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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']);
|
|
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.
|
|
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;
|
|
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 |
|
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
|
|
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});
|
|
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>
|
|
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">
|
|
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>
|
|
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 $command</p>
<p>Error output = <$!></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 $command</p>
<p>Error output = <$!></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>
|
|
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 ---- |
|
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},
|
|
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);
|
|
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 |
|
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 |
|
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);
|
|
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>
|
|
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 $command</p>
<p>Error output = <$!: $pk ></p>
EOE
} else {
push(@pks,$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>
|
|
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:
-->
|
|
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): |
|
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...> |
|
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 = $name;
|
|
From: <jas...@us...> - 2003-04-17 07:37:03
|
Update of /cvsroot/genex/genex-server/Genex/XMLUtils
In directory sc8-pr-cvs1:/tmp/cvs-serv4939/Genex/XMLUtils
Modified Files:
XMLUtils.pm.in
Log Message:
* XMLUtils/XMLUtils.pm.in (Repository):
major fix to handling inheritance of columns in views in xml2sql()
Index: XMLUtils.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/XMLUtils/XMLUtils.pm.in,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** XMLUtils.pm.in 16 Apr 2003 23:29:26 -0000 1.31
--- XMLUtils.pm.in 17 Apr 2003 07:36:59 -0000 1.32
***************
*** 541,546 ****
# will enforce it in the where clause, otherwise it's public
my @inherited_columns;
! if ($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";
|
|
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);
}
|
|
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 {
|
