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Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv25103
Modified Files:
add_user_to_group.html.in arrays.html.in authenticate.html.in
autohandler.in bioassay.html.in contact-insert.html.in
data-sources.html.in experiments.html.in
experimentset-create.html.in generate_group.html.in
generate_user.html.in group-create.html.in group-maint.html.in
kill-cookie.html.in noauth-autohandler.in query.html.in
user-insert.html.in workspace.html.in
Log Message:
removed all compile time '%%' substitutions in favor of runtime substitution
Index: add_user_to_group.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/add_user_to_group.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** add_user_to_group.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- add_user_to_group.html.in 21 Apr 2003 00:29:36 -0000 1.2
***************
*** 83,89 ****
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/add_user_to_group.html'
name=>'Associate Genex User With Group'
! path=>'%%GENEX_WORKSPACE_URL%%/add_user_to_group.html'
</%attr>
<%args>
--- 83,89 ----
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/add_user_to_group.html"
name=>'Associate Genex User With Group'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/add_user_to_group.html"
</%attr>
<%args>
***************
*** 106,109 ****
--- 106,110 ----
use Bio::Genex;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use Bio::Genex::GroupSec;
use Bio::Genex::UserSec;
***************
*** 112,122 ****
$OPTIONS{ro_groupname} = "public";
$OPTIONS{rw_groupname} = "superuser";
! $OPTIONS{SU_USERNAME} = "genex"; # this is now hard coded
! $OPTIONS{dbname} = "%%DB_NAME%%";
my $response_page;
my $db=Bio::Genex::Connect->new(
! USER=>$OPTIONS{SU_USERNAME},
! PASSWORD=>$OPTIONS{SU_PASSWORD},
! DBNAME=>$OPTIONS{dbname},
);
my @activegroups; # holds the names of the groups to which this user belongs
--- 113,122 ----
$OPTIONS{ro_groupname} = "public";
$OPTIONS{rw_groupname} = "superuser";
! $OPTIONS{dbname} = "$Bio::Genex::Congig->{DB_NAME}";
my $response_page;
my $db=Bio::Genex::Connect->new(
! USER=>$session->{username},
! PASSWORD=>$session->{password},
! DBNAME=>$session->{dbname},
);
my @activegroups; # holds the names of the groups to which this user belongs
Index: arrays.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/arrays.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** arrays.html.in 25 Nov 2002 21:45:32 -0000 1.1
--- arrays.html.in 21 Apr 2003 00:29:37 -0000 1.2
***************
*** 6,10 ****
<%attr>
name=>'GeneX DB BioAssay Display Page'
! path=>'%%GENEX_WORKSPACE_URL%%/array.html'
</%attr>
<%once>;
--- 6,10 ----
<%attr>
name=>'GeneX DB BioAssay Display Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/array.html"
</%attr>
<%once>;
***************
*** 20,26 ****
my $path = $m->current_comp->attr('path');
- $dbh->assert_table_defined('PhysicalBioAssay');
- $dbh->assert_table_defined('MeasuredBioAssay');
-
if ($type eq 'mba') {
my ($mba_db) = Bio::Genex::MeasuredBioAssay->get_objects($dbh, $id);
--- 20,23 ----
***************
*** 45,53 ****
$m->clear_buffer();
! my ($out_fh,$out_file) = tempfile(DIR=>'%%HTMLTMPDIR%%',
);
my $out_url = $out_file;
$out_url =~ s|.*/||;
! $out_url = "%%CGITMPURL%%/$out_url";
# print header
--- 42,50 ----
$m->clear_buffer();
! my ($out_fh,$out_file) = tempfile(DIR=>"$Bio::Genex::Config->{HTMLTMPDIR}",
);
my $out_url = $out_file;
$out_url =~ s|.*/||;
! $out_url = "$Bio::Genex::Config->{CGITMPURL}/$out_url";
# print header
Index: authenticate.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/authenticate.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** authenticate.html.in 20 Nov 2002 21:25:40 -0000 1.2
--- authenticate.html.in 21 Apr 2003 00:29:37 -0000 1.3
***************
*** 61,65 ****
<%attr>
name=>'GeneX DB Authentication Page'
! server=>'%%HTML_ROOT_URL%%'
</%attr>
<%args>
--- 61,65 ----
<%attr>
name=>'GeneX DB Authentication Page'
! server=>"$Bio::Genex::Config->{HTML_ROOT_URL}"
</%attr>
<%args>
***************
*** 67,75 ****
$login=>''
$password=>''
! $dbname=>'%%DB_NAME%%'
</%args>
<%once>;
use Bio::Genex::HTMLUtils;
use Bio::Genex::Connect;
</%once>
<%init>;
--- 67,76 ----
$login=>''
$password=>''
! $dbname=>"$Bio::Genex::Config->{DB_NAME}"
</%args>
<%once>;
use Bio::Genex::HTMLUtils;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
</%once>
<%init>;
Index: autohandler.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/autohandler.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** autohandler.in 26 Nov 2002 17:49:11 -0000 1.4
--- autohandler.in 21 Apr 2003 00:29:37 -0000 1.5
***************
*** 9,13 ****
<tr>
<td align=right valign=top>
! <img src="%%GENEX_GRAPHICS_URL%%/genex-banner-new.gif">
</td>
</tr>
--- 9,13 ----
<tr>
<td align=right valign=top>
! <img src="<% $src %>"/>
</td>
</tr>
***************
*** 18,24 ****
--- 18,27 ----
<p><% $DEBUG %></p>
+ <p>Go to workspace <a href="<% $index %>">index</a></p>
+
</body>
</html>
<%once>
+ use Bio::Genex::Config;
use Bio::Genex::HTMLUtils;
</%once>
***************
*** 29,32 ****
--- 32,37 ----
my $comp = $m->fetch_next();
my $name = $comp->attr('name');
+ my $src = "$Bio::Genex::Config->{GENEX_GRAPHICS_URL}/genex-banner-new.gif";
+ my $index = "$Bio::Genex::Config->{GENEX_MASON_URL}/index.html";
# we localize $dbh and $session so that they last only the duration of the request
Index: bioassay.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/bioassay.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** bioassay.html.in 20 Nov 2002 22:34:36 -0000 1.2
--- bioassay.html.in 21 Apr 2003 00:29:37 -0000 1.3
***************
*** 21,27 ****
</table>
- <hr noshade size=5>
-
- <input type="submit" name="submit" value="Load Data" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
--- 21,24 ----
***************
*** 38,48 ****
</%args>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
! name=>'GeneX DB Array Design Loader Page'
! path=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::MeasuredBioAssay;
--- 35,46 ----
</%args>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/bioassay.html"
! name=>'GeneX DB MeasuredBioAssay Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/bioassay.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use Bio::Genex::GroupSec;
use Bio::Genex::MeasuredBioAssay;
***************
*** 53,58 ****
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
-
- $dbh->assert_table_defined('MeasuredBioAssay');
my @bioassays;
--- 51,54 ----
Index: contact-insert.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/contact-insert.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** contact-insert.html.in 15 Apr 2003 17:47:28 -0000 1.1
--- contact-insert.html.in 21 Apr 2003 00:29:37 -0000 1.2
***************
*** 268,274 ****
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/contact-insert.html'
name=>'Create New Genex Contact'
! path=>'%%GENEX_WORKSPACE_URL%%/contact-insert.html'
</%attr>
<%args>
--- 268,274 ----
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/contact-insert.html"
name=>'Create New Genex Contact'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/contact-insert.html"
</%attr>
<%args>
Index: data-sources.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-sources.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** data-sources.html.in 20 Nov 2002 22:35:04 -0000 1.2
--- data-sources.html.in 21 Apr 2003 00:29:37 -0000 1.3
***************
*** 53,65 ****
</%args>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/query.html'
name=>'GeneX DB Data Source Selection Page'
! path=>'%%GENEX_WORKSPACE_URL%%/data-sources.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
!
! $dbh->assert_table_defined('G2G');
#
--- 53,64 ----
</%args>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/query.html"
name=>'GeneX DB Data Source Selection Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/data-sources.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
! use Bio::Genex::Config;
#
Index: experiments.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/experiments.html.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** experiments.html.in 25 Nov 2002 21:47:49 -0000 1.3
--- experiments.html.in 21 Apr 2003 00:29:37 -0000 1.4
***************
*** 55,64 ****
</%args>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/arrays.html'
name=>'GeneX DB Experiment Display Page'
! path=>'%%GENEX_WORKSPACE_URL%%/experiments.html'
</%attr>
<%once>;
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::HTMLUtils;
--- 55,65 ----
</%args>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/arrays.html"
name=>'GeneX DB Experiment Display Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/experiments.html"
</%attr>
<%once>;
use Bio::Genex;
+ use Bio::Genex::Config;
use Bio::Genex::Connect;
use Bio::Genex::HTMLUtils;
***************
*** 72,77 ****
my $action = $m->current_comp->attr('action');
- $dbh->assert_table_defined('PhysicalBioAssay');
- $dbh->assert_table_defined('MeasuredBioAssay');
my @exp_dbs = Bio::Genex::ExperimentSet->get_objects($dbh,
@experiments);
--- 73,76 ----
Index: experimentset-create.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/experimentset-create.html.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** experimentset-create.html.in 22 Nov 2002 00:38:37 -0000 1.3
--- experimentset-create.html.in 21 Apr 2003 00:29:37 -0000 1.4
***************
*** 172,178 ****
</%args>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/experimentset-create.html'
name=>'GeneX DB ExperimentSet Creation Page'
! path=>'%%GENEX_WORKSPACE_URL%%/experimentset-create.html'
</%attr>
<%once>
--- 172,178 ----
</%args>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/experimentset-create.html"
name=>'GeneX DB ExperimentSet Creation Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/experimentset-create.html"
</%attr>
<%once>
***************
*** 193,199 ****
# Apache::DB->handler;
- $dbh->assert_table_defined('GroupSec');
- $dbh->assert_table_defined('ExperimentSet');
-
my @groups;
my $no_type = 'NONE';
--- 193,196 ----
***************
*** 203,212 ****
if ($submit) {
$exp_name =~ s/\'//;
! my $cmd = '%%GENEX_BIN_DIR%%/experimentset-create.pl';
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
"--name='$exp_name'",
);
--- 200,209 ----
if ($submit) {
$exp_name =~ s/\'//;
! my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/experimentset-create.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
"--name='$exp_name'",
);
***************
*** 220,227 ****
}
if ($treatment_type ne $no_type) {
! push(@args,"--treatment_type=$treatment_type");
}
if ($quantity_series_type ne $no_type) {
! push(@args,"--quantity_series_type=$quantity_series_type");
}
--- 217,224 ----
}
if ($treatment_type ne $no_type) {
! push(@args,"--treatment_type='$treatment_type'");
}
if ($quantity_series_type ne $no_type) {
! push(@args,"--quantity_series_type='$quantity_series_type'");
}
Index: generate_group.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/generate_group.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** generate_group.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- generate_group.html.in 21 Apr 2003 00:29:37 -0000 1.2
***************
*** 128,134 ****
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/generate_group.html'
name=>'Create New Genex Group'
! path=>'%%GENEX_WORKSPACE_URL%%/generate_group.html'
</%attr>
<%args>
--- 128,134 ----
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/generate_group.html"
name=>'Create New Genex Group'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/generate_group.html"
</%attr>
<%args>
***************
*** 153,156 ****
--- 153,157 ----
use Bio::Genex::GroupSec;
use Bio::Genex::Contact;
+ use Bio::Genex::Config;
use Bio::Genex::GroupLink;
my %OPTIONS;
***************
*** 158,162 ****
$OPTIONS{rw_groupname} = "superuser";
$OPTIONS{SU_USERNAME} = "genex"; # this is now hard coded
! $OPTIONS{dbname} = "%%DB_NAME%%";
my $response_page;
--- 159,163 ----
$OPTIONS{rw_groupname} = "superuser";
$OPTIONS{SU_USERNAME} = "genex"; # this is now hard coded
! $OPTIONS{dbname} = "$Bio::Genex::Config->{DB_NAME}";
my $response_page;
Index: generate_user.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/generate_user.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** generate_user.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- generate_user.html.in 21 Apr 2003 00:29:37 -0000 1.2
***************
*** 235,241 ****
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/generate_user.html'
name=>'Create New Genex User'
! path=>'%%GENEX_WORKSPACE_URL%%/generate_user.html'
</%attr>
<%args>
--- 235,241 ----
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/generate_user.html"
name=>'Create New Genex User'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/generate_user.html"
</%attr>
<%args>
***************
*** 267,270 ****
--- 267,271 ----
use Bio::Genex;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use Bio::Genex::UserSec;
use Bio::Genex::Contact;
***************
*** 274,278 ****
$OPTIONS{ro_groupname} = "public";
$OPTIONS{rw_groupname} = "superuser";
! $OPTIONS{dbname} = "%%DB_NAME%%";
$OPTIONS{SU_USERNAME} = "genex";
$OPTIONS{SU_PASSWORD} = $SU_PASSWORD;
--- 275,279 ----
$OPTIONS{ro_groupname} = "public";
$OPTIONS{rw_groupname} = "superuser";
! $OPTIONS{dbname} = "$Bio::Genex::Config->{DB_NAME}";
$OPTIONS{SU_USERNAME} = "genex";
$OPTIONS{SU_PASSWORD} = $SU_PASSWORD;
Index: group-create.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/group-create.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** group-create.html.in 20 Nov 2002 22:33:09 -0000 1.2
--- group-create.html.in 21 Apr 2003 00:29:37 -0000 1.3
***************
*** 107,117 ****
</%args>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/group-create.html'
name=>'GeneX DB Group Creation Page'
! path=>'%%GENEX_WORKSPACE_URL%%/group-create.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
--- 107,118 ----
</%args>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/group-create.html"
name=>'GeneX DB Group Creation Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/group-create.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use Bio::Genex::GroupSec;
***************
*** 122,132 ****
my $action = $m->current_comp->attr('action');
- $dbh->assert_table_defined('GroupSec');
-
my @groups;
my $data = '';
if ($submit) {
$group_name =~ s/\'//;
! my $cmd = '%%GENEX_BIN_DIR%%/group-insert.pl';
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
--- 123,131 ----
my $action = $m->current_comp->attr('action');
my @groups;
my $data = '';
if ($submit) {
$group_name =~ s/\'//;
! my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/group-insert.pl";
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
***************
*** 160,164 ****
$data = <<EOT;
<p>Group <$pk> successfully created. You can now populate the group <a
! href="%%GENEX_WORKSPACE_URL%%/group-maint.html?submitted=true&groupname=$pk">here</a></p>
EOT
}
--- 159,163 ----
$data = <<EOT;
<p>Group <$pk> successfully created. You can now populate the group <a
! href="$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/group-maint.html?submitted=true&groupname=$pk">here</a></p>
EOT
}
Index: group-maint.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/group-maint.html.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** group-maint.html.in 9 Apr 2003 20:42:26 -0000 1.4
--- group-maint.html.in 21 Apr 2003 00:29:37 -0000 1.5
***************
*** 79,85 ****
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/group-maint.html'
name=>'Associate Genex User With Group'
! path=>'%%GENEX_WORKSPACE_URL%%/group-maint.html'
</%attr>
<%args>
--- 79,85 ----
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/group-maint.html"
name=>'Associate Genex User With Group'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/group-maint.html"
</%attr>
<%args>
***************
*** 92,95 ****
--- 92,96 ----
<%once>;
use Bio::Genex;
+ use Bio::Genex::Config;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
***************
*** 104,111 ****
my $action = $m->current_comp->attr('action');
-
- $dbh->assert_table_defined('UserSec');
- $dbh->assert_table_defined('GroupSec');
- $dbh->assert_table_defined('GroupLink');
my $response_page;
--- 105,108 ----
Index: kill-cookie.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/kill-cookie.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** kill-cookie.html.in 20 Nov 2002 21:21:28 -0000 1.1
--- kill-cookie.html.in 21 Apr 2003 00:29:37 -0000 1.2
***************
*** 8,15 ****
<%once>;
use CGI::Cookie;
</%once>
<%init>;
my $session_cookie = CGI::Cookie->new(-name=>"GENEX_SESSION_ID",
! -path=>'%%GENEX_SESSION_PATH%%',
-expires=>'now',
-value=>'ccc',
--- 8,16 ----
<%once>;
use CGI::Cookie;
+ use Bio::Genex::Config;
</%once>
<%init>;
my $session_cookie = CGI::Cookie->new(-name=>"GENEX_SESSION_ID",
! -path=>"$Bio::Genex::Config->{GENEX_SESSION_PATH}",
-expires=>'now',
-value=>'ccc',
Index: noauth-autohandler.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/noauth-autohandler.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** noauth-autohandler.in 20 Nov 2002 21:20:33 -0000 1.1
--- noauth-autohandler.in 21 Apr 2003 00:29:37 -0000 1.2
***************
*** 9,13 ****
<tr>
<td align=right valign=top>
! <img src="%%GENEX_GRAPHICS_URL%%/genex-banner-new.gif">
</td>
</tr>
--- 9,13 ----
<tr>
<td align=right valign=top>
! <img src="<% $src %>">
</td>
</tr>
***************
*** 23,28 ****
--- 23,32 ----
inherit => 'syshandler'
</%flags>
+ <%once>
+ use Bio::Genex::Config;
+ </%once>
<%init>;
my $comp = $m->fetch_next();
my $name = $comp->attr('name');
+ my $src = "$Bio::Genex::Config->{GENEX_GRAPHICS_URL}/genex-banner-new.gif";
</%init>
Index: query.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/query.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** query.html.in 20 Nov 2002 22:31:59 -0000 1.2
--- query.html.in 21 Apr 2003 00:29:37 -0000 1.3
***************
*** 74,78 ****
<%args>
@g2g => ()
! @local => ('%%DB_NAME%%')
$debug => 0
</%args>
--- 74,78 ----
<%args>
@g2g => ()
! @local => ("$Bio::Genex::Config->{DB_NAME}")
$debug => 0
</%args>
***************
*** 85,88 ****
--- 85,89 ----
use Bio::Genex;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use Bio::Genex::ExperimentSet;
use Bio::Genex::ArrayDesign;
***************
*** 114,120 ****
</%once>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/experiments.html'
name=>'GeneX DB Query Page'
! path=>'%%GENEX_WORKSPACE_URL%%/query.html'
</%attr>
<%init>;
--- 115,121 ----
</%once>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/experiments.html"
name=>'GeneX DB Query Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/query.html"
</%attr>
<%init>;
Index: user-insert.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/user-insert.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** user-insert.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- user-insert.html.in 21 Apr 2003 00:29:37 -0000 1.2
***************
*** 238,244 ****
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/user-insert.html'
name=>'Create New Genex User'
! path=>'%%GENEX_WORKSPACE_URL%%/user-insert.html'
</%attr>
<%args>
--- 238,244 ----
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/user-insert.html"
name=>'Create New Genex User'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/user-insert.html"
</%attr>
<%args>
***************
*** 274,277 ****
--- 274,278 ----
use Bio::Genex;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use Bio::Genex::UserSec;
use Bio::Genex::Contact;
***************
*** 279,283 ****
my %OPTIONS;
! $OPTIONS{dbname} = "%%DB_NAME%%";
# set predictable default if this variable doesn't exist;
--- 280,284 ----
my %OPTIONS;
! $OPTIONS{dbname} = "$Bio::Genex::Config->{DB_NAME}";
# set predictable default if this variable doesn't exist;
***************
*** 304,308 ****
DBNAME=>$OPTIONS{dbname},
);
! my $perl = '%%START_PERL%%' ;
$perl =~ s/^\#\!//;
$commandline = "$perl %%GENEX_BIN_DIR%%/user-insert.pl ".
--- 305,309 ----
DBNAME=>$OPTIONS{dbname},
);
! my $perl = "" ;
$perl =~ s/^\#\!//;
$commandline = "$perl %%GENEX_BIN_DIR%%/user-insert.pl ".
Index: workspace.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/workspace.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** workspace.html.in 20 Nov 2002 22:30:23 -0000 1.2
--- workspace.html.in 21 Apr 2003 00:29:37 -0000 1.3
***************
*** 42,58 ****
</table>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/experiments.html'
name=>'GeneX DB Workspace Page'
! path=>'%%GENEX_WORKSPACE_URL%%/workspace.html'
</%attr>
<%args>
@g2g => ()
! @local => ('%%DB_NAME%%')
$debug => 0
</%args>
<%once>;
use Bio::Genex;
! use Bio::Genex::Connect;
! use Bio::Genex::ExperimentSet;
</%once>
<%init>;
--- 42,57 ----
</table>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/experiments.html"
name=>'GeneX DB Workspace Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/workspace.html"
</%attr>
<%args>
@g2g => ()
! @local => ("$Bio::Genex::Config->{DB_NAME}")
$debug => 0
</%args>
<%once>;
use Bio::Genex;
! use Bio::Genex::Config;
</%once>
<%init>;
|
|
From: <jas...@us...> - 2003-04-21 00:27:27
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv24851
Modified Files:
index.html
Log Message:
reorganized
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/index.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** index.html 17 Apr 2003 17:57:05 -0000 1.6
--- index.html 21 Apr 2003 00:27:23 -0000 1.7
***************
*** 1,26 ****
<h1>Mason Index</h1>
<ul>
<li><a href="authenticate.html">authenticate.html</a></li>
<li><a href="check-cookie.html">check-cookie.html</a></li>
<li><a href="check-login.html">check-login.html</a></li>
- <li><a href="data-sources.html">data-sources.html</a></li>
- <li><a href="experiments.html">experiments.html</a></li>
<li><a href="kill-cookie.html">kill-cookie.html</a></li>
<li><a href="logout.html">logout.html</a></li>
! <li><a href="query.html">query.html</a></li>
! <li><a href="workspace.html">workspace.html</a></li>
<li><a href="generate_user.html">generate_user.html</a></li>
<li><a href="group-maint.html">group-maint.html</a></li>
- <li><a href="data-loader.html">data-loader.html</a></li>
- <li><a href="array-design.html">array-design.html</a></li>
- <li><a href="bioassay.html">bioassay.html</a></li>
- <li><a
- href="experimentset-create.html">experimentset-create.html</a></li>
<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>
<%attr>
--- 1,39 ----
<h1>Mason Index</h1>
<ul>
+ <!-- Pages that exist but shouldn't be directly used
<li><a href="authenticate.html">authenticate.html</a></li>
+ <li><a href="experiments.html">experiments.html</a></li>
+ -->
+
+ <h2>Utilities for controlling GeneX login</h2>
<li><a href="check-cookie.html">check-cookie.html</a></li>
<li><a href="check-login.html">check-login.html</a></li>
<li><a href="kill-cookie.html">kill-cookie.html</a></li>
<li><a href="logout.html">logout.html</a></li>
!
! <h2>Utilities for Managing GeneX Users and Groups</h2>
<li><a href="generate_user.html">generate_user.html</a></li>
<li><a href="group-maint.html">group-maint.html</a></li>
<li><a href="group-create.html">group-create.html</a></li>
<li><a href="contact-insert.html">contact-insert.html</a></li>
+
+ <h2>Experimental Utilities for looking at GeneX Data</h2>
+ <b><font color="green">These utilities are experimental and not
+ guaranteed to work at the moment. Try them as you wish, but don't be
+ surprised if you get a colorful Mason screen dump.</font></b>
+ <li><a href="data-sources.html">data-sources.html</a></li>
+ <li><a href="query.html">query.html</a></li>
+ <li><a href="workspace.html">workspace.html</a></li>
+ <li><a href="bioassay.html">bioassay.html</a></li>
+
+ <h2>Utilities for loading Data and Annotations</h2>
+ <li><a href="data-loader.html">data-loader.html</a></li>
+ <li><a href="array-design.html">array-design.html</a></li>
+ <li><a href="experimentset-create.html">experimentset-create.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>
+ <li><a href="sample-insert.html">sample-insert.html</a></li>
</ul>
<%attr>
|
|
From: <jas...@us...> - 2003-04-21 00:26:33
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv24520
Added Files:
sample-insert.html.in
Log Message:
sample GUI
--- NEW FILE: sample-insert.html.in ---
% if (($response_page eq 'NEW') || ($response_page eq 'ERROR')) {
<center>
<h1>Create New Genex Sample</h1>
<p>Required fields have their field names shown in <font size="+1" color="red"><b>red</b></font></p>
% if ($response eq 'ERROR') {
<h2><font color="red">ERROR</font></h2>
<p>Your input had the following error: </p>
<b><% $error %></b>
% }
<form action="<% $action %>"><br>
<br>
<center>
<table cellpadding="2" cellspacing="2" border="0"
style="width: 70%; text-align: left; margin-left: auto; margin-right: auto;"
title="enter the following information for your sample"
summary="information about the new genex sample">
<caption><br>
</caption> <tbody>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top"><font size="+1" color="red"><b>Name</b></font><br>
<br>
</td>
<td valign="top"><input type="text" name="sample_name" width="30" value="<% $sample_name %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Description<br>
</td>
<td valign="top" colspan="2"><textarea width="40" height="7" name="sample_description"><% $sample_description %></textarea></td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top"><font size="+1" color="red"><b>Species</b></font><br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"spc_fk",
array_ref=>\@species &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Pathology Description<br>
</td>
<td valign="top" colspan="2"><textarea width="40" height="7" name="sample_pathology_descr"><% $sample_pathology_descr %></textarea></td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Seed Supplier Catalog Number<br>
<br>
</td>
<td valign="top"><input type="text" name="seed_supplier_cat_num" width="30" value="<% $sample_seed_supplier_cat_num %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Cultivar Name<br>
<br>
</td>
<td valign="top"><input type="text" name="sample_cultivar_name" width="30" value="<% $sample_cultivar_name %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Variety<br>
<br>
</td>
<td valign="top"><input name="sample_variety" type="text" width="30" value="<% $sample_variety %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Strain<br>
<br>
</td>
<td valign="top"><input name="sample_strain" type="text" width="30" value="<% $sample_strain %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Cell Line<br>
<br>
</td>
<td valign="top"><input name="sample_cell_line" type="text" value="<% $sample_cell_line %>" width="30"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Genotype<br>
<br>
</td>
<td valign="top"><input name="sample_genotype" type="text" width="30" value="<% $sample_genotype %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Phenotype<br>
</td>
<td valign="top"><input name="sample_phenotype_name" type="text" width="30" value="<% $sample_phenotype_name %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Sex/Mating Type<br>
<br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"sample_sex_mating_type",
array_ref=>\@sample_sex_mating_type &>
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Age<br>
<br>
</td>
<td valign="top"><input name="sample_age" type="text" width="30" value="<% $sample_age %>"></td>
<td valign="right">Age Units
<& comps/query-drop-down.mason, name=>"sample_age_units",
array_ref=>\@sample_age_units &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Developmental Stage Time<br>
<br>
</td>
<td valign="right"><input name="sample_dev_stage_time" type="text" width="30" value="<% $sample_dev_stage_time %>"></td>
<td>Stage Units
<& comps/query-drop-down.mason, name=>"sample_dev_stage_units",
array_ref=>\@sample_dev_stage_units &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Developmental Stage Name<br>
<br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"sample_dev_stage_name",
array_ref=>\@sample_dev_stage_name &>
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Growth Condition<br>
<br>
</td>
<td valign="top"><input name="sample_growth_cond" type="text" width="30" value="<% $sample_growth_cond %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Common Accession Number<br>
<br>
</td>
<td valign="top"><input name="sample_common_acc_num" type="text" width="30" value="<% $sample_common_acc_num %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">ABRC Accession Number<br>
<br>
</td>
<td valign="top"><input name="sample_abrc_acc_num" type="text" width="30" value="<% $sample_abrc_acc_num %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
g <td valign="top">Nottingham Accession Number<br>
<br>
</td>
<td valign="top"><input name="sample_nottingham_acc_num" type="text" width="30" value="<% $sample_nottingham_acc_num %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Genetic Status<br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"sample_genetic_status",
array_ref=>\@sample_genetic_status &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Tissue Type<br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"sample_tissue_type",
array_ref=>\@sample_tissue_type &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Organ Type<br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"sample_organ_type",
array_ref=>\@sample_organ_type &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Primary Cell Type<br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"sample_primary_cell_type",
array_ref=>\@sample_primary_cell_type &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Organism Intactness<br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"sample_organism_intactness",
array_ref=>\@sample_organism_intactness &>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Genetic Status Comment<br>
</td>
<td valign="top" colspan="2"><textarea width="40" height="7" name="sample_genetic_status_comment"><% $sample_genetic_status_comment %></textarea></td>
</tr>
</tbody>
</table>
</center>
<hr noshade size=5>
<& comps/ro_rw_group.mason, type=>"Sample" &>
<hr noshade size=5>
<& comps/contacts.mason, type=>"Sample", required=>1 &>
<hr noshade size=5>
<br>
<input name="submitted" type="hidden" value="true">
<input type="submit" name="submit" value="Create This Sample"><br>
<br>
<br>
</center>
% }
% if ($response_page eq 'DONE'){
<div style="text-align: center;">
<h1>Genex Sample Created</h1>
<p>Created with primary key <% $response %></p>
</div>
% }
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/sample-insert.html"
name=>'Create New Genex Sample'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/sample-insert.html"
</%attr>
<%args>
$read_group => ""
$write_group => ""
$provider => ""
$spc_fk => ""
$sample_age_units => ""
$sample_dev_stage_units => ""
$sample_organism_intactness => ""
$sample_genetic_status => ""
$sample_organ_type => ""
$sample_tissue_type => ""
$sample_atcc_cell_type => ""
$sample_primary_cell_type => ""
$sample_pathology_descr => ""
$sample_dev_stage_time => ""
$sample_dev_stage_name => ""
$sample_growth_cond => ""
$sample_common_acc_num => ""
$sample_abrc_acc_num => ""
$sample_nottingham_acc_num => ""
$sample_genetic_status_comment => ""
$sample_strain => ""
$sample_name => ""
$sample_description => ""
$sample_seed_supplier_cat_num => ""
$sample_cultivar_name => ""
$sample_cell_line => ""
$sample_variety => ""
$sample_genotype => ""
$sample_phenotype_name => ""
$sample_age => ""
$sample_sex_mating_type => ""
$submitted => ""
$debug => 0
</%args>
<%once>;
my $VERSION = '$Id: sample-insert.html.in,v 1.1 2003/04/21 00:26:29 jason_e_stewart Exp $ ';
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%
use Bio::Genex;
use Bio::Genex::Config;
use Bio::Genex::Species;
use Bio::Genex::Sample;
use Bio::Genex::ControlledVocab;
</%once>
<%init>;
my $action = $m->current_comp->attr('action');
my $response_page;
my $response;
my $error;
my $commandline;
my @all;
my @species;
my $no_type = 'NONE';
my @sample_age_units = ([$no_type,$no_type]);
my @sample_dev_stage_name = ([$no_type,$no_type]);
my @sample_dev_stage_units = ([$no_type,$no_type]);
my @sample_genetic_status = ([$no_type,$no_type]);
my @sample_organ_type = ([$no_type,$no_type]);
my @sample_organism_intactness = ([$no_type,$no_type]);
my @sample_primary_cell_type = ([$no_type,$no_type]);
my @sample_sex_mating_type = ([$no_type,$no_type]);
my @sample_tissue_type = ([$no_type,$no_type]);
my @spc_dbs = Bio::Genex::Species->get_all_objects($dbh);
foreach my $spc_db (@spc_dbs) {
push(@species,[$spc_db->spc_pk,$spc_db->primary_scientific_name]);
}
my @cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_AgeUnits');
foreach my $cv_db (@cv_dbs) {
push(@sample_age_units,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_DevelopmentStageName');
foreach my $cv_db (@cv_dbs) {
push(@sample_dev_stage_name,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_DevelopmentStageUnits');
foreach my $cv_db (@cv_dbs) {
push(@sample_dev_stage_units,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_GeneticStatus');
foreach my $cv_db (@cv_dbs) {
push(@sample_genetic_status,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_OrganType');
foreach my $cv_db (@cv_dbs) {
push(@sample_organ_type,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_OrganismIntactness');
foreach my $cv_db (@cv_dbs) {
push(@sample_organism_intactness,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_PrimaryCellType');
foreach my $cv_db (@cv_dbs) {
push(@sample_primary_cell_type,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_SexMatingType');
foreach my $cv_db (@cv_dbs) {
push(@sample_sex_mating_type,[$cv_db->cv_pk,$cv_db->term_string]);
}
@cv_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'SMP_TissueType');
foreach my $cv_db (@cv_dbs) {
push(@sample_tissue_type,[$cv_db->cv_pk,$cv_db->term_string]);
}
unless ($submitted eq "true"){ # first time only, never clicked the button
$response_page="NEW";
} else {
unless ($sample_name) {
$error = "Must define Name for your Sample";
$response = 'ERROR';
goto FINISHED;
}
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/sample-insert.pl";
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
"--dbname=$session->{dbname}",
"--ro_group=$read_group",
"--rw_group=$write_group",
"--name='$sample_name'",
"--spc_fk='$spc_fk'",
"--con_fk='$provider'",
);
push(@args,'--description'=>$sample_description)
if $sample_description;
push(@args,'--seed_supplier_cat_num'=>$sample_seed_supplier_cat_num)
if $sample_seed_supplier_cat_num;
push(@args,'--cultivar_name'=>$sample_cultivar_name)
if $sample_cultivar_name;
push(@args,'--variety'=>$sample_variety)
if $sample_variety;
push(@args,'--strain'=>$sample_strain)
if $sample_strain;
push(@args,'--cell_line'=>$sample_cell_line)
if $sample_cell_line;
push(@args,'--genotype'=>$sample_genotype)
if $sample_genotype;
push(@args,'--phenotype_name'=>$sample_phenotype_name)
if $sample_phenotype_name;
if ($sample_age) {
unless ($sample_age_units ne $no_type) {
$response = 'ERROR';
$error = 'You must supply Age Units together with Age';
goto FINISHED;
} else {
push(@args,'--age'=>$sample_age);
push(@args,'--age_units'=>$sample_age_units);
}
}
if ($sample_dev_stage_time) {
unless ($sample_dev_stage_units ne $no_type) {
$response = 'ERROR';
$error = 'You must supply Stage Units together with Development Stage Time';
goto FINISHED;
} else {
push(@args,'--dev_stage_time'=>$sample_dev_stage_time);
push(@args,'--dev_stage_units'=>$sample_dev_stage_units);
}
}
push(@args,'--sex_mating_type'=>$sample_sex_mating_type)
if $sample_sex_mating_type and $sample_sex_mating_type ne $no_type;
push(@args,'--dev_stage_name'=>$sample_dev_stage_name)
if $sample_dev_stage_name and $sample_dev_stage_name ne $no_type;
push(@args,'--organ_type'=>$sample_organ_type)
if $sample_organ_type and $sample_organ_type ne $no_type;
push(@args,'--tissue_type'=>$sample_tissue_type)
if $sample_tissue_type and $sample_tissue_type ne $no_type;
push(@args,'--atcc_cell_type'=>$sample_atcc_cell_type)
if $sample_atcc_cell_type and $sample_atcc_cell_type ne $no_type;
push(@args,'--primary_cell_type'=>$sample_primary_cell_type)
if $sample_primary_cell_type and $sample_atcc_cell_type ne $no_type;
push(@args,'--organism_intactness'=>$sample_organism_intactness)
if $sample_organism_intactness and $sample_organism_intactness ne $no_type;
push(@args,'--genetic_status'=>$sample_genetic_status)
if $sample_genetic_status and $sample_genetic_status ne $no_type;
push(@args,'--genetic_status_comment'=>$sample_genetic_status_comment)
if $sample_genetic_status_comment;
push(@args,'--growth_cond'=>$sample_growth_cond)
if $sample_growth_cond;
push(@args,'--pathology_descr'=>$sample_pathology_descr)
if $sample_pathology_descr;
push(@args,'--common_acc_num'=>$sample_common_acc_num)
if $sample_common_acc_num;
push(@args,'--abrc_acc_num'=>$sample_abrc_acc_num)
if $sample_abrc_acc_num;
push(@args,'--nottingham_acc_num'=>$sample_nottingham_acc_num)
if $sample_nottingham_acc_num;
my $command = join(' ', $cmd, @args);
$response = `$command`;
if ($?) {
$response = 'ERROR';
$error = <<EOE;
<p>Executing $command</p>
<p>Error output = <$!></p>
EOE
}
FINISHED : {
if ($response eq 'ERROR') {
$response_page='ERROR';
} else {
$response_page='DONE';
}
}
}
</%init>
|
|
From: <jas...@us...> - 2003-04-21 00:25:50
|
Update of /cvsroot/genex/genex-server/Mason/workspace/comps
In directory sc8-pr-cvs1:/tmp/cvs-serv24401/comps
Added Files:
contacts.mason ro_rw_group.mason
Log Message:
new components for common HTML
--- NEW FILE: contacts.mason ---
<h2><% $title %></h2>
<p>Choose the <b>Contact</b> entry who provided the <% $type %>
(if any).</p>
<p>The entry must exist in the DB first, click <a
href="contact-insert.html">here</a> if you need to enter
the Contact 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>Provider Contact</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& query-drop-down.mason, name=>"provider", array_ref=>\@contacts &>
</td>
</tr>
</tbody>
</table>
<%args>
$type
$required => 0
</%args>
<%once>
use Bio::Genex::Contact;
</%once>
<%init>
my $no_type = 'NONE';
my @contacts;
my $title = 'Provider Contact';
if ($required) {
$title = qq[<font color="red">$title</font>];
} else {
push(@contacts,([$no_type,$no_type]));
}
my @con_dbs = Bio::Genex::Contact->get_all_objects($dbh);
foreach my $con_db (@con_dbs) {
push(@contacts,[$con_db->con_pk,'[' . $con_db->contact_person .
":" . $con_db->organization . ']']);
}
</%init>
--- NEW FILE: ro_rw_group.mason ---
<h2>Read Group and Write Group</h2>
<p>Choose the <b>read group</b> and the <b>write group</b>
that will be given to the <% $type %> entry you create.</p>
<table bgcolor="#D8E4F7" border="1" cols="2">
<thead bgcolor="#FFD78F">
<tr>
<th>Read Group</th>
<th>Write Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& query-drop-down.mason, name=>"read_group",
array_ref=>\@groups &>
</td>
<td>
<& query-drop-down.mason, name=>"write_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<%args>
$type
</%args>
<%once>
use Bio::Genex::GroupSec;
</%once>
<%init>
my @groups;
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
foreach my $gs_db (@gs_dbs) {
push(@groups,[$gs_db->name,$gs_db->name]);
}
</%init>
|
|
From: <jas...@us...> - 2003-04-21 00:24:49
|
Update of /cvsroot/genex/genex-server/Genex/scripts In directory sc8-pr-cvs1:/tmp/cvs-serv24090 Modified Files: .cvsignore Log Message: usual Index: .cvsignore =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/scripts/.cvsignore,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -d -r1.26 -r1.27 *** .cvsignore 17 Apr 2003 17:59:11 -0000 1.26 --- .cvsignore 21 Apr 2003 00:24:45 -0000 1.27 *************** *** 28,31 **** --- 28,32 ---- quant-dim-insert.pl reporter-insert.pl + sample-insert.pl scanner-insert.pl security-insert.pl |
|
From: <jas...@us...> - 2003-04-21 00:24:30
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv23973
Modified Files:
array-design-insert.pl.in
Log Message:
removed old cruft
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** array-design-insert.pl.in 9 Apr 2003 02:53:06 -0000 1.18
--- array-design-insert.pl.in 21 Apr 2003 00:24:26 -0000 1.19
***************
*** 105,122 ****
unless defined $CONTACT_GENEX;
- my ($GROUP_PUBLIC) = Bio::Genex::GroupSec->get_all_objects($dbh,
- column=>'name',
- value=>'public',
- );
- die "Couldn't get 'public' group"
- unless defined $GROUP_PUBLIC;
-
- my ($GROUP_SU) = Bio::Genex::GroupSec->get_all_objects($dbh,
- column=>'name',
- value=>'superuser',
- );
- die "Couldn't get 'superuser' group"
- unless defined $GROUP_SU;
-
my $curr_table = 'ArrayDesign';
--- 105,108 ----
|
|
From: <jas...@us...> - 2003-04-21 00:21:38
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv23206
Added Files:
sample-insert.pl.in
Log Message:
new app for inserting samples
--- NEW FILE: sample-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: sample-insert.pl.in,v 1.1 2003/04/21 00:21:35 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::Sample;
use Bio::Genex::Contact;
use Bio::Genex::Species;
use Bio::Genex::Config;
use Bio::Genex::GenexAdmin;
$Bio::Genex::GenexAdmin::DEBUG = 1;
$Bio::Genex::Sample::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',
'con_fk=i',
'spc_fk=i',
'age_units=s',
'dev_stage_units=s',
'organism_intactness=s',
'genetic_status=s',
'organ_type=s',
'tissue_type=s',
'atcc_cell_type=s',
'primary_cell_type=s',
'pathology_descr=s',
'dev_stage_time=s',
'dev_stage_name=s',
'growth_cond=s',
'common_acc_num=s',
'abrc_acc_num=s',
'nottingham_acc_num=s',
'genetic_status_comment=s',
'strain=s',
'name=s',
'description=s',
'seed_supplier_cat_num=s',
'cultivar_name=s',
'cell_line=s',
'variety=s',
'genotype=s',
'phenotype_name=s',
'age=s',
'sex_mating_type=s',
'ro_groupname=s',
'rw_groupname=s',
'username=s',
'password=s',
'help',
'debug',
);
my $USAGE = <<"EOU";
usage: $0 [required flags] [options]
required flags:
--spc_fk=num : the species foreign key
--con_fk=num : the provider foreign key
--name=name : the name of this sample
--username=name : the DB username to login as
--password=word : the DB password to login with
optional parameters:
[lots and lots of sample columns]
--dbname=name : the name of the DB to create
--ro_groupname=name : the name of the read-only group to use
--rw_groupname=name : the name of the read-write group to use
--debug : rollback instead of commit
--help : print this message
EOU
die "Bad option\n$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 $OPTIONS{name};
die "Must specify --spc_fk\n$USAGE"
unless exists $OPTIONS{spc_fk};
my ($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 $rw_group_db;
my ($con_db) = Bio::Genex::Contact->get_all_objects($dbh,
column=>'con_pk',
value=>$OPTIONS{con_fk},
);
$dbh->error(@error_args,
no_errstr=>1,
message=>"Couldn't locate $OPTIONS{con_fk} group")
unless defined $con_db;
my ($spc_db) = Bio::Genex::Species->get_all_objects($dbh,
column=>'spc_pk',
value=>$OPTIONS{spc_fk},
);
$dbh->error(@error_args,
no_errstr=>1,
message=>"Couldn't locate $OPTIONS{spc_fk} group")
unless defined $spc_db;
my $samp_db = Bio::Genex::Sample->new(ro_groupname_obj=>$ro_group_db,
rw_groupname_obj=>$rw_group_db,
name=>$OPTIONS{name},
provider_con_obj=>$con_db,
spc_obj=>$spc_db,
);
$samp_db->description($OPTIONS{description})
if $OPTIONS{description};
$samp_db->seed_supplier_cat_num($OPTIONS{seed_supplier_cat_num})
if $OPTIONS{seed_supplier_cat_num};
$samp_db->cultivar_name($OPTIONS{cultivar_name})
if $OPTIONS{cultivar_name};
$samp_db->variety($OPTIONS{variety})
if $OPTIONS{variety};
$samp_db->strain($OPTIONS{strain})
if $OPTIONS{strain};
$samp_db->cell_line($OPTIONS{cell_line})
if $OPTIONS{cell_line};
$samp_db->genotype($OPTIONS{genotype})
if $OPTIONS{genotype};
$samp_db->phenotype_name($OPTIONS{phenotype_name})
if $OPTIONS{phenotype_name};
$samp_db->sex_mating_type($OPTIONS{sex_mating_type})
if $OPTIONS{sex_mating_type};
if ($OPTIONS{age}) {
unless (exists $OPTIONS{age_units}) {
$dbh->error(@error_args,
no_errstr=>1,
message=>'You must supply Age Units together with Age');
} else {
$samp_db->age($OPTIONS{age});
$samp_db->age_units($OPTIONS{age_units});
}
}
if ($OPTIONS{dev_stage_time}) {
unless (exists $OPTIONS{dev_stage_units}) {
$dbh->error(@error_args,
no_errstr=>1,
message=>'You must supply Stage Units together with Development Stage Time');
} else {
$samp_db->dev_stage_time($OPTIONS{dev_stage_time});
$samp_db->dev_stage_units($OPTIONS{dev_stage_units});
}
}
$samp_db->dev_stage_name($OPTIONS{dev_stage_name})
if $OPTIONS{dev_stage_name};
$samp_db->organ_type($OPTIONS{organ_type})
if $OPTIONS{organ_type};
$samp_db->tissue_type($OPTIONS{tissue_type})
if $OPTIONS{tissue_type};
$samp_db->atcc_cell_type($OPTIONS{atcc_cell_type})
if $OPTIONS{atcc_cell_type};
$samp_db->primary_cell_type($OPTIONS{primary_cell_type})
if $OPTIONS{primary_cell_type};
$samp_db->organism_intactness($OPTIONS{organism_intactness})
if $OPTIONS{organism_intactness};
$samp_db->genetic_status($OPTIONS{genetic_status})
if $OPTIONS{genetic_status};
$samp_db->genetic_status_comment($OPTIONS{genetic_status_comment})
if $OPTIONS{genetic_status_comment};
$samp_db->growth_cond($OPTIONS{growth_cond})
if $OPTIONS{growth_cond};
$samp_db->pathology_descr($OPTIONS{pathology_descr})
if $OPTIONS{pathology_descr};
$samp_db->common_acc_num($OPTIONS{common_acc_num})
if $OPTIONS{common_acc_num};
$samp_db->abrc_acc_num($OPTIONS{abrc_acc_num})
if $OPTIONS{abrc_acc_num};
$samp_db->nottingham_acc_num($OPTIONS{nottingham_acc_num})
if $OPTIONS{nottingham_acc_num};
print STDERR "Adding Sample info\n";
my $pk = $samp_db->insert_db($dbh);
$dbh->error(@error_args,
message=>"Couldn't insert Sample",
) if $dbh->err;
print STDOUT "$pk\n";
print STDERR "Finished\n";
if (exists $OPTIONS{debug}) {
$dbh->rollback();
} else {
$dbh->commit();
}
$dbh->disconnect();
exit(0);
|
|
From: <jas...@us...> - 2003-04-20 02:11:01
|
Update of /cvsroot/genex/genex-server/Genex In directory sc8-pr-cvs1:/tmp/cvs-serv8169/Genex Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.132 retrieving revision 1.133 diff -C2 -d -r1.132 -r1.133 *** ChangeLog 17 Apr 2003 18:01:34 -0000 1.132 --- ChangeLog 20 Apr 2003 02:10:57 -0000 1.133 *************** *** 1,2 **** --- 1,9 ---- + 2003-04-19 Jason E. Stewart <ja...@op...> + + * HTMLUtils/HTMLUtils.pm.in (Repository): + Ported William Anderson's code for doing loggin of long-running + processes and the continually refreshing status page that + checks the log file. + 2003-04-17 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2003-04-20 02:11:00
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv8169 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.127 retrieving revision 1.128 diff -C2 -d -r1.127 -r1.128 *** ChangeLog 17 Apr 2003 18:04:11 -0000 1.127 --- ChangeLog 20 Apr 2003 02:10:56 -0000 1.128 *************** *** 1,2 **** --- 1,22 ---- + 2003-04-19 Jason E. Stewart <ja...@op...> + + * Mason/workspace/array-design.html.in (Repository): + added error status code output if array-design-insert.pl dies + + * apache/genex-2.conf.in (Repository): + allowing mason to handle the mason/ dir instead of only mason/workspace/ + + * Mason/status.html (Repository): + page that allows long running processes to log their output to a + file, and have it displayed in a refreshing buffer. When the + job is finished, this page then displays the output. + + * Mason/workspace/data-loader.html.in (Repository): + * Mason/workspace/array-design.html.in (Repository): + added support for status.html + + * Mason/workspace/data-loader.html.in (Repository): + added support for .TXT, .xls, and .XLS files + 2003-04-17 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2003-04-20 02:01:28
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv6767 Modified Files: data-loader.html.in Log Message: whitespace Index: data-loader.html.in =================================================================== RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** data-loader.html.in 20 Apr 2003 01:34:01 -0000 1.7 --- data-loader.html.in 20 Apr 2003 02:01:24 -0000 1.8 *************** *** 229,233 **** die $!; } - } # here we re-open the filehandle to write the SUCCESS line, if --- 229,232 ---- |
|
From: <jas...@us...> - 2003-04-20 02:00:52
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv6503
Modified Files:
array-design.html.in
Log Message:
* Mason/workspace/array-design.html.in (Repository):
added error status code output if array-design-insert.pl dies
Index: array-design.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/array-design.html.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** array-design.html.in 20 Apr 2003 01:34:00 -0000 1.3
--- array-design.html.in 20 Apr 2003 02:00:39 -0000 1.4
***************
*** 148,152 ****
my $command = join(" ", $cmd, @args, "--file=$file", "1>>$filename", '2>&1');
system($command);
! die $! if $?;
}
# here we re-open the filehandle to write the SUCCESS line, if
--- 148,157 ----
my $command = join(" ", $cmd, @args, "--file=$file", "1>>$filename", '2>&1');
system($command);
! if ($?) {
! $fh = IO::File->new(">> $filename");
! Bio::Genex::HTMLUtils::write_job_logfile($fh,
! 'FINISHED' => "ERROR\n");
! die $!;
! }
}
# here we re-open the filehandle to write the SUCCESS line, if
|
|
From: <jas...@us...> - 2003-04-20 01:51:23
|
Update of /cvsroot/genex/genex-server/apache
In directory sc8-pr-cvs1:/tmp/cvs-serv3780
Modified Files:
genex-2.conf.in
Log Message:
* apache/genex-2.conf.in (Repository):
allowing mason to handle the mason/ dir instead of only mason/workspace/
Index: genex-2.conf.in
===================================================================
RCS file: /cvsroot/genex/genex-server/apache/genex-2.conf.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** genex-2.conf.in 22 Nov 2002 00:37:50 -0000 1.4
--- genex-2.conf.in 20 Apr 2003 01:51:20 -0000 1.5
***************
*** 11,15 ****
PerlAddVar MasonAllowGlobals $DEBUG
! <Directory %%GENEX_WORKSPACE_DIR%%>
# PerlFixupHandler +Apache::DB
SetHandler perl-script
--- 11,15 ----
PerlAddVar MasonAllowGlobals $DEBUG
! <Directory %%GENEX_MASON_DIR%%>
# PerlFixupHandler +Apache::DB
SetHandler perl-script
|
|
From: <jas...@us...> - 2003-04-20 01:48:47
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv3128 Modified Files: MANIFEST.in Log Message: new files Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** MANIFEST.in 17 Apr 2003 18:04:11 -0000 1.9 --- MANIFEST.in 20 Apr 2003 01:48:44 -0000 1.10 *************** *** 29,32 **** --- 29,34 ---- 'apache/genex-2.conf' => '%%APACHE_CONF_DIR%%', + 'Mason/status.html' => '%%GENEX_MASON_DIR%%', + 'Mason/workspace/workspace.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/add_user_to_group.html' => '%%GENEX_WORKSPACE_DIR%%', |
|
From: <jas...@us...> - 2003-04-20 01:45:09
|
Update of /cvsroot/genex/genex-server/Genex/HTMLUtils
In directory sc8-pr-cvs1:/tmp/cvs-serv2215
Modified Files:
HTMLUtils.pm.in
Log Message:
* HTMLUtils/HTMLUtils.pm.in (Repository):
Ported William Anderson's code for doing loggin of long-running
processes and the continually refreshing status page that
checks the log file.
Index: HTMLUtils.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/HTMLUtils/HTMLUtils.pm.in,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** HTMLUtils.pm.in 11 Oct 2002 21:42:37 -0000 1.19
--- HTMLUtils.pm.in 20 Apr 2003 01:45:03 -0000 1.20
***************
*** 6,18 ****
use strict;
! use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $SERVER $CGIURL $DEBUG $PARAMS $SCRIPT @COOKIE_INFO);
use Carp;
use DBI;
use CGI qw(:standard);
use File::Basename;
use Apache::Session::Postgres;
use Bio::Genex qw(:ASSERT error);
use Bio::Genex::Connect;
use CGI::Cookie;
require Exporter;
--- 6,22 ----
use strict;
! use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $SERVER $CGIURL $DEBUG $PARAMS $SCRIPT @COOKIE_INFO $TAG);
use Carp;
+ use Digest::MD5 qw(md5_hex);
use DBI;
use CGI qw(:standard);
use File::Basename;
+ use File::Temp;
+ use IO::Handle;
use Apache::Session::Postgres;
use Bio::Genex qw(:ASSERT error);
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use CGI::Cookie;
require Exporter;
***************
*** 57,60 ****
--- 61,67 ----
);
+ # the begining of line tag for the logfiles
+ $TAG = '%%%%=';
+
=pod
***************
*** 770,775 ****
--- 777,927 ----
}
+ =item $digest = create_checksum($string)
+
+ This subroutine takes a string parameter and generates an MD5 hex
+ digest of the string and a shared secret, and returns the digest to
+ the calling program.
+
+ Return Value: a string containing the generated MD5 hex digest.
+
+ =cut
+
+ sub create_checksum {
+ my $str = shift;
+
+ # Append the secret value to the string.
+ $str .= $Bio::Genex::Config->{GENEX_SECRET};
+
+ # Calculate the MD5 digest and return to the caller
+ return md5_hex($str);
+ }
+
+ =item $bool = verify_checksum($str,$user_digest)
+
+ This subroutine takes two string parameters, a string and a MD5 checksum. The function
+ compares $user_digest with an MD5 checksum of $str and a shared secret.
+
+ Return Value: TRUE if $user_digest is valid, FALSE otherwise
+
+ =cut
+
+ sub verify_checksum {
+ my ($str,$user_digest) = @_;
+
+ # Append the secret value to the string.
+ $str .= $Bio::Genex::Config->{GENEX_SECRET};
+
+ # Calculate the MD5 digest.
+ my $digest = md5_hex($str);
+
+ # check to see if the digests match
+ return $user_digest eq $digest;
+ }
# Autoload methods go after =cut, and are processed by the autosplit program.
+
+ =item ($fh,$filename,$job_id) = create_job_logfile()
+
+ This subroutine creates a secure temporary file for logging
+ application output.
+
+ Return Value: $fh an open filehandle to the file, $filename is the
+ full path to the file, $job_id is the MD5 encoded string for use with
+ browsers.
+
+ =cut
+
+ sub create_job_logfile {
+ # create a secure temporary file
+ my ($fh,$filename) = File::Temp::tempfile('gxlogXXXXXX',
+ DIR => $Bio::Genex::Config->{SYSTMP});
+
+ # buffering screws things up
+ $fh->autoflush();
+
+ # print the job start info
+ write_job_logfile($fh,'START-TIME', time);
+ write_job_logfile($fh,'OUTPUT', "\n");
+
+ # $filename will be something like '/tmp/genex/gxlogd17Bac'
+ # we want to strip the leading path for the job id
+ my ($job_id) = $filename =~ m|/([^/]+)$|;
+
+ # create a secure digest of the filename
+ my $digest = create_checksum($job_id);
+
+ # return the pieces, creating the job id string
+ return ($fh,$filename,"$job_id-$digest");
+ }
+
+ =item write_job_logfile($fh,$key,$value)
+
+ This subroutine writes a $key/$value pair into a logfile using the
+ filehandle $fh.
+
+ Return Value: none
+
+ =cut
+
+ sub write_job_logfile {
+ my ($fh,$key,$value) = @_;
+
+ print $fh "$TAG$key|$value\n";
+ }
+
+ =item $value = read_job_logfile($filename,$key)
+
+ This subroutine reads the $value of the $key from the $filename
+ logfile.
+
+ Return Value: the $value of the key if it exists, or FALSE otherwise.
+
+ =cut
+
+ sub read_job_logfile {
+ my ($filename,$key) = @_;
+ my $found_regex = qr/^$TAG$key/;
+ my $tag_regex = qr/^$TAG/;
+ $filename = "$Bio::Genex::Config->{SYSTMP}/$filename";
+ open(FILE,$filename)
+ or die "Couldn't open logfile: $filename for reading";
+
+ my $output;
+ my $found;
+ while (<FILE>) {
+ if (m/$found_regex/) {
+ $found = 1;
+ ($output) = $_ =~ m/$found_regex\|(.*)/;
+ } elsif (m/$tag_regex/) {
+ if ($found) {
+ close FILE;
+ return $output;
+ }
+ } elsif ($found) {
+ $output .= $_;
+ }
+ }
+
+ # we got to the end of the file
+ close FILE;
+ return $output;
+ }
+
+ =item $job_id = extract_job_id($string)
+
+ Extracts a valid job_id from an MD5 encode web URL.
+
+ Return Value: a job_id string if $string is a valid job_id, FALSE otherwise.
+
+ =cut
+
+ sub extract_job_id {
+ my $string = shift;
+ my ($job_id,$digest) = split '-', $string;
+ if (verify_checksum($job_id,$digest)) {
+ return $job_id;
+ }
+ return 0;
+ }
1;
|
|
From: <jas...@us...> - 2003-04-20 01:37:01
|
Update of /cvsroot/genex/genex-server/Mason
In directory sc8-pr-cvs1:/tmp/cvs-serv354
Added Files:
status.html
Log Message:
* Mason/status.html (Repository):
page that allows long running processes to log their output to a
file, and have it displayed in a refreshing buffer. When the
job is finished, this page then displays the output.
--- NEW FILE: status.html ---
<html>
<head>
<title><% $title %></title>
% unless ($end_status) {
<meta http-equiv="REFRESH" content="3; URL="./status.pl?job_id=<% $job_id %>">
% }
</head>
<body bgcolor=#ffffff>
<div align=center>
<h1><% $title %></h1>
% if ($end_status) {
<p>Your job is finished. The status is: <% $end_status %></p>
<p>Output of the program:</p>
<table border=1 cellpadding=0 cellspacing=0 width="100%">
<tr><td><pre><% $output %> </pre></td></tr>
</table>
% } else {
<table width="100%">
<tr>
<td>
<p>Your job is being run by the system</p>
</td>
<tr>
<tr>
<td>
<p>Current run time is <% $runtime %> seconds.</p>
</td>
</tr>
<tr>
<td>
Output of the program:
<table border=1 cellpadding=0 cellspacing=0 width="100%">
<tr><td><pre><% $output %> </pre></td></tr>
</table>
</td>
</tr>
<tr>
<td>
<form action="<% $action %>" method="post">
<input type="hidden" name="job_id" value="<% $job_id %>"/>
<p>This page should automatically refresh in about 3 seconds.</p>
<input type="submit" value="Click here to update"/>
</form>
</td>
</tr>
</table>
% }
</div>
</body>
</html>
<%args>
$job_id
</%args>
<%once>
use Bio::Genex::HTMLUtils;
use Bio::Genex::Config;
</%once>
<%init>
$job_id = Bio::Genex::HTMLUtils::extract_job_id($job_id);
my $title = "Genex Job Status Page";
my $output;
my $runtime;
my $action;
my $end_status = Bio::Genex::HTMLUtils::read_job_logfile($job_id,'FINISHED');
if ($end_status) {
$output = Bio::Genex::HTMLUtils::read_job_logfile($job_id,'OUTPUT');
} else {
$runtime = Bio::Genex::HTMLUtils::read_job_logfile($job_id,'START-TIME');
$runtime = time - $runtime;
$output = Bio::Genex::HTMLUtils::read_job_logfile($job_id,'OUTPUT');
$action = "$Bio::Genex::Config->{GENEX_MASON_URL}/status.html";
}
</%init>
|
|
From: <jas...@us...> - 2003-04-20 01:34:04
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv32166
Modified Files:
array-design.html.in data-loader.html.in
Log Message:
* Mason/workspace/data-loader.html.in (Repository):
* Mason/workspace/array-design.html.in (Repository):
added support for status.html
Index: array-design.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/array-design.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** array-design.html.in 22 Nov 2002 00:42:45 -0000 1.2
--- array-design.html.in 20 Apr 2003 01:34:00 -0000 1.3
***************
*** 10,14 ****
% } else {
<h2>Read Group</h2>
! <p>Choose the <b>read group</b> that will be givne to create
the array design files that you load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
--- 10,14 ----
% } 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">
***************
*** 31,35 ****
<h2>Write Group</h2>
! <p>Choose the <b>write group</b> that will be givne to create
the array design files that you load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
--- 31,35 ----
<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">
***************
*** 71,75 ****
<hr noshade size=5>
! <input type="submit" name="submit" value="Load Data" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
--- 71,75 ----
<hr noshade size=5>
! <input type="submit" name="submit" value="Load Array Designs" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
***************
*** 87,99 ****
</%args>
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
name=>'GeneX DB Array Design Loader Page'
! path=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::ArrayDesign;
</%once>
--- 87,103 ----
</%args>
<%attr>
! action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/array-design.html"
name=>'GeneX DB Array Design Loader Page'
! path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/array-design.html"
</%attr>
<%once>
+ use Apache::Constants qw(:response);
+ use IO::File;
use Bio::Genex;
use Bio::Genex::Connect;
+ use Bio::Genex::Config;
use Bio::Genex::GroupSec;
use Bio::Genex::ArrayDesign;
+ use Bio::Genex::HTMLUtils;
</%once>
***************
*** 103,109 ****
my $action = $m->current_comp->attr('action');
- $dbh->assert_table_defined('GroupSec');
- $dbh->assert_table_defined('ArrayDesign');
-
my @groups;
my @data_files;
--- 107,110 ----
***************
*** 117,136 ****
}
! my $cmd = '%%GENEX_BIN_DIR%%/array-design-insert.pl';
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
! );
! my @pks;
! foreach my $file (@files) {
! my @params = ("--file=$file");
! my $command = join(' ', $cmd, @args, @params);
! my $pk = `$command`;
! die $! if $?;
! push(@pks,$pk);
}
- $data = "@pks";
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
--- 118,167 ----
}
! # open the job status logfile
! my ($fh,$filename,$job_id) = Bio::Genex::HTMLUtils::create_job_logfile();
! # for some bizarre buffering reason, we have to close this
! # filehandle even though we're going to re-open it to write the
! # SUCCESS line in a couple of lines
! close($fh);
!
! if (my $pid = fork) {
! # we erase any headers or HTML we might have created so far
! $m->clear_buffer();
!
! # now we redirect
! my @args = ($r,
! "$Bio::Genex::Config->{GENEX_MASON_URL}/status.html?job_id=$job_id",
! );
! Bio::Genex::HTMLUtils::call_page(@args);
! } else {
! my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/array-design-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
! );
! foreach my $file (@files) {
! # for some really bizarre reason, system() doesn't like the
! # STDOUT/STDERR redirection happening in a comma seperated
! # list, but it handles it just fine in a single string...
! my $command = join(" ", $cmd, @args, "--file=$file", "1>>$filename", '2>&1');
! system($command);
! die $! if $?;
! }
! # here we re-open the filehandle to write the SUCCESS line, if
! # we don't close(), and re-open this handle, the SUCCESS line
! # will get stamped write after the OUTPUT line, and not at the
! # end of the file like, you would want it to. I bet it has to
! # do with the filehandle thinking the EOF is at a certain
! # place, but since I've just written more info to the file in
! # the system() call above, it hasn't been updated. Doing the
! # re-open updates the info
! $fh = IO::File->new(">> $filename");
! Bio::Genex::HTMLUtils::write_job_logfile($fh,
! 'FINISHED' => "SUCCESS\n");
! $m->clear_buffer();
! $m->abort(DONE);
}
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
***************
*** 139,143 ****
}
! my @files = glob('%%GENEX_UPLOAD_DIR%%/*.xml');
foreach my $name (@files) {
my $short_name = $name;
--- 170,174 ----
}
! my @files = glob("$Bio::Genex::Config->{GENEX_UPLOAD_DIR}/*.xml");
foreach my $name (@files) {
my $short_name = $name;
Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** data-loader.html.in 20 Apr 2003 00:18:16 -0000 1.6
--- data-loader.html.in 20 Apr 2003 01:34:01 -0000 1.7
***************
*** 159,162 ****
--- 159,164 ----
</%attr>
<%once>
+ use Apache::Constants qw(:response);
+ use IO::File;
use Bio::Genex;
use Bio::Genex::Connect;
***************
*** 172,179 ****
my $action = $m->current_comp->attr('action');
- $dbh->assert_table_defined('ExperimentSet');
- $dbh->assert_table_defined('ArrayDesign');
- $dbh->assert_table_defined('FeatureExtractionSoftware');
-
my @groups;
my @data_files;
--- 174,177 ----
***************
*** 182,185 ****
--- 180,184 ----
my @array_designs;
my $data = '';
+
if ($submit) {
my @files;
***************
*** 190,214 ****
}
! my $cmd = '%%GENEX_BIN_DIR%%/mbad-insert.pl';
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
! "--es_pk=$es_pk",
! "--ad_pk=$ad_pk",
! "--fe_sw_pk=$fe_sw_pk",
! );
! my @pks;
! foreach my $file (@files) {
! my @params = ($file);
! my $command = join(' ', $cmd, @args, @params);
! my $pk = `$command`;
! die $! if $?;
! push(@pks,$pk);
! }
! $data = "@pks";
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
--- 189,248 ----
}
! # open the job status logfile
! my ($fh,$filename,$job_id) = Bio::Genex::HTMLUtils::create_job_logfile();
! # for some bizarre buffering reason, we have to close this
! # filehandle even though we're going to re-open it to write the
! # SUCCESS line in a couple of lines
! close($fh);
! if (my $pid = fork) {
! # we erase any headers or HTML we might have created so far
! $m->clear_buffer();
! # now we redirect
! my @args = ($r,
! "$Bio::Genex::Config->{GENEX_MASON_URL}/status.html?job_id=$job_id",
! );
! Bio::Genex::HTMLUtils::call_page(@args);
! } else {
! my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/mbad-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
! "--es_pk=$es_pk",
! "--ad_pk=$ad_pk",
! "--fe_sw_pk=$fe_sw_pk",
! );
!
! foreach my $file (@files) {
! # for some really bizarre reason, system() doesn't like the
! # STDOUT/STDERR redirection happening in a comma seperated
! # list, but it handles it just fine in a single string...
! my $command = join(' ', $cmd, @args, $file, "1>>$filename", '2>&1');
! system($command);
! if ($?) {
! $fh = IO::File->new(">> $filename");
! Bio::Genex::HTMLUtils::write_job_logfile($fh,
! 'FINISHED' => "ERROR\n");
! die $!;
! }
!
! }
! # here we re-open the filehandle to write the SUCCESS line, if
! # we don't close(), and re-open this handle, the SUCCESS line
! # will get stamped write after the OUTPUT line, and not at the
! # end of the file like, you would want it to. I bet it has to
! # do with the filehandle thinking the EOF is at a certain
! # place, but since I've just written more info to the file in
! # the system() call above, it hasn't been updated. Doing the
! # re-open updates the info
! $fh = IO::File->new(">> $filename");
! Bio::Genex::HTMLUtils::write_job_logfile($fh,
! 'FINISHED' => "SUCCESS\n");
! $m->clear_buffer();
! $m->abort(DONE);
! }
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
|
|
From: <jas...@us...> - 2003-04-20 00:18:21
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv13267
Modified Files:
data-loader.html.in
Log Message:
* Mason/workspace/data-loader.html.in (Repository):
added support for .TXT, .xls, and .XLS files
Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** data-loader.html.in 17 Apr 2003 07:37:28 -0000 1.5
--- data-loader.html.in 20 Apr 2003 00:18:16 -0000 1.6
***************
*** 232,236 ****
}
! my @files = glob("$Bio::Genex::Config->{GENEX_UPLOAD_DIR}/*.txt");
foreach my $name (@files) {
my $short_name = $name;
--- 232,236 ----
}
! my @files = glob("$Bio::Genex::Config->{GENEX_UPLOAD_DIR}/*.{txt,TXT,xls,XLS}");
foreach my $name (@files) {
my $short_name = $name;
|
|
From: <jas...@us...> - 2003-04-17 18:34:16
|
Update of /cvsroot/genex/genex-server/Genex/ProtocolApplicationLink In directory sc8-pr-cvs1:/tmp/cvs-serv30093/Genex/ProtocolApplicationLink Added Files: .cvsignore Log Message: usual --- NEW FILE: .cvsignore --- Makefile pm_to_blib |
|
From: <jas...@us...> - 2003-04-17 18:04:17
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv18602 Modified Files: ChangeLog MANIFEST.in Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.126 retrieving revision 1.127 diff -C2 -d -r1.126 -r1.127 *** ChangeLog 17 Apr 2003 07:37:49 -0000 1.126 --- ChangeLog 17 Apr 2003 18:04:11 -0000 1.127 *************** *** 1,4 **** --- 1,13 ---- 2003-04-17 Jason E. Stewart <ja...@op...> + * DB/xml/ProtocolStep.xml (Repository): + added inheritance from Identifiable + + * DB/xml/ParameterValue.xml (Repository): + added permissions, not through inheritance + + * Mason/workspace/protocol-insert.html (Repository): + changed URI to a text <input> + * Mason/workspace/data-loader.html.in (Repository): sw_pk => param_pk Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** MANIFEST.in 16 Apr 2003 23:30:38 -0000 1.8 --- MANIFEST.in 17 Apr 2003 18:04:11 -0000 1.9 *************** *** 54,58 **** --- 54,61 ---- 'Mason/workspace/query.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/contact-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/parameter-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/protocol-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/protocol-step-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/procedure-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', *************** *** 85,88 **** --- 88,94 ---- 'Genex/scripts/priveleges.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/protocol-insert.pl' => '%%GENEX_BIN_DIR%%', + 'Genex/scripts/parameter-insert.pl' => '%%GENEX_BIN_DIR%%', + 'Genex/scripts/protocol-step-insert.pl' => '%%GENEX_BIN_DIR%%', + 'Genex/scripts/procedure-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/qtdim-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/reporter-insert.pl' => '%%GENEX_BIN_DIR%%', |
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From: <jas...@us...> - 2003-04-17 18:03:54
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Update of /cvsroot/genex/genex-server/DB/controlled_vocab
In directory sc8-pr-cvs1:/tmp/cvs-serv18459/DB/controlled_vocab
Added Files:
PARAM_Type.xml
Log Message:
new vocab
--- NEW FILE: PARAM_Type.xml ---
<?xml version="1.0" standalone="yes"?>
<controlled_vocabulary db_table="Parameter" db_column="type" cv_table="PARAM_Type">
<comment type="definition">This table provides the restricted
vocabulary for the column type in the table Parameter and is used to
define the data types allowed by parameters
</comment>
<term name="int"
description="an integer"/>
<term name="float"
description="a floating point number"/>
<term name="string"
description="a text string"/>
<term name="other_parameter"
description="other"/>
</controlled_vocabulary>
<!--
*** emacs file mode definition ***
Local Variables:
ispell-personal-dictionary:"../.ispell-dict"
End:
-->
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From: <jas...@us...> - 2003-04-17 18:03:28
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Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv18273/DB/xml
Modified Files:
ProtocolStep.xml
Log Message:
* DB/xml/ProtocolStep.xml (Repository):
added inheritance from Identifiable
Index: ProtocolStep.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ProtocolStep.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ProtocolStep.xml 16 Apr 2003 21:21:47 -0000 1.1
--- ProtocolStep.xml 17 Apr 2003 18:03:24 -0000 1.2
***************
*** 4,7 ****
--- 4,8 ----
]>
<table name="&table_name;"
+ inherits_from="Identifiable"
type="&data_table;"
comment=" The &table_name; table contains the steps for protocols.">
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From: <jas...@us...> - 2003-04-17 18:02:53
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Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv17980/DB/xml
Modified Files:
ParameterValue.xml
Log Message:
* DB/xml/ParameterValue.xml (Repository):
added permissions, not through inheritance
Index: ParameterValue.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ParameterValue.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ParameterValue.xml 16 Apr 2003 21:21:47 -0000 1.1
--- ParameterValue.xml 17 Apr 2003 18:02:49 -0000 1.2
***************
*** 34,37 ****
--- 34,69 ----
foreign_table_pkey ="proto_step_pk"
fkey_type ="&fkey_oto;"/>
+ <column name="ro_groupname"
+ full_name="Read-Only Group Name"
+ not_null="true"
+ type="name"
+ comment="The group with permission to view this data"/>
+ <foreign_key column_id="ro_groupname"
+ foreign_table ="GroupSec"
+ foreign_table_pkey ="name"
+ fkey_type ="&fkey_oto;"/>
+ <column name="rw_groupname"
+ full_name="Read/Write Group Name"
+ not_null="true"
+ type="name"
+ comment="The group with permission to modify this data"/>
+ <foreign_key column_id="rw_groupname"
+ foreign_table ="GroupSec"
+ foreign_table_pkey ="name"
+ fkey_type ="&fkey_oto;"/>
+ <column name="audit_fk"
+ full_name="Audit"
+ not_null="true"
+ type="int4"
+ comment="The audit entry when this data was last modified, it
+ will be null if it is the creation event. We set the
+ write_sql attribute to be false so that Postgres doesn't put
+ a constraint on this column. It is automatically set by a
+ trigger. "/>
+ <foreign_key column_id="audit_fk"
+ write_sql="false"
+ foreign_table ="Audit"
+ foreign_table_pkey ="audit_pk"
+ fkey_type ="&fkey_oto;"/>
<primary_key column_id="param_value_pk"/>
</table>
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From: <jas...@us...> - 2003-04-17 18:02:13
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Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv17677/DB/xml
Added Files:
ProtocolApplicationLink.xml
Log Message:
new table
--- NEW FILE: ProtocolApplicationLink.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "ProtocolApplicationLink">
]>
<table name="&table_name;"
type="&data_table;"
comment=" The &table_name; table allows many protocols used in
an application to be specified. As many protocols as are
appropriate to describe the application may be used, and the same
protocol may be used in the different applications (a
many-to-many relationship).">
<column name="other_fk"
full_name="other_fk"
type="int4"
not_null="true"
comment="the foreign key to the table using the protocol. We do
not make this a foreign key constraint in the DB because this
can apply to many different tables."/>
<column name="proto_app_fk"
full_name="Protocol Application"
not_null="true"
type="int4"
comment=""/>
<foreign_key column_id="proto_app_fk"
foreign_table ="ProtocolApplication"
foreign_table_pkey ="proto_app_pk"
fkey_type ="&fkey_linking;"/>
<index name="palink_other_fk" column_id="other_fk"/>
<index name="palink_pa_fk" column_id="proto_app_fk"/>
<unique column_ids="other_fk proto_app_fk"/>
</table>
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From: <jas...@us...> - 2003-04-17 18:01:38
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Update of /cvsroot/genex/genex-server/Genex In directory sc8-pr-cvs1:/tmp/cvs-serv17471/Genex Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.131 retrieving revision 1.132 diff -C2 -d -r1.131 -r1.132 *** ChangeLog 17 Apr 2003 07:37:50 -0000 1.131 --- ChangeLog 17 Apr 2003 18:01:34 -0000 1.132 *************** *** 1,4 **** --- 1,7 ---- 2003-04-17 Jason E. Stewart <ja...@op...> + * Genex.pm.in (Repository): + new version (2.7.20030417) + * XMLUtils/XMLUtils.pm.in (Repository): major fix to handling inheritance of columns in views in xml2sql() |
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From: <jas...@us...> - 2003-04-17 18:01:17
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Update of /cvsroot/genex/genex-server/Genex
In directory sc8-pr-cvs1:/tmp/cvs-serv17306/Genex
Modified Files:
Genex.pm.in
Log Message:
* Genex.pm.in (Repository):
new version (2.7.20030417)
Index: Genex.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Genex.pm.in,v
retrieving revision 1.53
retrieving revision 1.54
diff -C2 -d -r1.53 -r1.54
*** Genex.pm.in 23 Nov 2002 10:16:21 -0000 1.53
--- Genex.pm.in 17 Apr 2003 18:01:12 -0000 1.54
***************
*** 58,62 ****
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20021123';
# Preloaded methods go here.
--- 58,62 ----
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20030417';
# Preloaded methods go here.
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