genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 12)

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[Genex-cvs-commit] genex-server/Genex/ProtocolStep ProtocolStep.pm,1.1,1.2

From: <jas...@us...> - 2003-04-17 18:00:41

Update of /cvsroot/genex/genex-server/Genex/ProtocolStep
In directory sc8-pr-cvs1:/tmp/cvs-serv17104/Genex/ProtocolStep

Modified Files:
	ProtocolStep.pm 
Log Message:
new columns


Index: ProtocolStep.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ProtocolStep/ProtocolStep.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ProtocolStep.pm	16 Apr 2003 23:23:52 -0000	1.1
--- ProtocolStep.pm	17 Apr 2003 18:00:36 -0000	1.2
***************
*** 20,24 ****
  use Bio::Genex::Procedure;
  use Bio::Genex::Protocol;
! 
  
  use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $FKEYS $COLUMN2NAME $NAME2COLUMN $COLUMN_NAMES %_CACHE $USE_CACHE $LIMIT $FKEY_OBJ2RAW $TABLE2PKEY $UNIQUE_COLUMNS $SUPER_CLASSES $TABLE_TYPE $PKEY_NAME $TABLE_NAME $DEBUG $TABLE_NAME_VIEW $COUNT);
--- 20,24 ----
  use Bio::Genex::Procedure;
  use Bio::Genex::Protocol;
! use Bio::Genex::Identifiable;
  
  use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $FKEYS $COLUMN2NAME $NAME2COLUMN $COLUMN_NAMES %_CACHE $USE_CACHE $LIMIT $FKEY_OBJ2RAW $TABLE2PKEY $UNIQUE_COLUMNS $SUPER_CLASSES $TABLE_TYPE $PKEY_NAME $TABLE_NAME $DEBUG $TABLE_NAME_VIEW $COUNT);
***************
*** 26,30 ****
  require Exporter;
  
! @ISA = qw(Bio::Genex Exporter Class::ObjectTemplate::DB);
  
  
--- 26,30 ----
  require Exporter;
  
! @ISA = qw(Bio::Genex Exporter Bio::Genex::Identifiable);
  
  
***************
*** 87,91 ****
          }
  ;
!   $SUPER_CLASSES = []
  ;
    $TABLE_NAME   = q[ProtocolStep];
--- 87,93 ----
          }
  ;
!   $SUPER_CLASSES = [
!           'Bio::Genex::Identifiable'
!         ]
  ;
    $TABLE_NAME   = q[ProtocolStep];
***************
*** 290,294 ****
  # this calls the Class::ObjectTemplate::attributes() method
  # to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['proto_step_pk', 'order', 'protocol_fk', 'proc_fk', 'protocol_obj', 'proc_obj']);
  
  
--- 292,297 ----
  # this calls the Class::ObjectTemplate::attributes() method
  # to initialize all the class attributes
! # we get the no_lookup attributes from our superclass
! attributes (lookup=>['proto_step_pk', 'order', 'protocol_fk', 'proc_fk', 'protocol_obj', 'proc_obj']);

[Genex-cvs-commit] genex-server/Genex/ParameterValue ParameterValue.pm,1.1,1.2

From: <jas...@us...> - 2003-04-17 18:00:39

Update of /cvsroot/genex/genex-server/Genex/ParameterValue
In directory sc8-pr-cvs1:/tmp/cvs-serv17104/Genex/ParameterValue

Modified Files:
	ParameterValue.pm 
Log Message:
new columns


Index: ParameterValue.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ParameterValue/ParameterValue.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ParameterValue.pm	16 Apr 2003 23:23:51 -0000	1.1
--- ParameterValue.pm	17 Apr 2003 18:00:34 -0000	1.2
***************
*** 18,21 ****
--- 18,23 ----
  
  use Class::ObjectTemplate::DB 0.27;
+ use Bio::Genex::GroupSec;
+ use Bio::Genex::Audit;
  use Bio::Genex::ProtocolStep;
  
***************
*** 44,48 ****
            'value',
            'proto_step_fk',
!           'parameter_fk'
          ]
  ;
--- 46,53 ----
            'value',
            'proto_step_fk',
!           'parameter_fk',
!           'ro_groupname',
!           'rw_groupname',
!           'audit_fk'
          ]
  ;
***************
*** 50,53 ****
--- 55,79 ----
  ;
   $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' ),
            'proto_step_obj' => bless( {
                                       'fkey_name' => 'proto_step_obj',
***************
*** 61,66 ****
--- 87,95 ----
  
    $COLUMN2NAME  = {
+           'audit_fk' => 'Audit',
            'value' => 'Value',
+           'ro_groupname' => 'Read-Only Group Name',
            'parameter_fk' => 'Parameter',
+           'rw_groupname' => 'Read/Write Group Name',
            'param_value_pk' => 'Accession Number',
            'proto_step_fk' => 'Protocol Step'
***************
*** 68,78 ****
--- 97,113 ----
  ;
    $NAME2COLUMN  = {
+           'Read-Only Group Name' => 'ro_groupname',
+           'Read/Write Group Name' => 'rw_groupname',
            'Value' => 'value',
            'Accession Number' => 'param_value_pk',
            'Protocol Step' => 'proto_step_fk',
+           'Audit' => 'audit_fk',
            'Parameter' => 'parameter_fk'
          }
  ;
    $FKEY_OBJ2RAW = {
+           'audit_obj' => 'audit_fk',
+           'rw_groupname_obj' => 'rw_groupname',
+           'ro_groupname_obj' => 'ro_groupname',
            'proto_step_obj' => 'proto_step_fk'
          }
***************
*** 132,135 ****
--- 167,179 ----
    $ParameterValue->parameter_fk($value);
  
+   my $ro_groupname_val = $ParameterValue->ro_groupname();
+   $ParameterValue->ro_groupname($value);
+ 
+   my $rw_groupname_val = $ParameterValue->rw_groupname();
+   $ParameterValue->rw_groupname($value);
+ 
+   my $audit_fk_val = $ParameterValue->audit_fk();
+   $ParameterValue->audit_fk($value);
+ 
  
  =head1 DESCRIPTION
***************
*** 281,285 ****
  # this calls the Class::ObjectTemplate::attributes() method
  # to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['param_value_pk', 'value', 'proto_step_fk', 'parameter_fk', 'proto_step_obj', 'proto_step_obj']);
  
  
--- 325,329 ----
  # this calls the Class::ObjectTemplate::attributes() method
  # to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['param_value_pk', 'value', 'proto_step_fk', 'parameter_fk', 'ro_groupname', 'rw_groupname', 'audit_fk', 'proto_step_obj', 'proto_step_obj', 'ro_groupname_obj', 'rw_groupname_obj', 'audit_obj']);
  
  
***************
*** 1253,1256 ****
--- 1297,1321 ----
  
  Methods for the parameter_fk attribute.
+ 
+ 
+ =item $value = ro_groupname();
+ 
+ =item ro_groupname($value);
+ 
+ Methods for the ro_groupname attribute.
+ 
+ 
+ =item $value = rw_groupname();
+ 
+ =item rw_groupname($value);
+ 
+ Methods for the rw_groupname attribute.
+ 
+ 
+ =item $value = audit_fk();
+ 
+ =item audit_fk($value);
+ 
+ Methods for the audit_fk attribute.

[Genex-cvs-commit] genex-server/Genex/ProtocolApplicationLink Makefile.PL,NONE,1.1 ProtocolApplicationLink.pm,NONE,1.1

From: <jas...@us...> - 2003-04-17 17:59:42

Update of /cvsroot/genex/genex-server/Genex/ProtocolApplicationLink
In directory sc8-pr-cvs1:/tmp/cvs-serv16683/Genex/ProtocolApplicationLink

Added Files:
	Makefile.PL ProtocolApplicationLink.pm 
Log Message:
new table


--- NEW FILE: Makefile.PL ---
sub MY::top_targets {
    package MY; # so that "SUPER" works right
    my $inherited = shift->SUPER::top_targets(@_);
    $inherited =~ s/(man|html)ifypods//g;
    $inherited;
}

WriteMakefile(
    'NAME'	=> 'Bio::Genex::ProtocolApplicationLink',
    'SKIP'      => [qw( test makeaperl manifypods htmlifypods xs_o static)],
    'VERSION_FROM' => '../Genex.pm', # finds $VERSION
);

--- NEW FILE: ProtocolApplicationLink.pm ---
##############################
#
# Bio::Genex::ProtocolApplicationLink
#
##############################
package Bio::Genex::ProtocolApplicationLink;

use strict;
use POSIX 'strftime';
use Carp;
use DBI;
use IO::File;
use Bio::Genex::Connect;

# import the fkey constants and undefined
use Bio::Genex qw(:ASSERT undefined error);
use Bio::Genex::Fkey qw(:FKEY);

use Class::ObjectTemplate::DB 0.27;
[...1009 lines suppressed...]

There exist other options such as C<Class::Struct> and
C<Class::MethodMaker> by Damian Conway which implement different forms
of automatic class creation.

=head1 BUGS

Please send bug reports to ge...@nc...

=head1 AUTHOR

Jason E. Stewart (je...@nc...)

=head1 SEE ALSO

perl(1).

=cut

1;

[Genex-cvs-commit] genex-server/Genex/scripts .cvsignore,1.25,1.26

From: <jas...@us...> - 2003-04-17 17:59:18

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv16509/Genex/scripts

Modified Files:
	.cvsignore 
Log Message:
usual


Index: .cvsignore
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/.cvsignore,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** .cvsignore	17 Apr 2003 15:42:55 -0000	1.25
--- .cvsignore	17 Apr 2003 17:59:11 -0000	1.26
***************
*** 20,26 ****
--- 20,28 ----
  layout.pl
  mbad-insert.pl
+ parameter-insert.pl
  priveleges.pl
  procedure-insert.pl
  protocol-insert.pl
+ protocol-step-insert.pl
  qtdim-insert.pl
  quant-dim-insert.pl

[Genex-cvs-commit] genex-server/Genex/t ParameterValue.t,1.1,1.2 ProtocolStep.t,1.1,1.2

From: <jas...@us...> - 2003-04-17 17:59:02

Update of /cvsroot/genex/genex-server/Genex/t
In directory sc8-pr-cvs1:/tmp/cvs-serv16363/Genex/t

Modified Files:
	ParameterValue.t ProtocolStep.t 
Log Message:
new columns


Index: ParameterValue.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/ParameterValue.t,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ParameterValue.t	16 Apr 2003 23:27:14 -0000	1.1
--- ParameterValue.t	17 Apr 2003 17:58:55 -0000	1.2
***************
*** 7,11 ****
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..25\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
--- 7,11 ----
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..34\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
***************
*** 48,51 ****
--- 48,63 ----
  result ($obj->parameter_fk() == 555);
  
+ # testing the ro_groupname attribute method
+ $obj->ro_groupname(555);
+ result ($obj->ro_groupname() == 555);
+ 
+ # testing the rw_groupname attribute method
+ $obj->rw_groupname(555);
+ result ($obj->rw_groupname() == 555);
+ 
+ # testing the audit_fk attribute method
+ $obj->audit_fk(555);
+ result ($obj->audit_fk() == 555);
+ 
  # testing the proto_step_obj attribute method
  $obj->proto_step_obj(555);
***************
*** 55,58 ****
--- 67,82 ----
  $obj->proto_step_obj(555);
  result ($obj->proto_step_obj() == 555);
+ 
+ # testing the ro_groupname_obj attribute method
+ $obj->ro_groupname_obj(555);
+ result ($obj->ro_groupname_obj() == 555);
+ 
+ # testing the rw_groupname_obj attribute method
+ $obj->rw_groupname_obj(555);
+ result ($obj->rw_groupname_obj() == 555);
+ 
+ # testing the audit_obj attribute method
+ $obj->audit_obj(555);
+ result ($obj->audit_obj() == 555);
  
  # testing the fetched attribute method

Index: ProtocolStep.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/ProtocolStep.t,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ProtocolStep.t	16 Apr 2003 23:27:14 -0000	1.1
--- ProtocolStep.t	17 Apr 2003 17:58:56 -0000	1.2
***************
*** 7,11 ****
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..25\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
--- 7,11 ----
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..26\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
***************
*** 135,138 ****
--- 135,141 ----
                 ));
  }
+ 
+ # testing superclass Bio::Genex::Identifiable
+ result($obj->isa(q[Bio::Genex::Identifiable]));
  
  # testing the column_names method

[Genex-cvs-commit] genex-server/Genex/t ProtocolApplicationLink.t,NONE,1.1

From: <jas...@us...> - 2003-04-17 17:58:47

Update of /cvsroot/genex/genex-server/Genex/t
In directory sc8-pr-cvs1:/tmp/cvs-serv16250/Genex/t

Added Files:
	ProtocolApplicationLink.t 
Log Message:
new table


--- NEW FILE: ProtocolApplicationLink.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl ProtocolApplicationLink.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..21\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::ProtocolApplicationLink;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::ProtocolApplicationLink->new();

# testing the other_fk attribute method
$obj->other_fk(555);
result ($obj->other_fk() == 555);

# testing the proto_app_fk attribute method
$obj->proto_app_fk(555);
result ($obj->proto_app_fk() == 555);

# testing the proto_app_obj attribute method
$obj->proto_app_obj(555);
result ($obj->proto_app_obj() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result(!defined $obj->pkey_name());


# testing the tablename method
result($obj->tablename() eq q[ProtocolApplicationLink]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::ProtocolApplicationLink::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::ProtocolApplicationLink::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::ProtocolApplicationLink::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::ProtocolApplicationLink::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::ProtocolApplicationLink::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::ProtocolApplicationLink::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::ProtocolApplicationLink::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::ProtocolApplicationLink::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::ProtocolApplicationLink::UNIQUE_COLUMNS});

[Genex-cvs-commit] genex-server/Mason/workspace protocol-insert.html,1.1,1.2

From: <jas...@us...> - 2003-04-17 17:58:26

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv16122/Mason/workspace

Modified Files:
	protocol-insert.html 
Log Message:
* Mason/workspace/protocol-insert.html (Repository): 
changed URI to a text <input>



Index: protocol-insert.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/protocol-insert.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** protocol-insert.html	16 Apr 2003 23:14:06 -0000	1.1
--- protocol-insert.html	17 Apr 2003 17:58:22 -0000	1.2
***************
*** 10,15 ****
  % } else {
  	<h2>Read Group</h2>
! 	<p>Choose the <b>read group</b> that will be given to create
! 	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">
--- 10,15 ----
  % } else {
  	<h2>Read Group</h2>
! 	<p>Choose the <b>read group</b> that will be given to the
! 	protocol you are creating.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">
***************
*** 31,36 ****
  
  	<h2>Write Group</h2>
! 	<p>Choose the <b>write group</b> that will be given to create
! 	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">
--- 31,36 ----
  
  	<h2>Write Group</h2>
! 	<p>Choose the <b>write group</b> that will be given to the
! 	protocol you are creating.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">
***************
*** 122,126 ****
   	  <tr>
   	    <td>
! 		      <textarea name="uri" rows="1" cols="65"></textarea>
   	    </td>
   	  </tr>
--- 122,126 ----
   	  <tr>
   	    <td>
! 		      <input type="text" name="uri" size="65" maxlength="128"/>
   	    </td>
   	  </tr>

[Genex-cvs-commit] genex-server/Mason/workspace procedure-insert.html,1.1,1.2

From: <jas...@us...> - 2003-04-17 17:57:46

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv15861/Mason/workspace

Modified Files:
	procedure-insert.html 
Log Message:
documentation changes


Index: procedure-insert.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/procedure-insert.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** procedure-insert.html	17 Apr 2003 15:41:44 -0000	1.1
--- procedure-insert.html	17 Apr 2003 17:57:40 -0000	1.2
***************
*** 10,15 ****
  % } else {
  	<h2>Read Group</h2>
! 	<p>Choose the <b>read group</b> that will be given to create
! 	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">
--- 10,15 ----
  % } else {
  	<h2>Read Group</h2>
! 	<p>Choose the <b>read group</b> that will be given to the
! 	procedure you are creating.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">
***************
*** 31,36 ****
  
  	<h2>Write Group</h2>
! 	<p>Choose the <b>write group</b> that will be given to create
! 	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">
--- 31,36 ----
  
  	<h2>Write Group</h2>
! 	<p>Choose the <b>write group</b> that will be given to the
! 	procedure you are creating.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
  	  <thead  bgcolor="#FFD78F">

[Genex-cvs-commit] genex-server/Mason/workspace index.html,1.5,1.6

From: <jas...@us...> - 2003-04-17 17:57:14

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv15605/Mason/workspace

Modified Files:
	index.html 
Log Message:
new guis


Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/index.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** index.html	17 Apr 2003 15:41:59 -0000	1.5
--- index.html	17 Apr 2003 17:57:05 -0000	1.6
***************
*** 19,23 ****
--- 19,25 ----
        <li><a href="group-create.html">group-create.html</a></li>
        <li><a href="contact-insert.html">contact-insert.html</a></li>
+       <li><a href="parameter-insert.html">parameter-insert.html</a></li>
        <li><a href="protocol-insert.html">protocol-insert.html</a></li>
+       <li><a href="protocol-step-insert.html">protocol-step-insert.html</a></li>
        <li><a href="procedure-insert.html">procedure-insert.html</a></li>
      </ul>

[Genex-cvs-commit] genex-server/Mason/workspace parameter-insert.html,NONE,1.1 protocol-step-insert.html,NONE,1.1

From: <jas...@us...> - 2003-04-17 17:56:55

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv15424/Mason/workspace

Added Files:
	parameter-insert.html protocol-step-insert.html 
Log Message:
new guis


--- NEW FILE: parameter-insert.html ---
    <h1 align="center"><% $name %></h1>
    <form action="<% $action %>" 
	  method="post" enctype="multipart/form-data">
      <div align="center">

% if ($submit) {

	<h2><% $data %></h2>

% } else {
	<h2>Read Group</h2>
	<p>Choose the <b>read group</b> that will be given to the
	parameter you are creating.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Read Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"read_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Write Group</h2>
	<p>Choose the <b>write group</b> that will be given to the
	parameter you are creating.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Write Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"write_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Procedure</h2>
	<p>Choose the <b>Procedure</b> to which this parameter belongs.</p>
	<p>The entry must exist in the DB first, click <a
	href="procedure-insert.html">here</a> if you need to enter the
	Procedure info, then
	return to this page and hit your browsers <b>Reload</b> button.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Procedure</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"proc_fk",
		   array_ref=>\@procs &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Parameter Type</h2>
	<p>Choose the <b>Parameter Type</b> that describes the type of
	parameter.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Parameter Type</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"parameter_type",
		   array_ref=>\@parameter_types &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Name</h2>
		<p> Provide an optional name used to specify this Parameter.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Name</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		      <input type="text" name="param_name" size="20" maxlength="128"/>
 	    </td>
 	  </tr>
	  </tbody>
	</table>
	<hr noshade size=5>

	<h2>Default Value</h2>
		<p> Provide a default value for this Parameter that
		will be used if none is specified.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Default Value</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		      <input type="text" name="default" size="20" maxlength="128"/>
 	    </td>
 	  </tr>
	  </tbody>
	</table>
	<hr noshade size=5>

	<input type="submit" name="submit" value="Create Parameter" size="33">
        <& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
	<hr noshade size=5>

% }
      </div>
    </form>

<%args>
    $debug => 0
    $submit => ''
    $read_group => ''
    $write_group => ''
    $default => ''
    $param_name => ''
    $parameter_type => ''
    $proc_fk => ''
</%args>
<%attr>
  action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/parameter-insert.html"
  name=>'GeneX DB Parameter Creation Page'
  path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/parameter-insert.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::GroupSec;
use Bio::Genex::Procedure;
use Bio::Genex::ControlledVocab;
# use Apache::DB ();

</%once>
<%init>;
    my $name = $m->current_comp->attr('name');
    my $path = $m->current_comp->attr('path');
    my $action = $m->current_comp->attr('action');

# Apache::DB->init;
# Apache::DB->handler;

    my @groups;
    my $no_type = 'NONE';
    my @protocols;
    my @procs;
    my @parameter_types;
    my $data = '';
    if ($submit) {
      my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/parameter-insert.pl";
      my @args = ("--user=$session->{username}",
		  "--password=$session->{password}",
		  "--dbname=$session->{dbname}",
		  "--ro_group=$read_group",
		  "--rw_group=$write_group",
		  "--type='$parameter_type'",
		  "--default='$default'",
		  "--name='$param_name'",
		  "--proc_fk='$proc_fk'",
		 );
      my @pks;
      my $command = join(' ', $cmd, @args);
      my $pk = `$command`;
      if ($?) {
	$data = <<EOE;
<p><b>ERROR</b></p>
<p>Executing $command</p>
<p>Error output = &lt;$!&gt;</p>
EOE
} else {
      push(@pks,$pk);
      $data = "Parameter Successfully Created";
}
    } else {
      my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
      foreach my $gs_db (@gs_dbs) {
	push(@groups,[$gs_db->name,$gs_db->name]);
      }

      my @proc_dbs = Bio::Genex::Procedure->get_all_objects($dbh);
      foreach my $proc_db (@proc_dbs) {
	push(@procs,[$proc_db->proc_pk, $proc_db->name]);
      }

      my @pt_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,
								column=>'vocab_name',
								value=>'PARAM_Type',
							       );
      foreach my $pt_db (@pt_dbs) {
	push(@parameter_types,[$pt_db->term_string,$pt_db->term_string]);
      }

    }
</%init>

--- NEW FILE: protocol-step-insert.html ---
    <h1 align="center"><% $name %></h1>
    <form action="<% $action %>" 
	  method="post" enctype="multipart/form-data">
      <div align="center">

% if ($submit) {

	<h2><% $data %></h2>

% } else {
	<h2>Read Group</h2>
	<p>Choose the <b>read group</b> that will be given to the
	protocol step you are creating.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Read Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"read_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Write Group</h2>
	<p>Choose the <b>write group</b> that will be given to the
	protocol step you are creating.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Write Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"write_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Order</h2>
	<p>Indicate the numerical order of this step in the protocol.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Order</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		  <input type="text" name="order" size="65" maxlength="128">
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Protocol</h2>
	<p>Choose the <b>Protocol</b> to which this step belongs.</p>
	<p>The entry must exist in the DB first, click <a
	href="protocol-insert.html">here</a> if you need to enter the
	Protocol info, then
	return to this page and hit your browsers <b>Reload</b> button.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Protocol</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"proto_fk",
		   array_ref=>\@protocols &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Procedure</h2>
	<p>Choose the <b>Procedure</b> to which this step belongs.</p>
	<p>The entry must exist in the DB first, click <a
	href="procedure-insert.html">here</a> if you need to enter the
	Procedure info, then
	return to this page and hit your browsers <b>Reload</b> button.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Procedure</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"proc_fk",
		   array_ref=>\@procs &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<input type="submit" name="submit" value="Create Protocol Step" size="33">
        <& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
	<hr noshade size=5>

% }
      </div>
    </form>

<%args>
    $debug => 0
    $submit => ''
    $read_group => ''
    $write_group => ''
    $order => ''
    $proto_fk => ''
    $proc_fk => ''
</%args>
<%attr>
  action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/protocol-step-insert.html"
  name=>'GeneX DB Protocol Step Creation Page'
  path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/protocol-step-insert.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::GroupSec;
use Bio::Genex::Protocol;
use Bio::Genex::Procedure;
# use Apache::DB ();

</%once>
<%init>;
    my $name = $m->current_comp->attr('name');
    my $path = $m->current_comp->attr('path');
    my $action = $m->current_comp->attr('action');

# Apache::DB->init;
# Apache::DB->handler;

    my @groups;
    my $no_type = 'NONE';
    my @protocols;
    my @procs;
    my @contacts = ([$no_type,$no_type]);
    my $data = '';
    if ($submit) {
      my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/protocol-step-insert.pl";
      my @args = ("--user=$session->{username}",
		  "--password=$session->{password}",
		  "--dbname=$session->{dbname}",
		  "--ro_group=$read_group",
		  "--rw_group=$write_group",
		  "--order='$order'",
		  "--proto_fk='$proto_fk'",
		  "--proc_fk='$proc_fk'",
		 );
      my @pks;
      my $command = join(' ', $cmd, @args);
      my $pk = `$command`;
      if ($?) {
	$data = <<EOE;
<p><b>ERROR</b></p>
<p>Executing $command</p>
<p>Error output = &lt;$!&gt;</p>
EOE
} else {
      push(@pks,$pk);
      $data = "Protocol Step Successfully Created";
}
    } else {
      my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
      foreach my $gs_db (@gs_dbs) {
	push(@groups,[$gs_db->name,$gs_db->name]);
      }

      my @proto_dbs = Bio::Genex::Protocol->get_all_objects($dbh);
      foreach my $proto_db (@proto_dbs) {
	push(@protocols,[$proto_db->protocol_pk, $proto_db->name]);
      }

      my @proc_dbs = Bio::Genex::Procedure->get_all_objects($dbh);
      foreach my $proc_db (@proc_dbs) {
	push(@procs,[$proc_db->proc_pk, $proc_db->name]);
      }

    }
</%init>

[Genex-cvs-commit] genex-server/Genex/scripts procedure-insert.pl.in,1.1,1.2

From: <jas...@us...> - 2003-04-17 17:56:09

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv15071/Genex/scripts

Modified Files:
	procedure-insert.pl.in 
Log Message:
removed cruft


Index: procedure-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/procedure-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** procedure-insert.pl.in	17 Apr 2003 15:42:41 -0000	1.1
--- procedure-insert.pl.in	17 Apr 2003 17:56:02 -0000	1.2
***************
*** 24,28 ****
  use Bio::Genex::GenexAdmin;
  
- $Bio::Genex::Contact::DEBUG = 1;
  $Bio::Genex::GenexAdmin::DEBUG = 1;
  $Bio::Genex::Procedure::DEBUG = 1;
--- 24,27 ----

[Genex-cvs-commit] genex-server/Genex/scripts make_classes.pl,1.29,1.30

From: <jas...@us...> - 2003-04-17 17:55:39

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv14834/Genex/scripts

Modified Files:
	make_classes.pl 
Log Message:
new classes


Index: make_classes.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/make_classes.pl,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** make_classes.pl	16 Apr 2003 23:25:19 -0000	1.29
--- make_classes.pl	17 Apr 2003 17:55:34 -0000	1.30
***************
*** 108,112 ****
         {target=>'Feature'},
         {target=>'ContactType'},
-        {target=>'AM_Spots'},
         {target=>'Chromosome'},
         {target=>'GenexAdmin'},
--- 108,111 ----
***************
*** 122,129 ****
         {target=>'QuantitationLink',linking=>1},
         {target=>'AM_FactorValues',linking=>1},
-        {target=>'AM_SuspectSpots',linking=>1},
         {target=>'HotSpots',linking=>1},
         {target=>'Treatment_AMs',linking=>1},
! #        {target=>'SampleProtocols',linking=>1},
         {target=>'SF_ExternalDBLink',linking=>1},
         {target=>'TL_FactorValues',linking=>1},
--- 121,127 ----
         {target=>'QuantitationLink',linking=>1},
         {target=>'AM_FactorValues',linking=>1},
         {target=>'HotSpots',linking=>1},
         {target=>'Treatment_AMs',linking=>1},
!        {target=>'ProtocolApplicationLink',linking=>1},
         {target=>'SF_ExternalDBLink',linking=>1},
         {target=>'TL_FactorValues',linking=>1},

[Genex-cvs-commit] genex-server/Genex/scripts parameter-insert.pl.in,NONE,1.1 protocol-step-insert.pl.in,NONE,1.1

From: <jas...@us...> - 2003-04-17 17:55:19

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv14648/Genex/scripts

Added Files:
	parameter-insert.pl.in protocol-step-insert.pl.in 
Log Message:
new data entry apps


--- NEW FILE: parameter-insert.pl.in ---
%%START_PERL%%
#
# parameter-insert.pl.in
#    first version Tue Oct 24 14:13:45 MST 2000
#    script for inserting parameter entries into genex DB
#
# author: Jason E. Stewart (ja...@op...)
# Copyright 2003 Jason E. Stewart
#
my $VERSION = '$Id: parameter-insert.pl.in,v 1.1 2003/04/17 17:55:14 jason_e_stewart Exp $ ';

use strict;
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%

# use blib;
use Bio::Genex qw(error);
use Bio::Genex::XMLUtils;
use Bio::Genex::Procedure;
use Bio::Genex::Parameter;
use Bio::Genex::Config;
use Bio::Genex::GenexAdmin;

$Bio::Genex::GenexAdmin::DEBUG = 1;
$Bio::Genex::Parameter::DEBUG = 1;

my $infile;
my %OPTIONS;
$OPTIONS{dbname} = $Bio::Genex::Connect::DBNAME;
$OPTIONS{ro_groupname} = 'public';
$OPTIONS{rw_groupname} = 'superuser';
my $rc = GetOptions(\%OPTIONS,
		    'dbname=s',
		    'default=s',
		    'type=s',
		    'name=s',
		    'proc_fk=i',
		    'ro_groupname=s',
		    'rw_groupname=s',
		    'username=s',
		    'password=s',
		    'help',
		    'debug',
		   );

my $USAGE = <<"EOU";
usage: $0 [required flags] [options]

  required flags:
    --proc_fk=num      : the procedure foreign key
    --username=name    : the DB username to login as
    --password=word    : the DB password to login with

  optional parameters:
    --default=value     : the default value of the parameter
    --type=name         : the parameter data type
    --name=name         : the name used to specify the parameter
    --dbname=name       : the name of the DB to create
    --ro_groupname=name : the name of the read-only group to use
    --rw_groupname=name : the name of the read-write group to use
    --debug           : rollback instead of commit
    --help            : print this message
EOU

die "Bad option\n$USAGE" unless $rc;
die $USAGE if exists $OPTIONS{help};

die "Must specify --username\n$USAGE"
  unless exists $OPTIONS{username};
die "Must specify --password\n$USAGE"
  unless exists $OPTIONS{password};

# open up a writeable connection
my $dbh = Bio::Genex::Connect->new(DBNAME=>$OPTIONS{dbname},
				   USER => $OPTIONS{username},
				   PASSWORD => $OPTIONS{password},
				   TRANSACTION => 1,
				  );

my @error_args = (caller=>$0);

die "Must specify --proc_fk\n$USAGE"
  unless exists $OPTIONS{proc_fk};

my ($ro_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
							  column=>'name',
							  value=>$OPTIONS{ro_groupname},
							 );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate $OPTIONS{ro_groupname} group")
  unless defined $ro_group_db;

my ($rw_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
							  column=>'name',
							  value=>$OPTIONS{rw_groupname},
							 );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate $OPTIONS{rw_groupname} group")
  unless defined $rw_group_db;

my $param_db = Bio::Genex::Parameter->new(ro_groupname_obj=>$ro_group_db,
					  rw_groupname_obj=>$rw_group_db,
					);

my ($proc_db) = Bio::Genex::Procedure->get_all_objects($dbh,
						       column=>'proc_pk',
						       value=>$OPTIONS{proc_fk},
						      );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate Procedure entry for value: $OPTIONS{proc_fk}")
  unless defined $proc_db;
$param_db->proc_obj($proc_db);

# handle the simple optional arguments
$param_db->name($OPTIONS{name})
  if exists $OPTIONS{name};
$param_db->type($OPTIONS{type})
  if exists $OPTIONS{type};
$param_db->default_value($OPTIONS{default})
  if exists $OPTIONS{default};

print "Adding Parameter info\n";
$param_db->insert_db($dbh);
$dbh->error(@error_args,
	    message=>"Couldn't insert Parameter",
	   ) if $dbh->err;


print STDERR "Finished\n";

if (exists $OPTIONS{debug}) {
  $dbh->rollback();
} else {
  $dbh->commit();
}
$dbh->disconnect();
exit(0);

--- NEW FILE: protocol-step-insert.pl.in ---
%%START_PERL%%
#
# procedure-insert.pl.in
#    first version Tue Oct 24 14:13:45 MST 2000
#    script for inserting procedure entries into genex DB
#
# author: Jason E. Stewart (ja...@op...)
# Copyright 2003 Jason E. Stewart
#
my $VERSION = '$Id: protocol-step-insert.pl.in,v 1.1 2003/04/17 17:55:14 jason_e_stewart Exp $ ';

use strict;
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%

# use blib;
use Bio::Genex qw(error);
use Bio::Genex::XMLUtils;
use Bio::Genex::ProtocolStep;
use Bio::Genex::Contact;
use Bio::Genex::Config;
use Bio::Genex::GenexAdmin;

$Bio::Genex::GenexAdmin::DEBUG = 1;
$Bio::Genex::ProtocolStep::DEBUG = 1;

my $infile;
my %OPTIONS;
$OPTIONS{dbname} = $Bio::Genex::Connect::DBNAME;
$OPTIONS{ro_groupname} = 'public';
$OPTIONS{rw_groupname} = 'superuser';
my $rc = GetOptions(\%OPTIONS,
		    'dbname=s',
		    'order=i',
		    'proto_fk=i',
		    'proc_fk=i',
		    'ro_groupname=s',
		    'rw_groupname=s',
		    'username=s',
		    'password=s',
		    'help',
		    'debug',
		   );

my $USAGE = <<"EOU";
usage: $0 [required flags] [options]

  required flags:
    --proto_fk=num     : the protocol foreign key
    --proto_fk=num     : the procedure foreign key
    --order=num        : the order of this step in the protocol
    --username=name    : the DB username to login as
    --password=word    : the DB password to login with

  optional parameters:
    --dbname=name       : the name of the DB to create
    --ro_groupname=name : the name of the read-only group to use
    --rw_groupname=name : the name of the read-write group to use
    --debug           : rollback instead of commit
    --help            : print this message
EOU

die "Bad option\n$USAGE" unless $rc;
die $USAGE if exists $OPTIONS{help};

die "Must specify --username\n$USAGE"
  unless exists $OPTIONS{username};
die "Must specify --password\n$USAGE"
  unless exists $OPTIONS{password};

# open up a writeable connection
my $dbh = Bio::Genex::Connect->new(DBNAME=>$OPTIONS{dbname},
				   USER => $OPTIONS{username},
				   PASSWORD => $OPTIONS{password},
				   TRANSACTION => 1,
				  );

my @error_args = (caller=>$0);

die "Must specify --order\n$USAGE"
  unless exists $OPTIONS{order};
die "Must specify --proto_fk\n$USAGE"
  unless exists $OPTIONS{proto_fk};
die "Must specify --proc_fk\n$USAGE"
  unless exists $OPTIONS{proc_fk};

my ($ro_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
							  column=>'name',
							  value=>$OPTIONS{ro_groupname},
							 );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate $OPTIONS{ro_groupname} group")
  unless defined $ro_group_db;

my ($rw_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
							  column=>'name',
							  value=>$OPTIONS{rw_groupname},
							 );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate $OPTIONS{rw_groupname} group")
  unless defined $rw_group_db;

my $ps_db = Bio::Genex::ProtocolStep->new(ro_groupname_obj=>$ro_group_db,
					    rw_groupname_obj=>$rw_group_db,
					    order=>$OPTIONS{order},
					);

my ($proto_db) = Bio::Genex::Protocol->get_all_objects($dbh,
						       column=>'protocol_pk',
						       value=>$OPTIONS{proto_fk},
						      );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate Protocol entry for value: $OPTIONS{proto_fk}")
  unless defined $proto_db;
$ps_db->protocol_obj($proto_db);

my ($proc_db) = Bio::Genex::Procedure->get_all_objects($dbh,
						       column=>'proc_pk',
						       value=>$OPTIONS{proc_fk},
						      );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate Procedure entry for value: $OPTIONS{proc_fk}")
  unless defined $proc_db;
$ps_db->proc_obj($proc_db);

print "Adding ProtocolStep info\n";
$ps_db->insert_db($dbh);
$dbh->error(@error_args,
	    message=>"Couldn't insert ProtocolStep",
	   ) if $dbh->err;


print STDERR "Finished\n";

if (exists $OPTIONS{debug}) {
  $dbh->rollback();
} else {
  $dbh->commit();
}
$dbh->disconnect();
exit(0);

[Genex-cvs-commit] genex-server/Genex/ProtocolApplicationLink - New directory

From: <jas...@us...> - 2003-04-17 17:54:30

Update of /cvsroot/genex/genex-server/Genex/ProtocolApplicationLink
In directory sc8-pr-cvs1:/tmp/cvs-serv14275/Genex/ProtocolApplicationLink

Log Message:
Directory /cvsroot/genex/genex-server/Genex/ProtocolApplicationLink added to the repository

[Genex-cvs-commit] genex-server/Genex/scripts .cvsignore,1.24,1.25

From: <jas...@us...> - 2003-04-17 15:43:00

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv5553

Modified Files:
	.cvsignore 
Log Message:
usual


Index: .cvsignore
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/.cvsignore,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** .cvsignore	7 Nov 2002 14:58:58 -0000	1.24
--- .cvsignore	17 Apr 2003 15:42:55 -0000	1.25
***************
*** 21,24 ****
--- 21,25 ----
  mbad-insert.pl
  priveleges.pl
+ procedure-insert.pl
  protocol-insert.pl
  qtdim-insert.pl

[Genex-cvs-commit] genex-server/Genex/scripts procedure-insert.pl.in,NONE,1.1

From: <jas...@us...> - 2003-04-17 15:42:44

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv5447

Added Files:
	procedure-insert.pl.in 
Log Message:
new app for inserting procedures


--- NEW FILE: procedure-insert.pl.in ---
%%START_PERL%%
#
# procedure-insert.pl.in
#    first version Tue Oct 24 14:13:45 MST 2000
#    script for inserting procedure entries into genex DB
#
# author: Jason E. Stewart (ja...@op...)
# Copyright 2003 Jason E. Stewart
#
my $VERSION = '$Id: procedure-insert.pl.in,v 1.1 2003/04/17 15:42:41 jason_e_stewart Exp $ ';

use strict;
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%

# use blib;
use Bio::Genex qw(error);
use Bio::Genex::XMLUtils;
use Bio::Genex::Procedure;
use Bio::Genex::Contact;
use Bio::Genex::Config;
use Bio::Genex::GenexAdmin;

$Bio::Genex::Contact::DEBUG = 1;
$Bio::Genex::GenexAdmin::DEBUG = 1;
$Bio::Genex::Procedure::DEBUG = 1;

my $infile;
my %OPTIONS;
$OPTIONS{dbname} = $Bio::Genex::Connect::DBNAME;
$OPTIONS{ro_groupname} = 'public';
$OPTIONS{rw_groupname} = 'superuser';
my $rc = GetOptions(\%OPTIONS,
		    'dbname=s',
		    'name=s',
		    'description=s',
		    'ro_groupname=s',
		    'rw_groupname=s',
		    'type=s',
		    'username=s',
		    'password=s',
		    'help',
		    'debug',
		   );

my $USAGE = <<"EOU";
usage: $0 [required flags] [options]

  required flags:
    --name=name        : the procedure name
    --description=text : the procedure description
    --username=name    : the DB username to login as
    --password=word    : the DB password to login with

  optional parameters:
    --type=name       : the procedure type (fkey)
    --dbname=name     : the name of the DB to create
    --ro_groupname=name : the name of the read-only group to use
    --rw_groupname=name : the name of the read-write group to use
    --debug           : rollback instead of commit
    --help            : print this message
EOU

die "Bad option\n$USAGE" unless $rc;
die $USAGE if exists $OPTIONS{help};

die "Must specify --username\n$USAGE"
  unless exists $OPTIONS{username};
die "Must specify --password\n$USAGE"
  unless exists $OPTIONS{password};

# open up a writeable connection
my $dbh = Bio::Genex::Connect->new(DBNAME=>$OPTIONS{dbname},
				   USER => $OPTIONS{username},
				   PASSWORD => $OPTIONS{password},
				   TRANSACTION => 1,
				  );

my @error_args = (caller=>$0);

die "Must specify --name\n$USAGE"
  unless exists $OPTIONS{name};
die "Must specify --description\n$USAGE"
  unless exists $OPTIONS{description};

# get all the arguments for a single procedure from the command line
my ($ro_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
							  column=>'name',
							  value=>$OPTIONS{ro_groupname},
							 );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate $OPTIONS{ro_groupname} group")
  unless defined $ro_group_db;

my ($rw_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
							  column=>'name',
							  value=>$OPTIONS{rw_groupname},
							 );
$dbh->error(@error_args,
	    no_errstr=>1,
	    message=>"Couldn't locate $OPTIONS{rw_groupname} group")
  unless defined $rw_group_db;

my $proc_db = Bio::Genex::Procedure->new(ro_groupname_obj=>$ro_group_db,
					 rw_groupname_obj=>$rw_group_db,
					 name=>$OPTIONS{name},
					 description=>$OPTIONS{description},

					);

# handle the simple optional arguments
$proc_db->type($OPTIONS{type})
  if exists $OPTIONS{type};

print "Adding procedure info\n";
$proc_db->insert_db($dbh);
$dbh->error(@error_args,
	    message=>"Couldn't insert procedure",
	   ) if $dbh->err;


print STDERR "Finished\n";

if (exists $OPTIONS{debug}) {
  $dbh->rollback();
} else {
  $dbh->commit();
}
$dbh->disconnect();
exit(0);

[Genex-cvs-commit] genex-server/Mason/workspace index.html,1.4,1.5

From: <jas...@us...> - 2003-04-17 15:42:04

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv5093a

Modified Files:
	index.html 
Log Message:
new file


Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/index.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** index.html	17 Apr 2003 04:42:46 -0000	1.4
--- index.html	17 Apr 2003 15:41:59 -0000	1.5
***************
*** 20,23 ****
--- 20,24 ----
        <li><a href="contact-insert.html">contact-insert.html</a></li>
        <li><a href="protocol-insert.html">protocol-insert.html</a></li>
+       <li><a href="procedure-insert.html">procedure-insert.html</a></li>
      </ul>
  <%attr>

[Genex-cvs-commit] genex-server/Mason/workspace procedure-insert.html,NONE,1.1

From: <jas...@us...> - 2003-04-17 15:41:50

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv4945

Added Files:
	procedure-insert.html 
Log Message:
procedure GUI


--- NEW FILE: procedure-insert.html ---
    <h1 align="center"><% $name %></h1>
    <form action="<% $action %>" 
	  method="post" enctype="multipart/form-data">
      <div align="center">

% if ($submit) {

	<h2><% $data %></h2>

% } else {
	<h2>Read Group</h2>
	<p>Choose the <b>read group</b> that will be given to create
	the array design files that you load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Read Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"read_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Write Group</h2>
	<p>Choose the <b>write group</b> that will be given to create
	the array design files that you load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Write Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"write_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Name</h2>
	<p>Choose a <b>Name</b> for your procedure. If you use single
	quotes, they will be removed, so don't.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Name</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		  <input type="text" name="proc_name" size="65" maxlength="128">
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Procedure Type</h2>
	<p>Choose the <b>Procedure Type</b> that describes the type of
	procedure.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Procedure Type</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"procedure_type",
		   array_ref=>\@procedure_types &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Procedure Description</h2> <p>Describe the procedure. If you
	use single quotes, they will be removed, so don't.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Procedure Description</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		      <textarea name="proc_desc" rows="5" cols="65"></textarea>
 	    </td>
 	  </tr>
	  </tbody>
	</table>
	<hr noshade size=5>

	<input type="submit" name="submit" value="Create Procedure" size="33">
        <& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
	<hr noshade size=5>

% }
      </div>
    </form>

<%args>
    $debug => 0
    $submit => ''
    $uri => ''
    $provider => ''
    $read_group => ''
    $write_group => ''
    $proc_desc => ''
    $procedure_type => ''
    $proc_name => ''
</%args>
<%attr>
  action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/procedure-insert.html"
  name=>'GeneX DB Procedure Creation Page'
  path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/procedure-insert.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::Contact;
use Bio::Genex::GroupSec;
use Bio::Genex::Procedure;
use Bio::Genex::ControlledVocab;
# use Apache::DB ();

</%once>
<%init>;
    my $name = $m->current_comp->attr('name');
    my $path = $m->current_comp->attr('path');
    my $action = $m->current_comp->attr('action');

# Apache::DB->init;
# Apache::DB->handler;

    $dbh->assert_table_defined('GroupSec');
    $dbh->assert_table_defined('Procedure');

    my @groups;
    my $no_type = 'NONE';
    my @procedure_types = ([$no_type,$no_type]);
    my @contacts = ([$no_type,$no_type]);
    my $data = '';
    if ($submit) {
      $proc_name =~ s/\'//;
      my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/procedure-insert.pl";
      my @args = ("--user=$session->{username}",
		  "--password=$session->{password}",
		  "--dbname=$session->{dbname}",
		  "--ro_group=$read_group",
		  "--rw_group=$write_group",
		  "--name='$proc_name'",
		 );
      if ($proc_desc) {
	$proc_desc =~ s/\'//;
	push(@args,"--description='$proc_desc'");
      }
      if ($procedure_type ne $no_type) {
	push(@args,"--type=$procedure_type");
      }

      my @pks;
      my $command = join(' ', $cmd, @args);
      my $pk = `$command`;
      if ($?) {
	$data = <<EOE;
<p><b>ERROR</b></p>
<p>Executing $command</p>
<p>Error output = &lt;$!: $pk &gt;</p>
EOE
} else {
      push(@pks,$pk);
      $data = "Procedure, $proc_name, Successfully Created";
}
    } else {
      my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
      foreach my $gs_db (@gs_dbs) {
	push(@groups,[$gs_db->name,$gs_db->name]);
      }

     my @pt_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,
								column=>'vocab_name',
								value=>'PROC_Type',
							       );
      foreach my $pt_db (@pt_dbs) {
	push(@procedure_types,[$pt_db->term_string,$pt_db->term_string]);
      }

    }
</%init>

[Genex-cvs-commit] genex-server/DB/controlled_vocab PROC_Type.xml,NONE,1.1

From: <jas...@us...> - 2003-04-17 15:40:26

Update of /cvsroot/genex/genex-server/DB/controlled_vocab
In directory sc8-pr-cvs1:/tmp/cvs-serv4435

Added Files:
	PROC_Type.xml 
Log Message:
cv's for procedures


--- NEW FILE: PROC_Type.xml ---
<?xml version="1.0" standalone="yes"?>
<controlled_vocabulary db_table="Procedure" db_column="type" cv_table="PROC_Type">
  <comment type="definition">This table provides the restricted
  vocabulary for the column type in the table Procedure and is used to
  give meaning to the types of low-level operations that make up a
  larger protocol.
</comment>
<term name="numerical"
        description="a mathematical manipulation of numerical data"/>
<term name="statistical"
        description="generating statistics of numerical data"/>
<term name="other_procedure"
        description="less general procedures"/>
</controlled_vocabulary>

<!--
*** emacs file mode definition ***
Local Variables:
ispell-personal-dictionary:"../.ispell-dict"
End:
-->

[Genex-cvs-commit] genex-server/Genex ChangeLog,1.130,1.131

From: <jas...@us...> - 2003-04-17 07:37:54

Update of /cvsroot/genex/genex-server/Genex
In directory sc8-pr-cvs1:/tmp/cvs-serv5210/Genex

Modified Files:
	ChangeLog 
Log Message:
usual


Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v
retrieving revision 1.130
retrieving revision 1.131
diff -C2 -d -r1.130 -r1.131
*** ChangeLog	16 Apr 2003 23:29:58 -0000	1.130
--- ChangeLog	17 Apr 2003 07:37:50 -0000	1.131
***************
*** 1,3 ****
--- 1,14 ----
+ 2003-04-17  Jason E. Stewart  <ja...@op...>
+ 
+ 	* XMLUtils/XMLUtils.pm.in (Repository): 
+ 	major fix to handling inheritance of columns in views in xml2sql()
+ 
+ 	* Connect/Connect.pm.in (Repository): 
+ 	minor fix in probably broken lookup_sw_id()
+ 
  2003-04-16  Jason E. Stewart  <ja...@op...>
+ 
+ 	* scripts/protocol-insert.pl.in (Repository): 
+ 	forgot to actually call insert_db()
  
  	* XMLUtils/XMLUtils.pm.in (Repository):

[Genex-cvs-commit] genex-server ChangeLog,1.125,1.126

From: <jas...@us...> - 2003-04-17 07:37:53

Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv5210

Modified Files:
	ChangeLog 
Log Message:
usual


Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.125
retrieving revision 1.126
diff -C2 -d -r1.125 -r1.126
*** ChangeLog	16 Apr 2003 23:30:20 -0000	1.125
--- ChangeLog	17 Apr 2003 07:37:49 -0000	1.126
***************
*** 1,2 ****
--- 1,7 ----
+ 2003-04-17  Jason E. Stewart  <ja...@op...>
+ 
+ 	* Mason/workspace/data-loader.html.in (Repository): 
+ 	sw_pk => param_pk
+ 
  2003-04-16  Jason E. Stewart  <ja...@op...>

[Genex-cvs-commit] genex-server/Mason/workspace data-loader.html.in,1.4,1.5

From: <jas...@us...> - 2003-04-17 07:37:31

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv5127/Mason/workspace

Modified Files:
	data-loader.html.in 
Log Message:
* Mason/workspace/data-loader.html.in (Repository): 
sw_pk => param_pk



Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** data-loader.html.in	16 Apr 2003 23:28:04 -0000	1.4
--- data-loader.html.in	17 Apr 2003 07:37:28 -0000	1.5
***************
*** 154,164 ****
  </%args>
  <%attr>
!   action=>'%%GENEX_WORKSPACE_URL%%/data-loader.html'
    name=>'GeneX DB Data Loader Page'
!   path=>'%%GENEX_WORKSPACE_URL%%/data-loader.html'
  </%attr>
  <%once>
  use Bio::Genex;
  use Bio::Genex::Connect;
  use Bio::Genex::ArrayDesign;
  use Bio::Genex::ExperimentSet;
--- 154,165 ----
  </%args>
  <%attr>
!   action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/data-loader.html"
    name=>'GeneX DB Data Loader Page'
!   path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/data-loader.html"
  </%attr>
  <%once>
  use Bio::Genex;
  use Bio::Genex::Connect;
+ use Bio::Genex::Config;
  use Bio::Genex::ArrayDesign;
  use Bio::Genex::ExperimentSet;
***************
*** 228,235 ****
        my @fe_dbs = Bio::Genex::FeatureExtractionSoftware->get_all_objects($dbh);
        foreach my $fe_db (@fe_dbs) {
! 	push(@feature_extractions,[$fe_db->sw_pk,$fe_db->name . ':' . $fe_db->version]);
        }
  
!       my @files = glob('%%GENEX_UPLOAD_DIR%%/*.txt');
        foreach my $name (@files) {
  	my $short_name = $name;
--- 229,236 ----
        my @fe_dbs = Bio::Genex::FeatureExtractionSoftware->get_all_objects($dbh);
        foreach my $fe_db (@fe_dbs) {
! 	push(@feature_extractions,[$fe_db->param_pk,$fe_db->name . ':' . $fe_db->version]);
        }
  
!       my @files = glob("$Bio::Genex::Config->{GENEX_UPLOAD_DIR}/*.txt");
        foreach my $name (@files) {
  	my $short_name = $name;

[Genex-cvs-commit] genex-server/Genex/XMLUtils XMLUtils.pm.in,1.31,1.32

From: <jas...@us...> - 2003-04-17 07:37:03

Update of /cvsroot/genex/genex-server/Genex/XMLUtils
In directory sc8-pr-cvs1:/tmp/cvs-serv4939/Genex/XMLUtils

Modified Files:
	XMLUtils.pm.in 
Log Message:
* XMLUtils/XMLUtils.pm.in (Repository): 
major fix to handling inheritance of columns in views in xml2sql()



Index: XMLUtils.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/XMLUtils/XMLUtils.pm.in,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** XMLUtils.pm.in	16 Apr 2003 23:29:26 -0000	1.31
--- XMLUtils.pm.in	17 Apr 2003 07:36:59 -0000	1.32
***************
*** 541,546 ****
      # will enforce it in the where clause, otherwise it's public
      my @inherited_columns;
!     if ($inherits_from ne 'none') {
!       @inherited_columns = $docs{$inherits_from}->getElementsByTagName('column');
      }
      my $view = "$ {table_name}_view";
--- 541,552 ----
      # will enforce it in the where clause, otherwise it's public
      my @inherited_columns;
!     my @inherits_from;
!     push(@inherits_from,$docs{$inherits_from})
!       if ($inherits_from ne 'none');
!     foreach my $doc (@inherits_from) {
!       push(@inherited_columns, $doc->getElementsByTagName('column'));
!       my $new_inherits_from = $doc->getDocumentElement->getAttribute('inherits_from');
!       push(@inherits_from,$docs{$new_inherits_from})
! 	if ($new_inherits_from ne 'none');
      }
      my $view = "$ {table_name}_view";

[Genex-cvs-commit] genex-server/Genex/Connect Connect.pm.in,1.10,1.11

From: <jas...@us...> - 2003-04-17 07:36:18

Update of /cvsroot/genex/genex-server/Genex/Connect
In directory sc8-pr-cvs1:/tmp/cvs-serv4606/Genex/Connect

Modified Files:
	Connect.pm.in 
Log Message:
* Connect/Connect.pm.in (Repository): 
minor fix in probably broken lookup_sw_id()



Index: Connect.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Connect/Connect.pm.in,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Connect.pm.in	17 Dec 2002 19:53:28 -0000	1.10
--- Connect.pm.in	17 Apr 2003 07:36:12 -0000	1.11
***************
*** 938,942 ****
    my ($dbh,$name,$approx) = @_;
  
!   return $dbh->lookup_id('Software','name','sw_pk',$name,$approx);
  }
  
--- 938,942 ----
    my ($dbh,$name,$approx) = @_;
  
!   return $dbh->lookup_id('Software','name','param_pk',$name,$approx);
  }

[Genex-cvs-commit] genex-server/Genex/scripts protocol-insert.pl.in,1.9,1.10

From: <jas...@us...> - 2003-04-17 05:06:30

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv23614

Modified Files:
	protocol-insert.pl.in 
Log Message:
* scripts/protocol-insert.pl.in (Repository): 
forgot to actually call insert_db()



Index: protocol-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/protocol-insert.pl.in,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** protocol-insert.pl.in	16 Apr 2003 23:25:06 -0000	1.9
--- protocol-insert.pl.in	17 Apr 2003 05:06:26 -0000	1.10
***************
*** 190,199 ****
        unless defined $con_db;
      $proto_db->provider_con_obj($con_db);
    }
  }
  
  print STDERR "Finished\n";
  
! if ($OPTIONS{debug}) {
    $dbh->rollback();
  } else {
--- 190,205 ----
        unless defined $con_db;
      $proto_db->provider_con_obj($con_db);
+ 
    }
+   print "Adding protocol info\n";
+   $proto_db->insert_db($dbh);
+   $dbh->error(@error_args,
+ 	      message=>"Couldn't insert protocol",
+ 	     ) if $dbh->err;
  }
  
  print STDERR "Finished\n";
  
! if (exists $OPTIONS{debug}) {
    $dbh->rollback();
  } else {

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