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From: Vladimir G. <vla...@du...> - 2009-12-23 18:55:25
|
Ok, you could be right about the current state of things. (For my education: where is that setting that instructs Hibernate on "NATIVE" vs "SEQUENCE"?) Then, how do we know which tables (besides the 2 you mentioned) we should take into account for computing the MAX value, to be set as the new seed for hibernate_sequence? Another concern: resetting hibernate_sequence now is likely to affect the subsequent TB1->TB2 import that we plan to do for the release. Someone must have given thought to all these issues already. All the reasons to relax and enjoy the holidays! --VG On Dec 23, 2009, at 1:19 PM, youjun guo wrote: > Vladimir, > > Based on the error massage I send to you, I am quite sure, right > now, treebase code simply ignored those xxxx_id_sequence you > mentioned in the treebase_dev. Those sequences only work for insert > via database like commandline but not working for treebase code. > > The hibernate only look at it own configuration unless you tell it > to do something else in its configration. > > Youjun > > On Wed, Dec 23, 2009 at 12:25 PM, Vladimir Gapeyev <vla...@du... > > wrote: > I think we need someone who is more aware about what is going on in > TB2 (Rutger? Bill?) to resolve this. > > Since the postgres sequence taxonlabel_id_sequence is declared in > the schema as the sequence for the taxonlabel table and since they > are perfectly in sync with each other, I presume that doing anything > to hibernate_sequence would be a mistake. > > --Vladimir > > > On Dec 23, 2009, at 11:37 AM, youjun guo wrote: > >> Hilmar & Vladimir, >> >> When hibernate insert a record into the database, it need to create >> a unique id (primer_key) for it. >> >> In treebase hibernate use sequence. yes It is a database object in >> treebase-dev. hibernate will ask for a key from this sequence object. >> >> By default hibernate will looking for a sequence object named >> "hibernate_sequence" unless some other sequence are explicitly >> appointed in hibernate configuration (NOT DATABASE SETUP). >> >> In the treebase code, I didn't find any other sequence defined in >> the hibernate configuration. I assume it will use default that is >> "hibernate_sequence". >> >> Most importantly the testing code do complain primer key conflict >> in these two tables, And the key hibernate got from the sequence do >> exist in the tables already. >> >> Only the owner of the treebase-dev can make change of the sequence. >> >> Youjun >> >> >> >> On Wed, Dec 23, 2009 at 10:29 AM, Vladimir Gapeyev <vla...@du... >> > wrote: >> In the schema, both taxonlabel and phylotreenode use their own >> sequences (taxonlabel_id_sequence and phylotreenode_id_sequence) >> whose >> current values are in sync with the tables. What is the purpose of >> the hibernate_sequence sequence? --VG >> >> >> On Dec 23, 2009, at 7:42 AM, youjun guo wrote: >> >> > Hilmar and Bill, >> > >> > In our database, the current hibernate_sequence value (1416) is >> much >> > smaller than max id value of table taxonlabel and phylotreenode, >> > that make primer key conflict when hibernate try to insert new data >> > into this two table. >> > >> > It need to be change to a bigger number so that the current value >> > big than max phylotreenode_id. >> > >> > I tried but the server said only the owner can alter it. >> > >> > Enjoy your holiday to all! >> > >> > Youjun >> > >> ------------------------------------------------------------------------------ >> > This SF.Net email is sponsored by the Verizon Developer Community >> > Take advantage of Verizon's best-in-class app development support >> > A streamlined, 14 day to market process makes app distribution fast >> > and easy >> > Join now and get one step closer to millions of Verizon customers >> > http://p.sf.net/sfu/verizon-dev2dev >> > _______________________________________________ >> > Treebase-devel mailing list >> > Tre...@li... >> > https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
|
From: youjun g. <you...@ya...> - 2009-12-23 18:19:17
|
Vladimir, Based on the error massage I send to you, I am quite sure, right now, treebase code simply ignored those xxxx_id_sequence you mentioned in the treebase_dev. Those sequences only work for insert via database like commandline but not working for treebase code. The hibernate only look at it own configuration unless you tell it to do something else in its configration. Youjun On Wed, Dec 23, 2009 at 12:25 PM, Vladimir Gapeyev < vla...@du...> wrote: > I think we need someone who is more aware about what is going on in TB2 > (Rutger? Bill?) to resolve this. > > Since the postgres sequence taxonlabel_id_sequence is declared in the > schema as the sequence for the taxonlabel table and since they are perfectly > in sync with each other, I presume that doing anything to hibernate_sequence > would be a mistake. > > --Vladimir > > > On Dec 23, 2009, at 11:37 AM, youjun guo wrote: > > Hilmar & Vladimir, > > When hibernate insert a record into the database, it need to create a > unique id (primer_key) for it. > > In treebase hibernate use sequence. yes It is a database object in > treebase-dev. hibernate will ask for a key from this sequence object. > > By default hibernate will looking for a sequence object named > "hibernate_sequence" unless some other sequence are explicitly appointed in > hibernate configuration (NOT DATABASE SETUP). > > In the treebase code, I didn't find any other sequence defined in the > hibernate configuration. I assume it will use default that is > "hibernate_sequence". > > Most importantly the testing code do complain primer key conflict in these > two tables, And the key hibernate got from the sequence do exist in the > tables already. > > Only the owner of the treebase-dev can make change of the sequence. > > Youjun > > > > On Wed, Dec 23, 2009 at 10:29 AM, Vladimir Gapeyev < > vla...@du...> wrote: > >> In the schema, both taxonlabel and phylotreenode use their own >> sequences (taxonlabel_id_sequence and phylotreenode_id_sequence) whose >> current values are in sync with the tables. What is the purpose of >> the hibernate_sequence sequence? --VG >> >> >> On Dec 23, 2009, at 7:42 AM, youjun guo wrote: >> >> > Hilmar and Bill, >> > >> > In our database, the current hibernate_sequence value (1416) is much >> > smaller than max id value of table taxonlabel and phylotreenode, >> > that make primer key conflict when hibernate try to insert new data >> > into this two table. >> > >> > It need to be change to a bigger number so that the current value >> > big than max phylotreenode_id. >> > >> > I tried but the server said only the owner can alter it. >> > >> > Enjoy your holiday to all! >> > >> > Youjun >> > >> ------------------------------------------------------------------------------ >> > This SF.Net email is sponsored by the Verizon Developer Community >> > Take advantage of Verizon's best-in-class app development support >> > A streamlined, 14 day to market process makes app distribution fast >> > and easy >> > Join now and get one step closer to millions of Verizon customers >> > http://p.sf.net/sfu/verizon-dev2dev >> > _______________________________________________ >> > Treebase-devel mailing list >> > Tre...@li... >> > https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast and >> easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and > easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and > easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
|
From: youjun g. <you...@ya...> - 2009-12-23 18:03:39
|
Hilmar,
Sounds like you prefer the treebase hibernate id generator to be setup as
"NATIVE", which tells hibernate to use the database native id generate
rules.
Both "SEQUENCE " and "NATIVE" are widely used in hibernate applications,
and I am fine with any one of these.
I don't know if there is any historical reasons for current setup, because
sometime developers want to explicitly operate on the id field in their
code. "NATIVE" setup will prevent this.
Youjun
On Wed, Dec 23, 2009 at 12:20 PM, Hilmar Lapp <hl...@ne...> wrote:
> Youjun - this smells like a hibernate misconfiguration. You can tell
> hibernate that the database will assign the primary key, rather than
> hibernate assigning it itself.
>
> More importantly, it needs to be consistent with the database. If the
> database has sequence definitions and auto-increment (SERIAL or
> DEFAULT('nextval XXXX' in PostgreSQL) for the primary key, then hibernate
> has got to be using them as well (i.e., database and not hibernate assigns
> primary keys). If hibernate assigns primary keys, then the database tables
> must not have auto-increment rules on its primary key columns.
>
> Right now it looks like the database has auto-increment rules *and*
> hibernate tries to do its own thing?
>
> -hilmar
>
> On Dec 23, 2009, at 11:37 AM, youjun guo wrote:
>
> Hilmar & Vladimir,
>
> When hibernate insert a record into the database, it need to create a
> unique id (primer_key) for it.
>
> In treebase hibernate use sequence. yes It is a database object in
> treebase-dev. hibernate will ask for a key from this sequence object.
>
> By default hibernate will looking for a sequence object named
> "hibernate_sequence" unless some other sequence are explicitly appointed in
> hibernate configuration (NOT DATABASE SETUP).
>
> In the treebase code, I didn't find any other sequence defined in the
> hibernate configuration. I assume it will use default that is
> "hibernate_sequence".
>
> Most importantly the testing code do complain primer key conflict in these
> two tables, And the key hibernate got from the sequence do exist in the
> tables already.
>
> Only the owner of the treebase-dev can make change of the sequence.
>
> Youjun
>
>
>
> On Wed, Dec 23, 2009 at 10:29 AM, Vladimir Gapeyev <
> vla...@du...> wrote:
>
>> In the schema, both taxonlabel and phylotreenode use their own
>> sequences (taxonlabel_id_sequence and phylotreenode_id_sequence) whose
>> current values are in sync with the tables. What is the purpose of
>> the hibernate_sequence sequence? --VG
>>
>>
>> On Dec 23, 2009, at 7:42 AM, youjun guo wrote:
>>
>> > Hilmar and Bill,
>> >
>> > In our database, the current hibernate_sequence value (1416) is much
>> > smaller than max id value of table taxonlabel and phylotreenode,
>> > that make primer key conflict when hibernate try to insert new data
>> > into this two table.
>> >
>> > It need to be change to a bigger number so that the current value
>> > big than max phylotreenode_id.
>> >
>> > I tried but the server said only the owner can alter it.
>> >
>> > Enjoy your holiday to all!
>> >
>> > Youjun
>> >
>> ------------------------------------------------------------------------------
>> > This SF.Net email is sponsored by the Verizon Developer Community
>> > Take advantage of Verizon's best-in-class app development support
>> > A streamlined, 14 day to market process makes app distribution fast
>> > and easy
>> > Join now and get one step closer to millions of Verizon customers
>> > http://p.sf.net/sfu/verizon-dev2dev
>> > _______________________________________________
>> > Treebase-devel mailing list
>> > Tre...@li...
>> > https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Verizon Developer Community
>> Take advantage of Verizon's best-in-class app development support
>> A streamlined, 14 day to market process makes app distribution fast and
>> easy
>> Join now and get one step closer to millions of Verizon customers
>> http://p.sf.net/sfu/verizon-dev2dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>
|
|
From: Vladimir G. <vla...@du...> - 2009-12-23 17:25:37
|
I think we need someone who is more aware about what is going on in TB2 (Rutger? Bill?) to resolve this. Since the postgres sequence taxonlabel_id_sequence is declared in the schema as the sequence for the taxonlabel table and since they are perfectly in sync with each other, I presume that doing anything to hibernate_sequence would be a mistake. --Vladimir On Dec 23, 2009, at 11:37 AM, youjun guo wrote: > Hilmar & Vladimir, > > When hibernate insert a record into the database, it need to create > a unique id (primer_key) for it. > > In treebase hibernate use sequence. yes It is a database object in > treebase-dev. hibernate will ask for a key from this sequence object. > > By default hibernate will looking for a sequence object named > "hibernate_sequence" unless some other sequence are explicitly > appointed in hibernate configuration (NOT DATABASE SETUP). > > In the treebase code, I didn't find any other sequence defined in > the hibernate configuration. I assume it will use default that is > "hibernate_sequence". > > Most importantly the testing code do complain primer key conflict in > these two tables, And the key hibernate got from the sequence do > exist in the tables already. > > Only the owner of the treebase-dev can make change of the sequence. > > Youjun > > > > On Wed, Dec 23, 2009 at 10:29 AM, Vladimir Gapeyev <vla...@du... > > wrote: > In the schema, both taxonlabel and phylotreenode use their own > sequences (taxonlabel_id_sequence and phylotreenode_id_sequence) whose > current values are in sync with the tables. What is the purpose of > the hibernate_sequence sequence? --VG > > > On Dec 23, 2009, at 7:42 AM, youjun guo wrote: > > > Hilmar and Bill, > > > > In our database, the current hibernate_sequence value (1416) is much > > smaller than max id value of table taxonlabel and phylotreenode, > > that make primer key conflict when hibernate try to insert new data > > into this two table. > > > > It need to be change to a bigger number so that the current value > > big than max phylotreenode_id. > > > > I tried but the server said only the owner can alter it. > > > > Enjoy your holiday to all! > > > > Youjun > > > ------------------------------------------------------------------------------ > > This SF.Net email is sponsored by the Verizon Developer Community > > Take advantage of Verizon's best-in-class app development support > > A streamlined, 14 day to market process makes app distribution fast > > and easy > > Join now and get one step closer to millions of Verizon customers > > http://p.sf.net/sfu/verizon-dev2dev > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
|
From: Hilmar L. <hl...@ne...> - 2009-12-23 17:21:02
|
Youjun - this smells like a hibernate misconfiguration. You can tell
hibernate that the database will assign the primary key, rather than
hibernate assigning it itself.
More importantly, it needs to be consistent with the database. If the
database has sequence definitions and auto-increment (SERIAL or
DEFAULT('nextval XXXX' in PostgreSQL) for the primary key, then
hibernate has got to be using them as well (i.e., database and not
hibernate assigns primary keys). If hibernate assigns primary keys,
then the database tables must not have auto-increment rules on its
primary key columns.
Right now it looks like the database has auto-increment rules *and*
hibernate tries to do its own thing?
-hilmar
On Dec 23, 2009, at 11:37 AM, youjun guo wrote:
> Hilmar & Vladimir,
>
> When hibernate insert a record into the database, it need to create
> a unique id (primer_key) for it.
>
> In treebase hibernate use sequence. yes It is a database object in
> treebase-dev. hibernate will ask for a key from this sequence object.
>
> By default hibernate will looking for a sequence object named
> "hibernate_sequence" unless some other sequence are explicitly
> appointed in hibernate configuration (NOT DATABASE SETUP).
>
> In the treebase code, I didn't find any other sequence defined in
> the hibernate configuration. I assume it will use default that is
> "hibernate_sequence".
>
> Most importantly the testing code do complain primer key conflict in
> these two tables, And the key hibernate got from the sequence do
> exist in the tables already.
>
> Only the owner of the treebase-dev can make change of the sequence.
>
> Youjun
>
>
>
> On Wed, Dec 23, 2009 at 10:29 AM, Vladimir Gapeyev <vla...@du...
> > wrote:
> In the schema, both taxonlabel and phylotreenode use their own
> sequences (taxonlabel_id_sequence and phylotreenode_id_sequence) whose
> current values are in sync with the tables. What is the purpose of
> the hibernate_sequence sequence? --VG
>
>
> On Dec 23, 2009, at 7:42 AM, youjun guo wrote:
>
> > Hilmar and Bill,
> >
> > In our database, the current hibernate_sequence value (1416) is much
> > smaller than max id value of table taxonlabel and phylotreenode,
> > that make primer key conflict when hibernate try to insert new data
> > into this two table.
> >
> > It need to be change to a bigger number so that the current value
> > big than max phylotreenode_id.
> >
> > I tried but the server said only the owner can alter it.
> >
> > Enjoy your holiday to all!
> >
> > Youjun
> >
> ------------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Verizon Developer Community
> > Take advantage of Verizon's best-in-class app development support
> > A streamlined, 14 day to market process makes app distribution fast
> > and easy
> > Join now and get one step closer to millions of Verizon customers
> > http://p.sf.net/sfu/verizon-dev2dev
> > _______________________________________________
> > Treebase-devel mailing list
> > Tre...@li...
> > https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast
> and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast
> and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
===========================================================
|
|
From: youjun g. <you...@ya...> - 2009-12-23 16:57:59
|
Vladimir,
Look at the end of this error massage which I got minutes ago, hibernate get
this id from sequence:
TAXONLABEL_ID =14220 that is far less than the max id in the table and it is
already exist.
To make change on the sequence run this sql query: alter sequence
hibernate_sequence restart with 300000.
300000 just a example, you can find the max id in these tables and make it
the bigest + 1.
Youjun
Tests run: 2, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.047 sec
<<< FAILURE!
testAddDelete(org.cipres.treebase.service.matrix.MatrixServiceImplTest)
Time elapsed: 1.016 sec <<< ERROR!
org.springframework.dao.DataIntegrityViolationException: Could not execute
JDBC batch update; nested exception is
org.hibernate.exception.ConstraintViolationException: Could not execute JDBC
batch update
Caused by: org.hibernate.exception.ConstraintViolationException: Could not
execute JDBC batch update
at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:71)
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:253)
at
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:92)
at
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:87)
at
org.hibernate.jdbc.AbstractBatcher.prepareBatchStatement(AbstractBatcher.java:222)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2229)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2665)
at
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:60)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:263)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
at
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
at
org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:578)
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:662)
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:632)
at
org.springframework.test.AbstractTransactionalSpringContextTests.endTransaction(AbstractTransactionalSpringContextTests.java:293)
at
org.cipres.treebase.service.matrix.MatrixServiceImplTest.testAddDelete(MatrixServiceImplTest.java:232)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at junit.framework.TestCase.runTest(TestCase.java:154)
at junit.framework.TestCase.runBare(TestCase.java:127)
at
org.springframework.test.ConditionalTestCase.runBare(ConditionalTestCase.java:69)
at junit.framework.TestResult$1.protect(TestResult.java:106)
at junit.framework.TestResult.runProtected(TestResult.java:124)
at junit.framework.TestResult.run(TestResult.java:109)
at junit.framework.TestCase.run(TestCase.java:118)
at junit.framework.TestSuite.runTest(TestSuite.java:208)
at junit.framework.TestSuite.run(TestSuite.java:203)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)
at
org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:140)
at
org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:127)
at org.apache.maven.surefire.Surefire.run(Surefire.java:177)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:338)
at
org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:997)
Caused by: java.sql.BatchUpdateException: Batch entry 0 insert into
TAXONLABEL (VERSION, LINKED, STUDY_ID, TaxonLabel, TAXONVARIANT_ID,
TAXONLABEL_ID) values (0, 0, NULL, testAddDelete test 0.3318026555702662,
NULL, 14220) was aborted. Call getNextException to see the cause.
|
|
From: youjun g. <you...@ya...> - 2009-12-23 16:38:08
|
Hilmar & Vladimir, When hibernate insert a record into the database, it need to create a unique id (primer_key) for it. In treebase hibernate use sequence. yes It is a database object in treebase-dev. hibernate will ask for a key from this sequence object. By default hibernate will looking for a sequence object named "hibernate_sequence" unless some other sequence are explicitly appointed in hibernate configuration (NOT DATABASE SETUP). In the treebase code, I didn't find any other sequence defined in the hibernate configuration. I assume it will use default that is "hibernate_sequence". Most importantly the testing code do complain primer key conflict in these two tables, And the key hibernate got from the sequence do exist in the tables already. Only the owner of the treebase-dev can make change of the sequence. Youjun On Wed, Dec 23, 2009 at 10:29 AM, Vladimir Gapeyev < vla...@du...> wrote: > In the schema, both taxonlabel and phylotreenode use their own > sequences (taxonlabel_id_sequence and phylotreenode_id_sequence) whose > current values are in sync with the tables. What is the purpose of > the hibernate_sequence sequence? --VG > > > On Dec 23, 2009, at 7:42 AM, youjun guo wrote: > > > Hilmar and Bill, > > > > In our database, the current hibernate_sequence value (1416) is much > > smaller than max id value of table taxonlabel and phylotreenode, > > that make primer key conflict when hibernate try to insert new data > > into this two table. > > > > It need to be change to a bigger number so that the current value > > big than max phylotreenode_id. > > > > I tried but the server said only the owner can alter it. > > > > Enjoy your holiday to all! > > > > Youjun > > > ------------------------------------------------------------------------------ > > This SF.Net email is sponsored by the Verizon Developer Community > > Take advantage of Verizon's best-in-class app development support > > A streamlined, 14 day to market process makes app distribution fast > > and easy > > Join now and get one step closer to millions of Verizon customers > > http://p.sf.net/sfu/verizon-dev2dev > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and > easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
|
From: Vladimir G. <vla...@du...> - 2009-12-23 15:29:18
|
In the schema, both taxonlabel and phylotreenode use their own sequences (taxonlabel_id_sequence and phylotreenode_id_sequence) whose current values are in sync with the tables. What is the purpose of the hibernate_sequence sequence? --VG On Dec 23, 2009, at 7:42 AM, youjun guo wrote: > Hilmar and Bill, > > In our database, the current hibernate_sequence value (1416) is much > smaller than max id value of table taxonlabel and phylotreenode, > that make primer key conflict when hibernate try to insert new data > into this two table. > > It need to be change to a bigger number so that the current value > big than max phylotreenode_id. > > I tried but the server said only the owner can alter it. > > Enjoy your holiday to all! > > Youjun > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
|
From: Hilmar L. <hl...@ne...> - 2009-12-23 15:06:36
|
The owner of what? And change where? Is that a database object? -hilmar Sent from away On Dec 23, 2009, at 7:42 AM, youjun guo <you...@ya...> wrote: > Hilmar and Bill, > > In our database, the current hibernate_sequence value (1416) is much > smaller than max id value of table taxonlabel and phylotreenode, > that make primer key conflict when hibernate try to insert new data > into this two table. > > It need to be change to a bigger number so that the current value > big than max phylotreenode_id. > > I tried but the server said only the owner can alter it. > > Enjoy your holiday to all! > > Youjun |
|
From: youjun g. <you...@ya...> - 2009-12-23 13:12:04
|
Hilmar and Bill, In our database, the current hibernate_sequence value (1416) is much smaller than max id value of table taxonlabel and phylotreenode, that make primer key conflict when hibernate try to insert new data into this two table. It need to be change to a bigger number so that the current value big than max phylotreenode_id. I tried but the server said only the owner can alter it. Enjoy your holiday to all! Youjun |
|
From: William P. <wil...@ya...> - 2009-12-23 05:14:25
|
On Dec 22, 2009, at 6:11 PM, Hilmar Lapp wrote: > That sounds good to me I've gone ahead with that. I created a user with the username "tb1" and email tb...@tr..., which happens to have generated a user_id of 14150. (why so big? I don't know). Then for the submission table I replaced user_id = NULL with user_id = 14150. Seems to work, in that when I log in as tb1, I see all of the migrated tb1 studies. Youjun can tell us if the relevant unit tests are now succeeding. bp |
|
From: Hilmar L. <hl...@ne...> - 2009-12-22 23:11:11
|
On Dec 22, 2009, at 1:17 PM, William Piel wrote: > I propose that I create a special new user who will serve as a > placeholder for the migrated data, and then just update the > submission table, replacing NULL with the ID of this special user. That sounds good to me; can we also put a not-null constraint on the column (and/or into the hibernate mapping if it's not already there) afterwards so that future violations are prevented? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: youjun g. <you...@ya...> - 2009-12-22 19:11:51
|
Hi, Rutger,
This unit test error may related to mesquite, please have a look on it.
Youjun
-------------------------------------------------------------------------------
Test set: org.cipres.treebase.service.matrix.RowSegmentServiceImplTest
-------------------------------------------------------------------------------
Tests run: 2, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 8.641 sec
<<< FAILURE!
testCreateRowSegments(org.cipres.treebase.service.matrix.RowSegmentServiceImplTest)
Time elapsed: 8.594 sec <<< ERROR!
java.lang.NullPointerException
at
org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:610)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at $Proxy81.addNexusFilesJDBC(Unknown Source)
at
org.cipres.treebase.service.matrix.RowSegmentServiceImplTest.testCreateRowSegments(RowSegmentServiceImplTest.java:182)
|
|
From: youjun g. <you...@ya...> - 2009-12-22 18:27:31
|
I checked with Bill and he get a solution. The column should not be null. It is very likely in our code, given a submission we want to retrieve the info of the submitter so a call like User user=submission.getSubmitter() if this returns null, then user.getXXX() will cause a null pointer.exception Youjun On Tue, Dec 22, 2009 at 11:44 AM, Hilmar Lapp <hl...@ne...> wrote: > What is supposed to be in this column? I gather that if null values are in > the column, then the data model actually permits this value to be missing. > If the application code assumes that it is always present, then either it is > making a wrong assumption and needs to be fixed, or the data model is wrong > in that it ought to be mandating a value for the column. > > Which of the two is the case? > > -hilmar > > On Dec 22, 2009, at 11:21 AM, youjun guo wrote: > > Dear All, > > Upon working on the unit test I found lots of "null" in table > "submission"/column "user_id", which cause null point exception on test > suite. > > Hilmar and Rutger, the table may need to be reloaded. > > Youjun > > > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > |
|
From: William P. <wil...@ya...> - 2009-12-22 18:17:59
|
On Dec 22, 2009, at 11:44 AM, Hilmar Lapp wrote: > What is supposed to be in this column? I gather that if null values are in the column, then the data model actually permits this value to be missing. If the application code assumes that it is always present, then either it is making a wrong assumption and needs to be fixed, or the data model is wrong in that it ought to be mandating a value for the column. The problem is because our TB1->TB2 migration violates constraints for normal operation. Under normal operation, each submission has an owner_id, a FK to the users table. But since data that are migrated to TB2 lacks a submitter, this FK remains null. I propose that I create a special new user who will serve as a placeholder for the migrated data, and then just update the submission table, replacing NULL with the ID of this special user. bp |
|
From: Hilmar L. <hl...@ne...> - 2009-12-22 16:45:06
|
What is supposed to be in this column? I gather that if null values are in the column, then the data model actually permits this value to be missing. If the application code assumes that it is always present, then either it is making a wrong assumption and needs to be fixed, or the data model is wrong in that it ought to be mandating a value for the column. Which of the two is the case? -hilmar On Dec 22, 2009, at 11:21 AM, youjun guo wrote: > Dear All, > > Upon working on the unit test I found lots of "null" in table > "submission"/column "user_id", which cause null point exception on > test suite. > > Hilmar and Rutger, the table may need to be reloaded. > > Youjun > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: youjun g. <you...@ya...> - 2009-12-22 16:22:09
|
Dear All, Upon working on the unit test I found lots of "null" in table "submission"/column "user_id", which cause null point exception on test suite. Hilmar and Rutger, the table may need to be reloaded. Youjun |
|
From: Vladimir G. <vla...@du...> - 2009-12-21 18:42:53
|
It would be very helpful for my introduction to the project if I could participate in repairing some of the unit tests. I would need some hand-holding in the beginning, though. Youjun, when you identify some tests from category #1, could you pass 2-3 simpler ones to me and could we talk then about what I should do to fix them? --Vladimir On Dec 21, 2009, at 10:09 AM, youjun guo wrote: > Hilmar and All, > > There are 10 failed test and 29 errors need to be fixed on > TreeBASE. The possibly cause include: > > 1. main java code change without synchronizing with the test suite; > 2. database schema change without synchronizing with the test suite; > 3. testing recode was lost from the database table; > 4. other issue like mesquite > > I think one developer can fix 4-5 of them per working day, because > most of us will not work from Dec 23rd to Jan 3rd, I expect the > whole work can be done by Jan 8th-10th. > > Rutger, can I send you those failed test that related to mesquite? > There maybe 2-3 of them. I can finish the rest unless by working on > them I found my estimation about the due day is too optimistic. > > I will let you know then. > > Thanks > > Youjun . > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
|
From: Vladimir G. <vga...@ne...> - 2009-12-21 18:25:18
|
I have put together a page https://sourceforge.net/apps/mediawiki/treebase/index.php?title=Infrastructure_and_Deployment_plan with a proposal how we should set up infrastructure for the remaining work on TB2 and for subsequent maintenance, as well as a summary of what space we have available right now to start the work. The infrastructure proposal may be ambitious and might be fully implemented only after the public release, but l post it in an attempt to to establish a shared understanding from the start, so that whatever we do prior to the release will fit with the eventual goal. Please raise your concerns! The Instances 0, 1, 2 described at the end are operational, but are completely empty (no data in DB, no WARs deployed). The first step is to set up these instances. Email me personally for access credentials, but let's make sure to coordinate on the list any work being done. --Vladimir |
|
From: Hilmar L. <hl...@ne...> - 2009-12-21 16:52:54
|
Thanks for the update, Youjun. I entered Jan 11 as target date into our release plan. -hilmar On Dec 21, 2009, at 10:09 AM, youjun guo wrote: > Hilmar and All, > > There are 10 failed test and 29 errors need to be fixed on > TreeBASE. The possibly cause include: > > 1. main java code change without synchronizing with the test suite; > 2. database schema change without synchronizing with the test suite; > 3. testing recode was lost from the database table; > 4. other issue like mesquite > > I think one developer can fix 4-5 of them per working day, because > most of us will not work from Dec 23rd to Jan 3rd, I expect the > whole work can be done by Jan 8th-10th. > > Rutger, can I send you those failed test that related to mesquite? > There maybe 2-3 of them. I can finish the rest unless by working on > them I found my estimation about the due day is too optimistic. > > I will let you know then. > > Thanks > > Youjun . -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: youjun g. <you...@ya...> - 2009-12-21 15:09:48
|
Hilmar and All, There are 10 failed test and 29 errors need to be fixed on TreeBASE. The possibly cause include: 1. main java code change without synchronizing with the test suite; 2. database schema change without synchronizing with the test suite; 3. testing recode was lost from the database table; 4. other issue like mesquite I think one developer can fix 4-5 of them per working day, because most of us will not work from Dec 23rd to Jan 3rd, I expect the whole work can be done by Jan 8th-10th. Rutger, can I send you those failed test that related to mesquite? There maybe 2-3 of them. I can finish the rest unless by working on them I found my estimation about the due day is too optimistic. I will let you know then. Thanks Youjun . |
|
From: youjun g. <you...@gm...> - 2009-12-21 14:33:30
|
Hi, Rutger, I just finished on this: 2854768 Editors and Administrators Cannot Edit Ready Submissions Code already submitted to source forge, please help me to redeploy. Youjun |
|
From: Vladimir G. <vga...@ne...> - 2009-12-18 21:26:19
|
I tried today to re-do, from scratch, the original Rutger's example configuration from http://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment . There are still a few more things to figure out. Actually, I went through all the instructions successfully, concluding with creating a Tomcat server in Eclipse Servers view. However, starting this server failed to start a treebase-web instance -- see the full log below. There are 2 visible problems: (1) Missing jdbc.properties. I do not know where it is missing from. I see that treebase-web/pom.xml has a task that copies $JDBC_HOME/jdbc.properties to treebase-web/src/main/resources. There is no similar task in treebase-core/pom.xml, and when I had earlier followed Youjun's advice in another setting, I did create treebase- core/src/main/resources/jdbc.properties by hand. I tried that now, but it did not help. (2) The class org/apache/commons/digester/Digester is missing. This is probably a build problem, since eclipse does complain that dependency M2_REPO/..../commons-digester-1.5.jar is missing (alongside with jta-1.0.1b.jar). Where should I add these dependencies and which steps in the instructions should I redo? Thanks, --Vladimir Dec 18, 2009 2:41:52 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent INFO: The Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: .:/Library/Java/Extensions:/System/Library/Java/ Extensions:/usr/lib/java Dec 18, 2009 2:41:52 PM org.apache.coyote.http11.Http11BaseProtocol init INFO: Initializing Coyote HTTP/1.1 on http-8080 Dec 18, 2009 2:41:52 PM org.apache.catalina.startup.Catalina load INFO: Initialization processed in 587 ms Dec 18, 2009 2:41:52 PM org.apache.catalina.core.StandardService start INFO: Starting service Catalina Dec 18, 2009 2:41:52 PM org.apache.catalina.core.StandardEngine start INFO: Starting Servlet Engine: Apache Tomcat/5.5.28 Dec 18, 2009 2:41:52 PM org.apache.catalina.core.StandardHost start INFO: XML validation disabled Dec 18, 2009 2:41:53 PM org.apache.catalina.loader.WebappClassLoader validateJarFile INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/devel2/treebase/ trunk/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/ treebase-web/WEB-INF/lib/geronimo-servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/ servlet/Servlet.class Dec 18, 2009 2:41:53 PM org.apache.catalina.loader.WebappClassLoader validateJarFile INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/devel2/treebase/ trunk/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/ treebase-web/WEB-INF/lib/servlet-api-2.4.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/ Servlet.class [main] DEBUG org.cipres.treebase.web.listeners.StartupListener - contextInitialized(ServletContextEvent) - FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart [main] ERROR org.springframework.web.context.ContextLoader - Context initialization failed org.springframework.beans.factory.BeanInitializationException: Could not load properties; nested exception is java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist Caused by: java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist at org .springframework .core.io.ClassPathResource.getInputStream(ClassPathResource.java:135) at org .springframework .core .io .support .PropertiesLoaderSupport.loadProperties(PropertiesLoaderSupport.java: 179) at org .springframework .core .io .support .PropertiesLoaderSupport.mergeProperties(PropertiesLoaderSupport.java: 158) at org .springframework .beans .factory .config .PropertyResourceConfigurer .postProcessBeanFactory(PropertyResourceConfigurer.java:68) at org .springframework .context .support .AbstractApplicationContext .invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:467) at org .springframework .context .support .AbstractApplicationContext.refresh(AbstractApplicationContext.java:334) at org.springframework.web.context.ContextLoader.createWebApplicationContext (ContextLoader.java:245) at org.springframework.web.context.ContextLoader.initWebApplicationContext (ContextLoader.java:188) at org.springframework.web.context.ContextLoaderListener.contextInitialized (ContextLoaderListener.java:49) at org .cipres .treebase .web.listeners.StartupListener.contextInitialized(StartupListener.java: 45) at org .apache .catalina.core.StandardContext.listenerStart(StandardContext.java:3795) at org.apache.catalina.core.StandardContext.start(StandardContext.java: 4252) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java: 700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 39) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 25) at java.lang.reflect.Method.invoke(Method.java:592) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina]. [localhost].[/treebase-web] - Exception sending context initialized event to listener instance of class org.cipres.treebase.web.listeners.StartupListener org.springframework.beans.factory.BeanInitializationException: Could not load properties; nested exception is java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist Caused by: java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist at org .springframework .core.io.ClassPathResource.getInputStream(ClassPathResource.java:135) at org .springframework .core .io .support .PropertiesLoaderSupport.loadProperties(PropertiesLoaderSupport.java: 179) at org .springframework .core .io .support .PropertiesLoaderSupport.mergeProperties(PropertiesLoaderSupport.java: 158) at org .springframework .beans .factory .config .PropertyResourceConfigurer .postProcessBeanFactory(PropertyResourceConfigurer.java:68) at org .springframework .context .support .AbstractApplicationContext .invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:467) at org .springframework .context .support .AbstractApplicationContext.refresh(AbstractApplicationContext.java:334) at org.springframework.web.context.ContextLoader.createWebApplicationContext (ContextLoader.java:245) at org.springframework.web.context.ContextLoader.initWebApplicationContext (ContextLoader.java:188) at org.springframework.web.context.ContextLoaderListener.contextInitialized (ContextLoaderListener.java:49) at org .cipres .treebase .web.listeners.StartupListener.contextInitialized(StartupListener.java: 45) at org .apache .catalina.core.StandardContext.listenerStart(StandardContext.java:3795) at org.apache.catalina.core.StandardContext.start(StandardContext.java: 4252) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java: 700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 39) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 25) at java.lang.reflect.Method.invoke(Method.java:592) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina]. [localhost].[/treebase-web] - Exception sending context initialized event to listener instance of class net.sf.navigator.menu.MenuContextListener java.lang.NoClassDefFoundError: org/apache/commons/digester/Digester at net.sf.navigator.menu.MenuRepository.initDigester(MenuRepository.java: 83) at net.sf.navigator.menu.MenuRepository.load(MenuRepository.java:210) at net .sf .navigator .menu.MenuContextListener.contextInitialized(MenuContextListener.java: 64) at org .apache .catalina.core.StandardContext.listenerStart(StandardContext.java:3795) at org.apache.catalina.core.StandardContext.start(StandardContext.java: 4252) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java: 700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 39) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 25) at java.lang.reflect.Method.invoke(Method.java:592) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) Dec 18, 2009 2:41:54 PM org.apache.catalina.core.StandardContext start SEVERE: Error listenerStart Dec 18, 2009 2:41:54 PM org.apache.catalina.core.StandardContext start SEVERE: Context [/treebase-web] startup failed due to previous errors WARN: The method class org.apache.commons.logging.impl.SLF4JLogFactory#release() was invoked. WARN: Please see http://www.slf4j.org/codes.html for an explanation. Dec 18, 2009 2:41:54 PM org.apache.coyote.http11.Http11BaseProtocol start INFO: Starting Coyote HTTP/1.1 on http-8080 Dec 18, 2009 2:41:54 PM org.apache.jk.common.ChannelSocket init INFO: JK: ajp13 listening on /0.0.0.0:8009 Dec 18, 2009 2:41:54 PM org.apache.jk.server.JkMain start INFO: Jk running ID=0 time=0/17 config=null Dec 18, 2009 2:41:54 PM org.apache.catalina.storeconfig.StoreLoader load INFO: Find registry server-registry.xml at classpath resource Dec 18, 2009 2:41:54 PM org.apache.catalina.startup.Catalina start INFO: Server startup in 1983 ms |
|
From: Rutger V. <rut...@gm...> - 2009-12-18 10:49:50
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>> The environment for this user should be setup from scratch instead of >> copied over from an existing user's home dir. > > Yes. Rutger, are the instructions for that now complete, including any > Mesquite environment variables? Yes. It's on the wiki, there's also a file with the same variables in /home/rvosa/vars >> BTW, I tired to start Rutger's instance of tomcat with sudo this morning >> and was not able to because it needed some environment variables to start. >> Will this be necessary on production? I would prefer not. I usually put >> those variables in tomcat5.conf or in the catalina.sh script. > > It sounds like we need to fix that too so they are indeed part of the tomcat > startup configuration. Is that part of the documented instructions above? Not yet. The configuration that is being suggested here is different from how I did it. I approached it as a programmer wanting to have all the required variables set in the shell, so I can run scripts, launch standalone mesquite, etc. What Jon is suggesting is a more sysadmin-oriented approach where everything is scoped inside tomcat so that there is no hidden "magic" in the outside environment. I guess the consensus is that that suggestion is better, so what we should probably do is set it up on tre...@tr..., then update the wiki. -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2009-12-17 21:19:15
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On Dec 16, 2009, at 1:22 PM, Jon Auman wrote: > I suggest that treebase-dev be configured to run from the treebase > account on the server. I agree. > CATALINA_HOME : /home/treebase/tomcat Ditto. > The environment for this user should be setup from scratch instead > of copied over from an existing user's home dir. Yes. Rutger, are the instructions for that now complete, including any Mesquite environment variables? > I'll create an initd script that starts tomcat on startup of the > server. All developers will be able to start and stop that instance > of tomcat as well. That sounds great. > BTW, I tired to start Rutger's instance of tomcat with sudo this > morning and was not able to because it needed some environment > variables to start. Will this be necessary on production? I would > prefer not. I usually put those variables in tomcat5.conf or in the > catalina.sh script. It sounds like we need to fix that too so they are indeed part of the tomcat startup configuration. Is that part of the documented instructions above? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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