gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] RAD3 Schema Questions

[Elisabetta M. <man...@pc...>]

Hi Paul,

> I had asked about the differences between the xxxElementImp and
> xxxElementResultImp tables, and that makes sense now.  I had been 
> confused by the presence of ARRAY_ID on both tables, but I guess this is 
> primarily just a denormalization then.

actually array_id is only an attribute in xxxElementImp. 
xxxElementResultImp has a quantification_id attribute, since the array_id 
can be inferred either by going to ElementImp or by going to Assay through 
Quantification->Acquisition->Assay.

> So, if I understand correctly, the querying process to go from a 
> BioMaterial to getting the corresponding Elements and ElementResults 
> would look something like this:
> ...
> In other words, I walk the table chain:
> BioMaterialImp -> AssayBioMaterial ->
> Acquisition -> Quantification ->
> ElementResultImp -> ElementImp

Yes, you have it right.

As for ElementResultImp, we typically have a view for each image 
quantification software (e.g. ArrayVisionElementResultImp, 
GenePixElementResultImp, etc.) and we use them to store ALL measurements 
output by that software package, EXCEPT for those that can be derived 
from other measurements already stored. Now, in the case of 2-channel data, we 
have 2 quantification_ids, one per channel, for each image analysis run. 
So, for each element, we store 2 complete groups of measurements in the 
corresponding ElementResultImp view, one for each of the two quantification_id. For 
those measurements, which are not derived, but which are typically 
identical for the two channels, e.g. the GenePix spot_diameter, or the 
mean_of_ratios, they will be stored redundantly, once for each channel.
(Note that the GenePix ratio_of_means is a derived measurement so we 
don't store it in GenePixElementResult, whereas the means_of_ratios is 
not. The schema browser 
http://www.cbil.upenn.edu/cgi-bin/GUS30/schemaBrowser.pl?db=GUS30 contains 
more detailed doc on the RAD tables and their attributes.) 
Given 2 related quantifications (as from the RelatedQuantification table) 
for a given 2-channel assay, you can retrieve the ElementResultImp 
measurements for each, and then the element_id will 
tell you which correspond to the same element. From this you can compute 
ratios for each element (e.g. ratios of background subtracted 
intensities).

> And then if I calculate a ratio or a normalized-value I would create a 
> new ElementResultImp view and store the values in there.  Is that about 
> right?

We do not create new views of ElementResultImp for derived or normalized 
values. The views of ElementResultImp are solely to store "raw" output 
from image quantification software packages.
We use the Processing tables (ProcessedIO, ProcessResult, 
ProcessInvocation, etc.) to store results of preprocessing. These tables 
are flexible enough to be used to store a variety of processings, 
including averaging within or across arrays, normalization results, etc.

Hope this helps,
Elisabetta
P.S. I'll be leaving tomorrow afternoon for meetings in Europe and I might 
not have easy access to my email while away (till June 15). In any 
case, should you have more questions, Angel or any other of the "Raddies" 
(who is on the this mailing list) should be able to help you.

---
On Mon, 2 Jun 2003, Paul Boutros wrote:

> Hi Elisabetta, Angel.
> 
> Thanks for your speedy and comprehensive replies -- it's very much appreciated!
> 
> I had asked about the differences between the xxxElementImp and 
> xxxElementResultImp tables, and that makes sense now.  I had been confused by 
> the presence of ARRAY_ID on both tables, but I guess this is primarily just a 
> denormalization then.
> 
> So, if I understand correctly, the querying process to go from a BioMaterial to 
> getting the corresponding Elements and ElementResults would look something like 
> this:
> 
> SELECT		ElementImp.tinystring1,
> 		ElementResultImp.foreground
> FROM		BioMaterialImp
> INNER JOIN	AssayBioMaterial
> ON		BioMaterialImp.bio_material_id = 
> AssayBioMaterial.bio_material_id
> INNER JOIN	Acquisition
> ON		AssayBioMaterial.assay_id = Acquisition.assay_id
> INNER JOIN	Quantificiation
> ON		Acquisition.acquisition_id = Quantification.acquisition_id
> INNER JOIN	ElementResultImp
> ON		Quantification.quantification_id = 
> ElementResultImp.quantification_id
> INNER JOIN	ElementImp
> ON		ElementResultImp.element_id = ElementImp.element_id;
> 
> In other words, I walk the table chain:
> BioMaterialImp -> AssayBioMaterial ->
> Acquisition -> Quantification ->
> ElementResultImp -> ElementImp
> 
> This is data for one channel of a multi-channel array.  The quantification and 
> acquisition relationships are stored in the RelatedXXX tables.  My 
> understanding is that to get access to data from both channels for a specific 
> array (e.g. to get ratios) I would need to do something like:
> 
> SELECT		ElementImp.tinystring1
> 		DECODE(BioMaterialID.label_method_id, 1, SUM
> (ElementResultImp.foreground), NULL),
> 		DECODE(BioMaterialID.label_method_id, 2, SUM
> (ElementResultImp.foreground), NULL)
> FROM		BioMaterialImp
> INNER JOIN	AssayBioMaterial
> ON		BioMaterialImp.bio_material_id = 
> AssayBioMaterial.bio_material_id
> INNER JOIN	Acquisition
> ON		AssayBioMaterial.assay_id = Acquisition.assay_id
> INNER JOIN	Quantification
> ON		Acquisition.acquisition_id = Quantification.acquisition_id
> INNER JOIN	ElementResultImp
> ON		Quantification.quantification_id = 
> ElementResultImp.quantification_id
> INNER JOIN	ElementImp
> ON		ElementResultImp.element_id = ElementImp.element_id
> WHERE		Assay.array_identifier = ?
> 
> Where I'm taking:
> label_method_id = 1 for a Cy3 channel
> label_method_id = 2 for a Cy5 channel
> 
> And then if I calculate a ratio or a normalized-value I would create a new 
> ElementResultImp view and store the values in there.  Is that about right?
> 
> Thanks for your patience with me,
> Paul
> 
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> 
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Re: [Gusdev-gusdev] RAD3 Schema Questions

[Paul B. <pcb...@en...>]

Hi Elisabetta, Angel.

Thanks for your speedy and comprehensive replies -- it's very much appreciated!

I had asked about the differences between the xxxElementImp and 
xxxElementResultImp tables, and that makes sense now.  I had been confused by 
the presence of ARRAY_ID on both tables, but I guess this is primarily just a 
denormalization then.

So, if I understand correctly, the querying process to go from a BioMaterial to 
getting the corresponding Elements and ElementResults would look something like 
this:

SELECT		ElementImp.tinystring1,
		ElementResultImp.foreground
FROM		BioMaterialImp
INNER JOIN	AssayBioMaterial
ON		BioMaterialImp.bio_material_id = 
AssayBioMaterial.bio_material_id
INNER JOIN	Acquisition
ON		AssayBioMaterial.assay_id = Acquisition.assay_id
INNER JOIN	Quantificiation
ON		Acquisition.acquisition_id = Quantification.acquisition_id
INNER JOIN	ElementResultImp
ON		Quantification.quantification_id = 
ElementResultImp.quantification_id
INNER JOIN	ElementImp
ON		ElementResultImp.element_id = ElementImp.element_id;

In other words, I walk the table chain:
BioMaterialImp -> AssayBioMaterial ->
Acquisition -> Quantification ->
ElementResultImp -> ElementImp

This is data for one channel of a multi-channel array.  The quantification and 
acquisition relationships are stored in the RelatedXXX tables.  My 
understanding is that to get access to data from both channels for a specific 
array (e.g. to get ratios) I would need to do something like:

SELECT		ElementImp.tinystring1
		DECODE(BioMaterialID.label_method_id, 1, SUM
(ElementResultImp.foreground), NULL),
		DECODE(BioMaterialID.label_method_id, 2, SUM
(ElementResultImp.foreground), NULL)
FROM		BioMaterialImp
INNER JOIN	AssayBioMaterial
ON		BioMaterialImp.bio_material_id = 
AssayBioMaterial.bio_material_id
INNER JOIN	Acquisition
ON		AssayBioMaterial.assay_id = Acquisition.assay_id
INNER JOIN	Quantification
ON		Acquisition.acquisition_id = Quantification.acquisition_id
INNER JOIN	ElementResultImp
ON		Quantification.quantification_id = 
ElementResultImp.quantification_id
INNER JOIN	ElementImp
ON		ElementResultImp.element_id = ElementImp.element_id
WHERE		Assay.array_identifier = ?

Where I'm taking:
label_method_id = 1 for a Cy3 channel
label_method_id = 2 for a Cy5 channel

And then if I calculate a ratio or a normalized-value I would create a new 
ElementResultImp view and store the values in there.  Is that about right?

Thanks for your patience with me,
Paul

----------------------------------------
This mail sent through www.mywaterloo.ca

Re: [Gusdev-gusdev] RAD3 Schema Questions

[Angel P. <an...@pc...>]

Paul,
Since I referred you her, I'll take point and answer these questions. 
See the comments below.

WE ask if you take/adapt any code, that you pay attention to the Apache 
inspired license and add references back to gusdb.org. Thanks!

Angel

Paul Boutros wrote:

>Hi all,
>
>Hopefully this is the right place for these questions.  If not, please let me 
>know where I can ask.
>
>I have a moderately extensive Oracle DB for cDNA microarray data.  As 
>requirements have increased it is now considered desirable to store Affy data 
>as well as enhanced sample Annotation.  I looked into MAGE-ML, and was referred 
>from a list there to GUS DB.
>
>I've started implementing a portion of your schema into my own DB, in 
>particular the annotation portion (e.g. ExternalDatabaseRelease, BioMaterialImp 
>& associated views, LabelMethod, etc.).
>
>I'm thinking about using an even larger fraction -- including the 
>CompositeElementImp/CompositeElementResultImp and ElementImp/ElementResultImp 
>tables -- because I really like the schema design you've done.
>
>But here is my problem.  I'm having some difficulty interpreting the meanings 
>of those tables.  My main questions:
>1. What are the differences between the xxxElementImp and xxxElementResultImp 
>tables?  What goes into each?  My understanding is that the xxxElementImp store 
>details about the array *layout* while the xxxElementResultImp store details 
>about the data from specific arrays.
>
This is correct. For example the Array table would contain "Affy array 
U74A", the ShortOligo view on the ElementImp table would contain the 
probe pair information and the ShortOligoFamily view on 
CompositeElementImp would contain information of the probe sets. For 
microarray data, Array = "MicroArray X" and the Spot view on ElementImp 
would contain the Features (e.g. physical locations) and the sequence 
that is spotted there. For MAGE purposes, we decided to put Reporter and 
CompositeSequence information in the SpotFamily view on the 
CompositeElementImp table.

The Results go into the various views on xxxElemenResultImp, such as 
ArrayVisionResult or AffymetrixMAS4.
Check out the documentation on the ArrayVision view from the GUS schema 
browser (look for the tables with the RAD prefix):

http://www.cbil.upenn.edu/cgi-bin/GUS30/schemaBrowser.pl?db=GUS30

http://www.cbil.upenn.edu/cgi-bin/GUS30/schemaBrowser.pl?db=GUS30&table=RAD3::ArrayVisionElementResult&path=RAD3::ArrayVisionElementResult

>2. If the above description is right, would that mean that for each physical 
>array (each "chip") there are records in all four tables?  Is that necessary 
>for cases with repeated chip "layouts"?
>
Well, it depends on what data you have and what you are going to use 
this DB for. But let me first state that this is actually the most space 
efficient way of storing array layouts and results. We separated the 
array layout information (as you noted) from the results in order to use 
the layouts repeatedly for multiple analysis on the same chips.

So to answer your question:
If your intent to provide a DB to keep track of LIMS information for 
something like a microarray core facility, (e.g. you are never going to 
work with the data from within the database) then you do not need the 
xxxElementResultImp tables at all. You can just store the Array 
definitions and the Hybridization information on the Assay -> 
Acquisition -> Quantification tables:
Assay = Hybridization ,
Acquisition = Scanning information and the location of the image file,
Quantification = Feature extraction / quantification software parameters 
and the location of the result file

But for our purposes let's assume that you need to store the data in the 
DB and work with it there:

For Affy, if you only produce / receive MAS* files, then you do not need 
the Element*Imp branch, since you will not need to store the individual 
probe pairs or the CEL file results on these probe pairs

For microarray data, if you do not want to group elements into some 
bigger concept, like a gene, or group the individual elements by source 
plate information, then you do not need the CompositeElement*Imp branch.

All other cases require you to fill in all four tables.

>3. Are the Ontologies used in RAD3::OntologyTerm publicly available?  I 
>couldn't find them in the 3.0-Beta release tar, but perhaps I just missed them?
>  
>
No they are not, for a variety of reasons. You raise a good point though 
and we will put this on our to-do list.

>Any help or suggested reading would be very much appreciated!
>Paul
>
Here are two references for the previous version of the schema that 
cover the major concepts/conventions used in RAD. Most of it still 
apply, module some schema details. If you can't get these, email me (off 
the list) and I'll try and get copies sent. A new manuscript is in 
preparation.

Stoeckert, C., Pizarro, A., Manduchi, E., Gibson, M., Brunk, B., 
Crabtree, J., Schug, S., Shen-Orr, S., Overton, G.C. (2001) A relational 
schema for both array-based and SAGE gene expression experiments. 
Bioinformatics 17(4), 300-308 (2001).

Manduchi, E., Pizarro, A., Stoeckert, C. (2001) RAD (RNA Abundance 
Database): an infrastructure for array data analysis. Proc. SPIE, vol 
4266, pp. 68-78.


Angel

Re: [Gusdev-gusdev] RAD3 Schema Questions

[Elisabetta M. <man...@pc...>]

Hi Paul,
thanks for your interest in RAD.

> 1. What are the differences between the xxxElementImp and xxxElementResultImp 
> tables?  What goes into each?  My understanding is that the xxxElementImp store 
> details about the array *layout* while the xxxElementResultImp store details 
> about the data from specific arrays.
> 2. If the above description is right, would that mean that for each 
physical array (each "chip") there are records in all four tables?  Is that 
> necessary for cases with repeated chip "layouts"?

The xxxElementImp tables indeed store information about arrays, that is 
what is spotted/synthesized at each location on the array. 
The xxxElementResultImp tables store the measurements output by image 
quantifications software for a given quantification.
Thus, for example, for a given array layout, you would store this once and 
for all using the xxxElementImp tables. Then,  for each image 
quantification of a hybridization done using such a chip, you would 
populate the xxxElementResultImp tables with the resulting data.

> 3. Are the Ontologies used in RAD3::OntologyTerm publicly available?  I 
> couldn't find them in the 3.0-Beta release tar, but perhaps I just missed them?

I guess you are referring to the RAD3.OntologyEntry table. The entries we 
store in this table typically point to entries stored in ontology tables 
which are in the SRes component of GUS. This includes the MGED Ontology 
which is available at http://mged.sourceforge.net/ontologies/index.php.

Elisabetta

[Gusdev-gusdev] RAD3 Schema Questions

[Paul B. <pcb...@en...>]

Hi all,

Hopefully this is the right place for these questions.  If not, please let me 
know where I can ask.

I have a moderately extensive Oracle DB for cDNA microarray data.  As 
requirements have increased it is now considered desirable to store Affy data 
as well as enhanced sample Annotation.  I looked into MAGE-ML, and was referred 
from a list there to GUS DB.

I've started implementing a portion of your schema into my own DB, in 
particular the annotation portion (e.g. ExternalDatabaseRelease, BioMaterialImp 
& associated views, LabelMethod, etc.).

I'm thinking about using an even larger fraction -- including the 
CompositeElementImp/CompositeElementResultImp and ElementImp/ElementResultImp 
tables -- because I really like the schema design you've done.

But here is my problem.  I'm having some difficulty interpreting the meanings 
of those tables.  My main questions:
1. What are the differences between the xxxElementImp and xxxElementResultImp 
tables?  What goes into each?  My understanding is that the xxxElementImp store 
details about the array *layout* while the xxxElementResultImp store details 
about the data from specific arrays.
2. If the above description is right, would that mean that for each physical 
array (each "chip") there are records in all four tables?  Is that necessary 
for cases with repeated chip "layouts"?
3. Are the Ontologies used in RAD3::OntologyTerm publicly available?  I 
couldn't find them in the 3.0-Beta release tar, but perhaps I just missed them?

Any help or suggested reading would be very much appreciated!
Paul

----------------------------------------
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Re: [Gusdev-gusdev] LoadNRDB newbie questions:

[Deborah F. P. <pi...@pc...>]

Hi Michael,

Try granting select to public. Was the temp table created?

I don't think the null error is due to the problem with granting
permissions. As you probably know, each nrdb record has a defline with
each of the databases that have that sequence. The databases are listed by
an abreviation, e.g. gb, emb, dbj, pir, etc. and the number of
abreviations is not static.  That is why there is such a long list of
database names and abreviations on the command line (--sourceDB). I should
have explained to you that you will have to supply a list that conforms to
what is in your database The external_database_release_id in the NRDBEntry
table is for each of these databases and not the NRDB database itself (you
have 135 for that and it is in the ExternalNASequence table).

The plugin fetches the external_database_release_id using the following 
SQL query:

select r.external_database_release_id from sres.externaldatabase d, 
sres.externaldatabaserelease r where upper(d.name) like ? and 
d.external_database_id=r.external_database_id and upper(r.version) = 
'UNKNOWN'

You will have to first enter each of the databases into ExternalDatabase 
and ExternalDatabaseRelease and then supply them on the command line using 
the model that I gave you.

The kicker is that you have to check this each time you are loading as not 
only do the number of databsaes change but also they can have different 
defline formats which means --sourceDB will have to change and the plugin 
will have to be modified to accomodate the additional format. NCBI gives 
you the information in its README files on the ftp site. 

                                                    Debbie


 On Thu, 29 May 2003, MICHAEL LUCHTAN wrote:

> Hey Debbie
> Thanks for the reply.  I tried to run the plugin with these arguments:
> 
> **********************************************************************
>  ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10
> --nrdb=/scratch/NCBI/nr
> --gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135
> --verbose --maketemp --temp_login=luchtan --temp_password=xxxxx
> --dbi_str='dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS' --plugin --delete
> --sourceDB 'GENBANK(NRDB):gb,EMBL DATA LIBRARY (NRDB):emb,DDBJ
> (NRDB):dbj,NBRF PIR (NRDB):pir,PROTEIN RESEARCH FOUNDATION
> (NRDB):prf,SWISS-PROT (NRDB):sp,BROOKHAVEN PROTEIN DATA BANK
> (NRDB):pdb,PATENTS (NRDB):pat,GENINFO BACKBONE ID (NRDB):bbs,GENERAL
> DATABASE IDENTIFIER (NRDB):gnl,NCBI REFERENCE SEQUENCE (NRDB):ref,LOCAL
> SEQUENCE IDENTIFIER:lcl,GENPEPT:genpept'
> ***********************************************************************
> 
> I am a little confused about what user to set the select permissions to
> instead of 'gusrw'.  I tried to code it as 'luchtan', but it said that I
> couldn't grant/revoke priveleges to/from myself:
> 
> ***********************************************************************
> DBD::Oracle::db do failed: ORA-01749: you may not GRANT/REVOKE privileges
> to/from yourself (DBD ERROR: OCIStmtExecute) at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 222
> ***********************************************************************
> 
> and then I get all these errors like:
> 
> ***********************************************************************
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("LUCHTAN"."NRDBTEMP"."EXTERNAL_DB_REL_ID") (DBD ERROR: OCIStmtExecute) at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 271, <NRDB>
> line 1.
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("LUCHTAN"."NRDBTEMP"."EXTERNAL_DB_REL_ID") (DBD ERROR: OCIStmtExecute) at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 271, <NRDB>
> line 11.
> ************************************************************************
> 
> Which I assume is a result of me not knowing who to grant permissions to.
> In my gus config file there is a readOnlyDatabaseLogin.  Should it be that
> user?
> 
> 
> So the plugin still ends up crashing.  Here is the rest of the output:
> (Any help would be much, much appreciate)
> **********************************************************************
> 
> 
> prepareAndExecute: select max(set_num) from luchtan.NRDBTemp
> Thu May 29 16:08:30 2003	 entries in temp table
> 
> 
> RetrieveFromDB: select * from DoTS.ExternalAASequence where  description =
> ? and  external_database_release_id = ? and  secondary_identifier = ? and
> source_id = ?
>   bindValues (unnamed protein product [Oryza sativa (japonica
> cultivar-group)], 135, 7228451, BAA92411.1)
> 
> RetrieveFromDB: select * from DoTS.NRDBEntry where
> external_database_release_id is NULL and  source_id = ?
>   bindValues (BAA92411.1)
> 
> 
> sqlExec:
>     INSERT INTO DoTS.ExternalAASequence (  description, row_user_id,
> user_write, group_write, secondary_identifier, row_project_id,
> external_database_release_id, subclass_view, group_read, sequence,
> aa_sequence_id, row_group_id, other_read, length, source_id,
> modification_date, user_read, row_alg_invocation_id, other_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?,
> ?, ? )
>   bindValues (unnamed protein product [Oryza sativa (japonica
> cultivar-group)], 6, 1, 1, 7228451, 2, 135, ExternalAASequence, 1,
> MCSYIRYDTPKLFTHVTKTPPKNQVSNSINDVGSRRATDRSVASCSSEKSVGTMSVKNASSISFEDIEKSISNWKIPKVNIKEIYHVDTDIHKVLTLNLQTSGYELELGSENISVTYRVYYKAMTTLAPCAKHYTPKGLTTLLQTNPNNRCTTPKTLKWDEITLPEKWVLSQAVEPKSMDQSEVESLIETPDGDVEITFASKQKAFLQSRPSVSLDSRPRTKPQNVVYATYEDNSDEPSISDFDINVIELDVGFVIAIEEDEFEIDKDLLKKELRLQKNRPKMKRYFERVDEPFRLKIRELWHKEMREQRKNIFFFDWYESSQVRHFEEFFKGKNMMKKEQKSEAEDLTVIKKVSTEWETTSGNKSSSSQSVSPMFVPTIDPNIKLGKQKAFGPAISEELVSELALKLNNLKVNKNINEISDNEKYDMVNKIFKPSTLTSTTRNYYPRPTYADLQFEEMPQIQNMTYYNGKEIVEWNLDGFTEYQIFTLCHQMIMYANACIANGNKEREAANMIVIGFSGQLKGWWNNYLNETQRQEILCAVKRDDQGRPLPDRDGNGNPTELKEGFHMEEKDEPIQEDDQVVGTIQKYTKQKWYAEVMYRFIDGSYFQHITLIDSGADVNCIREDEILDQLVQTKREQVVNSIYLHDNSFPKSMDLPDQKITEKRAKLQDIPHHEERLLDYREKKSRDGQDKLPMEVEQSMATNKNTKILLRAWLLST,
> 2, 3, 1, 719, BAA92411.1, 1, 252, 0)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec:
>     INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
> group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
> external_database_release_id, group_read, aa_sequence_id, row_group_id,
> other_read, gid, source_id, modification_date, user_read,
> row_alg_invocation_id, other_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, ?, SYSDATE, ?,
> ?, ? )
>   bindValues (unnamed protein product [Oryza sativa (japonica
> cultivar-group)], 6, 1, 1, 2, 1, 2, 142988, 1, 2, 3, 1, 7228451,
> BAA92411.1, 1, 252, 0)
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("DOTS"."NRDBENTRY"."EXTERNAL_DATABASE_RELEASE_ID") (DBD ERROR:
> OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
> 144, <NRDB> line 11.
> 
> 
> sqlExec:
>     UPDATE  Core.AlgorithmInvocation
>     SET
> 	end_time = SYSDATE,
> 	row_alg_invocation_id = ?,
> 	modification_date = SYSDATE
>     WHERE   algorithm_invocation_id = ?
>   bindValues (252, 252)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
>  SQL ERROR!! involving
> 
>     INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
> group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
> external_database_release_id, group_read, aa_sequence_id, row_group_id,
> other_read, gid, source_id, modification_date, user_read,
> row_alg_invocation_id, other_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, ?, SYSDATE, ?,
> ?, ? )
>  Values: unnamed protein product [Oryza sativa (japonica cultivar-group)],
> 6, 1, 1, 2, 1, 2, 142988, 1, 2, 3, 1, 7228451, BAA92411.1, 1, 252, 0 at
> /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> 
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85e7ea4)',
> '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NRDBEntry (  desc...')
> called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> 
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85e7ea4)',
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x417b0b58)', 'ARRAY(0x419d7d00)', '^J
> INSERT INTO DoTS.NRDBEntry (  description, row_user_id, use...') called at
> /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> 
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NRDBEntry=HASH(0x1043ae48)',
> 'HASH(0xfd8bd54)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> line 621
> 
> GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NRDBEntry=HASH(0x1043ae48)')
> called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> 
> GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x1043ae48)',
> undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765
> 
> GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0xf24a708)',
> 'GUS::Model::DoTS::NRDBEntry') called at
> /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746
> 
> GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0xf24a708)')
> called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
> 
> GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0xf24a708)')
> called at /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 345
> 
> GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x84bf844)',
> 'HASH(0x84f5eb4)', 'HASH(0x84f5bf0)', 135) called at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
> 
> GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x84bf844)',
> 'HASH(0x8765564)') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> 	eval {...} called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> 
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadNRDB') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> 
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadNRDB') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> 
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'ARRAY(0x8105184)') called at /home/gus_home/bin/ga line 11
> 
> 
> 
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
> 
> 
> On Thu, 29 May 2003, Deborah F. Pinney wrote:
> 
> >
> > Hi Michael,
> >
> > These are the arguments that I used:
> >
> > --temp_login "pinney" --sourceDB 'GENBANK
> > (NRDB):gb,EMBL DATA LIBRARY (NRDB):emb,DDBJ (NRDB):dbj,NBRF PIR
> > (NRDB):pir,PROTEIN RESEARCH FOUNDATION (NRDB):prf,SWISS-PROT
> > (NRDB):sp,BROOKHAVEN PROTEIN DATA BANK (NRDB):pdb,PATENTS
> > (NRDB):pat,GENINFO BACKBONE ID (NRDB):bbs,GENERAL DATABASE IDENTIFIER
> > (NRDB):gnl,NCBI REFERENCE SEQUENCE (NRDB):ref,LOCAL SEQUENCE
> > IDENTIFIER:lcl,GENPEPT:genpept' --temp_password "xxxxxxx" --dbi_str
> > 'dbi:Oracle:host=erebus.pcbi.upenn.edu;sid=gusdev'
> > --gitax /ptolemy/gi_taxid_prot.dmp --nrdb /ptolemy/nr --extDbRelId 4194
> > --maketemp --plugin --delete
> >
> >
> > The temp table is necessary for updating and even though you are only
> > filling the table for the first time, you will need to include this. I
> > think Jonathan answered the general questions about temp tables and why
> > you might need them. The plugin actually truncates, drops, creates the
> > nrdbtemp table and grants select permission to gusrw. That last one is an
> > error that will be fixed in the future but for now you may want to hard
> > code the appropriate login. I included --dbi_str  because I thought that
> > this could and might vary from your config file.
> >
> > The plugin runs in three sections, make the temp table, insert and update
> > into NRDBEntry and ExternalAASequence, and delete obsolete entries in
> > those two tables. Each section can be run separately and each is specified
> > as --maketemp, --plugin, --delete. They should be run sequentially but
> > for testing and in case of failure, they can be run at separate times. You
> > could skip the --delete.
> >
> > I hope this helps.
> >
> >                                                         Debbie
> >
> > On Thu, 29 May 2003, MICHAEL LUCHTAN wrote:
> >
> > > Hello All:
> > > I am trying to load the genbank nrdb database into GUS so that I will have
> > > what I blast against in the db so that I can load blast similarities.
> > > I have some questions regarding this plugin.
> > > What is the temp table for?  Why is it necessary?  Why must I proide
> > > another login to the database to create this table?  I would think that it
> > > could just use the login/information provided in my gus config file.
> > >
> > > Can anyone clarify the args --plugin, and --maketemp?  i.e. what happens
> > > if these are/are not provided?
> > >
> > > Which arguements are required?
> > >
> > >
> > > Also, I have tried to run the plugin with the following command:
> > > ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10
> > > --nrdb=/scratch/NCBI/nr
> > > --gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135
> > > --verbose --maketemp --temp_login=luchtan --temp_password=*******
> > > --dbi_str=dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS
> > >
> > > But I get an error like this:
> > >
> > > Thu May 29 12:01:35 2003	**COMMIT TURNED OFF**
> > >
> > > Thu May 29 12:01:35 2003	Testing on 10 insertions
> > >                 into temp table
> > >
> > > Thu May 29 12:01:35 2003	Testing on 10 insertions
> > >                 into NRDBEntry/ExternalAASequence
> > >
> > > There are 0 entries in the database hash
> > > Thu May 29 12:02:40 2003	There are 2900500 gi to taxon_id pairs
> > >
> > > DBI->connect(host=mango.ctegd.uga.edu) failed: ORA-12154: TNS:could not
> > > resolve service name (DBD ERROR: OCIServerAttach) at
> > > /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 216
> > >
> > >
> > > sqlExec:
> > >     UPDATE  Core.AlgorithmInvocation
> > >     SET
> > > 	end_time = SYSDATE,
> > > 	row_alg_invocation_id = ?,
> > > 	modification_date = SYSDATE
> > >     WHERE   algorithm_invocation_id = ?
> > >   bindValues (245, 245)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > Can't call method "do" on an undefined value at
> > > /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 219.
> > >
> > >
> > >
> > > I might be kind of "fresh" with regards to my interaction with Oracle, so
> > > I am not sure if the dbi_str argument is in the correct format.  Can
> > > anyone help me with this?
> > >
> > >
> > > Michael Luchtan
> > > http://www.cs.uga.edu/~luchtan
> > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: eBay
> > > Get office equipment for less on eBay!
> > > http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: eBay
> > Get office equipment for less on eBay!
> > http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: eBay
> Get office equipment for less on eBay!
> http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] LoadNRDB newbie questions:

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

Hey Debbie
Thanks for the reply.  I tried to run the plugin with these arguments:

**********************************************************************
 ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10
--nrdb=/scratch/NCBI/nr
--gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135
--verbose --maketemp --temp_login=luchtan --temp_password=xxxxx
--dbi_str='dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS' --plugin --delete
--sourceDB 'GENBANK(NRDB):gb,EMBL DATA LIBRARY (NRDB):emb,DDBJ
(NRDB):dbj,NBRF PIR (NRDB):pir,PROTEIN RESEARCH FOUNDATION
(NRDB):prf,SWISS-PROT (NRDB):sp,BROOKHAVEN PROTEIN DATA BANK
(NRDB):pdb,PATENTS (NRDB):pat,GENINFO BACKBONE ID (NRDB):bbs,GENERAL
DATABASE IDENTIFIER (NRDB):gnl,NCBI REFERENCE SEQUENCE (NRDB):ref,LOCAL
SEQUENCE IDENTIFIER:lcl,GENPEPT:genpept'
***********************************************************************

I am a little confused about what user to set the select permissions to
instead of 'gusrw'.  I tried to code it as 'luchtan', but it said that I
couldn't grant/revoke priveleges to/from myself:

***********************************************************************
DBD::Oracle::db do failed: ORA-01749: you may not GRANT/REVOKE privileges
to/from yourself (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 222
***********************************************************************

and then I get all these errors like:

***********************************************************************
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("LUCHTAN"."NRDBTEMP"."EXTERNAL_DB_REL_ID") (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 271, <NRDB>
line 1.
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("LUCHTAN"."NRDBTEMP"."EXTERNAL_DB_REL_ID") (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 271, <NRDB>
line 11.
************************************************************************

Which I assume is a result of me not knowing who to grant permissions to.
In my gus config file there is a readOnlyDatabaseLogin.  Should it be that
user?


So the plugin still ends up crashing.  Here is the rest of the output:
(Any help would be much, much appreciate)
**********************************************************************


prepareAndExecute: select max(set_num) from luchtan.NRDBTemp
Thu May 29 16:08:30 2003	 entries in temp table


RetrieveFromDB: select * from DoTS.ExternalAASequence where  description =
? and  external_database_release_id = ? and  secondary_identifier = ? and
source_id = ?
  bindValues (unnamed protein product [Oryza sativa (japonica
cultivar-group)], 135, 7228451, BAA92411.1)

RetrieveFromDB: select * from DoTS.NRDBEntry where
external_database_release_id is NULL and  source_id = ?
  bindValues (BAA92411.1)


sqlExec:
    INSERT INTO DoTS.ExternalAASequence (  description, row_user_id,
user_write, group_write, secondary_identifier, row_project_id,
external_database_release_id, subclass_view, group_read, sequence,
aa_sequence_id, row_group_id, other_read, length, source_id,
modification_date, user_read, row_alg_invocation_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?,
?, ? )
  bindValues (unnamed protein product [Oryza sativa (japonica
cultivar-group)], 6, 1, 1, 7228451, 2, 135, ExternalAASequence, 1,
MCSYIRYDTPKLFTHVTKTPPKNQVSNSINDVGSRRATDRSVASCSSEKSVGTMSVKNASSISFEDIEKSISNWKIPKVNIKEIYHVDTDIHKVLTLNLQTSGYELELGSENISVTYRVYYKAMTTLAPCAKHYTPKGLTTLLQTNPNNRCTTPKTLKWDEITLPEKWVLSQAVEPKSMDQSEVESLIETPDGDVEITFASKQKAFLQSRPSVSLDSRPRTKPQNVVYATYEDNSDEPSISDFDINVIELDVGFVIAIEEDEFEIDKDLLKKELRLQKNRPKMKRYFERVDEPFRLKIRELWHKEMREQRKNIFFFDWYESSQVRHFEEFFKGKNMMKKEQKSEAEDLTVIKKVSTEWETTSGNKSSSSQSVSPMFVPTIDPNIKLGKQKAFGPAISEELVSELALKLNNLKVNKNINEISDNEKYDMVNKIFKPSTLTSTTRNYYPRPTYADLQFEEMPQIQNMTYYNGKEIVEWNLDGFTEYQIFTLCHQMIMYANACIANGNKEREAANMIVIGFSGQLKGWWNNYLNETQRQEILCAVKRDDQGRPLPDRDGNGNPTELKEGFHMEEKDEPIQEDDQVVGTIQKYTKQKWYAEVMYRFIDGSYFQHITLIDSGADVNCIREDEILDQLVQTKREQVVNSIYLHDNSFPKSMDLPDQKITEKRAKLQDIPHHEERLLDYREKKSRDGQDKLPMEVEQSMATNKNTKILLRAWLLST,
2, 3, 1, 719, BAA92411.1, 1, 252, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
external_database_release_id, group_read, aa_sequence_id, row_group_id,
other_read, gid, source_id, modification_date, user_read,
row_alg_invocation_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, ?, SYSDATE, ?,
?, ? )
  bindValues (unnamed protein product [Oryza sativa (japonica
cultivar-group)], 6, 1, 1, 2, 1, 2, 142988, 1, 2, 3, 1, 7228451,
BAA92411.1, 1, 252, 0)
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("DOTS"."NRDBENTRY"."EXTERNAL_DATABASE_RELEASE_ID") (DBD ERROR:
OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
144, <NRDB> line 11.


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (252, 252)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

 SQL ERROR!! involving

    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
external_database_release_id, group_read, aa_sequence_id, row_group_id,
other_read, gid, source_id, modification_date, user_read,
row_alg_invocation_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, ?, SYSDATE, ?,
?, ? )
 Values: unnamed protein product [Oryza sativa (japonica cultivar-group)],
6, 1, 1, 2, 1, 2, 142988, 1, 2, 3, 1, 7228451, BAA92411.1, 1, 252, 0 at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85e7ea4)',
'^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NRDBEntry (  desc...')
called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85e7ea4)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x417b0b58)', 'ARRAY(0x419d7d00)', '^J
INSERT INTO DoTS.NRDBEntry (  description, row_user_id, use...') called at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NRDBEntry=HASH(0x1043ae48)',
'HASH(0xfd8bd54)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 621

GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NRDBEntry=HASH(0x1043ae48)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677

GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x1043ae48)',
undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765

GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0xf24a708)',
'GUS::Model::DoTS::NRDBEntry') called at
/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746

GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0xf24a708)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684

GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0xf24a708)')
called at /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 345

GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x84bf844)',
'HASH(0x84f5eb4)', 'HASH(0x84f5bf0)', 135) called at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127

GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x84bf844)',
'HASH(0x8765564)') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
	eval {...} called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadNRDB') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadNRDB') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105184)') called at /home/gus_home/bin/ga line 11



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


On Thu, 29 May 2003, Deborah F. Pinney wrote:

>
> Hi Michael,
>
> These are the arguments that I used:
>
> --temp_login "pinney" --sourceDB 'GENBANK
> (NRDB):gb,EMBL DATA LIBRARY (NRDB):emb,DDBJ (NRDB):dbj,NBRF PIR
> (NRDB):pir,PROTEIN RESEARCH FOUNDATION (NRDB):prf,SWISS-PROT
> (NRDB):sp,BROOKHAVEN PROTEIN DATA BANK (NRDB):pdb,PATENTS
> (NRDB):pat,GENINFO BACKBONE ID (NRDB):bbs,GENERAL DATABASE IDENTIFIER
> (NRDB):gnl,NCBI REFERENCE SEQUENCE (NRDB):ref,LOCAL SEQUENCE
> IDENTIFIER:lcl,GENPEPT:genpept' --temp_password "xxxxxxx" --dbi_str
> 'dbi:Oracle:host=erebus.pcbi.upenn.edu;sid=gusdev'
> --gitax /ptolemy/gi_taxid_prot.dmp --nrdb /ptolemy/nr --extDbRelId 4194
> --maketemp --plugin --delete
>
>
> The temp table is necessary for updating and even though you are only
> filling the table for the first time, you will need to include this. I
> think Jonathan answered the general questions about temp tables and why
> you might need them. The plugin actually truncates, drops, creates the
> nrdbtemp table and grants select permission to gusrw. That last one is an
> error that will be fixed in the future but for now you may want to hard
> code the appropriate login. I included --dbi_str  because I thought that
> this could and might vary from your config file.
>
> The plugin runs in three sections, make the temp table, insert and update
> into NRDBEntry and ExternalAASequence, and delete obsolete entries in
> those two tables. Each section can be run separately and each is specified
> as --maketemp, --plugin, --delete. They should be run sequentially but
> for testing and in case of failure, they can be run at separate times. You
> could skip the --delete.
>
> I hope this helps.
>
>                                                         Debbie
>
> On Thu, 29 May 2003, MICHAEL LUCHTAN wrote:
>
> > Hello All:
> > I am trying to load the genbank nrdb database into GUS so that I will have
> > what I blast against in the db so that I can load blast similarities.
> > I have some questions regarding this plugin.
> > What is the temp table for?  Why is it necessary?  Why must I proide
> > another login to the database to create this table?  I would think that it
> > could just use the login/information provided in my gus config file.
> >
> > Can anyone clarify the args --plugin, and --maketemp?  i.e. what happens
> > if these are/are not provided?
> >
> > Which arguements are required?
> >
> >
> > Also, I have tried to run the plugin with the following command:
> > ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10
> > --nrdb=/scratch/NCBI/nr
> > --gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135
> > --verbose --maketemp --temp_login=luchtan --temp_password=*******
> > --dbi_str=dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS
> >
> > But I get an error like this:
> >
> > Thu May 29 12:01:35 2003	**COMMIT TURNED OFF**
> >
> > Thu May 29 12:01:35 2003	Testing on 10 insertions
> >                 into temp table
> >
> > Thu May 29 12:01:35 2003	Testing on 10 insertions
> >                 into NRDBEntry/ExternalAASequence
> >
> > There are 0 entries in the database hash
> > Thu May 29 12:02:40 2003	There are 2900500 gi to taxon_id pairs
> >
> > DBI->connect(host=mango.ctegd.uga.edu) failed: ORA-12154: TNS:could not
> > resolve service name (DBD ERROR: OCIServerAttach) at
> > /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 216
> >
> >
> > sqlExec:
> >     UPDATE  Core.AlgorithmInvocation
> >     SET
> > 	end_time = SYSDATE,
> > 	row_alg_invocation_id = ?,
> > 	modification_date = SYSDATE
> >     WHERE   algorithm_invocation_id = ?
> >   bindValues (245, 245)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > Can't call method "do" on an undefined value at
> > /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 219.
> >
> >
> >
> > I might be kind of "fresh" with regards to my interaction with Oracle, so
> > I am not sure if the dbi_str argument is in the correct format.  Can
> > anyone help me with this?
> >
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: eBay
> > Get office equipment for less on eBay!
> > http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: eBay
> Get office equipment for less on eBay!
> http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5
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Re: [Gusdev-gusdev] LoadNRDB newbie questions:

[Deborah F. P. <pi...@pc...>]

Hi Michael,

These are the arguments that I used:

--temp_login "pinney" --sourceDB 'GENBANK 
(NRDB):gb,EMBL DATA LIBRARY (NRDB):emb,DDBJ (NRDB):dbj,NBRF PIR 
(NRDB):pir,PROTEIN RESEARCH FOUNDATION (NRDB):prf,SWISS-PROT 
(NRDB):sp,BROOKHAVEN PROTEIN DATA BANK (NRDB):pdb,PATENTS 
(NRDB):pat,GENINFO BACKBONE ID (NRDB):bbs,GENERAL DATABASE IDENTIFIER 
(NRDB):gnl,NCBI REFERENCE SEQUENCE (NRDB):ref,LOCAL SEQUENCE 
IDENTIFIER:lcl,GENPEPT:genpept' --temp_password "xxxxxxx" --dbi_str 
'dbi:Oracle:host=erebus.pcbi.upenn.edu;sid=gusdev' 
--gitax /ptolemy/gi_taxid_prot.dmp --nrdb /ptolemy/nr --extDbRelId 4194
--maketemp --plugin --delete


The temp table is necessary for updating and even though you are only 
filling the table for the first time, you will need to include this. I 
think Jonathan answered the general questions about temp tables and why 
you might need them. The plugin actually truncates, drops, creates the 
nrdbtemp table and grants select permission to gusrw. That last one is an 
error that will be fixed in the future but for now you may want to hard 
code the appropriate login. I included --dbi_str  because I thought that 
this could and might vary from your config file. 

The plugin runs in three sections, make the temp table, insert and update
into NRDBEntry and ExternalAASequence, and delete obsolete entries in
those two tables. Each section can be run separately and each is specified 
as --maketemp, --plugin, --delete. They should be run sequentially but 
for testing and in case of failure, they can be run at separate times. You 
could skip the --delete.

I hope this helps.

                                                        Debbie 

On Thu, 29 May 2003, MICHAEL LUCHTAN wrote:

> Hello All:
> I am trying to load the genbank nrdb database into GUS so that I will have
> what I blast against in the db so that I can load blast similarities.
> I have some questions regarding this plugin.
> What is the temp table for?  Why is it necessary?  Why must I proide
> another login to the database to create this table?  I would think that it
> could just use the login/information provided in my gus config file.
> 
> Can anyone clarify the args --plugin, and --maketemp?  i.e. what happens
> if these are/are not provided?
> 
> Which arguements are required?
> 
> 
> Also, I have tried to run the plugin with the following command:
> ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10
> --nrdb=/scratch/NCBI/nr
> --gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135
> --verbose --maketemp --temp_login=luchtan --temp_password=*******
> --dbi_str=dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS
> 
> But I get an error like this:
> 
> Thu May 29 12:01:35 2003	**COMMIT TURNED OFF**
> 
> Thu May 29 12:01:35 2003	Testing on 10 insertions
>                 into temp table
> 
> Thu May 29 12:01:35 2003	Testing on 10 insertions
>                 into NRDBEntry/ExternalAASequence
> 
> There are 0 entries in the database hash
> Thu May 29 12:02:40 2003	There are 2900500 gi to taxon_id pairs
> 
> DBI->connect(host=mango.ctegd.uga.edu) failed: ORA-12154: TNS:could not
> resolve service name (DBD ERROR: OCIServerAttach) at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 216
> 
> 
> sqlExec:
>     UPDATE  Core.AlgorithmInvocation
>     SET
> 	end_time = SYSDATE,
> 	row_alg_invocation_id = ?,
> 	modification_date = SYSDATE
>     WHERE   algorithm_invocation_id = ?
>   bindValues (245, 245)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> Can't call method "do" on an undefined value at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 219.
> 
> 
> 
> I might be kind of "fresh" with regards to my interaction with Oracle, so
> I am not sure if the dbi_str argument is in the correct format.  Can
> anyone help me with this?
> 
> 
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
> 
> 
> 
> 
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Re: [Gusdev-gusdev] LoadNRDB newbie questions:

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

Hi Michael-

MICHAEL LUCHTAN wrote:
> What is the temp table for?  Why is it necessary?  Why must I proide
> another login to the database to create this table?  I would think that it
> could just use the login/information provided in my gus config file.

My recollection is that Deborah Pinney worked on this plugin most recently;
Debbie, please correct me if I'm wrong on that count.  I don't know without
looking at the code what the temp. table is used for, but there are a couple
of different reasons why it's desirable to allow the user to supply a
different login under which to create it:

1. Prevents temp. tables from cluttering (even if only temporarily) the
    main GUS namespaces and/or shared database logins (like the "GUSrw"
    login we often use at CBIL.)
2. In the same vein, it allows two different users who are both running
    LoadNRDB to avoid trying to create or modify the same table.
3. The login specified in the config. file might not necessarily have
    CREATE TABLE privileges, since these are not needed for most GUS
    operations.

> Can anyone clarify the args --plugin, and --maketemp?  i.e. what happens
> if these are/are not provided?
 >
> Which arguements are required?

These are all very good questions and the answers certainly aren't clear
from the documentation of the plugin's arguments.

> Also, I have tried to run the plugin with the following command:
> ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10
> --nrdb=/scratch/NCBI/nr
> --gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135
> --verbose --maketemp --temp_login=luchtan --temp_password=*******
> --dbi_str=dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS
> 
> But I get an error like this:
> 
> Thu May 29 12:01:35 2003	**COMMIT TURNED OFF**
> 
> Thu May 29 12:01:35 2003	Testing on 10 insertions
>                 into temp table
> 
> Thu May 29 12:01:35 2003	Testing on 10 insertions
>                 into NRDBEntry/ExternalAASequence
> 
> There are 0 entries in the database hash
> Thu May 29 12:02:40 2003	There are 2900500 gi to taxon_id pairs
> 
> DBI->connect(host=mango.ctegd.uga.edu) failed: ORA-12154: TNS:could not
> resolve service name (DBD ERROR: OCIServerAttach) at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 216

Try the following two things (in this order, since the first item will
probably fix the problem):

1. Quote the DBI string on your plugin command line; your shell
    is probably trying to interpret the semicolon embedded therein.
    In other words, use the following argument for the dbi_str (single
    quotes should do the trick for csh/tcsh):

    --dbi_str='dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS'

2. Also double-check that your --dbi_str argument matches the "dbiDsn"
    parameter in your $GUS_CONFIG_FILE.  I'm not sure why the plugin
    makes you specify this value separately, since the code will almost
    certainly break if you specify an Oracle server different from the
    one that hosts GUS (i.e., the one identified in the config. file).

Jonathan

[Gusdev-gusdev] LoadNRDB newbie questions:

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

Hello All:
I am trying to load the genbank nrdb database into GUS so that I will have
what I blast against in the db so that I can load blast similarities.
I have some questions regarding this plugin.
What is the temp table for?  Why is it necessary?  Why must I proide
another login to the database to create this table?  I would think that it
could just use the login/information provided in my gus config file.

Can anyone clarify the args --plugin, and --maketemp?  i.e. what happens
if these are/are not provided?

Which arguements are required?


Also, I have tried to run the plugin with the following command:
ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10
--nrdb=/scratch/NCBI/nr
--gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135
--verbose --maketemp --temp_login=luchtan --temp_password=*******
--dbi_str=dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS

But I get an error like this:

Thu May 29 12:01:35 2003	**COMMIT TURNED OFF**

Thu May 29 12:01:35 2003	Testing on 10 insertions
                into temp table

Thu May 29 12:01:35 2003	Testing on 10 insertions
                into NRDBEntry/ExternalAASequence

There are 0 entries in the database hash
Thu May 29 12:02:40 2003	There are 2900500 gi to taxon_id pairs

DBI->connect(host=mango.ctegd.uga.edu) failed: ORA-12154: TNS:could not
resolve service name (DBD ERROR: OCIServerAttach) at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 216


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (245, 245)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Can't call method "do" on an undefined value at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 219.



I might be kind of "fresh" with regards to my interaction with Oracle, so
I am not sure if the dbi_str argument is in the correct format.  Can
anyone help me with this?


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

Re: [Gusdev-gusdev] LoadPfam plugin error:

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

Hey Jonathan:
I tried adding an entry into esternaldatabaserelease like so:
insert into Sres.Externaldatabaserelease
values(105,95,SYSDATE,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,SYSDATE,1,1,1,1,1,0,6,3,2,1);
which was inserted succesfully.  (I'm not sure what version of the medline
database I'm supposed to use, so I just put 1.  Actually, I don't even see
why the pfam plugin would require this to be there since medline is a
publications database)  Anyway, here is the error I get when executing the
the following:

[luchtan@mango luchtan]$ ga GUS::Common::Plugin::LoadPfam --release=8.0
--flat_file=/scratch/luchtan/Pfam-A.full --verbose
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
.
.
.

sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 231, 1, 3, 1, 1, 231, 2512, 493, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
ImportPfam: COMMIT OFF
ImportPfam: reading Pfam release 8.0 from /scratch/luchtan/Pfam-A.full
In readExternalDbReleases()


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (231, 231)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Can't use an undefined value as a HASH reference at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm line 285.


Any ideas what the deal here is?

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


On Thu, 29 May 2003, Jonathan Crabtree wrote:

>
> Michael-
>
> MICHAEL LUCHTAN wrote:
> > My first thought was to add an entry to the sres.externaldatabase table
> > like so:
> > insert into Sres.Externaldatabase
> > values(95,'medline','medline',SYSDATE,1,1,1,1,1,0,6,3,2,1);
> > But even after doing so I get the same error.
> >
> > Does anyone have any ideas?
>
> My guess is that you also need to add an entry to the ExternalDatabaseRelease
> table, since (as of version 3.0) GUS has split its representation of external
> databases into two tables: ExternalDatabase and ExternalDatabaseRelease.  The
> plugin has been updated accordingly, however, the error messages (and comments)
> still refer to the old schema (which only has the ExternalDatabase table).
> Here's the relevant part of the code.  Line 414 is the "die" statement,
> obviously:
>
>  ># Return the external_db_id of an ExternalDatabase given its name.
>  >#
>  >sub getExtDbRelId {
>  >    my($extDbRels, $name) = @_;
>  >
>  >    $name     =~ tr/A-Z/a-z/; # Normalize to lowercase
>  >
>  >    my $db    = $extDbRels->{$name};
>  >    my $relId = $db->{'external_database_release_id'} if defined($db);
>  >
>  >    die "Unable to find ID for ExternalDatabase $name" if (not defined($relId));
>  >    return $relId;
>  >}
>
> I've updated the plugin in CVS to make the comment and error message a
> little more accurate.
>
> Looking quickly at the rest of the code, it appears that the "getExtDbRelId"
> will always return the most recent ExternalDatabaseRelease (or, rather, its
> primary key value) for a given ExternalDatabase.name, based on
> ExternalDatabaseRelease.release_date.  This is ever-so-slightly dangerous,
> because the release_date is nullable, but should not be an issue so long as
> you specify one that's non-null.
>
> Jonathan
>
>
>
>

Re: [Gusdev-gusdev] LoadPfam plugin error:

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

Michael-

MICHAEL LUCHTAN wrote:
> My first thought was to add an entry to the sres.externaldatabase table
> like so:
> insert into Sres.Externaldatabase
> values(95,'medline','medline',SYSDATE,1,1,1,1,1,0,6,3,2,1);
> But even after doing so I get the same error.
> 
> Does anyone have any ideas?

My guess is that you also need to add an entry to the ExternalDatabaseRelease
table, since (as of version 3.0) GUS has split its representation of external
databases into two tables: ExternalDatabase and ExternalDatabaseRelease.  The
plugin has been updated accordingly, however, the error messages (and comments)
still refer to the old schema (which only has the ExternalDatabase table).
Here's the relevant part of the code.  Line 414 is the "die" statement,
obviously:

 ># Return the external_db_id of an ExternalDatabase given its name.
 >#
 >sub getExtDbRelId {
 >    my($extDbRels, $name) = @_;
 >
 >    $name     =~ tr/A-Z/a-z/; # Normalize to lowercase
 >
 >    my $db    = $extDbRels->{$name};
 >    my $relId = $db->{'external_database_release_id'} if defined($db);
 >
 >    die "Unable to find ID for ExternalDatabase $name" if (not defined($relId));
 >    return $relId;
 >}

I've updated the plugin in CVS to make the comment and error message a
little more accurate.

Looking quickly at the rest of the code, it appears that the "getExtDbRelId"
will always return the most recent ExternalDatabaseRelease (or, rather, its
primary key value) for a given ExternalDatabase.name, based on
ExternalDatabaseRelease.release_date.  This is ever-so-slightly dangerous,
because the release_date is nullable, but should not be an issue so long as
you specify one that's non-null.

Jonathan

[Gusdev-gusdev] LoadPfam plugin error:

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

Hello all
While attempting to use the LoadPfam plugin I have gotten the following
error messages:

[luchtan@mango luchtan]$ ga GUS::Common::Plugin::LoadPfam --release=8.0
--flat_file=/scratch/luchtan/Pfam-A.full --verbose
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.


prepareAndExecute:     SELECT *
      FROM Core.AlgorithmImplementation
     WHERE executable = 'GUS::Common::Plugin::LoadPfam'
       AND cvs_revision    = '1.8b'


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.


prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t,
Core.DatabaseInfo d where d.database_id = t.database_id
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.

RetrieveFromDB: select * from Core.AlgorithmImplementation where
algorithm_implementation_id = ?
  bindValues (102)


prepareAndExecute: select login,user_id from Core.UserInfo


prepareAndExecute: select name,group_id from Core.GroupInfo


prepareAndExecute: select name,project_id from Core.ProjectInfo


sqlExec:
    INSERT INTO Core.AlgorithmInvocation (  end_time, row_user_id,
user_write, group_write, cpu_time, algorithm_implementation_id,
row_project_id, algorithm_invocation_id, comment_string, group_read,
row_group_id, result, other_read, cpus_used, start_time,
modification_date, user_read, row_alg_invocation_id, other_write,
machine_id )
    VALUES   (  SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, SYSDATE,
SYSDATE, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 102, 2, 229, 1, 3, pending, 1, 1, 1, 1, 0, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKey where
algorithm_implementation_id = ?
  bindValues (102)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (2)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
)
  bindValues (6, 1, 1, 0, 0, 2, 1, 229, 1, 1, 3, 1, 1, 229, 2483, 474, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (0)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2484, 480, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
  bindValues (4)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2485, 479, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, /scratch/luchtan/Pfam-A.full, 3,
1, 1, 229, 2486, 477, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2487, 473, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, /home/luchtan/.gus.properties, 3,
1, 1, 229, 2488, 476, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2489, 482, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2490, 481, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, 8.0, 3, 1, 1, 229, 2491, 475, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
  bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2492, 478, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
ImportPfam: COMMIT OFF
ImportPfam: reading Pfam release 8.0 from /scratch/luchtan/Pfam-A.full
In readExternalDbReleases()
0: PF00244


sqlExec:
    INSERT INTO DoTS.PfamEntry (  row_user_id, alignment_method,
user_write, group_write, accession, row_project_id, group_read,
row_group_id, other_read, release, modification_date, user_read,
number_of_seqs, pfam_entry_id, row_alg_invocation_id, author, definition,
identifier, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?,
?, ? )
  bindValues (6, Clustalw, 1, 1, PF00244, 2, 1, 3, 1, 8.0, 1, 203, 9, 229,
Finn RD, 14-3-3 protein, 14-3-3, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (229, 229)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Unable to find ID for ExternalDatabase medline at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm line 414, <PFAM>
line 493.



***********************************************
My first thought was to add an entry to the sres.externaldatabase table
like so:
insert into Sres.Externaldatabase
values(95,'medline','medline',SYSDATE,1,1,1,1,1,0,6,3,2,1);
But even after doing so I get the same error.

Does anyone have any ideas?



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

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

Re: [Gusdev-gusdev] LoadPfam compile error and a question

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

Yep-
Good call- this fixes the problem. Changed description to 512 chars.
Thanks!

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


On Wed, 28 May 2003, Steve Fischer wrote:

> michael-
>
> not sure what is going on here.  you are calling ga +create correctly,
> and the same call worked here.
>
> the SQL error is telling you that one of the values you are inserting
> into the AlgorithmParamKey table is too big. (this table describes the
> allowed params to your plugin, and the values are taken from the easycsp
> declaration in LoadPfam.pm).
>
> i did a byte count on the description value, which is the help string
> starting with "Values: Flat file containing the release...", and it
> seems the string is about 350 bytes long.  in our instance of GUS, i
> used the describe function to see what the allowed size of the
> description field is, and it is 512 characters, which is big enough to
> hold the provided description.  maybe your instance of GUS allows only
> 256????
>
> steve
>
> SQL> describe Core.AlgorithmParamKey;
>  Name                                      Null?    Type
>  ----------------------------------------- --------
> ----------------------------
>  ALGORITHM_PARAM_KEY_ID                    NOT NULL NUMBER(5)
>  ALGORITHM_IMPLEMENTATION_ID               NOT NULL NUMBER(5)
>  ALGORITHM_PARAM_KEY                       NOT NULL VARCHAR2(60)
>  ALGORITHM_PARAM_KEY_TYPE_ID               NOT NULL NUMBER(3)
>  IS_LIST_VALUED                            NOT NULL NUMBER(1)
>  DESCRIPTION                                        VARCHAR2(512)
>  MODIFICATION_DATE                         NOT NULL DATE
>  USER_READ                                 NOT NULL NUMBER(1)
>  USER_WRITE                                NOT NULL NUMBER(1)
>  GROUP_READ                                NOT NULL NUMBER(1)
>  GROUP_WRITE                               NOT NULL NUMBER(1)
>  OTHER_READ                                NOT NULL NUMBER(1)
>  OTHER_WRITE                               NOT NULL NUMBER(1)
>  ROW_USER_ID                               NOT NULL NUMBER(12)
>  ROW_GROUP_ID                              NOT NULL NUMBER(3)
>  ROW_PROJECT_ID                            NOT NULL NUMBER(3)
>  ROW_ALG_INVOCATION_ID                     NOT NULL NUMBER(12)
>
>
>
>
> MICHAEL LUCHTAN wrote:
>
> >Hey steve-
> >I haven't used the +create option yet, but I get an error from the
> >following command:
> >ga +create GUS::Common::Plugin::LoadPfam
> >(and the same error with a --commit afterward).
> >The error:
> >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::st execute failed: ORA-01401: inserted value too large for
> >column (DBD ERROR: OCIStmtExecute) at
> >/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
> >
> > SQL ERROR!! involving
> >
> >    INSERT INTO Core.AlgorithmParamKey (  description, row_user_id,
> >algorithm_param_key, user_write, group_write, algorithm_implementation_id,
> >algorithm_param_key_type_id, row_project_id, group_read, row_group_id,
> >other_read, modification_date, user_read, row_alg_invocation_id,
> >algorithm_param_key_id, other_write, is_list_valued )
> >    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > Values: Flat file containing the release of Pfam to load.  Expects
> >			the file containing the annotation and full
> >alignments in Pfam
> >			format of all Pfam-A families (called
> >"Pfam-A.full" in release 5.2)
> >			The specified file may be in gzip (.gz) or
> >compressed (.Z) format., 6, flat_file, 1, 1, 100, 0, 2, 1, 3, 1, 1, 1,
> >462, 0, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> >
> >GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
> >'^J SQL ERROR!! involving^J ^J    INSERT INTO Core.AlgorithmParamKey...')
> >called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> >
> >GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
> >'GUS::ObjRelP::DbiDbHandle::st=HASH(0x84646e0)', 'ARRAY(0x8773f48)', '^J
> >INSERT INTO Core.AlgorithmParamKey (  description, row_user...') called at
> >/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> >
> >GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
> >'HASH(0x8773f18)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> >line 621
> >
> >GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)')
> >called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >
> >GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
> >undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765
> >
> >GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
> >'GUS::Model::Core::AlgorithmParamKey') called at
> >/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746
> >
> >GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)')
> >called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
> >
> >GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
> >undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765
> >
> >GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x86e849c)',
> >'GUS::Model::Core::AlgorithmImplementation') called at
> >/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746
> >
> >GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
> >called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
> >
> >GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
> >called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763
> >
> >GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >0, 'GUS::Common::Plugin::LoadPfam') called at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 411
> >
> >GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >'GUS::Common::Plugin::LoadPfam') called at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> >
> >GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >'GUS::Common::Plugin::LoadPfam') called at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> >
> >GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >'ARRAY(0x8105184)') called at /home/gus_home/bin/ga line 11
> >
> >
> >
> >Is this a problem with my syntax for a +create?
> >
> >
> >Michael Luchtan
> >http://www.cs.uga.edu/~luchtan
> >
> >
> >On Wed, 28 May 2003, Steve Fischer wrote:
> >
> >
> >
> >>Michael-
> >>
> >>you are getting the "can't  call method submit" error because:
> >>  1. you are trying to use ga +update on a plugin that hasn't yet been
> >>registered.  use ga +create instead
> >>  2. ga failed to properly detect that mistake.  i have fixed it in cvs
> >>so that it will now give a useful error message
> >>
> >>steve
> >>
> >>MICHAEL LUCHTAN wrote:
> >>
> >>
> >>
> >>>I figured this one out.  I didn't write the plugin, and I don't have CVS
> >>>write access, but someone might want to change lines like 124,125 from
> >>>   my $flatFile  = $self>getArgs->{'flat_file'};
> >>>   my $release   = $self>getArgs->{'release'};
> >>>to
> >>>   my $flatFile  = $self->getArgs->{'flat_file'};
> >>>   my $release   = $self->getArgs->{'release'};
> >>>Along with numerous other occurences of the same error in revision 1.8 of
> >>>LoadPfam.pm.
> >>>
> >>>Also, when I try to submit the newly built module, I get an error like so:
> >>>Can't call method "submit" on an undefined value at
> >>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.
> >>>
> >>>Can anyone help me with this?
> >>>
> >>>
> >>>Michael Luchtan
> >>>http://www.cs.uga.edu/~luchtan
> >>>
> >>>
> >>>On Thu, 22 May 2003, Chetna Warade wrote:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>Hi all,
> >>>>
> >>>>I am getting a compiler error for LoadPfam.pm
> >>>>Heres a snapshot:
> >>>>
> >>>>[chetna@mango chetna]$ ga
> >>>>GUS::Common::Plugin::LoadPfam
> >>>>Reading properties from
> >>>>/home/gus_home/config/GUS-PluginMgr.prop
> >>>>
> >>>>ERROR: Can't use bareword ("getArgs") as a HASH ref
> >>>>while "strict refs" in use at
> >>>>/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> >>>>line 125.
> >>>>Compilation failed in require at (eval 1) line 1.
> >>>>
> >>>>
> >>>>--------------------------- STACK TRACE
> >>>>-------------------------
> >>>>
> >>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>'Can\'t use bareword ("getArgs") as a HASH ref while
> >>>>"strict refs...') called at
> >>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>line 249
> >>>>
> >>>>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>'GUS::Common::Plugin::LoadPfam') called at
> >>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>line 362
> >>>>
> >>>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>'GUS::Common::Plugin::LoadPfam') called at
> >>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>line 284
> >>>>
> >>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>'GUS::Common::Plugin::LoadPfam') called at
> >>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>>>line 193
> >>>>
> >>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>>>'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
> >>>>line 11
> >>>>[chetna@mango chetna]$
> >>>>
> >>>>Look forward to chain of emails!,
> >>>>Chetna
> >>>>
> >>>>
> >>>>__________________________________
> >>>>Do you Yahoo!?
> >>>>The New Yahoo! Search - Faster. Easier. Bingo.
> >>>>http://search.yahoo.com
> >>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>This SF.net email is sponsored by: ObjectStore.
> >>>>If flattening out C++ or Java code to make your application fit in a
> >>>>relational database is painful, don't do it! Check out ObjectStore.
> >>>>Now part of Progress Software. http://www.objectstore.net/sourceforge
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.net email is sponsored by: ObjectStore.
> >>>If flattening out C++ or Java code to make your application fit in a
> >>>relational database is painful, don't do it! Check out ObjectStore.
> >>>Now part of Progress Software. http://www.objectstore.net/sourceforge
> >>>_______________________________________________
> >>>Gusdev-gusdev mailing list
> >>>Gus...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>
> >>>
> >>>
> >>>
> >>
> >>
>
>
>

Re: [Gusdev-gusdev] LoadPfam compile error and a question

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

michael-

not sure what is going on here.  you are calling ga +create correctly, 
and the same call worked here.

the SQL error is telling you that one of the values you are inserting 
into the AlgorithmParamKey table is too big. (this table describes the 
allowed params to your plugin, and the values are taken from the easycsp 
declaration in LoadPfam.pm).

i did a byte count on the description value, which is the help string 
starting with "Values: Flat file containing the release...", and it 
seems the string is about 350 bytes long.  in our instance of GUS, i 
used the describe function to see what the allowed size of the 
description field is, and it is 512 characters, which is big enough to 
hold the provided description.  maybe your instance of GUS allows only 
256????

steve

SQL> describe Core.AlgorithmParamKey;
 Name                                      Null?    Type
 ----------------------------------------- -------- 
----------------------------
 ALGORITHM_PARAM_KEY_ID                    NOT NULL NUMBER(5)
 ALGORITHM_IMPLEMENTATION_ID               NOT NULL NUMBER(5)
 ALGORITHM_PARAM_KEY                       NOT NULL VARCHAR2(60)
 ALGORITHM_PARAM_KEY_TYPE_ID               NOT NULL NUMBER(3)
 IS_LIST_VALUED                            NOT NULL NUMBER(1)
 DESCRIPTION                                        VARCHAR2(512)
 MODIFICATION_DATE                         NOT NULL DATE
 USER_READ                                 NOT NULL NUMBER(1)
 USER_WRITE                                NOT NULL NUMBER(1)
 GROUP_READ                                NOT NULL NUMBER(1)
 GROUP_WRITE                               NOT NULL NUMBER(1)
 OTHER_READ                                NOT NULL NUMBER(1)
 OTHER_WRITE                               NOT NULL NUMBER(1)
 ROW_USER_ID                               NOT NULL NUMBER(12)
 ROW_GROUP_ID                              NOT NULL NUMBER(3)
 ROW_PROJECT_ID                            NOT NULL NUMBER(3)
 ROW_ALG_INVOCATION_ID                     NOT NULL NUMBER(12)




MICHAEL LUCHTAN wrote:

>Hey steve-
>I haven't used the +create option yet, but I get an error from the
>following command:
>ga +create GUS::Common::Plugin::LoadPfam
>(and the same error with a --commit afterward).
>The error:
>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::st execute failed: ORA-01401: inserted value too large for
>column (DBD ERROR: OCIStmtExecute) at
>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
>
> SQL ERROR!! involving
>
>    INSERT INTO Core.AlgorithmParamKey (  description, row_user_id,
>algorithm_param_key, user_write, group_write, algorithm_implementation_id,
>algorithm_param_key_type_id, row_project_id, group_read, row_group_id,
>other_read, modification_date, user_read, row_alg_invocation_id,
>algorithm_param_key_id, other_write, is_list_valued )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> Values: Flat file containing the release of Pfam to load.  Expects
>			the file containing the annotation and full
>alignments in Pfam
>			format of all Pfam-A families (called
>"Pfam-A.full" in release 5.2)
>			The specified file may be in gzip (.gz) or
>compressed (.Z) format., 6, flat_file, 1, 1, 100, 0, 2, 1, 3, 1, 1, 1,
>462, 0, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
>
>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
>'^J SQL ERROR!! involving^J ^J    INSERT INTO Core.AlgorithmParamKey...')
>called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
>
>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
>'GUS::ObjRelP::DbiDbHandle::st=HASH(0x84646e0)', 'ARRAY(0x8773f48)', '^J
>INSERT INTO Core.AlgorithmParamKey (  description, row_user...') called at
>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
>
>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
>'HASH(0x8773f18)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
>line 621
>
>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)')
>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>
>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
>undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765
>
>GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
>'GUS::Model::Core::AlgorithmParamKey') called at
>/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746
>
>GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)')
>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
>undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765
>
>GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x86e849c)',
>'GUS::Model::Core::AlgorithmImplementation') called at
>/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746
>
>GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
>GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
>called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763
>
>GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>0, 'GUS::Common::Plugin::LoadPfam') called at
>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 411
>
>GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>'GUS::Common::Plugin::LoadPfam') called at
>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
>
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>'GUS::Common::Plugin::LoadPfam') called at
>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
>
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>'ARRAY(0x8105184)') called at /home/gus_home/bin/ga line 11
>
>
>
>Is this a problem with my syntax for a +create?
>
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Wed, 28 May 2003, Steve Fischer wrote:
>
>  
>
>>Michael-
>>
>>you are getting the "can't  call method submit" error because:
>>  1. you are trying to use ga +update on a plugin that hasn't yet been
>>registered.  use ga +create instead
>>  2. ga failed to properly detect that mistake.  i have fixed it in cvs
>>so that it will now give a useful error message
>>
>>steve
>>
>>MICHAEL LUCHTAN wrote:
>>
>>    
>>
>>>I figured this one out.  I didn't write the plugin, and I don't have CVS
>>>write access, but someone might want to change lines like 124,125 from
>>>   my $flatFile  = $self>getArgs->{'flat_file'};
>>>   my $release   = $self>getArgs->{'release'};
>>>to
>>>   my $flatFile  = $self->getArgs->{'flat_file'};
>>>   my $release   = $self->getArgs->{'release'};
>>>Along with numerous other occurences of the same error in revision 1.8 of
>>>LoadPfam.pm.
>>>
>>>Also, when I try to submit the newly built module, I get an error like so:
>>>Can't call method "submit" on an undefined value at
>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.
>>>
>>>Can anyone help me with this?
>>>
>>>
>>>Michael Luchtan
>>>http://www.cs.uga.edu/~luchtan
>>>
>>>
>>>On Thu, 22 May 2003, Chetna Warade wrote:
>>>
>>>
>>>
>>>      
>>>
>>>>Hi all,
>>>>
>>>>I am getting a compiler error for LoadPfam.pm
>>>>Heres a snapshot:
>>>>
>>>>[chetna@mango chetna]$ ga
>>>>GUS::Common::Plugin::LoadPfam
>>>>Reading properties from
>>>>/home/gus_home/config/GUS-PluginMgr.prop
>>>>
>>>>ERROR: Can't use bareword ("getArgs") as a HASH ref
>>>>while "strict refs" in use at
>>>>/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
>>>>line 125.
>>>>Compilation failed in require at (eval 1) line 1.
>>>>
>>>>
>>>>--------------------------- STACK TRACE
>>>>-------------------------
>>>>
>>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>'Can\'t use bareword ("getArgs") as a HASH ref while
>>>>"strict refs...') called at
>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 249
>>>>
>>>>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>'GUS::Common::Plugin::LoadPfam') called at
>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 362
>>>>
>>>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>'GUS::Common::Plugin::LoadPfam') called at
>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 284
>>>>
>>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>'GUS::Common::Plugin::LoadPfam') called at
>>>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 193
>>>>
>>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>>>'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
>>>>line 11
>>>>[chetna@mango chetna]$
>>>>
>>>>Look forward to chain of emails!,
>>>>Chetna
>>>>
>>>>
>>>>__________________________________
>>>>Do you Yahoo!?
>>>>The New Yahoo! Search - Faster. Easier. Bingo.
>>>>http://search.yahoo.com
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This SF.net email is sponsored by: ObjectStore.
>>>>If flattening out C++ or Java code to make your application fit in a
>>>>relational database is painful, don't do it! Check out ObjectStore.
>>>>Now part of Progress Software. http://www.objectstore.net/sourceforge
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This SF.net email is sponsored by: ObjectStore.
>>>If flattening out C++ or Java code to make your application fit in a
>>>relational database is painful, don't do it! Check out ObjectStore.
>>>Now part of Progress Software. http://www.objectstore.net/sourceforge
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>      
>>>
>>    
>>

Re: [Gusdev-gusdev] LoadPfam compile error and a question

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

Hey steve-
I haven't used the +create option yet, but I get an error from the
following command:
ga +create GUS::Common::Plugin::LoadPfam
(and the same error with a --commit afterward).
The error:
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::st execute failed: ORA-01401: inserted value too large for
column (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.

 SQL ERROR!! involving

    INSERT INTO Core.AlgorithmParamKey (  description, row_user_id,
algorithm_param_key, user_write, group_write, algorithm_implementation_id,
algorithm_param_key_type_id, row_project_id, group_read, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_key_id, other_write, is_list_valued )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
 Values: Flat file containing the release of Pfam to load.  Expects
			the file containing the annotation and full
alignments in Pfam
			format of all Pfam-A families (called
"Pfam-A.full" in release 5.2)
			The specified file may be in gzip (.gz) or
compressed (.Z) format., 6, flat_file, 1, 1, 100, 0, 2, 1, 3, 1, 1, 1,
462, 0, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
'^J SQL ERROR!! involving^J ^J    INSERT INTO Core.AlgorithmParamKey...')
called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x84646e0)', 'ARRAY(0x8773f48)', '^J
INSERT INTO Core.AlgorithmParamKey (  description, row_user...') called at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
'HASH(0x8773f18)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 621

GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677

GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765

GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
'GUS::Model::Core::AlgorithmParamKey') called at
/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746

GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684

GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765

GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x86e849c)',
'GUS::Model::Core::AlgorithmImplementation') called at
/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746

GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684

GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763

GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
0, 'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 411

GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105184)') called at /home/gus_home/bin/ga line 11



Is this a problem with my syntax for a +create?


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


On Wed, 28 May 2003, Steve Fischer wrote:

> Michael-
>
> you are getting the "can't  call method submit" error because:
>   1. you are trying to use ga +update on a plugin that hasn't yet been
> registered.  use ga +create instead
>   2. ga failed to properly detect that mistake.  i have fixed it in cvs
> so that it will now give a useful error message
>
> steve
>
> MICHAEL LUCHTAN wrote:
>
> >I figured this one out.  I didn't write the plugin, and I don't have CVS
> >write access, but someone might want to change lines like 124,125 from
> >    my $flatFile  = $self>getArgs->{'flat_file'};
> >    my $release   = $self>getArgs->{'release'};
> >to
> >    my $flatFile  = $self->getArgs->{'flat_file'};
> >    my $release   = $self->getArgs->{'release'};
> >Along with numerous other occurences of the same error in revision 1.8 of
> >LoadPfam.pm.
> >
> >Also, when I try to submit the newly built module, I get an error like so:
> >Can't call method "submit" on an undefined value at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.
> >
> >Can anyone help me with this?
> >
> >
> >Michael Luchtan
> >http://www.cs.uga.edu/~luchtan
> >
> >
> >On Thu, 22 May 2003, Chetna Warade wrote:
> >
> >
> >
> >>Hi all,
> >>
> >>I am getting a compiler error for LoadPfam.pm
> >>Heres a snapshot:
> >>
> >>[chetna@mango chetna]$ ga
> >>GUS::Common::Plugin::LoadPfam
> >>Reading properties from
> >>/home/gus_home/config/GUS-PluginMgr.prop
> >>
> >>ERROR: Can't use bareword ("getArgs") as a HASH ref
> >>while "strict refs" in use at
> >>/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> >>line 125.
> >>Compilation failed in require at (eval 1) line 1.
> >>
> >>
> >>--------------------------- STACK TRACE
> >>-------------------------
> >>
> >>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'Can\'t use bareword ("getArgs") as a HASH ref while
> >>"strict refs...') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 249
> >>
> >>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'GUS::Common::Plugin::LoadPfam') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 362
> >>
> >>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'GUS::Common::Plugin::LoadPfam') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 284
> >>
> >>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'GUS::Common::Plugin::LoadPfam') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 193
> >>
> >>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
> >>line 11
> >>[chetna@mango chetna]$
> >>
> >>Look forward to chain of emails!,
> >>Chetna
> >>
> >>
> >>__________________________________
> >>Do you Yahoo!?
> >>The New Yahoo! Search - Faster. Easier. Bingo.
> >>http://search.yahoo.com
> >>
> >>
> >>-------------------------------------------------------
> >>This SF.net email is sponsored by: ObjectStore.
> >>If flattening out C++ or Java code to make your application fit in a
> >>relational database is painful, don't do it! Check out ObjectStore.
> >>Now part of Progress Software. http://www.objectstore.net/sourceforge
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>
> >>
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.net email is sponsored by: ObjectStore.
> >If flattening out C++ or Java code to make your application fit in a
> >relational database is painful, don't do it! Check out ObjectStore.
> >Now part of Progress Software. http://www.objectstore.net/sourceforge
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
>

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
>
>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: ObjectStore.
>If flattening out C++ or Java code to make your application fit in a
>relational database is painful, don't do it! Check out ObjectStore.
>Now part of Progress Software. http://www.objectstore.net/sourceforge
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] LoadPfam compile error and a question

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

Michael-

you are getting the "can't  call method submit" error because:
  1. you are trying to use ga +update on a plugin that hasn't yet been 
registered.  use ga +create instead
  2. ga failed to properly detect that mistake.  i have fixed it in cvs 
so that it will now give a useful error message

steve

MICHAEL LUCHTAN wrote:

>I figured this one out.  I didn't write the plugin, and I don't have CVS
>write access, but someone might want to change lines like 124,125 from
>    my $flatFile  = $self>getArgs->{'flat_file'};
>    my $release   = $self>getArgs->{'release'};
>to
>    my $flatFile  = $self->getArgs->{'flat_file'};
>    my $release   = $self->getArgs->{'release'};
>Along with numerous other occurences of the same error in revision 1.8 of
>LoadPfam.pm.
>
>Also, when I try to submit the newly built module, I get an error like so:
>Can't call method "submit" on an undefined value at
>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.
>
>Can anyone help me with this?
>
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Thu, 22 May 2003, Chetna Warade wrote:
>
>  
>
>>Hi all,
>>
>>I am getting a compiler error for LoadPfam.pm
>>Heres a snapshot:
>>
>>[chetna@mango chetna]$ ga
>>GUS::Common::Plugin::LoadPfam
>>Reading properties from
>>/home/gus_home/config/GUS-PluginMgr.prop
>>
>>ERROR: Can't use bareword ("getArgs") as a HASH ref
>>while "strict refs" in use at
>>/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
>>line 125.
>>Compilation failed in require at (eval 1) line 1.
>>
>>
>>--------------------------- STACK TRACE
>>-------------------------
>>
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'Can\'t use bareword ("getArgs") as a HASH ref while
>>"strict refs...') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 249
>>
>>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'GUS::Common::Plugin::LoadPfam') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 362
>>
>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'GUS::Common::Plugin::LoadPfam') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 284
>>
>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'GUS::Common::Plugin::LoadPfam') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 193
>>
>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
>>line 11
>>[chetna@mango chetna]$
>>
>>Look forward to chain of emails!,
>>Chetna
>>
>>
>>__________________________________
>>Do you Yahoo!?
>>The New Yahoo! Search - Faster. Easier. Bingo.
>>http://search.yahoo.com
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: ObjectStore.
>>If flattening out C++ or Java code to make your application fit in a
>>relational database is painful, don't do it! Check out ObjectStore.
>>Now part of Progress Software. http://www.objectstore.net/sourceforge
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: ObjectStore.
>If flattening out C++ or Java code to make your application fit in a
>relational database is painful, don't do it! Check out ObjectStore.
>Now part of Progress Software. http://www.objectstore.net/sourceforge
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

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] LoadPfam compile error and a question

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

Michael-

1. in LoadPfam, it looks like somebody did a faulty search and replace, 
making all the self-> to be self>.  I have corrected that and checked it 
into cvs.

2. i am getting the GusApplication error you are describing, and am 
looking into it now.

steve

MICHAEL LUCHTAN wrote:

>I figured this one out.  I didn't write the plugin, and I don't have CVS
>write access, but someone might want to change lines like 124,125 from
>    my $flatFile  = $self>getArgs->{'flat_file'};
>    my $release   = $self>getArgs->{'release'};
>to
>    my $flatFile  = $self->getArgs->{'flat_file'};
>    my $release   = $self->getArgs->{'release'};
>Along with numerous other occurences of the same error in revision 1.8 of
>LoadPfam.pm.
>
>Also, when I try to submit the newly built module, I get an error like so:
>Can't call method "submit" on an undefined value at
>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.
>
>Can anyone help me with this?
>
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Thu, 22 May 2003, Chetna Warade wrote:
>
>  
>
>>Hi all,
>>
>>I am getting a compiler error for LoadPfam.pm
>>Heres a snapshot:
>>
>>[chetna@mango chetna]$ ga
>>GUS::Common::Plugin::LoadPfam
>>Reading properties from
>>/home/gus_home/config/GUS-PluginMgr.prop
>>
>>ERROR: Can't use bareword ("getArgs") as a HASH ref
>>while "strict refs" in use at
>>/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
>>line 125.
>>Compilation failed in require at (eval 1) line 1.
>>
>>
>>--------------------------- STACK TRACE
>>-------------------------
>>
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'Can\'t use bareword ("getArgs") as a HASH ref while
>>"strict refs...') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 249
>>
>>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'GUS::Common::Plugin::LoadPfam') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 362
>>
>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'GUS::Common::Plugin::LoadPfam') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 284
>>
>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'GUS::Common::Plugin::LoadPfam') called at
>>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 193
>>
>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
>>'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
>>line 11
>>[chetna@mango chetna]$
>>
>>Look forward to chain of emails!,
>>Chetna
>>
>>
>>__________________________________
>>Do you Yahoo!?
>>The New Yahoo! Search - Faster. Easier. Bingo.
>>http://search.yahoo.com
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: ObjectStore.
>>If flattening out C++ or Java code to make your application fit in a
>>relational database is painful, don't do it! Check out ObjectStore.
>>Now part of Progress Software. http://www.objectstore.net/sourceforge
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: ObjectStore.
>If flattening out C++ or Java code to make your application fit in a
>relational database is painful, don't do it! Check out ObjectStore.
>Now part of Progress Software. http://www.objectstore.net/sourceforge
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] LoadPfam compile error and a question

[pjm <pj...@sa...>]

I shall make the change in 5 mins - I presume its my fault....


MICHAEL LUCHTAN wrote:
> 
> I figured this one out.  I didn't write the plugin, and I don't have CVS
> write access, but someone might want to change lines like 124,125 from
>     my $flatFile  = $self>getArgs->{'flat_file'};
>     my $release   = $self>getArgs->{'release'};
> to
>     my $flatFile  = $self->getArgs->{'flat_file'};
>     my $release   = $self->getArgs->{'release'};
> Along with numerous other occurences of the same error in revision 1.8 of
> LoadPfam.pm.
> 
> Also, when I try to submit the newly built module, I get an error like so:
> Can't call method "submit" on an undefined value at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.
> 
> Can anyone help me with this?
> 
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
> 
> On Thu, 22 May 2003, Chetna Warade wrote:
> 
> > Hi all,
> >
> > I am getting a compiler error for LoadPfam.pm
> > Heres a snapshot:
> >
> > [chetna@mango chetna]$ ga
> > GUS::Common::Plugin::LoadPfam
> > Reading properties from
> > /home/gus_home/config/GUS-PluginMgr.prop
> >
> > ERROR: Can't use bareword ("getArgs") as a HASH ref
> > while "strict refs" in use at
> > /home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> > line 125.
> > Compilation failed in require at (eval 1) line 1.
> >
> >
> > --------------------------- STACK TRACE
> > -------------------------
> >
> > GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'Can\'t use bareword ("getArgs") as a HASH ref while
> > "strict refs...') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> > line 249
> >
> > GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::Common::Plugin::LoadPfam') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> > line 362
> >
> > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::Common::Plugin::LoadPfam') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> > line 284
> >
> > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::Common::Plugin::LoadPfam') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> > line 193
> >
> > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
> > line 11
> > [chetna@mango chetna]$
> >
> > Look forward to chain of emails!,
> > Chetna
> >
> >
> > __________________________________
> > Do you Yahoo!?
> > The New Yahoo! Search - Faster. Easier. Bingo.
> > http://search.yahoo.com
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: ObjectStore.
> > If flattening out C++ or Java code to make your application fit in a
> > relational database is painful, don't do it! Check out ObjectStore.
> > Now part of Progress Software. http://www.objectstore.net/sourceforge
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: ObjectStore.
> If flattening out C++ or Java code to make your application fit in a
> relational database is painful, don't do it! Check out ObjectStore.
> Now part of Progress Software. http://www.objectstore.net/sourceforge
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/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] LoadPfam compile error and a question

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

I figured this one out.  I didn't write the plugin, and I don't have CVS
write access, but someone might want to change lines like 124,125 from
    my $flatFile  = $self>getArgs->{'flat_file'};
    my $release   = $self>getArgs->{'release'};
to
    my $flatFile  = $self->getArgs->{'flat_file'};
    my $release   = $self->getArgs->{'release'};
Along with numerous other occurences of the same error in revision 1.8 of
LoadPfam.pm.

Also, when I try to submit the newly built module, I get an error like so:
Can't call method "submit" on an undefined value at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.

Can anyone help me with this?


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


On Thu, 22 May 2003, Chetna Warade wrote:

> Hi all,
>
> I am getting a compiler error for LoadPfam.pm
> Heres a snapshot:
>
> [chetna@mango chetna]$ ga
> GUS::Common::Plugin::LoadPfam
> Reading properties from
> /home/gus_home/config/GUS-PluginMgr.prop
>
> ERROR: Can't use bareword ("getArgs") as a HASH ref
> while "strict refs" in use at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> line 125.
> Compilation failed in require at (eval 1) line 1.
>
>
> --------------------------- STACK TRACE
> -------------------------
>
> GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'Can\'t use bareword ("getArgs") as a HASH ref while
> "strict refs...') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 249
>
> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 362
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 284
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 193
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
> line 11
> [chetna@mango chetna]$
>
> Look forward to chain of emails!,
> Chetna
>
>
> __________________________________
> Do you Yahoo!?
> The New Yahoo! Search - Faster. Easier. Bingo.
> http://search.yahoo.com
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: ObjectStore.
> If flattening out C++ or Java code to make your application fit in a
> relational database is painful, don't do it! Check out ObjectStore.
> Now part of Progress Software. http://www.objectstore.net/sourceforge
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] format of sequences for blast

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

The idea of the plugin is to store in gus a "similarity" association 
between each of the seqs you blasted and the seqs each one hit.  It only 
makes sense if the seqs you blasted against (the blastable db) are 
themselves also in gus.

In blast parlance, the seq you blast is the "query" and the seqs it hits 
in the blastable db are the "subjects".

so, the query table in your case is ExternalNaSequence.

I don't know how you made your blastable db, but, whatever table they 
came out of (and, they must have ids in their definition lines), is the 
subject table

steve

MICHAEL LUCHTAN wrote:

>Hello --
>
>I used the following script to get some data out of GUS:
>#!/usr/bin/perl
>
>use GUS::ObjRelP::DbiDatabase;
>use GUS::Common::GusConfig;
>
>my $gusconfig=
>GUS::Common::GusConfig->new("/home/luchtan/gus.properties");
>my $db= GUS::ObjRelP::DbiDatabase->new($gusconfig->getDbiDsn(),
>
>$gusconfig->getReadOnlyDatabaseLogin(),
>
>$gusconfig->getReadOnlyDatabasePassword,
>                                        1,1,1,
>                                        $gusconfig->getCoreSchemaName);
>my $dbh= $db->getQueryHandle();
>
>my $idStmt= $dbh->prepare("select '>'||na_sequence_id||' '||name||'\n'
>name_str,sequence from dots.externalnasequence");
>$idStmt->execute();
>open(TEMP, ">retrievedSeqForBLAST.tmp");
>while(my (@row)=$idStmt->fetchrow_array()){
>    print TEMP "@row\n";
>}
>close(TEMP);
>
>
>and blasted the resulting retrievedSeqForBLAST file.  Now I want to load
>the results into GUS using the plugin LoadBlastSimilaritiesPK.
>This plugin requires a subject_table and a query_table.  Perhaps it is a
>question of my unfamiliarity of the whole biology aspect of what is going
>on here(I'm just a programmer), but I am not sure what these tables are
>for.  Can anybody help me
>out?
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Thu, 22 May 2003, Jonathan Crabtree wrote:
>
>  
>
>>Jessie-
>>
>>Jessica Kissinger wrote:
>>    
>>
>>>    If memory serves me correct, once sequences were loaded into GUS, we
>>>then retrieved them along with their GUS ID to submit for blast searches.
>>>      
>>>
>>Yes, I think that's right.
>>
>>    
>>
>>>    When we retrieved the sequences, we created a custom format for the
>>>header line, such that the blast results once generated for these
>>>sequences could be easily parsed and loaded with the existing plug-in.
>>>
>>>    Can someone tell me what the format of the fasta header should be,
>>>i.e is it ">GUSID, External_NA _sequence Name" or the other way around
>>>and should there be any formatting, tabs, spaces etc.  If I remember
>>>correctly, the blast results were loaded by GUSID not "name", but I
>>>don't remember.
>>>      
>>>
>>My recollection is that the defline started as you said, with ">GUSID ".
>>I don't believe that the format is crucial, because (again, from what
>>I remember) when you run the plugin to load the BLAST similarities you
>>supply it with a regular expression that it uses to pick the GUSID
>>(an na_sequence_id for most of the PlasmoDB searches) out of the defline.
>>So as long as the regex matches the defline format, you should be OK,
>>and I don't think that the plugin uses anything on the defline except
>>for the GUSID.
>>
>>Jonathan
>>
>>
>>
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: ObjectStore.
>>If flattening out C++ or Java code to make your application fit in a
>>relational database is painful, don't do it! Check out ObjectStore.
>>Now part of Progress Software. http://www.objectstore.net/sourceforge
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: ObjectStore.
>If flattening out C++ or Java code to make your application fit in a
>relational database is painful, don't do it! Check out ObjectStore.
>Now part of Progress Software. http://www.objectstore.net/sourceforge
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>