/Intact/human.xml
XML File is Valid.
XML Type: PSI_MI
-----------------------------------------
Fatal Error: null
-----------------------------------------
The null error doesn't give me a clue, what could be wrong ;-)
The user/password exist and I can connect on command line to create the
database.
David.
David,
I think there are probably a few issues going on here:
1) It looks like you are using tomcat 5.5.9. Since 5.5.9 uses Java
1.5, and 1.5 is not yet available on the Mac, I can't replicate the
problem. We do all of our testing/deployment using Tomcat 4, but this
morning, I was able to install cPath using Tomcat 5.029, and it worked
fine.
So, my first suggestion is to try Tomcat 4 or 5.029, and see if that
fixes the first problem.
2) On the data validation, I am not sure. It could be a firewall
issue, as Iain suggests. Do you think this could be it? If so, you
could try replacing the schema location in the xml file with an absolute
path to the local copy of PSI-MI, e.g. ..cpath/testData/psi_mi/MIF.xsd.
Perhaps it's easiest if you emailed me a copy of human_small.xml, and I
will try to load it here, and email back with any progress I make.
Ethan Cerami
Apr 29, 2005, 11:47:31 AM4/29/05
to cpat...@googlegroups.com
David,
Try using the -d flag to print the stack trace, e.g.
./admin.pl -d -u tomcat -p kitty -f ../dbData/Intact/human.xml import
and, send me the stack trace.
Ethan
Try using the -d flag to print the stack trace, e.g.
./admin.pl -d -u tomcat -p kitty -f ../dbData/Intact/human.xml import
and, send me the stack trace.
Ethan
iain keddie
Apr 29, 2005, 12:06:09 PM4/29/05
to cpat...@googlegroups.com
Out of interest, what operating system are you running on?
Ethan can probably help a lot more with the error trace. However if you are on windows, check the "admin.pl" for some spare quotes. unix was ok with them but windows got all confused and gave me the same error you have now.
Ethan can probably help a lot more with the error trace. However if you are on windows, check the "admin.pl" for some spare quotes. unix was ok with them but windows got all confused and gave me the same error you have now.
David...@schering.de
May 1, 2005, 2:14:41 AM5/1/05
to cpat...@googlegroups.com
Hello,
I'm on unix (FreeBSD4.9). So this should not cause trouble.
Here comes the stack trace
Thanks for your help,
David.
XML File is Valid.
XML Type: PSI_MI
-----------------------------------------
Fatal Error: null
org.mskcc.pathdb.sql.dao.DaoException
at org.mskcc.pathdb.sql.dao.DaoImport.addRecord(DaoImport.java:200)
at
org.mskcc.pathdb.tool.LoadBioPaxPsi.importDataFile(LoadBioPaxPsi.java:64)
at org.mskcc.pathdb.tool.Admin.importPsiMiFile(Admin.java:209)
at
org.mskcc.pathdb.tool.Admin.importDataFromSingleFile(Admin.java:175)
at org.mskcc.pathdb.tool.Admin.importData(Admin.java:162)
at org.mskcc.pathdb.tool.Admin.main(Admin.java:96)
Caused by: java.sql.SQLException: Communication link failure:
java.io.IOException, underlying cause: Unexpected end of input stream
** BEGIN NESTED EXCEPTION **
java.io.IOException
MESSAGE: Unexpected end of input stream
STACKTRACE:
java.io.IOException: Unexpected end of input stream
at com.mysql.jdbc.MysqlIO.readPacket(MysqlIO.java:1096)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:626)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:1562)
at com.mysql.jdbc.Connection.<init>(Connection.java:491)
at
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:346)
at java.sql.DriverManager.getConnection(DriverManager.java:512)
at java.sql.DriverManager.getConnection(DriverManager.java:193)
at
org.apache.commons.dbcp.DriverManagerConnectionFactory.createConnection(DriverManagerConnectionFactory.java:92)
at
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:300)
at
org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:816)
at
org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:140)
at
org.mskcc.pathdb.sql.JdbcUtil.getCPathConnection(JdbcUtil.java:81)
at org.mskcc.pathdb.sql.dao.DaoImport.addRecord(DaoImport.java:164)
at
org.mskcc.pathdb.tool.LoadBioPaxPsi.importDataFile(LoadBioPaxPsi.java:64)
at org.mskcc.pathdb.tool.Admin.importPsiMiFile(Admin.java:209)
at
org.mskcc.pathdb.tool.Admin.importDataFromSingleFile(Admin.java:175)
at org.mskcc.pathdb.tool.Admin.importData(Admin.java:162)
at org.mskcc.pathdb.tool.Admin.main(Admin.java:96)
** END NESTED EXCEPTION **
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:699)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:1562)
at com.mysql.jdbc.Connection.<init>(Connection.java:491)
at
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:346)
at java.sql.DriverManager.getConnection(DriverManager.java:512)
at java.sql.DriverManager.getConnection(DriverManager.java:193)
at
org.apache.commons.dbcp.DriverManagerConnectionFactory.createConnection(DriverManagerConnectionFactory.java:92)
at
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:300)
at
org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:816)
at
org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:140)
at
org.mskcc.pathdb.sql.JdbcUtil.getCPathConnection(JdbcUtil.java:81)
at org.mskcc.pathdb.sql.dao.DaoImport.addRecord(DaoImport.java:164)
... 5 more
-----------------------------------------
David,
Try using the -d flag to print the stack trace, e.g.
./admin.pl -d -u tomcat -p kitty -f ../dbData/Intact/human.xml import
and, send me the stack trace.
Ethan
Ethan Cerami
May 5, 2005, 10:00:00 AM5/5/05
to cpat...@googlegroups.com
Hello David,
I haven't actually tested cPath with MySQL 4.1 (we are still primarily
running under MySQL 4.0). However, since your problem is specific to
4.1, my next guess is that our JDBC driver is incompatible with 4.1.
You could try downloading the very latest MySQL JDBC driver at:
http://dev.mysql.com/downloads/connector/j/3.1.html
And, then replace the jar file in cpath/lib.
I will also try to install MySQL 4.1 here and try the updated jar.
Ethan
I haven't actually tested cPath with MySQL 4.1 (we are still primarily
running under MySQL 4.0). However, since your problem is specific to
4.1, my next guess is that our JDBC driver is incompatible with 4.1.
You could try downloading the very latest MySQL JDBC driver at:
http://dev.mysql.com/downloads/connector/j/3.1.html
And, then replace the jar file in cpath/lib.
I will also try to install MySQL 4.1 here and try the updated jar.
Ethan
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