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From: <jas...@us...> - 2003-04-24 00:18:26
|
Update of /cvsroot/genex/genex-server/Genex/GenexAdmin
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/GenexAdmin
Modified Files:
GenexAdmin.pm
Log Message:
new files
Index: GenexAdmin.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/GenexAdmin/GenexAdmin.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** GenexAdmin.pm 23 Apr 2003 23:58:33 -0000 1.21
--- GenexAdmin.pm 24 Apr 2003 00:08:53 -0000 1.22
***************
*** 547,550 ****
--- 547,552 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:18:25
|
Update of /cvsroot/genex/genex-server/Genex/GroupSec
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/GroupSec
Modified Files:
GroupSec.pm
Log Message:
new files
Index: GroupSec.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/GroupSec/GroupSec.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** GroupSec.pm 23 Apr 2003 22:20:55 -0000 1.40
--- GroupSec.pm 24 Apr 2003 00:08:55 -0000 1.41
***************
*** 19,24 ****
use Class::ObjectTemplate::DB 0.27;
use Bio::Genex::GroupSec;
- use Bio::Genex::GroupLink;
use Bio::Genex::Audit;
--- 19,24 ----
use Class::ObjectTemplate::DB 0.27;
use Bio::Genex::GroupSec;
use Bio::Genex::Audit;
+ use Bio::Genex::GroupLink;
***************
*** 60,120 ****
$FKEYS = {
'audit_obj' => bless( {
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Audit'
! }, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'true',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
! 'ro_groupname_obj' => bless( {
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'true',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
'grouplink_obj' => bless( {
'fkey_name' => 'grouplink_obj',
- 'pkey_name' => 'groupname',
'can_self_reference' => undef,
! 'fkey_type' => 'ONE_TO_MANY_LINK_OO',
! 'table_name' => 'GroupLink'
}, 'Bio::Genex::Fkey' ),
! 'grouplink_fk' => bless( {
! 'fkey_name' => 'grouplink_fk',
! 'pkey_name' => 'groupname',
! 'fkey_type' => 'ONE_TO_MANY_LINK',
! 'table_name' => 'GroupLink'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
! 'audit_fk' => 'Audit',
! 'ro_groupname' => 'Read-Only Group Name',
! 'name' => 'Group Name',
'rw_groupname' => 'Read/Write Group Name',
! 'description' => 'Description'
}
;
$NAME2COLUMN = {
- 'Read-Only Group Name' => 'ro_groupname',
- 'Read/Write Group Name' => 'rw_groupname',
- 'Audit' => 'audit_fk',
'Description' => 'description',
! 'Group Name' => 'name'
}
;
$FKEY_OBJ2RAW = {
'audit_obj' => 'audit_fk',
'rw_groupname_obj' => 'rw_groupname',
! 'ro_groupname_obj' => 'ro_groupname',
! 'grouplink_obj' => 'grouplink_fk'
}
;
--- 60,120 ----
$FKEYS = {
'audit_obj' => bless( {
! 'table_name' => 'Audit',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk'
! }, 'Bio::Genex::Fkey' ),
! 'grouplink_fk' => bless( {
! 'table_name' => 'GroupLink',
! 'fkey_type' => 'ONE_TO_MANY_LINK',
! 'fkey_name' => 'grouplink_fk',
! 'pkey_name' => 'groupname'
! }, 'Bio::Genex::Fkey' ),
'grouplink_obj' => bless( {
+ 'fkey_type' => 'ONE_TO_MANY_LINK_OO',
+ 'table_name' => 'GroupLink',
'fkey_name' => 'grouplink_obj',
'can_self_reference' => undef,
! 'pkey_name' => 'groupname'
}, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'true',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' ),
! 'ro_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'true',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
! 'description' => 'Description',
'rw_groupname' => 'Read/Write Group Name',
! 'ro_groupname' => 'Read-Only Group Name',
! 'audit_fk' => 'Audit',
! 'name' => 'Group Name'
}
;
$NAME2COLUMN = {
'Description' => 'description',
! 'Audit' => 'audit_fk',
! 'Group Name' => 'name',
! 'Read/Write Group Name' => 'rw_groupname',
! 'Read-Only Group Name' => 'ro_groupname'
}
;
$FKEY_OBJ2RAW = {
'audit_obj' => 'audit_fk',
+ 'grouplink_obj' => 'grouplink_fk',
'rw_groupname_obj' => 'rw_groupname',
! 'ro_groupname_obj' => 'ro_groupname'
}
;
***************
*** 594,597 ****
--- 594,599 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:18:25
|
Update of /cvsroot/genex/genex-server/Genex/Hardware
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Hardware
Modified Files:
Hardware.pm
Log Message:
new files
Index: Hardware.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Hardware/Hardware.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Hardware.pm 23 Apr 2003 23:58:33 -0000 1.2
--- Hardware.pm 24 Apr 2003 00:08:55 -0000 1.3
***************
*** 559,562 ****
--- 559,564 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:16:14
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv18854/scripts
Modified Files:
create_genex_class.pl.in
Log Message:
corrected quote_identifier() call
Index: create_genex_class.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_class.pl.in,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** create_genex_class.pl.in 23 Apr 2003 23:54:38 -0000 1.22
--- create_genex_class.pl.in 24 Apr 2003 00:16:10 -0000 1.23
***************
*** 1655,1660 ****
# it fails for any one group we ext
foreach my \$uniques (\@{\$self->unique_columns}) {
- # we have to quote the column names in case they have reserved words
- \$unique = \$dbh->quote_identifier(\$unique);
foreach my \$unique (\@{\$uniques}) {
my \$value = \$self->get_attribute(\$unique);
--- 1655,1658 ----
***************
*** 1662,1666 ****
\$value =~ s/^\\s*(\\w)/\$1/;
\$value =~ s/(\\w)\\s*\$/\$1/;
! push(\@clauses,"\$unique=" . \$dbh->quote(\$value));
}
\$UNIQUE_WHERE = join(' AND ', \@clauses);
--- 1660,1666 ----
\$value =~ s/^\\s*(\\w)/\$1/;
\$value =~ s/(\\w)\\s*\$/\$1/;
! # we have to quote the column names in case they have reserved words
! \$unique = \$dbh->quote_identifier(\$unique);
! push(\@clauses,"\$unique=" . \$dbh->quote(\$value));
}
\$UNIQUE_WHERE = join(' AND ', \@clauses);
|
|
From: <jas...@us...> - 2003-04-24 00:09:31
|
Update of /cvsroot/genex/genex-server/Genex/Feature
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Feature
Modified Files:
Feature.pm
Log Message:
new files
Index: Feature.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Feature/Feature.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Feature.pm 23 Apr 2003 23:58:32 -0000 1.16
--- Feature.pm 24 Apr 2003 00:08:53 -0000 1.17
***************
*** 641,644 ****
--- 641,646 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:30
|
Update of /cvsroot/genex/genex-server/Genex/ExperimentSet
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/ExperimentSet
Modified Files:
ExperimentSet.pm
Log Message:
new files
Index: ExperimentSet.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ExperimentSet/ExperimentSet.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** ExperimentSet.pm 23 Apr 2003 22:20:49 -0000 1.40
--- ExperimentSet.pm 24 Apr 2003 00:08:50 -0000 1.41
***************
*** 18,30 ****
use Class::ObjectTemplate::DB 0.27;
- use Bio::Genex::GroupSec;
- use Bio::Genex::Contact;
- use Bio::Genex::MeasuredBioAssay;
use Bio::Genex::PhysicalBioAssay;
- use Bio::Genex::TreatmentLevel;
use Bio::Genex::HotSpots;
use Bio::Genex::Citation;
! use Bio::Genex::Audit;
use Bio::Genex::ExperimentFactors;
--- 18,30 ----
use Class::ObjectTemplate::DB 0.27;
use Bio::Genex::PhysicalBioAssay;
use Bio::Genex::HotSpots;
use Bio::Genex::Citation;
! use Bio::Genex::MeasuredBioAssay;
! use Bio::Genex::Contact;
! use Bio::Genex::GroupSec;
use Bio::Genex::ExperimentFactors;
+ use Bio::Genex::Audit;
+ use Bio::Genex::TreatmentLevel;
***************
*** 72,223 ****
;
$FKEYS = {
! 'experimentfactors_obj' => bless( {
! 'fkey_name' => 'experimentfactors_obj',
! 'pkey_name' => 'es_fk',
! 'can_self_reference' => undef,
! 'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'ExperimentFactors'
! }, 'Bio::Genex::Fkey' ),
! 'cit_obj' => bless( {
! 'fkey_name' => 'cit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'cit_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Citation'
! }, 'Bio::Genex::Fkey' ),
! 'physicalbioassay_fk' => bless( {
! 'fkey_name' => 'physicalbioassay_fk',
! 'pkey_name' => 'es_fk',
! 'fkey_type' => 'ONE_TO_MANY',
! 'table_name' => 'PhysicalBioAssay'
! }, 'Bio::Genex::Fkey' ),
'treatmentlevel_obj' => bless( {
'fkey_name' => 'treatmentlevel_obj',
- 'pkey_name' => 'es_fk',
'can_self_reference' => undef,
! 'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'TreatmentLevel'
}, 'Bio::Genex::Fkey' ),
! 'physicalbioassay_obj' => bless( {
! 'fkey_name' => 'physicalbioassay_obj',
! 'pkey_name' => 'es_fk',
! 'can_self_reference' => undef,
'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'PhysicalBioAssay'
}, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
! 'hotspots_fk' => bless( {
! 'fkey_name' => 'hotspots_fk',
! 'pkey_name' => 'es_fk',
! 'fkey_type' => 'ONE_TO_MANY_LINK',
! 'table_name' => 'HotSpots'
! }, 'Bio::Genex::Fkey' ),
'hotspots_obj' => bless( {
'fkey_name' => 'hotspots_obj',
- 'pkey_name' => 'es_fk',
'can_self_reference' => undef,
! 'fkey_type' => 'ONE_TO_MANY_LINK_OO',
! 'table_name' => 'HotSpots'
}, 'Bio::Genex::Fkey' ),
! 'measuredbioassay_obj' => bless( {
! 'fkey_name' => 'measuredbioassay_obj',
! 'pkey_name' => 'es_fk',
! 'can_self_reference' => undef,
'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'MeasuredBioAssay'
}, 'Bio::Genex::Fkey' ),
! 'measuredbioassay_fk' => bless( {
! 'fkey_name' => 'measuredbioassay_fk',
! 'pkey_name' => 'es_fk',
'fkey_type' => 'ONE_TO_MANY',
! 'table_name' => 'MeasuredBioAssay'
}, 'Bio::Genex::Fkey' ),
'audit_obj' => bless( {
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk',
'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Audit'
}, 'Bio::Genex::Fkey' ),
! 'ro_groupname_obj' => bless( {
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
! 'provider_con_obj' => bless( {
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Contact'
! }, 'Bio::Genex::Fkey' ),
! 'treatmentlevel_fk' => bless( {
! 'fkey_name' => 'treatmentlevel_fk',
! 'pkey_name' => 'es_fk',
! 'fkey_type' => 'ONE_TO_MANY',
! 'table_name' => 'TreatmentLevel'
! }, 'Bio::Genex::Fkey' ),
! 'experimentfactors_fk' => bless( {
! 'fkey_name' => 'experimentfactors_fk',
! 'pkey_name' => 'es_fk',
! 'fkey_type' => 'ONE_TO_MANY',
! 'table_name' => 'ExperimentFactors'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
- 'audit_fk' => 'Audit',
- 'provider_con_fk' => 'Data Provider',
'release_date' => 'Release Date',
- 'treatment_type' => 'Treatment Type',
'analysis_description' => 'Analysis Description',
'cit_fk' => 'Primary Citation',
'name' => 'Experiment Name',
'local_accession' => 'Local Accession Number',
- 'rw_groupname' => 'Read/Write Group Name',
- 'biology_description' => 'Biology Description',
- 'es_pk' => 'Accession Number',
- 'quantity_series_type' => 'Quantity Series Type',
'ro_groupname' => 'Read-Only Group Name',
! 'archive_bundle_ref' => 'Archive Bundle Reference'
}
;
$NAME2COLUMN = {
'Treatment Type' => 'treatment_type',
! 'Read-Only Group Name' => 'ro_groupname',
! 'Analysis Description' => 'analysis_description',
! 'Read/Write Group Name' => 'rw_groupname',
'Quantity Series Type' => 'quantity_series_type',
'Biology Description' => 'biology_description',
'Experiment Name' => 'name',
! 'Archive Bundle Reference' => 'archive_bundle_ref',
! 'Accession Number' => 'es_pk',
! 'Primary Citation' => 'cit_fk',
! 'Local Accession Number' => 'local_accession',
'Audit' => 'audit_fk',
! 'Release Date' => 'release_date',
! 'Data Provider' => 'provider_con_fk'
}
;
$FKEY_OBJ2RAW = {
- 'experimentfactors_obj' => 'experimentfactors_fk',
- 'cit_obj' => 'cit_fk',
'treatmentlevel_obj' => 'treatmentlevel_fk',
- 'physicalbioassay_obj' => 'physicalbioassay_fk',
'audit_obj' => 'audit_fk',
'rw_groupname_obj' => 'rw_groupname',
'ro_groupname_obj' => 'ro_groupname',
'hotspots_obj' => 'hotspots_fk',
! 'provider_con_obj' => 'provider_con_fk',
! 'measuredbioassay_obj' => 'measuredbioassay_fk'
}
;
--- 72,223 ----
;
$FKEYS = {
! 'treatmentlevel_fk' => bless( {
! 'table_name' => 'TreatmentLevel',
! 'fkey_type' => 'ONE_TO_MANY',
! 'fkey_name' => 'treatmentlevel_fk',
! 'pkey_name' => 'es_fk'
! }, 'Bio::Genex::Fkey' ),
'treatmentlevel_obj' => bless( {
+ 'fkey_type' => 'ONE_TO_MANY_OO',
+ 'table_name' => 'TreatmentLevel',
'fkey_name' => 'treatmentlevel_obj',
'can_self_reference' => undef,
! 'pkey_name' => 'es_fk'
}, 'Bio::Genex::Fkey' ),
! 'provider_con_obj' => bless( {
! 'table_name' => 'Contact',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk'
! }, 'Bio::Genex::Fkey' ),
! 'experimentfactors_fk' => bless( {
! 'table_name' => 'ExperimentFactors',
! 'fkey_type' => 'ONE_TO_MANY',
! 'fkey_name' => 'experimentfactors_fk',
! 'pkey_name' => 'es_fk'
! }, 'Bio::Genex::Fkey' ),
! 'measuredbioassay_obj' => bless( {
'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'MeasuredBioAssay',
! 'fkey_name' => 'measuredbioassay_obj',
! 'can_self_reference' => undef,
! 'pkey_name' => 'es_fk'
}, 'Bio::Genex::Fkey' ),
! 'ro_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' ),
'hotspots_obj' => bless( {
+ 'fkey_type' => 'ONE_TO_MANY_LINK_OO',
+ 'table_name' => 'HotSpots',
'fkey_name' => 'hotspots_obj',
'can_self_reference' => undef,
! 'pkey_name' => 'es_fk'
}, 'Bio::Genex::Fkey' ),
! 'physicalbioassay_obj' => bless( {
'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'PhysicalBioAssay',
! 'fkey_name' => 'physicalbioassay_obj',
! 'can_self_reference' => undef,
! 'pkey_name' => 'es_fk'
}, 'Bio::Genex::Fkey' ),
! 'physicalbioassay_fk' => bless( {
! 'table_name' => 'PhysicalBioAssay',
'fkey_type' => 'ONE_TO_MANY',
! 'fkey_name' => 'physicalbioassay_fk',
! 'pkey_name' => 'es_fk'
}, 'Bio::Genex::Fkey' ),
'audit_obj' => bless( {
! 'table_name' => 'Audit',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk'
! }, 'Bio::Genex::Fkey' ),
! 'measuredbioassay_fk' => bless( {
! 'table_name' => 'MeasuredBioAssay',
! 'fkey_type' => 'ONE_TO_MANY',
! 'fkey_name' => 'measuredbioassay_fk',
! 'pkey_name' => 'es_fk'
! }, 'Bio::Genex::Fkey' ),
! 'experimentfactors_obj' => bless( {
! 'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'ExperimentFactors',
! 'fkey_name' => 'experimentfactors_obj',
! 'can_self_reference' => undef,
! 'pkey_name' => 'es_fk'
! }, 'Bio::Genex::Fkey' ),
! 'cit_obj' => bless( {
! 'table_name' => 'Citation',
'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'cit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'cit_pk'
}, 'Bio::Genex::Fkey' ),
! 'hotspots_fk' => bless( {
! 'table_name' => 'HotSpots',
! 'fkey_type' => 'ONE_TO_MANY_LINK',
! 'fkey_name' => 'hotspots_fk',
! 'pkey_name' => 'es_fk'
! }, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
'release_date' => 'Release Date',
'analysis_description' => 'Analysis Description',
+ 'treatment_type' => 'Treatment Type',
+ 'provider_con_fk' => 'Data Provider',
+ 'archive_bundle_ref' => 'Archive Bundle Reference',
+ 'rw_groupname' => 'Read/Write Group Name',
'cit_fk' => 'Primary Citation',
'name' => 'Experiment Name',
'local_accession' => 'Local Accession Number',
'ro_groupname' => 'Read-Only Group Name',
! 'quantity_series_type' => 'Quantity Series Type',
! 'es_pk' => 'Accession Number',
! 'audit_fk' => 'Audit',
! 'biology_description' => 'Biology Description'
}
;
$NAME2COLUMN = {
+ 'Release Date' => 'release_date',
+ 'Accession Number' => 'es_pk',
'Treatment Type' => 'treatment_type',
! 'Archive Bundle Reference' => 'archive_bundle_ref',
'Quantity Series Type' => 'quantity_series_type',
'Biology Description' => 'biology_description',
'Experiment Name' => 'name',
! 'Analysis Description' => 'analysis_description',
'Audit' => 'audit_fk',
! 'Local Accession Number' => 'local_accession',
! 'Primary Citation' => 'cit_fk',
! 'Read/Write Group Name' => 'rw_groupname',
! 'Data Provider' => 'provider_con_fk',
! 'Read-Only Group Name' => 'ro_groupname'
}
;
$FKEY_OBJ2RAW = {
'treatmentlevel_obj' => 'treatmentlevel_fk',
'audit_obj' => 'audit_fk',
+ 'provider_con_obj' => 'provider_con_fk',
+ 'measuredbioassay_obj' => 'measuredbioassay_fk',
+ 'cit_obj' => 'cit_fk',
+ 'experimentfactors_obj' => 'experimentfactors_fk',
'rw_groupname_obj' => 'rw_groupname',
'ro_groupname_obj' => 'ro_groupname',
'hotspots_obj' => 'hotspots_fk',
! 'physicalbioassay_obj' => 'physicalbioassay_fk'
}
;
***************
*** 455,459 ****
# this calls the Class::ObjectTemplate::attributes() method
# to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['es_pk', 'name', 'cit_fk', 'provider_con_fk', 'ro_groupname', 'rw_groupname', 'audit_fk', 'biology_description', 'analysis_description', 'treatment_type', 'quantity_series_type', 'release_date', 'local_accession', 'archive_bundle_ref', 'cit_obj', 'provider_con_obj', 'ro_groupname_obj', 'rw_groupname_obj', 'audit_obj', 'measuredbioassay_obj', 'measuredbioassay_fk', 'experimentfactors_obj', 'experimentfactors_fk', 'physicalbioassay_obj', 'physicalbioassay_fk', 'treatmentlevel_obj', 'treatmentlevel_fk', 'hotspots_obj', 'hotspots_fk']);
--- 455,459 ----
# this calls the Class::ObjectTemplate::attributes() method
# to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['es_pk', 'name', 'cit_fk', 'provider_con_fk', 'ro_groupname', 'rw_groupname', 'audit_fk', 'biology_description', 'analysis_description', 'treatment_type', 'quantity_series_type', 'release_date', 'local_accession', 'archive_bundle_ref', 'cit_obj', 'provider_con_obj', 'ro_groupname_obj', 'rw_groupname_obj', 'audit_obj', 'physicalbioassay_obj', 'physicalbioassay_fk', 'measuredbioassay_obj', 'measuredbioassay_fk', 'experimentfactors_obj', 'experimentfactors_fk', 'treatmentlevel_obj', 'treatmentlevel_fk', 'hotspots_obj', 'hotspots_fk']);
***************
*** 715,718 ****
--- 715,720 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
***************
*** 1354,1377 ****
- =item @id_list = measuredbioassay_fk()
-
- =item @obj_list = measuredbioassay_obj()
-
- This is an attribute of type ONE_TO_MANY and refers to class
- L<Bio::Genex::MeasuredBioAssay>. The raw accessor method, C<measuredbioassay_fk()> returns a list of
- foreign key ids. The OO accessor method, C<measuredbioassay_obj()> returns a
- list of objects of class Bio::Genex::MeasuredBioAssay.
-
-
- =item @id_list = experimentfactors_fk()
-
- =item @obj_list = experimentfactors_obj()
-
- This is an attribute of type ONE_TO_MANY and refers to class
- L<Bio::Genex::ExperimentFactors>. The raw accessor method, C<experimentfactors_fk()> returns a list of
- foreign key ids. The OO accessor method, C<experimentfactors_obj()> returns a
- list of objects of class Bio::Genex::ExperimentFactors.
-
-
=item @id_list = physicalbioassay_fk()
--- 1356,1359 ----
***************
*** 1384,1387 ****
--- 1366,1379 ----
+ =item @id_list = measuredbioassay_fk()
+
+ =item @obj_list = measuredbioassay_obj()
+
+ This is an attribute of type ONE_TO_MANY and refers to class
+ L<Bio::Genex::MeasuredBioAssay>. The raw accessor method, C<measuredbioassay_fk()> returns a list of
+ foreign key ids. The OO accessor method, C<measuredbioassay_obj()> returns a
+ list of objects of class Bio::Genex::MeasuredBioAssay.
+
+
=item @id_list = hotspots_fk()
***************
*** 1392,1395 ****
--- 1384,1397 ----
foreign key ids. The OO accessor method, C<hotspots_obj()> returns a
list of objects of class Bio::Genex::HotSpots.
+
+
+ =item @id_list = experimentfactors_fk()
+
+ =item @obj_list = experimentfactors_obj()
+
+ This is an attribute of type ONE_TO_MANY and refers to class
+ L<Bio::Genex::ExperimentFactors>. The raw accessor method, C<experimentfactors_fk()> returns a list of
+ foreign key ids. The OO accessor method, C<experimentfactors_obj()> returns a
+ list of objects of class Bio::Genex::ExperimentFactors.
|
|
From: <jas...@us...> - 2003-04-24 00:09:30
|
Update of /cvsroot/genex/genex-server/Genex/ExternalDatabase
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/ExternalDatabase
Modified Files:
ExternalDatabase.pm
Log Message:
new files
Index: ExternalDatabase.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ExternalDatabase/ExternalDatabase.pm,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** ExternalDatabase.pm 23 Apr 2003 22:20:51 -0000 1.34
--- ExternalDatabase.pm 24 Apr 2003 00:08:51 -0000 1.35
***************
*** 59,103 ****
$FKEYS = {
'audit_obj' => bless( {
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Audit'
! }, 'Bio::Genex::Fkey' ),
'rw_groupname_obj' => bless( {
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
'ro_groupname_obj' => bless( {
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
- 'audit_fk' => 'Audit',
'main_url' => 'Main DB URL',
- 'ro_groupname' => 'Read-Only Group Name',
- 'name' => 'Database Name',
'ed_pk' => 'Accession Number',
'rw_groupname' => 'Read/Write Group Name',
! 'parameterized_url' => 'Parameterized URL'
}
;
$NAME2COLUMN = {
! 'Read-Only Group Name' => 'ro_groupname',
! 'Read/Write Group Name' => 'rw_groupname',
'Accession Number' => 'ed_pk',
'Main DB URL' => 'main_url',
! 'Database Name' => 'name',
! 'Audit' => 'audit_fk',
! 'Parameterized URL' => 'parameterized_url'
}
;
--- 59,103 ----
$FKEYS = {
'audit_obj' => bless( {
! 'table_name' => 'Audit',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk'
! }, 'Bio::Genex::Fkey' ),
'rw_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' ),
'ro_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
'main_url' => 'Main DB URL',
'ed_pk' => 'Accession Number',
'rw_groupname' => 'Read/Write Group Name',
! 'ro_groupname' => 'Read-Only Group Name',
! 'parameterized_url' => 'Parameterized URL',
! 'audit_fk' => 'Audit',
! 'name' => 'Database Name'
}
;
$NAME2COLUMN = {
! 'Audit' => 'audit_fk',
! 'Database Name' => 'name',
'Accession Number' => 'ed_pk',
+ 'Parameterized URL' => 'parameterized_url',
'Main DB URL' => 'main_url',
! 'Read/Write Group Name' => 'rw_groupname',
! 'Read-Only Group Name' => 'ro_groupname'
}
;
***************
*** 580,583 ****
--- 580,585 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:26
|
Update of /cvsroot/genex/genex-server/Genex/ContactType
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/ContactType
Modified Files:
ContactType.pm
Log Message:
new files
Index: ContactType.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ContactType/ContactType.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** ContactType.pm 23 Apr 2003 23:58:32 -0000 1.21
--- ContactType.pm 24 Apr 2003 00:08:47 -0000 1.22
***************
*** 534,537 ****
--- 534,539 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:25
|
Update of /cvsroot/genex/genex-server/Genex/Citation
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Citation
Modified Files:
Citation.pm
Log Message:
new files
Index: Citation.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Citation/Citation.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** Citation.pm 23 Apr 2003 23:58:32 -0000 1.40
--- Citation.pm 24 Apr 2003 00:08:46 -0000 1.41
***************
*** 595,598 ****
--- 595,600 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:25
|
Update of /cvsroot/genex/genex-server/Genex/Channel
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Channel
Modified Files:
Channel.pm
Log Message:
new files
Index: Channel.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Channel/Channel.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** Channel.pm 23 Apr 2003 23:58:31 -0000 1.12
--- Channel.pm 24 Apr 2003 00:08:45 -0000 1.13
***************
*** 515,518 ****
--- 515,520 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:25
|
Update of /cvsroot/genex/genex-server/Genex/Contact
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Contact
Modified Files:
Contact.pm
Log Message:
new files
Index: Contact.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Contact/Contact.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** Contact.pm 23 Apr 2003 22:20:43 -0000 1.40
--- Contact.pm 24 Apr 2003 00:08:46 -0000 1.41
***************
*** 18,24 ****
use Class::ObjectTemplate::DB 0.27;
- use Bio::Genex::ContactType;
use Bio::Genex::GroupSec;
use Bio::Genex::Audit;
--- 18,24 ----
use Class::ObjectTemplate::DB 0.27;
use Bio::Genex::GroupSec;
use Bio::Genex::Audit;
+ use Bio::Genex::ContactType;
***************
*** 68,139 ****
$FKEYS = {
'contacttype_obj' => bless( {
'fkey_name' => 'contacttype_obj',
- 'pkey_name' => 'con_fk',
'can_self_reference' => undef,
! 'fkey_type' => 'ONE_TO_MANY_OO',
! 'table_name' => 'ContactType'
}, 'Bio::Genex::Fkey' ),
'audit_obj' => bless( {
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Audit'
! }, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
'contacttype_fk' => bless( {
! 'fkey_name' => 'contacttype_fk',
! 'pkey_name' => 'con_fk',
'fkey_type' => 'ONE_TO_MANY',
! 'table_name' => 'ContactType'
}, 'Bio::Genex::Fkey' ),
'ro_groupname_obj' => bless( {
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
- 'audit_fk' => 'Audit',
- 'org_fax' => 'Organization Fax',
- 'org_mail_address' => 'Organization Mail Address',
- 'org_email' => 'Organization Email',
- 'contact_person_phone' => 'Contact Person Phone',
'con_pk' => 'Accession Number',
'rw_groupname' => 'Read/Write Group Name',
'contact_person' => 'Contact Person',
'org_toll_free_phone' => 'Organization Toll Free Phone',
! 'contact_person_email' => 'Contact Person Email',
'url' => 'URL',
'ro_groupname' => 'Read-Only Group Name',
! 'organization' => 'Organization',
! 'org_phone' => 'Organization Phone'
}
;
$NAME2COLUMN = {
! 'Read-Only Group Name' => 'ro_groupname',
! 'URL' => 'url',
! 'Read/Write Group Name' => 'rw_groupname',
'Organization Email' => 'org_email',
- 'Organization Mail Address' => 'org_mail_address',
'Organization Toll Free Phone' => 'org_toll_free_phone',
'Organization Phone' => 'org_phone',
! 'Contact Person Phone' => 'contact_person_phone',
'Contact Person Email' => 'contact_person_email',
! 'Accession Number' => 'con_pk',
! 'Audit' => 'audit_fk',
! 'Organization Fax' => 'org_fax',
'Organization' => 'organization',
! 'Contact Person' => 'contact_person'
}
;
--- 68,139 ----
$FKEYS = {
'contacttype_obj' => bless( {
+ 'fkey_type' => 'ONE_TO_MANY_OO',
+ 'table_name' => 'ContactType',
'fkey_name' => 'contacttype_obj',
'can_self_reference' => undef,
! 'pkey_name' => 'con_fk'
}, 'Bio::Genex::Fkey' ),
'audit_obj' => bless( {
! 'table_name' => 'Audit',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk'
! }, 'Bio::Genex::Fkey' ),
'contacttype_fk' => bless( {
! 'table_name' => 'ContactType',
'fkey_type' => 'ONE_TO_MANY',
! 'fkey_name' => 'contacttype_fk',
! 'pkey_name' => 'con_fk'
}, 'Bio::Genex::Fkey' ),
+ 'rw_groupname_obj' => bless( {
+ 'table_name' => 'GroupSec',
+ 'fkey_type' => 'ONE_TO_ONE_OO',
+ 'fkey_name' => 'rw_groupname_obj',
+ 'can_self_reference' => 'false',
+ 'pkey_name' => 'name'
+ }, 'Bio::Genex::Fkey' ),
'ro_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
'con_pk' => 'Accession Number',
'rw_groupname' => 'Read/Write Group Name',
'contact_person' => 'Contact Person',
'org_toll_free_phone' => 'Organization Toll Free Phone',
! 'org_fax' => 'Organization Fax',
! 'organization' => 'Organization',
'url' => 'URL',
'ro_groupname' => 'Read-Only Group Name',
! 'contact_person_phone' => 'Contact Person Phone',
! 'contact_person_email' => 'Contact Person Email',
! 'org_email' => 'Organization Email',
! 'audit_fk' => 'Audit',
! 'org_phone' => 'Organization Phone',
! 'org_mail_address' => 'Organization Mail Address'
}
;
$NAME2COLUMN = {
! 'Organization Fax' => 'org_fax',
! 'Accession Number' => 'con_pk',
'Organization Email' => 'org_email',
'Organization Toll Free Phone' => 'org_toll_free_phone',
'Organization Phone' => 'org_phone',
! 'URL' => 'url',
'Contact Person Email' => 'contact_person_email',
! 'Contact Person Phone' => 'contact_person_phone',
! 'Contact Person' => 'contact_person',
'Organization' => 'organization',
! 'Audit' => 'audit_fk',
! 'Organization Mail Address' => 'org_mail_address',
! 'Read/Write Group Name' => 'rw_groupname',
! 'Read-Only Group Name' => 'ro_groupname'
}
;
***************
*** 638,641 ****
--- 638,643 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:25
|
Update of /cvsroot/genex/genex-server/Genex/ControlledVocab
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/ControlledVocab
Modified Files:
ControlledVocab.pm
Log Message:
new files
Index: ControlledVocab.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ControlledVocab/ControlledVocab.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** ControlledVocab.pm 23 Apr 2003 22:20:46 -0000 1.33
--- ControlledVocab.pm 24 Apr 2003 00:08:47 -0000 1.34
***************
*** 67,115 ****
$FKEYS = {
'audit_obj' => bless( {
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Audit'
! }, 'Bio::Genex::Fkey' ),
'rw_groupname_obj' => bless( {
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
'ro_groupname_obj' => bless( {
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
- 'audit_fk' => 'Audit',
- 'vocab_name' => 'Vocabulary Name',
- 'rw_groupname' => 'Read/Write Group Name',
'description' => 'Description',
! 'cv_pk' => 'Accession Number',
'column_name' => 'Column Name',
! 'ro_groupname' => 'Read-Only Group Name',
'table_name' => 'Table Name',
! 'term_string' => 'Term String'
}
;
$NAME2COLUMN = {
! 'Read-Only Group Name' => 'ro_groupname',
! 'Read/Write Group Name' => 'rw_groupname',
! 'Term String' => 'term_string',
! 'Vocabulary Name' => 'vocab_name',
'Accession Number' => 'cv_pk',
'Column Name' => 'column_name',
! 'Audit' => 'audit_fk',
'Table Name' => 'table_name',
! 'Description' => 'description'
}
;
--- 67,115 ----
$FKEYS = {
'audit_obj' => bless( {
! 'table_name' => 'Audit',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk'
! }, 'Bio::Genex::Fkey' ),
'rw_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' ),
'ro_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
'description' => 'Description',
! 'term_string' => 'Term String',
'column_name' => 'Column Name',
! 'vocab_name' => 'Vocabulary Name',
! 'rw_groupname' => 'Read/Write Group Name',
'table_name' => 'Table Name',
! 'ro_groupname' => 'Read-Only Group Name',
! 'audit_fk' => 'Audit',
! 'cv_pk' => 'Accession Number'
}
;
$NAME2COLUMN = {
! 'Description' => 'description',
'Accession Number' => 'cv_pk',
'Column Name' => 'column_name',
! 'Term String' => 'term_string',
! 'Vocabulary Name' => 'vocab_name',
'Table Name' => 'table_name',
! 'Audit' => 'audit_fk',
! 'Read/Write Group Name' => 'rw_groupname',
! 'Read-Only Group Name' => 'ro_groupname'
}
;
***************
*** 598,601 ****
--- 598,603 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:25
|
Update of /cvsroot/genex/genex-server/Genex/BlastHits
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/BlastHits
Modified Files:
BlastHits.pm
Log Message:
new files
Index: BlastHits.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/BlastHits/BlastHits.pm,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** BlastHits.pm 23 Apr 2003 23:58:31 -0000 1.34
--- BlastHits.pm 24 Apr 2003 00:08:45 -0000 1.35
***************
*** 546,549 ****
--- 546,551 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:25
|
Update of /cvsroot/genex/genex-server/Genex/ExperimentFactors
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/ExperimentFactors
Modified Files:
ExperimentFactors.pm
Log Message:
new files
Index: ExperimentFactors.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ExperimentFactors/ExperimentFactors.pm,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** ExperimentFactors.pm 23 Apr 2003 23:58:32 -0000 1.34
--- ExperimentFactors.pm 24 Apr 2003 00:08:48 -0000 1.35
***************
*** 603,606 ****
--- 603,608 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:23
|
Update of /cvsroot/genex/genex-server/Genex/Chromosome
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Chromosome
Modified Files:
Chromosome.pm
Log Message:
new files
Index: Chromosome.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Chromosome/Chromosome.pm,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** Chromosome.pm 23 Apr 2003 23:58:31 -0000 1.44
--- Chromosome.pm 24 Apr 2003 00:08:45 -0000 1.45
***************
*** 561,564 ****
--- 561,566 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:19
|
Update of /cvsroot/genex/genex-server/Genex/ArrayDesign
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/ArrayDesign
Modified Files:
ArrayDesign.pm
Log Message:
new files
Index: ArrayDesign.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ArrayDesign/ArrayDesign.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** ArrayDesign.pm 23 Apr 2003 22:20:42 -0000 1.10
--- ArrayDesign.pm 24 Apr 2003 00:08:44 -0000 1.11
***************
*** 68,155 ****
;
$FKEYS = {
- 'audit_obj' => bless( {
- 'fkey_name' => 'audit_obj',
- 'can_self_reference' => 'false',
- 'pkey_name' => 'audit_pk',
- 'fkey_type' => 'ONE_TO_ONE_OO',
- 'table_name' => 'Audit'
- }, 'Bio::Genex::Fkey' ),
- 'rw_groupname_obj' => bless( {
- 'fkey_name' => 'rw_groupname_obj',
- 'can_self_reference' => 'false',
- 'pkey_name' => 'name',
- 'fkey_type' => 'ONE_TO_ONE_OO',
- 'table_name' => 'GroupSec'
- }, 'Bio::Genex::Fkey' ),
- 'feature_fk' => bless( {
- 'fkey_name' => 'feature_fk',
- 'pkey_name' => 'ad_fk',
- 'fkey_type' => 'ONE_TO_MANY_LT',
- 'table_name' => 'Feature'
- }, 'Bio::Genex::Fkey' ),
'feature_obj' => bless( {
'fkey_name' => 'feature_obj',
- 'pkey_name' => 'ad_fk',
'can_self_reference' => undef,
! 'fkey_type' => 'ONE_TO_MANY_LT_OO',
! 'table_name' => 'Feature'
}, 'Bio::Genex::Fkey' ),
- 'ro_groupname_obj' => bless( {
- 'fkey_name' => 'ro_groupname_obj',
- 'can_self_reference' => 'false',
- 'pkey_name' => 'name',
- 'fkey_type' => 'ONE_TO_ONE_OO',
- 'table_name' => 'GroupSec'
- }, 'Bio::Genex::Fkey' ),
'provider_con_obj' => bless( {
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Contact'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
- 'audit_fk' => 'Audit',
- 'default_spot_conc' => 'Default Spot Concentration',
'technology_type' => 'Technology Type',
'provider_con_fk' => 'Provider Contact',
! 'name' => 'Layout Name',
'default_spot_conc_units' => 'Default Spot Concentration Units',
- 'identifier_code' => 'Identifier Code',
'rw_groupname' => 'Read/Write Group Name',
! 'ad_pk' => 'Accession Number',
! 'description' => 'Description',
'coating' => 'Coating',
- 'medium' => 'Medium',
'ro_groupname' => 'Read-Only Group Name',
! 'default_spot_conc_error' => 'Default Spot Concentration Error'
}
;
$NAME2COLUMN = {
- 'Read-Only Group Name' => 'ro_groupname',
- 'Read/Write Group Name' => 'rw_groupname',
'Default Spot Concentration Error' => 'default_spot_conc_error',
'Technology Type' => 'technology_type',
'Layout Name' => 'name',
'Identifier Code' => 'identifier_code',
! 'Default Spot Concentration Units' => 'default_spot_conc_units',
! 'Accession Number' => 'ad_pk',
'Provider Contact' => 'provider_con_fk',
! 'Audit' => 'audit_fk',
! 'Coating' => 'coating',
! 'Medium' => 'medium',
! 'Description' => 'description',
! 'Default Spot Concentration' => 'default_spot_conc'
}
;
$FKEY_OBJ2RAW = {
'audit_obj' => 'audit_fk',
'rw_groupname_obj' => 'rw_groupname',
! 'feature_obj' => 'feature_fk',
! 'ro_groupname_obj' => 'ro_groupname',
! 'provider_con_obj' => 'provider_con_fk'
}
;
--- 68,155 ----
;
$FKEYS = {
'feature_obj' => bless( {
+ 'fkey_type' => 'ONE_TO_MANY_LT_OO',
+ 'table_name' => 'Feature',
'fkey_name' => 'feature_obj',
'can_self_reference' => undef,
! 'pkey_name' => 'ad_fk'
}, 'Bio::Genex::Fkey' ),
'provider_con_obj' => bless( {
! 'table_name' => 'Contact',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk'
! }, 'Bio::Genex::Fkey' ),
! 'audit_obj' => bless( {
! 'table_name' => 'Audit',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk'
! }, 'Bio::Genex::Fkey' ),
! 'feature_fk' => bless( {
! 'table_name' => 'Feature',
! 'fkey_type' => 'ONE_TO_MANY_LT',
! 'fkey_name' => 'feature_fk',
! 'pkey_name' => 'ad_fk'
! }, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' ),
! 'ro_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
'technology_type' => 'Technology Type',
+ 'description' => 'Description',
'provider_con_fk' => 'Provider Contact',
! 'default_spot_conc_error' => 'Default Spot Concentration Error',
'default_spot_conc_units' => 'Default Spot Concentration Units',
'rw_groupname' => 'Read/Write Group Name',
! 'default_spot_conc' => 'Default Spot Concentration',
! 'name' => 'Layout Name',
'coating' => 'Coating',
'ro_groupname' => 'Read-Only Group Name',
! 'ad_pk' => 'Accession Number',
! 'identifier_code' => 'Identifier Code',
! 'medium' => 'Medium',
! 'audit_fk' => 'Audit'
}
;
$NAME2COLUMN = {
'Default Spot Concentration Error' => 'default_spot_conc_error',
+ 'Default Spot Concentration Units' => 'default_spot_conc_units',
+ 'Coating' => 'coating',
+ 'Description' => 'description',
'Technology Type' => 'technology_type',
+ 'Audit' => 'audit_fk',
+ 'Accession Number' => 'ad_pk',
+ 'Default Spot Concentration' => 'default_spot_conc',
+ 'Medium' => 'medium',
'Layout Name' => 'name',
'Identifier Code' => 'identifier_code',
! 'Read/Write Group Name' => 'rw_groupname',
'Provider Contact' => 'provider_con_fk',
! 'Read-Only Group Name' => 'ro_groupname'
}
;
$FKEY_OBJ2RAW = {
+ 'feature_obj' => 'feature_fk',
+ 'provider_con_obj' => 'provider_con_fk',
'audit_obj' => 'audit_fk',
'rw_groupname_obj' => 'rw_groupname',
! 'ro_groupname_obj' => 'ro_groupname'
}
;
***************
*** 647,650 ****
--- 647,652 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:19
|
Update of /cvsroot/genex/genex-server/Genex/AM_FactorValues
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/AM_FactorValues
Modified Files:
AM_FactorValues.pm
Log Message:
new files
Index: AM_FactorValues.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/AM_FactorValues/AM_FactorValues.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** AM_FactorValues.pm 23 Apr 2003 23:58:30 -0000 1.33
--- AM_FactorValues.pm 24 Apr 2003 00:08:43 -0000 1.34
***************
*** 563,566 ****
--- 563,568 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:19
|
Update of /cvsroot/genex/genex-server/Genex/Array
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Array
Modified Files:
Array.pm
Log Message:
new files
Index: Array.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Array/Array.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Array.pm 23 Apr 2003 22:20:39 -0000 1.10
--- Array.pm 24 Apr 2003 00:08:43 -0000 1.11
***************
*** 19,26 ****
use Class::ObjectTemplate::DB 0.27;
use Bio::Genex::Contact;
- use Bio::Genex::GroupSec;
use Bio::Genex::Hardware;
! use Bio::Genex::Software;
use Bio::Genex::Audit;
use Bio::Genex::ArrayDesign;
--- 19,26 ----
use Class::ObjectTemplate::DB 0.27;
use Bio::Genex::Contact;
use Bio::Genex::Hardware;
! use Bio::Genex::GroupSec;
use Bio::Genex::Audit;
+ use Bio::Genex::Software;
use Bio::Genex::ArrayDesign;
***************
*** 73,186 ****
;
$FKEYS = {
'spotter_hw_obj' => bless( {
! 'fkey_name' => 'spotter_hw_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'param_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Hardware'
! }, 'Bio::Genex::Fkey' ),
! 'ad_obj' => bless( {
! 'fkey_name' => 'ad_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'ad_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'ArrayDesign'
! }, 'Bio::Genex::Fkey' ),
! 'audit_obj' => bless( {
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Audit'
! }, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name',
'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
! }, 'Bio::Genex::Fkey' ),
! 'sw_obj' => bless( {
! 'fkey_name' => 'sw_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'sw_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Software'
! }, 'Bio::Genex::Fkey' ),
! 'ro_groupname_obj' => bless( {
! 'fkey_name' => 'ro_groupname_obj',
'can_self_reference' => 'false',
! 'pkey_name' => 'name',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'GroupSec'
}, 'Bio::Genex::Fkey' ),
'provider_con_obj' => bless( {
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Contact'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
! 'array_identifier' => 'Array Identifier',
! 'audit_fk' => 'Audit',
'default_spot_conc' => 'Default Spot Concentration',
'spotter_hw_params' => 'Spotter Hardware Parameters',
'provider_con_fk' => 'Provider Contact',
'default_spot_conc_units' => 'Default Spot Concentration Units',
- 'identifier_code' => 'Identifier Code',
'rw_groupname' => 'Read/Write Group Name',
'coating' => 'Coating',
- 'tolerance' => 'Tolerance',
- 'medium' => 'Medium',
- 'sw_fk' => 'Software',
- 'manufacture_date' => 'Manufacture date',
- 'technology_type' => 'Technology Type',
'spotter_hw_fk' => 'Spotter Hardware',
- 'name' => 'Layout Name',
- 'description' => 'Description',
- 'spotter_sw_params' => 'Spotter Software Parameters',
- 'ad_fk' => 'Array Design',
'ro_groupname' => 'Read-Only Group Name',
'array_pk' => 'Accession Number',
! 'default_spot_conc_error' => 'Default Spot Concentration Error'
}
;
$NAME2COLUMN = {
! 'Manufacture date' => 'manufacture_date',
'Layout Name' => 'name',
! 'Identifier Code' => 'identifier_code',
'Default Spot Concentration Units' => 'default_spot_conc_units',
'Accession Number' => 'array_pk',
! 'Array Design' => 'ad_fk',
! 'Tolerance' => 'tolerance',
! 'Medium' => 'medium',
! 'Spotter Hardware Parameters' => 'spotter_hw_params',
! 'Spotter Software Parameters' => 'spotter_sw_params',
'Default Spot Concentration' => 'default_spot_conc',
! 'Read-Only Group Name' => 'ro_groupname',
'Read/Write Group Name' => 'rw_groupname',
- 'Default Spot Concentration Error' => 'default_spot_conc_error',
- 'Technology Type' => 'technology_type',
- 'Array Identifier' => 'array_identifier',
- 'Spotter Hardware' => 'spotter_hw_fk',
'Provider Contact' => 'provider_con_fk',
! 'Software' => 'sw_fk',
! 'Audit' => 'audit_fk',
! 'Coating' => 'coating',
! 'Description' => 'description'
}
;
$FKEY_OBJ2RAW = {
'spotter_hw_obj' => 'spotter_hw_fk',
'ad_obj' => 'ad_fk',
'audit_obj' => 'audit_fk',
'rw_groupname_obj' => 'rw_groupname',
! 'sw_obj' => 'sw_fk',
! 'ro_groupname_obj' => 'ro_groupname',
! 'provider_con_obj' => 'provider_con_fk'
}
;
--- 73,186 ----
;
$FKEYS = {
+ 'sw_obj' => bless( {
+ 'table_name' => 'Software',
+ 'fkey_type' => 'ONE_TO_ONE_OO',
+ 'fkey_name' => 'sw_obj',
+ 'can_self_reference' => 'false',
+ 'pkey_name' => 'sw_pk'
+ }, 'Bio::Genex::Fkey' ),
'spotter_hw_obj' => bless( {
! 'table_name' => 'Hardware',
'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'spotter_hw_obj',
'can_self_reference' => 'false',
! 'pkey_name' => 'param_pk'
}, 'Bio::Genex::Fkey' ),
'provider_con_obj' => bless( {
! 'table_name' => 'Contact',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk'
! }, 'Bio::Genex::Fkey' ),
! 'ad_obj' => bless( {
! 'table_name' => 'ArrayDesign',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ad_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'ad_pk'
! }, 'Bio::Genex::Fkey' ),
! 'audit_obj' => bless( {
! 'table_name' => 'Audit',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'audit_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'audit_pk'
! }, 'Bio::Genex::Fkey' ),
! 'rw_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'rw_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' ),
! 'ro_groupname_obj' => bless( {
! 'table_name' => 'GroupSec',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'ro_groupname_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'name'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
! 'technology_type' => 'Technology Type',
! 'description' => 'Description',
! 'default_spot_conc_error' => 'Default Spot Concentration Error',
'default_spot_conc' => 'Default Spot Concentration',
+ 'name' => 'Layout Name',
'spotter_hw_params' => 'Spotter Hardware Parameters',
+ 'spotter_sw_params' => 'Spotter Software Parameters',
+ 'manufacture_date' => 'Manufacture date',
+ 'tolerance' => 'Tolerance',
'provider_con_fk' => 'Provider Contact',
'default_spot_conc_units' => 'Default Spot Concentration Units',
'rw_groupname' => 'Read/Write Group Name',
+ 'ad_fk' => 'Array Design',
+ 'array_identifier' => 'Array Identifier',
'coating' => 'Coating',
'spotter_hw_fk' => 'Spotter Hardware',
'ro_groupname' => 'Read-Only Group Name',
+ 'identifier_code' => 'Identifier Code',
'array_pk' => 'Accession Number',
! 'medium' => 'Medium',
! 'audit_fk' => 'Audit',
! 'sw_fk' => 'Software'
}
;
$NAME2COLUMN = {
! 'Array Identifier' => 'array_identifier',
! 'Default Spot Concentration Error' => 'default_spot_conc_error',
! 'Description' => 'description',
! 'Technology Type' => 'technology_type',
! 'Spotter Hardware Parameters' => 'spotter_hw_params',
! 'Spotter Software Parameters' => 'spotter_sw_params',
! 'Software' => 'sw_fk',
'Layout Name' => 'name',
! 'Tolerance' => 'tolerance',
! 'Manufacture date' => 'manufacture_date',
! 'Array Design' => 'ad_fk',
'Default Spot Concentration Units' => 'default_spot_conc_units',
+ 'Spotter Hardware' => 'spotter_hw_fk',
'Accession Number' => 'array_pk',
! 'Coating' => 'coating',
! 'Audit' => 'audit_fk',
'Default Spot Concentration' => 'default_spot_conc',
! 'Medium' => 'medium',
'Read/Write Group Name' => 'rw_groupname',
'Provider Contact' => 'provider_con_fk',
! 'Identifier Code' => 'identifier_code',
! 'Read-Only Group Name' => 'ro_groupname'
}
;
$FKEY_OBJ2RAW = {
+ 'sw_obj' => 'sw_fk',
'spotter_hw_obj' => 'spotter_hw_fk',
+ 'provider_con_obj' => 'provider_con_fk',
'ad_obj' => 'ad_fk',
'audit_obj' => 'audit_fk',
'rw_groupname_obj' => 'rw_groupname',
! 'ro_groupname_obj' => 'ro_groupname'
}
;
***************
*** 702,705 ****
--- 702,707 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:09:19
|
Update of /cvsroot/genex/genex-server/Genex/Audit
In directory sc8-pr-cvs1:/tmp/cvs-serv16602/Audit
Modified Files:
Audit.pm
Log Message:
new files
Index: Audit.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Audit/Audit.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Audit.pm 23 Apr 2003 23:58:31 -0000 1.10
--- Audit.pm 24 Apr 2003 00:08:44 -0000 1.11
***************
*** 541,544 ****
--- 541,546 ----
# it fails for any one group we ext
foreach my $uniques (@{$self->unique_columns}) {
+ # we have to quote the column names in case they have reserved words
+ $unique = $dbh->quote_identifier($unique);
foreach my $unique (@{$uniques}) {
my $value = $self->get_attribute($unique);
|
|
From: <jas...@us...> - 2003-04-24 00:08:05
|
Update of /cvsroot/genex/genex-server/Genex/Protocol
In directory sc8-pr-cvs1:/tmp/cvs-serv12879/Protocol
Modified Files:
Protocol.pm
Log Message:
new files
Index: Protocol.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Protocol/Protocol.pm,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** Protocol.pm 16 Apr 2003 23:23:52 -0000 1.36
--- Protocol.pm 23 Apr 2003 23:58:34 -0000 1.37
***************
*** 58,84 ****
$FKEYS = {
'provider_con_obj' => bless( {
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Contact'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
! 'URI' => 'URI',
'provider_con_fk' => 'Protocol Provider',
! 'protocol_pk' => 'Accession Number',
'type' => 'Type',
! 'description' => 'Description'
}
;
$NAME2COLUMN = {
! 'Type' => 'type',
! 'URI' => 'URI',
'Accession Number' => 'protocol_pk',
'Protocol Provider' => 'provider_con_fk',
! 'Description' => 'description'
}
;
--- 58,84 ----
$FKEYS = {
'provider_con_obj' => bless( {
! 'table_name' => 'Contact',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'provider_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk'
! }, 'Bio::Genex::Fkey' )
}
;
$COLUMN2NAME = {
! 'description' => 'Description',
'provider_con_fk' => 'Protocol Provider',
! 'URI' => 'URI',
'type' => 'Type',
! 'protocol_pk' => 'Accession Number'
}
;
$NAME2COLUMN = {
! 'Description' => 'description',
'Accession Number' => 'protocol_pk',
+ 'URI' => 'URI',
'Protocol Provider' => 'provider_con_fk',
! 'Type' => 'type'
}
;
|
|
From: <jas...@us...> - 2003-04-24 00:08:04
|
Update of /cvsroot/genex/genex-server/Genex/ProtocolApplicationLink
In directory sc8-pr-cvs1:/tmp/cvs-serv12879/ProtocolApplicationLink
Modified Files:
ProtocolApplicationLink.pm
Log Message:
new files
Index: ProtocolApplicationLink.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ProtocolApplicationLink/ProtocolApplicationLink.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ProtocolApplicationLink.pm 17 Apr 2003 17:59:37 -0000 1.1
--- ProtocolApplicationLink.pm 23 Apr 2003 23:58:35 -0000 1.2
***************
*** 54,63 ****
$FKEYS = {
'proto_app_obj' => bless( {
! 'fkey_name' => 'proto_app_obj',
! 'pkey_name' => 'proto_app_pk',
! 'can_self_reference' => 'false',
! 'fkey_type' => 'LINKING_TABLE_OO',
! 'table_name' => 'ProtocolApplication'
! }, 'Bio::Genex::Fkey' )
}
;
--- 54,63 ----
$FKEYS = {
'proto_app_obj' => bless( {
! 'fkey_type' => 'LINKING_TABLE_OO',
! 'table_name' => 'ProtocolApplication',
! 'fkey_name' => 'proto_app_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'proto_app_pk'
! }, 'Bio::Genex::Fkey' )
}
;
|
|
From: <jas...@us...> - 2003-04-24 00:08:04
|
Update of /cvsroot/genex/genex-server/Genex/ProtocolApplication
In directory sc8-pr-cvs1:/tmp/cvs-serv12879/ProtocolApplication
Modified Files:
ProtocolApplication.pm
Log Message:
new files
Index: ProtocolApplication.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ProtocolApplication/ProtocolApplication.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ProtocolApplication.pm 16 Apr 2003 23:23:52 -0000 1.1
--- ProtocolApplication.pm 23 Apr 2003 23:58:35 -0000 1.2
***************
*** 52,68 ****
$FKEYS = {
'protocol_obj' => bless( {
! 'fkey_name' => 'protocol_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'protocol_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Protocol'
! }, 'Bio::Genex::Fkey' ),
'performer_con_obj' => bless( {
! 'fkey_name' => 'performer_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Contact'
! }, 'Bio::Genex::Fkey' )
}
;
--- 52,68 ----
$FKEYS = {
'protocol_obj' => bless( {
! 'table_name' => 'Protocol',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'protocol_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'protocol_pk'
! }, 'Bio::Genex::Fkey' ),
'performer_con_obj' => bless( {
! 'table_name' => 'Contact',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'performer_con_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'con_pk'
! }, 'Bio::Genex::Fkey' )
}
;
***************
*** 76,81 ****
;
$NAME2COLUMN = {
- 'Accession Number' => 'proto_app_pk',
'Protocol Performer' => 'performer_con_fk',
'Protocol' => 'protocol_fk',
'Activity Date' => 'activity_date'
--- 76,81 ----
;
$NAME2COLUMN = {
'Protocol Performer' => 'performer_con_fk',
+ 'Accession Number' => 'proto_app_pk',
'Protocol' => 'protocol_fk',
'Activity Date' => 'activity_date'
|
|
From: <jas...@us...> - 2003-04-24 00:08:04
|
Update of /cvsroot/genex/genex-server/Genex/Parameter
In directory sc8-pr-cvs1:/tmp/cvs-serv12879/Parameter
Modified Files:
Parameter.pm
Log Message:
new files
Index: Parameter.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Parameter/Parameter.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Parameter.pm 16 Apr 2003 23:23:50 -0000 1.1
--- Parameter.pm 23 Apr 2003 23:58:34 -0000 1.2
***************
*** 51,60 ****
$FKEYS = {
'proc_obj' => bless( {
! 'fkey_name' => 'proc_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'proc_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'Procedure'
! }, 'Bio::Genex::Fkey' )
}
;
--- 51,60 ----
$FKEYS = {
'proc_obj' => bless( {
! 'table_name' => 'Procedure',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'proc_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'proc_pk'
! }, 'Bio::Genex::Fkey' )
}
;
***************
*** 62,75 ****
$COLUMN2NAME = {
'parameter_pk' => 'Accession Number',
- 'default_value' => 'Default Value',
'proc_fk' => 'Procedure',
! 'type' => 'Type'
}
;
$NAME2COLUMN = {
'Procedure' => 'proc_fk',
! 'Type' => 'type',
'Accession Number' => 'parameter_pk',
! 'Default Value' => 'default_value'
}
;
--- 62,75 ----
$COLUMN2NAME = {
'parameter_pk' => 'Accession Number',
'proc_fk' => 'Procedure',
! 'type' => 'Type',
! 'default_value' => 'Default Value'
}
;
$NAME2COLUMN = {
'Procedure' => 'proc_fk',
! 'Default Value' => 'default_value',
'Accession Number' => 'parameter_pk',
! 'Type' => 'type'
}
;
|
|
From: <jas...@us...> - 2003-04-24 00:08:04
|
Update of /cvsroot/genex/genex-server/Genex/Procedure
In directory sc8-pr-cvs1:/tmp/cvs-serv12879/Procedure
Modified Files:
Procedure.pm
Log Message:
new files
Index: Procedure.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Procedure/Procedure.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Procedure.pm 16 Apr 2003 23:23:51 -0000 1.1
--- Procedure.pm 23 Apr 2003 23:58:34 -0000 1.2
***************
*** 51,63 ****
$COLUMN2NAME = {
'proc_pk' => 'Accession Number',
! 'type' => 'Type',
! 'description' => 'Description'
}
;
$NAME2COLUMN = {
! 'Type' => 'type',
'Accession Number' => 'proc_pk',
! 'Description' => 'description'
}
;
--- 51,63 ----
$COLUMN2NAME = {
+ 'description' => 'Description',
'proc_pk' => 'Accession Number',
! 'type' => 'Type'
}
;
$NAME2COLUMN = {
! 'Description' => 'description',
'Accession Number' => 'proc_pk',
! 'Type' => 'type'
}
;
|
|
From: <jas...@us...> - 2003-04-23 23:59:07
|
Update of /cvsroot/genex/genex-server/Genex/MeasuredBioAssay
In directory sc8-pr-cvs1:/tmp/cvs-serv12879/MeasuredBioAssay
Modified Files:
MeasuredBioAssay.pm
Log Message:
new files
Index: MeasuredBioAssay.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/MeasuredBioAssay/MeasuredBioAssay.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** MeasuredBioAssay.pm 16 Apr 2003 23:23:50 -0000 1.7
--- MeasuredBioAssay.pm 23 Apr 2003 23:58:34 -0000 1.8
***************
*** 18,23 ****
use Class::ObjectTemplate::DB 0.27;
- use Bio::Genex::ExperimentSet;
use Bio::Genex::FeatureExtractionSoftware;
use Bio::Genex::Identifiable;
--- 18,23 ----
use Class::ObjectTemplate::DB 0.27;
use Bio::Genex::FeatureExtractionSoftware;
+ use Bio::Genex::ExperimentSet;
use Bio::Genex::Identifiable;
***************
*** 51,68 ****
;
$FKEYS = {
- 'es_obj' => bless( {
- 'fkey_name' => 'es_obj',
- 'can_self_reference' => 'false',
- 'pkey_name' => 'es_pk',
- 'fkey_type' => 'MANY_TO_ONE_OO',
- 'table_name' => 'ExperimentSet'
- }, 'Bio::Genex::Fkey' ),
'sw_obj' => bless( {
! 'fkey_name' => 'sw_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'param_pk',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'table_name' => 'FeatureExtractionSoftware'
! }, 'Bio::Genex::Fkey' )
}
;
--- 51,68 ----
;
$FKEYS = {
'sw_obj' => bless( {
! 'table_name' => 'FeatureExtractionSoftware',
! 'fkey_type' => 'ONE_TO_ONE_OO',
! 'fkey_name' => 'sw_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'param_pk'
! }, 'Bio::Genex::Fkey' ),
! 'es_obj' => bless( {
! 'table_name' => 'ExperimentSet',
! 'fkey_type' => 'MANY_TO_ONE_OO',
! 'fkey_name' => 'es_obj',
! 'can_self_reference' => 'false',
! 'pkey_name' => 'es_pk'
! }, 'Bio::Genex::Fkey' )
}
;
***************
*** 70,88 ****
$COLUMN2NAME = {
'es_fk' => 'Primary Experiment Set',
- 'sw_fk' => 'Feature Extraction Software',
'description' => 'Description',
'mba_pk' => 'Accession Number'
}
;
$NAME2COLUMN = {
- 'Feature Extraction Software' => 'sw_fk',
- 'Accession Number' => 'mba_pk',
'Primary Experiment Set' => 'es_fk',
! 'Description' => 'description'
}
;
$FKEY_OBJ2RAW = {
! 'es_obj' => 'es_fk',
! 'sw_obj' => 'sw_fk'
}
;
--- 70,88 ----
$COLUMN2NAME = {
'es_fk' => 'Primary Experiment Set',
'description' => 'Description',
+ 'sw_fk' => 'Feature Extraction Software',
'mba_pk' => 'Accession Number'
}
;
$NAME2COLUMN = {
'Primary Experiment Set' => 'es_fk',
! 'Description' => 'description',
! 'Accession Number' => 'mba_pk',
! 'Feature Extraction Software' => 'sw_fk'
}
;
$FKEY_OBJ2RAW = {
! 'sw_obj' => 'sw_fk',
! 'es_obj' => 'es_fk'
}
;
|
