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From: <jas...@us...> - 2002-11-26 17:51:57
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv4776 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.115 retrieving revision 1.116 diff -C2 -d -r1.115 -r1.116 *** ChangeLog 25 Nov 2002 21:49:57 -0000 1.115 --- ChangeLog 26 Nov 2002 17:51:54 -0000 1.116 *************** *** 1,2 **** --- 1,13 ---- + 2002-11-26 Jason E. Stewart <ja...@op...> + + * Makefile (Repository): + added install_files target + fixed install_files to run substitute.pl as well + + * Mason/workspace/autohandler.in (Repository): + no longer keep the Apache::Session instance - by freeing this up + we remove the possibility of deadlock. Instead we copy the info + to a private hashref + 2002-11-25 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2002-11-26 17:51:38
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv4654a
Modified Files:
Makefile
Log Message:
* Makefile (Repository):
fixed install_files to run substitute.pl as well
Index: Makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/Makefile,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile 26 Nov 2002 17:49:41 -0000 1.2
--- Makefile 26 Nov 2002 17:51:35 -0000 1.3
***************
*** 17,20 ****
--- 17,21 ----
install_files: Bio/Genex/Config.pm
+ ./substitute.pl
${PERL} Install --files_only
|
|
From: <jas...@us...> - 2002-11-26 17:49:45
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv3856
Modified Files:
Makefile
Log Message:
* Makefile (Repository):
added install_files target
Index: Makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/Makefile,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile 11 Oct 2002 01:18:23 -0000 1.1
--- Makefile 26 Nov 2002 17:49:41 -0000 1.2
***************
*** 16,19 ****
--- 16,22 ----
${PERL} Install
+ install_files: Bio/Genex/Config.pm
+ ${PERL} Install --files_only
+
Bio/Genex/Config.pm:
@echo Using Perl interpreter: ${PERL}
|
|
From: <jas...@us...> - 2002-11-26 17:49:14
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv3714/Mason/workspace
Modified Files:
autohandler.in
Log Message:
* Mason/workspace/autohandler.in (Repository):
no longer keep the Apache::Session instance - by freeing this up
we remove the possibility of deadlock. Instead we copy the info
to a private hashref
Index: autohandler.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/autohandler.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** autohandler.in 22 Nov 2002 00:40:31 -0000 1.3
--- autohandler.in 26 Nov 2002 17:49:11 -0000 1.4
***************
*** 30,58 ****
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}) {
! $m->clear_buffer();
! # $r is the global variable for the Apache request object
! # $m is the global variable for the Mason request object
! Bio::Genex::HTMLUtils::call_page($r,
! '%%GENEX_WORKSPACE_URL%%/authenticate.html',
! $comp->attr('path'),
! );
! $m->abort(301);
! }
! if ($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>
--- 30,64 ----
my $name = $comp->attr('name');
! # we localize $dbh and $session so that they last only the duration of the request
! local $dbh;
! local $session;
! {
! # we must keep $session lexical - Apache::Session::Postgres locks the
! # the row in the Sessions table and this will cause deadlocks if we
! # make it global
! my $apache_session = Bio::Genex::HTMLUtils::get_session_cookie($r);
! unless (defined $apache_session and exists $apache_session->{username}) {
! $m->clear_buffer();
! # $r is the global variable for the Apache request object
! # $m is the global variable for the Mason request object
! Bio::Genex::HTMLUtils::call_page($r,
! '%%GENEX_WORKSPACE_URL%%/authenticate.html',
! $comp->attr('path'),
! );
! $m->abort(301);
! }
! # we now copy the Apache::Session info into a private hashref so
! # that any further components in the component chain are free to
! # call get_session() without fear of causing a deadlock
! foreach my $arg (keys %{$apache_session}) {
! $session->{$arg} = $apache_session->{$arg};
}
}
! $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
! PASSWORD=>$session->{password},
! DBNAME=>$session->{dbname},
! );
</%init>
|
|
From: <tw...@us...> - 2002-11-26 14:29:19
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv12919
Modified Files:
Tag: Rel-1_0_1-branch
sessionlib.pl chgrp1.pl chgrp1.html chgrp2.pl
Log Message:
refinements to study permission setting, comments.
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.8
retrieving revision 1.1.2.9
diff -C2 -d -r1.1.2.8 -r1.1.2.9
*** sessionlib.pl 25 Nov 2002 21:39:49 -0000 1.1.2.8
--- sessionlib.pl 26 Nov 2002 14:29:15 -0000 1.1.2.9
***************
*** 690,698 ****
# system is identical to Unix, but we'll never use x.
#
! # Read the values for each position vertically. For example, 512 decimal is 400 octal.
#
! # 516 318 421
! # 124 26
! # 28
#
# 421 421 421
--- 690,698 ----
# system is identical to Unix, but we'll never use x.
#
! # Read the values for each position vertically. For example, 256 decimal is 400 octal.
#
! # 216 318 421
! # 524 26
! # 68
#
# 421 421 421
***************
*** 713,720 ****
my $sql;
my $sth;
! my $priv_mask = 288; #\440 uga read-only. decimal 288
if ($unlock == 1)
{
! $priv_mask = 416; # octal \640 rw- r-- --- u+rw,g+r
}
$sql = "select smp_pk from sample where oi_fk=$oi_pk";
--- 713,720 ----
my $sql;
my $sth;
! my $priv_mask = 0440; # 288; #\440 uga read-only. decimal 288
if ($unlock == 1)
{
! $priv_mask = 0640; # 416; # octal \640 rw- r-- --- u+rw,g+r
}
$sql = "select smp_pk from sample where oi_fk=$oi_pk";
***************
*** 755,759 ****
--- 755,762 ----
}
+ #
# Called from lock_order. Probably not useful otherwise.
+ # This really locks the experimental conditions of the study, and nothing else.
+ #
sub lock_study
{
***************
*** 763,770 ****
my $sql;
my $sth;
! my $priv_mask = 288; #\440 uga read-only. decimal 288
if ($unlock == 1)
{
! $priv_mask = 416; # octal \640 rw- r-- --- u+rw,g+r
}
$sql = "select ec_pk from exp_condition where sty_fk=$sty_pk";
--- 766,773 ----
my $sql;
my $sth;
! my $priv_mask = 0440; # 288; #\440 uga read-only. decimal 288
if ($unlock == 1)
{
! $priv_mask = 0640; # 416; # octal \640 rw- r-- --- u+rw,g+r
}
$sql = "select ec_pk from exp_condition where sty_fk=$sty_pk";
Index: chgrp1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp1.pl,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** chgrp1.pl 25 Nov 2002 22:15:41 -0000 1.1.2.3
--- chgrp1.pl 26 Nov 2002 14:29:15 -0000 1.1.2.4
***************
*** 37,45 ****
# write_log("sn: $hr->{study_name}");
$hr->{select_gs_name} = select_gs_name($dbh);
my $loop_instance = $loop_template;
$loop_instance =~ s/{(.*?)}/$hr->{$1}/gs;
$loop_instance = fixselect("select_gs_name", $hr->{gs_fk}, $loop_instance);
- # $loop_instance = fixradiocheck("user_read", $hr->{user_read}, "checkbox", $loop_instance);
- # $loop_instance = fixradiocheck("user_write", $hr->{user_write}, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_read", $hr->{group_read}, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_write", $hr->{group_write}, "checkbox", $loop_instance);
--- 37,56 ----
# write_log("sn: $hr->{study_name}");
$hr->{select_gs_name} = select_gs_name($dbh);
+ $hr->{octal_permissions} = sprintf("%o", $hr->{permissions});
+ if ($hr->{user_read} == 1)
+ {
+ $hr->{user_read} = "Yes";
+ }
+ if ($hr->{user_write} == 1)
+ {
+ $hr->{user_write} = "Yes";
+ }
+ else
+ {
+ $hr->{user_write} = "Locked";
+ }
my $loop_instance = $loop_template;
$loop_instance =~ s/{(.*?)}/$hr->{$1}/gs;
$loop_instance = fixselect("select_gs_name", $hr->{gs_fk}, $loop_instance);
$loop_instance = fixradiocheck("group_read", $hr->{group_read}, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_write", $hr->{group_write}, "checkbox", $loop_instance);
Index: chgrp1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp1.html,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** chgrp1.html 25 Nov 2002 22:15:41 -0000 1.1.2.3
--- chgrp1.html 26 Nov 2002 14:29:15 -0000 1.1.2.4
***************
*** 1,6 ****
! <html><head><title>Manage ownership and permissions</title></head>
<body bgcolor="#FFFFFF">
<table width="600" border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX MAS5 Hybridization Analysis<br><br>
<a href="./">Return to Genex Member Home</a>
<br><br clear=all><br>
--- 1,6 ----
! <html><head><title>Manage Study group ownership and permissions</title></head>
<body bgcolor="#FFFFFF">
<table width="600" border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">Change Study group, permissions<br><br>
<a href="./">Return to Genex Member Home</a>
<br><br clear=all><br>
***************
*** 22,25 ****
--- 22,26 ----
<td valign=top width="127"> Group Read</td>
<td valign=top width="114"> Group Write</td>
+ <td valign=top > Permissions (octal)</td>
</tr>
***************
*** 35,42 ****
<td valign=top width="72"> {select_gs_name} </td>
<td valign=top width="105">
! <input type="checkbox" name="user_read" value="1">
</td>
<td valign=top width="102">
! <input type="checkbox" name="user_write" value="1">
</td>
<td valign=top width="126">
--- 36,43 ----
<td valign=top width="72"> {select_gs_name} </td>
<td valign=top width="105">
! {user_read}
</td>
<td valign=top width="102">
! {user_write}
</td>
<td valign=top width="126">
***************
*** 45,48 ****
--- 46,52 ----
<td valign=top width="110">
<input type="checkbox" name="group_write" value="1">
+ </td>
+ <td valign=top>
+ {octal_permissions}
</td>
</tr>
Index: chgrp2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp2.pl,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** chgrp2.pl 25 Nov 2002 22:15:39 -0000 1.1.2.3
--- chgrp2.pl 26 Nov 2002 14:29:15 -0000 1.1.2.4
***************
*** 33,51 ****
if ($ch{"group_read_$xx"})
{
! $perm |= 32; # set 32
}
else
{
! $perm &= (511-32); # clear 32
}
! if ($ch{"group_write_$xx"} && ($ch{"permissions_$xx"} & 128))
{
! $perm |= 16; # set 16
}
else
{
! $perm &= (511-16); # clear 16
}
! my $tp = ($ch{"permissions_$xx"} & 128);
my $pp = $ch{"permissions_$xx"};
write_log("tp:$tp p:$pp");
--- 33,51 ----
if ($ch{"group_read_$xx"})
{
! $perm |= 040; # 040 octal = 32 decimal
}
else
{
! $perm &= 0730; # 0730 is 0770-040 or in decimal (511-32)
}
! if ($ch{"group_write_$xx"} && ($ch{"permissions_$xx"} & 0200))
{
! $perm |= 020; # 020 is 16 decimal
}
else
{
! $perm &= 0750; # 0750 is 0770-020 or in decimal (511-16)
}
! my $tp = ($ch{"permissions_$xx"} & 0200);
my $pp = $ch{"permissions_$xx"};
write_log("tp:$tp p:$pp");
***************
*** 66,70 ****
$sth = getq("update_gp", $dbh);
$sth->execute($perm, $ch{"select_gs_name_$xx"}, $ch{"ref_fk_$xx"}) || die "Query update_gp execute fails.\n$DBI::errstr\n";
! $message .= "21m";
}
else
--- 66,73 ----
$sth = getq("update_gp", $dbh);
$sth->execute($perm, $ch{"select_gs_name_$xx"}, $ch{"ref_fk_$xx"}) || die "Query update_gp execute fails.\n$DBI::errstr\n";
! if ($message !~ m/^21m|m21m/ )
! {
! $message .= "21m"; # see messages() in sessionlib.pl
! }
}
else
|
|
From: <tw...@us...> - 2002-11-25 22:15:45
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv3802
Modified Files:
Tag: Rel-1_0_1-branch
chgrp2.pl chgrp1.pl chgrp1.html
Log Message:
Switched UI over to allowing setting of any/all privs and ownership of
all the records displayed from one visit to the web page.
Previous UI was one record changed at each page visit.
New, more elegant field number resolution on the read side of the CGI.
Index: chgrp2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp2.pl,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** chgrp2.pl 25 Nov 2002 21:39:49 -0000 1.1.2.2
--- chgrp2.pl 25 Nov 2002 22:15:39 -0000 1.1.2.3
***************
*** 13,60 ****
my %ch = $q->Vars;
my $ref_fk = $ch{ref_fk};
- my $perm = $ch{permissions};
my $message = "";
#
! # Users can't change user read or user write under most circumstances.
! # If not user_write, don't allow group_write
! #
! if ($ch{group_read})
! {
! $perm |= 32; # set 32
! }
! else
! {
! $perm &= (511-32); # clear 32
! }
! if ($ch{group_write} && $ch{user_write})
! {
! $perm |= 16; # set 16
! }
! else
! {
! $perm &= (511-16); # clear 16
! }
! write_log("p:$ch{permissions} gr:$ch{group_read} gw:$ch{group_write} final:$perm");
! #
! # Check that $ch{select_gs_name} is a group I own
! # The update_db query also has this constraint.
#
! my $sth = getq("select_gs_name", $dbh);
! $sth->execute() || die "Query select_gs_name execute fails.\n$DBI::errstr\n";
! my %gname;
! while( (my $gs_pk, my $gs_name) = $sth->fetchrow_array())
{
! $gname{$gs_pk} = $gs_name;
! }
! if (exists($gname{$ch{select_gs_name}}))
! {
! $sth = getq("update_gp", $dbh);
! $sth->execute($perm, $ch{select_gs_name}, $ch{ref_fk}) || die "Query update_gp execute fails.\n$DBI::errstr\n";
! $message .= "21m";
! }
! else
! {
! write_log("User is not owner of $ch{select_gs_name}");
}
$dbh->commit();
--- 13,76 ----
my %ch = $q->Vars;
my $ref_fk = $ch{ref_fk};
my $message = "";
+
+
#
! # This is a powerful (and robust?) way to process
! # as many _xx fields as existed in the submitted CGI form.
! # The older scripts counted some field to get a max xx. This is more elegant.
! # The older stuff also required two hashes %all_ch and %ch.
! # Here we only have one hash, but the keys must always have the _$xx on the end,
! # and the keys must always be interpolated.
#
! for(my $xx=0; exists($ch{"gs_fk_$xx"}); $xx++)
{
! my $perm = $ch{"permissions_$xx"};
! #
! # Users can't change user read or user write under most circumstances.
! # If not user_write, don't allow group_write
! #
! if ($ch{"group_read_$xx"})
! {
! $perm |= 32; # set 32
! }
! else
! {
! $perm &= (511-32); # clear 32
! }
! if ($ch{"group_write_$xx"} && ($ch{"permissions_$xx"} & 128))
! {
! $perm |= 16; # set 16
! }
! else
! {
! $perm &= (511-16); # clear 16
! }
! my $tp = ($ch{"permissions_$xx"} & 128);
! my $pp = $ch{"permissions_$xx"};
! write_log("tp:$tp p:$pp");
! #
! # Check that $ch{"select_gs_name_$xx"} is a group I own
! # The update_db query also has this constraint.
! #
! my $sth = getq("select_gs_name", $dbh);
! $sth->execute() || die "Query select_gs_name execute fails.\n$DBI::errstr\n";
! my %gname;
! while( (my $gs_pk, my $gs_name) = $sth->fetchrow_array())
! {
! $gname{$gs_pk} = $gs_name;
! }
! if (exists($gname{$ch{"select_gs_name_$xx"}}))
! {
! $sth = getq("update_gp", $dbh);
! $sth->execute($perm, $ch{"select_gs_name_$xx"}, $ch{"ref_fk_$xx"}) || die "Query update_gp execute fails.\n$DBI::errstr\n";
! $message .= "21m";
! }
! else
! {
! my $selected_gs = $ch{"select_gs_name_$xx"};
! write_log("User is not owner of $selected_gs");
! }
}
$dbh->commit();
Index: chgrp1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp1.pl,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** chgrp1.pl 25 Nov 2002 21:39:47 -0000 1.1.2.2
--- chgrp1.pl 25 Nov 2002 22:15:41 -0000 1.1.2.3
***************
*** 23,33 ****
(my $all_html, my $loop_template) = readtemplate("chgrp1.html");
my $sth = getq("studies_i_own", $dbh);
$sth->execute() || die "Query studies_i_own execute fails.\n$DBI::errstr\n";
my $rows = $sth->rows();
my $hr; #hash ref
while( $hr = $sth->fetchrow_hashref())
{
! # study_name, ref_fk, gs_fk, gs_name, user_read, user_write, group_read, group_write
# write_log("sn: $hr->{study_name}");
$hr->{select_gs_name} = select_gs_name($dbh);
--- 23,38 ----
(my $all_html, my $loop_template) = readtemplate("chgrp1.html");
+ #
+ # Do the whole field_xx thing so all fields are in one big form,
+ # and any number of records can be change with a single submit.
+ #
my $sth = getq("studies_i_own", $dbh);
$sth->execute() || die "Query studies_i_own execute fails.\n$DBI::errstr\n";
my $rows = $sth->rows();
my $hr; #hash ref
+ my $xx = 0;
while( $hr = $sth->fetchrow_hashref())
{
! # study_name, ref_fk, gs_fk, gs_name, permissions, user_read, user_write, group_read, group_write
# write_log("sn: $hr->{study_name}");
$hr->{select_gs_name} = select_gs_name($dbh);
***************
*** 35,42 ****
$loop_instance =~ s/{(.*?)}/$hr->{$1}/gs;
$loop_instance = fixselect("select_gs_name", $hr->{gs_fk}, $loop_instance);
! $loop_instance = fixradiocheck("user_read", $hr->{user_read}, "checkbox", $loop_instance);
! $loop_instance = fixradiocheck("user_write", $hr->{user_write}, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_read", $hr->{group_read}, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_write", $hr->{group_write}, "checkbox", $loop_instance);
$all_html =~ s/<loop_here>/$loop_instance<loop_here>/s;
}
--- 40,49 ----
$loop_instance =~ s/{(.*?)}/$hr->{$1}/gs;
$loop_instance = fixselect("select_gs_name", $hr->{gs_fk}, $loop_instance);
! # $loop_instance = fixradiocheck("user_read", $hr->{user_read}, "checkbox", $loop_instance);
! # $loop_instance = fixradiocheck("user_write", $hr->{user_write}, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_read", $hr->{group_read}, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_write", $hr->{group_write}, "checkbox", $loop_instance);
+ $loop_instance =~ s/name=\"(.*?)\"/name=\"$1_$xx\"/g;
+ $xx++;
$all_html =~ s/<loop_here>/$loop_instance<loop_here>/s;
}
Index: chgrp1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp1.html,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** chgrp1.html 25 Nov 2002 21:39:49 -0000 1.1.2.2
--- chgrp1.html 25 Nov 2002 22:15:41 -0000 1.1.2.3
***************
*** 10,14 ****
</tr>
</table>
! <table width="800" border=1 cellspacing=0 cellpadding=3>
<tr bgcolor="#ccccff">
<td valign=top width="83"> </td>
--- 10,17 ----
</tr>
</table>
! <br>
! <form action="chgrp2.pl" method="post">
! <input type="submit" name="submit" value="Update">
! <table width="800" border=1 cellspacing=0 cellpadding=3>
<tr bgcolor="#ccccff">
<td valign=top width="83"> </td>
***************
*** 20,32 ****
<td valign=top width="114"> Group Write</td>
</tr>
! </table>
! <br>
<loop>
! <form action="chgrp2.pl" method="post">
! <table width="800" border=1 cellspacing=0 cellpadding=3>
<tr>
! <td valign=top width="84">
! <input type="submit" name="submit2" value="Update">
! </td>
<td valign=top width="84"> {study_name}
<input type="hidden" name="ref_fk" value="{ref_fk}">
--- 23,31 ----
<td valign=top width="114"> Group Write</td>
</tr>
!
<loop>
!
<tr>
! <td valign=top width="84"> </td>
<td valign=top width="84"> {study_name}
<input type="hidden" name="ref_fk" value="{ref_fk}">
***************
*** 48,56 ****
</td>
</tr>
</table>
</form>
- </loop>
-
</body>
</html>
--- 47,56 ----
</td>
</tr>
+
+ </loop>
</table>
+ <input type="submit" name="submit" value="Update">
</form>
</body>
</html>
|
|
From: <jas...@us...> - 2002-11-25 21:50:33
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv24120 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.114 retrieving revision 1.115 diff -C2 -d -r1.114 -r1.115 *** ChangeLog 23 Nov 2002 10:25:42 -0000 1.114 --- ChangeLog 25 Nov 2002 21:49:57 -0000 1.115 *************** *** 1,3 **** --- 1,14 ---- + 2002-11-25 Jason E. Stewart <ja...@op...> + + * Install (Repository): + added --files_only + + * Mason/workspace/experiments.html.in (Repository): + now creates simple links to array.html + 2002-11-23 Jason E. Stewart <ja...@op...> + + * Mason/workspace/data-loader.html.in (Repository): + renamed fesw_pk => sw_pk * DB/xml/functions-sql.xml.in (Repository): |
|
From: <jas...@us...> - 2002-11-25 21:50:33
|
Update of /cvsroot/genex/genex-server/Genex In directory sc8-pr-cvs1:/tmp/cvs-serv24120/Genex Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.125 retrieving revision 1.126 diff -C2 -d -r1.125 -r1.126 *** ChangeLog 23 Nov 2002 10:59:10 -0000 1.125 --- ChangeLog 25 Nov 2002 21:49:59 -0000 1.126 *************** *** 1,4 **** --- 1,10 ---- 2002-11-23 Jason E. Stewart <ja...@op...> + * scripts/gendb.pl.in (Repository): + fixed regex escape + + * scripts/mbad-insert.pl.in (Repository): + starting to handle missing values - convert empty values to NULL + * scripts/array-design-insert.pl.in (Repository): added --matrix |
|
From: <jas...@us...> - 2002-11-25 21:50:05
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv24120/Mason/workspace Modified Files: .cvsignore Log Message: usual Index: .cvsignore =================================================================== RCS file: /cvsroot/genex/genex-server/Mason/workspace/.cvsignore,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** .cvsignore 23 Nov 2002 08:01:49 -0000 1.2 --- .cvsignore 25 Nov 2002 21:49:59 -0000 1.3 *************** *** 1,4 **** --- 1,5 ---- add_user_to_group.html array-design.html + arrays.html authenticate.html autohandler |
|
From: <jas...@us...> - 2002-11-25 21:49:29
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv23948
Modified Files:
Install
Log Message:
* Install (Repository):
added --files_only
Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Install 23 Nov 2002 00:00:58 -0000 1.17
--- Install 25 Nov 2002 21:49:24 -0000 1.18
***************
*** 78,81 ****
--- 78,85 ----
use Getopt::Long;
use Term::ReadKey;
+ my %OPTIONS;
+ my $rc = GetOptions(\%OPTIONS,
+ "files_only",
+ );
***************
*** 100,103 ****
--- 104,110 ----
}
+ goto FILES_ONLY
+ if exists $OPTIONS{files_only};
+
print STDOUT <<"EOM";
***************
*** 565,568 ****
--- 572,577 ----
slow() if ($SLOW);
+ FILES_ONLY: {};
+
# now go through the MANIFEST and install all the files
print STDERR "\nCopying all files to their locations\n";
***************
*** 574,577 ****
--- 583,589 ----
genex_system("cp $file $FILES{$file}");
}
+
+ exit(0)
+ if exists $OPTIONS{files_only};
print STDERR <<EOT;
|
|
From: <jas...@us...> - 2002-11-25 21:48:51
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv23723 Modified Files: MANIFEST.in Log Message: new file Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** MANIFEST.in 23 Nov 2002 00:01:20 -0000 1.4 --- MANIFEST.in 25 Nov 2002 21:48:47 -0000 1.5 *************** *** 5,8 **** --- 5,9 ---- 'Mason/workspace/add_user_to_group.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/array-design.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/arrays.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/authenticate.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/autohandler' => '%%GENEX_WORKSPACE_DIR%%', |
|
From: <jas...@us...> - 2002-11-25 21:47:52
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv23199/Mason/workspace
Modified Files:
experiments.html.in
Log Message:
* Mason/workspace/experiments.html.in (Repository):
now creates simple links to array.html
Index: experiments.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/experiments.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** experiments.html.in 20 Nov 2002 22:35:26 -0000 1.2
--- experiments.html.in 25 Nov 2002 21:47:49 -0000 1.3
***************
*** 8,12 ****
<thead>
<tr bgcolor="#FFB6C1" align=center>
! <td>Arrays for Experiment: <% $exp_db->name %></td>
</tr>
</thead>
--- 8,12 ----
<thead>
<tr bgcolor="#FFB6C1" align=center>
! <td>PhysicalBioAssay's for Experiment: <% $exp_db->name %></td>
</tr>
</thead>
***************
*** 19,22 ****
--- 19,42 ----
</table>
<hr noshade size=5>
+
+ <table bgcolor="#A2FBC9" border="1">
+ <thead>
+ <tr bgcolor="#FFB6C1" align=center>
+ <td>MeasuredBioAssay's for Experiment: <% $exp_db->name %></td>
+ </tr>
+ </thead>
+ <tbody>
+ % foreach my $array (@{$table_ref->[1]}) {
+ <tr>
+ <td><p>Found array:
+ <a href="<% $action %>?type=mba&id=<% $array->id %>">
+ <% $array->name %>
+ </a></p>
+ </td>
+ </tr>
+ % }
+ </tbody>
+ </table>
+ <hr noshade size=5>
% }
<input type="submit" name="submit" value="Retrieve Data" size="33">
***************
*** 53,56 ****
--- 73,77 ----
$dbh->assert_table_defined('PhysicalBioAssay');
+ $dbh->assert_table_defined('MeasuredBioAssay');
my @exp_dbs = Bio::Genex::ExperimentSet->get_objects($dbh,
@experiments);
***************
*** 59,63 ****
my @pba_dbs = Bio::Genex::PhysicalBioAssay->get_all_objects($dbh,
column=>'es_fk',value=>$exp->es_pk);
! push(@exps,[$exp,\@pba_dbs]);
}
--- 80,86 ----
my @pba_dbs = Bio::Genex::PhysicalBioAssay->get_all_objects($dbh,
column=>'es_fk',value=>$exp->es_pk);
! my @mba_dbs = Bio::Genex::MeasuredBioAssay->get_all_objects($dbh,
! column=>'es_fk',value=>$exp->es_pk);
! push(@exps,[$exp,\@pba_dbs,\@mba_dbs]);
}
|
|
From: <jas...@us...> - 2002-11-25 21:45:39
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv22126/Mason/workspace
Added Files:
arrays.html.in
Log Message:
new
--- NEW FILE: arrays.html.in ---
<%args>
$type
$id
$debug => 0
</%args>
<%attr>
name=>'GeneX DB BioAssay Display Page'
path=>'%%GENEX_WORKSPACE_URL%%/array.html'
</%attr>
<%once>;
use Bio::Genex;
use Bio::Genex::Config;
use Bio::Genex::MeasuredBioAssay;
use Bio::Genex::PhysicalBioAssay;
use File::Temp qw(tempfile);
</%once>
<%init>
my $name = $m->current_comp->attr('name');
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);
my $table_name = $mba_db->sw_obj->qd_obj->data_table_name();
$table_name .= '_view';
# my $name = $mba_db->name();
my $sql = $dbh->create_select_sql(FROM=>[$table_name],
COLUMNS=>['*'],
WHERE=>"mba_fk=$id",
);
my $sth = $dbh->prepare($sql)
or $dbh->error(caller=>'arrays.html',
message=>"Couldn't prepare data fetch for MeasuredBioAssay:$id",
sql=>$sql,
);
$sth->execute()
or $dbh->error(caller=>'arrays.html',
message=>"Couldn't execute fetch for MeasuredBioAssay:$id",
sth=>$sth,
);
$m->clear_buffer();
my ($out_fh,$out_file) = tempfile(DIR=>'%%HTMLTMPDIR%%',
);
my $out_url = $out_file;
$out_url =~ s|.*/||;
$out_url = "%%CGITMPURL%%/$out_url";
# print header
my $cols = $sth->{NUM_OF_FIELDS};
print $out_fh '# ' . join("\t", @{$sth->{NAME}}[2..$cols]) . "\n";
while (my $array_ref = $sth->fetchrow_arrayref) {
$dbh->error(caller=>'arrays.html',
message=>"Couldn't fetch row MeasuredBioAssay:$id",
sth=>$sth,
)
if $sth->err;
print $out_fh join("\t", @{$array_ref}[2..$cols]) . "\n";
}
$m->print("<H2>Data for MeasuredBioAssay: $id written to file. Click <a href='$out_url'>here</a> to dowload</H2>");
} else {
my $pba_db = Bio::Genex::PhysicalBioAssay->get_objects($dbh, $id);
}
</%init>
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv19198
Modified Files:
Tag: Rel-1_0_1-branch
sql_lib.pl chgrp1.pl chgrp1.html chgrp2.pl sessionlib.pl
Log Message:
changing group and setting group privs is working.
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.15
retrieving revision 1.1.2.16
diff -C2 -d -r1.1.2.15 -r1.1.2.16
*** sql_lib.pl 25 Nov 2002 16:32:40 -0000 1.1.2.15
--- sql_lib.pl 25 Nov 2002 21:39:44 -0000 1.1.2.16
***************
*** 128,131 ****
--- 128,132 ----
gs_fk,
gs_name,
+ permissions,
(permissions&256=256) as user_read,
(permissions&128=128) as user_write,
***************
*** 137,143 ****
groupref.us_fk=$us_fk AND
groupref.gs_fk=groupsec.gs_pk AND
! groupref.us_fk=groupsec.gs_owner AND
! groupsec.gs_pk=groupsec.gs_owner AND
! ref_fk=sty_pk";
}
elsif ($q_name eq "select_gs_name")
--- 138,146 ----
groupref.us_fk=$us_fk AND
groupref.gs_fk=groupsec.gs_pk AND
! (groupref.us_fk=groupsec.gs_owner OR
! groupsec.gs_pk=groupsec.gs_owner) AND
! ref_fk=sty_pk
! ORDER BY
! study_name";
}
elsif ($q_name eq "select_gs_name")
***************
*** 153,157 ****
# Keep us_fk=$us_fk as a constraint. Only the owner of the record is allowed to change permissions
! $sql = "update groupref (permissions, gs_fk) values (?,?) where ref_fk=? and us_fk=$us_fk";
}
elsif ($q_name eq "groupref_table_name")
--- 156,160 ----
# Keep us_fk=$us_fk as a constraint. Only the owner of the record is allowed to change permissions
! $sql = "update groupref set permissions=?, gs_fk=? where ref_fk=? and us_fk=$us_fk";
}
elsif ($q_name eq "groupref_table_name")
***************
*** 201,206 ****
as table_select where count>0
";
-
}
# write_log("sql: $sql");
if (defined($sql))
--- 204,211 ----
as table_select where count>0
";
}
+
+
+
# write_log("sql: $sql");
if (defined($sql))
Index: chgrp1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp1.pl,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** chgrp1.pl 25 Nov 2002 14:29:12 -0000 1.1.2.1
--- chgrp1.pl 25 Nov 2002 21:39:47 -0000 1.1.2.2
***************
*** 11,14 ****
--- 11,22 ----
my $q = new CGI;
my $dbh = new_connection();
+ my %ch = $q->Vars();
+ #
+ # Turn message param in the form 0m1m2m back into a message text.
+ # Use the wonderful and dangerous /e switch to eval the right side
+ # of the regex. See sub messages() in sessionlib.pl
+ #
+ $ch{message} =~ s/(\d+)m/messages($1)/eg;
+
# list all the studies, orders, files I own
***************
*** 26,37 ****
my $loop_instance = $loop_template;
$loop_instance =~ s/{(.*?)}/$hr->{$1}/gs;
! $loop_instance = fixselect("select_gs_name", $hr->{gs_name}, $loop_instance);
! $loop_instance = fixradiocheck("user_read", 1, "checkbox", $loop_instance);
! $loop_instance = fixradiocheck("user_write", 1, "checkbox", $loop_instance);
! $loop_instance = fixradiocheck("group_read", 1, "checkbox", $loop_instance);
! $loop_instance = fixradiocheck("group_write", 1, "checkbox", $loop_instance);
$all_html =~ s/<loop_here>/$loop_instance<loop_here>/s;
}
$all_html =~ s/<loop_here>//s;
print "Content-type: text/html\n\n$all_html\n";
--- 34,46 ----
my $loop_instance = $loop_template;
$loop_instance =~ s/{(.*?)}/$hr->{$1}/gs;
! $loop_instance = fixselect("select_gs_name", $hr->{gs_fk}, $loop_instance);
! $loop_instance = fixradiocheck("user_read", $hr->{user_read}, "checkbox", $loop_instance);
! $loop_instance = fixradiocheck("user_write", $hr->{user_write}, "checkbox", $loop_instance);
! $loop_instance = fixradiocheck("group_read", $hr->{group_read}, "checkbox", $loop_instance);
! $loop_instance = fixradiocheck("group_write", $hr->{group_write}, "checkbox", $loop_instance);
$all_html =~ s/<loop_here>/$loop_instance<loop_here>/s;
}
$all_html =~ s/<loop_here>//s;
+ $all_html =~ s/{(.*?)}/$ch{$1}/sg;
print "Content-type: text/html\n\n$all_html\n";
Index: chgrp1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp1.html,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** chgrp1.html 25 Nov 2002 14:29:12 -0000 1.1.2.1
--- chgrp1.html 25 Nov 2002 21:39:49 -0000 1.1.2.2
***************
*** 32,48 ****
<input type="hidden" name="ref_fk" value="{ref_fk}">
<input type="hidden" name="gs_fk" value="{gs_fk}">
</td>
<td valign=top width="72"> {select_gs_name} </td>
<td valign=top width="105">
! <input type="checkbox" name="user_read" value="{user_read}">
</td>
<td valign=top width="102">
! <input type="checkbox" name="user_write" value="{user_write}">
</td>
<td valign=top width="126">
! <input type="checkbox" name="group_read" value="{group_read}">
</td>
<td valign=top width="110">
! <input type="checkbox" name="group_write" value="{group_write}">
</td>
</tr>
--- 32,49 ----
<input type="hidden" name="ref_fk" value="{ref_fk}">
<input type="hidden" name="gs_fk" value="{gs_fk}">
+ <input type="hidden" name="permissions" value="{permissions}">
</td>
<td valign=top width="72"> {select_gs_name} </td>
<td valign=top width="105">
! <input type="checkbox" name="user_read" value="1">
</td>
<td valign=top width="102">
! <input type="checkbox" name="user_write" value="1">
</td>
<td valign=top width="126">
! <input type="checkbox" name="group_read" value="1">
</td>
<td valign=top width="110">
! <input type="checkbox" name="group_write" value="1">
</td>
</tr>
Index: chgrp2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp2.pl,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** chgrp2.pl 25 Nov 2002 14:29:12 -0000 1.1.2.1
--- chgrp2.pl 25 Nov 2002 21:39:49 -0000 1.1.2.2
***************
*** 5,9 ****
use CGI::Carp qw(fatalsToBrowser);
! require "sessionlib.pl";
main:
--- 5,9 ----
use CGI::Carp qw(fatalsToBrowser);
! require "./sessionlib.pl";
main:
***************
*** 13,17 ****
my %ch = $q->Vars;
my $ref_fk = $ch{ref_fk};
! my $perm = 0;
#
# Users can't change user read or user write under most circumstances.
--- 13,18 ----
my %ch = $q->Vars;
my $ref_fk = $ch{ref_fk};
! my $perm = $ch{permissions};
! my $message = "";
#
# Users can't change user read or user write under most circumstances.
***************
*** 20,30 ****
if ($ch{group_read})
{
! $perm |= 32;
}
if ($ch{group_write} && $ch{user_write})
{
! $perm |= 16;
}
- my $sth = getq("update_gp", $dbh);
- $sth->execute($perm, $ch{select_gs_name}, $ch{ref_fk});
}
--- 21,74 ----
if ($ch{group_read})
{
! $perm |= 32; # set 32
! }
! else
! {
! $perm &= (511-32); # clear 32
}
if ($ch{group_write} && $ch{user_write})
{
! $perm |= 16; # set 16
! }
! else
! {
! $perm &= (511-16); # clear 16
! }
! write_log("p:$ch{permissions} gr:$ch{group_read} gw:$ch{group_write} final:$perm");
! #
! # Check that $ch{select_gs_name} is a group I own
! # The update_db query also has this constraint.
! #
! my $sth = getq("select_gs_name", $dbh);
! $sth->execute() || die "Query select_gs_name execute fails.\n$DBI::errstr\n";
! my %gname;
! while( (my $gs_pk, my $gs_name) = $sth->fetchrow_array())
! {
! $gname{$gs_pk} = $gs_name;
! }
!
! if (exists($gname{$ch{select_gs_name}}))
! {
! $sth = getq("update_gp", $dbh);
! $sth->execute($perm, $ch{select_gs_name}, $ch{ref_fk}) || die "Query update_gp execute fails.\n$DBI::errstr\n";
! $message .= "21m";
! }
! else
! {
! write_log("User is not owner of $ch{select_gs_name}");
! }
! $dbh->commit();
! $dbh->disconnect();
! if ((length($message) > 0))
! {
! my $url = index_url(); # see sessionlib.pl
! $url =~ s/(.*)\/.*/$1\/chgrp1.pl/;
! print "Location: $url?message=$message\n\n";
! exit();
! }
! else
! {
! my $url = index_url(); # see sessionlib.pl
! print "Location: $url\n\n";
}
}
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.7
retrieving revision 1.1.2.8
diff -C2 -d -r1.1.2.7 -r1.1.2.8
*** sessionlib.pl 25 Nov 2002 14:29:12 -0000 1.1.2.7
--- sessionlib.pl 25 Nov 2002 21:39:49 -0000 1.1.2.8
***************
*** 53,56 ****
--- 53,58 ----
$messages[19] = "One or more sample hybridizations does not have a chip selected. A chip must be selected on which to run the sample(s).<br>\n";
$messages[20] = "One or more samples have no Study/Experimental Condition selected.<br>\n";
+ $messages[21] = "Successfully updated group/permission info.<br>\n";
+
return $messages[$_[0]];
}
|
|
From: <jl...@us...> - 2002-11-25 16:32:47
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv2988
Modified Files:
Tag: Rel-1_0_1-branch
sql_lib.pl
Log Message:
added SQL query for groupref_table_name.pl
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.14
retrieving revision 1.1.2.15
diff -C2 -d -r1.1.2.14 -r1.1.2.15
*** sql_lib.pl 25 Nov 2002 15:18:20 -0000 1.1.2.14
--- sql_lib.pl 25 Nov 2002 16:32:40 -0000 1.1.2.15
***************
*** 9,16 ****
my $q_name = $_[0];
my $dbh = $_[1];
! if ($_[2])
! {
! my @args = @{$_[2]};
! }
if (! defined($dbh))
{
--- 9,14 ----
my $q_name = $_[0];
my $dbh = $_[1];
! my @args;
! $args[0]=$_[2];
if (! defined($dbh))
{
***************
*** 157,161 ****
--- 155,206 ----
$sql = "update groupref (permissions, gs_fk) values (?,?) where ref_fk=? and us_fk=$us_fk";
}
+ elsif ($q_name eq "groupref_table_name")
+ {
+
+ $sql = "
+ SELECT * from (
+ SELECT count(*), 'bh_pk' as table from blasthits where bh_pk=$args[0]
+ UNION
+ SELECT count(*), 'chr_pk' as table from chromosome where chr_pk=$args[0]
+ UNION
+ SELECT count(*), 'ef_pk' as table from experimentfactors where ef_pk=$args[0]
+ UNION
+ SELECT count(*), 'smp_pk' as table from sample where smp_pk=$args[0]
+ UNION
+ SELECT count(*), 'tl_pk' as table from treatmentlevel where tl_pk=$args[0]
+ UNION
+ SELECT count(*), 'prt_pk' as table from protocol where prt_pk=$args[0]
+ UNION
+ SELECT count(*), 'scn_pk' as table from scanner where scn_pk=$args[0]
+ UNION
+ SELECT count(*), 'sptr_pk' as table from spotter where sptr_pk=$args[0]
+ UNION
+ SELECT count(*), 'cit_pk' as table from citation where cit_pk=$args[0]
+ UNION
+ SELECT count(*), 'sw_pk' as table from software where sw_pk=$args[0]
+ UNION
+ SELECT count(*), 'spc_pk' as table from species where spc_pk=$args[0]
+ UNION
+ SELECT count(*), 'sty_pk' as table from study where sty_pk=$args[0]
+ UNION
+ SELECT count(*), 'ec_pk' as table from exp_condition where ec_pk=$args[0]
+ UNION
+ SELECT count(*), 'am_pk' as table from arraymeasurement where am_pk=$args[0]
+ UNION
+ SELECT count(*), 'al_pk' as table from arraylayout where al_pk=$args[0]
+ UNION
+ SELECT count(*), 'qc_pk' as table from quality_control where qc_pk=$args[0]
+ UNION
+ SELECT count(*), 'oi_pk' as table from order_info where oi_pk=$args[0]
+ UNION
+ SELECT count(*), 'fi_pk' as table from file_info where fi_pk=$args[0]
+ UNION
+ SELECT count(*), 'tree_pk' as table from tree where tree_pk=$args[0]
+ UNION
+ SELECT count(*), 'node_pk' as table from node where node_pk=$args[0])
+ as table_select where count>0
+ ";
+ }
# write_log("sql: $sql");
if (defined($sql))
***************
*** 171,173 ****
! 1;
--- 216,218 ----
! ;
|
|
From: <jl...@us...> - 2002-11-25 16:31:44
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv2288
Added Files:
Tag: Rel-1_0_1-branch
groupref_table_name.pl
Log Message:
script to identify table associated with secured record in groupref table
--- NEW FILE: groupref_table_name.pl ---
#!/usr/bin/perl
use strict;
require "./sessionlib.pl";
main:
{
my $dbh = new_connection();
my $sth = getq("groupref_table_name",$dbh, $ARGV[0]);
$sth->execute();
(my $count, my $table) = $sth->fetchrow_array();
print "Count: $count Table: $table \n";
$sth->finish();
$dbh->disconnect();
}
|
|
From: <tw...@us...> - 2002-11-25 15:39:30
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv25473
Modified Files:
Tag: Rel-1_0_1-branch
sql_lib.pl
Log Message:
working on update privs
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.13
retrieving revision 1.1.2.14
diff -C2 -d -r1.1.2.13 -r1.1.2.14
*** sql_lib.pl 25 Nov 2002 14:29:12 -0000 1.1.2.13
--- sql_lib.pl 25 Nov 2002 15:18:20 -0000 1.1.2.14
***************
*** 153,157 ****
# select permissions and only allow group_write to be set if user_write
# need some exclusive or comb like (?&(128/8)&16)
! $sql = "update groupref (permissions, gs_fk) values (?,?) where ref_fk=?";
}
--- 153,159 ----
# select permissions and only allow group_write to be set if user_write
# need some exclusive or comb like (?&(128/8)&16)
!
! # Keep us_fk=$us_fk as a constraint. Only the owner of the record is allowed to change permissions
! $sql = "update groupref (permissions, gs_fk) values (?,?) where ref_fk=? and us_fk=$us_fk";
}
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv22659
Modified Files:
Tag: Rel-1_0_1-branch
edit_atree1.html sql_lib.pl sessionlib.pl
Added Files:
Tag: Rel-1_0_1-branch
chgrp2.pl chgrp1.html chgrp1.pl
Log Message:
chgrp web pages will display studies and ownership
atree edit updated with on-page instructions.
--- NEW FILE: chgrp2.pl ---
#!/usr/bin/perl
use strict;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
require "sessionlib.pl";
main:
{
my $q = new CGI;
my $dbh = new_connection();
my %ch = $q->Vars;
my $ref_fk = $ch{ref_fk};
my $perm = 0;
#
# Users can't change user read or user write under most circumstances.
# If not user_write, don't allow group_write
#
if ($ch{group_read})
{
$perm |= 32;
}
if ($ch{group_write} && $ch{user_write})
{
$perm |= 16;
}
my $sth = getq("update_gp", $dbh);
$sth->execute($perm, $ch{select_gs_name}, $ch{ref_fk});
}
--- NEW FILE: chgrp1.html ---
<html><head><title>Manage ownership and permissions</title></head>
<body bgcolor="#FFFFFF">
<table width="600" border=0 cellpadding=0 cellspacing=0>
<tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX MAS5 Hybridization Analysis<br><br>
<a href="./">Return to Genex Member Home</a>
<br><br clear=all><br>
Change the group and/or read-write permissions.<br>
<font color="#FF0000">{message}</font>
</td>
</tr>
</table>
<table width="800" border=1 cellspacing=0 cellpadding=3>
<tr bgcolor="#ccccff">
<td valign=top width="83"> </td>
<td valign=top width="99"> Name</td>
<td valign=top width="112"> Group</td>
<td valign=top width="104"> User Read</td>
<td valign=top width="103"> User Write</td>
<td valign=top width="127"> Group Read</td>
<td valign=top width="114"> Group Write</td>
</tr>
</table>
<br>
<loop>
<form action="chgrp2.pl" method="post">
<table width="800" border=1 cellspacing=0 cellpadding=3>
<tr>
<td valign=top width="84">
<input type="submit" name="submit2" value="Update">
</td>
<td valign=top width="84"> {study_name}
<input type="hidden" name="ref_fk" value="{ref_fk}">
<input type="hidden" name="gs_fk" value="{gs_fk}">
</td>
<td valign=top width="72"> {select_gs_name} </td>
<td valign=top width="105">
<input type="checkbox" name="user_read" value="{user_read}">
</td>
<td valign=top width="102">
<input type="checkbox" name="user_write" value="{user_write}">
</td>
<td valign=top width="126">
<input type="checkbox" name="group_read" value="{group_read}">
</td>
<td valign=top width="110">
<input type="checkbox" name="group_write" value="{group_write}">
</td>
</tr>
</table>
</form>
</loop>
</body>
</html>
--- NEW FILE: chgrp1.pl ---
#!/usr/bin/perl
use strict;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
require "sessionlib.pl";
main:
{
my $q = new CGI;
my $dbh = new_connection();
# list all the studies, orders, files I own
(my $all_html, my $loop_template) = readtemplate("chgrp1.html");
my $sth = getq("studies_i_own", $dbh);
$sth->execute() || die "Query studies_i_own execute fails.\n$DBI::errstr\n";
my $rows = $sth->rows();
my $hr; #hash ref
while( $hr = $sth->fetchrow_hashref())
{
# study_name, ref_fk, gs_fk, gs_name, user_read, user_write, group_read, group_write
# write_log("sn: $hr->{study_name}");
$hr->{select_gs_name} = select_gs_name($dbh);
my $loop_instance = $loop_template;
$loop_instance =~ s/{(.*?)}/$hr->{$1}/gs;
$loop_instance = fixselect("select_gs_name", $hr->{gs_name}, $loop_instance);
$loop_instance = fixradiocheck("user_read", 1, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("user_write", 1, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_read", 1, "checkbox", $loop_instance);
$loop_instance = fixradiocheck("group_write", 1, "checkbox", $loop_instance);
$all_html =~ s/<loop_here>/$loop_instance<loop_here>/s;
}
$all_html =~ s/<loop_here>//s;
print "Content-type: text/html\n\n$all_html\n";
$dbh->disconnect();
}
sub select_gs_name
{
my $dbh = $_[0];
my $sth = getq("select_gs_name", $dbh);
$sth->execute();
my $sel = "<select name=\"select_gs_name\">\n";
while((my $gs_pk, my $gs_name) = $sth->fetchrow_array())
{
$sel .= "<option value=\"$gs_pk\">$gs_name</option>\n";
}
$sel .= "</select>\n";
return $sel;
}
Index: edit_atree1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.html,v
retrieving revision 1.1.2.6
retrieving revision 1.1.2.7
diff -C2 -d -r1.1.2.6 -r1.1.2.7
*** edit_atree1.html 12 Nov 2002 22:34:36 -0000 1.1.2.6
--- edit_atree1.html 25 Nov 2002 14:29:12 -0000 1.1.2.7
***************
*** 7,10 ****
--- 7,12 ----
</tr>
</table>
+ Click the radio button of the node you wish to modify.<br>
+ Node properties are not yet implemented.
<br>
<font color="#FF0000">{message}</font>
***************
*** 21,25 ****
<table border="0">
<tr>
! <td> </td><td><input type=submit name="add" value="Add Node"></td>
</tr>
--- 23,32 ----
<table border="0">
<tr>
! <td> </td><td>Click the radio button of the node you wish to modify.<br>
! Choose an analysis from the list, then "Add Node" or "Change Node"<br></td>
! </tr>
!
! <tr>
! <td>Analysis List</td><td><input type=submit name="add" value="Add Node"></td>
</tr>
***************
*** 34,38 ****
</form>
<br>
! * Please complete these fields. This information is required before your analysis
will run.<br>
</body>
--- 41,45 ----
</form>
<br>
! * (Node properties will eventually contain required fields.) Please complete these fields. This information is required before your analysis
will run.<br>
</body>
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.12
retrieving revision 1.1.2.13
diff -C2 -d -r1.1.2.12 -r1.1.2.13
*** sql_lib.pl 22 Nov 2002 14:15:49 -0000 1.1.2.12
--- sql_lib.pl 25 Nov 2002 14:29:12 -0000 1.1.2.13
***************
*** 123,130 ****
elsif ($q_name eq "studies_i_own")
{
! my $us_fk = get_us_fk($dbh);
! $sql = "select study_name as name,ref_fk,gs_fk,permissions from study,groupref where us_fk=$us_fk and ref_fk=sty_pk";
}
if (defined($sql))
{
--- 123,160 ----
elsif ($q_name eq "studies_i_own")
{
! my $us_fk = get_us_fk($dbh);
! $sql = "
! SELECT
! study_name,
! ref_fk,
! gs_fk,
! gs_name,
! (permissions&256=256) as user_read,
! (permissions&128=128) as user_write,
! (permissions&32=32) as group_read,
! (permissions&16=16) as group_write
! FROM
! study,groupref,groupsec
! WHERE
! groupref.us_fk=$us_fk AND
! groupref.gs_fk=groupsec.gs_pk AND
! groupref.us_fk=groupsec.gs_owner AND
! groupsec.gs_pk=groupsec.gs_owner AND
! ref_fk=sty_pk";
! }
! elsif ($q_name eq "select_gs_name")
! {
! my $us_fk = get_us_fk($dbh);
! $sql = "select gs_pk,gs_name from groupsec where gs_owner=$us_fk";
! }
! elsif ($q_name eq "update_gp")
! {
! my $us_fk = get_us_fk($dbh);
! # select permissions and only allow group_write to be set if user_write
! # need some exclusive or comb like (?&(128/8)&16)
! $sql = "update groupref (permissions, gs_fk) values (?,?) where ref_fk=?";
}
+ # write_log("sql: $sql");
if (defined($sql))
{
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.6
retrieving revision 1.1.2.7
diff -C2 -d -r1.1.2.6 -r1.1.2.7
*** sessionlib.pl 18 Nov 2002 19:09:20 -0000 1.1.2.6
--- sessionlib.pl 25 Nov 2002 14:29:12 -0000 1.1.2.7
***************
*** 504,508 ****
my $key;
my $value;
! my %Vars;
if (! open(OR, "< options.reminders"))
--- 504,508 ----
my $key;
my $value;
! my %vars;
if (! open(OR, "< options.reminders"))
***************
*** 525,529 ****
$value =~ s/^\s*(.*?)\s*$/$1/; # remove zero or more leading and/or trailing whitespace chars
! $Vars{$key} = $value;
}
#
--- 525,529 ----
$value =~ s/^\s*(.*?)\s*$/$1/; # remove zero or more leading and/or trailing whitespace chars
! $vars{$key} = $value;
}
#
***************
*** 531,576 ****
#
! $Vars{MOTHERDIR} = `pwd`; # where we start from.
! chomp($Vars{MOTHERDIR});
! $Vars{CURR_LOGIN} = getpwuid($<);
# aug 13 2002 tom: need a var for the webtools destination directory.
! $Vars{WEBTOOLS} = "$Vars{HTMLDIR}/$Vars{GENEX_DIR}/webtools";
! $Vars{GENEX_CGI_URL} = "$Vars{CGI_ROOT_URL}/$Vars{GENEX_DIR}";
! $Vars{GENEX_URL_QUERY} = "$Vars{GENEX_CGI_URL}/gxquery";
! $Vars{GENEX_URL_CUR_TOOL} = "$Vars{GENEX_CGI_URL}/curation-tool";
! $Vars{GENEX_URL_EXAMPLE} = "$Vars{GENEX_CGI_URL}/samples";
! $Vars{GENEX_HTM_URL} = "$Vars{HTML_ROOT_URL}/$Vars{GENEX_DIR}";
! $Vars{GENEX_GRAPHICS_URL} = "$Vars{GENEX_HTM_URL}/graphics";
! $Vars{CYBERT_DIR} = "$Vars{GENEX_DIR}/cybert";
! $Vars{GXQUERY_DIR} = "$Vars{GENEX_DIR}/gxquery";
! $Vars{RCLUST_DIR} = "$Vars{GENEX_DIR}/rcluster";
! $Vars{CURA_TOOL} = "$Vars{GENEX_DIR}/curation-tool";
! $Vars{LOGIN_DIR} = "$Vars{GENEX_DIR}/login";
! $Vars{MERGEM_DIR} = "$Vars{GENEX_DIR}/mergem";
! $Vars{GENEX_CGIDIR} = "$Vars{CGIDIR}/$Vars{GENEX_DIR}";
! $Vars{GENEX_QUERY_DIR} = "$Vars{GENEX_CGIDIR}/gxquery";
! $Vars{GENEX_EXAMPLE_DIR} = "$Vars{GENEX_CGIDIR}/samples";
! $Vars{GENEX_CUR_TOOL_DIR} = "$Vars{GENEX_CGIDIR}/curation-tool";
! $Vars{DOWNLOAD_DIR} = "$Vars{GENEX_DIR}/download";
! $Vars{CyberT_Demo_DIR} = "$Vars{GENEX_DIR}/CyberT-Demo";
! $Vars{DTD_DIR} = "$Vars{GENEX_DIR}/DTD";
! $Vars{GENEXML_URL} = "$Vars{HTML_ROOT_URL}/$Vars{DTD_DIR}";
! $Vars{DTD_HTML_URL} = "$Vars{GENEXML_URL}/genexml-html";
! $Vars{RCluster_Demo_DIR} = "$Vars{GENEX_DIR}/RCluster-Demo";
! $Vars{GRAPHICS_DIR} = "$Vars{GENEX_DIR}/graphics";
! $Vars{INCLUDE_DIR} = "$Vars{GENEX_DIR}/include";
! $Vars{TOP_LEVEL_DIR} = "$Vars{GENEX_DIR}/top_level";
! $Vars{XCLUSTER_DIR} = "$Vars{GENEX_DIR}/xcluster";
! $Vars{RCLUSTER_PERL_LIB} = "$Vars{PREFIX}/RCluster";
! if ($Vars{PREFIX}) {
! $Vars{GENEX_MAN1} = "$Vars{LOCAL_ROOT}/man/man1";
! $Vars{GENEX_MAN3} = "$Vars{LOCAL_ROOT}/man/man3";
! $Vars{GENEX_INSTALLSITE} = $Vars{PREFIX};
}
--- 531,576 ----
#
! $vars{MOTHERDIR} = `pwd`; # where we start from.
! chomp($vars{MOTHERDIR});
! $vars{CURR_LOGIN} = getpwuid($<);
# aug 13 2002 tom: need a var for the webtools destination directory.
! $vars{WEBTOOLS} = "$vars{HTMLDIR}/$vars{GENEX_DIR}/webtools";
! $vars{GENEX_CGI_URL} = "$vars{CGI_ROOT_URL}/$vars{GENEX_DIR}";
! $vars{GENEX_URL_QUERY} = "$vars{GENEX_CGI_URL}/gxquery";
! $vars{GENEX_URL_CUR_TOOL} = "$vars{GENEX_CGI_URL}/curation-tool";
! $vars{GENEX_URL_EXAMPLE} = "$vars{GENEX_CGI_URL}/samples";
! $vars{GENEX_HTM_URL} = "$vars{HTML_ROOT_URL}/$vars{GENEX_DIR}";
! $vars{GENEX_GRAPHICS_URL} = "$vars{GENEX_HTM_URL}/graphics";
! $vars{CYBERT_DIR} = "$vars{GENEX_DIR}/cybert";
! $vars{GXQUERY_DIR} = "$vars{GENEX_DIR}/gxquery";
! $vars{RCLUST_DIR} = "$vars{GENEX_DIR}/rcluster";
! $vars{CURA_TOOL} = "$vars{GENEX_DIR}/curation-tool";
! $vars{LOGIN_DIR} = "$vars{GENEX_DIR}/login";
! $vars{MERGEM_DIR} = "$vars{GENEX_DIR}/mergem";
! $vars{GENEX_CGIDIR} = "$vars{CGIDIR}/$vars{GENEX_DIR}";
! $vars{GENEX_QUERY_DIR} = "$vars{GENEX_CGIDIR}/gxquery";
! $vars{GENEX_EXAMPLE_DIR} = "$vars{GENEX_CGIDIR}/samples";
! $vars{GENEX_CUR_TOOL_DIR} = "$vars{GENEX_CGIDIR}/curation-tool";
! $vars{DOWNLOAD_DIR} = "$vars{GENEX_DIR}/download";
! $vars{CyberT_Demo_DIR} = "$vars{GENEX_DIR}/CyberT-Demo";
! $vars{DTD_DIR} = "$vars{GENEX_DIR}/DTD";
! $vars{GENEXML_URL} = "$vars{HTML_ROOT_URL}/$vars{DTD_DIR}";
! $vars{DTD_HTML_URL} = "$vars{GENEXML_URL}/genexml-html";
! $vars{RCluster_Demo_DIR} = "$vars{GENEX_DIR}/RCluster-Demo";
! $vars{GRAPHICS_DIR} = "$vars{GENEX_DIR}/graphics";
! $vars{INCLUDE_DIR} = "$vars{GENEX_DIR}/include";
! $vars{TOP_LEVEL_DIR} = "$vars{GENEX_DIR}/top_level";
! $vars{XCLUSTER_DIR} = "$vars{GENEX_DIR}/xcluster";
! $vars{RCLUSTER_PERL_LIB} = "$vars{PREFIX}/RCluster";
! if ($vars{PREFIX}) {
! $vars{GENEX_MAN1} = "$vars{LOCAL_ROOT}/man/man1";
! $vars{GENEX_MAN3} = "$vars{LOCAL_ROOT}/man/man3";
! $vars{GENEX_INSTALLSITE} = $vars{PREFIX};
}
***************
*** 580,584 ****
# weak desire to maintain legacy options. See sub new_connection.
#
! $Vars{'GENEX_CONNECT'} = "dbi:$Vars{GENEX_DBMS}:dbname=$Vars{DB_NAME};host=$Vars{GENEX_HOST};port=$Vars{GENEX_PORT}";
#
--- 580,584 ----
# weak desire to maintain legacy options. See sub new_connection.
#
! $vars{'GENEX_CONNECT'} = "dbi:$vars{GENEX_DBMS}:dbname=$vars{DB_NAME};host=$vars{GENEX_HOST};port=$vars{GENEX_PORT}";
#
***************
*** 586,593 ****
# Used to use strftime() but that stopped working.
#
! $Vars{GENEX_SERVER_INSTALLATION_DATE} = `date +\"$Vars{ISO8601_DATE_FORMAT}\"`;
! chomp($Vars{GENEX_SERVER_INSTALLATION_DATE});
! return %Vars;
} # end read_optionsdotreminders()
--- 586,593 ----
# Used to use strftime() but that stopped working.
#
! $vars{GENEX_SERVER_INSTALLATION_DATE} = `date +\"$vars{ISO8601_DATE_FORMAT}\"`;
! chomp($vars{GENEX_SERVER_INSTALLATION_DATE});
! return %vars;
} # end read_optionsdotreminders()
***************
*** 1018,1024 ****
# fix radio and checkboxes
# returns string fixed_html = fixradiocheck(string name attribute,
! # string value attribute,
! # string "checkbox" | "radio",
! # string the_html_to_fix )
#
sub fixradiocheck
--- 1018,1024 ----
# fix radio and checkboxes
# returns string fixed_html = fixradiocheck(string name attribute,
! # string value attribute,
! # string "checkbox" | "radio",
! # string the_html_to_fix )
#
sub fixradiocheck
***************
*** 1070,1074 ****
}
!
sub fixselect
{
--- 1070,1078 ----
}
! #
! # returns string fixed_html = fixselect(string HTML attriute "name",
! # string HTML attribute "value",
! # string the_html_to_fix);
! #
sub fixselect
{
|
|
From: <jas...@us...> - 2002-11-24 02:08:44
|
Update of /cvsroot/genex/genex-server/Genex/scripts In directory sc8-pr-cvs1:/tmp/cvs-serv31895 Modified Files: gendb.pl.in Log Message: * scripts/gendb.pl.in (Repository): fixed regex escape Index: gendb.pl.in =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/scripts/gendb.pl.in,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** gendb.pl.in 15 Nov 2002 22:01:07 -0000 1.8 --- gendb.pl.in 24 Nov 2002 02:08:41 -0000 1.9 *************** *** 201,205 **** '--version=3.0', '--feat="1.2.3.4"', ! '--data_start_regex1=^Begin\s+Data', '--data_start_regex2=^Number', '--data_end_regex=^End', --- 201,205 ---- '--version=3.0', '--feat="1.2.3.4"', ! '--data_start_regex1=^Begin\\s+Data', '--data_start_regex2=^Number', '--data_end_regex=^End', |
|
From: <jas...@us...> - 2002-11-24 01:59:45
|
Update of /cvsroot/genex/genex-server/Mason/workspace/workspace-comps
In directory sc8-pr-cvs1:/tmp/cvs-serv16840/workspace-comps
Modified Files:
footer.mason.in header.mason.in main.mason.in nav.mason.in
Log Message:
removed residual calls to get_session
Index: footer.mason.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/workspace-comps/footer.mason.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** footer.mason.in 20 Nov 2002 00:19:39 -0000 1.1
--- footer.mason.in 24 Nov 2002 01:59:42 -0000 1.2
***************
*** 13,18 ****
$debug => 0
</%args>
- <%once>;
- </%once>
- <%init>;
- </%init>
--- 13,14 ----
Index: header.mason.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/workspace-comps/header.mason.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** header.mason.in 20 Nov 2002 00:19:39 -0000 1.1
--- header.mason.in 24 Nov 2002 01:59:42 -0000 1.2
***************
*** 17,21 ****
</%once>
<%init>;
- my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $user = $session->{username};
</%init>
--- 17,20 ----
Index: main.mason.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/workspace-comps/main.mason.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** main.mason.in 20 Nov 2002 00:19:39 -0000 1.1
--- main.mason.in 24 Nov 2002 01:59:42 -0000 1.2
***************
*** 32,40 ****
</%once>
<%init>;
- 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('PhysicalBioAssay');
--- 32,35 ----
Index: nav.mason.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/workspace-comps/nav.mason.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** nav.mason.in 20 Nov 2002 00:19:39 -0000 1.1
--- nav.mason.in 24 Nov 2002 01:59:42 -0000 1.2
***************
*** 19,24 ****
$debug => 0
</%args>
- <%once>;
- </%once>
- <%init>;
- </%init>
--- 19,20 ----
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From: <jas...@us...> - 2002-11-24 01:59:18
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv16694
Modified Files:
data-loader.html.in
Log Message:
* Mason/workspace/data-loader.html.in (Repository):
renamed fesw_pk => sw_pk
Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** data-loader.html.in 20 Nov 2002 22:34:15 -0000 1.2
--- data-loader.html.in 24 Nov 2002 01:59:15 -0000 1.3
***************
*** 228,232 ****
my @fe_dbs = Bio::Genex::FeatureExtractionSoftware->get_all_objects($dbh);
foreach my $fe_db (@fe_dbs) {
! push(@feature_extractions,[$fe_db->fesw_pk,$fe_db->name . ':' . $fe_db->version]);
}
--- 228,232 ----
my @fe_dbs = Bio::Genex::FeatureExtractionSoftware->get_all_objects($dbh);
foreach my $fe_db (@fe_dbs) {
! push(@feature_extractions,[$fe_db->sw_pk,$fe_db->name . ':' . $fe_db->version]);
}
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|
From: <jas...@us...> - 2002-11-23 22:27:08
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv21408
Modified Files:
mbad-insert.pl.in
Log Message:
* scripts/mbad-insert.pl.in (Repository):
starting to handle missing values - convert empty values to NULL
Index: mbad-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/mbad-insert.pl.in,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** mbad-insert.pl.in 23 Nov 2002 10:25:13 -0000 1.8
--- mbad-insert.pl.in 23 Nov 2002 22:27:05 -0000 1.9
***************
*** 279,286 ****
my $id = eval "$feature_id_string";
print STDERR "Found id: <$id>\n" if $OPTIONS{debug};
- print STDERR "Found feature: <$features{$id}>\n" if $OPTIONS{debug};
- my @vals = eval qq[($data_string)];
- print STDERR "Found vals: <@vals>\n" if $OPTIONS{debug};
my $feature_id = $features{$id};
$dbh->error(@error_args,
--- 279,283 ----
***************
*** 288,291 ****
--- 285,294 ----
message=>"Could't find feature identifier for id: $id")
unless defined $feature_id;
+ print STDERR "Found feature: <$features{$id}>\n" if $OPTIONS{debug};
+
+ my @vals = eval qq[($data_string)];
+ # handle missing values convert them empty string to undef
+ @vals = map {$_ eq '' ? undef : $_} @vals;
+ print STDERR "Found vals: <@vals>\n" if $OPTIONS{debug};
unshift(@vals,$feature_id, $mba_pk);
|
|
From: <jas...@us...> - 2002-11-23 10:59:13
|
Update of /cvsroot/genex/genex-server/Genex In directory sc8-pr-cvs1:/tmp/cvs-serv15028/Genex Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.124 retrieving revision 1.125 diff -C2 -d -r1.124 -r1.125 *** ChangeLog 23 Nov 2002 10:25:31 -0000 1.124 --- ChangeLog 23 Nov 2002 10:59:10 -0000 1.125 *************** *** 1,4 **** --- 1,9 ---- 2002-11-23 Jason E. Stewart <ja...@op...> + * scripts/array-design-insert.pl.in (Repository): + added --matrix + added back ability to insert one reporter at a time + fixed typo in debug output + * scripts/create_genex_db.pl.in (Repository): removed TableAdmin |
|
From: <jas...@us...> - 2002-11-23 10:56:30
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv14255/Genex/scripts
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Repository):
fixed typo in debug output
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** array-design-insert.pl.in 23 Nov 2002 10:39:22 -0000 1.12
--- array-design-insert.pl.in 23 Nov 2002 10:56:25 -0000 1.13
***************
*** 187,191 ****
$REPORTERS{$name} = $rep_pk
unless exists $OPTIONS{reporters_only};
! print STDERR "Handled $count Reporters",
}
}
--- 187,192 ----
$REPORTERS{$name} = $rep_pk
unless exists $OPTIONS{reporters_only};
! print STDERR "Handled $count Reporters\n",
! if exists $OPTIONS{count} and ($count % $OPTIONS{count} == 0);
}
}
|
|
From: <jas...@us...> - 2002-11-23 10:39:25
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv10414/Genex/scripts
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Repository):
added --matrix
added back ability to insert one reporter at a time
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** array-design-insert.pl.in 21 Nov 2002 12:38:23 -0000 1.11
--- array-design-insert.pl.in 23 Nov 2002 10:39:22 -0000 1.12
***************
*** 46,49 ****
--- 46,50 ----
'no_reporters',
'reporters_only',
+ 'matrix',
'help',
'debug',
***************
*** 63,66 ****
--- 64,68 ----
--no_reporters : do not process reporters
--reporters_only : only process reporters
+ --matrix : process reporters using insert_matrix()
--count=num : print output every num tags
--help : print this message
***************
*** 166,173 ****
my $type = 'clone_name'; # FIXME
! push(@names,$name);
! push(@matrix,[$name,$type,$con_fk,$OPTIONS{ro_group},$OPTIONS{rw_group}]);
! print STDERR "Added $count Reporters to matrix\n"
! if exists $OPTIONS{count} and ($count % $OPTIONS{count} == 0);
}
if ($OPTIONS{count}) {
--- 168,192 ----
my $type = 'clone_name'; # FIXME
! if (exists $OPTIONS{matrix}) {
! push(@names,$name);
! push(@matrix,[$name,$type,$con_fk,$OPTIONS{ro_group},$OPTIONS{rw_group}]);
! print STDERR "Added $count Reporters to matrix\n"
! if exists $OPTIONS{count} and ($count % $OPTIONS{count} == 0);
! } else {
! # we should figure out how to enable a contact for the reporters FIXME
! my $rep_db = Bio::Genex::Reporter->new(rep_name=>$name,
! rep_type=>$type,
! provider_con_obj=>$CONTACT_GENEX,
! ro_groupname=>$OPTIONS{ro_group},
! rw_groupname=>$OPTIONS{rw_group},
! );
! my $rep_pk = $rep_db->insert_db(dbh=>$dbh,no_genex_admin=>1);
! $dbh->error(@error_args,
! message=>"couldn't insert record for reporter: $name")
! if $dbh->err;
! $REPORTERS{$name} = $rep_pk
! unless exists $OPTIONS{reporters_only};
! print STDERR "Handled $count Reporters",
! }
}
if ($OPTIONS{count}) {
***************
*** 175,184 ****
$Bio::Genex::Reporter::COUNT = $OPTIONS{count};
}
! if (exists $OPTIONS{reporters_only}) {
! Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,
! matrix=>\@matrix);
! } else {
! $REPORTERS{@names} = Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,
! matrix=>\@matrix);
}
--- 194,205 ----
$Bio::Genex::Reporter::COUNT = $OPTIONS{count};
}
! if (exists $OPTIONS{matrix}) {
! if (exists $OPTIONS{reporters_only}) {
! Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,
! matrix=>\@matrix);
! } else {
! $REPORTERS{@names} = Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,
! matrix=>\@matrix);
! }
}
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