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From: <jas...@us...> - 2002-11-20 23:23:50
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv22737
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Repository):
uses 'identifier' for rep_name if 'name' isn't defined
uses BioSequence name/identifier for rep_name if defined
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** array-design-insert.pl.in 19 Nov 2002 22:33:25 -0000 1.5
--- array-design-insert.pl.in 20 Nov 2002 23:23:47 -0000 1.6
***************
*** 153,157 ****
$start = new Benchmark;
foreach my $mage_reporter (@mage_reporters) {
! my $name = $mage_reporter->getName();
my $type = 'clone_name'; # FIXME
--- 153,161 ----
$start = new Benchmark;
foreach my $mage_reporter (@mage_reporters) {
! my $name = $mage_reporter->getName() || $mage_reporter->getIdentifier();
! if (defined $mage_reporter->getImmobilizedCharacteristics()) {
! my $mage_biosequences = $mage_reporter->getImmobilizedCharacteristics();
! $name = $mage_biosequences->[0]->getName || $mage_biosequences->[0]->getIdentifier;
! }
my $type = 'clone_name'; # FIXME
|
|
From: <jas...@us...> - 2002-11-20 22:43:08
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv4313 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.109 retrieving revision 1.110 diff -C2 -d -r1.109 -r1.110 *** ChangeLog 20 Nov 2002 00:22:41 -0000 1.109 --- ChangeLog 20 Nov 2002 22:43:04 -0000 1.110 *************** *** 1,2 **** --- 1,36 ---- + 2002-11-20 Jason E. Stewart <ja...@op...> + + * MANIFEST.in (Message): + new files + + * Mason/workspace/experiments.html.in (Repository): + * Mason/workspace/data-sources.html.in (Repository): + * Mason/workspace/bioassay.html.in (Repository): + * Mason/workspace/data-loader.html.in (Repository): + * Mason/workspace/experimentset-create.html.in (Repository): + * Mason/workspace/group-create.html.in (Repository): + * Mason/workspace/group-maint.html.in (Repository): + * Mason/workspace/query.html.in (Repository): + * Mason/workspace/workspace.html.in (Repository): + $dbh and $session are now global + + * Mason/workspace/logout.html (Repository): + * Mason/workspace/index.html (Repository): + * Mason/workspace/check-login.html (Repository): + * Mason/workspace/check-cookie.html (Repository): + * Mason/workspace/authenticate.html.in (Repository): + inherits from noauth-autohandler + + * Mason/workspace/autohandler.in (Repository): + inherits from syshandler + removed no-auth cruft + localized $dbh and $session + + * Mason/workspace/comps/authenticate.mason.in (Repository): + removed attr's, put them directly into the code + + * apache/genex-2.conf.in (Repository): + added globals: $dbh $session $DEBUG + 2002-11-19 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2002-11-20 22:42:56
|
Update of /cvsroot/genex/genex-server/DB/xml In directory sc8-pr-cvs1:/tmp/cvs-serv4203/DB/xml Added Files: .cvsignore Log Message: usual --- NEW FILE: .cvsignore --- functions-sql.xml |
|
From: <jas...@us...> - 2002-11-20 22:42:36
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv4036/Mason/workspace Added Files: test.html Log Message: random test script, not for mortals --- NEW FILE: test.html --- <p>dbh: <% $dbh %></p> <p>session: <% $session %></p> <%attr> name=>'GeneX DB Foo Page' </%attr> |
|
From: <jas...@us...> - 2002-11-20 22:40:02
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv2734 Modified Files: MANIFEST.in Log Message: new files Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** MANIFEST.in 20 Nov 2002 00:24:51 -0000 1.2 --- MANIFEST.in 20 Nov 2002 22:39:59 -0000 1.3 *************** *** 7,10 **** --- 7,13 ---- 'Mason/workspace/authenticate.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/autohandler' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/noauth-autohandler' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/test.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/syshandler' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/bioassay.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/check-cookie.html' => '%%GENEX_WORKSPACE_DIR%%', |
|
From: <jas...@us...> - 2002-11-20 22:35:28
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv788
Modified Files:
experiments.html.in
Log Message:
* Mason/workspace/experiments.html.in (Repository):
$dbh and $session are now global
Index: experiments.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/experiments.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** experiments.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- experiments.html.in 20 Nov 2002 22:35:26 -0000 1.2
***************
*** 51,55 ****
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
- my $dbh = Bio::Genex::Connect->new(DBNAME=>$local[0]);
$dbh->assert_table_defined('PhysicalBioAssay');
--- 51,54 ----
|
|
From: <jas...@us...> - 2002-11-20 22:35:08
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv652
Modified Files:
data-sources.html.in
Log Message:
* Mason/workspace/data-sources.html.in (Repository):
$dbh and $session are now global
Index: data-sources.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-sources.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** data-sources.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- data-sources.html.in 20 Nov 2002 22:35:04 -0000 1.2
***************
*** 61,66 ****
use Bio::Genex::Connect;
- my $dbh = Bio::Genex::Connect->new();
-
$dbh->assert_table_defined('G2G');
--- 61,64 ----
|
|
From: <jas...@us...> - 2002-11-20 22:34:39
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv421
Modified Files:
bioassay.html.in
Log Message:
* Mason/workspace/bioassay.html.in (Repository):
$dbh and $session are now global
Index: bioassay.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/bioassay.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** bioassay.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- bioassay.html.in 20 Nov 2002 22:34:36 -0000 1.2
***************
*** 54,65 ****
my $action = $m->current_comp->attr('action');
- my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
-
- my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
- PASSWORD=>$session->{password},
- DBNAME=>$session->{dbname},
- );
-
-
$dbh->assert_table_defined('MeasuredBioAssay');
--- 54,57 ----
|
|
From: <jas...@us...> - 2002-11-20 22:34:18
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv32723
Modified Files:
data-loader.html.in
Log Message:
* Mason/workspace/data-loader.html.in (Repository):
$dbh and $session are now global
Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** data-loader.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- data-loader.html.in 20 Nov 2002 22:34:15 -0000 1.2
***************
*** 171,182 ****
my $action = $m->current_comp->attr('action');
- my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
-
- my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
- PASSWORD=>$session->{password},
- DBNAME=>$session->{dbname},
- );
-
-
$dbh->assert_table_defined('ExperimentSet');
$dbh->assert_table_defined('ArrayDesign');
--- 171,174 ----
|
|
From: <jas...@us...> - 2002-11-20 22:33:54
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv32551
Modified Files:
experimentset-create.html.in
Log Message:
* Mason/workspace/experimentset-create.html.in (Repository):
$dbh and $session are now global
Index: experimentset-create.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/experimentset-create.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** experimentset-create.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- experimentset-create.html.in 20 Nov 2002 22:33:51 -0000 1.2
***************
*** 189,199 ****
my $action = $m->current_comp->attr('action');
- my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
- my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
- PASSWORD=>$session->{password},
- DBNAME=>$session->{dbname},
- );
-
-
$dbh->assert_table_defined('GroupSec');
$dbh->assert_table_defined('ExperimentSet');
--- 189,192 ----
***************
*** 265,268 ****
}
-
</%init>
--- 258,260 ----
|
|
From: <jas...@us...> - 2002-11-20 22:33:12
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv32282
Modified Files:
group-create.html.in
Log Message:
* Mason/workspace/group-create.html.in (Repository):
$dbh and $session are now global
Index: group-create.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/group-create.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** group-create.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- group-create.html.in 20 Nov 2002 22:33:09 -0000 1.2
***************
*** 122,132 ****
my $action = $m->current_comp->attr('action');
- my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
- my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
- PASSWORD=>$session->{password},
- DBNAME=>$session->{dbname},
- );
-
-
$dbh->assert_table_defined('GroupSec');
--- 122,125 ----
|
|
From: <jas...@us...> - 2002-11-20 22:32:24
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv31945
Modified Files:
group-maint.html.in
Log Message:
* Mason/workspace/group-maint.html.in (Repository):
$dbh and $session are now global
Index: group-maint.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/group-maint.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** group-maint.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- group-maint.html.in 20 Nov 2002 22:32:21 -0000 1.2
***************
*** 104,114 ****
my $action = $m->current_comp->attr('action');
- my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
-
- my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
- PASSWORD=>$session->{password},
- DBNAME=>$session->{dbname},
- );
-
$dbh->assert_table_defined('UserSec');
--- 104,107 ----
|
|
From: <jas...@us...> - 2002-11-20 22:32:01
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv31767
Modified Files:
query.html.in
Log Message:
* Mason/workspace/query.html.in (Repository):
$dbh and $session are now global
Index: query.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/query.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** query.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- query.html.in 20 Nov 2002 22:31:59 -0000 1.2
***************
*** 90,94 ****
use Bio::Genex::Provider;
use Env qw(LANG); # bogus bug fix for Xerces
- my $dbh;
$LANG = 'en_US';
--- 90,93 ----
***************
*** 129,138 ****
my @data_provider_names;
my @treatment_types;
- my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
-
- $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
- PASSWORD=>$session->{password},
- DBNAME=>$local[0],
- );
print STDERR "using DB: ", $dbh->db_name(), "\n";
--- 128,131 ----
|
|
From: <jas...@us...> - 2002-11-20 22:30:26
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv31024
Modified Files:
workspace.html.in
Log Message:
* Mason/workspace/workspace.html.in (Repository):
$dbh and $session are now global
Index: workspace.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/workspace.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** workspace.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- workspace.html.in 20 Nov 2002 22:30:23 -0000 1.2
***************
*** 60,71 ****
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
-
- # my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
- #
- # my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
- # PASSWORD=>$session->{password},
- # DBNAME=>$session->{dbname},
- # );
-
-
</%init>
--- 60,62 ----
|
|
From: <jas...@us...> - 2002-11-20 22:29:00
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv30378
Modified Files:
logout.html
Log Message:
* Mason/workspace/logout.html (Repository):
inherits from noauth-autohandler
Index: logout.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/logout.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** logout.html 20 Nov 2002 00:19:38 -0000 1.1
--- logout.html 20 Nov 2002 22:28:58 -0000 1.2
***************
*** 1,8 ****
- <html>
- <head><title><% $name %></title></head>
- <body bgcolor=white>
<h2>You been logged out of GeneX</h2>
! </body>
! </html>
<%attr>
name=>'GeneX DB Logout Page'
--- 1,6 ----
<h2>You been logged out of GeneX</h2>
! <%flags>
! inherit => 'noauth-autohandler'
! </%flags>
<%attr>
name=>'GeneX DB Logout Page'
***************
*** 12,16 ****
</%once>
<%init>;
- my $name = $m->current_comp->attr('name');
Bio::Genex::HTMLUtils::session_logout_cookie($r);
</%init>
--- 10,13 ----
|
|
From: <jas...@us...> - 2002-11-20 22:28:29
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv30161
Modified Files:
index.html
Log Message:
* Mason/workspace/index.html (Repository):
inherits from noauth-autohandler
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/index.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** index.html 20 Nov 2002 00:19:38 -0000 1.1
--- index.html 20 Nov 2002 22:28:26 -0000 1.2
***************
*** 22,23 ****
--- 22,26 ----
name=>'GeneX Mason Component Index Page'
</%attr>
+ <%flags>
+ inherit => 'noauth-autohandler'
+ </%flags>
|
|
From: <jas...@us...> - 2002-11-20 22:27:45
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv29799
Modified Files:
check-login.html
Log Message:
* Mason/workspace/check-login.html (Repository):
inherits from noauth-autohandler
Index: check-login.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/check-login.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** check-login.html 20 Nov 2002 00:19:38 -0000 1.1
--- check-login.html 20 Nov 2002 22:27:43 -0000 1.2
***************
*** 1,6 ****
- <html>
- <head><title><% $name %></title></head>
- <body bgcolor=white>
-
% if (defined $login) {
--- 1,2 ----
***************
*** 12,18 ****
% }
!
! </body>
! </html>
<%attr>
name=>'GeneX DB Authentication Check Page'
--- 8,14 ----
% }
! <%flags>
! inherit => 'noauth-autohandler'
! </%flags>
<%attr>
name=>'GeneX DB Authentication Check Page'
***************
*** 22,34 ****
</%once>
<%init>;
! my $name = $m->current_comp->attr('name');
! my $login;
! my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
! if (defined $session) {
! warn "check: retrieving session";
! foreach my $arg (keys %{$session}) {
! warn "check: session arg: $arg: $session->{$arg}";
! }
! $login = $session->{username};
}
</%init>
--- 18,30 ----
</%once>
<%init>;
! my $name = $m->current_comp->attr('name');
! my $login;
! my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
! if (defined $session) {
! warn "check: retrieving session";
! foreach my $arg (keys %{$session}) {
! warn "check: session arg: $arg: $session->{$arg}";
}
+ $login = $session->{username};
+ }
</%init>
|
|
From: <jas...@us...> - 2002-11-20 22:26:23
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv29093
Modified Files:
check-cookie.html
Log Message:
* Mason/workspace/check-cookie.html (Repository):
inherits from noauth-autohandler
Index: check-cookie.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/check-cookie.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** check-cookie.html 20 Nov 2002 00:19:38 -0000 1.1
--- check-cookie.html 20 Nov 2002 22:26:20 -0000 1.2
***************
*** 1,6 ****
- <html>
- <head><title><% $name %></title></head>
- <body bgcolor=white>
-
% if (defined $session_id) {
--- 1,2 ----
***************
*** 16,23 ****
<p>all your cookies:</p>
<% $cookies %>
!
!
! </body>
! </html>
<%attr>
name=>'GeneX DB Cookie Check Page'
--- 12,18 ----
<p>all your cookies:</p>
<% $cookies %>
! <%flags>
! inherit => 'noauth-autohandler'
! </%flags>
<%attr>
name=>'GeneX DB Cookie Check Page'
|
|
From: <jas...@us...> - 2002-11-20 22:25:41
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv28665
Modified Files:
autohandler.in
Log Message:
* Mason/workspace/autohandler.in (Repository):
inherits from syshandler
removed no-auth cruft
localized $dbh and $session
Index: autohandler.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/autohandler.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** autohandler.in 20 Nov 2002 00:19:38 -0000 1.1
--- autohandler.in 20 Nov 2002 22:25:38 -0000 1.2
***************
*** 23,54 ****
use Bio::Genex::HTMLUtils;
</%once>
<%init>;
- my $DEBUG = '';
my $comp = $m->fetch_next();
my $name = $comp->attr('name');
! my @no_auth = qw(check-login.html
! check-cookie.html
! index.html
! kill-cookie.html
! authenticate.html
! logout.html
! );
! unless (grep {$comp->path =~ $_} @no_auth) {
! my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
! if ($ARGS{debug}) {
! warn "authohandler: retrieving session";
! foreach my $arg (keys %{$session}) {
! warn "authohandler: session arg: $arg: $session->{$arg}";
! }
! }
! unless (defined $session and exists $session->{username}) {
! my $path = $comp->attr('path');
! $m->comp('comps/authenticate.mason', caller=>$path);
! }
}
if ($ARGS{debug}) {
! $DEBUG = $m->comp('../comps/debug-args.mason','args'=>\%ARGS);
}
</%init>
--- 23,52 ----
use Bio::Genex::HTMLUtils;
</%once>
+ <%flags>
+ inherit => 'syshandler'
+ </%flags>
<%init>;
my $comp = $m->fetch_next();
my $name = $comp->attr('name');
!
! # we localize $session so that it lasts only the duration of the request
! local $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
!
! unless (defined $session and exists $session->{username}) {
! my $path = $comp->attr('path');
! $m->comp('comps/authenticate.mason', caller=>$path);
}
if ($ARGS{debug}) {
! warn "authohandler: retrieving session";
! foreach my $arg (keys %{$session}) {
! warn "authohandler: session arg: $arg: $session->{$arg}";
! }
}
+ # we localize $dbh so that it lasts only the duration of the request
+ local $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
+ PASSWORD=>$session->{password},
+ DBNAME=>$session->{dbname},
+ );
</%init>
|
|
From: <jas...@us...> - 2002-11-20 21:25:43
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv28864/Mason/workspace
Modified Files:
authenticate.html.in
Log Message:
* Mason/workspace/authenticate.html.in (Repository):
inherits from noauth-autohandler
Index: authenticate.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/authenticate.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** authenticate.html.in 20 Nov 2002 00:19:38 -0000 1.1
--- authenticate.html.in 20 Nov 2002 21:25:40 -0000 1.2
***************
*** 1,13 ****
- <html>
- <head>
- <title><% $name %></title>
-
- % if (0) {
% if (defined $session) {
! <meta HTTP-EQUIV="refresh" Content="2;URL=<% $caller %>">
% }
- % }
</head>
--- 1,7 ----
% if (defined $session) {
! <meta HTTP-EQUIV="refresh" Content="2; URL=<% $caller %>">
% }
</head>
***************
*** 62,68 ****
% }
!
! </body>
! </html>
<%attr>
name=>'GeneX DB Authentication Page'
--- 56,62 ----
% }
! <%flags>
! inherit => 'noauth-autohandler'
! </%flags>
<%attr>
name=>'GeneX DB Authentication Page'
***************
*** 86,90 ****
unless ($password) {
$error = 'You must provide a valid password';
! } else { # not $login
my $dbh = eval {Bio::Genex::Connect->new(USER=>$login,
DBNAME=>$dbname,
--- 80,84 ----
unless ($password) {
$error = 'You must provide a valid password';
! } else { # not $login
my $dbh = eval {Bio::Genex::Connect->new(USER=>$login,
DBNAME=>$dbname,
***************
*** 95,103 ****
# first get the session
$session =
! Bio::Genex::HTMLUtils::set_session_cookie(username=>$login,
! password=>$password,
! dbname=>$dbname,
! request=>$r,
! );
foreach my $arg (keys %{$session}) {
warn "authenticate: session arg: $arg: $session->{$arg}";
--- 89,97 ----
# first get the session
$session =
! Bio::Genex::HTMLUtils::set_session_cookie(username=>$login,
! password=>$password,
! dbname=>$dbname,
! request=>$r,
! );
foreach my $arg (keys %{$session}) {
warn "authenticate: session arg: $arg: $session->{$arg}";
***************
*** 105,119 ****
warn "authenticate: cookie: ", $r->headers_out->{'Set-Cookie'};
- # my $page = $m->current_comp->attr('server');;
- # $page .= $m->interp->comp_root . $caller;
- #
- # $m->clear_buffer();
- # warn "authenticate: cookie: ", $r->headers_out->{'Set-Cookie'};
- # Bio::Genex::HTMLUtils::call_page($r,
- # $caller,
- # );
- # $m->abort(301);
- # warn "authenticate: cookie: ",
- # $r->headers_out->{'Set-Cookie'};
}
}
--- 99,102 ----
|
|
From: <jas...@us...> - 2002-11-20 21:24:12
|
Update of /cvsroot/genex/genex-server/Mason/workspace/comps
In directory sc8-pr-cvs1:/tmp/cvs-serv28425/Mason/workspace/comps
Modified Files:
authenticate.mason.in
Log Message:
* Mason/workspace/comps/authenticate.mason.in (Repository):
removed attr's, put them directly into the code
Index: authenticate.mason.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/comps/authenticate.mason.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** authenticate.mason.in 20 Nov 2002 00:19:38 -0000 1.1
--- authenticate.mason.in 20 Nov 2002 21:24:09 -0000 1.2
***************
*** 1,6 ****
- <%attr>
- name=>'GeneX DB Authentication Checker'
- page=>'%%GENEX_WORKSPACE_URL%%/authenticate.html'
- </%attr>
<%args>
$caller
--- 1,2 ----
***************
*** 14,18 ****
# $m is the global variable for the Mason request object
Bio::Genex::HTMLUtils::call_page($r,
! $m->current_comp->attr('page'),
$caller
);
--- 10,14 ----
# $m is the global variable for the Mason request object
Bio::Genex::HTMLUtils::call_page($r,
! '%%GENEX_WORKSPACE_URL%%/authenticate.html',
$caller
);
|
|
From: <jas...@us...> - 2002-11-20 21:23:07
|
Update of /cvsroot/genex/genex-server/apache
In directory sc8-pr-cvs1:/tmp/cvs-serv27859/apache
Modified Files:
genex-2.conf.in
Log Message:
* apache/genex-2.conf.in (Repository):
added globals: $dbh $session $DEBUG
Index: genex-2.conf.in
===================================================================
RCS file: /cvsroot/genex/genex-server/apache/genex-2.conf.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** genex-2.conf.in 20 Oct 2002 19:55:52 -0000 1.2
--- genex-2.conf.in 20 Nov 2002 21:23:05 -0000 1.3
***************
*** 5,8 ****
--- 5,12 ----
PerlModule HTML::Mason::ApacheHandler
+ PerlSetVar MasonAllowGlobals $dbh
+ PerlAddVar MasonAllowGlobals $session
+ PerlAddVar MasonAllowGlobals $DEBUG
+
<Directory %%GENEX_WORKSPACE_DIR%%>
SetHandler perl-script
|
|
From: <jas...@us...> - 2002-11-20 21:22:19
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv27173/Mason/workspace Added Files: .cvsignore Log Message: usual --- NEW FILE: .cvsignore --- add_user_to_group.html array-design.html authenticate.html autohandler bioassay.html data-loader.html data-sources.html experiments.html experimentset-create.html generate_group.html generate_user.html group-create.html group-maint.html noauth-autohandler query.html user-insert.html workspace.html |
|
From: <jas...@us...> - 2002-11-20 21:21:31
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv26716/Mason/workspace
Added Files:
kill-cookie.html.in
Removed Files:
kill-cookie.html
Log Message:
made substitutable because of cookie path
--- NEW FILE: kill-cookie.html.in ---
<h2>You GeneX cookie has been eradicated</h2>
<%flags>
inherit => 'noauth-autohandler'
</%flags>
<%attr>
name=>'GeneX DB Cookie Death Page'
</%attr>
<%once>;
use CGI::Cookie;
</%once>
<%init>;
my $session_cookie = CGI::Cookie->new(-name=>"GENEX_SESSION_ID",
-path=>'%%GENEX_SESSION_PATH%%',
-expires=>'now',
-value=>'ccc',
);
$r->header_out('Set-Cookie' => $session_cookie);
</%init>
--- kill-cookie.html DELETED ---
|
|
From: <jas...@us...> - 2002-11-20 21:20:36
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv26218/Mason/workspace
Added Files:
noauth-autohandler.in
Log Message:
new base component for components that don't need authentication
--- NEW FILE: noauth-autohandler.in ---
<html>
<head>
<title><% $name %></title>
</head>
<body>
<table border=0 cellpadding=0 cellspacing=0>
<tr>
<td align=right valign=top>
<img src="%%GENEX_GRAPHICS_URL%%/genex-banner-new.gif">
</td>
</tr>
</table>
<% $m->call_next() %>
<p><% $DEBUG %></p>
</body>
</html>
<%flags>
inherit => 'syshandler'
</%flags>
<%init>;
my $comp = $m->fetch_next();
my $name = $comp->attr('name');
</%init>
|
