gusdev-gusdev — Topics concerning GUS development

[Gusdev-gusdev] Problem with GBParser

[Thomas O. <ot...@fi...>]

Hello,

I have a little problem trying to insert a sequence from Genbank with 
the GBParser. (Errormessage and sequence-file (a cutted version) see below!)

Looks like, that the table doesn't exists! Do I have to create the table 
or is the GBParser not able to insert this type of entries in general.

I will continue to resolve the problem, but maybe someone might help me.

Thanks a lot,
Thomas


Error msg:
Invalid child name: 'GUS::Model::DoTS::AAFeatureComment' at 
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line 851        
GUS::ObjRelP::DbiTable::addToChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...) 
called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line 844
        
GUS::ObjRelP::DbiTable::setChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...) 
called at /home/oracle/gus_home/lib/perl/GUS/Model/DoTS/Source_Table.pm 
line 16
        
GUS::Model::DoTS::Source_Table::setDefaultParams('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)') 
called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line 38
        
GUS::ObjRelP::DbiTable::new('GUS::Model::DoTS::Source_Table','GUS::Model::DoTS::Source','GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)') 
called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 179
        
GUS::ObjRelP::DbiDatabase::getTable('GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)','GUS::Model::DoTS::Source') 
called
at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 30
        
GUS::ObjRelP::DbiRow::new('GUS::ObjRelP::DbiRow','GUS::Model::DoTS::Source','HASH(0x8fcb890)','undef','undef') 
called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 25
        
GUS::Model::GusRow::new('GUS::Model::DoTS::Source','HASH(0x8fcb890)') 
called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm 
line 486
        
GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::Entry=HASH(0x8ec70f4)','GUS::Model::DoTS::ExternalNASequence=HASH(0x8f95ea8)') 
called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm 
line 251
        
GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::ArrayStream=HASH(0x8ec7088)') 
called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm 
line 185
        eval {...} called at 
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
        
GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','HASH(0x8e53714)') 
called at /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
line 430
        eval {...} called at 
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
        
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser') 
called at /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
line 283
        
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser') 
called at /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
line 192
        
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x80606b0)') 
called at /home/oracle/gus_home/bin/ga line 11

Re: [Gusdev-gusdev] fixing GBParser to add topology

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

ok, thanks fidel.   we'll fold these changes in.

steve

Fidel Salas wrote:

>To get GBParser to fill-in the topology attribute, I had to make
>manual changes to two files (see below).  Creation of Perl objects
>automatically created setTopology and getTopology methods in 
>GUS::Model::DoTS::NAEntry_Row (after creating initial DB instance with
>modified schema).
>
>Fidel
>
>
>Here are the diffs:
>CBIL::Bio::GenBank::Locus
>*** /tmp/Locus.pm	Thu Mar  4 15:03:49 2004
>--- /tmp/Locus.pm-original	Thu Mar  4 15:03:49 2004
>***************
>*** 9,15 ****
>  sub setType     { $_[0]->{TYP} = $_[1]; $_[0] }
>  sub setDivision { $_[0]->{DIV} = $_[1]; $_[0] }
>  sub setDate     { $_[0]->{DAT} = $_[1]; $_[0] }
>- sub setTopology { $_[0]->{TOP} = $_[1]; $_[0] }
>  
>  sub getId       { $_[0]->{ID}  }
>  sub getLength   { $_[0]->{LEN} }
>--- 9,14 ----
>***************
>*** 16,22 ****
>  sub getType     { $_[0]->{TYP} }
>  sub getDivision { $_[0]->{DIV} }
>  sub getDate     { $_[0]->{DAT} }
>- sub getTopology { $_[0]->{TOP} }
>  
>  # ........................................
>  
>--- 15,20 ----
>***************
>*** 27,35 ****
>    my $line = $IOS->getLine();
>  
>  	my @A = split /\s+/, $line;
>!   my ( $LOCUS, $id, $length, $bp, $type, $topology, $div, $date );
>  	if (@A > 7) {
>! 		( $LOCUS, $id, $length, $bp, $type, $topology, $div, $date ) = @A;
>  	} elsif (@A == 7) {
>  		( $LOCUS, $id, $length, $bp, $type, $div, $date ) = @A;
>  	}	else {
>--- 25,33 ----
>    my $line = $IOS->getLine();
>  
>  	my @A = split /\s+/, $line;
>!   my ( $LOCUS, $id, $length, $bp, $type, $circular, $div, $date );
>  	if (@A > 7) {
>! 		( $LOCUS, $id, $length, $bp, $type, $circular, $div, $date ) = @A;
>  	} elsif (@A == 7) {
>  		( $LOCUS, $id, $length, $bp, $type, $div, $date ) = @A;
>  	}	else {
>***************
>*** 43,49 ****
>    $M->setType(     $type );
>    $M->setDivision( $div );
>    $M->setDate(     $date );
>-   $M->setTopology( $topology );
>  
>    $M;
>  }
>--- 41,46 ----
>
>
>GUS::Common::Plugin::GBParser
>*** /tmp/GBParser.pm	Thu Mar  4 15:15:26 2004
>--- /tmp/GBParser.pm~	Thu Mar  4 15:15:26 2004
>***************
>*** 348,354 ****
>    my %h = ('source_id' =>  $e->{ACCESSION}->[0]->getAccession(), 
>  	   'division' => $e->{LOCUS}->[0]->getDivision(),
>  	   'version' => $e->{VERSION}->[0]->getSeqVersion(),
>- 	   'topology' => $e->{LOCUS}->[0]->getTopology(),
>  	  ) ;
>    my $date = &formatDate($e->{LOCUS}->[0]->getDate());
>    if ($chkdif) { 
>--- 345,350 ----
>
>
>
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[Gusdev-gusdev] wdk update

[Thomas O. <ot...@fi...>]

Hi,

I read that that the wdk will be replaced by another module (JSP 
based?). How far is this effort, because we are thinking to use the wdk 
frontend - but if the new one will come out soon.

Thanks,
Thomas

[Gusdev-gusdev] fixing GBParser to add topology

[Fidel S. <fi...@vb...>]

To get GBParser to fill-in the topology attribute, I had to make
manual changes to two files (see below).  Creation of Perl objects
automatically created setTopology and getTopology methods in 
GUS::Model::DoTS::NAEntry_Row (after creating initial DB instance with
modified schema).

Fidel


Here are the diffs:
CBIL::Bio::GenBank::Locus
*** /tmp/Locus.pm	Thu Mar  4 15:03:49 2004
--- /tmp/Locus.pm-original	Thu Mar  4 15:03:49 2004
***************
*** 9,15 ****
  sub setType     { $_[0]->{TYP} = $_[1]; $_[0] }
  sub setDivision { $_[0]->{DIV} = $_[1]; $_[0] }
  sub setDate     { $_[0]->{DAT} = $_[1]; $_[0] }
- sub setTopology { $_[0]->{TOP} = $_[1]; $_[0] }
  
  sub getId       { $_[0]->{ID}  }
  sub getLength   { $_[0]->{LEN} }
--- 9,14 ----
***************
*** 16,22 ****
  sub getType     { $_[0]->{TYP} }
  sub getDivision { $_[0]->{DIV} }
  sub getDate     { $_[0]->{DAT} }
- sub getTopology { $_[0]->{TOP} }
  
  # ........................................
  
--- 15,20 ----
***************
*** 27,35 ****
    my $line = $IOS->getLine();
  
  	my @A = split /\s+/, $line;
!   my ( $LOCUS, $id, $length, $bp, $type, $topology, $div, $date );
  	if (@A > 7) {
! 		( $LOCUS, $id, $length, $bp, $type, $topology, $div, $date ) = @A;
  	} elsif (@A == 7) {
  		( $LOCUS, $id, $length, $bp, $type, $div, $date ) = @A;
  	}	else {
--- 25,33 ----
    my $line = $IOS->getLine();
  
  	my @A = split /\s+/, $line;
!   my ( $LOCUS, $id, $length, $bp, $type, $circular, $div, $date );
  	if (@A > 7) {
! 		( $LOCUS, $id, $length, $bp, $type, $circular, $div, $date ) = @A;
  	} elsif (@A == 7) {
  		( $LOCUS, $id, $length, $bp, $type, $div, $date ) = @A;
  	}	else {
***************
*** 43,49 ****
    $M->setType(     $type );
    $M->setDivision( $div );
    $M->setDate(     $date );
-   $M->setTopology( $topology );
  
    $M;
  }
--- 41,46 ----


GUS::Common::Plugin::GBParser
*** /tmp/GBParser.pm	Thu Mar  4 15:15:26 2004
--- /tmp/GBParser.pm~	Thu Mar  4 15:15:26 2004
***************
*** 348,354 ****
    my %h = ('source_id' =>  $e->{ACCESSION}->[0]->getAccession(), 
  	   'division' => $e->{LOCUS}->[0]->getDivision(),
  	   'version' => $e->{VERSION}->[0]->getSeqVersion(),
- 	   'topology' => $e->{LOCUS}->[0]->getTopology(),
  	  ) ;
    my $date = &formatDate($e->{LOCUS}->[0]->getDate());
    if ($chkdif) { 
--- 345,350 ----

Re: [Gusdev-gusdev] GUS to PostgreSQL

[Laurie K. <lk...@mo...>]

Angel Pizarro wrote:

> We use NUMBER mainly for integers, so one of the int types would do. 
> What is the
> precision of these ints? Are these signed ints?  -99 > int2 > +99


Yes.

-32768 >= int2 >= +32767    (int2 == smallint)

-2147483648 >= int4 >= +2147483647   (int4 == integer)

-9223372036854775808 >= int8 >= 9223372036854775807   (int8 == bigint)


Neither int2 nor int8 values are recommended for use in indexed fields.
My vote is to use the "integer" keyword for most attributes, reserving
"smallint" for those with just a few values, unless they are indexed.
Other opinions?

> BTW thanks very much for the converted SQL.
>
You're welcome.  I learned a lot.
Laurie

Re: [Gusdev-gusdev] GUS to PostgreSQL

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

i don't have time right now to digest this, but...

hey, wow, this is great.

steve

Laurie Kramer wrote:

> Steve wrote on Feb 13:
>
>> ok, to follow on this with a new subject heading...
>>
>> For those groups that are gearing up to port GUS to PostgreSQL, here 
>> are some quick thoughts on getting started.
>>
>> The two main tasks, to start with, I think, are:
>>   - porting the schema creation scripts to postgres
>>   - remove the oracle dependencies from the perl object layer
>>
>> Porting the Schema
>> As mentioned below, one way to go here is using a system-neutral 
>> syntax (xml) to create the schemas.   I think this should be the long 
>> term goal.  But, for a quick solution, there must be some way for us 
>> to manually transform the existing oracle-specific syntax to 
>> postgres.   I envision some kind of ad hoc scripts to do the 
>> transform.   This shouldn't be too big a deal.
>>
>> I would say the first step is to identify what the transforms will be.
>>
>>
>> Object Layer
>> I just did a quick look in the object layer code (Perl).  (we can 
>> defer for now on the java object layer since its not in wide use).   
>> Only two files seem to use oracle system tables, both in 
>> $PROJECT_HOME/GUS/ObjRelP/lib/perl:  DbiTable.pm and 
>> DbiDatabase.pm.   There are about 10 separate sql queries that use 
>> the oracle system tables (listed below).   A quick fix would be to 
>> supply an Oracle.pm and a PostgreSQL.pm which have methods that 
>> provide the correct sql for those queries.   IF postgres has parallel 
>> tables, then this should be trivial.  if not...?    here are the 
>> tables used:
>>
>> all_sequences
>> all_cons_columns
>> all_constraints
>> all_tab_columns
>> all_views
>>  
>>
>
> I am joining this discussion late, but would like to get involved as
> soon as possible in order to get GUS up and running here at Princeton.
> on PostgreSQL 7.3 (is that what others are using?) Steve and Angel,
> have either of you looked into the ora2pg perl module?  It is at
> http://www.samse.fr/GPL/ora2pg/ and requires an Oracle connection
> in order to run.
>
> In response to Steve's identification of the Oracle metadata queries
> which need to be converted, I have completed and tested all of them
> and only have trouble with this one from DbiTable.pm:
>
>        select column_name, data_type, nullable, column_id,
>                data_precision, data_length, data_scale
>        from    all_tab_columns
>        where   table_name = '$table_name' and owner = '$owner'
>        order by column_id
>
> Here is my best attempt at a conversion:
>
>        select  a.attname, t.typname,
>                case when a.attnotnull then 'N' else 'Y' end as nullable,
>                a.attnum,
>                case when t.typlen < 1 then null else t.typlen end as 
> data_precision,
>                case when a.atttypmod < 0 then null else a.atttypmod-4 
> end  as data_length,
>                null as data_scale
>        from    pg_attribute a, pg_class c, pg_type t
>        where    a.attrelid = c.oid and c.relname = 'assay' and 
> a.atttypid = t.oid and a.attnum > 0
>        order by a.attnum;
>
> Using RAD3.assay, the Oracle results yield the following:
>
>
> COLUMN_NAME                   DATA_TYPE  NULLABLE col_id  precision 
> length  scale
> ----------------------------  ---------  -------- ------  --------- 
> ------  ----------
> ASSAY_ID                      NUMBER     N        1       8         
> 22      0
> ARRAY_ID                      NUMBER     N        2       4         
> 22      0
> PROTOCOL_ID                   NUMBER     Y        3       10        
> 22      0
> ASSAY_DATE                    DATE       Y        4       null      
> 7       null
> ARRAY_IDENTIFIER              VARCHAR2   Y        5       null      
> 100     null
> ARRAY_BATCH_IDENTIFIER        VARCHAR2   Y        6       null      
> 100     null
> OPERATOR_ID                   NUMBER     N        7       10        
> 22      0
> EXTERNAL_DATABASE_RELEASE_ID  NUMBER     Y        8       5         
> 22      0
> SOURCE_ID                     VARCHAR2   Y        9       null      
> 50      null
> NAME                          VARCHAR2   Y        10      null      
> 100     null
> DESCRIPTION                   VARCHAR2   Y        11      null      
> 500     null
> MODIFICATION_DATE             DATE       N        12      null      
> 7       null
> USER_READ                     NUMBER     N        13      1         
> 22      0
> USER_WRITE                    NUMBER     N        14      1         
> 22      0
> GROUP_READ                    NUMBER     N        15      1         
> 22      0
> GROUP_WRITE                   NUMBER     N        16      1         
> 22      0
> OTHER_READ                    NUMBER     N        17      1         
> 22      0
> OTHER_WRITE                   NUMBER     N        18      1         
> 22      0
> ROW_USER_ID                   NUMBER     N        19      12        
> 22      0
> ROW_GROUP_ID                  NUMBER     N        20      3         
> 22      0
> ROW_PROJECT_ID                NUMBER     N        21      4         
> 22      0
> ROW_ALG_INVOCATION_ID         NUMBER     N        22      12        
> 22      0
>
> while the PostgreSQL results yield:
>
>           attname            | typname | nullable | attnum | 
> data_precision | data_length | data_scale
> ------------------------------+---------+----------+--------+----------------+-------------+------------ 
>
> assay_id                     | int8    | N        |      1 
> |              8 |             |
> array_id                     | int4    | N        |      2 
> |              4 |             |
> protocol_id                  | int8    | Y        |      3 
> |              8 |             |
> assay_date                   | date    | Y        |      4 
> |              4 |             |
> array_identifier             | varchar | Y        |      5 
> |                |         100 |
> array_batch_identifier       | varchar | Y        |      6 
> |                |         100 |
> operator_id                  | int8    | N        |      7 
> |              8 |             |
> external_database_release_id | int4    | Y        |      8 
> |              4 |             |
> source_id                    | varchar | Y        |      9 
> |                |          50 |
> name                         | varchar | Y        |     10 
> |                |         100 |
> description                  | varchar | Y        |     11 
> |                |         500 |
> modification_date            | date    | N        |     12 
> |              4 |             |
> user_read                    | int2    | N        |     13 
> |              2 |             |
> user_write                   | int2    | N        |     14 
> |              2 |             |
> group_read                   | int2    | N        |     15 
> |              2 |             |
> group_write                  | int2    | N        |     16 
> |              2 |             |
> other_read                   | int2    | N        |     17 
> |              2 |             |
> other_write                  | int2    | N        |     18 
> |              2 |             |
> row_user_id                  | int8    | N        |     19 
> |              8 |             |
> row_group_id                 | int4    | N        |     20 
> |              4 |             |
> row_project_id               | int4    | N        |     21 
> |              4 |             |
> row_alg_invocation_id        | int8    | N        |     22 
> |              8 |             |
>
> The PostgreSQL numeric data types are different from those in Oracle 
> and this
> raises the issue of how to convert them.  There is no equivalent of 
> the NUMBER(10)
> or NUMBER(12) in the assay table above, for example, in PostgreSQL.  
> The common
> integer types are int2, int4 and int8.  There is a numeric type which 
> supports
> precision and scale but it is much slower than the integer types.  
> Hence, we
> *must* come to agreement on this conversion issue.  Do I hear any 
> volunteers?
>
> Here are the other queries, successfully converted.
> ============
> DbiTable.pm
> ============
> Oracle:
>
>        select    text
>        from    all_views
>        where    owner = '$owner' and
>                view_name = '$table'
>
>
> PostgreSQL:
>
>        select    definition
>        from    pg_views
>        where    schemaname = '$owner' and
>                viewname = '$table'
>
> -------------------------------------------
>
> Oracle:
>
>        select    ac.owner,                 accs.table_name,
>                accs.column_name,
>                accr.owner,
>                accr.table_name,
>                accr.column_name
>        from    all_cons_columns accr,
>                all_cons_columns accs,
>                all_constraints ac
>        where    accs.owner = '$owner' and
>                ac.table_name = '$table' and
>                ac.owner = '$owner' and
>                ac.constraint_type = 'R' and
>                accr.constraint_name = ac.r_constraint_name and
>                ac.r_owner = accr.owner and
>                accs.constraint_name = ac.constraint_name
>       PostgreSQL:
>
>        select  n1.nspname,
>                r1.relname,
>                a1.attname,
>                n2.nspname,
>                r2.relname,
>                a2.attname
>        from    pg_namespace n1,
>                pg_namespace n2,
>                pg_class r1,
>                pg_class r2,
>                pg_attribute a1,
>                pg_attribute a2,
>                pg_constraint c
>        where   r1.relname = '$table' and
>                n1.nspname = '$owner' and
>                r1.relnamespace = n1.oid and
>                r1.oid = c.conrelid and
>                r1.oid = a1.attrelid and
>                c.contype = 'f' and
>                c.confrelid = r2.oid and
>                r2.relnamespace = n2.oid and
>                c.conkey[1] = a1.attnum and
>                c.confkey[1] = a2.attnum and
>                a2.attrelid = r2.oid
>
> -------------------------------------------
>
> Oracle:
>
>        select    distinct acc.column_name
>        from    all_cons_columns acc, all_constraints ac
>        where    acc.owner = '$owner' and
>                ac.table_name = '$queryTable' and
>                ac.constraint_type = 'P' and
>                acc.constraint_name = ac.constraint_name
>
> PostgreSQL:
>
>        select    distinct a.attname           from    pg_namespace n,
>                pg_class r,
>                pg_attribute a,
>                pg_constraint c
>        where    n.nspname = '$owner' and
>                r.relname = '$table' and
>                n.oid = r.relnamespace and
>                r.oid = a.attrelid and
>                r.oid = c.conrelid and
>                c.contype = 'p' and
>                c.conkey[1] = a.attnum;
>
> ============
> DbiDatabase.pm
> ============
>
> Oracle:
>
>        select    sequence_owner,sequence_name
>        from    all_sequences
>
> PostgreSQL:
>
>        select    schemaname, relname
>        from    pg_statio_user_sequences;
>
>
> -------------------------------------------
>
> Oracle:
>
>        select    
> acon.owner,acc1.owner,acc1.table_name,acc1.column_name, 
> acon.table_name ,acc2.column_name
>        from    all_cons_columns acc1, all_constraints 
> acon,all_cons_columns acc2
>        where    acon.r_constraint_name = acc1.constraint_name and
>                acc1.owner = '$owner' and
>                acon.r_owner = acc1.owner and
>                acc2.constraint_name = acon.constraint_name and
>                acc2.owner = acon.owner
>               PostgreSQL:
>
>        select  n1.nspname,
>                n2.nspname,
>                r1.relname,
>                a1.attname,
>                r2.relname,
>                a2.attname
>        from    pg_namespace n1,
>                pg_namespace n2,
>                pg_class r1,
>                pg_class r2,
>                pg_attribute a1,
>                pg_attribute a2,
>                pg_constraint c
>        where   r1.nspname = '$owner' and
>                r1.relnamespace = n1.oid and
>                r1.oid = c.conrelid and
>                r1.oid = a1.attrelid and
>                c.contype = 'f' and
>                c.confrelid = r2.oid and
>                r2.relnamespace = n2.oid and
>                c.conkey[1] = a1.attnum and
>                c.confkey[1] = a2.attnum and
>                a2.attrelid = r2.oid
>
> The next topic to tackle is CLOBs.
>
>
> Laurie
>
> -------------------------------
> Laurie Kramer
> Department of Molecular Biology
> Princeton University
> lk...@mo...
> 609.258.5657
>
>
>
>
>
>
> -------------------------------------------------------
> SF.Net is sponsored by: Speed Start Your Linux Apps Now.
> Build and deploy apps & Web services for Linux with
> a free DVD software kit from IBM. Click Now!
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> _______________________________________________
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> Gus...@li...
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Re: [Gusdev-gusdev] GUS to PostgreSQL

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

On Feb 20, 2004, at 3:46 PM, Laurie Kramer wrote:
>
> I am joining this discussion late, but would like to get involved as
> soon as possible in order to get GUS up and running here at Princeton.
> on PostgreSQL 7.3 (is that what others are using?) Steve and Angel,
> have either of you looked into the ora2pg perl module?  It is at
> http://www.samse.fr/GPL/ora2pg/ and requires an Oracle connection
> in order to run.
>
No I have not. When I get some time next week, I'll look into it.

>
> The PostgreSQL numeric data types are different from those in Oracle 
> and this
> raises the issue of how to convert them.  There is no equivalent of 
> the NUMBER(10)
> or NUMBER(12) in the assay table above, for example, in PostgreSQL.  
> The common
> integer types are int2, int4 and int8.  There is a numeric type which 
> supports
> precision and scale but it is much slower than the integer types.  
> Hence, we
> *must* come to agreement on this conversion issue.  Do I hear any 
> volunteers?
>
We use NUMBER mainly for integers, so one of the int types would do. 
What is the precision of these ints? Are these signed ints?
  -99 > int2 > +99

BTW thanks very much for the converted SQL.

Angel

Re: [Gusdev-gusdev] GUS to PostgreSQL

[Laurie K. <lk...@mo...>]

Steve wrote on Feb 13:

>ok, to follow on this with a new subject heading...
>
>For those groups that are gearing up to port GUS to PostgreSQL, here are 
>some quick thoughts on getting started.
>
>The two main tasks, to start with, I think, are:
>   - porting the schema creation scripts to postgres
>   - remove the oracle dependencies from the perl object layer
>
>Porting the Schema
>As mentioned below, one way to go here is using a system-neutral syntax 
>(xml) to create the schemas.   I think this should be the long term 
>goal.  But, for a quick solution, there must be some way for us to 
>manually transform the existing oracle-specific syntax to postgres.   I 
>envision some kind of ad hoc scripts to do the transform.   This 
>shouldn't be too big a deal.
>
>I would say the first step is to identify what the transforms will be.
>
>
>Object Layer
>I just did a quick look in the object layer code (Perl).  (we can defer 
>for now on the java object layer since its not in wide use).   Only two 
>files seem to use oracle system tables, both in 
> $PROJECT_HOME/GUS/ObjRelP/lib/perl:  DbiTable.pm and DbiDatabase.pm.   
> There are about 10 separate sql queries that use the oracle system 
>tables (listed below).   A quick fix would be to supply an Oracle.pm and 
>a PostgreSQL.pm which have methods that provide the correct sql for 
>those queries.   IF postgres has parallel tables, then this should be 
>trivial.  if not...?    here are the tables used:
>
>all_sequences
>all_cons_columns
>all_constraints
>all_tab_columns
>all_views
>  
>

I am joining this discussion late, but would like to get involved as
soon as possible in order to get GUS up and running here at Princeton.
on PostgreSQL 7.3 (is that what others are using?) Steve and Angel,
have either of you looked into the ora2pg perl module?  It is at
http://www.samse.fr/GPL/ora2pg/ and requires an Oracle connection
in order to run.

In response to Steve's identification of the Oracle metadata queries
which need to be converted, I have completed and tested all of them
and only have trouble with this one from DbiTable.pm:

        select column_name, data_type, nullable, column_id,
                data_precision, data_length, data_scale
        from    all_tab_columns
        where   table_name = '$table_name' and owner = '$owner'
        order by column_id

Here is my best attempt at a conversion:

        select  a.attname, t.typname,
                case when a.attnotnull then 'N' else 'Y' end as nullable,
                a.attnum,
                case when t.typlen < 1 then null else t.typlen end as 
data_precision,
                case when a.atttypmod < 0 then null else a.atttypmod-4 
end  as data_length,
                null as data_scale
        from    pg_attribute a, pg_class c, pg_type t
        where    a.attrelid = c.oid and c.relname = 'assay' and 
a.atttypid = t.oid and a.attnum > 0
        order by a.attnum;

Using RAD3.assay, the Oracle results yield the following:


COLUMN_NAME                   DATA_TYPE  NULLABLE col_id  precision 
length  scale
----------------------------  ---------  -------- ------  --------- 
------  ----------
ASSAY_ID                      NUMBER     N        1       8         
22      0
ARRAY_ID                      NUMBER     N        2       4         
22      0
PROTOCOL_ID                   NUMBER     Y        3       10        
22      0
ASSAY_DATE                    DATE       Y        4       null      
7       null
ARRAY_IDENTIFIER              VARCHAR2   Y        5       null      
100     null
ARRAY_BATCH_IDENTIFIER        VARCHAR2   Y        6       null      
100     null
OPERATOR_ID                   NUMBER     N        7       10        
22      0
EXTERNAL_DATABASE_RELEASE_ID  NUMBER     Y        8       5         
22      0
SOURCE_ID                     VARCHAR2   Y        9       null      
50      null
NAME                          VARCHAR2   Y        10      null      
100     null
DESCRIPTION                   VARCHAR2   Y        11      null      
500     null
MODIFICATION_DATE             DATE       N        12      null      
7       null
USER_READ                     NUMBER     N        13      1         
22      0
USER_WRITE                    NUMBER     N        14      1         
22      0
GROUP_READ                    NUMBER     N        15      1         
22      0
GROUP_WRITE                   NUMBER     N        16      1         
22      0
OTHER_READ                    NUMBER     N        17      1         
22      0
OTHER_WRITE                   NUMBER     N        18      1         
22      0
ROW_USER_ID                   NUMBER     N        19      12        
22      0
ROW_GROUP_ID                  NUMBER     N        20      3         
22      0
ROW_PROJECT_ID                NUMBER     N        21      4         
22      0
ROW_ALG_INVOCATION_ID         NUMBER     N        22      12        
22      0

while the PostgreSQL results yield:

           attname            | typname | nullable | attnum | 
data_precision | data_length | data_scale
------------------------------+---------+----------+--------+----------------+-------------+------------
 assay_id                     | int8    | N        |      1 
|              8 |             |
 array_id                     | int4    | N        |      2 
|              4 |             |
 protocol_id                  | int8    | Y        |      3 
|              8 |             |
 assay_date                   | date    | Y        |      4 
|              4 |             |
 array_identifier             | varchar | Y        |      5 
|                |         100 |
 array_batch_identifier       | varchar | Y        |      6 
|                |         100 |
 operator_id                  | int8    | N        |      7 
|              8 |             |
 external_database_release_id | int4    | Y        |      8 
|              4 |             |
 source_id                    | varchar | Y        |      9 
|                |          50 |
 name                         | varchar | Y        |     10 
|                |         100 |
 description                  | varchar | Y        |     11 
|                |         500 |
 modification_date            | date    | N        |     12 
|              4 |             |
 user_read                    | int2    | N        |     13 
|              2 |             |
 user_write                   | int2    | N        |     14 
|              2 |             |
 group_read                   | int2    | N        |     15 
|              2 |             |
 group_write                  | int2    | N        |     16 
|              2 |             |
 other_read                   | int2    | N        |     17 
|              2 |             |
 other_write                  | int2    | N        |     18 
|              2 |             |
 row_user_id                  | int8    | N        |     19 
|              8 |             |
 row_group_id                 | int4    | N        |     20 
|              4 |             |
 row_project_id               | int4    | N        |     21 
|              4 |             |
 row_alg_invocation_id        | int8    | N        |     22 
|              8 |             |

The PostgreSQL numeric data types are different from those in Oracle and 
this
raises the issue of how to convert them.  There is no equivalent of the 
NUMBER(10)
or NUMBER(12) in the assay table above, for example, in PostgreSQL.  The 
common
integer types are int2, int4 and int8.  There is a numeric type which 
supports
precision and scale but it is much slower than the integer types.  
Hence, we
*must* come to agreement on this conversion issue.  Do I hear any 
volunteers?

Here are the other queries, successfully converted. 

============
DbiTable.pm
============
Oracle:

        select    text
        from    all_views
        where    owner = '$owner' and
                view_name = '$table'


PostgreSQL:

        select    definition
        from    pg_views
        where    schemaname = '$owner' and
                viewname = '$table'

-------------------------------------------

Oracle:

        select    ac.owner,  
                accs.table_name,
                accs.column_name,
                accr.owner,
                accr.table_name,
                accr.column_name
        from    all_cons_columns accr,
                all_cons_columns accs,
                all_constraints ac
        where    accs.owner = '$owner' and
                ac.table_name = '$table' and
                ac.owner = '$owner' and
                ac.constraint_type = 'R' and
                accr.constraint_name = ac.r_constraint_name and
                ac.r_owner = accr.owner and
                accs.constraint_name = ac.constraint_name
       
PostgreSQL:

        select  n1.nspname,
                r1.relname,
                a1.attname,
                n2.nspname,
                r2.relname,
                a2.attname
        from    pg_namespace n1,
                pg_namespace n2,
                pg_class r1,
                pg_class r2,
                pg_attribute a1,
                pg_attribute a2,
                pg_constraint c
        where   r1.relname = '$table' and
                n1.nspname = '$owner' and
                r1.relnamespace = n1.oid and
                r1.oid = c.conrelid and
                r1.oid = a1.attrelid and
                c.contype = 'f' and
                c.confrelid = r2.oid and
                r2.relnamespace = n2.oid and
                c.conkey[1] = a1.attnum and
                c.confkey[1] = a2.attnum and
                a2.attrelid = r2.oid

-------------------------------------------

Oracle:

        select    distinct acc.column_name
        from    all_cons_columns acc, all_constraints ac
        where    acc.owner = '$owner' and
                ac.table_name = '$queryTable' and
                ac.constraint_type = 'P' and
                acc.constraint_name = ac.constraint_name

PostgreSQL:

        select    distinct a.attname    
        from    pg_namespace n,
                pg_class r,
                pg_attribute a,
                pg_constraint c
        where    n.nspname = '$owner' and
                r.relname = '$table' and
                n.oid = r.relnamespace and
                r.oid = a.attrelid and
                r.oid = c.conrelid and
                c.contype = 'p' and
                c.conkey[1] = a.attnum;

============
DbiDatabase.pm
============

Oracle:

        select    sequence_owner,sequence_name
        from    all_sequences

PostgreSQL:

        select    schemaname, relname
        from    pg_statio_user_sequences;


-------------------------------------------

Oracle:

        select    
acon.owner,acc1.owner,acc1.table_name,acc1.column_name, acon.table_name 
,acc2.column_name
        from    all_cons_columns acc1, all_constraints 
acon,all_cons_columns acc2
        where    acon.r_constraint_name = acc1.constraint_name and
                acc1.owner = '$owner' and
                acon.r_owner = acc1.owner and
                acc2.constraint_name = acon.constraint_name and
                acc2.owner = acon.owner
               
PostgreSQL:

        select  n1.nspname,
                n2.nspname,
                r1.relname,
                a1.attname,
                r2.relname,
                a2.attname
        from    pg_namespace n1,
                pg_namespace n2,
                pg_class r1,
                pg_class r2,
                pg_attribute a1,
                pg_attribute a2,
                pg_constraint c
        where   r1.nspname = '$owner' and
                r1.relnamespace = n1.oid and
                r1.oid = c.conrelid and
                r1.oid = a1.attrelid and
                c.contype = 'f' and
                c.confrelid = r2.oid and
                r2.relnamespace = n2.oid and
                c.conkey[1] = a1.attnum and
                c.confkey[1] = a2.attnum and
                a2.attrelid = r2.oid

The next topic to tackle is CLOBs.


Laurie

-------------------------------
Laurie Kramer
Department of Molecular Biology
Princeton University
lk...@mo...
609.258.5657

[Gusdev-gusdev] WDKinstall PageFormat options

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

Hello-

The WDK-classic provides to the user the htdocs/cgi-bins/etc for the
allgenes.org website, and the java file AllgenesPageFormatter for jsp
results.  We will need to have a CTEGDPageFormatter here at CTEGD, and
would like it to more closely resemble PlasmoDB than allgenes.  I realize
that the PlasmoDBPageFormatter is provided with the WDK-classic, but the
htdocs/etc needed for it are not.  Is there any way to get ahold of those?

Thanks,
Michael Luchtan

Re: [Gusdev-gusdev] GUS: unique table names

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

Here is my opinion:
The instance where a table will have a FK to two tables with the same 
name but different schemas is going to be rare. I think analogous to 
the views having two foreign keys to different subclass views of the 
same table. Probably even rarer.

Make the common case fast and easy. Keep the "getGene()" syntax. When 
there is such a clash, then use the schema name "getDotsGene()" & 
"getFooGene()"

The ability to have a modular schema is more important in my opinion.

cheers,
Angel
On Feb 17, 2004, at 6:58 PM, Steve Fischer wrote:

> folks-
>
> i think that we should consider a rule about GUS table names:
>
>   "table names are unique across schema spaces"
>
> there are pros and cons here.
>
> pros:
>   - this way, in our object layer, we can have simpler accessor names, 
> such as getGene().   Otherwise, we need to have getDoTSGene() (yuck)
>   - this may help us port, if we need to, to systems which don't 
> support schema spaces
>
> cons:
>   - the obvious one:  schema spaces are no longer truly modular.  the 
> must be aware of other schema spaces that are or *might be* used in 
> the same system.
>
> Comments???
>
> Which do people see as the lesser of the two evils?
>
> steve
>
>
>
> -------------------------------------------------------
> SF.Net is sponsored by: Speed Start Your Linux Apps Now.
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[Gusdev-gusdev] GUS: unique table names

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

folks-

i think that we should consider a rule about GUS table names:

   "table names are unique across schema spaces"

there are pros and cons here.

pros:
   - this way, in our object layer, we can have simpler accessor names, 
such as getGene().   Otherwise, we need to have getDoTSGene() (yuck)
   - this may help us port, if we need to, to systems which don't 
support schema spaces

cons:
   - the obvious one:  schema spaces are no longer truly modular.  the 
must be aware of other schema spaces that are or *might be* used in the 
same system.

Comments???

Which do people see as the lesser of the two evils?

steve

[Gusdev-gusdev] GUS 3.2 tentative release

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

Hey folks,
I just dumped the GUS schema again, and went through all of the files to 
fix errors here and there.

I tagged GUS/Model with "GUS_3_2" so you can check out the changes, 
surmised below:

GUS/DBAdmin/bin/dumpSchema.pl
    Changed a typo that caused the --target-index-tablespace-list option 
to use values from --target-tablespace-list. Not really a part of the 
release, but if you use this, please update.


GUS/Model/schema/oracle:
    Core:
          Added a few entries into TableInfo
          Added WorkFlowNode superclass view

    Sres:
        No schema changes. Just date update on the dump files
    DoTS:
        Added some tables for RejectedMotif  that the annotators use to 
say that particular motif similarities
         are of no predictive value and they should be ignored.
    RAD: Added some new ElementResult views. Removed the constraints on 
the superclass views.
             Fix the remaining references to the string 'RAD3' in all files
    TESS: No schema changes
    App: No schema changes

  GUS/Model/schema/VERSION : Updated version to "3.2"

Note, I call this a tentative release b/c the GUS/RAD component has not 
yet been updated to use a substitution string for the "RAD" schema 
space. Also you will note that the files are still prefixed with  'rad3' 
. Hence for the GUS/Model/config/schema.prop.sample file the default 
substitution name is still "RAD3". Hopefully one day this will all be an 
issue of the past.

Also, there may or may not be some funny business here and there, 
although I tested out a build of GUS (no schema install) and everything 
seems A-OK. Email any errors to the list. I'll keep testing as time allows.

Thanks to Mathew for sending me the errors and Fidel for continually 
egging me on to commit the changes. Appreciate it.

Angel

Re: [Gusdev-gusdev] bug in SubmitRow

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

Thomas-

Yes, i think you are correct.  thanks for clarifying.

I will improve the error message.  it should say:
 
Error:  You have provided primary key "sequence_type_id = 1"  which does 
not exist.  When inserting, do not provide a primary key (one will be 
generated automatically).  When updating, provide an existing primary key.

steve

Thomas Otto wrote:

> Hi,
>
> I had the same problem... the thing is, that the primary key will be 
> set automatically, so you cannot set it. If the primary key exists, a 
> update will be done.
> So just write command without the primarykey (sequence_type_id).
>
> Cheers,
> Thomas
>
> Fidel Salas wrote:
>
>> Steve,
>>
>> Revision 1.7, I believe, has a bug not found in revision 1.4.
>> It is expressed when one tries to insert a row with an id that does
>> not yet exist in the database.  The bug is the updateRow method.  See
>> the following insert invocation:
>>
>> ga GUS::Common::Plugin::SubmitRow --tablename DoTS::SequenceType 
>> --attrlist 
>> sequence_type_id,nucleotide_type,sub_type,strand,hierarchy,parent_sequence_type_id,name,description 
>> --valuelist "1^^^DNA^^^null^^^null^^^1^^^1^^^DNA^^^unkown 
>> strandedness" --commit
>> Reading properties from 
>> /home/fisal/GUS/dev/gushome/config/GUS-PluginMgr.prop
>> Reading properties from /home/fisal/GUS/dev/.gus.properties
>> Tue Feb 17 12:19:19 2004    ALGINVID    78
>> Tue Feb 17 12:19:19 2004    COMMIT    commit on
>>
>> ERROR: Can't update.  No row found with primary key sequence_type_id = 1
>>
>>
>> Anyway,  I went back to using revision 1.4.
>>
>> Fidel
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net is sponsored by: Speed Start Your Linux Apps Now.
>> Build and deploy apps & Web services for Linux with
>> a free DVD software kit from IBM. Click Now!
>> http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>  
>>
>
>
>
>
> -------------------------------------------------------
> SF.Net is sponsored by: Speed Start Your Linux Apps Now.
> Build and deploy apps & Web services for Linux with
> a free DVD software kit from IBM. Click Now!
> http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] bug in SubmitRow

[Thomas O. <ot...@fi...>]

Hi,

I had the same problem... the thing is, that the primary key will be set 
automatically, so you cannot set it. If the primary key exists, a update 
will be done.
So just write command without the primarykey (sequence_type_id).

Cheers,
Thomas

Fidel Salas wrote:

>Steve,
>
>Revision 1.7, I believe, has a bug not found in revision 1.4.
>It is expressed when one tries to insert a row with an id that does
>not yet exist in the database.  The bug is the updateRow method.  See
>the following insert invocation:
>
>ga GUS::Common::Plugin::SubmitRow --tablename DoTS::SequenceType --attrlist sequence_type_id,nucleotide_type,sub_type,strand,hierarchy,parent_sequence_type_id,name,description --valuelist "1^^^DNA^^^null^^^null^^^1^^^1^^^DNA^^^unkown strandedness" --commit
>Reading properties from /home/fisal/GUS/dev/gushome/config/GUS-PluginMgr.prop
>Reading properties from /home/fisal/GUS/dev/.gus.properties
>Tue Feb 17 12:19:19 2004	ALGINVID	78
>Tue Feb 17 12:19:19 2004	COMMIT	commit on
>
>ERROR: Can't update.  No row found with primary key sequence_type_id = 1
>
>
>Anyway,  I went back to using revision 1.4.
>
>Fidel
>
>
>
>-------------------------------------------------------
>SF.Net is sponsored by: Speed Start Your Linux Apps Now.
>Build and deploy apps & Web services for Linux with
>a free DVD software kit from IBM. Click Now!
>http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

[Gusdev-gusdev] bug in SubmitRow

[Fidel S. <fi...@vb...>]

Steve,

Revision 1.7, I believe, has a bug not found in revision 1.4.
It is expressed when one tries to insert a row with an id that does
not yet exist in the database.  The bug is the updateRow method.  See
the following insert invocation:

ga GUS::Common::Plugin::SubmitRow --tablename DoTS::SequenceType --attrlist sequence_type_id,nucleotide_type,sub_type,strand,hierarchy,parent_sequence_type_id,name,description --valuelist "1^^^DNA^^^null^^^null^^^1^^^1^^^DNA^^^unkown strandedness" --commit
Reading properties from /home/fisal/GUS/dev/gushome/config/GUS-PluginMgr.prop
Reading properties from /home/fisal/GUS/dev/.gus.properties
Tue Feb 17 12:19:19 2004	ALGINVID	78
Tue Feb 17 12:19:19 2004	COMMIT	commit on

ERROR: Can't update.  No row found with primary key sequence_type_id = 1


Anyway,  I went back to using revision 1.4.

Fidel

[Gusdev-gusdev] Re: the nasty java package question

[Adrian R. T. <ar...@sa...>]

As probably the third largest sponsor of Java, I guess Oracle are allowed to
break the rules sometimes!

The only place it really makes a difference is in imports, ie not very often.
(When I come across packages that don't obey the JLS package naming rules it
always rings a little alarm bell in the back of my head.) For the sake of 4
letters I'd keep the org. 

A related question - why org.gusdev rather than org.gusdb?


> folks-
> 
> i am gearing up to right my first WDK java code (xml parser using 
> digester).  this is also my first java code for GUS.
> 
> and so, i am confronted with the nasty package name question.
> 
> officially, this is kind of what i think the package name should be, 
> but, its so darn long:
>    org.gusdev.gus.wdk.model.config.Parser;
> 
> ie, organization_type.organization.project.component.subcomponent.package
> 
> note that while we don't yet, we do expect to have other projects, such 
> as rad, be under the gusdev umbrella.

But presumably the web interface will want to talk to rad etc. Will there be a
org.gusdev.rad.wdk... etc or something else?

Adrian

> 
> i did a quick surf to see if others are having this problem.  here is 
> the first package name i stumbled on:
> 
> oracle.security.rdbms.server.AppCtx.AppCtxManager
> 
> I suppose we could drop the leading org:
> 
>   gusdev.gus.wdk.model.config.Parser
> 
> any ideas?
> 

[Gusdev-gusdev] e-mail Test - please ignore

[Adrian R. T. <ar...@sa...>]

Just a quick test - sorry

[Gusdev-gusdev] change to build system--better java compiling

[Dave B. <db...@pc...>]

Folks--

I checked in a small change to the build system to better handle java 
compiling.  After you do a cvs update on the ant build.xml files (after 
the appropriate changes have been made--see below), from now on, when you 
want to build a component that has to compile java code, simply add the 
'-compileJava' flag to the build command.

Previously, when you wanted to build a component that had java 
code to compile, you had to go into the build.xml file and uncomment a 
line that, by default, turned off java compiling.  I have updated the 
GUS/Model and GUS/ObjRelJ components so that they no longer have this 
behavior.  There still may be components that compile java code that other 
people are working with that need updates, so whoever is in charge of build system 
administration for those components should make the appropriate changes  
(drop me a line if they're not obvious.)

thanks,
Dave

[Gusdev-gusdev] SubmitRow with cvs revision '1.7' and cvs

[Fidel S. <fi...@vb...>]

Steve,

The pm file is missing a closing parens on line 111.

Fidel

[Gusdev-gusdev] GUS to PostgreSQL

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

ok, to follow on this with a new subject heading...

For those groups that are gearing up to port GUS to PostgreSQL, here are 
some quick thoughts on getting started.

The two main tasks, to start with, I think, are:
   - porting the schema creation scripts to postgres
   - remove the oracle dependencies from the perl object layer

Porting the Schema
As mentioned below, one way to go here is using a system-neutral syntax 
(xml) to create the schemas.   I think this should be the long term 
goal.  But, for a quick solution, there must be some way for us to 
manually transform the existing oracle-specific syntax to postgres.   I 
envision some kind of ad hoc scripts to do the transform.   This 
shouldn't be too big a deal.

I would say the first step is to identify what the transforms will be.


Object Layer
I just did a quick look in the object layer code (Perl).  (we can defer 
for now on the java object layer since its not in wide use).   Only two 
files seem to use oracle system tables, both in 
 $PROJECT_HOME/GUS/ObjRelP/lib/perl:  DbiTable.pm and DbiDatabase.pm.   
 There are about 10 separate sql queries that use the oracle system 
tables (listed below).   A quick fix would be to supply an Oracle.pm and 
a PostgreSQL.pm which have methods that provide the correct sql for 
those queries.   IF postgres has parallel tables, then this should be 
trivial.  if not...?    here are the tables used:

all_sequences
all_cons_columns
all_constraints
all_tab_columns
all_views


steve

:
Angel Pizarro wrote:

> Steve,
> This is a very accurate and complete synopsis of the issues we have 
> discussed so far. Without actually starting the project, I don't 
> foresee us coming up with anything else.
>
> As for translation between DB platforms, there is a Sourceforge.net 
> project that Allen Day belongs to named SQLFairy. See more about it at 
> http://sqlfairy.sourceforge.net/
>
> They claim to translate between Oracle and PostgreSQL, but this has 
> not worked in practice for me when I tried to translate the GUS schema 
> files to postgresql. Part of the problem is that we separate tables, 
> views and constraints into their own files in addition to separate 
> file groups for schemas. It also had trouble with multi-line comments.
>
> They have listed a platform independent XML syntax, but they as yet do 
> not have a formal DTD or XML schema (I asked already) . They said they 
> were willing to formalize on an XML schema if we provide it and is 
> close to what they have already. I don't see any reason to re-invent 
> the wheel here.
>
> Angel
>
> Steve Fischer wrote:
>
>> (Cesare and Giuseppe, are you on the gusdev mailing list?  If not, 
>> you can subscribe at: 
>> http://lists.sourceforge.net/lists/listinfo/gusdev-gusdev)
>>
>> Folks-
>>
>> Here is a quick outline of what might need to be done to make GUS 
>> RDBMS independent.    I discuss the two major subsystems of GUS:  the 
>> schema and the application framework.
>>
>> Please bear in mind that i am not a DB expert.   Comments and 
>> corrections encouraged.
>>
>> GUS Schema
>>   - schema definition.     it appears that different RDBMSs have 
>> differences in their data types and in the way they create tables and 
>> specify constraints.   it seems that this we need to define the 
>> schema in a system neutral syntax, say, xml, and then transform that 
>> into system-specific syntax.   i wonder if there are third party 
>> tools to do this.
>>
>>    - schema spaces.   the definition of the schema currently assumes 
>> "schema name spaces."     for example, we have RAD.Process.    For 
>> systems that don't support this, we may need to define the schema as, 
>> say, RAD_Process.   In other words, prepend the schema name to the 
>> table names.
>>
>>   - schema installation.    this will need to be system-specific, and 
>> will probably be generated by transforming a schema definition in a 
>> neutral syntax
>>
>>
>> GUS Application Framework
>>    - the application framework currently uses DBI and JDBC.   these 
>> are fine.
>>
>>   - the object layer API (and all the code that uses it) assumes that 
>> there is a schema space.   worse still, it hard codes the names as 
>> DoTS, RAD, Core, TESS and SRes.   The changes I envision here are:
>>           - removing hard coded references to schema names, replacing 
>> them with logical names.
>>           - allow the API to *keep* the schema space assumption.    
>> however, inside the object layer, use a RDBMS-specific "driver" to 
>> handle them in a system specific way.   for example, it would use '.' 
>> as the concatenation character for oracle and '_' for mySql.
>>            - the object layer's code generator (generates all the 
>> objects) has a system-specific module for discovering 
>> meta-information about the tables.   this is segregated into system 
>> specific modules.   for any new system, we would need to write new 
>> ones.    note:  any system that we support would need to offer this 
>> meta information somehow!!!!
>>
>>    - sql code.   there is plenty of direct SQL in our application 
>> code and in plugins.   here are the problems:
>>           - Wherever this sql refers to table names, the sql would 
>> need to be modified to get the table names from an API which can 
>> provide them in correct syntax.            - some of the code relies 
>> on system specific optimization directives.   i don't know how we'll 
>> handle this.
>>           - are there any other sql incompatibilities?   how about 
>> join and/or outer join syntax?
>>
>> Any other ideas?
>>
>> Steve
>>
>>
>>
>> Giuseppe Jurman wrote:
>>
>>>> Thanks Elisabetta,
>>>>
>>>> An important question would be also why PostgreSQL and not MySQL, the
>>>> latter appears to be evolved well and have now a good support to
>>>> transactions via InnoDB, etc. I am very inclined to use Gmod and chado
>>>> por our project, but would like to have a final check on the potential
>>>> of GUS before starting things.
>>>>   
>>>
>>>
>>> ITC-irst has started a working group for a full open source version of
>>> GUS, so to allow the substitution of the Oracle database management
>>> system for data tables and relations within GUS with an open source
>>> solution. In principle we are not oriented to the substitution
>>> of Oracle with another specific DMBS.
>>>
>>> It might be worthwhile to consider the possibility to turn DB
>>> independent the whole object-related part of GUS and then choosing the
>>> suitable DB-dedicated driver depending on the user's system. The first
>>> (heavy) step towards this option requires to check the existing code
>>> looking for the Oracle-specific SQL, and then designing an ad-hoc
>>> strategy to transform into either a DBI (better) or into a DBD (here
>>> the choice of the DBMS becomes a constraint).
>>>
>>> An important issue, for us, is how to align the DBD portions of the
>>> code along the next releases of GUS. In this view, we see the need of
>>> a DBI-DBD separation really relevant.
>>>
>>> We would like to perform the Oracle-PostgreSQL conversion in the most
>>> automated way possible. Before, the Oracle proprietary SQL code has to
>>> be somehow moved to the upper Perl Object Layer level, or to a new
>>> Perl Object Layer.
>>>
>>> Comments welcomed
>>>
>>>
>>> Giuseppe Jurman
>>> Cersare Furlanello
>>>
>>>  
>>>
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] Upload AA - aquivalent to GBParser

[Thomas O. <ot...@fi...>]

Hello,

I tried to read for this the forum - but there are some connect problems...

I want to upload AA entries from Genbank. The GBParser seem only to 
upload NA. The ImportPlasmoDBAAFeatures.pm doesn't seem to import all 
the information.

Who can help, or should I program a new module?

Cheers,
Thomas

Re: [Gusdev-gusdev] Re: [Fwd: Porting GUS to a Open SourceDB ?]

[Alberto D. <da...@io...>]

Hi Angel,

We have plans to give a try to the translation between Oracle and
PostgreSQL (or MySQL) using the SQLFairy, could you share some more
details of your tentatives, please ? If you think there are not too many
dependencies, then we would like to help. Please kindly keep Pablo
(pab...@uf...) in the loop.

Thanks and best regards, 

Alberto



On Tue, 2004-02-10 at 14:54, Angel Pizarro wrote:
> Steve,
> This is a very accurate and complete synopsis of the issues we have 
> discussed so far. Without actually starting the project, I don't foresee 
> us coming up with anything else.
> 
> As for translation between DB platforms, there is a Sourceforge.net 
> project that Allen Day belongs to named SQLFairy. See more about it at 
> http://sqlfairy.sourceforge.net/
> 
> They claim to translate between Oracle and PostgreSQL, but this has not 
> worked in practice for me when I tried to translate the GUS schema files 
> to postgresql. Part of the problem is that we separate tables, views and 
> constraints into their own files in addition to separate file groups for 
> schemas. It also had trouble with multi-line comments.
> 
> They have listed a platform independent XML syntax, but they as yet do 
> not have a formal DTD or XML schema (I asked already) . They said they 
> were willing to formalize on an XML schema if we provide it and is close 
> to what they have already. I don't see any reason to re-invent the wheel 
> here.
> 
> Angel
> 
> Steve Fischer wrote:
> 
> > (Cesare and Giuseppe, are you on the gusdev mailing list?  If not, you 
> > can subscribe at: 
> > http://lists.sourceforge.net/lists/listinfo/gusdev-gusdev)
> >
> > Folks-
> >
> > Here is a quick outline of what might need to be done to make GUS 
> > RDBMS independent.    I discuss the two major subsystems of GUS:  the 
> > schema and the application framework.
> >
> > Please bear in mind that i am not a DB expert.   Comments and 
> > corrections encouraged.
> >
> > GUS Schema
> >   - schema definition.     it appears that different RDBMSs have 
> > differences in their data types and in the way they create tables and 
> > specify constraints.   it seems that this we need to define the schema 
> > in a system neutral syntax, say, xml, and then transform that into 
> > system-specific syntax.   i wonder if there are third party tools to 
> > do this.
> >
> >    - schema spaces.   the definition of the schema currently assumes 
> > "schema name spaces."     for example, we have RAD.Process.    For 
> > systems that don't support this, we may need to define the schema as, 
> > say, RAD_Process.   In other words, prepend the schema name to the 
> > table names.
> >
> >   - schema installation.    this will need to be system-specific, and 
> > will probably be generated by transforming a schema definition in a 
> > neutral syntax
> >
> >
> > GUS Application Framework
> >    - the application framework currently uses DBI and JDBC.   these 
> > are fine.
> >
> >   - the object layer API (and all the code that uses it) assumes that 
> > there is a schema space.   worse still, it hard codes the names as 
> > DoTS, RAD, Core, TESS and SRes.   The changes I envision here are:
> >           - removing hard coded references to schema names, replacing 
> > them with logical names.
> >           - allow the API to *keep* the schema space assumption.    
> > however, inside the object layer, use a RDBMS-specific "driver" to 
> > handle them in a system specific way.   for example, it would use '.' 
> > as the concatenation character for oracle and '_' for mySql.
> >            - the object layer's code generator (generates all the 
> > objects) has a system-specific module for discovering meta-information 
> > about the tables.   this is segregated into system specific modules.   
> > for any new system, we would need to write new ones.    note:  any 
> > system that we support would need to offer this meta information 
> > somehow!!!!
> >
> >    - sql code.   there is plenty of direct SQL in our application code 
> > and in plugins.   here are the problems:
> >           - Wherever this sql refers to table names, the sql would 
> > need to be modified to get the table names from an API which can 
> > provide them in correct syntax.  
> >           - some of the code relies on system specific optimization 
> > directives.   i don't know how we'll handle this.
> >           - are there any other sql incompatibilities?   how about 
> > join and/or outer join syntax?
> >
> > Any other ideas?
> >
> > Steve
> >
> >
> >
> > Giuseppe Jurman wrote:
> >
> >>>Thanks Elisabetta,
> >>>
> >>>An important question would be also why PostgreSQL and not MySQL, the
> >>>latter appears to be evolved well and have now a good support to
> >>>transactions via InnoDB, etc. I am very inclined to use Gmod and chado
> >>>por our project, but would like to have a final check on the potential
> >>>of GUS before starting things.
> >>>    
> >>>
> >>
> >>ITC-irst has started a working group for a full open source version of
> >>GUS, so to allow the substitution of the Oracle database management
> >>system for data tables and relations within GUS with an open source
> >>solution. In principle we are not oriented to the substitution
> >>of Oracle with another specific DMBS.
> >>
> >>It might be worthwhile to consider the possibility to turn DB
> >>independent the whole object-related part of GUS and then choosing the
> >>suitable DB-dedicated driver depending on the user's system. The first
> >>(heavy) step towards this option requires to check the existing code
> >>looking for the Oracle-specific SQL, and then designing an ad-hoc
> >>strategy to transform into either a DBI (better) or into a DBD (here
> >>the choice of the DBMS becomes a constraint).
> >>
> >>An important issue, for us, is how to align the DBD portions of the
> >>code along the next releases of GUS. In this view, we see the need of
> >>a DBI-DBD separation really relevant.
> >>
> >>We would like to perform the Oracle-PostgreSQL conversion in the most
> >>automated way possible. Before, the Oracle proprietary SQL code has to
> >>be somehow moved to the upper Perl Object Layer level, or to a new
> >>Perl Object Layer.
> >>
> >>Comments welcomed
> >>
> >>
> >>Giuseppe Jurman
> >>Cersare Furlanello
> >>

Re: [Gusdev-gusdev] Re: [Fwd: Porting GUS to a Open SourceDB ?]

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

I think we need to find out ASAP whether postgres and/or mysql have 
system tables that offer the kind of info we need.

steve

Angel Pizarro wrote:

> Steve,
> This is a very accurate and complete synopsis of the issues we have 
> discussed so far. Without actually starting the project, I don't 
> foresee us coming up with anything else.
>
> As for translation between DB platforms, there is a Sourceforge.net 
> project that Allen Day belongs to named SQLFairy. See more about it at 
> http://sqlfairy.sourceforge.net/
>
> They claim to translate between Oracle and PostgreSQL, but this has 
> not worked in practice for me when I tried to translate the GUS schema 
> files to postgresql. Part of the problem is that we separate tables, 
> views and constraints into their own files in addition to separate 
> file groups for schemas. It also had trouble with multi-line comments.
>
> They have listed a platform independent XML syntax, but they as yet do 
> not have a formal DTD or XML schema (I asked already) . They said they 
> were willing to formalize on an XML schema if we provide it and is 
> close to what they have already. I don't see any reason to re-invent 
> the wheel here.
>
> Angel
>
> Steve Fischer wrote:
>
>> (Cesare and Giuseppe, are you on the gusdev mailing list?  If not, 
>> you can subscribe at: 
>> http://lists.sourceforge.net/lists/listinfo/gusdev-gusdev)
>>
>> Folks-
>>
>> Here is a quick outline of what might need to be done to make GUS 
>> RDBMS independent.    I discuss the two major subsystems of GUS:  the 
>> schema and the application framework.
>>
>> Please bear in mind that i am not a DB expert.   Comments and 
>> corrections encouraged.
>>
>> GUS Schema
>>   - schema definition.     it appears that different RDBMSs have 
>> differences in their data types and in the way they create tables and 
>> specify constraints.   it seems that this we need to define the 
>> schema in a system neutral syntax, say, xml, and then transform that 
>> into system-specific syntax.   i wonder if there are third party 
>> tools to do this.
>>
>>    - schema spaces.   the definition of the schema currently assumes 
>> "schema name spaces."     for example, we have RAD.Process.    For 
>> systems that don't support this, we may need to define the schema as, 
>> say, RAD_Process.   In other words, prepend the schema name to the 
>> table names.
>>
>>   - schema installation.    this will need to be system-specific, and 
>> will probably be generated by transforming a schema definition in a 
>> neutral syntax
>>
>>
>> GUS Application Framework
>>    - the application framework currently uses DBI and JDBC.   these 
>> are fine.
>>
>>   - the object layer API (and all the code that uses it) assumes that 
>> there is a schema space.   worse still, it hard codes the names as 
>> DoTS, RAD, Core, TESS and SRes.   The changes I envision here are:
>>           - removing hard coded references to schema names, replacing 
>> them with logical names.
>>           - allow the API to *keep* the schema space assumption.    
>> however, inside the object layer, use a RDBMS-specific "driver" to 
>> handle them in a system specific way.   for example, it would use '.' 
>> as the concatenation character for oracle and '_' for mySql.
>>            - the object layer's code generator (generates all the 
>> objects) has a system-specific module for discovering 
>> meta-information about the tables.   this is segregated into system 
>> specific modules.   for any new system, we would need to write new 
>> ones.    note:  any system that we support would need to offer this 
>> meta information somehow!!!!
>>
>>    - sql code.   there is plenty of direct SQL in our application 
>> code and in plugins.   here are the problems:
>>           - Wherever this sql refers to table names, the sql would 
>> need to be modified to get the table names from an API which can 
>> provide them in correct syntax.            - some of the code relies 
>> on system specific optimization directives.   i don't know how we'll 
>> handle this.
>>           - are there any other sql incompatibilities?   how about 
>> join and/or outer join syntax?
>>
>> Any other ideas?
>>
>> Steve
>>
>>
>>
>> Giuseppe Jurman wrote:
>>
>>>> Thanks Elisabetta,
>>>>
>>>> An important question would be also why PostgreSQL and not MySQL, the
>>>> latter appears to be evolved well and have now a good support to
>>>> transactions via InnoDB, etc. I am very inclined to use Gmod and chado
>>>> por our project, but would like to have a final check on the potential
>>>> of GUS before starting things.
>>>>   
>>>
>>>
>>> ITC-irst has started a working group for a full open source version of
>>> GUS, so to allow the substitution of the Oracle database management
>>> system for data tables and relations within GUS with an open source
>>> solution. In principle we are not oriented to the substitution
>>> of Oracle with another specific DMBS.
>>>
>>> It might be worthwhile to consider the possibility to turn DB
>>> independent the whole object-related part of GUS and then choosing the
>>> suitable DB-dedicated driver depending on the user's system. The first
>>> (heavy) step towards this option requires to check the existing code
>>> looking for the Oracle-specific SQL, and then designing an ad-hoc
>>> strategy to transform into either a DBI (better) or into a DBD (here
>>> the choice of the DBMS becomes a constraint).
>>>
>>> An important issue, for us, is how to align the DBD portions of the
>>> code along the next releases of GUS. In this view, we see the need of
>>> a DBI-DBD separation really relevant.
>>>
>>> We would like to perform the Oracle-PostgreSQL conversion in the most
>>> automated way possible. Before, the Oracle proprietary SQL code has to
>>> be somehow moved to the upper Perl Object Layer level, or to a new
>>> Perl Object Layer.
>>>
>>> Comments welcomed
>>>
>>>
>>> Giuseppe Jurman
>>> Cersare Furlanello
>>>
>>>  
>>>
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] WDK classic install, setting sql

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

No problem.
BTW, your SQL should enclose the string as in sjingle quotes and 
probably use the 'like' operator, instead of the "="

gseqDescrQ.SQL=select *\
  from dots.ExternalNASequence\
  where external_database_release_id = $$0$$ \
  and source_id like  '$$1$$'

Angel




MICHAEL LUCHTAN wrote:

>Gracies-
>That works, and saves a lot of hunting, I'm sure.
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Tue, 10 Feb 2004, Angel Pizarro wrote:
>
>  
>
>>query parameters (eg. "$$0$$", "$$1$$") get set by the "Params"
>>attribute. In your case :
>>
>>gseqDescrQ.Params=intP
>>
>>where "intP" is defined later in the file as :
>>
>>intP.class=IntParam
>>intP.Prompt=Integer
>>
>>You must define two parameters for "$$0$$" and $$1$$ in your query.
>>
>>gseqDescrQ.SQL=select *\
>>  from dots.ExternalNASequence\
>>  where external_database_release_id = $$0$$ \
>>  and source_id = $$1$$
>>
>>you can keep "intP" for $$0$$, since this is an integer, but source_id is a string, hence you must use a StringParam
>>
>>change "gseqDescrQ.Params=intP" to "gseqDescrQ.Params=intP,stringP" since "stringP" is already defined in this config file as:
>>
>>stringP.class=StringParam
>>stringP.Prompt=Enter a string:
>>stringP.Description=String
>>
>>
>>Angel
>>
>>
>>MICHAEL LUCHTAN wrote:
>>
>>    
>>
>>>Just a quick question, in case anyone knows.  Elsewise I'll still be
>>>digging around:
>>>
>>>In the WDK-classic installation, you supply a configuration file which
>>>specifies which pages you want to serve up, and certain paramaters, like
>>>the sql statement that is used.  I've changed some stuff for
>>>GenomicSequencePage to make it more applicable to CTEGD web apps, and
>>>altered following in the supplied config file:
>>>
>>>gseqDescrQ.SQL=select ena.source_id, ena.name, ena.description, ed.name
>>>dbname, \
>>> tn.name, ena.length \
>>> from dots.ExternalNASequence ena, sres.TaxonName tn,
>>>sres.ExternalDatabase ed, \
>>> sres.ExternalDatabaseRelease edr \
>>> where ena.na_sequence_id = $$0$$ \
>>> and ena.taxon_id = tn.taxon_id \
>>> and tn.name_class = 'scientific name' \
>>> and ena.external_database_release_id = edr.external_database_release_id \
>>> and edr.external_database_id = ed.external_database_id \
>>> and edr.external_database_release_id not in (@PRIVATE_SEQ_DB_IDS@)
>>>
>>>to:
>>>
>>>gseqDescrQ.SQL=select *\
>>> from dots.ExternalNASequence\
>>> where external_database_release_id = $$0$$ \
>>> and source_id = $$1$$
>>>
>>>I know that this gets set, but for some reason the number of parameters
>>>does not change.  Is this hard coded somewhere?  In my error
>>>file(CATALINA.OUT) I get the following:
>>>
>>>Running query:
>>>select *  from dots.ExternalNASequence  where external_database_release_id
>>>= 35   and source_id = $$1$$
>>>java.sql.SQLException: ORA-00911: invalid character
>>>
>>>But I know that I am passing an array with two elements in it, and it is
>>>obviously getting the first one.
>>>
>>>
>>>If any knows why it won't insert the second parameter, please let me know.
>>>
>>>
>>>Michael Luchtan
>>>http://www.cs.uga.edu/~luchtan
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>The SF.Net email is sponsored by EclipseCon 2004
>>>Premiere Conference on Open Tools Development and Integration
>>>See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
>>>http://www.eclipsecon.org/osdn
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>      
>>>
>>    
>>

Re: [Gusdev-gusdev] WDK classic install, setting sql

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

Gracies-
That works, and saves a lot of hunting, I'm sure.

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


On Tue, 10 Feb 2004, Angel Pizarro wrote:

> query parameters (eg. "$$0$$", "$$1$$") get set by the "Params"
> attribute. In your case :
>
> gseqDescrQ.Params=intP
>
> where "intP" is defined later in the file as :
>
> intP.class=IntParam
> intP.Prompt=Integer
>
> You must define two parameters for "$$0$$" and $$1$$ in your query.
>
> gseqDescrQ.SQL=select *\
>   from dots.ExternalNASequence\
>   where external_database_release_id = $$0$$ \
>   and source_id = $$1$$
>
> you can keep "intP" for $$0$$, since this is an integer, but source_id is a string, hence you must use a StringParam
>
> change "gseqDescrQ.Params=intP" to "gseqDescrQ.Params=intP,stringP" since "stringP" is already defined in this config file as:
>
> stringP.class=StringParam
> stringP.Prompt=Enter a string:
> stringP.Description=String
>
>
> Angel
>
>
> MICHAEL LUCHTAN wrote:
>
> >Just a quick question, in case anyone knows.  Elsewise I'll still be
> >digging around:
> >
> >In the WDK-classic installation, you supply a configuration file which
> >specifies which pages you want to serve up, and certain paramaters, like
> >the sql statement that is used.  I've changed some stuff for
> >GenomicSequencePage to make it more applicable to CTEGD web apps, and
> >altered following in the supplied config file:
> >
> >gseqDescrQ.SQL=select ena.source_id, ena.name, ena.description, ed.name
> >dbname, \
> >  tn.name, ena.length \
> >  from dots.ExternalNASequence ena, sres.TaxonName tn,
> >sres.ExternalDatabase ed, \
> >  sres.ExternalDatabaseRelease edr \
> >  where ena.na_sequence_id = $$0$$ \
> >  and ena.taxon_id = tn.taxon_id \
> >  and tn.name_class = 'scientific name' \
> >  and ena.external_database_release_id = edr.external_database_release_id \
> >  and edr.external_database_id = ed.external_database_id \
> >  and edr.external_database_release_id not in (@PRIVATE_SEQ_DB_IDS@)
> >
> >to:
> >
> >gseqDescrQ.SQL=select *\
> >  from dots.ExternalNASequence\
> >  where external_database_release_id = $$0$$ \
> >  and source_id = $$1$$
> >
> >I know that this gets set, but for some reason the number of parameters
> >does not change.  Is this hard coded somewhere?  In my error
> >file(CATALINA.OUT) I get the following:
> >
> >Running query:
> >select *  from dots.ExternalNASequence  where external_database_release_id
> >= 35   and source_id = $$1$$
> >java.sql.SQLException: ORA-00911: invalid character
> >
> >But I know that I am passing an array with two elements in it, and it is
> >obviously getting the first one.
> >
> >
> >If any knows why it won't insert the second parameter, please let me know.
> >
> >
> >Michael Luchtan
> >http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
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>