[Gmod-help] Re: [Gmod-schema] Apollo and Chado problems
Scott Cain
scott at scottcain.net
Thu Dec 3 23:07:09 EST 2009
That's not a problem. That was just introduced to the codebase within
the last few weeks and I need to fix it, but it is calling a commit at
the end of the load when it isn't needed.
Scott
On Thu, Dec 3, 2009 at 5:46 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
> Hi,
>
> At the end of loading the GFF file (using gmod_bulk_load_gff3.pl) into
> Chado, I get something I did not get before:
>
> commit ineffective with AutoCommit enabled
>
> Is that just a warning and the data was loaded anyway, or does it mean the
> commit failed? If I knew the schema better, I could check some tables, but
> there are so many...
>
> Thanks
> J
>
> Scott Cain wrote:
>>
>> Hi J,
>>
>> Yes, getting schema/trunk is sufficient. Since we moved to svn pretty
>> recently, there are likely to be other holes in documentation where
>> cvs was assumed.
>>
>> As for further questions, it depends on what they are concerning. If
>> apollo webstart is causing you problems, you can ask about it on the
>> apollo mailing list, GBrowse questions to the gbrowse list, and most
>> other questions would go to the schema mailing list.
>>
>> Scott
>>
>> On Thu, Dec 3, 2009 at 12:15 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
>>>
>>> Hi,
>>>
>>> Thanks for the answer, that helped. I was following the instructions from
>>> http://gmod.org/wiki/Chado_-_Getting_Started but I missed the part about
>>> ant
>>> (because I was originally not installing from SVN) -- have that installed
>>> now. I didn't see anything about the checking out of the whole schema
>>> though.
>>>
>>> What I did was this:
>>>
>>> svn co https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk
>>>
>>> It does check out GMODTools and other stuff. Is that sufficient? It did
>>> take
>>> care of all the errors at any rate.
>>>
>>> I'm now loading the ontologies into my database, and will next load the
>>> S.
>>> cerevisiae GFF into the DB for testing (as described at
>>> http://gmod.org/wiki/Load_GFF_Into_Chado).
>>>
>>> Thanks again
>>> J
>>>
>>> PS: quick question, I'm using the community annotation server (VMware
>>> image
>>> available from http://gmod.org/wiki/Community_Annotation_System) you
>>> have,
>>> and it's mostly working (webstarted Apollo is giving a little trouble). I
>>> do
>>> have some problems and questions about it though. Which list should I
>>> direct
>>> them to?
>>>
>>>
>>> Scott Cain wrote:
>>>>
>>>> Hi J,
>>>>
>>>> I don't know how I missed a few emails in this thread, but the problem
>>>> you are having is because you need to checkout the entire schema
>>>> repository, not just the chado subdirectory. You must have ant
>>>> installed, and you need to have the GMODTools directory, which is at
>>>> the same level as the chado directory.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Wed, Dec 2, 2009 at 4:11 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
>>>>>
>>>>> Hi, Dave
>>>>>
>>>>> Thanks, that did help -- although the two lines you mention were
>>>>> *already*
>>>>> commented out. I also had to comment out the following:
>>>>>
>>>>> if ($ant or !-e "$working_dir/../GMODTools") {
>>>>> push @exe_files, 'bin/gmod_bulkfiles.pl', 'bin/gmod_gff2biomart5.pl';
>>>>> }
>>>>>
>>>>> These are currently lines 493-5 of Makefile.PL
>>>>>
>>>>> After that, it did finish without problems, apparently.
>>>>>
>>>>> I am currently updating from the gmod-1.0 file found on SourceForge to
>>>>> the
>>>>> SVN code. Do I need to uninstall the old version (how? 'make uninstall'
>>>>> does
>>>>> not do it, just gives a list of things to delete) or is just installing
>>>>> on
>>>>> top of the one I have right now fine?
>>>>>
>>>>> Thanks
>>>>> J
>>>>>
>>>>> Dave Clements, GMOD Help Desk wrote:
>>>>>>
>>>>>> Hi J,
>>>>>>
>>>>>> We generally recommend searching using Nabble:
>>>>>>
>>>>>> http://www.nabble.com/Generic-Model-Organism-System-Database-f3491.html
>>>>>>
>>>>>> And, using Nabble, I found a thread from 2007
>>>>>>
>>>>>>
>>>>>> (http://old.nabble.com/Blast-input-file-for-CHADO-to9828403.html#a9847174)
>>>>>> where someone had the same problem. I have no idea why you are having
>>>>>> the problem, but a workaround is:
>>>>>>
>>>>>> But, it works after commenting out the following lines in
>>>>>> Makefile.PL.
>>>>>> #'bin/gmod_bulkfiles.pl', line no 522
>>>>>> #'bin/gmod_gff2biomart5.pl', line no 523
>>>>>>
>>>>>> You don't need the biomart script unless you are using BioMart too.
>>>>>> Does that work for you?
>>>>>>
>>>>>> Dave C.
>>>>>>
>>>>>> On Mon, Nov 30, 2009 at 1:44 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
>>>>>>>
>>>>>>> Thanks, Scott
>>>>>>>
>>>>>>> I just subscribed to the list. BTW, is there a way to search it? I
>>>>>>> looked there, but the Sourceforge interface is terrible, and the
>>>>>>> search
>>>>>>> box on the top right searches all the site's project names instead of
>>>>>>> the list archives.
>>>>>>>
>>>>>>> I ask because, following your advice, I checked out the svn version.
>>>>>>> Then I got a warning during perl Makefile.PL that the kit was missing
>>>>>>> files, contact author:
>>>>>>>
>>>>>>> ===========================================
>>>>>>> Checking if your kit is complete...
>>>>>>> Warning: the following files are missing in your kit:
>>>>>>> bin/cxgn/load_cvterms.pl
>>>>>>> bin/gmod_bulkfiles.pl
>>>>>>> bin/gmod_gff2biomart5.pl
>>>>>>> conf/bulkfiles/anogam.xml
>>>>>>> conf/bulkfiles/blastfiles.xml
>>>>>>> conf/bulkfiles/bulkfiles_template.xml
>>>>>>> conf/bulkfiles/chadofeatconv.xml
>>>>>>> conf/bulkfiles/chadofeatsql.xml
>>>>>>> conf/bulkfiles/chadogenepagesql.xml
>>>>>>> conf/bulkfiles/dmelhetfeatconv.xml
>>>>>>> conf/bulkfiles/dmelr420.xml
>>>>>>> conf/bulkfiles/dmelr430.xml
>>>>>>> conf/bulkfiles/dpsebulk-p4.xml
>>>>>>> conf/bulkfiles/dpsebulk-p5.xml
>>>>>>> conf/bulkfiles/dpsebulk-r2.xml
>>>>>>> conf/bulkfiles/drosmelgb.xml
>>>>>>> conf/bulkfiles/fastawriter.xml
>>>>>>> conf/bulkfiles/fbbulk-hetr3.xml
>>>>>>> conf/bulkfiles/fbbulk-r3.xml
>>>>>>> conf/bulkfiles/fbbulk-r3h.xml
>>>>>>> conf/bulkfiles/fbbulk-r4.xml
>>>>>>> conf/bulkfiles/fbbulk-r41.xml
>>>>>>> conf/bulkfiles/fbbulk-r411.xml
>>>>>>> conf/bulkfiles/fbreleases.xml
>>>>>>> conf/bulkfiles/featuresets.xml
>>>>>>> conf/bulkfiles/filesets.xml
>>>>>>> conf/bulkfiles/gbrowseconf.xml
>>>>>>> conf/bulkfiles/gbrowseconf_fb.xml
>>>>>>> conf/bulkfiles/genbanksubmit.xml
>>>>>>> conf/bulkfiles/genomeweb.xml
>>>>>>> conf/bulkfiles/organisms.xml
>>>>>>> conf/bulkfiles/sgdbulk.xml
>>>>>>> conf/bulkfiles/sgdbulk1.xml
>>>>>>> conf/bulkfiles/sgdfeatconf.xml
>>>>>>> conf/bulkfiles/site_defaults.xml
>>>>>>> conf/bulkfiles/site_eugenes_defaults.xml
>>>>>>> conf/bulkfiles/spbase.xml
>>>>>>> conf/bulkfiles/spbasefeatconf.xml
>>>>>>> conf/bulkfiles/tablewriter.xml
>>>>>>> conf/bulkfiles/toacode.xml
>>>>>>> conf/bulkfiles/tognomap.xml
>>>>>>> conf/chado2apollo-apache.conf
>>>>>>> doc/about-gff2biomart.pod
>>>>>>> doc/COPYRIGHT
>>>>>>> doc/gff2biomart-update.note
>>>>>>> doc/gmod-tools-readme.pod
>>>>>>> lib/Bio/GMOD/Bulkfiles.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/AcodeWriter.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/BlastWriter.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/BulkWriter.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/FastaWriter.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/GnomapWriter.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/MyLargePrimarySeq.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/MySplitLocation.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm
>>>>>>> lib/Bio/GMOD/Bulkfiles/TableWriter.pm
>>>>>>> lib/Bio/GMOD/Config2.pm
>>>>>>> lib/Bio/GMOD/SeqUtils.pm
>>>>>>> Please inform the author.
>>>>>>> ===========================================
>>>>>>>
>>>>>>> When I "make", it finishes quite early, with:
>>>>>>>
>>>>>>> make: *** No rule to make target `bin/gmod_gff2biomart5.pl', needed
>>>>>>> by
>>>>>>> `blib/script/gmod_gff2biomart5.pl'. Stop.
>>>>>>>
>>>>>>> (the full output of "make" is below)
>>>>>>>
>>>>>>> Has anyone seen this problem? Is it a problem? (it seems to me...)
>>>>>>> And
>>>>>>> any idea what to do, please?
>>>>>>>
>>>>>>> Thanks
>>>>>>> J
>>>>>>>
>>>>>>> ===========================================
>>>>>>> ~/prog/chado$ make
>>>>>>> Skip blib/lib/Bio/GMOD/Load.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/FeatureIO/chado.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/GMOD/DB/Config.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/Chado/Config.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/Chado/LoadDBI.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/GMOD/Load/GFF.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/GMOD/Config.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/FeatureIO/chadobulk.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/GMOD/DB/Adapter.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/GMOD/DB/Adapter/Wormbase.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/Chado/AutoDBI.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/GMOD/DB/Adapter/FeatureIterator.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/GMOD/DB/Tools/ETA.pm (unchanged)
>>>>>>> Skip blib/lib/Bio/Chado/Builder.pm (unchanged)
>>>>>>> make[1]: Entering directory `/home/jmalves/prog/chado/chaos-xml'
>>>>>>> cp lib/Bio/Chaos/ChaosGraph.pm ../blib/lib/Bio/Chaos/ChaosGraph.pm
>>>>>>> cp lib/Bio/Chaos/FeatureUtil.pm ../blib/lib/Bio/Chaos/FeatureUtil.pm
>>>>>>> cp lib/Bio/Chaos/XSLTHelper.pm ../blib/lib/Bio/Chaos/XSLTHelper.pm
>>>>>>> cp lib/Bio/Chaos/Root.pm ../blib/lib/Bio/Chaos/Root.pm
>>>>>>> cp bin/cx-download-enscore.pl ../blib/script/cx-download-enscore.pl
>>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>>> ../blib/script/cx-download-enscore.pl
>>>>>>> cp bin/cx-genbank2chaos.pl ../blib/script/cx-genbank2chaos.pl
>>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>>> ../blib/script/cx-genbank2chaos.pl
>>>>>>> cp bin/cx-enscore2chaos.pl ../blib/script/cx-enscore2chaos.pl
>>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>>> ../blib/script/cx-enscore2chaos.pl
>>>>>>> cp bin/cx-chadoxml2chaos.pl ../blib/script/cx-chadoxml2chaos.pl
>>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>>> ../blib/script/cx-chadoxml2chaos.pl
>>>>>>> cp bin/cx-chaos-report.pl ../blib/script/cx-chaos-report.pl
>>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>>> ../blib/script/cx-chaos-report.pl
>>>>>>> Manifying ../blib/man1/cx-genbank2chaos.pl.1p
>>>>>>> Manifying ../blib/man1/cx-chadoxml2chaos.pl.1p
>>>>>>> Manifying ../blib/man1/cx-chaos-report.pl.1p
>>>>>>> Manifying ../blib/man3/Bio::Chaos::ChaosGraph.3pm
>>>>>>> Manifying ../blib/man3/Bio::Chaos::FeatureUtil.3pm
>>>>>>> Manifying ../blib/man3/Bio::Chaos::XSLTHelper.3pm
>>>>>>> Manifying ../blib/man3/Bio::Chaos::Root.3pm
>>>>>>> make[1]: Leaving directory `/home/jmalves/prog/chado/chaos-xml'
>>>>>>> make: *** No rule to make target `bin/gmod_gff2biomart5.pl', needed
>>>>>>> by
>>>>>>> `blib/script/gmod_gff2biomart5.pl'. Stop.
>>>>>>> ===========================================
>>>>>>>
>>>>>>> Scott Cain wrote:
>>>>>>>>
>>>>>>>> Hello J,
>>>>>>>>
>>>>>>>> I'm cc'ing this response to the schema mailing list, which is where
>>>>>>>> Chado discussion usually occurs. For the problem you are
>>>>>>>> describing,
>>>>>>>> there or the Apollo list (or both) would be a good place to start
>>>>>>>> when
>>>>>>>> looking for solutions.
>>>>>>>>
>>>>>>>> For using Apollo with Chado, I would suggest that you first take a
>>>>>>>> look at the the tutorial on the GMOD website:
>>>>>>>>
>>>>>>>> http://gmod.org/wiki/Apollo_Tutorial
>>>>>>>>
>>>>>>>> Additionally, I would suggest you consider using chado checked out
>>>>>>>> from svn instead of the 1.0 release; it is getting pretty old at
>>>>>>>> this
>>>>>>>> point. I am working on a 1.1 release that I plan to have out by the
>>>>>>>> end of the year, but what is in svn now is quite stable.
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Nov 25, 2009 at 1:23 PM, J.M.P. Alves <jmalves at vcu.edu>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I am following the instructions from README.Apollo in the GMOD 1.0
>>>>>>>>> distribution, and have found a couple of problems.
>>>>>>>>>
>>>>>>>>> When running
>>>>>>>>>
>>>>>>>>> psql chadodb < modules/sequence/apollo-bridge/apollo.inserts
>>>>>>>>>
>>>>>>>>> I got a couple of errors. The first:
>>>>>>>>>
>>>>>>>>> ERROR: null value in column "cv_id" violates not-null constraint
>>>>>>>>>
>>>>>>>>> I checked the offending part of the sql and it tries to find a
>>>>>>>>> cv_if
>>>>>>>>> for the
>>>>>>>>> record with "Relationship Ontology" as name. But in the schema I
>>>>>>>>> installed
>>>>>>>>> there is no such record. The closest I could find was one called
>>>>>>>>> "relationship" and one called "pub relationship type". Which is the
>>>>>>>>> correct
>>>>>>>>> one?
>>>>>>>>>
>>>>>>>>> The second error was:
>>>>>>>>>
>>>>>>>>> ERROR: aggregates not allowed in WHERE clause
>>>>>>>>>
>>>>>>>>> This was triggered by the command:
>>>>>>>>>
>>>>>>>>> delete from feature_namegenerator where feature_namegenerator_id
>>>>>>>>> not
>>>>>>>>> in
>>>>>>>>> (select feature_namegenerator_id from feature_namegenerator where
>>>>>>>>> count
>>>>>>>>> =
>>>>>>>>> max(count) group by name,type_id);
>>>>>>>>>
>>>>>>>>> I haven't figured out how to solve this one, since I have no
>>>>>>>>> experience
>>>>>>>>> with
>>>>>>>>> PostgreSQL.
>>>>>>>>>
>>>>>>>>> Regards
>>>>>>>>> J
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> P.S.: I wrote a few minutes ago about a problem with GBrowse's
>>>>>>>>> Chado
>>>>>>>>> documentation. I spoke too soon, there was another problem that I
>>>>>>>>> found
>>>>>>>>> when
>>>>>>>>> I clicked on the examples in GBrowse (gene name). Adding the
>>>>>>>>> following
>>>>>>>>> table
>>>>>>>>> to the permissions solved it:
>>>>>>>>>
>>>>>>>>> GRANT SELECT ON all_feature_names TO "www-data";
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> -------------------------------
>>>>>>>>> João Marcelo Pereira Alves (J)
>>>>>>>>> Post-doctoral fellow
>>>>>>>>> MCV / VCU - Richmond, VA
>>>>>>>>> http://bioinfo.lpb.mic.vcu.edu
>>>>>>>>> f. 1-804-828-3897
>>>>>>>>>
>>>>>>>>>
>>>>>>> --
>>>>>>> -------------------------------
>>>>>>> João Marcelo Pereira Alves (J)
>>>>>>> Post-doctoral fellow
>>>>>>> MCV / VCU - Richmond, VA
>>>>>>> http://bioinfo.lpb.mic.vcu.edu
>>>>>>> f. 1-804-828-3897
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Join us December 9, 2009 for the Red Hat Virtual Experience,
>>>>>>> a free event focused on virtualization and cloud computing.
>>>>>>> Attend in-depth sessions from your desk. Your couch. Anywhere.
>>>>>>> http://p.sf.net/sfu/redhat-sfdev2dev
>>>>>>> _______________________________________________
>>>>>>> Gmod-schema mailing list
>>>>>>> Gmod-schema at lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>
>>>>>>
>>>>> --
>>>>> -------------------------------
>>>>> João Marcelo Pereira Alves (J)
>>>>> Post-doctoral fellow
>>>>> MCV / VCU - Richmond, VA
>>>>> http://bioinfo.lpb.mic.vcu.edu
>>>>> f. 1-804-828-3897
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>> --
>>> -------------------------------
>>> João Marcelo Pereira Alves (J)
>>> Post-doctoral fellow
>>> MCV / VCU - Richmond, VA
>>> http://bioinfo.lpb.mic.vcu.edu
>>> f. 1-804-828-3897
>>>
>>>
>>
>>
>>
>
> --
> -------------------------------
> João Marcelo Pereira Alves (J)
> Post-doctoral fellow
> MCV / VCU - Richmond, VA
> http://bioinfo.lpb.mic.vcu.edu
> f. 1-804-828-3897
>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
More information about the Gmod-help
mailing list