Menu
▾
▴
genex-cvs-commit — CVS commit messages
You can subscribe to this list here.
| 2002 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(267) |
Nov
(344) |
Dec
(119) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2003 |
Jan
(23) |
Feb
(15) |
Mar
(16) |
Apr
(388) |
May
|
Jun
(4) |
Jul
|
Aug
|
Sep
(4) |
Oct
|
Nov
|
Dec
|
|
From: <tw...@us...> - 2002-10-29 19:09:20
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv24153
Added Files:
Tag: Rel-1_0_1-branch
analysis_tree_lib.pl
Log Message:
New library of subs for analysis tree support.
--- NEW FILE: analysis_tree_lib.pl ---
#!/usr/bin/perl
use strict;
my @tree;
my @parent;
my @children;
my %node2g;
my @generation;
main:
{
read_db();
analyze_tree();
print "\n";
for(my $xx=0; $xx<=$#parent; $xx++)
{
if ($xx == 0)
{
print "\"$tree[$xx][0]\" is the root. ";
}
else
{
print "\"$tree[$xx][0]\"'s parent is \"$tree[$parent[$xx]][0]\". ";
}
my $num_children = $#{$children[$xx]}+1;
if ($num_children > 0)
{
if ($num_children == 1)
{
print "$num_children child. ";
}
else
{
print "$num_children children. ";
}
foreach my $child (@{$children[$xx]})
{
print "\"$tree[$child][0]\" ";
}
}
else
{
print "No children. ";
}
print "\n";
}
for(my $xx=0; $xx<=$#generation; $xx++)
{
print "Generation $xx: ";
for(my $yy=0; $yy<=$#{$generation[$xx]}; $yy++)
{
print "$generation[$xx][$yy] ";
}
print "\n";
}
}
sub read_db
{
# id,name,parent
# 1,"get data",0
# 2,"Quality Control",1
# 3,"Stat Analysis",2
# 4,"Westfall & Young",2
@{$tree[0]} = ("Choose Hybs", 0); # root has itself as parent
@{$tree[1]} = ("Quality Control", 0);
@{$tree[2]} = ("Stat Analysis", 1);
@{$tree[3]} = ("Westfall & Young", 1);
@{$tree[4]} = ("Cyber T", 1);
@{$tree[5]} = ("R Cluster", 4);
return (@tree,2);
}
sub analyze_tree
{
#
# who is my parent
# the number of parent is always one.
#
my $node;
my $curr_node;
my $xx;
my $yy;
#
# Hard code the root generation info.
# If we had a situation where the root generation could have
# multiple nodes, this would need to be changed to take that
# into account.
#
$node2g{0} = 0;
push(@{$generation[$node2g{0}]}, 0);
for($xx = 0; $xx<=$#tree; $xx++)
{
for($yy = $xx+1; $yy<=$#tree; $yy++)
{
if ($tree[$yy][1] == $xx)
{
print "$xx $tree[$xx][0] is parent of $tree[$yy][0] $tree[$yy][1]\n";
$parent[$yy] = $xx; # we can only have one parent
push(@{$children[$xx]}, $yy); # we might have several children
$node2g{$yy} = $node2g{$parent[$yy]} + 1;
push(@{$generation[$node2g{$yy}]}, $yy);
}
}
}
#
# number of children
# who is my child??
#
}
sub draw_sibs
{
my @tree = @{$_[0]};
foreach my $tree_pk (@tree)
{
}
}
|
|
From: <tw...@us...> - 2002-10-29 15:13:58
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv5797
Modified Files:
Tag: Rel-1_0_1-branch
choose_hybs.html
Log Message:
page layout fixes
Index: choose_hybs.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_hybs.html,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** choose_hybs.html 29 Oct 2002 15:08:36 -0000 1.1.2.4
--- choose_hybs.html 29 Oct 2002 15:13:54 -0000 1.1.2.5
***************
*** 5,10 ****
<a href="./">Return to Genex Member Home</a>
<br><br clear=all><br>
! Choose hybridizations to analyze, then choose one or more analyses to run.
! <br>
<font color="#FF0000">{message}</font>
</td>
--- 5,9 ----
<a href="./">Return to Genex Member Home</a>
<br><br clear=all><br>
! Choose hybridizations to analyze, and change the grouping as necessary.<br>
<font color="#FF0000">{message}</font>
</td>
***************
*** 13,24 ****
<br>
<form action="qc.pl" method="post">
! <input type="submit" name="submit" value="Run Analysis">
! <br>
! <br>
! <input type="checkbox" name="qualityControl" value="1"> Quality Control<br>
! <input type="checkbox" name="statAnalysis" value="1"> Stat Analysis<br>
! <input type="checkbox" name="westfallYoung" value="1"> Westfall & Young<br>
<br>
! Comments:<br><input type="text" name="comments" value="{comments}" size=50>
<br>
<br>
--- 12,19 ----
<br>
<form action="qc.pl" method="post">
! <input type="submit" name="submit" value="Next">
<br>
! Comments:<br>
! <input type="text" name="comments" value="{comments}" size=50>
<br>
<br>
***************
*** 59,63 ****
</loop>
<br>
! <input type="submit" name="submit" value="Run Analysis">
</form>
--- 54,58 ----
</loop>
<br>
! <input type="submit" name="submit" value="Next">
</form>
|
|
From: <tw...@us...> - 2002-10-29 15:08:40
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv2916
Modified Files:
Tag: Rel-1_0_1-branch
choose_hybs.html
Log Message:
html formatting fix
Index: choose_hybs.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_hybs.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
*** choose_hybs.html 29 Oct 2002 15:06:47 -0000 1.1.2.3
--- choose_hybs.html 29 Oct 2002 15:08:36 -0000 1.1.2.4
***************
*** 24,28 ****
<br>
<loop>
! <table width="600" border=0 cellspacing=0 cellpadding=3>
<tr bgcolor="#CCCCFF">
<td valign="top" width="21"> </td>
--- 24,28 ----
<br>
<loop>
! <table width="600" border=0 cellspacing=0 cellpadding=3>
<tr bgcolor="#CCCCFF">
<td valign="top" width="21"> </td>
***************
*** 30,38 ****
</tr>
<tr>
- <td valign="top" width="21"> </td>
- <td valign="top" width="561">Study/<br>
- Exp. Cond.</td>
- </tr>
- <tr>
<td valign="top" width="21">
<input type="checkbox" name="am_pk" value="{am_pk}">
--- 30,33 ----
***************
*** 40,45 ****
<td valign="top" width="561">{select_exp}</td>
</tr>
!
! </table> <table width="600" border=1 cellspacing=0 cellpadding=3>
<tr>
<td valign=top width="84"> Hybridization Comments </td>
--- 35,40 ----
<td valign="top" width="561">{select_exp}</td>
</tr>
! </table>
! <table width="600" border=1 cellspacing=0 cellpadding=3>
<tr>
<td valign=top width="84"> Hybridization Comments </td>
|
|
From: <tw...@us...> - 2002-10-29 15:06:54
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv2147
Modified Files:
Tag: Rel-1_0_1-branch
choose_hybs.html
Log Message:
html design change
Index: choose_hybs.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_hybs.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
*** choose_hybs.html 29 Oct 2002 14:59:34 -0000 1.1.2.2
--- choose_hybs.html 29 Oct 2002 15:06:47 -0000 1.1.2.3
***************
*** 23,31 ****
<br>
<br>
! <table width="600" border=1 cellspacing=0 cellpadding=3>
<tr>
! <td valign="top" width="22"> </td>
! <td valign="top" width="39">Study/<br>
Exp. Cond.</td>
<td valign=top width="84"> Hybridization Comments </td>
<td valign=top width="72"> Experiment Notes </td>
--- 23,46 ----
<br>
<br>
! <loop>
! <table width="600" border=0 cellspacing=0 cellpadding=3>
! <tr bgcolor="#CCCCFF">
! <td valign="top" width="21"> </td>
! <td valign="top" width="561"> </td>
! </tr>
<tr>
! <td valign="top" width="21"> </td>
! <td valign="top" width="561">Study/<br>
Exp. Cond.</td>
+ </tr>
+ <tr>
+ <td valign="top" width="21">
+ <input type="checkbox" name="am_pk" value="{am_pk}">
+ </td>
+ <td valign="top" width="561">{select_exp}</td>
+ </tr>
+
+ </table> <table width="600" border=1 cellspacing=0 cellpadding=3>
+ <tr>
<td valign=top width="84"> Hybridization Comments </td>
<td valign=top width="72"> Experiment Notes </td>
***************
*** 36,45 ****
<td valign=top width="51"> UserID </td>
</tr>
! <loop>
<tr>
- <td valign="top" width="22">
- <input type="checkbox" name="am_pk" value="{am_pk}">
- </td>
- <td valign="top" width="39">{select_exp}</td>
<td valign=top width="84"> {comments} </td>
<td valign=top width="72"> {notes} </td>
--- 51,56 ----
<td valign=top width="51"> UserID </td>
</tr>
!
<tr>
<td valign=top width="84"> {comments} </td>
<td valign=top width="72"> {notes} </td>
***************
*** 50,56 ****
<td valign=top width="51"> {login} </td>
</tr>
- </loop>
</table>
! <br>
<input type="submit" name="submit" value="Run Analysis">
</form>
--- 61,67 ----
<td valign=top width="51"> {login} </td>
</tr>
</table>
! </loop>
! <br>
<input type="submit" name="submit" value="Run Analysis">
</form>
|
|
From: <tw...@us...> - 2002-10-29 14:59:37
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv31019
Modified Files:
Tag: Rel-1_0_1-branch
choose_hybs.pl choose_hybs.html
Log Message:
Add group selection.
Index: choose_hybs.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_hybs.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
*** choose_hybs.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- choose_hybs.pl 29 Oct 2002 14:59:33 -0000 1.1.2.2
***************
*** 38,43 ****
my $owner_sth = $dbh->prepare($owner_sql) || die "$owner_sql\n$DBI::errstr\n";
! my $sample_sql = "select notes, abbrev_name, description from sample,exp_condition where sample.smp_pk=? and sample.ec_fk=exp_condition.ec_pk";
my $sample_sth = $dbh->prepare($sample_sql) || die "$sample_sql\n$DBI::errstr\n";
while($e_hr = $sth->fetchrow_hashref())
{
--- 38,45 ----
my $owner_sth = $dbh->prepare($owner_sql) || die "$owner_sql\n$DBI::errstr\n";
! my $sample_sql = "select ec_pk,notes, abbrev_name, description from sample,exp_condition where sample.smp_pk=? and sample.ec_fk=exp_condition.ec_pk";
my $sample_sth = $dbh->prepare($sample_sql) || die "$sample_sql\n$DBI::errstr\n";
+
+ my $select_exp = select_exp($dbh, $us_fk, "ec_pk");
while($e_hr = $sth->fetchrow_hashref())
{
***************
*** 53,62 ****
($e_hr->{login}, $e_hr->{contact_fname}, $e_hr->{contact_lname}) = $owner_sth->fetchrow_array();
! ($e_hr->{notes}, $e_hr->{abbrev_name}, $e_hr->{description}) = $sample_sth->fetchrow_array();
my $loop_instance = $loop_template;
$loop_instance =~ s/name=\"(.*?)\"/name=\"$1_$xx\"/g;
$xx++;
- $loop_instance =~ s/{(.*?)}/$e_hr->{$1}/g;
$allhtml =~ s/<loop_here>/$loop_instance\n<loop_here>/;
}
--- 55,67 ----
($e_hr->{login}, $e_hr->{contact_fname}, $e_hr->{contact_lname}) = $owner_sth->fetchrow_array();
! ($e_hr->{ec_pk}, $e_hr->{notes}, $e_hr->{abbrev_name}, $e_hr->{description}) = $sample_sth->fetchrow_array();
!
! $e_hr->{select_exp} = fixselect("ec_pk",$e_hr->{ec_pk}, $select_exp);
my $loop_instance = $loop_template;
+
+ $loop_instance =~ s/{(.*?)}/$e_hr->{$1}/g;
$loop_instance =~ s/name=\"(.*?)\"/name=\"$1_$xx\"/g;
$xx++;
$allhtml =~ s/<loop_here>/$loop_instance\n<loop_here>/;
}
Index: choose_hybs.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_hybs.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
*** choose_hybs.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- choose_hybs.html 29 Oct 2002 14:59:34 -0000 1.1.2.2
***************
*** 23,93 ****
<br>
<br>
! <table width="600" border=1 cellspacing=0 cellpadding=3>
!
! <tr>
! <td valign="top">
!
! </td>
! <td valign=top>
! Hybridization Comments
! </td>
! <td valign=top>
! Experiment Notes
! </td>
! <td valign=top>
! Short Exp. Name
! </td>
! <td valign=top>
! Exp. Cond. Description
! </td>
!
! <td valign=top>
! Hybridization Name
! </td>
!
! <td valign=top>
! Owner
! </td>
!
! <td valign=top>
! UserID
! </td>
! </tr>
!
! <loop>
!
! <tr>
! <td valign="top">
! <input type="checkbox" name="am_pk" value="{am_pk}">
! </td>
! <td valign=top>
! {comments}
! </td>
! <td valign=top>
! {notes}
! </td>
! <td valign=top>
! {abbrev_name}
! </td>
! <td valign=top>
! {description}
! </td>
!
! <td valign=top>
! {hybridization_name}
! </td>
!
! <td valign=top>
! {contact_fname} {contact_lname}
! </td>
!
! <td valign=top>
! {login}
! </td>
! </tr>
!
! </loop>
!
! </table>
<br>
<input type="submit" name="submit" value="Run Analysis">
--- 23,55 ----
<br>
<br>
! <table width="600" border=1 cellspacing=0 cellpadding=3>
! <tr>
! <td valign="top" width="22"> </td>
! <td valign="top" width="39">Study/<br>
! Exp. Cond.</td>
! <td valign=top width="84"> Hybridization Comments </td>
! <td valign=top width="72"> Experiment Notes </td>
! <td valign=top width="105"> Short Exp. Name </td>
! <td valign=top width="102"> Exp. Cond. Description </td>
! <td valign=top width="126"> Hybridization Name </td>
! <td valign=top width="110"> Owner </td>
! <td valign=top width="51"> UserID </td>
! </tr>
! <loop>
! <tr>
! <td valign="top" width="22">
! <input type="checkbox" name="am_pk" value="{am_pk}">
! </td>
! <td valign="top" width="39">{select_exp}</td>
! <td valign=top width="84"> {comments} </td>
! <td valign=top width="72"> {notes} </td>
! <td valign=top width="105"> {abbrev_name} </td>
! <td valign=top width="102"> {description} </td>
! <td valign=top width="126"> {hybridization_name} </td>
! <td valign=top width="110"> {contact_fname} {contact_lname} </td>
! <td valign=top width="51"> {login} </td>
! </tr>
! </loop>
! </table>
<br>
<input type="submit" name="submit" value="Run Analysis">
|
|
From: <tw...@us...> - 2002-10-29 14:49:24
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv26350
Modified Files:
Tag: Rel-1_0_1-branch
install_lib.pl
Log Message:
Added warnings when open() fails.
Index: install_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/Attic/install_lib.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
*** install_lib.pl 28 Oct 2002 19:53:49 -0000 1.1.2.2
--- install_lib.pl 29 Oct 2002 14:49:21 -0000 1.1.2.3
***************
*** 58,66 ****
my @stat_array = stat("$origin/$filename");
my $temp;
! open(IN, "< $origin/$filename");
sysread(IN, $temp, $stat_array[7]);
close(IN);
$temp =~ s/\%\%(.*?)\%\%/$Vars{$1}/g;
! open(OUT, "> $destination/$filename") || warn "Can't open $destination/$filename\n";
print OUT "$temp";
close(OUT);
--- 58,66 ----
my @stat_array = stat("$origin/$filename");
my $temp;
! open(IN, "< $origin/$filename") || warn "Can't open $origin/$filename for read.\n";
sysread(IN, $temp, $stat_array[7]);
close(IN);
$temp =~ s/\%\%(.*?)\%\%/$Vars{$1}/g;
! open(OUT, "> $destination/$filename") || warn "Can't open $destination/$filename for write.\n";
print OUT "$temp";
close(OUT);
|
|
From: <tw...@us...> - 2002-10-29 14:48:53
|
Update of /cvsroot/genex/genex-server/site
In directory usw-pr-cvs1:/tmp/cvs-serv26104
Modified Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
Fix arg to install_lib.pl
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/Attic/makefile,v
retrieving revision 1.1.2.5
retrieving revision 1.1.2.6
diff -C2 -d -r1.1.2.5 -r1.1.2.6
*** makefile 29 Oct 2002 14:42:16 -0000 1.1.2.5
--- makefile 29 Oct 2002 14:48:47 -0000 1.1.2.6
***************
*** 14,18 ****
html_files : $(html_srcs)
$(DEST)/%.html : ./%.html
! cd ../; ./install_lib.pl ./site/$< ./html $(DEST)
jpg_srcs := $(patsubst %.jpg,$(DEST)/%.jpg,$(wildcard graphics/*.jpg))
--- 14,18 ----
html_files : $(html_srcs)
$(DEST)/%.html : ./%.html
! cd ../; ./install_lib.pl $< ./site $(DEST)
jpg_srcs := $(patsubst %.jpg,$(DEST)/%.jpg,$(wildcard graphics/*.jpg))
|
|
From: <tw...@us...> - 2002-10-29 14:42:19
|
Update of /cvsroot/genex/genex-server/site
In directory usw-pr-cvs1:/tmp/cvs-serv22952
Modified Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
$< needs to be ./site/$<
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/Attic/makefile,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** makefile 29 Oct 2002 14:31:59 -0000 1.1.2.4
--- makefile 29 Oct 2002 14:42:16 -0000 1.1.2.5
***************
*** 14,18 ****
html_files : $(html_srcs)
$(DEST)/%.html : ./%.html
! cd ../; ./install_lib.pl $< ./html $(DEST)
jpg_srcs := $(patsubst %.jpg,$(DEST)/%.jpg,$(wildcard graphics/*.jpg))
--- 14,18 ----
html_files : $(html_srcs)
$(DEST)/%.html : ./%.html
! cd ../; ./install_lib.pl ./site/$< ./html $(DEST)
jpg_srcs := $(patsubst %.jpg,$(DEST)/%.jpg,$(wildcard graphics/*.jpg))
|
|
From: <tw...@us...> - 2002-10-29 14:32:02
|
Update of /cvsroot/genex/genex-server/site
In directory usw-pr-cvs1:/tmp/cvs-serv18542
Modified Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
fix a path problem calling install_lib.pl for .html files.
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/Attic/makefile,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** makefile 28 Oct 2002 19:52:52 -0000 1.1.2.3
--- makefile 29 Oct 2002 14:31:59 -0000 1.1.2.4
***************
*** 14,18 ****
html_files : $(html_srcs)
$(DEST)/%.html : ./%.html
! ../install_lib.pl $< ./html $(DEST)
jpg_srcs := $(patsubst %.jpg,$(DEST)/%.jpg,$(wildcard graphics/*.jpg))
--- 14,18 ----
html_files : $(html_srcs)
$(DEST)/%.html : ./%.html
! cd ../; ./install_lib.pl $< ./html $(DEST)
jpg_srcs := $(patsubst %.jpg,$(DEST)/%.jpg,$(wildcard graphics/*.jpg))
|
|
From: <mwi...@us...> - 2002-10-29 02:05:08
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv26672
Modified Files:
add_user_to_group.html.in generate_group.html.in
generate_user.html.in
Log Message:
fixed errors from my last commit. There are still additional changes that need to be made to these scripts as per the conversation with Jason on Monday AM, Oct 28th. I will start working on those now. These include having the mason pages call on the standalone scripts to generate new users and groups. Also, something has to be done with the authentication as it is currently hard-coded.
Index: add_user_to_group.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/add_user_to_group.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** add_user_to_group.html.in 22 Oct 2002 16:33:14 -0000 1.2
--- add_user_to_group.html.in 29 Oct 2002 02:05:04 -0000 1.3
***************
*** 109,117 ****
use Bio::Genex::UserSec;
use Bio::Genex::GroupLink;
!
! my $OPTIONS{ro_groupname} = "public";
! my $OPTIONS{rw_groupname} = "superuser";
! my $OPTIONS{SU_USERNAME} = "genex"; # this is now hard coded
! my $OPTIONS{dbname} = "%%DB_NAME%%";
my $response_page;
my $db=Bio::Genex::Connect->new(
--- 109,117 ----
use Bio::Genex::UserSec;
use Bio::Genex::GroupLink;
! my %OPTIONS;
! $OPTIONS{ro_groupname} = "public";
! $OPTIONS{rw_groupname} = "superuser";
! $OPTIONS{SU_USERNAME} = "genex"; # this is now hard coded
! $OPTIONS{dbname} = "%%DB_NAME%%";
my $response_page;
my $db=Bio::Genex::Connect->new(
***************
*** 137,141 ****
# set predictable default if this variable doesnt exist
! $rw_groupname = $rw_groupname?$rw_groupname:"superuser";
if ($submitted ne "true"){
--- 137,141 ----
# set predictable default if this variable doesnt exist
! $OPTIONS{rw_groupname} = $OPTIONS{rw_groupname}?$OPTIONS{rw_groupname}:"superuser";
if ($submitted ne "true"){
Index: generate_group.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/generate_group.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** generate_group.html.in 22 Oct 2002 16:33:14 -0000 1.1
--- generate_group.html.in 29 Oct 2002 02:05:04 -0000 1.2
***************
*** 159,163 ****
$OPTIONS{SU_USERNAME} = "genex"; # this is now hard coded
$OPTIONS{dbname} = "%%DB_NAME%%";
! $response_page;
# get list of all valid groups for various purposes
--- 159,163 ----
$OPTIONS{SU_USERNAME} = "genex"; # this is now hard coded
$OPTIONS{dbname} = "%%DB_NAME%%";
! my $response_page;
# get list of all valid groups for various purposes
Index: generate_user.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/generate_user.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** generate_user.html.in 22 Oct 2002 16:33:14 -0000 1.2
--- generate_user.html.in 29 Oct 2002 02:05:04 -0000 1.3
***************
*** 315,330 ****
$c->url($url);
! $c->ro_groupname($ro_groupname);
! $c->rw_groupname($rw_groupname);
my $cid = $c->insert_db($db);
$u->con_fk($cid);
! $u->ro_groupname($ro_groupname);
! $u->rw_groupname($rw_groupname);
$u->insert_db($db);
my $gl = Bio::Genex::GroupLink->new;
$gl->username($u->username);
! $gl->groupname($ro_groupname);
$gl->insert_db($db);
$response_page="DONE";
--- 315,330 ----
$c->url($url);
! $c->ro_groupname($OPTIONS{ro_groupname});
! $c->rw_groupname($OPTIONS{rw_groupname});
my $cid = $c->insert_db($db);
$u->con_fk($cid);
! $u->ro_groupname($OPTIONS{ro_groupname});
! $u->rw_groupname($OPTIONS{rw_groupname});
$u->insert_db($db);
my $gl = Bio::Genex::GroupLink->new;
$gl->username($u->username);
! $gl->groupname($OPTIONS{ro_groupname});
$gl->insert_db($db);
$response_page="DONE";
|
|
From: <tw...@us...> - 2002-10-28 21:07:24
|
Update of /cvsroot/genex/genex-server/archive
In directory usw-pr-cvs1:/tmp/cvs-serv30510
Modified Files:
Tag: Rel-1_0_1-branch
old_genex.tar
Log Message:
a better copy? the original got munged. don't know how.
Index: old_genex.tar
===================================================================
RCS file: /cvsroot/genex/genex-server/archive/Attic/old_genex.tar,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
Binary files /tmp/cvsPQYMXu and /tmp/cvspDFQto differ
|
|
From: <tw...@us...> - 2002-10-28 20:18:45
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv14197
Removed Files:
Tag: Rel-1_0_1-branch
init-dump.pl.in
Log Message:
no longer used.
--- init-dump.pl.in DELETED ---
|
|
From: <tw...@us...> - 2002-10-28 20:17:02
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv13297
Removed Files:
Tag: Rel-1_0_1-branch
db-update-0.8.1-0.9.pl.in
Log Message:
no longer used.
--- db-update-0.8.1-0.9.pl.in DELETED ---
|
|
From: <tw...@us...> - 2002-10-28 19:53:59
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv1306
Modified Files:
Tag: Rel-1_0_1-branch
makefile install_lib.pl
Log Message:
Fixes added for options.reminders symlinks, some invocation paths fixed,
improved dependencies.
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/Attic/makefile,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** makefile 24 Oct 2002 21:07:05 -0000 1.1.2.1
--- makefile 28 Oct 2002 19:53:49 -0000 1.1.2.2
***************
*** 1,12 ****
! all : repository html webtools
! # Make a function that will return this, something like
! # the install_lib.pl -D elsewhere.
! REP = /var/genres
! repository :
-mkdir $(REP)
-chown apache:users $(REP)
-chmod 775 $(REP)
html :
--- 1,23 ----
! all : repository symlinks html webtools
+ REP = $(shell ./install_lib.pl -R)
+ repository : $(REP)
! $(REP) :
-mkdir $(REP)
-chown apache:users $(REP)
-chmod 775 $(REP)
+
+ #
+ # We need a symlink to options.reminders in a couple of directories
+ # since we need to read it for installation options
+ #
+ symlinks : ./site/options.reminders ./site/webtools/options.reminders
+
+ ./site/options.reminders :
+ -cd site; ln -s ../options.reminders;
+
+ ./site/webtools/options.reminders :
+ -cd site/webtools; ln -s ../../options.reminders
html :
Index: install_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/Attic/install_lib.pl,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** install_lib.pl 4 Sep 2002 14:12:06 -0000 1.1.2.1
--- install_lib.pl 28 Oct 2002 19:53:49 -0000 1.1.2.2
***************
*** 14,28 ****
if (! defined(eval('$sessionlib_loaded')))
{
! require "./webtools/sessionlib.pl";
}
main:
{
if ($ARGV[0] =~ m/\-D/)
{
- my %Vars = read_optionsdotreminders();
print "$Vars{HTMLDIR}/$Vars{GENEX_DIR}\n";
exit(0);
}
if ($0 =~ m/install_lib/)
--- 14,34 ----
if (! defined(eval('$sessionlib_loaded')))
{
! require "./site/webtools/sessionlib.pl";
}
+ my %Vars = read_optionsdotreminders();
+
main:
{
if ($ARGV[0] =~ m/\-D/)
{
print "$Vars{HTMLDIR}/$Vars{GENEX_DIR}\n";
exit(0);
}
+ if ($ARGV[0] =~ m/\-R/)
+ {
+ print "$Vars{USER_DATA_DIR}\n";
+ exit(0);
+ }
if ($0 =~ m/install_lib/)
***************
*** 42,49 ****
my $origin = $_[1];
my $destination = $_[2];
#
# Use Perl's goofy RPN if() so we don't have a scoping problem with %Vars
#
! my %Vars = read_optionsdotreminders() if (! defined(eval('%Vars')));
my @stat_array = stat("$origin/$filename");
--- 48,58 ----
my $origin = $_[1];
my $destination = $_[2];
+
+ # Oct 28, 2002 Tom: Just make %Vars a global at the top, and run read_optionsdotreminders()
+ # at the beginning of runtime.
#
# Use Perl's goofy RPN if() so we don't have a scoping problem with %Vars
#
! # my %Vars = read_optionsdotreminders() if (! defined(eval('%Vars')));
my @stat_array = stat("$origin/$filename");
|
|
From: <tw...@us...> - 2002-10-28 19:52:57
|
Update of /cvsroot/genex/genex-server/site
In directory usw-pr-cvs1:/tmp/cvs-serv939
Modified Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
Fixed the makefile to work better with the options.reminders
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/Attic/makefile,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** makefile 24 Oct 2002 19:18:43 -0000 1.1.2.2
--- makefile 28 Oct 2002 19:52:52 -0000 1.1.2.3
***************
*** 6,10 ****
# from options.reminders
#
! DEST = $(shell ../install_lib.pl -D)
test :
--- 6,10 ----
# from options.reminders
#
! DEST = $(shell cd ../; ./install_lib.pl -D)
test :
|
|
From: <tw...@us...> - 2002-10-25 07:01:54
|
Update of /cvsroot/genex/genex-server/site
In directory usw-pr-cvs1:/tmp/cvs-serv5480
Added Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
Adding file.
--- NEW FILE: makefile ---
install : html_files
NOOP = $(SHELL) -c true
#
# install_lib.pl -D arg will return HTMLDIR/GENEX_DIR
# from options.reminders
#
DEST = $(shell cd ..; ./install_lib.pl -D)
test :
@echo $(html_srcs)
#
# I guess it would be nice to combine the .html and .shtml into
# a single rule. Or we could just change everything to .html since
# we aren't using SSI any more.
#
html_srcs := $(patsubst %.html,$(DEST)/%.html,$(wildcard *.html))
shtml_srcs := $(patsubst %.shtml,$(DEST)/%.shtml,$(wildcard *.shtml))
html_files : $(html_srcs) $(shtml_srcs)
$(DEST)/%.html : ./%.html
cd ..; ./install_lib.pl $< ./html $(DEST)
$(DEST)/%.shtml : ./%.shtml
cd ..; ./install_lib.pl $< ./html $(DEST)
|
Update of /cvsroot/genex/genex-server/html
In directory usw-pr-cvs1:/tmp/cvs-serv24215
Removed Files:
Tag: Rel-1_0_1-branch
aa_pagebits.html analysis_tools.shtml background.shtml
curation_tool.shtml data_file_creation.html
genex_contact.shtml genex_info.shtml header.shtml index.shtml
layout_creation.html makefile schema_changes.html schema.html
security.html web_interface.html workflow.shtml
Log Message:
rearranging the site source files to mirror the actual site.
It is more rational, and more suited to web page building.
--- aa_pagebits.html DELETED ---
--- analysis_tools.shtml DELETED ---
--- background.shtml DELETED ---
--- curation_tool.shtml DELETED ---
--- data_file_creation.html DELETED ---
--- genex_contact.shtml DELETED ---
--- genex_info.shtml DELETED ---
--- header.shtml DELETED ---
--- index.shtml DELETED ---
--- layout_creation.html DELETED ---
--- makefile DELETED ---
--- schema_changes.html DELETED ---
--- schema.html DELETED ---
--- security.html DELETED ---
--- web_interface.html DELETED ---
--- workflow.shtml DELETED ---
|
Update of /cvsroot/genex/genex-server/site/graphics
In directory usw-pr-cvs1:/tmp/cvs-serv5729
Added Files:
Tag: Rel-1_0_1-branch
experimentset_a.jpg experimentset_a.pdf experimentset_b.jpg
experimentset_b.pdf GeneX101602_1.jpg GeneX101602_2.jpg
GeneX101602_3.jpg GeneX101602_4.jpg genex_acct.jpg
genex_logo.jpg genex_order.jpg genex_study.jpg
layout_spots.jpg order_sample_qc.jpg study_exp_spots.jpg x.jpg
Log Message:
Adding files.
--- NEW FILE: experimentset_a.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: experimentset_a.pdf ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: experimentset_b.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: experimentset_b.pdf ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: GeneX101602_1.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: GeneX101602_2.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: GeneX101602_3.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: GeneX101602_4.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: genex_acct.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: genex_logo.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: genex_order.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: genex_study.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: layout_spots.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: order_sample_qc.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: study_exp_spots.jpg ---
(This appears to be a binary file; contents omitted.)
--- NEW FILE: x.jpg ---
(This appears to be a binary file; contents omitted.)
|
|
From: <tw...@us...> - 2002-10-25 05:16:21
|
Update of /cvsroot/genex/genex-server/site/webtools In directory usw-pr-cvs1:/tmp/cvs-serv29722/webtools Log Message: Directory /cvsroot/genex/genex-server/site/webtools added to the repository --> Using per-directory sticky tag `Rel-1_0_1-branch' |
|
From: <tw...@us...> - 2002-10-25 05:16:10
|
Update of /cvsroot/genex/genex-server/site/graphics In directory usw-pr-cvs1:/tmp/cvs-serv29559/graphics Log Message: Directory /cvsroot/genex/genex-server/site/graphics added to the repository --> Using per-directory sticky tag `Rel-1_0_1-branch' |
|
From: <tw...@us...> - 2002-10-25 05:15:46
|
Update of /cvsroot/genex/genex-server/site In directory usw-pr-cvs1:/tmp/cvs-serv29147/site Log Message: Directory /cvsroot/genex/genex-server/site added to the repository --> Using per-directory sticky tag `Rel-1_0_1-branch' |
|
From: <tw...@us...> - 2002-10-25 05:15:18
|
Update of /cvsroot/genex/genex-server/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv28032/webtools
Removed Files:
Tag: Rel-1_0_1-branch
.htaccess
Log Message:
deleteing the webtools directory?
--- .htaccess DELETED ---
|
Update of /cvsroot/genex/genex-server/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv23440
Removed Files:
Tag: Rel-1_0_1-branch
choose_order_curator.html edit_study1.html edit_study2.pl
edit_study1.pl sessionlib.pl edit_sample1.pl
sourceSPLUSbioinfo.ssc statAnalysis.rw view_orders.html
view_orders.pl westfallYoung.rw loadam_spots.pl load_data2.pl
makefile new_order.pl qc.pl qualitycontrol.R qualityControl.rw
insert_order.pl insert_sample.pl insert_study.html
insert_study.pl job.html load_data1.html load_data1.pl
load_data2.html insert_exp_conditions.pl getfile.pl
groups2.html groups.html groups.pl index.html index.pl
insert_am.pl edit_am2.pl edit_expset1.pl edit_expset2.pl
edit_expset.html edit_order_curator1.html
edit_order_curator1.pl edit_order_curator2.pl edit_qc1.html
edit_qc1.pl edit_qc2.pl edit_sample1.html edit_sample2.pl
files.html files.pl files_refresh.pl delete_sample.pl
delete_study1.html delete_study1.pl delete_study2.pl
edit_am1.html edit_am1.pl choose_study.html choose_study.pl
config.pl create_group.html create_group.pl delete_order1.html
delete_order1.pl delete_order2.pl admin_email.html
cant_delete_study.html choose_hybs.html choose_hybs.pl
choose_order_curator.pl choose_order.html choose_order.pl
choose_qc.html account.html account.pl admin_cli.pl
AffyDataReader.pm AffyTextDataReader.pm Rwrapper.pl
Log Message:
rearranging site.
--- choose_order_curator.html DELETED ---
--- edit_study1.html DELETED ---
--- edit_study2.pl DELETED ---
--- edit_study1.pl DELETED ---
--- sessionlib.pl DELETED ---
--- edit_sample1.pl DELETED ---
--- sourceSPLUSbioinfo.ssc DELETED ---
--- statAnalysis.rw DELETED ---
--- view_orders.html DELETED ---
--- view_orders.pl DELETED ---
--- westfallYoung.rw DELETED ---
--- loadam_spots.pl DELETED ---
--- load_data2.pl DELETED ---
--- makefile DELETED ---
--- new_order.pl DELETED ---
--- qc.pl DELETED ---
--- qualitycontrol.R DELETED ---
--- qualityControl.rw DELETED ---
--- insert_order.pl DELETED ---
--- insert_sample.pl DELETED ---
--- insert_study.html DELETED ---
--- insert_study.pl DELETED ---
--- job.html DELETED ---
--- load_data1.html DELETED ---
--- load_data1.pl DELETED ---
--- load_data2.html DELETED ---
--- insert_exp_conditions.pl DELETED ---
--- getfile.pl DELETED ---
--- groups2.html DELETED ---
--- groups.html DELETED ---
--- groups.pl DELETED ---
--- index.html DELETED ---
--- index.pl DELETED ---
--- insert_am.pl DELETED ---
--- edit_am2.pl DELETED ---
--- edit_expset1.pl DELETED ---
--- edit_expset2.pl DELETED ---
--- edit_expset.html DELETED ---
--- edit_order_curator1.html DELETED ---
--- edit_order_curator1.pl DELETED ---
--- edit_order_curator2.pl DELETED ---
--- edit_qc1.html DELETED ---
--- edit_qc1.pl DELETED ---
--- edit_qc2.pl DELETED ---
--- edit_sample1.html DELETED ---
--- edit_sample2.pl DELETED ---
--- files.html DELETED ---
--- files.pl DELETED ---
--- files_refresh.pl DELETED ---
--- delete_sample.pl DELETED ---
--- delete_study1.html DELETED ---
--- delete_study1.pl DELETED ---
--- delete_study2.pl DELETED ---
--- edit_am1.html DELETED ---
--- edit_am1.pl DELETED ---
--- choose_study.html DELETED ---
--- choose_study.pl DELETED ---
--- config.pl DELETED ---
--- create_group.html DELETED ---
--- create_group.pl DELETED ---
--- delete_order1.html DELETED ---
--- delete_order1.pl DELETED ---
--- delete_order2.pl DELETED ---
--- admin_email.html DELETED ---
--- cant_delete_study.html DELETED ---
--- choose_hybs.html DELETED ---
--- choose_hybs.pl DELETED ---
--- choose_order_curator.pl DELETED ---
--- choose_order.html DELETED ---
--- choose_order.pl DELETED ---
--- choose_qc.html DELETED ---
--- account.html DELETED ---
--- account.pl DELETED ---
--- admin_cli.pl DELETED ---
--- AffyDataReader.pm DELETED ---
--- AffyTextDataReader.pm DELETED ---
--- Rwrapper.pl DELETED ---
|
Update of /cvsroot/genex/genex-server/html/graphics
In directory usw-pr-cvs1:/tmp/cvs-serv26273
Removed Files:
Tag: Rel-1_0_1-branch
experimentset_a.jpg experimentset_a.pdf experimentset_b.jpg
experimentset_b.pdf GeneX101602_1.jpg GeneX101602_2.jpg
GeneX101602_3.jpg GeneX101602_4.jpg genex_acct.jpg
genex_order.jpg genex_study.jpg layout_spots.jpg
order_sample_qc.jpg study_exp_spots.jpg x.jpg
Log Message:
rearranging the site source files.
--- experimentset_a.jpg DELETED ---
--- experimentset_a.pdf DELETED ---
--- experimentset_b.jpg DELETED ---
--- experimentset_b.pdf DELETED ---
--- GeneX101602_1.jpg DELETED ---
--- GeneX101602_2.jpg DELETED ---
--- GeneX101602_3.jpg DELETED ---
--- GeneX101602_4.jpg DELETED ---
--- genex_acct.jpg DELETED ---
--- genex_order.jpg DELETED ---
--- genex_study.jpg DELETED ---
--- layout_spots.jpg DELETED ---
--- order_sample_qc.jpg DELETED ---
--- study_exp_spots.jpg DELETED ---
--- x.jpg DELETED ---
|
|
From: <tw...@us...> - 2002-10-25 05:10:11
|
Update of /cvsroot/genex/genex-server/site
In directory usw-pr-cvs1:/tmp/cvs-serv5649
Modified Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
Fixed for new directory structure, and some improved dependencies.
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/Attic/makefile,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** makefile 24 Oct 2002 18:35:43 -0000 1.1.2.1
--- makefile 24 Oct 2002 19:18:43 -0000 1.1.2.2
***************
*** 1,3 ****
! install : html_files
NOOP = $(SHELL) -c true
--- 1,3 ----
! install : html_files graphics_srcs
NOOP = $(SHELL) -c true
***************
*** 6,27 ****
# from options.reminders
#
! DEST = $(shell cd ..; ./install_lib.pl -D)
test :
! @echo $(html_srcs)
- #
- # I guess it would be nice to combine the .html and .shtml into
- # a single rule. Or we could just change everything to .html since
- # we aren't using SSI any more.
- #
html_srcs := $(patsubst %.html,$(DEST)/%.html,$(wildcard *.html))
! shtml_srcs := $(patsubst %.shtml,$(DEST)/%.shtml,$(wildcard *.shtml))
! html_files : $(html_srcs) $(shtml_srcs)
$(DEST)/%.html : ./%.html
! cd ..; ./install_lib.pl $< ./html $(DEST)
! $(DEST)/%.shtml : ./%.shtml
! cd ..; ./install_lib.pl $< ./html $(DEST)
--- 6,36 ----
# from options.reminders
#
! DEST = $(shell ../install_lib.pl -D)
test :
! @echo $(DEST); echo $(jpg_srcs)
html_srcs := $(patsubst %.html,$(DEST)/%.html,$(wildcard *.html))
! html_files : $(html_srcs)
$(DEST)/%.html : ./%.html
! ../install_lib.pl $< ./html $(DEST)
! jpg_srcs := $(patsubst %.jpg,$(DEST)/%.jpg,$(wildcard graphics/*.jpg))
! jpg_files : $(jpg_srcs)
! $(DEST)/%.jpg : ./%.jpg
! cp -f $< $(DEST)/graphics
!
! gif_srcs := $(patsubst %.gif,$(DEST)/%.gif,$(wildcard graphics/*.gif))
! gif_files : $(gif_srcs)
! $(DEST)/%.gif : ./%.gif
! cp -f $< $(DEST)/graphics
!
! pdf_srcs := $(patsubst %.pdf,$(DEST)/%.pdf,$(wildcard graphics/*.pdf))
! pdf_files : $(pdf_srcs)
! $(DEST)/%.pdf : ./%.pdf
! cp -f $< $(DEST)/graphics
!
!
! graphics_srcs : jpg_files gif_files pdf_files
|
