gusdev-gusdev

[Gusdev-gusdev] LoadGeneFeaturesFromXML error

[MICHAEL L. <lu...@cs...>]

Hello all-
While trying to run the LoadGeneFeaturesFromXML plugin, I get the
following error:
 ga GUS::Common::Plugin::LoadGeneFeaturesFromXML --XmlFile=tca1.8.xml
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
Wed May 28 10:27:42 2003	ALGINVID	218
Wed May 28 10:27:42 2003	COMMIT	commit off
Wed May 28 10:27:42 2003	ARGS	ComponentGoCvsVersion	2.249
Wed May 28 10:27:42 2003	ARGS	Display
Wed May 28 10:27:42 2003	ARGS	FunctionGoCvsVersion	2.483
Wed May 28 10:27:42 2003	ARGS	GoSynonymFile
/usr/local/db/others/GO/2002-09-17/synonyms.tab
Wed May 28 10:27:42 2003	ARGS	ProcessGoCvsVersion	2.571
Wed May 28 10:27:42 2003	ARGS	Project	PlasmodiumDB-4.0
Wed May 28 10:27:42 2003	ARGS	Survey
Wed May 28 10:27:42 2003	ARGS	Taxon	Plasmodium falciparum
Wed May 28 10:27:42 2003	ARGS	XmlFile	tca1.8.xml
Wed May 28 10:27:42 2003	ARGS	algoinvo	1
Wed May 28 10:27:42 2003	ARGS	chr
Wed May 28 10:27:42 2003	ARGS	chrnum
Wed May 28 10:27:42 2003	ARGS	comment
Wed May 28 10:27:42 2003	ARGS	commit
Wed May 28 10:27:42 2003	ARGS	debug
Wed May 28 10:27:42 2003	ARGS	group
Wed May 28 10:27:42 2003	ARGS	gusconfigfile
/home/luchtan/.gus.properties
Wed May 28 10:27:42 2003	ARGS	project
Wed May 28 10:27:42 2003	ARGS	seqFlag	0
Wed May 28 10:27:42 2003	ARGS	taskFlag
Wed May 28 10:27:42 2003	ARGS	usage
Wed May 28 10:27:42 2003	ARGS	user
Wed May 28 10:27:42 2003	ARGS	verbose
Wed May 28 10:27:42 2003	ARGS	veryVerbose
Wed May 28 10:27:42 2003	Finding Algorithm
ERROR in returning AlgId
Wed May 28 10:27:42 2003	RESULT	1


Why would it not be able to find the AlgID?  Anybody?

Michael Luchtan
http://www.cs.uga.edu/~luchtan

Re: [Gusdev-gusdev] LoadGeneFeaturesFromXML error

[MICHAEL L. <lu...@cs...>]

Some more information:
Error occurs in method setAlgId, which sets name to 'Pf Annotation'.
So when running this module with --verbose, there is an error like:


RetrieveFromDB: select * from Core.Algorithm where  name = ?
  bindValues (Pf Annotation)
ERROR in returning AlgId
Wed May 28 10:55:43 2003	RESULT	1



And here is what I get from a
select name from core.algorithm:


SQL> select name from core.algorithm;

NAME
--------------------------------------------------------------------------------
GA-Plugin
GUS::Common::Plugin::LoadTaxon
GUS::Common::Plugin::AnnotatorsInterfaceSubmitter
GUS::Common::Plugin::dbEST
GUS::Common::Plugin::DeleteSimilarities
GUS::Common::Plugin::InsertNewExternalSequences
GUS::Common::Plugin::LoadDocumentation
GUS::Common::Plugin::LoadNRDB
GUS::Common::Plugin::MakeIndexWordLink
GUS::Common::Plugin::MakeIndexWordSimLink
GUS::Common::Plugin::OrthologGroupsMCL

NAME
--------------------------------------------------------------------------------
GUS::Common::Plugin::SubmitRow
GUS::Common::Plugin::UpdateGusFromCla
GUS::Common::Plugin::UpdateGusFromXML
GUS::GOPredict::Plugin::LoadGoAssoc
GUS::GOPredict::Plugin::LoadGoOntology
GUS::Common::Plugin::LoadGeneFeaturesFromXML
SQL*PLUS
GUS::Common::Plugin::GBParser
GUS::Common::Plugin::LoadBlastSimilaritiesPK

20 rows selected.


Do I need to change line 216 in LoadGeneFeaturesFromXML from
 my %alg = ( name => 'Pf Annotation' );
to
 my %alg = ( name => 'GUS::Common::Plugin::LoadGeneFeaturesFromXML' );
??

Michael Luchtan
http://www.cs.uga.edu/~luchtan

Re: [Gusdev-gusdev] LoadGeneFeaturesFromXML error

[Steve F. <st...@pc...>]

Michael-

i don't know what the state of that plugin is.  it may be under 
construction.  you'l have to work with bindu on that.

bi...@sa...

steve

MICHAEL LUCHTAN wrote:

>Some more information:
>Error occurs in method setAlgId, which sets name to 'Pf Annotation'.
>So when running this module with --verbose, there is an error like:
>
>
>RetrieveFromDB: select * from Core.Algorithm where  name = ?
>  bindValues (Pf Annotation)
>ERROR in returning AlgId
>Wed May 28 10:55:43 2003	RESULT	1
>
>
>
>And here is what I get from a
>select name from core.algorithm:
>
>
>SQL> select name from core.algorithm;
>
>NAME
>--------------------------------------------------------------------------------
>GA-Plugin
>GUS::Common::Plugin::LoadTaxon
>GUS::Common::Plugin::AnnotatorsInterfaceSubmitter
>GUS::Common::Plugin::dbEST
>GUS::Common::Plugin::DeleteSimilarities
>GUS::Common::Plugin::InsertNewExternalSequences
>GUS::Common::Plugin::LoadDocumentation
>GUS::Common::Plugin::LoadNRDB
>GUS::Common::Plugin::MakeIndexWordLink
>GUS::Common::Plugin::MakeIndexWordSimLink
>GUS::Common::Plugin::OrthologGroupsMCL
>
>NAME
>--------------------------------------------------------------------------------
>GUS::Common::Plugin::SubmitRow
>GUS::Common::Plugin::UpdateGusFromCla
>GUS::Common::Plugin::UpdateGusFromXML
>GUS::GOPredict::Plugin::LoadGoAssoc
>GUS::GOPredict::Plugin::LoadGoOntology
>GUS::Common::Plugin::LoadGeneFeaturesFromXML
>SQL*PLUS
>GUS::Common::Plugin::GBParser
>GUS::Common::Plugin::LoadBlastSimilaritiesPK
>
>20 rows selected.
>
>
>Do I need to change line 216 in LoadGeneFeaturesFromXML from
> my %alg = ( name => 'Pf Annotation' );
>to
> my %alg = ( name => 'GUS::Common::Plugin::LoadGeneFeaturesFromXML' );
>??
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>
>
>
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Re: [Gusdev-gusdev] LoadGeneFeaturesFromXML error

[Jonathan C. <cra...@pc...>]

Hi Michael-

MICHAEL LUCHTAN wrote:
> Some more information:
> Error occurs in method setAlgId, which sets name to 'Pf Annotation'.
> So when running this module with --verbose, there is an error like:

This is a relatively straightforward case of a plugin making a (perhaps
un- or not-so-well documented) assumption about the initial state of the
database.  In this case, the plugin expects to find an entry in
core.Algorithm with the name "Pf Annotation".  We use the Algorithm table
to represent not only GUS plugins, but also "external" programs/algorithms
like Genscan, BLAST, etc.  For gene predictions in particular, the
GeneFeature table has a prediction_algorithm_id which we use to indicate
the gene predictor that generated the gene model.  In the PlasmoDB project
we have an Algorithm called "Pf Annotation", which is not a formal algorithm
per se, but rather a placeholder to indicate that the gene model in question
is an "annotated gene" (i.e., it may have come from an automated gene
prediction program initially, but it has since been modified and/or reviewed
by an annotator, and then released as part of the official annotation.)

> Do I need to change line 216 in LoadGeneFeaturesFromXML from
>  my %alg = ( name => 'Pf Annotation' );
> to
>  my %alg = ( name => 'GUS::Common::Plugin::LoadGeneFeaturesFromXML' );
> ??

No; you should instead add an appropriate entry into the Algorithm table.  If
you're loading official Plasmodium falciparum gene predictions, then you should
make an entry for "Pf Annotation"; otherwise you should enter whatever best
describes the source of the genes that you're loading.  I know that we have
used the same plugin to load gene models from Plasmodium yoelii, so it
shouldn't be hard-coded to look for "Pf Annotation", but it's possible that
this oversight hasn't been fixed yet.  If it hasn't been done already, the
name of the algorithm should be made into a command-line parameter to the plugin.
The plugin should also behave better if the requested Algorithm cannot be
found (and it should perhaps even create a new entry, although that could lead
to trouble once the inevitable spelling mistakes are made.)

Jonathan