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From: <tw...@us...> - 2002-12-23 21:48:16
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv5539
Modified Files:
Tag: Rel-1_0_1-branch
genex_schema.sql
Log Message:
new extraction table
Index: genex_schema.sql
===================================================================
RCS file: /cvsroot/genex/genex-server/genex_schema.sql,v
retrieving revision 1.3.2.19
retrieving revision 1.3.2.20
diff -C2 -d -r1.3.2.19 -r1.3.2.20
*** genex_schema.sql 21 Nov 2002 16:49:50 -0000 1.3.2.19
--- genex_schema.sql 23 Dec 2002 21:48:08 -0000 1.3.2.20
***************
*** 2851,2854 ****
--- 2851,2871 ----
GRANT SELECT on "tree" to "readonly";
+ --Table: extraction
+ --Tom 2002-12-23
+ --This table stores column headers and condition labels for exported data.
+ --Machine readable (aka GeneX readable) data needs the extraction info
+ --for column names and condLabels arguments to R.
+ --Human readabla exported data does not use this table, but instead
+ --puts this info into the data file as header rows.
+
+ CREATE TABLE "extraction" (
+ "fi_data_fk" integer,
+ "conds" text,
+ "cond_labels" character varying(128)
+ ) without OIDs;
+
+ REVOKE ALL on "extraction" from PUBLIC;
+ GRANT ALL on "extraction" to "genex";
+ GRANT SELECT on "extraction" to "readonly";
--Table: node
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv1906
Modified Files:
Tag: Rel-1_0_1-branch
analysis_tree_lib.pl sql_lib.pl delete_atree1.pl
delete_atree2.pl
Log Message:
full tree delete works, has UI
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.42
retrieving revision 1.1.2.43
diff -C2 -d -r1.1.2.42 -r1.1.2.43
*** analysis_tree_lib.pl 20 Dec 2002 22:21:33 -0000 1.1.2.42
--- analysis_tree_lib.pl 23 Dec 2002 19:59:39 -0000 1.1.2.43
***************
*** 261,266 ****
--- 261,288 ----
sub delete_tree
{
+ my $dbh = $_[0];
+ my $tree_pk = $_[1];
+ my %tree = read_db($dbh, $tree_pk);
+ my $sth = getq("get_tree_root_node", $dbh);
+ $sth->execute($tree{tree_pk}) || die "Query get_tree_root_node execute fails.\n$DBI::errstr\n";
+ my $gtrn_rows = $sth->rows();
+ if ($gtrn_rows != 1)
+ {
+ write_log("get_tree_root_node returns $gtrn_rows rows instead of one row for $tree{tree_pk}");
+ die "Query get_tree_root_node returns wrong number of records: $gtrn_rows for $tree{tree_pk}\n";
+ }
+ (my $root_node_pk) = $sth->fetchrow_array();
+ $sth->finish();
+ if ($root_node_pk != $tree{root})
+ {
+ write_log("root nodes don't match: $root_node_pk $tree{root}");
+ die "root nodes don't match: $root_node_pk $tree{root}\n";
+ }
+ $sth = getq("delete_tree", $dbh);
+ $sth->execute($tree{tree_pk});
+ $tree{delete_node_pk} = $root_node_pk; # delete all nodes!
+ delete_node($dbh, \%tree);
}
***************
*** 449,452 ****
--- 471,478 ----
# write_log("pk:$node_pk n:$an_name p:$parent_key a:$an_fk t:$tree_pk");
}
+
+ # $tree{properties_node_pk} = $ch{properties_node_pk};
+ $tree{tree_pk} = $tree_pk;
+
# I know... %tree is a package global, and we're returning it.
return %tree;
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.28
retrieving revision 1.1.2.29
diff -C2 -d -r1.1.2.28 -r1.1.2.29
*** sql_lib.pl 20 Dec 2002 21:54:30 -0000 1.1.2.28
--- sql_lib.pl 23 Dec 2002 19:59:39 -0000 1.1.2.29
***************
*** 62,65 ****
--- 62,72 ----
tree_name";
}
+ elsif ($q_name eq "get_tree_root_node")
+ {
+ my $us_fk = get_us_fk($dbh);
+ (my $fclause, my $wclause) = write_where_clause("tree", "tree_pk", $us_fk );
+ $sql = "select node_pk from node,tree,$fclause where tree_pk=? and tree_pk=tree_fk and parent_key=-1 and $wclause";
+ write_log("$sql");
+ }
elsif ($q_name eq "insert_tree")
{
***************
*** 99,102 ****
--- 106,113 ----
{
$sql = "select an_name,an_pk from analysis order by an_name";
+ }
+ elsif ($q_name eq "delete_tree")
+ {
+ $sql = "delete from tree where tree_pk=?";
}
elsif ($q_name eq "delete_tree_node")
Index: delete_atree1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/delete_atree1.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
*** delete_atree1.pl 20 Dec 2002 21:54:30 -0000 1.1.2.1
--- delete_atree1.pl 23 Dec 2002 19:59:39 -0000 1.1.2.2
***************
*** 20,24 ****
$sth->finish();
! $allhtml =~ s/{(.*?)}/$hr->{$1}/sg;
print "Content-type: text/html\n\n";
--- 20,24 ----
$sth->finish();
! $all_html =~ s/{(.*?)}/$hr->{$1}/sg;
print "Content-type: text/html\n\n";
Index: delete_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/delete_atree2.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
*** delete_atree2.pl 20 Dec 2002 22:21:33 -0000 1.1.2.2
--- delete_atree2.pl 23 Dec 2002 19:59:39 -0000 1.1.2.3
***************
*** 13,17 ****
my $dbh = new_connection();
! delete_tree($ch{tree_pk});
$dbh->commit;
--- 13,17 ----
my $dbh = new_connection();
! delete_tree($dbh, $ch{tree_pk});
$dbh->commit;
|
|
From: <tw...@us...> - 2002-12-20 22:21:38
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv27216
Modified Files:
Tag: Rel-1_0_1-branch
analysis_tree_lib.pl delete_atree2.pl edit_atree2.pl
Log Message:
node delete fixes, tree rename fix
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.41
retrieving revision 1.1.2.42
diff -C2 -d -r1.1.2.41 -r1.1.2.42
*** analysis_tree_lib.pl 20 Dec 2002 21:54:30 -0000 1.1.2.41
--- analysis_tree_lib.pl 20 Dec 2002 22:21:33 -0000 1.1.2.42
***************
*** 259,262 ****
--- 259,268 ----
}
+ sub delete_tree
+ {
+
+
+ }
+
sub delete_node
{
***************
*** 315,331 ****
$sth = getq("select_tree", $dbh);
$sth->execute();
! my %tn;
! while( (my $tree_name) = $sth->fetchrow_array())
{
! $tn{$tree_name} = 1;
}
my $t_suffix = 0;
! if (exists($tn{$tree{tree_name}}))
{
$message .= "22m";
! while(exists($tn{$tree{tree_name}}))
{
- $tree{tree_name} .= $t_suffix;
$t_suffix++;
if ($t_suffix >= 50)
{
--- 321,345 ----
$sth = getq("select_tree", $dbh);
$sth->execute();
! my $tn;
! while( (my $tree_name, my $tree_pk) = $sth->fetchrow_array())
{
! #
! # Only worry about the names of other trees. The current tree
! # can't have a name conflict with itself.
! #
! if ($tree_pk != $tree{tree_pk})
! {
! $tn .= "\t$tree_name\t";
! }
}
my $t_suffix = 0;
! if ($tn =~ m/\t$tree{tree_name}\t/i)
{
$message .= "22m";
! my $name_test = "$tree{tree_name}_$t_suffix";
! while($tn =~ m/\t$name_test\t/i)
{
$t_suffix++;
+ $name_test = "$tree{tree_name}_$t_suffix";
if ($t_suffix >= 50)
{
***************
*** 334,337 ****
--- 348,352 ----
}
}
+ $tree{tree_name} = $name_test;
}
$sth = getq("update_tree_name", $dbh);
Index: delete_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/delete_atree2.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
*** delete_atree2.pl 20 Dec 2002 21:54:30 -0000 1.1.2.1
--- delete_atree2.pl 20 Dec 2002 22:21:33 -0000 1.1.2.2
***************
*** 10,16 ****
{
my $q = new CGI;
my $dbh = new_connection();
! delete_order_info($dbh, $oi_pk);
$dbh->commit;
--- 10,17 ----
{
my $q = new CGI;
+ my %ch = $q->Vars();
my $dbh = new_connection();
! delete_tree($ch{tree_pk});
$dbh->commit;
***************
*** 19,23 ****
#
# This script has no web page output. It only redirects
! # back to choose_order.pl
#
my $url = index_url(); # see sessionlib.pl
--- 20,24 ----
#
# This script has no web page output. It only redirects
! # back to choose_tree.pl
#
my $url = index_url(); # see sessionlib.pl
Index: edit_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree2.pl,v
retrieving revision 1.1.2.17
retrieving revision 1.1.2.18
diff -C2 -d -r1.1.2.17 -r1.1.2.18
*** edit_atree2.pl 20 Dec 2002 21:54:30 -0000 1.1.2.17
--- edit_atree2.pl 20 Dec 2002 22:21:33 -0000 1.1.2.18
***************
*** 17,21 ****
my %tree = read_tree($q);
! write_db($dbh, \%tree);
my $url = index_url(); # see sessionlib.pl
--- 17,21 ----
my %tree = read_tree($q);
! $message = write_db($dbh, \%tree);
my $url = index_url(); # see sessionlib.pl
***************
*** 24,28 ****
{
# It is easier (and maybe better) to call this with $tree_pk and $us_pk
! my $temp = `./runtree.pl --treeName $ch{tree_name} --owner $ENV{REMOTE_USER}`;
$url =~ s/(.*)\/.*/$1\/files.pl/;
print "Location: $url\n\n";
--- 24,28 ----
{
# It is easier (and maybe better) to call this with $tree_pk and $us_pk
! my $temp = `./runtree.pl --treeName $ch{tree_pk} --owner $ENV{REMOTE_USER}`;
$url =~ s/(.*)\/.*/$1\/files.pl/;
print "Location: $url\n\n";
***************
*** 37,45 ****
if (exists($ch{node_pk}) && ! exists($tree{delete_node_pk}))
{
! print "Location: $url?tree_pk=$ch{tree_pk}&node_pk=$ch{node_pk}\n\n";
}
else
{
! print "Location: $url?tree_pk=$ch{tree_pk}\n\n";
}
}
--- 37,45 ----
if (exists($ch{node_pk}) && ! exists($tree{delete_node_pk}))
{
! print "Location: $url?tree_pk=$ch{tree_pk}&node_pk=$ch{node_pk}&message=$message\n\n";
}
else
{
! print "Location: $url?tree_pk=$ch{tree_pk}&message=$message\n\n";
}
}
|
|
From: <tw...@us...> - 2002-12-20 21:54:33
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv18346
Modified Files:
Tag: Rel-1_0_1-branch
edit_atree2.pl analysis_tree_lib.pl edit_atree1.pl
delete_order1.html sql_lib.pl choose_tree.pl choose_tree.html
Added Files:
Tag: Rel-1_0_1-branch
delete_atree2.pl delete_atree1.html delete_atree1.pl
Log Message:
fix html, fix node delete
--- NEW FILE: delete_atree2.pl ---
#!/usr/bin/perl
use strict;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
require "sessionlib.pl";
main:
{
my $q = new CGI;
my $dbh = new_connection();
delete_order_info($dbh, $oi_pk);
$dbh->commit;
$dbh->disconnect;
#
# This script has no web page output. It only redirects
# back to choose_order.pl
#
my $url = index_url(); # see sessionlib.pl
$url =~ s/(.*)\/.*/$1\/choose_tree.pl/;
print "Location: $url\n\n";
exit();
}
--- NEW FILE: delete_atree1.html ---
<html><head><title>Confirm Analysis tree delete</title></head>
<body bgcolor="#FFFFFF">
<table width="600" border="0" cellpadding="0" cellspacing="0">
<tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
<td> </td>
<td valign="top">Va GeneX confirm Analysis tree delete<br><br>
<a href="./">Return to Genex Member Home</a>
</td>
</tr>
</table>
<table width=700 border=1 cellpadding=0 cellspacing=0>
<tr>
<td valign="top">
Tree name: <b>{tree_name}</b><br>
Number of nodes: {number_of_nodes}<br>
</td>
<td valign="top" width="30%">
<form action="delete_atree2.pl" method=POST>
<input type="hidden" name="tree_pk" value="{tree_pk}">
<input type="submit" name="submit" value="Delete this tree now">
</form>
This will delete tree {tree_name} and all {number_of_nodes} node(s) in this tree.<br>
If you have previously run the tree, any existing files/reports produced will be unchanged.<br>
</td>
</tr>
</table>
<br>
<br>
</body>
</html>
--- NEW FILE: delete_atree1.pl ---
#!/usr/bin/perl
use strict;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
require "sessionlib.pl";
main:
{
my $q = new CGI;
my %ch = $q->Vars();
my $dbh = new_connection(); # sessionlib.pl
(my $all_html) = readtemplate("delete_atree1.html"); # readfile() is in sessionlib.pl
my $sth = getq("select_tree_nc_by_pk", $dbh);
$sth->execute($ch{tree_pk});
my $hr = $sth->fetchrow_hashref();
$sth->finish();
$allhtml =~ s/{(.*?)}/$hr->{$1}/sg;
print "Content-type: text/html\n\n";
print "$all_html\n";
$dbh->disconnect;
exit(0);
}
Index: edit_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree2.pl,v
retrieving revision 1.1.2.16
retrieving revision 1.1.2.17
diff -C2 -d -r1.1.2.16 -r1.1.2.17
*** edit_atree2.pl 20 Dec 2002 14:25:36 -0000 1.1.2.16
--- edit_atree2.pl 20 Dec 2002 21:54:30 -0000 1.1.2.17
***************
*** 24,30 ****
{
# It is easier (and maybe better) to call this with $tree_pk and $us_pk
- write_log("runtree is next: $ch{tree_name}");
my $temp = `./runtree.pl --treeName $ch{tree_name} --owner $ENV{REMOTE_USER}`;
- write_log("rt: $temp");
$url =~ s/(.*)\/.*/$1\/files.pl/;
print "Location: $url\n\n";
--- 24,28 ----
***************
*** 33,37 ****
{
$url =~ s/(.*)\/.*/$1\/edit_atree1.pl/;
! if (exists($ch{node_pk}))
{
print "Location: $url?tree_pk=$ch{tree_pk}&node_pk=$ch{node_pk}\n\n";
--- 31,39 ----
{
$url =~ s/(.*)\/.*/$1\/edit_atree1.pl/;
! #
! # A deleted node will also be the active node. It can't be active
! # after it has been deleted, so drop through to the else.
! #
! if (exists($ch{node_pk}) && ! exists($tree{delete_node_pk}))
{
print "Location: $url?tree_pk=$ch{tree_pk}&node_pk=$ch{node_pk}\n\n";
***************
*** 54,58 ****
foreach my $key (keys(%ch))
{
- # write_log("parse CGI key:$key");
#
# Capture name_nnn fields where nnn is an integer starting with zero
--- 56,59 ----
***************
*** 73,77 ****
{
$tree{$key} = $ch{$key};
- # write_log("$key: $ch{$key}");
}
}
--- 74,77 ----
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.40
retrieving revision 1.1.2.41
diff -C2 -d -r1.1.2.40 -r1.1.2.41
*** analysis_tree_lib.pl 20 Dec 2002 16:43:18 -0000 1.1.2.40
--- analysis_tree_lib.pl 20 Dec 2002 21:54:30 -0000 1.1.2.41
***************
*** 259,262 ****
--- 259,306 ----
}
+ sub delete_node
+ {
+ my $dbh = $_[0];
+ my %tree = %{$_[1]};
+
+ my @nstack;
+ push(@nstack, $tree{delete_node_pk});
+ # delete the extra hash element created as a delete carrier
+ delete($tree{delete_node_pk});
+
+ my $lc = 0; # loop counter
+ my $sth = getq("delete_tree_node", $dbh);
+ my $ds_sth = getq("delete_spv", $dbh);
+ my $du_sth = getq("delete_upv", $dbh);
+ while($#nstack >= 0)
+ {
+ my $s_node = pop(@nstack);
+ # delete the record, delete the upv and spv records
+ $sth->execute($s_node) || die "Query delete_tree_node execute fails.\n$DBI::errstr\n";
+ $ds_sth->execute($s_node) || die "Query delete_upv execute fails.\n$DBI::errstr\n";
+ $du_sth->execute($s_node) || die "Query delete_spv execute fails.\n$DBI::errstr\n";
+
+ delete($tree{$s_node}); # delete the element
+ foreach my $node (keys(%tree))
+ {
+ if ($node !~ m/^\d+$/)
+ {
+ next; # only do numeric nodes. We now have $tree{"root"}, $tree{delete}, etc.
+ }
+ if ($tree{$node}[1] == $s_node)
+ {
+ push(@nstack, $node);
+ }
+ $lc++;
+ if ($lc > 100)
+ {
+ die "inf. loop\n";
+ }
+ }
+ }
+ return %tree;
+ }
+
+
#
# local copy of %tree since this one comes from the web page?
***************
*** 269,273 ****
my $message;
! $sth = getq("get_tree_names", $dbh);
$sth->execute();
my %tn;
--- 313,317 ----
my $message;
! $sth = getq("select_tree", $dbh);
$sth->execute();
my %tn;
***************
*** 351,357 ****
{
# delete node
- my $s_node;
- my @nstack;
- $sth = getq("delete_tree_node", $dbh);
if ($tree{delete}[1] == $tree{root})
{
--- 395,398 ----
***************
*** 359,394 ****
return $message ; # don't allow deletion of the root of the tree;
}
! push(@nstack, $tree{delete_node_pk});
! # delete the extra hash element created as a delete carrier
! delete($tree{delete_node_pk});
! my $lc = 0; # loop counter
! my $ds_sth = getq("delete_spv", $dbh);
! my $du_sth = getq("delete_upv", $dbh);
! while($#nstack >= 0)
! {
! $s_node = pop(@nstack);
! # delete the record, delete the upv and spv records
! $sth->execute($s_node) || die "Query delete_tree_node execute fails.\n$DBI::errstr\n";
! $ds_sth->execute($s_node) || die "Query delete_upv execute fails.\n$DBI::errstr\n";
! $du_sth->execute($s_node) || die "Query delete_spv execute fails.\n$DBI::errstr\n";
!
! delete($tree{$s_node}); # delete the element
! foreach my $node (keys(%tree))
! {
! if ($node !~ m/^\d+$/)
! {
! next; # only do numeric nodes. We now have $tree{"root"}, $tree{delete}, etc.
! }
! if ($tree{$node}[1] == $s_node)
! {
! push(@nstack, $node);
! }
! $lc++;
! if ($lc > 100)
! {
! die "inf. loop\n";
! }
! }
! }
}
return $message;
--- 400,404 ----
return $message ; # don't allow deletion of the root of the tree;
}
! delete_node($dbh,\%tree);
}
return $message;
Index: edit_atree1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.pl,v
retrieving revision 1.1.2.11
retrieving revision 1.1.2.12
diff -C2 -d -r1.1.2.11 -r1.1.2.12
*** edit_atree1.pl 20 Dec 2002 14:25:36 -0000 1.1.2.11
--- edit_atree1.pl 20 Dec 2002 21:54:30 -0000 1.1.2.12
***************
*** 53,57 ****
{
my $temp = CGI::escape($hr->{up_value});
- write_log("t: $temp");
if ($hr->{up_type} eq "text")
{
--- 53,56 ----
Index: delete_order1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/delete_order1.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
*** delete_order1.html 27 Nov 2002 14:29:48 -0000 1.1.2.2
--- delete_order1.html 20 Dec 2002 21:54:30 -0000 1.1.2.3
***************
*** 1,13 ****
<html><head><title>Confirm order delete</title></head>
<body bgcolor="#FFFFFF">
! <table border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">Confirm order delete<br><br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
</table>
- <a href="./choose_order.pl">Cancel</a> <br>
- <br>
<loop>
--- 1,13 ----
<html><head><title>Confirm order delete</title></head>
<body bgcolor="#FFFFFF">
! <table width="600" border="0" cellpadding="0" cellspacing="0">
! <tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
! <td> </td>
! <td valign="top">Confirm order delete<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
</table>
<loop>
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.27
retrieving revision 1.1.2.28
diff -C2 -d -r1.1.2.27 -r1.1.2.28
*** sql_lib.pl 20 Dec 2002 15:25:18 -0000 1.1.2.27
--- sql_lib.pl 20 Dec 2002 21:54:30 -0000 1.1.2.28
***************
*** 25,28 ****
--- 25,65 ----
$sql = "select tree_name,tree_pk from tree,$fclause where $wclause order by tree_name";
}
+ elsif ($q_name eq "select_tree_nc")
+ {
+ my $us_fk = get_us_fk($dbh);
+ (my $fclause, my $wclause) = write_where_clause("tree", "tree_pk", $us_fk );
+ $sql = "SELECT
+ tree_name,
+ tree_pk,
+ number_of_nodes
+ FROM
+ tree,
+ $fclause,
+ (SELECT COUNT(tree_fk) AS number_of_nodes, tree_fk FROM node GROUP BY tree_fk) AS node_count
+ WHERE
+ node_count.tree_fk=tree_pk AND
+ $wclause
+ ORDER BY
+ tree_name";
+ }
+ elsif ($q_name eq "select_tree_nc_by_pk")
+ {
+ my $us_fk = get_us_fk($dbh);
+ (my $fclause, my $wclause) = write_where_clause("tree", "tree_pk", $us_fk );
+ $sql = "SELECT
+ tree_name,
+ tree_pk,
+ number_of_nodes
+ FROM
+ tree,
+ $fclause,
+ (SELECT COUNT(tree_fk) AS number_of_nodes, tree_fk FROM node GROUP BY tree_fk) AS node_count
+ WHERE
+ tree_pk=? AND
+ node_count.tree_fk=tree_pk AND
+ $wclause
+ ORDER BY
+ tree_name";
+ }
elsif ($q_name eq "insert_tree")
{
***************
*** 74,83 ****
{
$sql = "update tree set tree_name=trim(?) where tree_pk=?";
- }
- elsif ($q_name eq "get_tree_names")
- {
- my $us_fk = get_us_fk($dbh);
- (my $fclause, my $wclause) = write_where_clause("tree", "tree_pk", $us_fk );
- $sql = "select tree_name,tree_pk from tree,$fclause where $wclause";
}
elsif ($q_name eq "update_billing_code")
--- 111,114 ----
Index: choose_tree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_tree.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_tree.pl 8 Nov 2002 21:22:53 -0000 1.1.2.1
--- choose_tree.pl 20 Dec 2002 21:54:30 -0000 1.1.2.2
***************
*** 10,16 ****
{
my $dbh = new_connection();
! (my $all_html) = readtemplate("choose_tree.html");
! my $select_tree = select_tree($dbh); # analysis_tree_lib.pl
! $all_html =~ s/{select_tree}/$select_tree/;
print "Content-type: text/html\n\n$all_html\n";
$dbh->disconnect();
--- 10,26 ----
{
my $dbh = new_connection();
! (my $all_html, my $loop_template) = readtemplate("choose_tree.html");
!
! my $sth = getq("select_tree_nc", $dbh);
! $sth->execute() || die "Query select_tree_nc execute fails.\n$DBI::errstr\n";
! my $hr;
! while( $hr = $sth->fetchrow_hashref())
! {
! my $loop_instance = $loop_template;
! $loop_instance =~ s/{(.*?)}/$hr->{$1}/sg;
! $all_html =~ s/<loop_here>/$loop_instance<loop_here>/s;
! }
! $all_html =~ s/<loop_here>//s;
!
print "Content-type: text/html\n\n$all_html\n";
$dbh->disconnect();
Index: choose_tree.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_tree.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_tree.html 20 Dec 2002 18:43:49 -0000 1.1.2.2
--- choose_tree.html 20 Dec 2002 21:54:30 -0000 1.1.2.3
***************
*** 1,8 ****
! <html><head><title>Update Experimental Conditions</title></head>
<body bgcolor="#FFFFFF">
<table width="600" border="0" cellpadding="0" cellspacing="0">
<tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
<td> </td>
! <td valign="top">GeneX Experimental Conditions Update<br><br>
<a href="./">Return to Genex Member Home</a>
</td>
--- 1,8 ----
! <html><head><title>Choose a Study</title></head>
<body bgcolor="#FFFFFF">
<table width="600" border="0" cellpadding="0" cellspacing="0">
<tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
<td> </td>
! <td valign="top">GeneX Analysis tree selection<br><br>
<a href="./">Return to Genex Member Home</a>
</td>
***************
*** 10,20 ****
</table>
! <form action="edit_atree1.pl" method=POST>
! {select_tree} <br>
! <br>
! <br>
! <input type="submit" name="Submit" value="Next">
! <a href="./">Cancel</a>
! </form>
<br>
</body>
--- 10,61 ----
</table>
! <a href="./">Cancel</a><br><br>
! <loop>
! <table width="700" border=0 cellspacing=0 cellpadding=3>
! <tr>
! <td valign="top" bgcolor="#99CC99">
! <table width="100%" border="0" cellspacing="5" cellpadding="0" bgcolor="#FFFFFF">
! <tr>
! <td width="70%">
! <form action="edit_atree1.pl" method="post">
! <div align="right">
! <input type=submit name=submit2 value="Edit {tree_name}">
! <input type="image" border="0" name="imageField" src="../graphics/pencil.gif" width="25" height="25">
! <input type=hidden name="tree_pk" value="{tree_pk}">
! </div>
! </form>
! </td>
! <td width="30%"> </td>
! </tr>
! <tr>
! <td width="70%">
! <div align="right">Tree name:</div>
! </td>
! <td width="30%">{tree_name}</td>
! </tr>
! <tr>
! <td width="70%">
! <div align="right">Number of nodes:</div>
! </td>
! <td width="30%">{number_of_nodes}</td>
! </tr>
! <tr>
! <td width="70%">
! <form action="delete_atree1.pl" method="post">
! <div align="right">
! <input type="submit" name="submit" value="Delete {tree_name}">
! <input type="image" border="0" name="imageField2" src="../graphics/trash.gif" width="25" height="25">
! <input type="hidden" name="tree_pk" value="{tree_pk}">
! </div>
! </form>
! </td>
! <td width="30%"> </td>
! </tr>
! </table>
! </td>
! </tr>
! </table>
! <br>
! </loop> <br>
<br>
</body>
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv5620
Modified Files:
Tag: Rel-1_0_1-branch
create_group.html groups.html account.html choose_tree.html
get_data1.html choose_order_curator.html
Log Message:
format fixes
Index: create_group.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/create_group.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
*** create_group.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- create_group.html 20 Dec 2002 18:43:48 -0000 1.1.2.2
***************
*** 1,13 ****
<html><head><title>Create a new group</title></head>
<body bgcolor="#FFFFFF">
! <table border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">Create new group<br><br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
</table>
! <br>
! <br>
! {message}<br><br>
<form action="create_group.pl" method=POST>
<table border=0 cellpadding=0 cellspacing=0>
--- 1,17 ----
<html><head><title>Create a new group</title></head>
<body bgcolor="#FFFFFF">
! <table width="600" border="0" cellpadding="0" cellspacing="0">
! <tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
! <td> </td>
! <td valign="top">Create new group<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
</table>
!
! <br>
! {message}
! <br><br>
!
<form action="create_group.pl" method=POST>
<table border=0 cellpadding=0 cellspacing=0>
Index: groups.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/groups.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
*** groups.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- groups.html 20 Dec 2002 18:43:49 -0000 1.1.2.2
***************
*** 2,8 ****
<head><title>GeneX Account Update Login</title></head>
<body bgcolor=white>
! <table border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Account Update<br><br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
--- 2,10 ----
<head><title>GeneX Account Update Login</title></head>
<body bgcolor=white>
! <table width="600" border="0" cellpadding="0" cellspacing="0">
! <tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
! <td> </td>
! <td valign="top">GeneX Account Update<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
Index: account.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/account.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
*** account.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- account.html 20 Dec 2002 18:43:49 -0000 1.1.2.2
***************
*** 2,8 ****
<head><title>GeneX Account Update Login</title></head>
<body bgcolor=white>
! <img src="../graphics/genex_logo.jpg" align="left">GeneX Account Update<br>
! <a href="./"><br>Return to Genex Member Home</a>
! <br><br clear=all><br>
<form method="POST" action="account.pl">
--- 2,13 ----
<head><title>GeneX Account Update Login</title></head>
<body bgcolor=white>
! <table width="600" border="0" cellpadding="0" cellspacing="0">
! <tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
! <td> </td>
! <td valign="top">GeneX Account Update<br><br>
! <a href="./">Return to Genex Member Home</a>
! </td>
! </tr>
! </table>
<form method="POST" action="account.pl">
Index: choose_tree.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_tree.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_tree.html 8 Nov 2002 21:22:53 -0000 1.1.2.1
--- choose_tree.html 20 Dec 2002 18:43:49 -0000 1.1.2.2
***************
*** 1,11 ****
<html><head><title>Update Experimental Conditions</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 Experimental Conditions Update<br><br>
! <a href="./">Return to Genex Member Home</a><br>
</td>
</tr>
</table>
- <br>
<form action="edit_atree1.pl" method=POST>
--- 1,12 ----
<html><head><title>Update Experimental Conditions</title></head>
<body bgcolor="#FFFFFF">
! <table width="600" border="0" cellpadding="0" cellspacing="0">
! <tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
! <td> </td>
! <td valign="top">GeneX Experimental Conditions Update<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
</table>
<form action="edit_atree1.pl" method=POST>
Index: get_data1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/get_data1.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
*** get_data1.html 12 Dec 2002 20:50:26 -0000 1.1.2.3
--- get_data1.html 20 Dec 2002 18:43:49 -0000 1.1.2.4
***************
*** 1,8 ****
<html><head><title>Choose MAS5 hybridizations</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>
Choose hybridizations to export.<br>
The next version will allow experimental group changes, but that feature
--- 1,10 ----
<html><head><title>Choose MAS5 hybridizations</title></head>
<body bgcolor="#FFFFFF">
! <table width="600" border="0" cellpadding="0" cellspacing="0">
! <tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
! <td> </td>
! <td valign="top">GeneX MAS5 hybridization data export<br><br>
<a href="./">Return to Genex Member Home</a>
! <br>
Choose hybridizations to export.<br>
The next version will allow experimental group changes, but that feature
***************
*** 13,17 ****
</tr>
</table>
! <br>
<form action="get_data2.pl" method="post">
<input type="submit" name="submit" value="Next">
--- 15,19 ----
</tr>
</table>
!
<form action="get_data2.pl" method="post">
<input type="submit" name="submit" value="Next">
Index: choose_order_curator.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_order_curator.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_order_curator.html 18 Nov 2002 21:20:53 -0000 1.1.2.2
--- choose_order_curator.html 20 Dec 2002 18:43:49 -0000 1.1.2.3
***************
*** 1,10 ****
<html><head><title>Choose an order</title></head>
<body bgcolor="#FFFFFF">
! <table border=0 cellpadding=0 cellspacing=0>
! <tr>
! <td align=top><img src="../graphics/genex_logo.jpg" align="left" width="100" height="60">GeneX
! Account Update<br>
! <br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
--- 1,9 ----
<html><head><title>Choose an order</title></head>
<body bgcolor="#FFFFFF">
! <table width="600" border="0" cellpadding="0" cellspacing="0">
! <tr><td valign="top" width="207"><a href="./"><img src="../graphics/genex_logo.jpg" border="0" width="207" height="87"></a></td>
! <td> </td>
! <td valign="top">GeneX Account Update<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv14027
Modified Files:
Tag: Rel-1_0_1-branch
AffyTextDataReader.pm loadam_spots.pl sessionlib.pl
analysis_tree_lib.pl
Log Message:
AffyTextDataReader.pm fix to account for pre-increment
Index: AffyTextDataReader.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/AffyTextDataReader.pm,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** AffyTextDataReader.pm 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- AffyTextDataReader.pm 20 Dec 2002 16:43:18 -0000 1.1.2.2
***************
*** 71,80 ****
my $header_row = $datasheet->[$thisRow][0];
- #if ($header_row =~ m/^Expression Analysis/)
- #{
- #undef $header_row;
- #$this->{row_count} += 3;
- #$this->{end_of_header} = 1;
- #}
if ($header_row =~ m/^Probe Set Name/)
{
--- 71,74 ----
***************
*** 98,102 ****
}
undef $header_row; # This row isn't part of the header.
! $this->{row_count} += 1; # Data starts next row.
$this->{end_of_header} = 1; # Header is all done.
}
--- 92,98 ----
}
undef $header_row; # This row isn't part of the header.
! # 2002-12-20 Guess what! get_next_datarow() PRE increments!!
! # DO NOT increment row_count here.
! # $this->{row_count} += 1; # Data starts next row.
$this->{end_of_header} = 1; # Header is all done.
}
***************
*** 114,117 ****
--- 110,117 ----
my $datasheet=$this->{datasheet};
my $thisRow;
+ #
+ # 2002-12-20. Pre incrementing on a read seems weird.
+ # do loops bite. Rewrite this someday so mere mortals can understand it.
+ #
do
{
Index: loadam_spots.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/loadam_spots.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
*** loadam_spots.pl 21 Nov 2002 21:48:47 -0000 1.1.2.2
--- loadam_spots.pl 20 Dec 2002 16:43:18 -0000 1.1.2.3
***************
*** 122,131 ****
#Now set up arrays for spots from the first data row
#
! print "Getting first data row\n";
! my $refRow = $array_reader->get_next_datarow();
!
!
! die "No data row found \n" if !defined($refRow);
#
# Tom Laudeman 2002-04-30
# The workflow has changed drastically. Arraymeasurement is now
--- 122,135 ----
#Now set up arrays for spots from the first data row
#
!
! # 2002-12-20 This was really bad. It reads the first row of data, and this reallly is the
! # first row of data. This row is never used, which means it is lost.
! # I've commented out this glaring bug.
#
+ # print "Getting first data row\n";
+ # my $refRow = $array_reader->get_next_datarow();
+ # die "No data row found \n" if !defined($refRow);
+ #
+
# Tom Laudeman 2002-04-30
# The workflow has changed drastically. Arraymeasurement is now
***************
*** 186,193 ****
#
# Read spots and insert into db.
! # First row previously retrieved to get names of columns.
#
while ($refRow = $array_reader->get_next_datarow())
{
if (exists($skh{$refRow->{ProbeSet}}))
{
--- 190,216 ----
#
# Read spots and insert into db.
! # get_next_headerrow() from AffyTextDataReader.pm or AffyDataReader.pm
! # has been called to read in the headers, so we know whether this
! # is MAS4 or MAS5 data.
#
+ # 2002-12-20
+ # There was a spurious get_next_datarow() up above (now commented out). That lost one row of data.
+ # There was confusion about pre-incrementing before reading data
+ # and that lost another row of data.
+ # I've added code to print the first and last probe set names to verify.
+ #
+
+ my $first_flag = 1;
+ my $first_probeset = "";
+ my $last_probeset = "";
+ my $refRow;
while ($refRow = $array_reader->get_next_datarow())
{
+ if ($first_flag)
+ {
+ $first_probeset = $refRow->{ProbeSet};
+ $first_flag = 0;
+ }
+ $last_probeset = $refRow->{ProbeSet}; # assigning every time is crude, but we'll have the last one.
if (exists($skh{$refRow->{ProbeSet}}))
{
***************
*** 227,230 ****
--- 250,255 ----
}
}
+ print "First Probe Set Name: $first_probeset\n";
+ print " Last Probe Set Name: $last_probeset\n";
if (exists($options{nocommit})) {
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.22
retrieving revision 1.1.2.23
diff -C2 -d -r1.1.2.22 -r1.1.2.23
*** sessionlib.pl 20 Dec 2002 14:32:21 -0000 1.1.2.22
--- sessionlib.pl 20 Dec 2002 16:43:18 -0000 1.1.2.23
***************
*** 54,57 ****
--- 54,60 ----
$messages[20] = "One or more samples have no Study/Experimental Condition selected.<br>\n";
$messages[21] = "Successfully updated group/permission info.<br>\n";
+ $messages[22] = "Duplicate tree name was given a numerical suffix to make it unique.<br>\n";
+ $messages[23] = "The node is already the type you chose. No change to node type.<br>\n";
+ $messages[24] = "You cannot delete the root node.<br>\n";
return $messages[$_[0]];
***************
*** 1259,1263 ****
# If owner or group read permissions are true, a record is readable.
# The where clause that we return includes surrounding ()
! @ since the calling code almost always does something like
# "select * from table,$from_clause where table_pk=1 and $where_clause";
#
--- 1262,1266 ----
# If owner or group read permissions are true, a record is readable.
# The where clause that we return includes surrounding ()
! # since the calling code almost always does something like
# "select * from table,$from_clause where table_pk=1 and $where_clause";
#
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.39
retrieving revision 1.1.2.40
diff -C2 -d -r1.1.2.39 -r1.1.2.40
*** analysis_tree_lib.pl 20 Dec 2002 14:25:36 -0000 1.1.2.39
--- analysis_tree_lib.pl 20 Dec 2002 16:43:18 -0000 1.1.2.40
***************
*** 19,24 ****
{
my $dbh = $_[0];
! my $sth = getq("insert_tree", $dbh);
! $sth->execute() || die "Query insert_tree execute fails. $DBI::errstr\n";
my $us_fk = get_us_fk($dbh);
--- 19,34 ----
{
my $dbh = $_[0];
! my $t_suffix = 0;
! my $sth = getq("select_tree", $dbh);
! $sth->execute() || die "Query select_tree execute error: $DBI::errstr\n";
! while((my $name, my $tree_pk) = $sth->fetchrow_array())
! {
! if ($name eq "Tree $t_suffix")
! {
! $t_suffix++;
! }
! }
! $sth = getq("insert_tree", $dbh);
! $sth->execute("Tree $t_suffix") || die "Query insert_tree execute fails. $DBI::errstr\n";
my $us_fk = get_us_fk($dbh);
***************
*** 36,60 ****
init_node($dbh, $node_pk, $default_an_pk);
- # $sth = getq("default_upv", $dbh);
- # $sth->execute($default_an_pk) || die "Query default_upv execute error. $DBI::errstr\n";
- # my $sth_insert = getq("insert_upv", $dbh);
- # my $hr;
- # while ($hr = $sth->fetchrow_hashref())
- # {
- # $sth_insert->execute($node_pk,
- # $hr->{up_default},
- # $hr->{upn_pk}) || die "Query insert_upv execute error. $DBI::errstr\n";
- # }
-
- # $sth = getq("default_spv", $dbh);
- # $sth->execute($default_an_pk) || die "Query default_spv execute error. $DBI::errstr\n";
- # $sth_insert = getq("insert_spv", $dbh);
- # while ($hr = $sth->fetchrow_hashref())
- # {
- # $sth_insert->execute($node_pk,
- # $hr->{sp_default},
- # $hr->{spn_pk}) || die "Query insert_spv execute error. $DBI::errstr\n";
- # }
-
$dbh->commit;
return $tree_pk;
--- 46,49 ----
***************
*** 278,282 ****
my %tree = %{$_[1]};
my $sth;
!
$sth = getq("update_tree_name", $dbh);
$sth->execute($tree{tree_name}, $tree{tree_pk});
--- 267,294 ----
my %tree = %{$_[1]};
my $sth;
! my $message;
!
! $sth = getq("get_tree_names", $dbh);
! $sth->execute();
! my %tn;
! while( (my $tree_name) = $sth->fetchrow_array())
! {
! $tn{$tree_name} = 1;
! }
! my $t_suffix = 0;
! if (exists($tn{$tree{tree_name}}))
! {
! $message .= "22m";
! while(exists($tn{$tree{tree_name}}))
! {
! $tree{tree_name} .= $t_suffix;
! $t_suffix++;
! if ($t_suffix >= 50)
! {
! write_log("tree name suffix went over 50");
! die "Please click the back button, and enter a different tree name\n";
! }
! }
! }
$sth = getq("update_tree_name", $dbh);
$sth->execute($tree{tree_name}, $tree{tree_pk});
***************
*** 319,323 ****
{
# hasn't changed, do nothing, return.
! return ;
}
# has changed, delete old upv and spv
--- 331,336 ----
{
# hasn't changed, do nothing, return.
! $message .= "23m";
! return $message;
}
# has changed, delete old upv and spv
***************
*** 343,347 ****
if ($tree{delete}[1] == $tree{root})
{
! return ; # don't allow deletion of the root of the tree;
}
push(@nstack, $tree{delete_node_pk});
--- 356,361 ----
if ($tree{delete}[1] == $tree{root})
{
! $message .= "24m";
! return $message ; # don't allow deletion of the root of the tree;
}
push(@nstack, $tree{delete_node_pk});
***************
*** 378,381 ****
--- 392,396 ----
}
}
+ return $message;
}
|
|
From: <tw...@us...> - 2002-12-20 15:25:21
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv11335
Modified Files:
Tag: Rel-1_0_1-branch
sql_lib.pl
Log Message:
new get_tree_names query
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.26
retrieving revision 1.1.2.27
diff -C2 -d -r1.1.2.26 -r1.1.2.27
*** sql_lib.pl 20 Dec 2002 14:25:36 -0000 1.1.2.26
--- sql_lib.pl 20 Dec 2002 15:25:18 -0000 1.1.2.27
***************
*** 27,31 ****
elsif ($q_name eq "insert_tree")
{
! $sql = "insert into tree (tree_name) values ('Tree')";
}
elsif ($q_name eq "insert_tree_node")
--- 27,31 ----
elsif ($q_name eq "insert_tree")
{
! $sql = "insert into tree (tree_name) values (?)";
}
elsif ($q_name eq "insert_tree_node")
***************
*** 49,53 ****
$fclause
WHERE
! tree_fk=? AND
tree_pk=tree_fk AND
an_fk=an_pk AND
--- 49,53 ----
$fclause
WHERE
! tree_pk=? AND
tree_pk=tree_fk AND
an_fk=an_pk AND
***************
*** 74,77 ****
--- 74,83 ----
{
$sql = "update tree set tree_name=trim(?) where tree_pk=?";
+ }
+ elsif ($q_name eq "get_tree_names")
+ {
+ my $us_fk = get_us_fk($dbh);
+ (my $fclause, my $wclause) = write_where_clause("tree", "tree_pk", $us_fk );
+ $sql = "select tree_name,tree_pk from tree,$fclause where $wclause";
}
elsif ($q_name eq "update_billing_code")
|
|
From: <tw...@us...> - 2002-12-20 14:36:51
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv20701
Modified Files:
Tag: Rel-1_0_1-branch
sessionlib.pl
Log Message:
improved comments
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.21
retrieving revision 1.1.2.22
diff -C2 -d -r1.1.2.21 -r1.1.2.22
*** sessionlib.pl 20 Dec 2002 14:25:36 -0000 1.1.2.21
--- sessionlib.pl 20 Dec 2002 14:32:21 -0000 1.1.2.22
***************
*** 1255,1263 ****
#
! # select * from experimentset where date=today and $where_clause
#
! # select to match group
! # The where clause returned MUST be enclosed in () since the calling code may do something
! # like "select * from table,$from where field=1 and $where_clause";
#
# jul 29 2002 Tom
--- 1255,1264 ----
#
! # (my $from_clause, my $where_clause) = read_where_clause(string table, string primary_key_field_name, integer userid)
#
! # If owner or group read permissions are true, a record is readable.
! # The where clause that we return includes surrounding ()
! @ since the calling code almost always does something like
! # "select * from table,$from_clause where table_pk=1 and $where_clause";
#
# jul 29 2002 Tom
|
|
From: <tw...@us...> - 2002-12-20 14:25:39
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv17720
Modified Files:
Tag: Rel-1_0_1-branch
sql_lib.pl sessionlib.pl edit_atree1.pl edit_atree2.pl
edit_atree1.html analysis_tree_lib.pl makefile config.pl
Log Message:
atree node init fixes
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.25
retrieving revision 1.1.2.26
diff -C2 -d -r1.1.2.25 -r1.1.2.26
*** sql_lib.pl 17 Dec 2002 15:02:08 -0000 1.1.2.25
--- sql_lib.pl 20 Dec 2002 14:25:36 -0000 1.1.2.26
***************
*** 35,39 ****
elsif ($q_name eq "read_tree")
{
! $sql = "select tree_name, node_pk, an_name, parent_key, an_fk from tree, node, analysis where tree_fk=? and tree_pk=tree_fk and an_fk=an_pk order by node_pk";
}
elsif ($q_name eq "update_tree_node")
--- 35,57 ----
elsif ($q_name eq "read_tree")
{
! my $us_fk = get_us_fk($dbh);
! (my $fclause, my $wclause) = write_where_clause("tree", "tree_pk", $us_fk );
! $sql = "SELECT
! tree_name,
! node_pk,
! an_name,
! parent_key,
! an_fk
! FROM
! tree,
! node,
! analysis,
! $fclause
! WHERE
! tree_fk=? AND
! tree_pk=tree_fk AND
! an_fk=an_pk AND
! $wclause
! ORDER BY node_pk";
}
elsif ($q_name eq "update_tree_node")
***************
*** 304,307 ****
--- 322,338 ----
$sql = "update user_parameter_values set up_value=? where upv_pk=?";
}
+ elsif ($q_name eq "select_an_fk")
+ {
+ $sql = "select an_fk from node where node_pk=?";
+ }
+ elsif ($q_name eq "delete_upv")
+ {
+ $sql = "delete from user_parameter_values where node_fk=?";
+ }
+ elsif ($q_name eq "delete_spv")
+ {
+ $sql = "delete from sys_parameter_values where node_fk=?";
+ }
+
# write_log("sql: $sql");
***************
*** 317,321 ****
}
}
!
!
! ;
--- 348,350 ----
}
}
! 1;
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.20
retrieving revision 1.1.2.21
diff -C2 -d -r1.1.2.20 -r1.1.2.21
*** sessionlib.pl 18 Dec 2002 18:18:07 -0000 1.1.2.20
--- sessionlib.pl 20 Dec 2002 14:25:36 -0000 1.1.2.21
***************
*** 1285,1291 ****
#
# select all records that $userid is allowed to write
! # The where clause returned MUST be enclosed in () since the calling code may do something
! # like "select * from table,$from where field=1 and $where_clause";
#
# jul 29 2002 Tom
--- 1285,1294 ----
#
+ # (my $from_clause, my $where_clause) = write_where_clause(string $table, string $primary_key_field_name, integer $userid);
+ #
# select all records that $userid is allowed to write
! # The where clause returned includes enclosing () since the
! # calling code almost always does something like
! # "select * from table,$from_clause where table_pk=1 and $where_clause";
#
# jul 29 2002 Tom
Index: edit_atree1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.pl,v
retrieving revision 1.1.2.10
retrieving revision 1.1.2.11
diff -C2 -d -r1.1.2.10 -r1.1.2.11
*** edit_atree1.pl 17 Dec 2002 21:33:32 -0000 1.1.2.10
--- edit_atree1.pl 20 Dec 2002 14:25:36 -0000 1.1.2.11
***************
*** 56,60 ****
if ($hr->{up_type} eq "text")
{
- # $results .= "<tr><td valign=\"top\">$hr->{up_display_name} <br><br></td><td valign=\"top\"><input type=\"text\" name=\"upv_pk_$hr->{upv_pk}\" value=\"$hr->{up_value} \"size=\"30\" maxlength=\"128\"></td></tr>\n";
$results .= "<tr><td valign=\"top\">$hr->{up_display_name} <br><br></td><td valign=\"top\"><textarea name=\"upv_pk_$hr->{upv_pk}\" cols=30 rows=1 wrap=off>$hr->{up_value}</textarea></td></tr>\n";
}
--- 56,59 ----
***************
*** 79,83 ****
while( $hr = $sth->fetchrow_hashref())
{
! $results .= "<tr><td valign=\"top\">$hr->{sp_name} <br><br></td><td valign=\"top\">$hr->{sp_value}</td></tr>\n";
}
$results .= "</table>\n";
--- 78,82 ----
while( $hr = $sth->fetchrow_hashref())
{
! $results .= "<tr><td valign=\"top\">$hr->{sp_name} <br><br></td><td valign=\"top\">$hr->{sp_value}</td></tr>\n";
}
$results .= "</table>\n";
Index: edit_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree2.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
*** edit_atree2.pl 18 Dec 2002 03:32:13 -0000 1.1.2.15
--- edit_atree2.pl 20 Dec 2002 14:25:36 -0000 1.1.2.16
***************
*** 81,84 ****
--- 81,92 ----
$active_node = $ch{node_pk};
}
+ foreach my $key (keys(%ch))
+ {
+ if ($key =~ m/edit_(\d+)\.x/)
+ {
+ $active_node = $1;
+ last;
+ }
+ }
if (exists($ch{add}))
{
Index: edit_atree1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.html,v
retrieving revision 1.1.2.13
retrieving revision 1.1.2.14
diff -C2 -d -r1.1.2.13 -r1.1.2.14
*** edit_atree1.html 17 Dec 2002 21:33:32 -0000 1.1.2.13
--- edit_atree1.html 20 Dec 2002 14:25:36 -0000 1.1.2.14
***************
*** 15,18 ****
--- 15,19 ----
</tr>
</table>
+ <br>
<form action="edit_atree2.pl" method=GET>
Analysis tree name: {tree_name}
***************
*** 24,29 ****
<table width="760" border="0" cellpadding="0" cellspacing="4">
<tr>
! <td width="50%">
{atree} <br>
</td>
<td bgcolor="#00CC99" width="1%"></td>
--- 25,49 ----
<table width="760" border="0" cellpadding="0" cellspacing="4">
<tr>
! <td valign="top" width="50%">
{atree} <br>
+ <table width="100%"><tr><td bgcolor="$00CC99"><div align="center">Add a node or Change node's type</div></td></tr></table>
+ <table border="0" cellpadding="5" cellspacing="0">
+ <tr>
+ <td>(1) Click a radio button above</td><td></td>
+ </tr>
+
+ <tr>
+ <td>(2) Choose: <br></td><td>{select_node}</td>
+ </tr>
+
+ <tr>
+ <td>(3) Add or Change: <br></td><td><input type=submit name="add" value="Add Node"></td>
+ </tr>
+
+ <tr>
+ <td> </td><td><input type=submit name="change" value="Change Node"></td>
+ </tr>
+
+ </table>
</td>
<td bgcolor="#00CC99" width="1%"></td>
***************
*** 33,54 ****
<br>
<br>
- <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>
-
- <tr>
- <td>{select_node}</td><td> </td>
- </tr>
-
- <tr>
- <td> </td><td><input type=submit name="change" value="Change Node"></td>
- </tr>
- </table>
</form>
<br>
--- 53,56 ----
***************
*** 69,73 ****
To delete a node, click the node's radio button, then click the trash can. There is no
confirmation: we assume that since you clicked both the radio button and the trash can,
! you really meant it, and the node is immediately deleted as well as all the nodes children!
<br>
</td></tr></table>
--- 71,75 ----
To delete a node, click the node's radio button, then click the trash can. There is no
confirmation: we assume that since you clicked both the radio button and the trash can,
! you really meant it, and the node is immediately deleted as well as all the node's children!
<br>
</td></tr></table>
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.38
retrieving revision 1.1.2.39
diff -C2 -d -r1.1.2.38 -r1.1.2.39
*** analysis_tree_lib.pl 17 Dec 2002 15:02:14 -0000 1.1.2.38
--- analysis_tree_lib.pl 20 Dec 2002 14:25:36 -0000 1.1.2.39
***************
*** 34,57 ****
my $node_pk = insert_security($dbh, $us_fk, $us_fk, 0);
! $sth = getq("default_upv", $dbh);
! $sth->execute($default_an_pk) || die "Query default_upv execute error. $DBI::errstr\n";
! my $sth_insert = getq("insert_upv", $dbh);
! my $hr;
! while ($hr = $sth->fetchrow_hashref())
! {
! $sth_insert->execute($node_pk,
! $hr->{up_default},
! $hr->{upn_pk}) || die "Query insert_upv execute error. $DBI::errstr\n";
! }
! $sth = getq("default_spv", $dbh);
! $sth->execute($default_an_pk) || die "Query default_spv execute error. $DBI::errstr\n";
! $sth_insert = getq("insert_spv", $dbh);
! while ($hr = $sth->fetchrow_hashref())
! {
! $sth_insert->execute($node_pk,
! $hr->{sp_default},
! $hr->{spn_pk}) || die "Query insert_spv execute error. $DBI::errstr\n";
! }
$dbh->commit;
--- 34,59 ----
my $node_pk = insert_security($dbh, $us_fk, $us_fk, 0);
! init_node($dbh, $node_pk, $default_an_pk);
! # $sth = getq("default_upv", $dbh);
! # $sth->execute($default_an_pk) || die "Query default_upv execute error. $DBI::errstr\n";
! # my $sth_insert = getq("insert_upv", $dbh);
! # my $hr;
! # while ($hr = $sth->fetchrow_hashref())
! # {
! # $sth_insert->execute($node_pk,
! # $hr->{up_default},
! # $hr->{upn_pk}) || die "Query insert_upv execute error. $DBI::errstr\n";
! # }
!
! # $sth = getq("default_spv", $dbh);
! # $sth->execute($default_an_pk) || die "Query default_spv execute error. $DBI::errstr\n";
! # $sth_insert = getq("insert_spv", $dbh);
! # while ($hr = $sth->fetchrow_hashref())
! # {
! # $sth_insert->execute($node_pk,
! # $hr->{sp_default},
! # $hr->{spn_pk}) || die "Query insert_spv execute error. $DBI::errstr\n";
! # }
$dbh->commit;
***************
*** 236,239 ****
--- 238,274 ----
#
+ # Call this anytime you insert a new node, or
+ # when you update a node and change the nodes's an_fk.
+ #
+ sub init_node
+ {
+ my $dbh = $_[0];
+ my $node_pk = $_[1];
+ my $add_an_fk = $_[2];
+
+ my $sth = getq("default_upv", $dbh);
+ $sth->execute($add_an_fk) || die "Query default_upv execute error. $DBI::errstr\n";
+ my $sth_insert = getq("insert_upv", $dbh);
+ my $hr;
+ while ($hr = $sth->fetchrow_hashref())
+ {
+ $sth_insert->execute($node_pk,
+ $hr->{up_default},
+ $hr->{upn_pk}) || die "Query insert_upv execute error. $DBI::errstr\n";
+ }
+
+ $sth = getq("default_spv", $dbh);
+ $sth->execute($add_an_fk) || die "Query default_spv execute error. $DBI::errstr\n";
+ $sth_insert = getq("insert_spv", $dbh);
+ while ($hr = $sth->fetchrow_hashref())
+ {
+ # write_log("d:$hr->{sp_default} p:$hr->{spn_fk} n:$node_pk");
+ $sth_insert->execute($node_pk,
+ $hr->{sp_default},
+ $hr->{spn_pk}) || die "Query insert_spv execute error. $DBI::errstr\n";
+ }
+ }
+
+ #
# local copy of %tree since this one comes from the web page?
#
***************
*** 247,251 ****
$sth->execute($tree{tree_name}, $tree{tree_pk});
! # This better exist!
if (exists($tree{properties_node_pk}))
{
--- 282,286 ----
$sth->execute($tree{tree_name}, $tree{tree_pk});
! # $tree{properties_node_pk} better exist!
if (exists($tree{properties_node_pk}))
{
***************
*** 268,303 ****
# insert node
$sth = getq("insert_tree_node", $dbh);
! $sth->execute($tree{tree_pk}, $tree{add_parent}, $tree{add_an_fk}); # my tree's tree_pk, my parent's node_pk, analysis an_pk
my $us_fk = get_us_fk($dbh);
my $node_pk = insert_security($dbh, $us_fk, $us_fk, 0);
!
! $sth = getq("default_upv", $dbh);
! $sth->execute($tree{add_an_fk}) || die "Query default_upv execute error. $DBI::errstr\n";
! my $sth_insert = getq("insert_upv", $dbh);
! my $hr;
! while ($hr = $sth->fetchrow_hashref())
! {
! $sth_insert->execute($node_pk,
! $hr->{up_default},
! $hr->{upn_pk}) || die "Query insert_upv execute error. $DBI::errstr\n";
! }
!
! $sth = getq("default_spv", $dbh);
! $sth->execute($tree{add_an_fk}) || die "Query default_spv execute error. $DBI::errstr\n";
! $sth_insert = getq("insert_spv", $dbh);
! while ($hr = $sth->fetchrow_hashref())
! {
! # write_log("d:$hr->{sp_default} p:$hr->{spn_fk} n:$node_pk");
! $sth_insert->execute($node_pk,
! $hr->{sp_default},
! $hr->{spn_pk}) || die "Query insert_spv execute error. $DBI::errstr\n";
! }
}
elsif (exists($tree{update_node_pk}))
{
! # update node
$sth = getq("update_tree_node", $dbh);
# ana_fk, node_pk
$sth->execute($tree{update_an_fk}, $tree{update_node_pk});
}
elsif (exists($tree{delete_node_pk}))
--- 303,337 ----
# insert node
$sth = getq("insert_tree_node", $dbh);
! # my tree's tree_pk, my parent's node_pk, analysis an_pk
! $sth->execute($tree{tree_pk}, $tree{add_parent}, $tree{add_an_fk});
my $us_fk = get_us_fk($dbh);
my $node_pk = insert_security($dbh, $us_fk, $us_fk, 0);
! init_node($dbh, $node_pk, $tree{add_an_fk},);
}
elsif (exists($tree{update_node_pk}))
{
! # update node aka rename
! $sth = getq("select_an_fk", $dbh);
! $sth->execute($tree{update_node_pk});
! (my $old_an_fk) = $sth->fetchrow_array();
! # has it really changed?
! if ($old_an_fk == $tree{update_an_fk})
! {
! # hasn't changed, do nothing, return.
! return ;
! }
! # has changed, delete old upv and spv
! my $du_sth = getq("delete_upv", $dbh);
! my $ds_sth = getq("delete_spv", $dbh);
! $du_sth->execute($tree{update_node_pk});
! $ds_sth->execute($tree{update_node_pk});
!
! # change node an_fk
$sth = getq("update_tree_node", $dbh);
# ana_fk, node_pk
$sth->execute($tree{update_an_fk}, $tree{update_node_pk});
+
+ # init the essentially new node with default values
+ init_node($dbh, $tree{update_node_pk}, $tree{update_an_fk});
}
elsif (exists($tree{delete_node_pk}))
***************
*** 312,325 ****
}
push(@nstack, $tree{delete_node_pk});
! delete($tree{delete_node_pk}); # delete the extra hash element created as a delete carrier
! my $lc = 0;
while($#nstack >= 0)
{
$s_node = pop(@nstack);
! $sth->execute($s_node); # delete the record
delete($tree{$s_node}); # delete the element
foreach my $node (keys(%tree))
{
! if ($node !~ m/\d+/)
{
next; # only do numeric nodes. We now have $tree{"root"}, $tree{delete}, etc.
--- 346,366 ----
}
push(@nstack, $tree{delete_node_pk});
! # delete the extra hash element created as a delete carrier
! delete($tree{delete_node_pk});
! my $lc = 0; # loop counter
! my $ds_sth = getq("delete_spv", $dbh);
! my $du_sth = getq("delete_upv", $dbh);
while($#nstack >= 0)
{
$s_node = pop(@nstack);
! # delete the record, delete the upv and spv records
! $sth->execute($s_node) || die "Query delete_tree_node execute fails.\n$DBI::errstr\n";
! $ds_sth->execute($s_node) || die "Query delete_upv execute fails.\n$DBI::errstr\n";
! $du_sth->execute($s_node) || die "Query delete_spv execute fails.\n$DBI::errstr\n";
!
delete($tree{$s_node}); # delete the element
foreach my $node (keys(%tree))
{
! if ($node !~ m/^\d+$/)
{
next; # only do numeric nodes. We now have $tree{"root"}, $tree{delete}, etc.
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/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 17 Dec 2002 17:24:23 -0000 1.1.2.3
--- makefile 20 Dec 2002 14:25:36 -0000 1.1.2.4
***************
*** 1,3 ****
! all: pl_files pm_files html_files htaccess_src rw_files ssc_files options
# Dec 17 2002 analysis stuff is in ./analysis
--- 1,3 ----
! all: pl_files an_pl_files pm_files html_files htaccess_src options
# Dec 17 2002 analysis stuff is in ./analysis
***************
*** 11,14 ****
--- 11,26 ----
./config.pl $<
+ #
+ # 2002-12-19
+ # This picks up symlinks too.
+ # Fixed config.pl to ignore symlinks
+ #
+ an_pl_srcs := $(patsubst ./analysis/%.pl,$(DEST)/analysis/%.pl,$(wildcard ./analysis/*.pl))
+ an_pl_files : $(an_pl_srcs)
+ $(DEST)/analysis/%.pl : ./analysis/%.pl
+ ./config.pl $<
+ #show :
+ # @echo $(an_pl_srcs)
+
pm_srcs := $(patsubst %.pm,$(DEST)/%.pm,$(wildcard *.pm))
pm_files: $(pm_srcs)
***************
*** 25,42 ****
# Dec 17 2002 analysis stuff is in ./analysis
- rw_srcs := $(patsubst ./%.rw,$(DEST)/%.rw,$(wildcard *.rw))
- rw_files : $(rw_srcs)
- $(DEST)/%.rw : $(ANA)/%.rw
- cp -f $< $(DEST)
-
- show_srcs :
- @echo $(rw_srcs)
- # @echo $(html_srcs)
-
-
- ssc_srcs := $(patsubst %.ssc,$(DEST)/%.ssc,$(wildcard *.ssc))
- ssc_files : $(ssc_srcs)
- $(DEST)/%.ssc : ./%.ssc
- cp -f $< $(DEST)
--- 37,40 ----
Index: config.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/config.pl,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** config.pl 10 Dec 2002 19:19:20 -0000 1.1.2.4
--- config.pl 20 Dec 2002 14:25:36 -0000 1.1.2.5
***************
*** 74,78 ****
foreach my $file (@ls)
{
! my $all = readfile("$file"); # readfile() is in sessionlib.pl
#
--- 74,92 ----
foreach my $file (@ls)
{
! #
! # 2002-12-19 fixed to only process real files.
! # This is so we'll ignore symlinks.
! #
! my $all;
! if (-f $file)
! {
! # only process real files.
! $all = readfile("$file"); # readfile() is in sessionlib.pl
! }
! else
! {
! print "$file is not a file (probably a symlink). Skipping.\n";
! next;
! }
#
|
Update of /cvsroot/genex/genex-server/CyberT-Demo In directory sc8-pr-cvs1:/tmp/cvs-serv27597/CyberT-Demo Removed Files: .cvsignore AboutBasic_CyberT_Demo.shtml Basic_CyberT_Demo.shtml.in CyberT_Demos.html CyberT_Demos.shtml CyberT_Paired_DataSet yeast64.cybert.demo.txt Log Message: deleted the hated demo dirs for CyberT and rcluster --- .cvsignore DELETED --- --- AboutBasic_CyberT_Demo.shtml DELETED --- --- Basic_CyberT_Demo.shtml.in DELETED --- --- CyberT_Demos.html DELETED --- --- CyberT_Demos.shtml DELETED --- --- CyberT_Paired_DataSet DELETED --- --- yeast64.cybert.demo.txt DELETED --- |
Update of /cvsroot/genex/genex-server/RCluster-Demo In directory sc8-pr-cvs1:/tmp/cvs-serv27597/RCluster-Demo Removed Files: .cvsignore AboutRCluster-Demo.html.in RCluster-Demo.html.in RCluster-Demos.html.in yeast64.rclust.demo.txt Log Message: deleted the hated demo dirs for CyberT and rcluster --- .cvsignore DELETED --- --- AboutRCluster-Demo.html.in DELETED --- --- RCluster-Demo.html.in DELETED --- --- RCluster-Demos.html.in DELETED --- --- yeast64.rclust.demo.txt DELETED --- |
|
From: <man...@us...> - 2002-12-20 05:35:07
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv24379
Modified Files:
ChangeLog GeneSpring.notes GenexUtils.pm INSTALL MANIFEST.in
Makefile
Log Message:
various doc mods to top-level docs - see ChangeLog for details
Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.116
retrieving revision 1.117
diff -C2 -d -r1.116 -r1.117
*** ChangeLog 26 Nov 2002 17:51:54 -0000 1.116
--- ChangeLog 20 Dec 2002 05:35:04 -0000 1.117
***************
*** 1,2 ****
--- 1,29 ----
+ 2002-11-19 Harry Mangalam <hj...@ta...>
+ * more mods to INSTALL doc to bring it up to date (added more pkgs to
+ the apt-get list, noted inconsistencies in the pkgs.
+ * change of Install and Configure files to allow installation of the
+ analysis apps separately. (*have* to install the GeneX DB package and
+ the apps separately tho).
+ * more changes to the CyberT analysis package to sync the Web and lib versions
+ and make the R xgobi package work with GeneX. still some details broke tho.
+
+ * Added app files to the MANIFEST system and had all the data-loading scripts
+ copied to the /usr/local/genex/ (aka $LOCAL_LIB) directory so they could all
+ be called with the same prefix.
+ * small textual changes to GenexUtils.pm
+ * small changes to Makefile to add apps capability.
+ * sync'ed AI_Configure to Configure
+ * sync'ed AI_Install to Install
+ - removed invalid (and mostly commented out) explicit file copies
+ - removed Cyber-T Demo installation stuff - all the demo stuff should be
+ completely removed
+ - removed the mergem installation stuff - outdated, replaced by scut
+ if we want to add it back in
+ - removed rcluster demo installation stuff - should also be removed
+ from the CVS tree.
+ - removed the 'include' dir installation - could also be removed from cvs
+ - re-org'ed the installation flow of apps to mesh with JES's file
+ installation mods.
+
2002-11-26 Jason E. Stewart <ja...@op...>
***************
*** 125,128 ****
--- 152,156 ----
how to configure the Windows and *nix clients to access the server using
ODBC and JDBC.
+ * submitted KAS's new permcluster.
Index: GeneSpring.notes
===================================================================
RCS file: /cvsroot/genex/genex-server/GeneSpring.notes,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** GeneSpring.notes 18 Nov 2002 04:29:14 -0000 1.1
--- GeneSpring.notes 20 Dec 2002 05:35:04 -0000 1.2
***************
*** 1,3 ****
! GeneSpring Notes:
For both Windows and Linux/Unix GeneSpring clients to connect to the GeneX DB, the GeneX/Postgresql server will need the JDBC driver installed. This can be installed and configured automatically for Debian systems by installing the
--- 1,5 ----
! GeneSpring Notes:
!
! These notes refer only to GeneSpring 5, which is the only version I have access to.
For both Windows and Linux/Unix GeneSpring clients to connect to the GeneX DB, the GeneX/Postgresql server will need the JDBC driver installed. This can be installed and configured automatically for Debian systems by installing the
***************
*** 5,16 ****
For Windows, to connect GeneSpring to GeneX, you will in addition need:
! - the ODBC driver installed and configured on Windows
! - the JDBC driver installed and configured on Windows
! - the ODBC postgresql driver installed on the GeneX server. This can be automatically installed and configured by installing the debian 'libiodbc2' 'unixodbc', and 'odbc-postgresql' pkgs.
For Linux/Unix, to connect GeneSpring to GeneX, you will need:
! - the JDBC driver installed so that your Java VM can find and use it (typically, it is installed in the <java_root>/jre/lib/ext/ directory.
! - GeneSpring configured to use the JDBC driver appropriately. This is done by specifying it in GeneSpring -> Edit -> Preferences -> Database -> JDBC driver : [org.postgresql.Driver]. Alternatively, you can enter it direclty in the GeneSpring preference file: <genespring_home>/data/GeneSpring\ Preferences
! - additionally, you should use the suppplied JVM or Sun's JRE 1.4.1_01.
! - you dhould upgrade to the latest GeneSpring jar by using the upgrade utility within GeneSpring or downloading the latest demo which has the identical new jar. ja...@si... was very helpful in assisting with some of this debugging.
--- 7,117 ----
For Windows, to connect GeneSpring to GeneX, you will in addition need:
!
! - the ODBC driver installed and configured on Windows.
! You can find the PostgreSQL ODBC driver at:
! http://odbc.postgresql.org/ftpsite/odbc/versions/full/
! Once unzipped, it is a standard Windows installer and will install the psqlodbc driver in the correct place. Once that's done, you have to add the appropriate ODBC data source using the "Data SOurces" control panel (in the Administrative Tools on Win2K (dunno on other versions). Click the 'Add' button, select the PostgreSQL driver, and fill out the rest of the Data Source data. The GeneX database will be available to all ODBC-capable applications under the name you chose to label it. Verify with Excel (Data -> Get External Data -> New Database Query -> select your Genex Data Source from the list.
!
! - the JDBC driver installed and configured on Windows; I believe that GeneSpring on Windows uses the JDBC-ODBC bridge, which is a part of the JDK (I believe - I'm using GeneSpring on Linux, which uses the JDBC layer directly).
!
! - the ODBC postgresql driver installed on the GeneX server. This can be automatically installed and configured by installing the debian 'libiodbc2' 'unixodbc', and 'odbc-postgresql' pkgs. I believe that only the last is needed but I installed all 3 & they don't conflict either during the installation process or in usage.
For Linux/Unix, to connect GeneSpring to GeneX, you will need:
!
! - the JDBC driver installed so that your Java VM can find and use it (typically, the jar file is installed in the <java_root>/jre/lib/ext/ directory. It is available directly from Postgres:
! http://jdbc.postgresql.org/download.html (as of this writing, the correct version is: http://jdbc.postgresql.org/download/pgjdbc2.jar
!
! - GeneSpring configured to use the JDBC driver appropriately. This is done by specifying it in GeneSpring -> Edit -> Preferences -> Database -> JDBC driver : [org.postgresql.Driver]. Alternatively, you can enter it directly in the GeneSpring preference file: <genespring_home>/data/GeneSpring\ Preferences
!
! - you should DEFINITELY use GeneSpring's suppplied JVM or Sun's JRE 1.4.1_01. GeneSpring will not run acceptably on IBM's JDK. (Yes, one JDK per application - isn't portability a great thing?)
!
! - you should also upgrade to the latest GeneSpring jar by using the upgrade utility within GeneSpring or downloading the latest demo which has the identical new jar. ja...@si... was very helpful in assisting with some of this debugging.
!
+ The remaining process is very data-dependent. You have to create or modify a GeneSpring database connection file to select the correct data from the database for GeneSpring to present to the user. GeneSpring offers 2 such '.database' config files for GATC databases running on Oracle and MS SQL server (supplied in <genespring_root>/GeneSpring/data/Databases), which are largely useless for GeneX. However, you can get an idea of what they're trying to pull from the database and thus figure out (with difficulty) what they're trying to retrieve.
+
+ The GeneSpring - GeneX mapping will be different for each data format that you want to access - GenePix will probabaly be different from QuantArray will be different
+
+ Joe Roden from JPL has also supplied some further notes that I include here unedited:
+ 8< - - - - - - 8< - - - - - - 8< - - - - - - 8< - - - - - - 8< - - - - - - 8<
+ Recall that I did this once with GeneX 1.? and
+ GeneSpring 4.1 At the time I simply created a view
+ of the data inside GeneX and pointed GeneSpring to it.
+ The hardest part was getting the exact syntax for the
+ GeneSpring database description, thereby setting up
+ GeneSpring to point to postgres & GeneX. I have been
+ trying dig up my (minimal) notes on this to share...
+ here's what I've come up with:
+
+ This is the file you have to create to tell GeneSpring about
+ your database. Sort of a mapping from your DB schema into
+ GeneSpring concepts.
+
+ The file is:
+
+ /usr/software/genespring/4.1/GeneSpring/data/Databases/GeneX.database
+
+ The file's contents are shown here between the brackets:
+
+ ----- begin included file -----
+
+ Name : Genex DB
+ UserName : roden
+ Password :
+ Link : jdbc:postgresql:genex
+ ExperimentTableName : jcr_gene_expression_table
+ ExperimentTableIndex : smp_pk
+ QuoteExperimentID : false
+
+ SpecifyTableHeadings : true
+ GeneColumn : usf_name
+ IntensityColumn : spot_value
+ SQLgetExperimentIDsAndIndices : select smp_pk, smp_pk, strain, cell_line, age,
+ age_units, genetic_status_comment from sample
+ debug : true
+
+ NormalizeEachGene : true
+ NormaliseNoControl : true
+ SpecifyNormalizations : true
+
+ SpecifyDisplayOptions : true
+ SignalLow : 0
+ SignalMedium : 0
+ SignalHigh : 0
+
+ ----- end included file -----
+
+ Also I had created a view in GeneX that put the data in a
+ form that GeneSpring could work with. Here's that SQL:
+
+ CREATE VIEW jcr_gene_expression_table AS
+ SELECT smp.smp_pk, usf.usf_name, ams.spot_value
+ FROM am_spots ams
+ JOIN usersequencefeature usf
+ ON usf_fk = usf_pk
+ JOIN arraymeasurement am
+ ON am_fk = am_pk
+ JOIN sample smp
+ ON am.smp_fk = smp_pk
+
+ Lastly, I recall I needed to point GeneSpring to the JDBC
+ driver... my notes say I used /usr/share/java/postgresql.jar
+ However, which one is appropriate depends on the version of
+ postgres, and of Java. They're all available on the postgres
+ web site.
+
+ Recall we had efficiency problems when loading an experiment
+ to GeneSpring. We never tried creating an index on the GeneX
+ side... that'd be the first thing to try.
+
+ If you need more info, I recall iterating once with a Silicon
+ Genetics tech support person. If I can find that email exchange
+ we might have more details.
+
+ Don't forget to look at the latest GeneSpring docs and examples
+ (and web site?) as your first source of info. I don't expect
+ that their interface approach has changed much, but of course
+ the GeneX view would be completely different today.
+
+ Joe
+ 8< - - - - - - 8< - - - - - - 8< - - - - - - 8< - - - - - - 8< - - - - - - 8<
Index: GenexUtils.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/GenexUtils.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** GenexUtils.pm 22 Nov 2002 23:58:38 -0000 1.2
--- GenexUtils.pm 20 Dec 2002 05:35:04 -0000 1.3
***************
*** 184,191 ****
$command
! If this is *not* what you want (like if this is your root dir, '/')
then it is likely that something got entered incorrectly during the
! configuration process, so hit control-C (^C) now and re-run 'make
! configure'.
EOW
--- 184,193 ----
$command
! If this is *not* what you want (ie: if this is your root dir, '/')
then it is likely that something got entered incorrectly during the
! configuration process, so hit control-C (^C) now and re-run
! 'make configure' or 'make configure_apps'.
!
! If this is OK, then hit [Enter] to continue.
EOW
Index: INSTALL
===================================================================
RCS file: /cvsroot/genex/genex-server/INSTALL,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** INSTALL 18 Nov 2002 04:29:14 -0000 1.24
--- INSTALL 20 Dec 2002 05:35:04 -0000 1.25
***************
*** 56,73 ****
deb http://woldlab.caltech.edu/software woldlab main
! the following line (as root) will install and configure all the pieces noted
! apt-get install postgresql postgresql-dev libdbd-pg-perl expat \
! perlSGML libxeres17 libxeres17-dev libxml-xerces-perl libxaw7-dev \
! apache-dev libapache-mod-perl libdevel-symdump-perl
for genespring/odbc connectivity
! libiodbc2 unixodbc odbc-postgresql
for jdbc (to service direct jdbc calls)
! libpgjava
! for guis:
! pgaccess unixodbc-bin
Required Utilities
--- 56,86 ----
deb http://woldlab.caltech.edu/software woldlab main
! The following command (as root) will install everything you need to support
! GeneX (except the Perl Bio::MAGE package, which hasn't been packaged for
! Debian yet and the DBD::Pg pkg as the Debian woody pkg is too old (req.
! >=1.12):
! apt-get install postgresql postgresql-dev postgresql-client \
! postgresql-doc libpgtcl libpgperl expat perlSGML libxerces17 \
! libxerces17-dev libxml-xerces-perl libxaw7-dev apache-dev \
! libapache-mod-perl libdevel-symdump-perl odbc-postgresql libpgjava \
! pgaccess unixodbc-bin xgobi vncserver perlSGML libcgi-pm-perl \
! libterm-readkey-perl libapache-session-perl libapache-request-perl \
! libdigest-md5-perl libdbd-pg-perl libdbi-perl libhtml-mason-perl \
! libtie-ixhash-perl libclass-objecttemplate-perl \
! libclass-objecttemplate-db-perl libxerces17 libxerces17-dev \
! libxml-xerces-perl r-base-core r-recommended r-base r-base-dev \
! r-base-html
for genespring/odbc connectivity
! odbc-postgresql (definitely needed)
! libiodbc2 unixodbc (possibly needed_
for jdbc (to service direct jdbc calls)
! libpgjava (for genespring on linux)
! for GUIs tha might help understand how GeneX is laid out:
! pgaccess unixodbc-bin
!
Required Utilities
***************
*** 101,104 ****
--- 114,119 ----
install genex without it, but you will not be able to use many
of the analysis tools
+
+ Debian pkgs are called:
* g77 GNU Fortran compiler (req. to compile R from source)
***************
*** 114,118 ****
of the DTDs - if you didn't use the apt-get command above)
* xcluster => http://genome-www.stanford.edu/~sherlock/cluster.html
! * jythonc => http://www.jython.org (only to recompile the jar file
from supplied python - usually only needed by especially
masochistic developers)
--- 129,133 ----
of the DTDs - if you didn't use the apt-get command above)
* xcluster => http://genome-www.stanford.edu/~sherlock/cluster.html
! * jythonc => http://www.jython.org (only to recompile the jar file
from supplied python - usually only needed by especially
masochistic developers)
***************
*** 158,168 ****
a standalone system and then configure for TCP access. The additional work
is trivial. You need to change the 'pg_hba.conf' file to include a line
! like th eone below (changing the params for your case.
# TYPE DATABASE IP_ADDRESS MASK AUTH_TYPE AUTH_ARGUMENT
host genex 192.168.1.0 255.255.255.0 password
! which allows machines from a private net (192.168.1.0, masked 255.255.255.0)
! to access only the genex DB if they are known postgres users and supply the
correct postgresql password. There are more (and less) stringent
authentication schemes described in the comments in 'pg_hba.conf'.
--- 173,190 ----
a standalone system and then configure for TCP access. The additional work
is trivial. You need to change the 'pg_hba.conf' file to include a line
! like the one below (changing the params for your case).
+ # (NET_ADRESS)
# TYPE DATABASE IP_ADDRESS MASK AUTH_TYPE AUTH_ARGUMENT
host genex 192.168.1.0 255.255.255.0 password
! These two fields specify to which client machines a host or hostssl
! record applies, based on their IP address. The precise logic is that
! (actual-IP-address xor IP-address-field) and IP-mask-field
! must be zero for the record to match.
!
! In the above example, the line allows machines from a private net (192.168.1.0, masked 255.255.255.0)
! to access only the genex DB and only if they are known postgres users and
! supply the
correct postgresql password. There are more (and less) stringent
authentication schemes described in the comments in 'pg_hba.conf'.
***************
*** 198,206 ****
-- Modules with known problems (see below) --
! DBD::Pg - for the Postgres installation (see Known Problems below)
! XML::Xerces - used by the GeneXML utils (see Known Problems below)
! Bio::MAGE - used for importing and exporting MAGE-ML; may have to
! download it manually if CPAN refuses to acknowledge its
! existance... try:
http://search.cpan.org/CPAN/authors/id/J/JA/JASONS/Bio-MAGE-2002-09-02_0.tar.gz
--- 220,230 ----
-- Modules with known problems (see below) --
! DBD::Pg - for the Postgres installation - you only need to install
! this manually if you did not install 'libdbd-pg-perl' via
! the Debian package method above.
! XML::Xerces - used by the GeneXML utils.
! Bio::MAGE - used for importing and exporting MAGE-ML; may have to
! download it manually if CPAN refuses to acknowledge its
! existance... try:
http://search.cpan.org/CPAN/authors/id/J/JA/JASONS/Bio-MAGE-2002-09-02_0.tar.gz
***************
*** 208,212 ****
--------------------------------------------------
! * DBD::Pg: Before running CPAN, you must set two environment
variables (POSTGRES_INCLUDE and POSTGRES_LIB), or the build will
fail. When running 'install DBD::Pg', make test will fail if
--- 232,237 ----
--------------------------------------------------
! * DBD::Pg: (Again, only if installing manually)
! Before running CPAN, you must set two environment
variables (POSTGRES_INCLUDE and POSTGRES_LIB), or the build will
fail. When running 'install DBD::Pg', make test will fail if
***************
*** 214,222 ****
'force install DBD::Pg'.
For the RedHat RPMs mentioned above, Ron Ophir mentioned that
! POSTGRES_LIB = /usr/lib
! but setting POSTGRES_INCLUDE wasn't required (YMMV)
! * XML::Xerces: you cannot ask CPAN to install this module. Instead
! do the following:
1) download version 1.7 of the Xerces-C C++ library from Apache:
--- 239,247 ----
'force install DBD::Pg'.
For the RedHat RPMs mentioned above, Ron Ophir mentioned that
! POSTGRES_LIB = /usr/lib
! was required but setting POSTGRES_INCLUDE wasn't required (YMMV)
! * XML::Xerces: you cannot ask CPAN to install this module. If you cannot
! use Diane's debs (see above), do the following:
1) download version 1.7 of the Xerces-C C++ library from Apache:
***************
*** 254,258 ****
* genex database owner = genex (password=yeastecol1),
* user with SELECT only access = readonly (password=readonly).
! These are configurable during the installation, so if you want the
user names and passwords to be different, you're free to set them to
whatever you want, provided you have the two accounts.
--- 279,283 ----
* genex database owner = genex (password=yeastecol1),
* user with SELECT only access = readonly (password=readonly).
! NB: These ARE CONFIGURABLE DURING THE INSTALLATION, so if you want the
user names and passwords to be different, you're free to set them to
whatever you want, provided you have the two accounts.
***************
*** 392,398 ****
% cd GeneX-Server-X.Y.Z/
! % make configure
! % make install
Once having installed the parts above, cd to the directory formed by
--- 417,447 ----
% cd GeneX-Server-X.Y.Z/
! To install the database server, type:
!
! - 'make configure'
! (as normal user and anser all the questions, then as root:
!
! - 'make install'
! (answer a few more questions, and you should finish with a
! more or less complete GeneX installation)
!
! - finish by adding the required extra line to your apache config
! and restarting apache.
!
! To install the analysis apps, type:
! - 'make configure_apps'
! (as normal user and anser all the questions, then as root:
!
! - 'make install_apps'
! (answer a few more questions, and you should finish with a
! more or less complete installation of CyberT, Xcluster (minus
! the app itself, which has to be licensed direct form Stanford),
! and rcluster. Depending on what development is ongoing, bit of
! them may not work as expected.
!
! - finish by adding the required extra line to your apache config
! and restarting apache.
!
Once having installed the parts above, cd to the directory formed by
***************
*** 514,523 ****
software with us).
! We have a Bugzilla bug-tracking site set up to monitor bugs, but it's
! admittedly difficult for a beginner to use. While you're welcome to
! use it, we'd rather hear from you in ANY form rather than NOT hear
! from you in an official Bugzilla log, so if you come across a bug, or
! even something that you think should be done differently, please just
! send us an email at: gen...@li....
Thanks for reading through this to this point.
--- 563,568 ----
software with us).
! If you come across a bug, or even something that you think should be done
! differently, please just send us an email at: gen...@li....
Thanks for reading through this to this point.
Index: MANIFEST.in
===================================================================
RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** MANIFEST.in 25 Nov 2002 21:48:47 -0000 1.5
--- MANIFEST.in 20 Dec 2002 05:35:04 -0000 1.6
***************
*** 1,3 ****
--- 1,30 ----
$FILES = {
+ 'CyberT-dist/index.html' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/CyberT_C+E_DataSet' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/CyberT_Paired_DataSet' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/hdarray' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/hdarray_3.66' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/runa.c' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/runa.so' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/README' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/CTHelp.html' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/xgobi.R' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/xgobi_1.2-7.tar.gz' => '%%HTMLDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/CyberT-7.1.form.pl' => '%%CGIDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/CyberTDB-7.1.pl' => '%%CGIDIR%%/%%CYBERT_DIR%%',
+ 'CyberT-dist/cyberfilter.pl' => '%%GENEX_BIN_DIR%%',
+ 'CyberT-dist/munge4R.pl' => '%%GENEX_BIN_DIR%%',
+ 'CyberT-dist/genex_reaper.pl' => '%%GENEX_BIN_DIR%%',
+ 'CyberT-dist/xgobi.R' => '%%LOCAL_LIB%%/R/library/xgobi/R/xgobi',
+ 'CyberT-dist/hdarray' => '%%LOCAL_LIB%%/R/library/hdarray/R',
+ 'CyberT-dist/runa.so' => '%%LOCAL_LIB%%/R/library/hdarray/R',
+ 'CyberT-dist/hdarray_DESCRIPTION' => '%%LOCAL_LIB%%/R/library/hdarray/DESCRIPTION',
+
+ 'xcluster/xcluster.help.html' => '%%HTMLDIR%%/%%XCLUSTER_DIR%%',
+ 'xcluster/xcluster.notes' => '%%HTMLDIR%%/%%XCLUSTER_DIR%%',
+ 'xcluster/xcluster.test.dataset' => '%%HTMLDIR%%/%%XCLUSTER_DIR%%',
+ 'xcluster/xcluster_handler.pl' => '%%CGIDIR%%/%%XCLUSTER_DIR%%',
+ 'xcluster/xcluster.form.pl' => '%%CGIDIR%%/%%XCLUSTER_DIR%%',
+
'apache/genex-2.conf' => '%%APACHE_CONF_DIR%%',
***************
*** 66,70 ****
'Genex/scripts/xml2form.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/xml2sql.pl' => '%%GENEX_BIN_DIR%%',
!
'DB/controlled_vocab/ALS_SpotType.xml' => '%%GENEX_VOCAB_DIR%%',
--- 93,99 ----
'Genex/scripts/xml2form.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/xml2sql.pl' => '%%GENEX_BIN_DIR%%',
!
! 'DB/scripts/fix-array.pl' => '%%GENEX_BIN_DIR%%',
! 'DB/scripts/tab2AD.pl' => '%%GENEX_BIN_DIR%%',
'DB/controlled_vocab/ALS_SpotType.xml' => '%%GENEX_VOCAB_DIR%%',
Index: Makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/Makefile,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Makefile 26 Nov 2002 17:51:35 -0000 1.3
--- Makefile 20 Dec 2002 05:35:04 -0000 1.4
***************
*** 11,14 ****
--- 11,18 ----
@${PERL} Configure
+ configure_apps:
+ @echo Using Perl interpreter: ${PERL}
+ @${PERL} AI_Configure --ANALYSES_ONLY
+
build: Bio/Genex/Config.pm
***************
*** 19,22 ****
--- 23,29 ----
./substitute.pl
${PERL} Install --files_only
+
+ install_apps: Bio/Genex/Config.pm
+ ${PERL} AI_Install --ANALYSES_ONLY
Bio/Genex/Config.pm:
|
|
From: <man...@us...> - 2002-12-20 05:16:26
|
Update of /cvsroot/genex/genex-server/CyberT-dist In directory sc8-pr-cvs1:/tmp/cvs-serv20350/CyberT-dist Added Files: hdarray_DESCRIPTION Log Message: added DESCRIPTION for cybert, now needed for R --- NEW FILE: hdarray_DESCRIPTION --- Package: hdarray Version: 3.66 Priority: extra Title: The hdarray microarray analysis library Author: Tony D. Long, Pierre Baldi, Harry Mangalam Maintainer: Tony D. Long (td...@uc...) & Harry Mangalam (hj...@ta...) Description: Significance testing for both Paired & 'Control/Experimental' License: GPL Version 2 or later. Built: R 1.6.1; i686-pc-linux-gnu; Tue Oct 8 13:09:48 PDT 2002 |
|
From: <man...@us...> - 2002-12-20 05:13:45
|
Update of /cvsroot/genex/genex-server/xcluster
In directory sc8-pr-cvs1:/tmp/cvs-serv19516/xcluster
Modified Files:
xcluster.form.pl.in xcluster_handler.pl.in
Log Message:
lots of changes to docs and some apps - check ChangeLogs for 12.19.02
Index: xcluster.form.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/xcluster/xcluster.form.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** xcluster.form.pl.in 8 Jan 2001 22:49:29 -0000 1.2
--- xcluster.form.pl.in 20 Dec 2002 05:13:42 -0000 1.3
***************
*** 3,7 ****
# Copyright 2000, National Center for Genome Resources
# All Rights Reserved
! # Coding: Harry Mangalam (hj...@nc... || man...@ho...)
#
--- 3,7 ----
# Copyright 2000, National Center for Genome Resources
# All Rights Reserved
! # Coding: Harry Mangalam (hj...@ta...)
#
Index: xcluster_handler.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/xcluster/xcluster_handler.pl.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** xcluster_handler.pl.in 11 Oct 2002 02:19:55 -0000 1.4
--- xcluster_handler.pl.in 20 Dec 2002 05:13:42 -0000 1.5
***************
*** 3,7 ****
# Copyright 2000, National Center for Genome Resources
# All Rights Reserved
! # Coding: Harry Mangalam (hj...@nc... || man...@ho...)
#
--- 3,7 ----
# Copyright 2000, National Center for Genome Resources
# All Rights Reserved
! # Coding: Harry Mangalam (hj...@ta...)
#
***************
*** 282,286 ****
</pre>
back to the GeneX developers by :
! <a href="mailto:mangalam\@home.com?subject=commandline that coredumps xcluster">
clicking this mailto URL</a> and pasting the commandline above into the message.
<small>(yes, I could have done this automatically, but that wouldn't have been polite) </small>.
--- 282,286 ----
</pre>
back to the GeneX developers by :
! <a href="mailto:hjm\@tacgi.com?subject=commandline that coredumps xcluster">
clicking this mailto URL</a> and pasting the commandline above into the message.
<small>(yes, I could have done this automatically, but that wouldn't have been polite) </small>.
|
|
From: <man...@us...> - 2002-12-20 05:13:45
|
Update of /cvsroot/genex/genex-server/CyberT-dist
In directory sc8-pr-cvs1:/tmp/cvs-serv19516/CyberT-dist
Modified Files:
.cvsignore CyberT-7.1.form.pl.in CyberTDB-7.1.pl.in
index.html.in
Log Message:
lots of changes to docs and some apps - check ChangeLogs for 12.19.02
Index: .cvsignore
===================================================================
RCS file: /cvsroot/genex/genex-server/CyberT-dist/.cvsignore,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** .cvsignore 1 May 2001 22:46:20 -0000 1.7
--- .cvsignore 20 Dec 2002 05:13:42 -0000 1.8
***************
*** 14,15 ****
--- 14,18 ----
CyberT-7.0.form.pl
cyberfilter.pl
+ xgobi.R
+ index.html
+ hdarray_3.66
Index: CyberT-7.1.form.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/CyberT-dist/CyberT-7.1.form.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** CyberT-7.1.form.pl.in 14 Nov 2002 04:19:28 -0000 1.1
--- CyberT-7.1.form.pl.in 20 Dec 2002 05:13:42 -0000 1.2
***************
*** 3,9 ****
# Copyright 2000, National Center for Genome Resources
# All Rights Reserved
! # Coding: Harry Mangalam (hj...@nc... || man...@ho...)
! # file: CyberT-7.01.form.pl - consolidation of C+E & Paired form
# see ChangeLog for details
--- 3,9 ----
# Copyright 2000, National Center for Genome Resources
# All Rights Reserved
! # Coding: Harry Mangalam (hj...@ta...)
! # file: CyberT-7.1.form.pl - consolidation of C+E & Paired form
# see ChangeLog for details
***************
*** 66,70 ****
<tr align=center>
<td><a href="$HTML_ROOT_URL/$CYBERT_DIR/CTHelp.html"><b>General Help</b></a></td>
! <td><a href="mailto:mangalam\@home.com?subject=CyberT Registration"><b><i>Please Click to Register</i></b></a><br>
(to count users for grant appl'ns and for bug notifications)
</td>
--- 66,70 ----
<tr align=center>
<td><a href="$HTML_ROOT_URL/$CYBERT_DIR/CTHelp.html"><b>General Help</b></a></td>
! <td><a href="mailto:hjm\@tacgi.com?subject=CyberT Registration"><b><i>Please Click to Register</i></b></a><br>
(to count users for grant appl'ns and for bug notifications)
</td>
Index: CyberTDB-7.1.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/CyberT-dist/CyberTDB-7.1.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** CyberTDB-7.1.pl.in 14 Nov 2002 04:19:28 -0000 1.1
--- CyberTDB-7.1.pl.in 20 Dec 2002 05:13:42 -0000 1.2
***************
*** 5,9 ****
# Coding: Harry Mangalam (hj...@ta...)
#
! # file: CyberTDB-7.03.pl - includes functionality for both C+E and Paired
# This script handles the standard "Control + Experimental" type of
--- 5,9 ----
# Coding: Harry Mangalam (hj...@ta...)
#
! # file: CyberTDB-7.1.pl - includes functionality for both C+E and Paired
# This script handles the standard "Control + Experimental" type of
***************
*** 372,380 ****
}
}
! $tempstring .= "$val\t";
}
- if (defined $paired_expr_col) { #if we need to do Bayesian for the PAIRED, need this additional col.
- $tempstring .= "$L[$paired_expr_col]\t";
- }
}
chop $tempstring; # kill the last tab and ..
--- 372,380 ----
}
}
! $tempstring .= "$val\t";
! }
! if (defined $paired_expr_col) { #if we need to do Bayesian for the PAIRED, need this additional col.
! $tempstring .= "$L[$paired_expr_col]\t";
}
}
chop $tempstring; # kill the last tab and ..
***************
*** 392,396 ****
}
! if ($DataType eq 'CE') { # CE /P split
# 2nd the Control columns
for ($r = 0; $r < $N_Con_Cols; $r++) {
--- 392,396 ----
}
! if ($DataType eq 'CE') { # CE /P split
# 2nd the Control columns
for ($r = 0; $r < $N_Con_Cols; $r++) {
***************
*** 438,443 ****
$FinalColumn = $N_Lab_Cols + $N_Ratio_Cols; # (=5)
if (defined $paired_expr_col) { # calc the col -> pierre.paired & bump up $FinalColumn
! $FinalColumn++; # if the PEV is being used, then it adds a column to the setup
! $pec4R = $FinalColumn;
}
}
--- 438,443 ----
$FinalColumn = $N_Lab_Cols + $N_Ratio_Cols; # (=5)
if (defined $paired_expr_col) { # calc the col -> pierre.paired & bump up $FinalColumn
! $FinalColumn++; # if the PEV is being used, then it adds a column to the setup
! $pec4R = $FinalColumn;
}
}
***************
*** 487,497 ****
# these columns headers need to be inserted in the middle bc pierre() adds extra columns
# By = Bayesian
- $header .= "\"#obs\"\t\"Mn\"\t\"SD\"\t\"RunAvgSD\"\t\"t\"\t\"BySD\"\t\"By-t\"\t\"p\"\t\"By-p\"\n";
- $keycol = $N_Lab_Cols + $N_Ratio_Cols + $keycol + 3; # w/ Bayes, reg_p is 3 cols over.
- } else {
$header .= "\"EstExpr\"\t\"#obs\"\t\"Mn\"\t\"SD\"\t\"RunAvgSD\"\t\"t\"\t\"BySD\"\t\"By-t\"\t\"p\"\t\"By-p\"\n";
$keycol = $N_Lab_Cols + $N_Ratio_Cols + $keycol + 5; # w/ Bayes, sorting on Bayes_p - 5 cols over.
}
! }
# R inserts a stupid label field that has to be considered, hence this hack
--- 487,499 ----
# these columns headers need to be inserted in the middle bc pierre() adds extra columns
# By = Bayesian
$header .= "\"EstExpr\"\t\"#obs\"\t\"Mn\"\t\"SD\"\t\"RunAvgSD\"\t\"t\"\t\"BySD\"\t\"By-t\"\t\"p\"\t\"By-p\"\n";
$keycol = $N_Lab_Cols + $N_Ratio_Cols + $keycol + 5; # w/ Bayes, sorting on Bayes_p - 5 cols over.
+ # print "<P>PAIRED: with BAYES<br><B>key col = $keycol</B><p>\n";
+ } else {
+ $header .= "\"#obs\"\t\"Mn\"\t\"SD\"\t\"reg_t\"\t\"reg_p\"\n";
+ $keycol = $N_Lab_Cols + $N_Ratio_Cols + $keycol; # wo/ Bayes
+ print "<P>PAIRED: without BAYES<br><B>key col = $keycol</B><p>\n";
}
! }
# R inserts a stupid label field that has to be considered, hence this hack
***************
*** 539,543 ****
print CMD "system(\"$GNUTAIL +2 $sortfile | $GNUSORT -k $KC -g | $MUNGE4R --num=$xgobi --keycol=$keycol --startcol=1 >> $xginput\")\n";
print CMD "xg <- read.table(\"$xginput\",header=TRUE, sep=\"\\t\")\n";
! print CMD "library(xgobi)\n";
print CMD "xgobi(xg,display=\"$DISPLAY\",keep=TRUE,permfile=\"$dirname/xgobidata\")\n"; # h is the dataframe for allgenes;
}
--- 541,545 ----
print CMD "system(\"$GNUTAIL +2 $sortfile | $GNUSORT -k $KC -g | $MUNGE4R --num=$xgobi --keycol=$keycol --startcol=1 >> $xginput\")\n";
print CMD "xg <- read.table(\"$xginput\",header=TRUE, sep=\"\\t\")\n";
! print CMD "library(xgobi, lib.loc = '%%LOCAL_LIB%%/R/library')\n";
print CMD "xgobi(xg,display=\"$DISPLAY\",keep=TRUE,permfile=\"$dirname/xgobidata\")\n"; # h is the dataframe for allgenes;
}
Index: index.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/CyberT-dist/index.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** index.html.in 14 Nov 2002 04:30:34 -0000 1.1
--- index.html.in 20 Dec 2002 05:13:42 -0000 1.2
***************
*** 37,40 ****
--- 37,46 ----
<HR noshade size=2>
+ <i>Related</i><br>
+ <A HREF="%%CGI_ROOT_URL%%/%%XCLUSTER_DIR%%/xcluster.form.pl">
+ Go to the <b>xcluster</b> analysis page</A>,
+ <BR> if you have a data set that is ready for clustering.
+ <HR noshade size=2>
+
<A HREF="CTHelp.html">Browse thru the Help Page</A> (a concatenation of all the various help sections).
|
|
From: <td...@us...> - 2002-12-19 21:08:36
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv20632
Modified Files:
Tag: Rel-1_0_1-branch
runtree.pl
Log Message:
Fixed faulty comment
Index: runtree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/runtree.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
*** runtree.pl 19 Dec 2002 21:04:39 -0000 1.1.2.7
--- runtree.pl 19 Dec 2002 21:08:32 -0000 1.1.2.8
***************
*** 12,16 ****
=head1 DESCRIPTION
!
=cut
--- 12,21 ----
=head1 DESCRIPTION
!
! This script is intended for use as part of the genex system. It
! will select a tree structure from the database and initiate
! running of each tree node.
!
! Log files are created for each node in the users directory.
=cut
***************
*** 87,91 ****
print LOG "\n Running tree: $name owner: $treeOwner\n";
! # processTree($dbh, $tree_pk, LOG);
close(LOG);
--- 92,96 ----
print LOG "\n Running tree: $name owner: $treeOwner\n";
! processTree($dbh, $tree_pk, LOG);
close(LOG);
|
|
From: <td...@us...> - 2002-12-19 21:04:43
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv18291
Modified Files:
Tag: Rel-1_0_1-branch
runtree.pl
Log Message:
Changed to accept pk or name
Index: runtree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/runtree.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
*** runtree.pl 18 Dec 2002 03:32:13 -0000 1.1.2.6
--- runtree.pl 19 Dec 2002 21:04:39 -0000 1.1.2.7
***************
*** 2,22 ****
#TODO - change to accomodate version number as part of name
- # use strict;
! # =head1 NAME
! # runtree - initiates execution of an analysis tree stored in the db
! # =head1 SYNOPSIS
! # ./runtree.pl --treeName <tree_name> --owner <owner>
! # =head1 DESCRIPTION
! # =cut
! # use strict;
! use DBI;
use Getopt::Long 2.13;
--- 2,21 ----
#TODO - change to accomodate version number as part of name
! =head1 NAME
! runtree - initiates execution of an analysis tree stored in the db
! =head1 SYNOPSIS
! ./runtree.pl --tree <tree pk or tree name> --owner <owner>
! =head1 DESCRIPTION
! =cut
! use strict;
! use DBI;
use Getopt::Long 2.13;
***************
*** 25,29 ****
#command line options
my $debug ='';
! my $treeName ='';
my $owner='';
--- 24,28 ----
#command line options
my $debug ='';
! my $tree = '';
my $owner='';
***************
*** 33,42 ****
getOptions();
! write_log("running $treeName, $owner");
! runChain($treeName, $owner);
}
sub runChain
{
! my ($treeName, $treeOwner) = @_;
my $dbh = new_connection();
--- 32,42 ----
getOptions();
! write_log("running $tree, $owner");
! runChain($tree, $owner);
}
+
sub runChain
{
! my ($tree, $treeOwner) = @_;
my $dbh = new_connection();
***************
*** 44,49 ****
# TODO - how do we check owner stuff - remember to make unnecessary
! my $stm=
! "select * from tree where tree_name = '$treeName'";
my $sth = $dbh->prepare($stm);
$sth->execute();
--- 44,56 ----
# TODO - how do we check owner stuff - remember to make unnecessary
! my $stm;
! if ($tree =~ /^[0-9]+$/)
! {
! $stm = "select * from tree where tree_pk = '$tree'";
! }
! else
! {
! $stm= "select * from tree where tree_name = '$tree'";
! }
my $sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 54,59 ****
{
$dbh->disconnect;
! write_log("Tree: $treeName doesn't exist in db");
! exit();
}
--- 61,66 ----
{
$dbh->disconnect;
! write_log("Tree: $tree doesn't exist in db");
! exit();
}
***************
*** 61,65 ****
{
write_log("Too many tree records with name $name and owner $owner.\n");
! exit();
}
--- 68,72 ----
{
write_log("Too many tree records with name $name and owner $owner.\n");
! exit();
}
***************
*** 69,73 ****
# $sth->execute;
# my ($logfile) = $sth->fetchrow_array;
! my $logfile = $treeName;
$logfile = lc($logfile);
$logfile =~ s/[^a-z0-9]/_/g;
--- 76,80 ----
# $sth->execute;
# my ($logfile) = $sth->fetchrow_array;
! my $logfile = $name;
$logfile = lc($logfile);
$logfile =~ s/[^a-z0-9]/_/g;
***************
*** 77,96 ****
open(LOG, "> $logfile") || die "Unable to open $logfile: $!\n";
-
- write_log("pt next1");
-
print LOG `date`;
! write_log("pt next2");
!
! print LOG "\n Running tree: $treeName owner: $treeOwner\n";
!
! write_log("pt next3");
!
! processTree($dbh, $tree_pk, LOG);
close(LOG);
my $us_fk = get_us_fk($dbh);
! fi_update($dbh, $us_fk, $us_fk, $logfile, "$treeName log");
# TODO - stat logfile
--- 84,95 ----
open(LOG, "> $logfile") || die "Unable to open $logfile: $!\n";
print LOG `date`;
+ print LOG "\n Running tree: $name owner: $treeOwner\n";
! # processTree($dbh, $tree_pk, LOG);
close(LOG);
my $us_fk = get_us_fk($dbh);
! fi_update($dbh, $us_fk, $us_fk, $logfile, "$name log");
# TODO - stat logfile
***************
*** 390,394 ****
GetOptions(
'owner=s' => \$owner,
! 'treeName=s' => \$treeName,
'help|?' => \$help,
'debug!' => \$debug,
--- 389,393 ----
GetOptions(
'owner=s' => \$owner,
! 'tree=s' => \$tree,
'help|?' => \$help,
'debug!' => \$debug,
***************
*** 396,410 ****
} #have command line args
! if ($treeName eq "")
{
! print "Must specify a treeName to run.\n";
usage();
}
! if ($owner eq "")
! {
! print "Must specify a owner to run.\n";
! usage();
! }
usage() if ($help);
--- 395,409 ----
} #have command line args
! if ($tree eq "")
{
! print "Must specify a tree name or a tree pk to run.\n";
usage();
}
! #if ($owner eq "")
! #{
! # print "Must specify a owner to run.\n";
! # usage();
! #}
usage() if ($help);
***************
*** 415,419 ****
{
print "Usage: \n";
! print " ./runTree --treeName=<treeName> --owner=<owner>\n";
exit;
} #usage
--- 414,418 ----
{
print "Usage: \n";
! print " ./runTree --tree=<tree pk or tree name> --owner=<owner>\n";
exit;
} #usage
|
|
From: <jl...@us...> - 2002-12-18 18:21:03
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv517
Modified Files:
Tag: Rel-1_0_1-branch
admin_email.html
Log Message:
modified file to reflect updated URL title
Index: admin_email.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/admin_email.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
*** admin_email.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- admin_email.html 18 Dec 2002 18:21:00 -0000 1.1.2.2
***************
*** 10,14 ****
The admin will contact you via phone to give you your password.
! Your account is already active. You can now use the "Manage Your Account"
features of GeneX. Please check the contact information.
--- 10,14 ----
The admin will contact you via phone to give you your password.
! Your account is already active. You can now use the "GeneX Login"
features of GeneX. Please check the contact information.
|
|
From: <tw...@us...> - 2002-12-18 18:18:10
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv32098
Modified Files:
Tag: Rel-1_0_1-branch
sessionlib.pl
Log Message:
fixed nextURL email login url
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.19
retrieving revision 1.1.2.20
diff -C2 -d -r1.1.2.19 -r1.1.2.20
*** sessionlib.pl 16 Dec 2002 15:53:16 -0000 1.1.2.19
--- sessionlib.pl 18 Dec 2002 18:18:07 -0000 1.1.2.20
***************
*** 675,678 ****
--- 675,679 ----
my $file_name = $_[3];
my $fi_comments = $_[4];
+ my $fi_pk;
my $sql = "select fi_pk from file_info where file_name='$file_name'";
***************
*** 697,701 ****
if ($sth->rows() >= 1)
{
! (my $fi_pk) = $sth->fetchrow_array();
$sql = "update file_info set fi_comments=trim('$fi_comments'), fi_checksum=? where fi_pk=$fi_pk";
--- 698,702 ----
if ($sth->rows() >= 1)
{
! ($fi_pk) = $sth->fetchrow_array();
$sql = "update file_info set fi_comments=trim('$fi_comments'), fi_checksum=? where fi_pk=$fi_pk";
***************
*** 718,723 ****
$sth = $dbh->prepare($sql);
$sth->execute($file_name, $fi_comments, $md5);
! insert_security($dbh, $us_fk, $gs_fk, 0);
}
}
--- 719,725 ----
$sth = $dbh->prepare($sql);
$sth->execute($file_name, $fi_comments, $md5);
! $fi_pk = insert_security($dbh, $us_fk, $gs_fk, 0);
}
+ return $fi_pk;
}
***************
*** 1210,1213 ****
--- 1212,1219 ----
exit();
}
+ if (!exists($ENV{REMOTE_USER}))
+ {
+ die "Environment variable REMOTE_USER not set.\n";
+ }
my $sql = "select us_pk from usersec where login='$login'";
(my $us_fk) = $dbh->selectrow_array($sql) || die "sql: $sql\n$DBI::errstr\n";
***************
*** 1507,1511 ****
%opts = read_optionsdotreminders();
! $info{nextURL} = "http://$opts{WWWHOST}/webtools/account.pl";
$info{fromMail} = "nobody\@$opts{WWWHOST}";
$info{ccMail} = $opts{CONTACT_EMAIL};
--- 1513,1517 ----
%opts = read_optionsdotreminders();
! $info{nextURL} = "http://$opts{WWWHOST}/";
$info{fromMail} = "nobody\@$opts{WWWHOST}";
$info{ccMail} = $opts{CONTACT_EMAIL};
|
|
From: <tw...@us...> - 2002-12-18 15:05:41
|
Update of /cvsroot/genex/genex-server/site
In directory sc8-pr-cvs1:/tmp/cvs-serv21729
Modified Files:
Tag: Rel-1_0_1-branch
index.html
Log Message:
fixes
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/Attic/index.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
*** index.html 18 Dec 2002 14:53:46 -0000 1.1.2.4
--- index.html 18 Dec 2002 15:05:37 -0000 1.1.2.5
***************
*** 1,130 ****
! <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
! <HTML>
! <HEAD>
! <TITLE>GeneX Home Page</TITLE>
! </HEAD>
!
!
! <BODY bgcolor="#FFFFFF" marginheight="0" marginwidth="0" topmargin="0"
! leftmargin="0" link="#006633" vlink="#666633">
! <table width="600" border="0" cellspacing="0" cellpadding="6">
! <tr valign="top">
! <td bgcolor="990066">
! <p align="center"> </p></td>
! <td><div align="left"><img src="graphics/genex_logo.jpg" width="207" height="87"></div></td>
! </tr>
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490"> <hr noshade color="990066">
! <p><font face="Verdana, Arial, Helvetica, sans-serif" size="+1">UVA Gene
! Expression Database and Analysis<br>
! Home Page</font></p>
! <p><b>Welcome to the %%ORGANIZATION_NAME%% GeneX server .</b>
! </p>
! <p>If you have not used this system before, please review the <a href="intro_to_genex.html">Introduction
! to GeneX</a> document. </td>
! </tr>
!
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490">
! <p>GeneX is an Open Source Gene Expression Database made available under
! the <a href="http://www.fsf.org/copyleft/lesser.html"> Free Software Foundation's
! Lesser General Public License (LGPL)</a>. It is available as a stand-alone
! package for Solaris Unix or Linux. </p>
! <hr noshade color="990066">
! <p><strong>Using GeneX</strong>: </p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="webtools/">GeneX Login</a><br>
! Registered users only. Login to your account to create studies, orders,
! analyze data, and download files.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="mailto:%%GENEX_SERVER_INSTALLED_BY%%">%%GENEX_SERVER_INSTALLED_BY%%</a><br>
! Contact your local GeneX system administrator to request an account, or
! to report a problem.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT"><a href="stepbystep/filelist.xml">Step-by-step
! guide</a> <br>
! Instructions on how to use the the Web forms.</p>
! <hr noshade color="990066">
! <p><strong>General Information:</strong></p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="background.html">Background</a><br>
! An in-depth introduction to Genex. </p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_info.html">Introduction</a><br>
! Description of the GeneX repository and the built in tools and capabilities.</p>
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="workflow.html">Data
! Curation Workflow Overview</a><br>
! Flow charts of the web pages and scripts involved with documenting data,
! and importing chip expression data into GeneX. End user tools and curator
! tools are both described.<br>
! <br>
! <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="schema.html">Schema
! Description and Images</a><br>
! The descriptions are still being developed, but here are the more interesting
! and important parts of the schema in JPEG form. This is far from complete,
! but shows the critical core tables.
! <hr noshade color="990066">
! <p><b>For software developers:</b></p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="layout_creation.html">Creating Affymetrix layout files</a><br>
! The steps necessary to create layout files describing the probe set layout on Affymetrix chips. Describes using the NetAffx web site (preferred method) and the classic Affymetrix EASI software method.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="data_file_creation.html">Creating Affymetrix data files</a><br>
! This covers the process of creating and loading Affymetrix data files. Includes instructions for using MAS 5.0 to create data spread sheets, loading MAS 5.0 data, and loading DChip data.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="security.html">GeneX
! Security System Description</a><br>
! Description of the tables, SQL, and functions involved with the new 1.x security system.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="web_interface.html">GeneX Web Interface and CGI Scripts</a><br>
! Description of the HTML pages and Perl CGI scripts that make up the Web interface. (See the Data Curation Workflow Overview above)</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="http://genex.sourceforge.net">GeneX
! Development Site at Sourceforge</a><br>
! GeneX development details and downloads.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_contact.html">Contact
! Genex</a><br>
! Contact Information for the GeneX developers.</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14">
! <a href="schema_changes.html">Schema Changes</a><br>
! Database Schema Changes since 1.0.4</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="%%BUG_REPORT_URL%%">Bugzilla
! URL</a><br>
! This link points to a web site where you can report bugs.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="download.html">How
! to get GeneX 1.x</a><br>
! How to download your own copy of Genex</p>
!
! </td>
! </tr>
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490"> <hr noshade color="990066">
! <div align="center">GeneX 1.5.15</div>
! </td>
! </tr>
! </table>
!
! <br>
! </BODY>
! </HTML>
!
!
--- 1,130 ----
! <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
! <HTML>
! <HEAD>
! <TITLE>GeneX Home Page</TITLE>
! </HEAD>
!
!
! <BODY bgcolor="#FFFFFF" marginheight="0" marginwidth="0" topmargin="0"
! leftmargin="0" link="#006633" vlink="#666633">
! <table width="600" border="0" cellspacing="0" cellpadding="6">
! <tr valign="top">
! <td bgcolor="990066">
! <p align="center"> </p></td>
! <td><div align="left"><img src="graphics/genex_logo.jpg" width="207" height="87"></div></td>
! </tr>
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490"> <hr noshade color="990066">
! <p><font face="Verdana, Arial, Helvetica, sans-serif" size="+1">UVA Gene
! Expression Database and Analysis<br>
! Home Page</font></p>
! <p><b>Welcome to the %%ORGANIZATION_NAME%% GeneX server .</b>
! </p>
! <p>If you have not used this system before, please review the <a href="intro_to_genex.html">Introduction
! to GeneX</a> document. </td>
! </tr>
!
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490">
! <p>GeneX is an Open Source Gene Expression Database made available under
! the <a href="http://www.fsf.org/copyleft/lesser.html"> Free Software Foundation's
! Lesser General Public License (LGPL)</a>. It is available as a stand-alone
! package for Solaris Unix or Linux. </p>
! <hr noshade color="990066">
! <p><strong>Using GeneX</strong>: </p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="webtools/">GeneX Login</a><br>
! Registered users only. Login to your account to create studies, orders,
! analyze data, and download files.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="mailto:%%GENEX_SERVER_INSTALLED_BY%%">%%GENEX_SERVER_INSTALLED_BY%%</a><br>
! Contact your local GeneX system administrator to request an account, or
! to report a problem.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT"><a href="stepbystep.html">Step-by-step
! guide</a> <br>
! Instructions on how to use the the Web forms.</p>
! <hr noshade color="990066">
! <p><strong>General Information:</strong></p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="background.html">Background</a><br>
! An in-depth introduction to Genex. </p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_info.html">Introduction</a><br>
! Description of the GeneX repository and the built in tools and capabilities.</p>
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="workflow.html">Data
! Curation Workflow Overview</a><br>
! Flow charts of the web pages and scripts involved with documenting data,
! and importing chip expression data into GeneX. End user tools and curator
! tools are both described.<br>
! <br>
! <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="schema.html">Schema
! Description and Images</a><br>
! The descriptions are still being developed, but here are the more interesting
! and important parts of the schema in JPEG form. This is far from complete,
! but shows the critical core tables.
! <hr noshade color="990066">
! <p><b>For software developers:</b></p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="layout_creation.html">Creating Affymetrix layout files</a><br>
! The steps necessary to create layout files describing the probe set layout on Affymetrix chips. Describes using the NetAffx web site (preferred method) and the classic Affymetrix EASI software method.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="data_file_creation.html">Creating Affymetrix data files</a><br>
! This covers the process of creating and loading Affymetrix data files. Includes instructions for using MAS 5.0 to create data spread sheets, loading MAS 5.0 data, and loading DChip data.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="security.html">GeneX
! Security System Description</a><br>
! Description of the tables, SQL, and functions involved with the new 1.x security system.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="web_interface.html">GeneX Web Interface and CGI Scripts</a><br>
! Description of the HTML pages and Perl CGI scripts that make up the Web interface. (See the Data Curation Workflow Overview above)</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="http://genex.sourceforge.net">GeneX
! Development Site at Sourceforge</a><br>
! GeneX development details and downloads.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_contact.html">Contact
! Genex</a><br>
! Contact Information for the GeneX developers.</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14">
! <a href="schema_changes.html">Schema Changes</a><br>
! Database Schema Changes since 1.0.4</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="%%BUG_REPORT_URL%%">Bugzilla
! URL</a><br>
! This link points to a web site where you can report bugs.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="download.html">How
! to get GeneX 1.x</a><br>
! How to download your own copy of Genex</p>
!
! </td>
! </tr>
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490"> <hr noshade color="990066">
! <div align="center">GeneX 1.5.15</div>
! </td>
! </tr>
! </table>
!
! <br>
! </BODY>
! </HTML>
!
!
|
|
From: <tw...@us...> - 2002-12-18 15:03:34
|
Update of /cvsroot/genex/genex-server/site
In directory sc8-pr-cvs1:/tmp/cvs-serv20867
Added Files:
Tag: Rel-1_0_1-branch
stepbystep.html
Log Message:
new docs
--- NEW FILE: stepbystep.html ---
<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
<link rel=Edit-Time-Data href="./stepbystep_files/editdata.mso">
<link rel=OLE-Object-Data href="./stepbystep_files/oledata.mso">
<title>GeneX Instructions for Web Interface</title>
<style><!--
.Normal
{font-size:12.0pt;
font-family:"Times New Roman";}
-->
</style>
</head>
<body lang=EN-US link=blue vlink=purple bgcolor="#FFFFFF" class="Normal">
<p align=center style='text-align:center'><span
style='font-size:14.0pt;'>Step-By-Step Guide to GeneX Web Pages</span></p>
<p>The purpose of this document is to guide you through the GeneX database user
interface. You will be able to add information pertaining to your studies, experimental
conditions, orders, samples, and hybridizations. This data will then be viewed
and processed accordingly by the Biomolecular Research Facility (BRF).<span style='font-size:14.0pt;'><br>
<br>
</span></p>
<p> <span style='font-size:11.0pt;
'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span> <span style='font-size:11.0pt;'>The main GeneX page can be reached
by visiting <a
href="http://genes.med.virginia.edu/">http://genes.med.virginia.edu/</a>. There
are a number of links to various kinds of documentation. The link to follow
when you are ready to enter data is the GeneX Login link. <br>
<br>
<img border=0 width=466 height=470
src="graphics/image002.jpg" v:shapes="_x0000_i1025"> <br>
<br>
</span></p>
<p> <span style='font-size:11.0pt;
'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span> <span style='font-size:11.0pt;'>When you click on the GeneX
Login link you will be prompted to sign on to the system. If you have questions
about your account please contact the GeneX Database Administrator via email
at gen...@vi....<br>
<br>
<img border=0 width=406 height=182
src="graphics/image004.jpg" v:shapes="_x0000_i1026"> <br>
<br>
<br>
</span></p>
<p> <span style='font-size:11.0pt;
'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span> <span style='font-size:11.0pt;'>Once you have signed on to the
system you will be brought to the GeneX Member Home Page.<br>
<br>
<img border=0 width=530 height=457
src="graphics/image006.jpg" v:shapes="_x0000_i1027"> <br>
<br>
</span></p>
<p> <span style='font-size:11.0pt;
'>4)<span style='font:7.0pt "Times New Roman"'>
</span></span> <span style='font-size:11.0pt;'>The system requires that you
enter data pertaining to each of your studies. Please click on the link to Create
new study when you are ready to begin entering data.<br>
<br>
Enter the <i>Study Name, Study Start Date, </i>and any <i>Comments</i> regarding
the study that you may find useful at a later time. <br>
* It is highly recommended that you keep your study names unique. A listing
of all study names currently in use will be listed on the bottom of the screen
for your convenience.<br>
<br>
<br>
<img border=0 width=721 height=324
src="graphics/image008.gif" v:shapes="_x0000_i1028"> </span></p>
<p> <span style='font-size:11.0pt;
'>5)<span style='font:7.0pt "Times New Roman"'>
</span></span> There are two ways to add experimental conditions to your study.
This data is your conceptual criteria for the experiments. <br>
You can click the Add a blank empty experimental condition or choose to copy
data you submitted from a previous experimental condition. To do so simply choose
that condition from the drop down list and click Paste. Repeat this process
again for each experimental condition that you plan to add. You will see the
<i>No. of Experimental Conditions</i> incrementing as you proceed. <br>
a) Enter the <i>Experimental Condition Name </i>as defined by the Investigator.
Experimental Condition names <br>
should be unique. You will receive a warning if you attempt to reuse
an experimental condition name <br>
within the same study.<br>
b) Enter a <i>Short name </i>as an abbreviated version of your Experimental
Condition Name. This short name <br>
should be no more than 6 characters and will be used by the BRF
and system only.<br>
c) The <i>Notes</i> field can be used to record any extra details pertaining
to the experiment.<br>
d) Choose a <i>Species</i> from the list. If you do not see your species
listed please contact the GeneX Database <br>
Administrator via email at gen...@vi....<br>
e) Make a selection from the list of <i>Sample Types.<br>
</i>f) Fill in <i>Cell Line/Cell Type</i> or <i>Tissue Type</i> depending
on which Sample Type was chosen.<br>
g) The <i>Description </i>field should be used to record any description
relating to the sample.<br>
<br>
If you find that you have added too many experimental condition entries you
can simply click the <i>Delete</i> checkbox and that condition will be deleted
upon submission of entries.<br>
<br>
Click the FINISH button at the bottom of the page when complete.<br>
<br>
<img border=0 width=624 height=436
src="graphics/image010.jpg" v:shapes="_x0000_i1029"> <br>
<br>
<br>
</p>
<p> <span style='font-size:11.0pt;
'>6)<span style='font:7.0pt "Times New Roman"'>
</span></span> <span style='font-size:11.0pt;'>You can edit your studies and
experimental conditions by clicking on the Update an existing study link located
on the GeneX Member Home Page. <br>
Once the BRF has reviewed and accepted your order the experimental conditions
will be locked. You can still add conditions at this point but you will not
be allowed to edit the conditions that existed when the BRF reviewed and locked
the order.</span></p>
<p><span style='font-size:11.0pt;
'> <img border=0 width=721 height=188
src="graphics/image012.gif" v:shapes="_x0000_i1030"> <br>
<br>
</span></p>
<p> <span style='font-size:11.0pt;
'>7)<span style='font:7.0pt "Times New Roman"'>
</span></span> You can change the group ownership and/or group read-write permissions
for your studies by clicking on the Change study group ownership and read/write
permissions link located on the GeneX Member Home Page. The experimental conditions
for each study will be changed to reflect study permissions (as appropriate).
<br>
Any individual who is a member of your group will be affected by the settings
here. Read privileges allow the members of a particular group to read data pertaining
to the specific study. Write privileges will allow those same users to modify
(and delete where appropriate) this data. If you have individuals who will only
be allowed to read or write to <u>some</u> of your data then you need to create
a specific group for those individuals (see section #16 of this document). <br>
*Note: those individuals who have access to ALL of your data will need to be
listed as members in all of your groups.<span style='font-size:11.0pt;
'></span></p>
<p> <img border=0 width=631 height=112
src="graphics/image014.jpg" v:shapes="_x0000_i1031"> <span
style='font-size:11.0pt;'><br>
<br>
<br>
<br>
</span></p>
<p> <span style='font-size:11.0pt;
'>8)<span style='font:7.0pt "Times New Roman"'>
</span></span> Click on the Create a new order link to create an order, describe
the samples that you will deliver to the chip lab, and to enter hybridization
information.<br>
a) Enter your billing code in the space provided. This value is typically
a PTAO and is used by the BRF.<br>
b) Identify your <i>Study+Experimental Condition/Protocol</i> by choosing
from the drop down list. <br>
c) Enter the <i>Sample collection date.</i><br>
d) Enter your <i>Lab Notebook ID</i> and the <i>Lab book owner</i>.<br>
When you are ready to enter your hybridization information click on the Next
(HybridizationInfo) button.<br>
<br>
<br>
<img border=0 width=551 height=331
src="graphics/image016.jpg" v:shapes="_x0000_i1032"> </p>
<p> <span style='font-size:11.0pt;
'>9)<span style='font:7.0pt "Times New Roman"'>
</span></span> The Hybridization entry form will allow you to identify which
chip you would like your sample(s) hybridized to. If you require more than one
hybridization please click on the Add Hybridization button as many times as
necessary. <br>
a) Choose an Affymetrix chip from the drop down list. If you need to
add an Affymetrix chip to the list <br>
please contact the GeneX Database Administrator via email at gen...@vi....<br>
b) Make any <i>comments</i> you may find useful at a later date.<br>
<br>
<img border=0 width=453 height=310
src="graphics/image018.jpg" v:shapes="_x0000_i1033"> <br>
<br>
<br>
</p>
<p> <span style='font-size:11.0pt;
'>10)<span style='font:7.0pt "Times New Roman"'> </span></span> <span style='font-size:11.0pt;'>You
can edit your order up until the time that the BRF has reviewed your order and
placed it in a locked status. This status is necessary to preserve data integrity.
If you need to have an order unlocked please contact the BRF or the GeneX Database
Administrator(gen...@vi...).</span></p>
<p><span style='font-size:11.0pt;
'><br>
<br>
<img border=0 width=719 height=214
src="graphics/image020.gif" v:shapes="_x0000_i1034"> </span></p>
<p> 11)<span style='font:7.0pt "Times New Roman"'> </span> You can change
the group and/or read-write permissions of your orders by clicking on the Change
order group ownership and read/write permissions link located on the GeneX
Member Home Page. <br>
Samples and hybridizations within a given order will be given the same permissions
as the order. <br>
<br>
</p>
<p> <img border=0 width=674 height=184
src="graphics/image022.jpg" v:shapes="_x0000_i1035"> <br>
<br>
</p>
<p> 12)<span style='font:7.0pt "Times New Roman"'> </span> At the main GeneX
page you can view a listing of your files by following the View my files link.
This list includes all files that are currently in your personal repository
and should include all raw, processed, and Affymetrix generated files. Each
file can be viewed by clicking on the associated link.<br>
<br>
<img border=0 width=530 height=293
src="graphics/image024.jpg" v:shapes="_x0000_i1036"> <br>
<br>
</p>
<p> 13)<span style='font:7.0pt "Times New Roman"'> </span> You can change
the group ownership and/or group read-write permissions of your files by clicking
on the Change file group ownership and read/write permissions link located
on the GeneX Member Home Page. File permissions for the owner of the data are
determined by the system. We do not allow users to remove read/write permissions
for themselves.<br>
<br>
<img border=0 width=714 height=294
src="graphics/image026.gif" v:shapes="_x0000_i1037"> <br>
<br>
</p>
<p> 14)<span style='font:7.0pt "Times New Roman"'> </span> To verify that
your contact information is accurate follow the Update my info link at the
bottom of the main GeneX web page. You can modify this information as needed.<br>
<br>
<img border=0 width=441 height=511
src="graphics/image028.gif" v:shapes="_x0000_i1038"> <br>
</p>
<p> 15)<span style='font:7.0pt "Times New Roman"'> </span> You can add
and remove members from your group by clicking on the Manage membership of
my groups link at the bottom of the main GeneX page. All members of your group
will be able to read your data. If you need to break your data up such that
groups of individuals have access to certain subsets of your data then you will
need to set up groups (see next screen shot).<br>
<br>
<img border=0 width=269 height=269
src="graphics/image030.jpg" v:shapes="_x0000_i1039"> </p>
<p> 16)<span style='font:7.0pt "Times New Roman"'> </span> To create groups
click on the link to Create a new group on the bottom of the main GeneX web
page. <br>
Enter <i>Group name</i> of your preference. Please do not use hyphens in your
group names.<br>
<br>
<img border=0 width=285 height=170
src="graphics/image032.jpg" v:shapes="_x0000_i1040"> <br>
<br>
<br>
</p>
<p>If you have any questions or concerns regarding the instructions listed above
please contact the Database Administrator via email at gen...@vi....<br>
<br>
<br>
<br>
</p>
</body>
</html>
|
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image010.jpg image012.gif image014.jpg image016.jpg
image018.jpg image020.gif image022.jpg image024.jpg
image026.gif image028.gif image030.jpg image032.jpg
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|
|
From: <jl...@us...> - 2002-12-18 14:53:50
|
Update of /cvsroot/genex/genex-server/site
In directory sc8-pr-cvs1:/tmp/cvs-serv17004
Modified Files:
Tag: Rel-1_0_1-branch
index.html
Added Files:
Tag: Rel-1_0_1-branch
intro_to_genex.html
Log Message:
updates
--- NEW FILE: intro_to_genex.html ---
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<TITLE>GeneX Home Page</TITLE>
</HEAD>
<BODY bgcolor="#FFFFFF" marginheight="0" marginwidth="0" topmargin="0"
leftmargin="0" link="#006633" vlink="#666633">
<table width="600" border="0" cellspacing="0" cellpadding="6">
<tr>
<td bgcolor="990066"> </td>
<td><a href="index.html"><img src="graphics/genex_logo.jpg" width="207" height="87" border="0"></a></td>
</tr>
<tr>
<td width="100" bgcolor="990066"> </td>
<td width="490"> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="+1">Initiation
of GeneChip/Microarray Study Using UVA GeneX System</font></p>
<p>In support of genome-wide microarray studies at the University of Virginia,
a secure GeneX database system has been established to efficiently archive
and analyze vast amounts of complex gene expression data. This development
has resulted from a collaborative effort between members of the Biomolecular
Research Facility (BRF), Academic Computing Health Sciences (ACHS), and
the GeneChip/Micorarray Bioinformatics Core (GMB) of the University of
Virginia School of Medicine. The UVA GeneX system is providing full security
for all array data under each investigator’s discretion. </p>
<p>Thanks to this development, all investigators using the BRF microarray
facility are strongly encouraged to initiate their array studies starting
on <strong>November 1, 2002</strong>. Once an investigator has an account
created, he/she needs to initiate each array study by filling in the web
order form. Assistance with first time data entry is being offered through
the ACHS department. Please email <a href="mailto:gen...@vi...">gen...@vi...</a>
if you would like to schedule a brief training session. </p>
<p>Detailed instructions can also be found at the following URL:</p>
<blockquote><a href="http://genes.med.virginia.edu">http://genes.med.virginia.edu</a></blockquote>
<p>Follow the “Step By Step Guide” link.</p>
<p>If you have technical questions regarding web access and/or your UVA
GeneX account please send an email to gen...@vi....</p>
<p>If you have general questions about your array study, such as RNA sample
preparation, chip selection, and costs, you can address them to Paul Gallagher
(pgg3a, 3-9689), Alyson Prorock (ajp7x, 3-9689), Yongde Bao, Ph.D., Manager
of Microarray Facility (yb8d, 2-2551), or Jay Fox, Ph.D., BRF Director
(jwf8x, 4-0050). </p>
<p> <strong>GMB array data analysis service </strong></p>
<p>In addition to the automated service of the GeneX database and analysis
system, the GMB Core offers a formal analysis service to University array
users. This analysis service will provide the results of quality control,
statistical evaluation and discovery of differential expression, clustering
& classification analysis, and some annotation analysis for each array
study. This service is partially supported by the UVA School of Medicine,
but some partial fees will be assessed starting in January 1, 2003. The
BRF will continuously provide basic analysis of each array data set using
Affymetrix MicroArray Suite (MAS) 5.0 software. Questions regarding the
array analysis service can be addressed to Mir Siadaty, M.S., (mss4x,
2-4436) or Jae Lee, Ph.D., GMB Director (jkl7n, 2-1033).</p></td>
</tr>
</table>
<p> </p>
<p> </p>
</BODY>
</HTML>
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/Attic/index.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
*** index.html 10 Dec 2002 19:21:02 -0000 1.1.2.3
--- index.html 18 Dec 2002 14:53:46 -0000 1.1.2.4
***************
*** 1,126 ****
! <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
! <HTML>
! <HEAD>
! <TITLE>GeneX Home Page</TITLE>
! </HEAD>
!
!
! <BODY bgcolor="#FFFFFF" marginheight="0" marginwidth="0" topmargin="0"
! leftmargin="0" link="#006633" vlink="#666633">
! <table width="600" border="0" cellspacing="0" cellpadding="0">
! <tr valign="top">
! <td width="110"><font face="Verdana, Arial, Helvetica, sans-serif" size="+1">GeneX</font></td>
! <td width="490"><font face="Verdana, Arial, Helvetica, sans-serif" size="+1">
! Gene Expression<br>
! Analysis and Database <br>
! Home Page</font><br>
! <br>
! <b>Welcome to the GeneX server running at %%ORGANIZATION_NAME%%.</b>
! <p>GeneX is an Open Source Gene Expression Database made available under
! the <a href="http://www.fsf.org/copyleft/lesser.html"> Free Software Foundation's
! Lesser General Public License (LGPL)</a>. It is available as a stand-alone
! package for Solaris Unix or Linux.
! </td>
! </tr>
! </table>
! <br>
! <table width="600" border="0" cellspacing="0" cellpadding="0">
! <tr valign="top">
! <td width="110"> </td>
! <td width="490">
! <p><b>General information:</b></p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="webtools/">GeneX Login</a><br>
! Registered users only. Login to your account to create studies, orders,
! analyze data, and download files.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="mailto:%%GENEX_SERVER_INSTALLED_BY%%">%%GENEX_SERVER_INSTALLED_BY%%</a><br>
! Contact your local GeneX system administrator to request an account, or
! to report a problem.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="background.html">Background</a><br>
! An in-depth introduction to Genex. </p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_info.html">Introduction</a><br>
! Description of the GeneX repository and the built in tools and capabilities.</p>
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="analysis_tools.html">Analysis/Query</a><br>
! Links to Genex analysis tools.<br>
! <br>
! <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="workflow.html">Data
! Curation Workflow Overview</a><br>
! Flow charts of the web pages and scripts involved with documenting data,
! and importing chip expression data into GeneX. End user tools and curator
! tools are both described.<br>
! <br>
!
! <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="schema.html">Schema Description and Images</a><br>
! The descriptions are still being developed, but here are the more interesting and important parts
! of the schema in JPEG form. This is far from complete, but shows the critical core tables.<br>
! <br>
!
!
! <p><b>For software developers:</b></p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="layout_creation.html">Creating Affymetrix layout files</a><br>
! The steps necessary to create layout files describing the probe set layout on Affymetrix chips. Describes using the NetAffx web site (preferred method) and the classic Affymetrix EASI software method.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="data_file_creation.html">Creating Affymetrix data files</a><br>
! This covers the process of creating and loading Affymetrix data files. Includes instructions for using MAS 5.0 to create data spread sheets, loading MAS 5.0 data, and loading DChip data.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="security.html">GeneX
! Security System Description</a><br>
! Description of the tables, SQL, and functions involved with the new 1.x security system.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="web_interface.html">GeneX Web Interface and CGI Scripts</a><br>
! Description of the HTML pages and Perl CGI scripts that make up the Web interface. (See the Data Curation Workflow Overview above)</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="http://genex.sourceforge.net">GeneX
! Development Site at Sourceforge</a><br>
! GeneX development details and downloads.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_contact.html">Contact
! Genex</a><br>
! Contact Information for the GeneX developers.</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14">
! <a href="schema_changes.html">Schema Changes</a><br>
! Database Schema Changes since 1.0.4</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="%%BUG_REPORT_URL%%">Bugzilla
! URL</a><br>
! This link points to a web site where you can report bugs.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="download.html">How
! to get GeneX 1.x</a><br>
! How to download your own copy of Genex</p>
!
! </td>
! </tr>
! <tr valign="top">
! <td width="110"> </td>
! <td width="490">
! <hr align="center">
! <div align="center">GeneX 1.x</div>
! </td>
! </tr>
! </table>
!
! <br>
! </BODY>
! </HTML>
!
!
--- 1,130 ----
! <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
! <HTML>
! <HEAD>
! <TITLE>GeneX Home Page</TITLE>
! </HEAD>
!
!
! <BODY bgcolor="#FFFFFF" marginheight="0" marginwidth="0" topmargin="0"
! leftmargin="0" link="#006633" vlink="#666633">
! <table width="600" border="0" cellspacing="0" cellpadding="6">
! <tr valign="top">
! <td bgcolor="990066">
! <p align="center"> </p></td>
! <td><div align="left"><img src="graphics/genex_logo.jpg" width="207" height="87"></div></td>
! </tr>
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490"> <hr noshade color="990066">
! <p><font face="Verdana, Arial, Helvetica, sans-serif" size="+1">UVA Gene
! Expression Database and Analysis<br>
! Home Page</font></p>
! <p><b>Welcome to the %%ORGANIZATION_NAME%% GeneX server .</b>
! </p>
! <p>If you have not used this system before, please review the <a href="intro_to_genex.html">Introduction
! to GeneX</a> document. </td>
! </tr>
!
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490">
! <p>GeneX is an Open Source Gene Expression Database made available under
! the <a href="http://www.fsf.org/copyleft/lesser.html"> Free Software Foundation's
! Lesser General Public License (LGPL)</a>. It is available as a stand-alone
! package for Solaris Unix or Linux. </p>
! <hr noshade color="990066">
! <p><strong>Using GeneX</strong>: </p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="webtools/">GeneX Login</a><br>
! Registered users only. Login to your account to create studies, orders,
! analyze data, and download files.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" width="14" height="14">
! <a href="mailto:%%GENEX_SERVER_INSTALLED_BY%%">%%GENEX_SERVER_INSTALLED_BY%%</a><br>
! Contact your local GeneX system administrator to request an account, or
! to report a problem.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT"><a href="stepbystep/filelist.xml">Step-by-step
! guide</a> <br>
! Instructions on how to use the the Web forms.</p>
! <hr noshade color="990066">
! <p><strong>General Information:</strong></p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="background.html">Background</a><br>
! An in-depth introduction to Genex. </p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_info.html">Introduction</a><br>
! Description of the GeneX repository and the built in tools and capabilities.</p>
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="workflow.html">Data
! Curation Workflow Overview</a><br>
! Flow charts of the web pages and scripts involved with documenting data,
! and importing chip expression data into GeneX. End user tools and curator
! tools are both described.<br>
! <br>
! <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="schema.html">Schema
! Description and Images</a><br>
! The descriptions are still being developed, but here are the more interesting
! and important parts of the schema in JPEG form. This is far from complete,
! but shows the critical core tables.
! <hr noshade color="990066">
! <p><b>For software developers:</b></p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="layout_creation.html">Creating Affymetrix layout files</a><br>
! The steps necessary to create layout files describing the probe set layout on Affymetrix chips. Describes using the NetAffx web site (preferred method) and the classic Affymetrix EASI software method.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="data_file_creation.html">Creating Affymetrix data files</a><br>
! This covers the process of creating and loading Affymetrix data files. Includes instructions for using MAS 5.0 to create data spread sheets, loading MAS 5.0 data, and loading DChip data.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="security.html">GeneX
! Security System Description</a><br>
! Description of the tables, SQL, and functions involved with the new 1.x security system.</p>
!
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="web_interface.html">GeneX Web Interface and CGI Scripts</a><br>
! Description of the HTML pages and Perl CGI scripts that make up the Web interface. (See the Data Curation Workflow Overview above)</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="http://genex.sourceforge.net">GeneX
! Development Site at Sourceforge</a><br>
! GeneX development details and downloads.</p>
!
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="genex_contact.html">Contact
! Genex</a><br>
! Contact Information for the GeneX developers.</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14">
! <a href="schema_changes.html">Schema Changes</a><br>
! Database Schema Changes since 1.0.4</p>
!
! <p> <img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="%%BUG_REPORT_URL%%">Bugzilla
! URL</a><br>
! This link points to a web site where you can report bugs.</p>
! <p><img src="graphics/x.jpg" alt="x" align="LEFT" border="0"
! hspace="0" vspace="0" width="14" height="14"> <a href="download.html">How
! to get GeneX 1.x</a><br>
! How to download your own copy of Genex</p>
!
! </td>
! </tr>
! <tr valign="top">
! <td width="110" bgcolor="990066"> </td>
! <td width="490"> <hr noshade color="990066">
! <div align="center">GeneX 1.5.15</div>
! </td>
! </tr>
! </table>
!
! <br>
! </BODY>
! </HTML>
!
!
|
|
From: <tw...@us...> - 2002-12-18 03:57:48
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Update of /cvsroot/genex/genex-server/site/webtools/analysis/test
In directory sc8-pr-cvs1:/tmp/cvs-serv25559
Modified Files:
Tag: Rel-1_0_1-branch
depopulate populate
Log Message:
init fixes
Index: depopulate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/depopulate,v
retrieving revision 1.1.2.5
retrieving revision 1.1.2.6
diff -C2 -d -r1.1.2.5 -r1.1.2.6
*** depopulate 17 Dec 2002 21:52:41 -0000 1.1.2.5
--- depopulate 18 Dec 2002 03:57:45 -0000 1.1.2.6
***************
*** 1,8 ****
./test_quality.pl --action remove
! ./test_tree.pl --action remove
../../add_analysis.pl --configfile ../qualityControl.cfg --action remove
../../add_analysis.pl --configfile ../statAnalysis.cfg --action remove
../../add_analysis.pl --configfile ../foldChange.cfg --action remove
../../add_analysis.pl --configfile ../cluster.cfg --action remove
../../add_analysis.pl --configfile ../genBank.cfg --action remove
../../add_analysis.pl --configfile ../geneOnt.cfg --action remove
--- 1,10 ----
./test_quality.pl --action remove
! #./test_tree.pl --action remove
../../add_analysis.pl --configfile ../qualityControl.cfg --action remove
../../add_analysis.pl --configfile ../statAnalysis.cfg --action remove
../../add_analysis.pl --configfile ../foldChange.cfg --action remove
../../add_analysis.pl --configfile ../cluster.cfg --action remove
+ ../../add_analysis.pl --configfile ../k_cluster.cfg --action remove
+ ../../add_analysis.pl --configfile ../h_cluster.cfg --action remove
../../add_analysis.pl --configfile ../genBank.cfg --action remove
../../add_analysis.pl --configfile ../geneOnt.cfg --action remove
***************
*** 11,24 ****
../../add_analysis.pl --configfile ../unigene.cfg --action remove
../../add_analysis.pl --configfile ../ttest.cfg --action remove
! ../../add_analysis.pl --configfile demo4.cfg --action remove
! ../../add_analysis.pl --configfile demo3.cfg --action remove
! ../../add_analysis.pl --configfile demo2.cfg --action remove
! ../../add_analysis.pl --configfile demo1.cfg --action remove
! ../../add_analysis.pl --configfile demo.cfg --action remove
! ../../add_analysis.pl --configfile demo4.cfg --action remove
! ../../add_analysis.pl --configfile demo3.cfg --action remove
! ../../add_analysis.pl --configfile demo2.cfg --action remove
! ../../add_analysis.pl --configfile demo1.cfg --action remove
! ../../add_analysis.pl --configfile demo.cfg --action remove
! rm /tmp/initial_in
# should delete rows created in file_info from runTree
--- 13,26 ----
../../add_analysis.pl --configfile ../unigene.cfg --action remove
../../add_analysis.pl --configfile ../ttest.cfg --action remove
! #../../add_analysis.pl --configfile demo4.cfg --action remove
! #../../add_analysis.pl --configfile demo3.cfg --action remove
! #../../add_analysis.pl --configfile demo2.cfg --action remove
! #../../add_analysis.pl --configfile demo1.cfg --action remove
! #../../add_analysis.pl --configfile demo.cfg --action remove
! #../../add_analysis.pl --configfile demo4.cfg --action remove
! #../../add_analysis.pl --configfile demo3.cfg --action remove
! #../../add_analysis.pl --configfile demo2.cfg --action remove
! #../../add_analysis.pl --configfile demo1.cfg --action remove
! #../../add_analysis.pl --configfile demo.cfg --action remove
! #rm /tmp/initial_in
# should delete rows created in file_info from runTree
Index: populate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/populate,v
retrieving revision 1.1.2.6
retrieving revision 1.1.2.7
diff -C2 -d -r1.1.2.6 -r1.1.2.7
*** populate 18 Dec 2002 03:28:53 -0000 1.1.2.6
--- populate 18 Dec 2002 03:57:45 -0000 1.1.2.7
***************
*** 3,6 ****
--- 3,8 ----
../../add_analysis.pl --configfile ../foldChange.cfg --action insert
../../add_analysis.pl --configfile ../cluster.cfg --action insert
+ ../../add_analysis.pl --configfile ../k_cluster.cfg --action insert
+ ../../add_analysis.pl --configfile ../h_cluster.cfg --action insert
../../add_analysis.pl --configfile ../genBank.cfg --action insert
../../add_analysis.pl --configfile ../geneOnt.cfg --action insert
***************
*** 9,24 ****
../../add_analysis.pl --configfile ../unigene.cfg --action insert
../../add_analysis.pl --configfile ../ttest.cfg --action insert
! ../../add_analysis.pl --configfile ./demo.cfg --action insert
! ../../add_analysis.pl --configfile ./demo1.cfg --action insert
! ../../add_analysis.pl --configfile ./demo2.cfg --action insert
! ../../add_analysis.pl --configfile ./demo3.cfg --action insert
! ../../add_analysis.pl --configfile ./demo4.cfg --action insert
! ./test_tree.pl --action insert
./test_quality.pl --action insert
! cat > /tmp/initial_in << EOF
! This is the
! initial input
! for
! the
! demo test scripts.
! EOF
--- 11,26 ----
../../add_analysis.pl --configfile ../unigene.cfg --action insert
../../add_analysis.pl --configfile ../ttest.cfg --action insert
! #../../add_analysis.pl --configfile ./demo.cfg --action insert
! #../../add_analysis.pl --configfile ./demo1.cfg --action insert
! #../../add_analysis.pl --configfile ./demo2.cfg --action insert
! #../../add_analysis.pl --configfile ./demo3.cfg --action insert
! #../../add_analysis.pl --configfile ./demo4.cfg --action insert
! #./test_tree.pl --action insert
./test_quality.pl --action insert
! #cat > /tmp/initial_in << EOF
! #This is the
! #initial input
! #for
! ##the
! ##demo test scripts.
! #EOF
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From: <tw...@us...> - 2002-12-18 03:57:19
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Update of /cvsroot/genex/genex-server/site/webtools/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv25396
Modified Files:
Tag: Rel-1_0_1-branch
makefile
Added Files:
Tag: Rel-1_0_1-branch
h_cluster.cfg k_cluster.cfg
Log Message:
tree init fixes
--- NEW FILE: h_cluster.cfg ---
## filetypes
filetype = name=h_clusterin
filetype = comment=Input file for clusering
filetype = arg_name=--infile
filetype = name=h_clusterout
filetype = comment=Data output for clusering
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=h_clusterin
extension = ext=lnin
extension = filetype=h_clusterout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = H_clustering
cmdstr = ./analysis/Rwrapper.pl --kind h_cluster
#analysis_filetypes_link
analysisfile = filetype=h_clusterin
analysisfile = input =1
analysisfile = filetype=h_clusterout
analysisfile = input =0
analysisfile = filetype=log
analysisfile = input =0
#user_parameter_names
up = name=--settings condLabels
up = display_name=Labels for each of the conditions
up = type=text
up = name=--outfile
up = display_name = Data filename to pass on to other analyses
up = type= text
up = name=--logfile
up = display_name = Log filename
up = type= text
#sys_parameter_names
sp = name=--settings conds
sp = name=--infile
--- NEW FILE: k_cluster.cfg ---
## filetypes
filetype = name=k_clusterin
filetype = comment=Input file for clusering
filetype = arg_name=--infile
filetype = name=k_clusterout
filetype = comment=Data output for clusering
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=k_clusterin
extension = ext=lnin
extension = filetype=k_clusterout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = K_clustering
cmdstr = ./analysis/Rwrapper.pl --kind k_cluster
#analysis_filetypes_link
analysisfile = filetype=k_clusterin
analysisfile = input =1
analysisfile = filetype=k_clusterout
analysisfile = input =0
analysisfile = filetype=log
analysisfile = input =0
#user_parameter_names
up = name=--settings condLabels
up = display_name=Labels for each of the conditions
up = type=text
up = name=--outfile
up = display_name = Data filename to pass on to other analyses
up = type= text
up = name=--logfile
up = display_name = Log filename
up = type= text
#sys_parameter_names
sp = name=--settings conds
sp = name=--infile
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/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 17 Dec 2002 21:38:32 -0000 1.1.2.1
--- makefile 18 Dec 2002 03:57:16 -0000 1.1.2.2
***************
*** 2,6 ****
NOOP = $(SHELL) -c true
! DEST = /var/www/html/genex/webtools
--- 2,6 ----
NOOP = $(SHELL) -c true
! DEST = /var/www/html/genex/webtools/analysis
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