gusdev-gusdev — Topics concerning GUS development

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[<an...@ne...>]

Hello,
did anyone have the time to look into the issue I submitted and confirm i=
t?

Thank you very much,

Antonio

Quoting an...@ne...:

> Quoting Michael Saffitz <m...@sa...>:
>
> > Antonio is correct here-- it looks like the postgres triggers aren't =
being
> > correctly generated for this table. I had thought I had fixed this, b=
ut I
> > guess not.  These are in the db writer for postgres within the db adm=
in
> > package.  Search for 'ON INSERT TO'.  Antonio-- it may help if you fo=
rward
> > along your install logs (that include all SQL used in generating the
> > instance).
> > Steve's also correct-- bug 177 appears to track a different issue.
>
> I fear that while the database error does appear to be different, the
> underlying issue is exactly the same.
>
> Following Steve's advice to try suggesting a fix, I've been digging fur=
ther.
> If I got your code correctly, all this wreck is generated when the sche=
ma
> hierarchy gets converted, in
>
>  GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter=
.java
>
> In function 'buildSuperClassView', (around line 440 in GUS 3.5; but
> 'buildSubClassView' exhibits the same issue) the code goes like this:
>
> -----------------------------------------------------------------------=
-----
> // Housekeeping Columns and complete for the Version View
> if (impTable.isVersioned()) {
>   superClassView.setVersioned(true);
>   verSql =3D sql.concat(" ");
>
>   for (Iterator i =3D verHousekeepingColumns.iterator(); i.hasNext();) =
{
>     Column column =3D (Column)i.next();
>     verSql =3D verSql.concat(", " + column.getName());
>     superClassView.getVersionView().addColumn(new
> ColumnPair(column.getName(),
>              column.getName()));
>   }
>   verSql =3D verSql.concat(
>     " FROM " +
>     impTable.getVersionTable().getSchema().getName() +
>     "." + impTable.getVersionTable().getName() +
>     ";");
>   superClassView.getVersionView().setSql(verSql);
> }
> -----------------------------------------------------------------------=
-----
>
> Now, the problem is that while 'verSql' is correctly generated (because=
 it
> starts with 'sql'), the original view's colums are not copied at all.
>
> The reason is that GusView behaves differently from GusTable, since its
> 'setVersioned()' method does not copy the base view colums as one might=
 have
> expected after having looked at GusTable.
>
> As far as I can tell this has no relation to the actual database instan=
ce in
> use, but I'd say that this is the core of the problem.
>
> HTH,
>
> Antonio
>
>
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>
>
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Re: [GUSDEV] [CBIL] forgot this Re: sres.author table

[Marie-Adele R. <ma...@sa...>]

Thanks for checking.  The PSU no longer has a need for these tables.

Marie-Adele Rajandream

Pathogen Sequencing Unit

-----Original Message-----
From: gus...@li...
[mailto:gus...@li...] On Behalf Of Trish
Whetzel
Sent: 10 October 2006 17:34
To: Junmin Liu
Cc: gus...@li...; cb...@pc...
Subject: Re: [GUSDEV] [CBIL] forgot this Re: sres.author table

As I recall, these 'redundant' tables were left in the schema because
they=20
were requested by PSU based on how they handle this type of information.

Does PSU still have a need for these tables?

Trish


> Looks like these are the ghost tables, people never use it since 2002.
> ---junmin
>
> On Mon, 9 Oct 2006, Junmin Liu wrote:
>
>> Hi, all
>> By looking at gus schema browser, I just realized that we have couple
new
>> tables in SRes: sres.author, sres.bibRefAuthor. I searched the GUS
tracker to
>> find the cause for this, but couldn't find any.
>>
>> I have couple questions:
>> 1. why we need this? what are the use cases? I understand the
"authors"
>> column in biblographRefernce may not be optimized, but I think
practically it
>> works well, even you want to search for authors.
>>
>> 2. what the difference between this author table and sres.contact
table? Why
>> we cann't use sres.contact table?
>>
>> 3. where is the documentation saying "when we use sres.contact and
when we
>> use sres.author"? I don't find any difference between these two,
except the
>> names.
>>
>> 4. please note in the FuGE uml model, or MAGE model, the developers
simply
>> user "authors" column too, and don't borther to create this author
and
>> linking table.
>>
>> Thanks,
>> ---junmin

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Re: [GUSDEV] [CBIL] forgot this Re: sres.author table

[Trish W. <wh...@pc...>]

As I recall, these 'redundant' tables were left in the schema because they 
were requested by PSU based on how they handle this type of information. 
Does PSU still have a need for these tables?

Trish


> Looks like these are the ghost tables, people never use it since 2002.
> ---junmin
>
> On Mon, 9 Oct 2006, Junmin Liu wrote:
>
>> Hi, all
>> By looking at gus schema browser, I just realized that we have couple new
>> tables in SRes: sres.author, sres.bibRefAuthor. I searched the GUS tracker to
>> find the cause for this, but couldn't find any.
>>
>> I have couple questions:
>> 1. why we need this? what are the use cases? I understand the "authors"
>> column in biblographRefernce may not be optimized, but I think practically it
>> works well, even you want to search for authors.
>>
>> 2. what the difference between this author table and sres.contact table? Why
>> we cann't use sres.contact table?
>>
>> 3. where is the documentation saying "when we use sres.contact and when we
>> use sres.author"? I don't find any difference between these two, except the
>> names.
>>
>> 4. please note in the FuGE uml model, or MAGE model, the developers simply
>> user "authors" column too, and don't borther to create this author and
>> linking table.
>>
>> Thanks,
>> ---junmin

[GUSDEV] forgot this Re: sres.author table

[Junmin L. <ju...@pc...>]

Looks like these are the ghost tables, people never use it since 2002.
---junmin

On Mon, 9 Oct 2006, Junmin Liu wrote:

> Hi, all
> By looking at gus schema browser, I just realized that we have couple new 
> tables in SRes: sres.author, sres.bibRefAuthor. I searched the GUS tracker to 
> find the cause for this, but couldn't find any.
>
> I have couple questions:
> 1. why we need this? what are the use cases? I understand the "authors" 
> column in biblographRefernce may not be optimized, but I think practically it 
> works well, even you want to search for authors.
>
> 2. what the difference between this author table and sres.contact table? Why 
> we cann't use sres.contact table?
>
> 3. where is the documentation saying "when we use sres.contact and when we 
> use sres.author"? I don't find any difference between these two, except the 
> names.
>
> 4. please note in the FuGE uml model, or MAGE model, the developers simply 
> user "authors" column too, and don't borther to create this author and 
> linking table.
>
> Thanks,
> ---junmin
>
>
>

[GUSDEV] sres.author table

[Junmin L. <ju...@pc...>]

Hi, all
By looking at gus schema browser, I just realized that we have couple new 
tables in SRes: sres.author, sres.bibRefAuthor. I searched the GUS 
tracker to find the cause for this, but couldn't find any.

I have couple questions:
1. why we need this? what are the use cases? I understand the "authors" 
column in biblographRefernce may not be optimized, but I think 
practically it works well, even you want to search for authors.

2. what the difference between this author table and sres.contact table? 
Why we cann't use sres.contact table?

3. where is the documentation saying "when we use sres.contact and when 
we use sres.author"? I don't find any difference between these two, except 
the names.

4. please note in the FuGE uml model, or MAGE model, the developers simply 
user "authors" column too, and don't borther to create this author and 
linking table.

Thanks,
---junmin

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[<an...@ne...>]

Quoting Michael Saffitz <m...@sa...>:

> Antonio is correct here-- it looks like the postgres triggers aren't be=
ing
> correctly generated for this table. I had thought I had fixed this, but=
 I
> guess not.  These are in the db writer for postgres within the db admin
> package.  Search for 'ON INSERT TO'.  Antonio-- it may help if you forw=
ard
> along your install logs (that include all SQL used in generating the
> instance).
> Steve's also correct-- bug 177 appears to track a different issue.

I fear that while the database error does appear to be different, the
underlying issue is exactly the same.

Following Steve's advice to try suggesting a fix, I've been digging furth=
er.
If I got your code correctly, all this wreck is generated when the schema
hierarchy gets converted, in

 GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.j=
ava

In function 'buildSuperClassView', (around line 440 in GUS 3.5; but
'buildSubClassView' exhibits the same issue) the code goes like this:

-------------------------------------------------------------------------=
---
// Housekeeping Columns and complete for the Version View
if (impTable.isVersioned()) {
  superClassView.setVersioned(true);
  verSql =3D sql.concat(" ");

  for (Iterator i =3D verHousekeepingColumns.iterator(); i.hasNext();) {
    Column column =3D (Column)i.next();
    verSql =3D verSql.concat(", " + column.getName());
    superClassView.getVersionView().addColumn(new ColumnPair(column.getNa=
me(),
             column.getName()));
  }
  verSql =3D verSql.concat(
    " FROM " +
    impTable.getVersionTable().getSchema().getName() +
    "." + impTable.getVersionTable().getName() +
    ";");
  superClassView.getVersionView().setSql(verSql);
}
-------------------------------------------------------------------------=
---

Now, the problem is that while 'verSql' is correctly generated (because i=
t
starts with 'sql'), the original view's colums are not copied at all.

The reason is that GusView behaves differently from GusTable, since its
'setVersioned()' method does not copy the base view colums as one might h=
ave
expected after having looked at GusTable.

As far as I can tell this has no relation to the actual database instance=
 in
use, but I'd say that this is the core of the problem.

HTH,

Antonio


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This message was sent using IMP, the Internet Messaging Program.

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[Michael S. <m...@sa...>]

Antonio is correct here-- it looks like the postgres triggers aren't being 
correctly generated for this table.  I had thought I had fixed this, but I 
guess not.  These are in the db writer for postgres within the db admin 
package.  Search for 'ON INSERT TO'.  Antonio-- it may help if you forward 
along your install logs (that include all SQL used in generating the 
instance).

Steve's also correct-- bug 177 appears to track a different issue.

--Mike

----- Original Message ----- 
From: "Chris Stoeckert" <sto...@pc...>
To: "Steve Fischer" <sfi...@pc...>
Cc: <gus...@li...>
Sent: Saturday, October 07, 2006 2:39 PM
Subject: Re: [GUSDEV] bug in GUS schema,evidentiated by 
InsertSequenceFeatures


> John Iodice in our group is working on a postgres instance of GUS so
> will ask him to help but if anyone else out there has some ideas that
> would be great to hear.
> Chris
>
> On Oct 7, 2006, at 10:08 AM, Steve Fischer wrote:
>
>> Antonio-
>>
>> i don't think this is the same problem as bug 177.   in that bug,
>> there
>> was a uniqueness constraint violation, not a non-null constraint
>> violation.
>>
>> we don't have much postgres expertise in-house.  i'll see if
>> anybody can
>> help  on this.
>>
>> otherwise, you might need to propose a solution yourself.
>>
>> steve
>>
>> an...@ne... wrote:
>>> Hello all,
>>> using ISF I've found a bug of the schema very similar to the one
>>> signalled
>>> here: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=177
>>>
>>> When using ISF like this:
>>>
>>> ga GUS::Supported::Plugin::InsertSequenceFeatures \
>>>  --mapFile $GUS_HOME/config/genbank2gus.xml \
>>>  --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank \
>>>  --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16 \
>>>  --veryVerbose --sqlVerbose --commit
>>>
>>> the procedure does complete the insert of all relevant data, but
>>> this single
>>> SQL instruction fails:
>>>
>>> sqlExec:
>>>  INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from
>>> DoTS.Source v
>>>  where v.na_feature_id = ?
>>>  bindValues (5)
>>>
>>> DBD::Pg::st execute failed: ERROR:  null value in column
>>> "na_feature_id"
>>> violates not-null constraint at
>>> /hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>>> line 147,
>>> <GEN39> line 368238.
>>>
>>> The SQL instruction is indeed incorrect: trying it manually in
>>> PostgreSQL
>>>
>>> dbgus=# INSERT INTO DoTSVer.SourceVer
>>>   select v.*,215,now(),30 from DoTS.Source v where v.na_feature_id
>>> = 5
>>> ;
>>>
>>> gives the very same error.
>>>
>>> The problem lies in the INSERT trigger for the view
>>> DoTSVer.SourceVer, which
>>> PostgreSQL spells out as follows:
>>>
>>> ON INSERT TO dotsver.sourcever DO INSTEAD
>>>   INSERT INTO dotsver.nafeatureimpver (
>>>     modification_date, user_read, user_write, group_read,
>>> group_write,
>>>     other_read, other_write, row_user_id, row_group_id,
>>> row_project_id,
>>>     row_alg_invocation_id, version_alg_invocation_id, version_date,
>>>     version_transaction_id
>>>   ) VALUES (
>>>     new.modification_date, new.user_read, new.user_write,
>>> new.group_read,
>>>     new.group_write, new.other_read, new.other_write,
>>> new.row_user_id,
>>>     new.row_group_id, new.row_project_id, new.row_alg_invocation_id,
>>>     new.version_alg_invocation_id, new.version_date,
>>> new.version_transaction_id
>>>   )
>>>
>>> Now, the description for underlying table DoTS.NAFeatureimpVer
>>> starts with
>>>
>>> dbgus=# \d dotsver.nafeatureimpver
>>>                     Table "dotsver.nafeatureimpver"
>>>             Column            |            Type             |
>>> Modifiers
>>> ------------------------------+----------------------------- 
>>> +-----------
>>>  na_feature_id                | numeric(10,0)               | not
>>> null
>>>
>>> Clearly the DoTSVer.SourceVer trigger for INSERTs is wrong, since
>>> it misses
>>> to set the (provided) value to na_feature_id column.
>>>
>>> Bug #177 signalled in you Bugzilla is generated by the very same
>>> problem, but
>>> on view DoTSVer.TranslatedAAFeatureVer (and using Oracle), so
>>> quite likely
>>> this might a more general issue related to how DoTSVer views are
>>> created.
>>>
>>> Let me know if you need more information for tackling the problem,
>>>
>>> Antonio Galea
>>>
>>>
>>>
>>> ----------------------------------------------------------------
>>> Net Wise webmail system - http://www.netwise.it
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>>
>>> --------------------------------------------------------------------- 
>>> ----
>>> Take Surveys. Earn Cash. Influence the Future of IT
>>> Join SourceForge.net's Techsay panel and you'll get the chance to
>>> share your
>>> opinions on IT & business topics through brief surveys -- and earn
>>> cash
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>>> page=join.php&p=sourceforge&CID=DEVDEV
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>>>
>>
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>> Join SourceForge.net's Techsay panel and you'll get the chance to
>> share your
>> opinions on IT & business topics through brief surveys -- and earn
>> cash
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>
>
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> 

Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[Chris S. <sto...@pc...>]

John Iodice in our group is working on a postgres instance of GUS so  
will ask him to help but if anyone else out there has some ideas that  
would be great to hear.
Chris

On Oct 7, 2006, at 10:08 AM, Steve Fischer wrote:

> Antonio-
>
> i don't think this is the same problem as bug 177.   in that bug,  
> there
> was a uniqueness constraint violation, not a non-null constraint  
> violation.
>
> we don't have much postgres expertise in-house.  i'll see if  
> anybody can
> help  on this.
>
> otherwise, you might need to propose a solution yourself.
>
> steve
>
> an...@ne... wrote:
>> Hello all,
>> using ISF I've found a bug of the schema very similar to the one  
>> signalled
>> here: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=177
>>
>> When using ISF like this:
>>
>> ga GUS::Supported::Plugin::InsertSequenceFeatures \
>>  --mapFile $GUS_HOME/config/genbank2gus.xml \
>>  --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank \
>>  --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16 \
>>  --veryVerbose --sqlVerbose --commit
>>
>> the procedure does complete the insert of all relevant data, but  
>> this single
>> SQL instruction fails:
>>
>> sqlExec:
>>  INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from  
>> DoTS.Source v
>>  where v.na_feature_id = ?
>>  bindValues (5)
>>
>> DBD::Pg::st execute failed: ERROR:  null value in column  
>> "na_feature_id"
>> violates not-null constraint at
>> /hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm  
>> line 147,
>> <GEN39> line 368238.
>>
>> The SQL instruction is indeed incorrect: trying it manually in  
>> PostgreSQL
>>
>> dbgus=# INSERT INTO DoTSVer.SourceVer
>>   select v.*,215,now(),30 from DoTS.Source v where v.na_feature_id  
>> = 5
>> ;
>>
>> gives the very same error.
>>
>> The problem lies in the INSERT trigger for the view  
>> DoTSVer.SourceVer, which
>> PostgreSQL spells out as follows:
>>
>> ON INSERT TO dotsver.sourcever DO INSTEAD
>>   INSERT INTO dotsver.nafeatureimpver (
>>     modification_date, user_read, user_write, group_read,  
>> group_write,
>>     other_read, other_write, row_user_id, row_group_id,  
>> row_project_id,
>>     row_alg_invocation_id, version_alg_invocation_id, version_date,
>>     version_transaction_id
>>   ) VALUES (
>>     new.modification_date, new.user_read, new.user_write,  
>> new.group_read,
>>     new.group_write, new.other_read, new.other_write,  
>> new.row_user_id,
>>     new.row_group_id, new.row_project_id, new.row_alg_invocation_id,
>>     new.version_alg_invocation_id, new.version_date,  
>> new.version_transaction_id
>>   )
>>
>> Now, the description for underlying table DoTS.NAFeatureimpVer  
>> starts with
>>
>> dbgus=# \d dotsver.nafeatureimpver
>>                     Table "dotsver.nafeatureimpver"
>>             Column            |            Type             |  
>> Modifiers
>> ------------------------------+----------------------------- 
>> +-----------
>>  na_feature_id                | numeric(10,0)               | not  
>> null
>>
>> Clearly the DoTSVer.SourceVer trigger for INSERTs is wrong, since  
>> it misses
>> to set the (provided) value to na_feature_id column.
>>
>> Bug #177 signalled in you Bugzilla is generated by the very same  
>> problem, but
>> on view DoTSVer.TranslatedAAFeatureVer (and using Oracle), so  
>> quite likely
>> this might a more general issue related to how DoTSVer views are  
>> created.
>>
>> Let me know if you need more information for tackling the problem,
>>
>> Antonio Galea
>>
>>
>>
>> ----------------------------------------------------------------
>> Net Wise webmail system - http://www.netwise.it
>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to  
>> share your
>> opinions on IT & business topics through brief surveys -- and earn  
>> cash
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>> page=join.php&p=sourceforge&CID=DEVDEV
>> _______________________________________________
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>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
> ---------------------------------------------------------------------- 
> ---
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> Join SourceForge.net's Techsay panel and you'll get the chance to  
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Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

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

Antonio-

i don't think this is the same problem as bug 177.   in that bug, there 
was a uniqueness constraint violation, not a non-null constraint violation.

we don't have much postgres expertise in-house.  i'll see if anybody can 
help  on this. 

otherwise, you might need to propose a solution yourself.

steve

an...@ne... wrote:
> Hello all,
> using ISF I've found a bug of the schema very similar to the one signalled
> here: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=177
>
> When using ISF like this:
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures \
>  --mapFile $GUS_HOME/config/genbank2gus.xml \
>  --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank \
>  --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16 \
>  --veryVerbose --sqlVerbose --commit
>
> the procedure does complete the insert of all relevant data, but this single
> SQL instruction fails:
>
> sqlExec:
>  INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from DoTS.Source v
>  where v.na_feature_id = ?
>  bindValues (5)
>
> DBD::Pg::st execute failed: ERROR:  null value in column "na_feature_id"
> violates not-null constraint at
> /hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147,
> <GEN39> line 368238.
>
> The SQL instruction is indeed incorrect: trying it manually in PostgreSQL
>
> dbgus=# INSERT INTO DoTSVer.SourceVer
>   select v.*,215,now(),30 from DoTS.Source v where v.na_feature_id = 5
> ;
>
> gives the very same error.
>
> The problem lies in the INSERT trigger for the view DoTSVer.SourceVer, which
> PostgreSQL spells out as follows:
>
> ON INSERT TO dotsver.sourcever DO INSTEAD
>   INSERT INTO dotsver.nafeatureimpver (
>     modification_date, user_read, user_write, group_read, group_write,
>     other_read, other_write, row_user_id, row_group_id, row_project_id,
>     row_alg_invocation_id, version_alg_invocation_id, version_date,
>     version_transaction_id
>   ) VALUES (
>     new.modification_date, new.user_read, new.user_write, new.group_read,
>     new.group_write, new.other_read, new.other_write, new.row_user_id,
>     new.row_group_id, new.row_project_id, new.row_alg_invocation_id,
>     new.version_alg_invocation_id, new.version_date, new.version_transaction_id
>   )
>
> Now, the description for underlying table DoTS.NAFeatureimpVer starts with
>
> dbgus=# \d dotsver.nafeatureimpver
>                     Table "dotsver.nafeatureimpver"
>             Column            |            Type             | Modifiers
> ------------------------------+-----------------------------+-----------
>  na_feature_id                | numeric(10,0)               | not null
>
> Clearly the DoTSVer.SourceVer trigger for INSERTs is wrong, since it misses
> to set the (provided) value to na_feature_id column.
>
> Bug #177 signalled in you Bugzilla is generated by the very same problem, but
> on view DoTSVer.TranslatedAAFeatureVer (and using Oracle), so quite likely
> this might a more general issue related to how DoTSVer views are created.
>
> Let me know if you need more information for tackling the problem,
>
> Antonio Galea
>
>
>
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>   

[GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures

[<an...@ne...>]

Hello all,
using ISF I've found a bug of the schema very similar to the one signalle=
d
here: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D177

When using ISF like this:

ga GUS::Supported::Plugin::InsertSequenceFeatures \
 --mapFile $GUS_HOME/config/genbank2gus.xml \
 --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank \
 --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16 \
 --veryVerbose --sqlVerbose --commit

the procedure does complete the insert of all relevant data, but this sin=
gle
SQL instruction fails:

sqlExec:
 INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from DoTS.Source v
 where v.na_feature_id =3D ?
 bindValues (5)

DBD::Pg::st execute failed: ERROR:  null value in column "na_feature_id"
violates not-null constraint at
/hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 14=
7,
<GEN39> line 368238.

The SQL instruction is indeed incorrect: trying it manually in PostgreSQL

dbgus=3D# INSERT INTO DoTSVer.SourceVer
  select v.*,215,now(),30 from DoTS.Source v where v.na_feature_id =3D 5
;

gives the very same error.

The problem lies in the INSERT trigger for the view DoTSVer.SourceVer, wh=
ich
PostgreSQL spells out as follows:

ON INSERT TO dotsver.sourcever DO INSTEAD
  INSERT INTO dotsver.nafeatureimpver (
    modification_date, user_read, user_write, group_read, group_write,
    other_read, other_write, row_user_id, row_group_id, row_project_id,
    row_alg_invocation_id, version_alg_invocation_id, version_date,
    version_transaction_id
  ) VALUES (
    new.modification_date, new.user_read, new.user_write, new.group_read,
    new.group_write, new.other_read, new.other_write, new.row_user_id,
    new.row_group_id, new.row_project_id, new.row_alg_invocation_id,
    new.version_alg_invocation_id, new.version_date, new.version_transact=
ion_id
  )

Now, the description for underlying table DoTS.NAFeatureimpVer starts wit=
h

dbgus=3D# \d dotsver.nafeatureimpver
                    Table "dotsver.nafeatureimpver"
            Column            |            Type             | Modifiers
------------------------------+-----------------------------+-----------
 na_feature_id                | numeric(10,0)               | not null

Clearly the DoTSVer.SourceVer trigger for INSERTs is wrong, since it miss=
es
to set the (provided) value to na_feature_id column.

Bug #177 signalled in you Bugzilla is generated by the very same problem,=
 but
on view DoTSVer.TranslatedAAFeatureVer (and using Oracle), so quite likel=
y
this might a more general issue related to how DoTSVer views are created.

Let me know if you need more information for tackling the problem,

Antonio Galea



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Re: [GUSDEV] Question regarding "InsertSequenceFeature"

[Kumar, S. <San...@ng...>]

Hi Steve,
   You are absolutely right. That is Why I am going to right small perl
program to parse each genome sequence to be loaded to get the date and
accession, and then I will search in the database to see whether  the
accession exists in the "nasequenceimp" table or not. If accession
doesn't exists then it will be considered as a new load and if exists
the we will compare the date (which we are talking about), if the new
file's date is later, then we will delete the old sequence and load the
updated sequence.
This way we will save "lot of data processing time".
    Since, we are dealing with Flu sequences we have total count of more
than 38000 sequences and with so many numbers I felt it will be time
consuming to rebuild the whole database.

Thanks
Sanjeev

-----Original Message-----
From: Steve Fischer [mailto:sfi...@pc...]=20
Sent: Thursday, October 05, 2006 12:15 PM
To: Kumar, Sanjeev
Cc: gus...@li...
Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"

kumar-

a problem i see is that InsertSequenceFeatures is not designed to do
updates.  (In GUS/Supported, when a plugin name starts with Insert that
means that it only inserts and doesn't update.  plugins that insert
and/or update start with Load).

the reason that ISF doesn't do that is that updating can be tricky.  the
strategy we have for PlasmoDB is that we just rebuild the whole
database, rather than doing updates.

steve

Kumar, Sanjeev wrote:

>Hi Steve,
>   This date will be used to check whether the same genome sequence has

>been updated by genBank or not.
>   Here my understanding is that whenever genBank changes any old=20
>genomsequence/or its annotations they
>   change this date. And that comparision we will let me know whether I

>need to reload the updated
>   sequence or not.
>   What do you think, is it a big change or small change?=20
>
>Thanks
>Sanjeev
>
>-----Original Message-----
>From: Steve Fischer [mailto:sfi...@pc...]
>Sent: Tuesday, October 03, 2006 6:23 PM
>To: Kumar, Sanjeev
>Cc: gus...@li...
>Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"
>
>ok, i guess it doesn't.  what is it that you are hoping to accomplish?
>
>steve
>
>Kumar, Sanjeev wrote:
> =20
>
>>Hi Steve,
>>   thanks for your reply. As you suggested I looked into the=20
>>InsertSequenceFeatures.pm code,
>>   and I found some commnets that says
>>  # Annotations we haven't used yet
>>  #	SEGMENT 	segment		SimpleValue e.g. " 1 of 2"
>>  #   ORIGIN 	origin		SimpleValue e.g. " X Chromosome"
>>  #   INV		date_changed	SimpleValue e.g. "08-JUL-1994"
>> Other than that I didn't see any where we are reading this
>>   =20
>>
>annotation.
> =20
>
>>Does this mean that the plugin doesn't read it.
>>
>>Thanks
>>Sanjeev
>>
>>-----Original Message-----
>>From: sfi...@pc... [mailto:sfi...@pc...]
>>Sent: Friday, September 29, 2006 6:21 PM
>>To: Kumar, Sanjeev
>>Cc: gus...@li...
>>Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"
>>
>>sanjeev-
>>
>>i believe it does.  take a look at the code in the plugin to see if=20
>>you can find where it is parsing that line.
>>
>>steve
>>
>>Quoting "Kumar, Sanjeev" <San...@ng...>:
>>
>> =20
>>   =20
>>
>>>Hi Group,
>>>  I have a question regarding InsertSequenceFeature plugin.
>>>  Following are the first few lines of NCBI genBank genome sequence
>>>file:
>>>*******************************
>>>  LOCUS          AB255391                 978 bp    RNA     linear
>>>VRL 22-JUN-2006
>>>  DEFINITION     Influenza A virus (A/Aichi/17/2006(H1N1)) gene for
>>>hemagglutinin,
>>>                     partial cds.
>>>  ACCESSION         AB255391
>>>  VERSION       AB255391.1  GI:109452180
>>>  KEYWORDS    .
>>>  .
>>>  .
>>>*************************
>>>My question is does the plugin parses and store the date shown in=20
>>>first line above (22-JUN-2006).
>>>I tried to look in various dbref table but no luck.
>>>
>>>Any help will be appreciated.
>>>
>>>Thanks
>>>Sanjeev
>>>
>>>---------------------------------------------------------------------
>>>-
>>>--- Take Surveys. Earn Cash. Influence the Future of IT Join=20
>>>SourceForge.net's Techsay panel and you'll get the chance to share=20
>>>your opinions on IT & business topics through brief surveys -- and=20
>>>earn cash=20
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=3DDE
>>>V DEV _______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>   =20
>>>     =20
>>>
>>
>> =20
>>   =20
>>
>
>-----------------------------------------------------------------------
>-- Take Surveys. Earn Cash. Influence the Future of IT Join=20
>SourceForge.net's Techsay panel and you'll get the chance to share your

>opinions on IT & business topics through brief surveys -- and earn cash

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DEVD
>EV _______________________________________________
>Gusdev-gusdev mailing list
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>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

Re: [GUSDEV] Question regarding "InsertSequenceFeature"

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

kumar-

a problem i see is that InsertSequenceFeatures is not designed to do 
updates.  (In GUS/Supported, when a plugin name starts with Insert that 
means that it only inserts and doesn't update.  plugins that insert 
and/or update start with Load).

the reason that ISF doesn't do that is that updating can be tricky.  the 
strategy we have for PlasmoDB is that we just rebuild the whole 
database, rather than doing updates.

steve

Kumar, Sanjeev wrote:

>Hi Steve,
>   This date will be used to check whether the same genome sequence has
>been updated by genBank or not.
>   Here my understanding is that whenever genBank changes any old
>genomsequence/or its annotations they 
>   change this date. And that comparision we will let me know whether I
>need to reload the updated 
>   sequence or not.
>   What do you think, is it a big change or small change? 
>
>Thanks
>Sanjeev 
>
>-----Original Message-----
>From: Steve Fischer [mailto:sfi...@pc...] 
>Sent: Tuesday, October 03, 2006 6:23 PM
>To: Kumar, Sanjeev
>Cc: gus...@li...
>Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"
>
>ok, i guess it doesn't.  what is it that you are hoping to accomplish?
>
>steve
>
>Kumar, Sanjeev wrote:
>  
>
>>Hi Steve,
>>   thanks for your reply. As you suggested I looked into the 
>>InsertSequenceFeatures.pm code,
>>   and I found some commnets that says
>>  # Annotations we haven't used yet
>>  #	SEGMENT 	segment		SimpleValue e.g. " 1 of 2"
>>  #   ORIGIN 	origin		SimpleValue e.g. " X Chromosome"
>>  #   INV		date_changed	SimpleValue e.g. "08-JUL-1994"
>> Other than that I didn't see any where we are reading this
>>    
>>
>annotation.
>  
>
>>Does this mean that the plugin doesn't read it.
>>
>>Thanks
>>Sanjeev
>>
>>-----Original Message-----
>>From: sfi...@pc... [mailto:sfi...@pc...]
>>Sent: Friday, September 29, 2006 6:21 PM
>>To: Kumar, Sanjeev
>>Cc: gus...@li...
>>Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"
>>
>>sanjeev-
>>
>>i believe it does.  take a look at the code in the plugin to see if 
>>you can find where it is parsing that line.
>>
>>steve
>>
>>Quoting "Kumar, Sanjeev" <San...@ng...>:
>>
>>  
>>    
>>
>>>Hi Group,
>>>  I have a question regarding InsertSequenceFeature plugin.
>>>  Following are the first few lines of NCBI genBank genome sequence
>>>file:
>>>*******************************
>>>  LOCUS          AB255391                 978 bp    RNA     linear
>>>VRL 22-JUN-2006
>>>  DEFINITION     Influenza A virus (A/Aichi/17/2006(H1N1)) gene for
>>>hemagglutinin,
>>>                     partial cds.
>>>  ACCESSION         AB255391
>>>  VERSION       AB255391.1  GI:109452180
>>>  KEYWORDS    .
>>>  .
>>>  .
>>>*************************
>>>My question is does the plugin parses and store the date shown in 
>>>first line above (22-JUN-2006).
>>>I tried to look in various dbref table but no luck.
>>>
>>>Any help will be appreciated.
>>>
>>>Thanks
>>>Sanjeev
>>>
>>>---------------------------------------------------------------------
>>>-
>>>--- Take Surveys. Earn Cash. Influence the Future of IT Join 
>>>SourceForge.net's Techsay panel and you'll get the chance to share 
>>>your opinions on IT & business topics through brief surveys -- and 
>>>earn cash 
>>>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DE
>>>V DEV _______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>    
>>>      
>>>
>>
>>  
>>    
>>
>
>-------------------------------------------------------------------------
>Take Surveys. Earn Cash. Influence the Future of IT
>Join SourceForge.net's Techsay panel and you'll get the chance to share your
>opinions on IT & business topics through brief surveys -- and earn cash
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>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [GUSDEV] Question regarding "InsertSequenceFeature"

[Kumar, S. <San...@ng...>]

Hi Steve,
   This date will be used to check whether the same genome sequence has
been updated by genBank or not.
   Here my understanding is that whenever genBank changes any old
genomsequence/or its annotations they=20
   change this date. And that comparision we will let me know whether I
need to reload the updated=20
   sequence or not.
   What do you think, is it a big change or small change?=20

Thanks
Sanjeev=20

-----Original Message-----
From: Steve Fischer [mailto:sfi...@pc...]=20
Sent: Tuesday, October 03, 2006 6:23 PM
To: Kumar, Sanjeev
Cc: gus...@li...
Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"

ok, i guess it doesn't.  what is it that you are hoping to accomplish?

steve

Kumar, Sanjeev wrote:
> Hi Steve,
>    thanks for your reply. As you suggested I looked into the=20
> InsertSequenceFeatures.pm code,
>    and I found some commnets that says
>   # Annotations we haven't used yet
>   #	SEGMENT 	segment		SimpleValue e.g. " 1 of 2"
>   #   ORIGIN 	origin		SimpleValue e.g. " X Chromosome"
>   #   INV		date_changed	SimpleValue e.g. "08-JUL-1994"
>  Other than that I didn't see any where we are reading this
annotation.
> Does this mean that the plugin doesn't read it.
>
> Thanks
> Sanjeev
>
> -----Original Message-----
> From: sfi...@pc... [mailto:sfi...@pc...]
> Sent: Friday, September 29, 2006 6:21 PM
> To: Kumar, Sanjeev
> Cc: gus...@li...
> Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"
>
> sanjeev-
>
> i believe it does.  take a look at the code in the plugin to see if=20
> you can find where it is parsing that line.
>
> steve
>
> Quoting "Kumar, Sanjeev" <San...@ng...>:
>
>  =20
>> Hi Group,
>>   I have a question regarding InsertSequenceFeature plugin.
>>   Following are the first few lines of NCBI genBank genome sequence
>> file:
>> *******************************
>>   LOCUS          AB255391                 978 bp    RNA     linear
>> VRL 22-JUN-2006
>>   DEFINITION     Influenza A virus (A/Aichi/17/2006(H1N1)) gene for
>> hemagglutinin,
>>                      partial cds.
>>   ACCESSION         AB255391
>>   VERSION       AB255391.1  GI:109452180
>>   KEYWORDS    .
>>   .
>>   .
>> *************************
>> My question is does the plugin parses and store the date shown in=20
>> first line above (22-JUN-2006).
>> I tried to look in various dbref table but no luck.
>>
>> Any help will be appreciated.
>>
>> Thanks
>> Sanjeev
>>
>> ---------------------------------------------------------------------
>> -
>> --- Take Surveys. Earn Cash. Influence the Future of IT Join=20
>> SourceForge.net's Techsay panel and you'll get the chance to share=20
>> your opinions on IT & business topics through brief surveys -- and=20
>> earn cash=20
>> =
http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DE
>> V DEV _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    =20
>
>
>
>  =20

Re: [GUSDEV] Question regarding "InsertSequenceFeature"

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

ok, i guess it doesn't.  what is it that you are hoping to accomplish?

steve

Kumar, Sanjeev wrote:
> Hi Steve,
>    thanks for your reply. As you suggested I looked into the
> InsertSequenceFeatures.pm code,
>    and I found some commnets that says
>   # Annotations we haven't used yet
>   #	SEGMENT 	segment		SimpleValue e.g. " 1 of 2"
>   #   ORIGIN 	origin		SimpleValue e.g. " X Chromosome"
>   #   INV		date_changed	SimpleValue e.g. "08-JUL-1994"
>  Other than that I didn't see any where we are reading this annotation.
> Does this mean that the plugin doesn't read it.
>
> Thanks
> Sanjeev
>
> -----Original Message-----
> From: sfi...@pc... [mailto:sfi...@pc...] 
> Sent: Friday, September 29, 2006 6:21 PM
> To: Kumar, Sanjeev
> Cc: gus...@li...
> Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"
>
> sanjeev-
>
> i believe it does.  take a look at the code in the plugin to see if you
> can find where it is parsing that line.
>
> steve
>
> Quoting "Kumar, Sanjeev" <San...@ng...>:
>
>   
>> Hi Group,
>>   I have a question regarding InsertSequenceFeature plugin.
>>   Following are the first few lines of NCBI genBank genome sequence
>> file:
>> *******************************
>>   LOCUS          AB255391                 978 bp    RNA     linear
>> VRL 22-JUN-2006
>>   DEFINITION     Influenza A virus (A/Aichi/17/2006(H1N1)) gene for
>> hemagglutinin,
>>                      partial cds.
>>   ACCESSION         AB255391
>>   VERSION       AB255391.1  GI:109452180
>>   KEYWORDS    .
>>   .
>>   .
>> *************************
>> My question is does the plugin parses and store the date shown in 
>> first line above (22-JUN-2006).
>> I tried to look in various dbref table but no luck.
>>
>> Any help will be appreciated.
>>
>> Thanks
>> Sanjeev
>>
>> ----------------------------------------------------------------------
>> --- Take Surveys. Earn Cash. Influence the Future of IT Join 
>> SourceForge.net's Techsay panel and you'll get the chance to share 
>> your opinions on IT & business topics through brief surveys -- and 
>> earn cash 
>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEV
>> DEV _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>     
>
>
>
>   

Re: [GUSDEV] Question regarding "InsertSequenceFeature"

[Kumar, S. <San...@ng...>]

Hi Steve,
   thanks for your reply. As you suggested I looked into the
InsertSequenceFeatures.pm code,
   and I found some commnets that says
  # Annotations we haven't used yet
  #	SEGMENT 	segment		SimpleValue e.g. " 1 of 2"
  #   ORIGIN 	origin		SimpleValue e.g. " X Chromosome"
  #   INV		date_changed	SimpleValue e.g. "08-JUL-1994"
 Other than that I didn't see any where we are reading this annotation.
Does this mean that the plugin doesn't read it.

Thanks
Sanjeev

-----Original Message-----
From: sfi...@pc... [mailto:sfi...@pc...]=20
Sent: Friday, September 29, 2006 6:21 PM
To: Kumar, Sanjeev
Cc: gus...@li...
Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"

sanjeev-

i believe it does.  take a look at the code in the plugin to see if you
can find where it is parsing that line.

steve

Quoting "Kumar, Sanjeev" <San...@ng...>:

>
> Hi Group,
>   I have a question regarding InsertSequenceFeature plugin.
>   Following are the first few lines of NCBI genBank genome sequence
> file:
> *******************************
>   LOCUS          AB255391                 978 bp    RNA     linear
> VRL 22-JUN-2006
>   DEFINITION     Influenza A virus (A/Aichi/17/2006(H1N1)) gene for
> hemagglutinin,
>                      partial cds.
>   ACCESSION         AB255391
>   VERSION       AB255391.1  GI:109452180
>   KEYWORDS    .
>   .
>   .
> *************************
> My question is does the plugin parses and store the date shown in=20
> first line above (22-JUN-2006).
> I tried to look in various dbref table but no luck.
>
> Any help will be appreciated.
>
> Thanks
> Sanjeev
>
> ----------------------------------------------------------------------
> --- Take Surveys. Earn Cash. Influence the Future of IT Join=20
> SourceForge.net's Techsay panel and you'll get the chance to share=20
> your opinions on IT & business topics through brief surveys -- and=20
> earn cash=20
> =
http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEV
> DEV _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] Concurrent inserts into GUS

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

jeetendra-   see below.   -steve

Quoting Jeetendra Soneja <so...@vb...>:

>
> Steve,
>
> Thanks for your reply.
>
> No, I haven't tried such concurrent runs of plug-ins yet. However, I might
> have to do so in the near future.
>
> You said that objects written in one submit() function call are atomic.
> So, if I add a NALocation object as a child of NAFeature object, and I
> call submit() on NAFeature, do these two inserts become one atomic
> transaction ?

yes.   but, i don't think you need to do that.  i am not clear on why 
you think
you will have conflicts.  just running two plugins concurrently should not
cause a problem.

>
> Thanks,
> Jeetendra.
>
> On Fri, September 29, 2006 6:25 pm, sfi...@pc... wrote:
>> jeetendra-
>>
>> no, they are not atomic.  in gus plugins whatever objects are written in
>> one submit() function call are atomic.  but in this case it seems the
>> features are written first and the locations second.
>>
>> however, i do not think this will cause inconsistent data.
>>
>> do you have inconsistent data?
>>
>> steve
>>
>> Quoting Jeetendra Soneja <so...@vb...>:
>>
>>
>>>
>>> I had a question regarding concurrent inserts into GUS. Are the inserts
>>>  into GUS synchronized ? If I have multiple plug-ins inserting data at
>>> the same time, into same tables, can this lead to inconsistent data ?
>>> There are certain cases where the newly inserted primary key is
>>> referenced by other tables. For example, if we are inserting features and
>>> their locations, the plug-in inserts feature first, and uses the primary
>>> key (na_feature_id) of the feature to insert its location(s). Are such
>>> inserts done as one atomic and synchonized transaction ?
>>>
>>> Please let me know.
>>>
>>>
>>> Thank you for your help,
>>> Jeetendra.
>>>
>>>
>>>
>>> -----------------------------------------------------------------------
>>> --
>>> Take Surveys. Earn Cash. Influence the Future of IT
>>> Join SourceForge.net's Techsay panel and you'll get the chance to share
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>>> EV
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>>
>>
>>
>> -------------------------------------------------------------------------
>>  Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to share
>> your opinions on IT & business topics through brief surveys -- and earn
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>>
>>
>
>
> --
> Jeetendra Soneja
> Research Associate (Software Engineer)
> Virginia Bioinformatics Institute
> 0477 Washington St, Phase II - 162-04
> Blacksburg, VA 24060, USA
> Phone: (540)-231-2789
> http://www.vbi.vt.edu
>
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
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Re: [GUSDEV] Concurrent inserts into GUS

[Jeetendra S. <so...@vb...>]

Steve,

Thanks for your reply.

No, I haven't tried such concurrent runs of plug-ins yet. However, I might
have to do so in the near future.

You said that objects written in one submit() function call are atomic.
So, if I add a NALocation object as a child of NAFeature object, and I
call submit() on NAFeature, do these two inserts become one atomic
transaction ?

Thanks,
Jeetendra.

On Fri, September 29, 2006 6:25 pm, sfi...@pc... wrote:
> jeetendra-
>
> no, they are not atomic.  in gus plugins whatever objects are written in
> one submit() function call are atomic.  but in this case it seems the
> features are written first and the locations second.
>
> however, i do not think this will cause inconsistent data.
>
> do you have inconsistent data?
>
> steve
>
> Quoting Jeetendra Soneja <so...@vb...>:
>
>
>>
>> I had a question regarding concurrent inserts into GUS. Are the inserts
>>  into GUS synchronized ? If I have multiple plug-ins inserting data at
>> the same time, into same tables, can this lead to inconsistent data ?
>> There are certain cases where the newly inserted primary key is
>> referenced by other tables. For example, if we are inserting features and
>> their locations, the plug-in inserts feature first, and uses the primary
>> key (na_feature_id) of the feature to insert its location(s). Are such
>> inserts done as one atomic and synchonized transaction ?
>>
>> Please let me know.
>>
>>
>> Thank you for your help,
>> Jeetendra.
>>
>>
>>
>> -----------------------------------------------------------------------
>> --
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>
>
>
>
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-- 
Jeetendra Soneja
Research Associate (Software Engineer)
Virginia Bioinformatics Institute
0477 Washington St, Phase II - 162-04
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

Re: [GUSDEV] Concurrent inserts into GUS

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

jeetendra-

no, they are not atomic.  in gus plugins whatever objects are written in one
submit() function call are atomic.  but in this case it seems the features are
written first and the locations second.

however, i do not think this will cause inconsistent data.

do you have inconsistent data?

steve

Quoting Jeetendra Soneja <so...@vb...>:

>
> I had a question regarding concurrent inserts into GUS. Are the inserts
> into GUS synchronized ? If I have multiple plug-ins inserting data at
> the same time, into same tables, can this lead to inconsistent data ?
> There are certain cases where the newly inserted primary key is
> referenced by other tables. For example, if we are inserting features
> and their locations, the plug-in inserts feature first, and uses the
> primary key (na_feature_id) of the feature to insert its location(s).
> Are such inserts done as one atomic and synchonized transaction ?
>
> Please let me know.
>
> Thank you for your help,
> Jeetendra.
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
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Re: [GUSDEV] Question regarding "InsertSequenceFeature"

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

sanjeev-

i believe it does.  take a look at the code in the plugin to see if you 
can find
where it is parsing that line.

steve

Quoting "Kumar, Sanjeev" <San...@ng...>:

>
> Hi Group,
>   I have a question regarding InsertSequenceFeature plugin.
>   Following are the first few lines of NCBI genBank genome sequence
> file:
> *******************************
>   LOCUS          AB255391                 978 bp    RNA     linear
> VRL 22-JUN-2006
>   DEFINITION     Influenza A virus (A/Aichi/17/2006(H1N1)) gene for
> hemagglutinin,
>                      partial cds.
>   ACCESSION         AB255391
>   VERSION       AB255391.1  GI:109452180
>   KEYWORDS    .
>   .
>   .
> *************************
> My question is does the plugin parses and store the date shown in first
> line above (22-JUN-2006).
> I tried to look in various dbref table but no luck.
>
> Any help will be appreciated.
>
> Thanks
> Sanjeev
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
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[GUSDEV] Question regarding "InsertSequenceFeature"

[Kumar, S. <San...@ng...>]

 Hi Group,
   I have a question regarding InsertSequenceFeature plugin.
   Following are the first few lines of NCBI genBank genome sequence
file:
*******************************
   LOCUS          AB255391                 978 bp    RNA     linear
VRL 22-JUN-2006
   DEFINITION     Influenza A virus (A/Aichi/17/2006(H1N1)) gene for
hemagglutinin,
                      partial cds.
   ACCESSION         AB255391
   VERSION       AB255391.1  GI:109452180
   KEYWORDS    .
   .
   .
*************************
My question is does the plugin parses and store the date shown in first
line above (22-JUN-2006).
I tried to look in various dbref table but no luck.

Any help will be appreciated.

Thanks
Sanjeev

[GUSDEV] Concurrent inserts into GUS

[Jeetendra S. <so...@vb...>]

I had a question regarding concurrent inserts into GUS. Are the inserts 
into GUS synchronized ? If I have multiple plug-ins inserting data at 
the same time, into same tables, can this lead to inconsistent data ? 
There are certain cases where the newly inserted primary key is 
referenced by other tables. For example, if we are inserting features 
and their locations, the plug-in inserts feature first, and uses the 
primary key (na_feature_id) of the feature to insert its location(s). 
Are such inserts done as one atomic and synchonized transaction ?

Please let me know.

Thank you for your help,
Jeetendra.

Re: [GUSDEV] InsertSequenceFeatures.pm

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

michael-

i suspect the problem is that you have downloaded and installed
InsertSequenceFeature.pm into  your previously existing gus installation.

but, it needs other support files.

you might be ok if you get all of GUS/Supported.   save your old GUS/Supported
as a backup.

let's see how that goes.  you might need more.

steve

Quoting mro...@cs...:

> Hi everybody,
>
>
> In InsertSequenceFeatures.pm at line 308 I changed
>
>   cvsRevision => '$Revision$',
> to cvsRevision => '$Revision: 1000 $',
>
> and the revision error in no longer with me
>
>
> Then I run
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures
> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml
> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk
> --fileFormat genbank
> --extDbName "Pseudomonas_aeruginosa"
> --extDbRlsVer "unknown"
> --commit
>
> and got
>
> ================================
> Thu Sep 28 18:24:00 2006        ARGS    algoinvo        1
> Thu Sep 28 18:24:00 2006        ARGS    comment
> Thu Sep 28 18:24:00 2006        ARGS    commit  1
> Thu Sep 28 18:24:00 2006        ARGS    debug   0
> Thu Sep 28 18:24:00 2006        ARGS    defaultOrganism
> Thu Sep 28 18:24:00 2006        ARGS    extDbName
> Pseudomonas_aeruginosa
> Thu Sep 28 18:24:00 2006        ARGS    extDbRlsVer     unknown
> Thu Sep 28 18:24:00 2006        ARGS    fileFormat      genbank
> Thu Sep 28 18:24:00 2006        ARGS    gff2GroupTag
> Thu Sep 28 18:24:00 2006        ARGS    group
> Thu Sep 28 18:24:00 2006        ARGS    gusconfigfile
> /home/acrl-storage-1/gusdb/GUS/gus.properties
> Thu Sep 28 18:24:00 2006        ARGS    handlerExternalDbs
> Thu Sep 28 18:24:00 2006        ARGS    help
> Thu Sep 28 18:24:00 2006        ARGS    helpHTML
> Thu Sep 28 18:24:00 2006        ARGS    inputFileExtension
> Thu Sep 28 18:24:00 2006        ARGS    inputFileOrDir
> /home/biorg-srv-2/mrobi002/pseudomonas aeruginosa/pa01/NC_002516.gbk
> Thu Sep 28 18:24:00 2006        ARGS    makeSourceids
> Thu Sep 28 18:24:00 2006        ARGS    mapFile
> /home/biorg-srv-2/mrobi002/pseudomonas aeruginosa/pa01/genbank2gus.xml
> Thu Sep 28 18:24:00 2006        ARGS    naSequenceSubclass
> Thu Sep 28 18:24:00 2006        ARGS    organism
> Thu Sep 28 18:24:00 2006        ARGS    project
> Thu Sep 28 18:24:00 2006        ARGS    seqExtDbName
> Thu Sep 28 18:24:00 2006        ARGS    seqExtDbRlsVer
> Thu Sep 28 18:24:00 2006        ARGS    seqIdColumn     source_id
> Thu Sep 28 18:24:00 2006        ARGS    seqSoTerm
> Thu Sep 28 18:24:00 2006        ARGS    seqType
> Thu Sep 28 18:24:00 2006        ARGS    soCvsVersion
> Thu Sep 28 18:24:00 2006        ARGS    sqlVerbose      0
> Thu Sep 28 18:24:00 2006        ARGS    testNumber
> Thu Sep 28 18:24:00 2006        ARGS    user
> Thu Sep 28 18:24:00 2006        ARGS    verbose 0
> Thu Sep 28 18:24:00 2006        ARGS    veryVerbose     0
> Thu Sep 28 18:24:00 2006        COMMIT  commit on
> Thu Sep 28 18:24:00 2006        ALGINVID        12
>
> ERROR:
> Can't locate object method "new" via package
> "GUS::Supported::BioperlFeatMapperSet" (perhaps you forgot to load
> "GUS::Supported::BioperlFeatMapperSet"?) at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 319.
>
> STACK TRACE:
> at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 319
>        
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x854891c)',
> 'HASH(0x8ea8aa8)') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 469
>        eval {...} called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 461
>        
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 380
>        
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 288
>        
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 197
>        
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'ARRAY(0x80f8ee4)') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/bin/ga line 11
> ==========================================
>
>
> I went to line 319 in InsertSequenceFeatures.pm and I get:
>
>
>  $self->{mapperSet} =
>    GUS::Supported::BioperlFeatMapperSet->new($self->getArg('mapFile'),
> $self)
>
>
> So should I assume that there is a problem with mapFile genbank2gus.xml?
>
> I have not modified any other Plugins, do I need to?
>
> In the Gus-dev I found that the other similar times with this problem it
> was caused by Source Repository being temporary unavailable.
>
>
> Thank you
>
>
> Michael
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
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[GUSDEV] InsertSequenceFeatures.pm

[<mro...@cs...>]

Hi everybody,


In InsertSequenceFeatures.pm at line 308 I changed

   cvsRevision =3D> '$Revision$',
to cvsRevision =3D> '$Revision: 1000 $',

and the revision error in no longer with me


Then I run

ga GUS::Supported::Plugin::InsertSequenceFeatures
--mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml
--inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk
--fileFormat genbank
--extDbName "Pseudomonas_aeruginosa"
--extDbRlsVer "unknown"
--commit

and got

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
Thu Sep 28 18:24:00 2006        ARGS    algoinvo        1
Thu Sep 28 18:24:00 2006        ARGS    comment
Thu Sep 28 18:24:00 2006        ARGS    commit  1
Thu Sep 28 18:24:00 2006        ARGS    debug   0
Thu Sep 28 18:24:00 2006        ARGS    defaultOrganism
Thu Sep 28 18:24:00 2006        ARGS    extDbName     =20
Pseudomonas_aeruginosa
Thu Sep 28 18:24:00 2006        ARGS    extDbRlsVer     unknown
Thu Sep 28 18:24:00 2006        ARGS    fileFormat      genbank
Thu Sep 28 18:24:00 2006        ARGS    gff2GroupTag
Thu Sep 28 18:24:00 2006        ARGS    group
Thu Sep 28 18:24:00 2006        ARGS    gusconfigfile =20
/home/acrl-storage-1/gusdb/GUS/gus.properties
Thu Sep 28 18:24:00 2006        ARGS    handlerExternalDbs
Thu Sep 28 18:24:00 2006        ARGS    help
Thu Sep 28 18:24:00 2006        ARGS    helpHTML
Thu Sep 28 18:24:00 2006        ARGS    inputFileExtension
Thu Sep 28 18:24:00 2006        ARGS    inputFileOrDir=20
/home/biorg-srv-2/mrobi002/pseudomonas aeruginosa/pa01/NC_002516.gbk
Thu Sep 28 18:24:00 2006        ARGS    makeSourceids
Thu Sep 28 18:24:00 2006        ARGS    mapFile
/home/biorg-srv-2/mrobi002/pseudomonas aeruginosa/pa01/genbank2gus.xml
Thu Sep 28 18:24:00 2006        ARGS    naSequenceSubclass
Thu Sep 28 18:24:00 2006        ARGS    organism
Thu Sep 28 18:24:00 2006        ARGS    project
Thu Sep 28 18:24:00 2006        ARGS    seqExtDbName
Thu Sep 28 18:24:00 2006        ARGS    seqExtDbRlsVer
Thu Sep 28 18:24:00 2006        ARGS    seqIdColumn     source_id
Thu Sep 28 18:24:00 2006        ARGS    seqSoTerm
Thu Sep 28 18:24:00 2006        ARGS    seqType
Thu Sep 28 18:24:00 2006        ARGS    soCvsVersion
Thu Sep 28 18:24:00 2006        ARGS    sqlVerbose      0
Thu Sep 28 18:24:00 2006        ARGS    testNumber
Thu Sep 28 18:24:00 2006        ARGS    user
Thu Sep 28 18:24:00 2006        ARGS    verbose 0
Thu Sep 28 18:24:00 2006        ARGS    veryVerbose     0
Thu Sep 28 18:24:00 2006        COMMIT  commit on
Thu Sep 28 18:24:00 2006        ALGINVID        12

ERROR:
Can't locate object method "new" via package
"GUS::Supported::BioperlFeatMapperSet" (perhaps you forgot to load
"GUS::Supported::BioperlFeatMapperSet"?) at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin/Ins=
ertSequenceFeatures.pm
line 319.

STACK TRACE:
 at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin/Ins=
ertSequenceFeatures.pm
line 319
        GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Support=
ed::Plugin::InsertSequenceFeatures=3DHASH(0x854891c)',
'HASH(0x8ea8aa8)') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 469
        eval {...} called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 461
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plu=
ginMgr::GusApplication=3DHASH(0x80f1174)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 380
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::=
GusApplication=3DHASH(0x80f1174)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 288
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusA=
pplication=3DHASH(0x80f1174)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 197
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusA=
pplication=3DHASH(0x80f1174)',
'ARRAY(0x80f8ee4)') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/bin/ga line 11
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


I went to line 319 in InsertSequenceFeatures.pm and I get:


  $self->{mapperSet} =3D
    GUS::Supported::BioperlFeatMapperSet->new($self->getArg('mapFile'),
$self)


So should I assume that there is a problem with mapFile genbank2gus.xml?

I have not modified any other Plugins, do I need to?

In the Gus-dev I found that the other similar times with this problem it
was caused by Source Repository being temporary unavailable.


Thank you


Michael

Re: [GUSDEV] genes with more than one EC number

[Fernan A. <fe...@ii...>]

+----[ Mark Heiges <mh...@ug...> (26.Sep.2006 23:02):
|
| You need a SpecialCaseQualifierHandlers module to process multi-value  
| tags. See "...some qualifiers do not fit neatly into a column in the  
| feature table..." in the ISF plugin notes.
| 
| GUS::Supported::SpecialCaseQualifierHandlers is an example.

Yes, we've already written a few of these ... but the
problem with EC numbers was that even with a special
handler, dots.transcript has only one column for ec_number.

| I will send you another example off-list that includes a subroutine  
| for handling ECs.
|
+----]

Thanks, that's what I thought was the right thing ... a
separate table implementing a one-to-many ... I was not
aware of the dots.aasequenceenzymeclass table ... thanks for
the pointer!

Fernan

Re: [GUSDEV] genes with more than one EC number

[Mark S. H. <mh...@ug...>]

You need a SpecialCaseQualifierHandlers module to process multi-value  
tags. See "...some qualifiers do not fit neatly into a column in the  
feature table..." in the ISF plugin notes.

GUS::Supported::SpecialCaseQualifierHandlers is an example.

I will send you another example off-list that includes a subroutine  
for handling ECs.

On Sep 26, 2006, at 9:25 PM, Fernan Aguero wrote:

> Hi,
>
> we're having problems loading files where genes have more
> than one EC number (we're using the supported
> InsertSequenceFeatures plugin).
>
> Depending on how you view the problem it could be an issue
> of the plugin, the underlying schema, or both.
>
> Given that it is not unexpected that proteins could have
> more than one EC number, this should not be the standard
> behaviour (maybe give a warning but still continue loading?).
>
> Is this a known bug? Anyone has already worked around this?
>
> If not, I'll be submitting an issue to the tracker,
>
> Fernan
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
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> opinions on IT & business topics through brief surveys -- and earn  
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