treebase-devel

[Treebase-devel] hibernate_sequence takes charge in treebasedev

[Vladimir G. <vga...@ne...>]

As of late afternoon Fri Jan 22, all tables in treebase- 
dev.nescent.org/treebasedev draw their PK ids from hibernate_sequence,  
which was updated to start with 16000000000.

Running 'mvn test' seemingly hangs forever on  
org.cipres.treebase.service.matrix.MatrixServiceImplTest.  This might  
be due to an intrinsic problem with the test, or maybe because the  
test's transaction bumped into someone else's transaction?  [I did  
manage to run this test successfully individually earlier in the day,  
but that time only 3 tables were switched to hibernate_sequence.]

I see a couple that could be done to verify success:
  - Check that unit tests now execute correctly (Youjun?)
  - Check that data entry operations from UI work (Bill?)


A few more remarks:

  - Repeating the sequence re-targeting procedure on another db  
instance will take me about an hour (there is manual work  
involved).    It's not too bad, but still means we should perform it  
on all instances as soon as treebasedev is confirmed to function  
correctly.

  - The huge starting number for hibernate_sequence is probably due to  
tests.  This suggests we should never run tests on the production  
instance.

  - All sequences but hibernate_sequence can now be dropped, I think.

Re: [Treebase-devel] hibernate_sequence takes charge in treebasedev

[Hilmar L. <hl...@ne...>]

Hmm - could there be a deadlock situation brought about by the test by  
having two transactions open on the same resource in two connections?

	-hilmar

On Jan 22, 2010, at 6:34 PM, Vladimir Gapeyev wrote:

> As of late afternoon Fri Jan 22, all tables in treebase-
> dev.nescent.org/treebasedev draw their PK ids from hibernate_sequence,
> which was updated to start with 16000000000.
>
> Running 'mvn test' seemingly hangs forever on
> org.cipres.treebase.service.matrix.MatrixServiceImplTest.  This might
> be due to an intrinsic problem with the test, or maybe because the
> test's transaction bumped into someone else's transaction?  [I did
> manage to run this test successfully individually earlier in the day,
> but that time only 3 tables were switched to hibernate_sequence.]
>
> I see a couple that could be done to verify success:
>  - Check that unit tests now execute correctly (Youjun?)
>  - Check that data entry operations from UI work (Bill?)
>
>
> A few more remarks:
>
>  - Repeating the sequence re-targeting procedure on another db
> instance will take me about an hour (there is manual work
> involved).    It's not too bad, but still means we should perform it
> on all instances as soon as treebasedev is confirmed to function
> correctly.
>
>  - The huge starting number for hibernate_sequence is probably due to
> tests.  This suggests we should never run tests on the production
> instance.
>
>  - All sequences but hibernate_sequence can now be dropped, I think.
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts  
> the
> world's best and brightest in the field, creating opportunities for  
> Conference
> attendees to learn about information security's most important  
> issues through
> interactions with peers, luminaries and emerging and established  
> companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] hibernate_sequence takes charge in treebasedev

[Vladimir G. <vga...@ne...>]

I hope you do not suggest that hibernate_sequence is the resource!  -vg

On Jan 22, 2010, at 6:37 PM, Hilmar Lapp wrote:

> Hmm - could there be a deadlock situation brought about by the test  
> by having two transactions open on the same resource in two  
> connections?
>
> 	-hilmar
>
> On Jan 22, 2010, at 6:34 PM, Vladimir Gapeyev wrote:
>
>> As of late afternoon Fri Jan 22, all tables in treebase-
>> dev.nescent.org/treebasedev draw their PK ids from  
>> hibernate_sequence,
>> which was updated to start with 16000000000.
>>
>> Running 'mvn test' seemingly hangs forever on
>> org.cipres.treebase.service.matrix.MatrixServiceImplTest.  This might
>> be due to an intrinsic problem with the test, or maybe because the
>> test's transaction bumped into someone else's transaction?  [I did
>> manage to run this test successfully individually earlier in the day,
>> but that time only 3 tables were switched to hibernate_sequence.]
>>
>> I see a couple that could be done to verify success:
>> - Check that unit tests now execute correctly (Youjun?)
>> - Check that data entry operations from UI work (Bill?)
>>
>>
>> A few more remarks:
>>
>> - Repeating the sequence re-targeting procedure on another db
>> instance will take me about an hour (there is manual work
>> involved).    It's not too bad, but still means we should perform it
>> on all instances as soon as treebasedev is confirmed to function
>> correctly.
>>
>> - The huge starting number for hibernate_sequence is probably due to
>> tests.  This suggests we should never run tests on the production
>> instance.
>>
>> - All sequences but hibernate_sequence can now be dropped, I think.
>>
>>
>> ------------------------------------------------------------------------------
>> Throughout its 18-year history, RSA Conference consistently  
>> attracts the
>> world's best and brightest in the field, creating opportunities for  
>> Conference
>> attendees to learn about information security's most important  
>> issues through
>> interactions with peers, luminaries and emerging and established  
>> companies.
>> http://p.sf.net/sfu/rsaconf-dev2dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>

Re: [Treebase-devel] hibernate_sequence takes charge in treebasedev

[youjun g. <you...@ya...>]

Thanks Vladimir,

The sequence works,  and MatrixServiceImplTest problem solved.

Youjun

On Fri, Jan 22, 2010 at 6:34 PM, Vladimir Gapeyev <vga...@ne...>wrote:

> As of late afternoon Fri Jan 22, all tables in treebase-
> dev.nescent.org/treebasedev draw their PK ids from hibernate_sequence,
> which was updated to start with 16000000000.
>
> Running 'mvn test' seemingly hangs forever on
> org.cipres.treebase.service.matrix.MatrixServiceImplTest.  This might
> be due to an intrinsic problem with the test, or maybe because the
> test's transaction bumped into someone else's transaction?  [I did
> manage to run this test successfully individually earlier in the day,
> but that time only 3 tables were switched to hibernate_sequence.]
>
> I see a couple that could be done to verify success:
>  - Check that unit tests now execute correctly (Youjun?)
>  - Check that data entry operations from UI work (Bill?)
>
>
> A few more remarks:
>
>  - Repeating the sequence re-targeting procedure on another db
> instance will take me about an hour (there is manual work
> involved).    It's not too bad, but still means we should perform it
> on all instances as soon as treebasedev is confirmed to function
> correctly.
>
>  - The huge starting number for hibernate_sequence is probably due to
> tests.  This suggests we should never run tests on the production
> instance.
>
>  - All sequences but hibernate_sequence can now be dropped, I think.
>
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>

Re: [Treebase-devel] hibernate_sequence takes charge in treebasedev

[Hilmar L. <hl...@ne...>]

Awesome! One more check mark on the way to release.

	-hilmar

On Jan 26, 2010, at 9:18 AM, youjun guo wrote:

> Thanks Vladimir,
>
> The sequence works,  and MatrixServiceImplTest problem solved.
>
> Youjun
>
> On Fri, Jan 22, 2010 at 6:34 PM, Vladimir Gapeyev <vga...@ne... 
> > wrote:
> As of late afternoon Fri Jan 22, all tables in treebase-
> dev.nescent.org/treebasedev draw their PK ids from hibernate_sequence,
> which was updated to start with 16000000000.
>
> Running 'mvn test' seemingly hangs forever on
> org.cipres.treebase.service.matrix.MatrixServiceImplTest.  This might
> be due to an intrinsic problem with the test, or maybe because the
> test's transaction bumped into someone else's transaction?  [I did
> manage to run this test successfully individually earlier in the day,
> but that time only 3 tables were switched to hibernate_sequence.]
>
> I see a couple that could be done to verify success:
>  - Check that unit tests now execute correctly (Youjun?)
>  - Check that data entry operations from UI work (Bill?)
>
>
> A few more remarks:
>
>  - Repeating the sequence re-targeting procedure on another db
> instance will take me about an hour (there is manual work
> involved).    It's not too bad, but still means we should perform it
> on all instances as soon as treebasedev is confirmed to function
> correctly.
>
>  - The huge starting number for hibernate_sequence is probably due to
> tests.  This suggests we should never run tests on the production
> instance.
>
>  - All sequences but hibernate_sequence can now be dropped, I think.
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts  
> the
> world's best and brightest in the field, creating opportunities for  
> Conference
> attendees to learn about information security's most important  
> issues through
> interactions with peers, luminaries and emerging and established  
> companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
> ------------------------------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] hibernate_sequence takes charge in treebasedev

[Rutger V. <rut...@gm...>]

That's great news!


On Tuesday, January 26, 2010, youjun guo <you...@ya...> wrote:
> Thanks Vladimir,
>
> The sequence works,  and MatrixServiceImplTest problem solved.
>
> Youjun
>
> On Fri, Jan 22, 2010 at 6:34 PM, Vladimir Gapeyev <vga...@ne...> wrote:
> As of late afternoon Fri Jan 22, all tables in treebase-
> dev.nescent.org/treebasedev draw their PK ids from hibernate_sequence,
> which was updated to start with 16000000000.
>
> Running 'mvn test' seemingly hangs forever on
> org.cipres.treebase.service.matrix.MatrixServiceImplTest.  This might
> be due to an intrinsic problem with the test, or maybe because the
> test's transaction bumped into someone else's transaction?  [I did
> manage to run this test successfully individually earlier in the day,
> but that time only 3 tables were switched to hibernate_sequence.]
>
> I see a couple that could be done to verify success:
>   - Check that unit tests now execute correctly (Youjun?)
>   - Check that data entry operations from UI work (Bill?)
>
>
> A few more remarks:
>
>   - Repeating the sequence re-targeting procedure on another db
> instance will take me about an hour (there is manual work
> involved).    It's not too bad, but still means we should perform it
> on all instances as soon as treebasedev is confirmed to function
> correctly.
>
>   - The huge starting number for hibernate_sequence is probably due to
> tests.  This suggests we should never run tests on the production
> instance.
>
>   - All sequences but hibernate_sequence can now be dropped, I think.
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for Conference
> attendees to learn about information security's most important issues through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>

-- 
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

Re: [Treebase-devel] hibernate_sequence takes charge in treebasedev

[Vladimir G. <vga...@ne...>]

On Jan 26, 2010, at 9:18 AM, youjun guo wrote:

> Thanks Vladimir,
>
> The sequence works,  and MatrixServiceImplTest problem solved.
>

When I run 'mvn test', I get

Tests in error:
    
testFindMatricesByTaxon 
(org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest)
    
testFindTaxonVariantWithSubstring 
(org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest)
   testSetAuthors(org.cipres.treebase.domain.study.CitationTest)
   testUpdateNewickString(org.cipres.treebase.domain.tree.PhyloTreeTest)
   testDelete(org.cipres.treebase.dao.admin.PersonDAOTest)
   testFindByID(org.cipres.treebase.dao.admin.PersonDAOTest)
    
testFindMatricesByTaxonLabel 
(org.cipres.treebase.domain.taxon.TaxonLabelTest)
    
testFindMatricesByTaxonVariant 
(org.cipres.treebase.domain.taxon.TaxonLabelTest)
    
testConvertToMatrices 
(org.cipres.treebase.domain.search.SearchResultsTest)
    
testConvertFromMatrices 
(org.cipres.treebase.domain.search.SearchResultsTest)
    
testConvertToTrees(org.cipres.treebase.domain.search.SearchResultsTest)
    
testConvertFromTrees 
(org.cipres.treebase.domain.search.SearchResultsTest)

Tests run: 263, Failures: 0, Errors: 12, Skipped: 0


Do you get the same or there is something wrong on my side?

--VG