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From: <tw...@us...> - 2002-12-18 03:32:17
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv17636
Modified Files:
Tag: Rel-1_0_1-branch
runtree.pl edit_atree2.pl
Log Message:
logging
Index: runtree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/runtree.pl,v
retrieving revision 1.1.2.5
retrieving revision 1.1.2.6
diff -C2 -d -r1.1.2.5 -r1.1.2.6
*** runtree.pl 18 Dec 2002 02:16:36 -0000 1.1.2.5
--- runtree.pl 18 Dec 2002 03:32:13 -0000 1.1.2.6
***************
*** 30,35 ****
main:
{
getOptions();
!
runChain($treeName, $owner);
}
--- 30,37 ----
main:
{
+ write_log("runtree");
getOptions();
!
! write_log("running $treeName, $owner");
runChain($treeName, $owner);
}
***************
*** 39,42 ****
--- 41,45 ----
my $dbh = new_connection();
+ write_log("rc: new conn");
# TODO - how do we check owner stuff - remember to make unnecessary
***************
*** 71,78 ****
$logfile = "/var/genres/$ENV{REMOTE_USER}/$logfile.log";
! open(LOG, "> $logfile") or die "Unable to open $logfile: $!\n";
print LOG `date`;
print LOG "\n Running tree: $treeName owner: $treeOwner\n";
processTree($dbh, $tree_pk, LOG);
close(LOG);
--- 74,91 ----
$logfile = "/var/genres/$ENV{REMOTE_USER}/$logfile.log";
! write_log("log: $logfile");
!
! 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);
***************
*** 80,87 ****
my $us_fk = get_us_fk($dbh);
fi_update($dbh, $us_fk, $us_fk, $logfile, "$treeName log");
!
# TODO - stat logfile
! $sth->finish;
$dbh->disconnect();
} #runChain
--- 93,100 ----
my $us_fk = get_us_fk($dbh);
fi_update($dbh, $us_fk, $us_fk, $logfile, "$treeName log");
!
# TODO - stat logfile
! $dbh->commit;
$dbh->disconnect();
} #runChain
Index: edit_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree2.pl,v
retrieving revision 1.1.2.14
retrieving revision 1.1.2.15
diff -C2 -d -r1.1.2.14 -r1.1.2.15
*** edit_atree2.pl 18 Dec 2002 02:16:36 -0000 1.1.2.14
--- edit_atree2.pl 18 Dec 2002 03:32:13 -0000 1.1.2.15
***************
*** 24,35 ****
{
# It is easier (and maybe better) to call this with $tree_pk and $us_pk
! my $sth = getq("select_tree", $dbh);
! $sth->execute();
! (my $tree_name, my $tree_pk) = $sth->fetchrow_array();
! $sth->finish();
! `./runtree.pl --treeName $tree_name --treeOwner $ENV{REMOTE_USER}`;
$url =~ s/(.*)\/.*/$1\/files.pl/;
print "Location: $url\n\n";
! 2 }
else
{
--- 24,33 ----
{
# 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";
! }
else
{
|
|
From: <tw...@us...> - 2002-12-18 03:29:54
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv16303
Modified Files:
Tag: Rel-1_0_1-branch
Rwrapper.pl
Log Message:
more logging
Index: Rwrapper.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/Attic/Rwrapper.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
*** Rwrapper.pl 17 Dec 2002 18:24:21 -0000 1.1.2.2
--- Rwrapper.pl 18 Dec 2002 03:29:51 -0000 1.1.2.3
***************
*** 97,101 ****
if (-s $lockFile)
{
! die "You can only run one $kind analysis at a time\n";
}
else
--- 97,103 ----
if (-s $lockFile)
{
! print "Found lock $lockFile\n";
! print "You can only run one $kind analysis at a time\n";
! exit(1);
}
else
***************
*** 344,348 ****
else
{
! warn "Email address needs a \\ in front of \@. Remember to use double quotes from the command line.\n";
}
}
--- 346,350 ----
else
{
! warn "Email address $email needs a \\ in front of \@. Remember to use double quotes from the command line.\n";
}
}
|
|
From: <tw...@us...> - 2002-12-18 03:28:56
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis/test
In directory sc8-pr-cvs1:/tmp/cvs-serv15557
Modified Files:
Tag: Rel-1_0_1-branch
populate test_quality.pl
Log Message:
fix init stuff
make tree owned by owner
Index: populate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/populate,v
retrieving revision 1.1.2.5
retrieving revision 1.1.2.6
diff -C2 -d -r1.1.2.5 -r1.1.2.6
*** populate 17 Dec 2002 21:52:41 -0000 1.1.2.5
--- populate 18 Dec 2002 03:28:53 -0000 1.1.2.6
***************
*** 1,2 ****
--- 1,3 ----
+ ../../add_analysis.pl --configfile ../qualityControl.cfg --action insert
../../add_analysis.pl --configfile ../statAnalysis.cfg --action insert
../../add_analysis.pl --configfile ../foldChange.cfg --action insert
***************
*** 9,13 ****
../../add_analysis.pl --configfile ../ttest.cfg --action insert
../../add_analysis.pl --configfile ./demo.cfg --action insert
- ../../add_analysis.pl --configfile ../qualityControl.cfg --action insert
../../add_analysis.pl --configfile ./demo1.cfg --action insert
../../add_analysis.pl --configfile ./demo2.cfg --action insert
--- 10,13 ----
Index: test_quality.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/test_quality.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
*** test_quality.pl 17 Dec 2002 18:20:51 -0000 1.1.2.1
--- test_quality.pl 18 Dec 2002 03:28:53 -0000 1.1.2.2
***************
*** 38,44 ****
# insert initial input file values
$stm = "insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (NULL, '/tmp/in.qcin', 't', 'initial input file for qualityControl');";
$stm .="insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (NULL, '/tmp/qctreelog.txt', 'f', 'logfile for qualityControl');";
my $sth = $dbh->prepare($stm);
$sth->execute();
--- 38,44 ----
# insert initial input file values
$stm = "insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (NULL, 'in.qcin', 't', 'initial input file for qualityControl');";
$stm .="insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (NULL, 'qctreelog.txt', 'f', 'logfile for qualityControl');";
my $sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 84,95 ****
$stm = "insert into tree (tree_name, fi_input_fk, fi_log_fk) values ('qcTree', $fi_ifk, $fi_lfk)";
}
else
{
! $stm = "delete from tree where tree_name = 'qcTree'";
}
- $sth = $dbh->prepare($stm);
- $sth->execute();
$dbh->commit();
--- 84,99 ----
$stm = "insert into tree (tree_name, fi_input_fk, fi_log_fk) values ('qcTree', $fi_ifk, $fi_lfk)";
+ $sth = $dbh->prepare($stm);
+ $sth->execute();
+ my $us_fk = get_us_fk($dbh);
+ my $in_pk = insert_security($dbh, $us_fk, $us_fk, 0);
}
else
{
! $stm = "delete from tree where tree_name = 'qcTree'";
! $sth = $dbh->prepare($stm);
! $sth->execute();
}
$dbh->commit();
***************
*** 189,193 ****
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, '=/tmp/out.qcout', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 193,197 ----
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, 'out.qcout', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 200,204 ****
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, '=/tmp/qclog.log', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 204,208 ----
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, 'qclog.log', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 211,215 ****
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, '=/tmp/qc.txt', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 215,219 ----
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, 'qc.txt', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 222,226 ****
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, '=/tmp/qc.jpg', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 226,230 ----
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
! " values ($node_fk, 'qc.jpg', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 280,288 ****
my $spn_fk = $sth->fetchrow_array;
! my $email = "=tdj4mvirginia.edu";
! $stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
! " values ($node_fk, '$email', $spn_fk);";
$sth = $dbh->prepare($stm);
! $sth->execute();
$stm = "select spn_pk from sys_parameter_names " .
--- 284,291 ----
my $spn_fk = $sth->fetchrow_array;
! my $email = 'tdj4\@mvirginia.edu';
! $stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk) values ($node_fk,?, $spn_fk);";
$sth = $dbh->prepare($stm);
! $sth->execute($email);
$stm = "select spn_pk from sys_parameter_names " .
***************
*** 304,308 ****
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
! " values ($node_fk, '=/tmp', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 307,311 ----
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
! " values ($node_fk, '', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 315,319 ****
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
! " values ($node_fk, '=/tmp', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 318,322 ----
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
! " values ($node_fk, '', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 327,331 ****
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
! " values ($node_fk, '=/tmp/in.qcin', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 330,334 ----
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
! " values ($node_fk, 'in.qcin', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
|
|
From: <tw...@us...> - 2002-12-18 02:16:39
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv17186
Modified Files:
Tag: Rel-1_0_1-branch
runtree.pl getfile.pl edit_atree2.pl
Log Message:
integration tree fixes
Index: runtree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/runtree.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
*** runtree.pl 17 Dec 2002 18:25:27 -0000 1.1.2.4
--- runtree.pl 18 Dec 2002 02:16:36 -0000 1.1.2.5
***************
*** 4,35 ****
# 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;
! require "sessionlib.pl";
! #command line options
! my $debug ='';
! my $treeName ='';
! my $owner='';
getOptions();
!
runChain($treeName, $owner);
!
sub runChain
{
--- 4,37 ----
# 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;
! require "sessionlib.pl";
! #command line options
! my $debug ='';
! my $treeName ='';
! my $owner='';
+ main:
+ {
getOptions();
!
runChain($treeName, $owner);
! }
sub runChain
{
***************
*** 49,66 ****
{
$dbh->disconnect;
! die "Tree: $treeName doesn't exist in db";
}
if ($sth->fetchrow_array())
{
! die "Too many tree records with name $name and owner $owner.\n";
}
# determine log name
! $stm="select file_name from file_info,tree where fi_pk = fi_log_fk and tree_pk = $tree_pk";
! $sth=$dbh->prepare($stm);
! $sth->execute;
!
! my ($logfile) = $sth->fetchrow_array;
open(LOG, "> $logfile") or die "Unable to open $logfile: $!\n";
print LOG `date`;
--- 51,74 ----
{
$dbh->disconnect;
! write_log("Tree: $treeName doesn't exist in db");
! exit();
}
if ($sth->fetchrow_array())
{
! write_log("Too many tree records with name $name and owner $owner.\n");
! exit();
}
# determine log name
! # $stm="select file_name from file_info,tree where fi_pk = fi_log_fk and tree_pk = $tree_pk";
! #$sth=$dbh->prepare($stm);
! # $sth->execute;
! # my ($logfile) = $sth->fetchrow_array;
! my $logfile = $treeName;
! $logfile = lc($logfile);
! $logfile =~ s/[^a-z0-9]/_/g;
! $logfile = "/var/genres/$ENV{REMOTE_USER}/$logfile.log";
!
open(LOG, "> $logfile") or die "Unable to open $logfile: $!\n";
print LOG `date`;
***************
*** 69,72 ****
--- 77,83 ----
processTree($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
***************
*** 157,161 ****
if ($found == 1)
{
! warn "Great trauma! There are two appropriate input files. infile:$infile";
}
$found = 1;
--- 168,172 ----
if ($found == 1)
{
! write_log( "Great trauma! There are two appropriate input files. infile:$infile");
}
$found = 1;
***************
*** 178,182 ****
if ($found == 0)
{
! warn "No input file with type: $ext for node: $child_node_pk an_pk: $child_an_fk\n";
$have_all_inputs = 0;
}
--- 189,193 ----
if ($found == 0)
{
! write_log( "No input file with type: $ext for node: $child_node_pk an_pk: $child_an_fk\n");
$have_all_inputs = 0;
}
***************
*** 191,196 ****
{
my ($dbh, $node_pk, $an_fk, $logfile) = @_;
-
my ($stm, $sth);
# get command string from analysis
--- 202,207 ----
{
my ($dbh, $node_pk, $an_fk, $logfile) = @_;
my ($stm, $sth);
+ my @created_files;
# get command string from analysis
***************
*** 203,207 ****
{
print $logfile "Unable to cmdstr for analysis key: $an_fk";
! warn "Unable to cmdstr for analysis key: $an_fk";
}
--- 214,218 ----
{
print $logfile "Unable to cmdstr for analysis key: $an_fk";
! write_log( "Unable to cmdstr for analysis key: $an_fk");
}
***************
*** 227,234 ****
if ($sth2->fetchrow_array)
{
! warn "Uh oh!! Never should have multiple returns!";
}
! $userParams .= $up_name . "$up_value ";
# TODO - do I need to use default or does Tom set?
}
--- 238,257 ----
if ($sth2->fetchrow_array)
{
! write_log( "Uh oh!! Never should have multiple returns!");
}
! if ($up_value =~ m/\=/)
! {
! $userParams .= "$up_name$up_value ";
! }
! elsif ($up_name =~ m/file|out/i)
! {
! $userParams .= "$up_name=/var/genres/$ENV{REMOTE_USER}/$up_value ";
! push(@created_files, "/var/genres/$ENV{REMOTE_USER}/$up_value");
! }
! else
! {
! $userParams .= "$up_name=$up_value ";
! }
# TODO - do I need to use default or does Tom set?
}
***************
*** 255,262 ****
if ($sth2->fetchrow_array)
{
! warn "Uh oh!! Never should have multiple returns!";
}
! $sysParams .= $sp_name . "$sp_value ";
# TODO - do I need to use default or does Tom set?
}
--- 278,298 ----
if ($sth2->fetchrow_array)
{
! write_log( "Uh oh!! Never should have multiple returns!");
}
! if ($sp_value =~ m/\=/)
! {
! $sysParams .= "$sp_name$sp_value ";
! #$userParams .= "$up_name$up_value ";
! }
! elsif ($sp_name =~ m/file|path/i) # what a hack.
! {
! $sysParams .= "$sp_name=/var/genres/$ENV{REMOTE_USER}/$sp_value ";
! }
! else
! {
! $sysParams .= "$sp_name=$sp_value ";
! #$userParams .= "$up_name=$up_value ";
! }
# TODO - do I need to use default or does Tom set?
}
***************
*** 266,285 ****
print $logfile "Running cmd:\n$cmd\n";
my $rc = system("$cmd");
! warn "Bad return value from: $cmd" if $rc;
#verify existence of output files and insert into file_info table
-
- $stm="select arg_name from analysis_filetypes_link," .
- " filetypes,analysis,node where input='f' and " .
- " ft_pk=ft_fk and analysis_filetypes_link.an_fk = an_pk ".
- " and an_pk=node.an_fk and node_pk = $node_pk";
- my $sth2 = $dbh->prepare($stm);
- $sth2->execute();
! while (my ($fileprefix) = $sth2->fetchrow_array)
{
! $userParams =~ /$fileprefix\s*'?([\S]+)'?\s/;
! my $filename = $1;
! insertFile($dbh, $node_pk, $filename);
}
--- 302,334 ----
print $logfile "Running cmd:\n$cmd\n";
my $rc = system("$cmd");
! write_log( "Bad return value from: $cmd") if $rc;
#verify existence of output files and insert into file_info table
! foreach my $created (@created_files)
{
! if ((-e $created) and (! -d $created))
! {
! insertFile($dbh, $node_pk, $created);
! }
! }
!
! if (0 == 1)
! {
!
! $stm="select arg_name from analysis_filetypes_link," .
! " filetypes,analysis,node where input='f' and " .
! " ft_pk=ft_fk and analysis_filetypes_link.an_fk = an_pk ".
! " and an_pk=node.an_fk and node_pk = $node_pk";
! my $sth2 = $dbh->prepare($stm);
! $sth2->execute();
!
! while (my ($fileprefix) = $sth2->fetchrow_array)
! {
! $userParams =~ /$fileprefix\s*'?([\S]+)'?\s/;
! my $filename = $1;
! write_log("f:$filename up:$userParams");
! insertFile($dbh, $node_pk, $filename);
! }
}
***************
*** 302,305 ****
--- 351,356 ----
# my $sth= $dbh->prepare($stm);
# $sth->execute();
+
+ $file =~ s/^\=//; # remove leading =
my $fi_pk = fi_update($dbh, $us_fk, $us_fk, $file, $comments);
Index: getfile.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/getfile.pl,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** getfile.pl 10 Dec 2002 21:39:15 -0000 1.1.2.4
--- getfile.pl 18 Dec 2002 02:16:36 -0000 1.1.2.5
***************
*** 93,97 ****
print "$::all_lines";
}
! elsif ($file =~ m/\.txt|.rpt|.exp/)
{
#
--- 93,97 ----
print "$::all_lines";
}
! elsif ($file =~ m/\.txt|.rpt|.exp|.log|.qcout/)
{
#
Index: edit_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree2.pl,v
retrieving revision 1.1.2.13
retrieving revision 1.1.2.14
diff -C2 -d -r1.1.2.13 -r1.1.2.14
*** edit_atree2.pl 17 Dec 2002 21:33:32 -0000 1.1.2.13
--- edit_atree2.pl 18 Dec 2002 02:16:36 -0000 1.1.2.14
***************
*** 16,22 ****
my $us_fk = get_us_fk($dbh);
-
-
-
my %tree = read_tree($q);
write_db($dbh, \%tree);
--- 16,19 ----
***************
*** 56,64 ****
my %ch = $q->Vars();
my %tree;
-
- foreach my $key (keys(%ENV))
- {
- write_log("$key: $ENV{$key}");
- }
foreach my $key (keys(%ch))
--- 53,56 ----
|
|
From: <tw...@us...> - 2002-12-17 22:06:28
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv17725
Modified Files:
Tag: Rel-1_0_1-branch
edit_atree1.pl edit_atree1.html edit_atree2.pl
Log Message:
fixes
Index: edit_atree1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.pl,v
retrieving revision 1.1.2.9
retrieving revision 1.1.2.10
diff -C2 -d -r1.1.2.9 -r1.1.2.10
*** edit_atree1.pl 17 Dec 2002 15:02:05 -0000 1.1.2.9
--- edit_atree1.pl 17 Dec 2002 21:33:32 -0000 1.1.2.10
***************
*** 52,58 ****
while( $hr = $sth->fetchrow_hashref())
{
if ($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";
}
elsif ($hr->{up_type} =~ m/^radio/)
--- 52,61 ----
while( $hr = $sth->fetchrow_hashref())
{
+ my $temp = CGI::escape($hr->{up_value});
+ write_log("t: $temp");
if ($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";
}
elsif ($hr->{up_type} =~ m/^radio/)
Index: edit_atree1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.html,v
retrieving revision 1.1.2.12
retrieving revision 1.1.2.13
diff -C2 -d -r1.1.2.12 -r1.1.2.13
*** edit_atree1.html 17 Dec 2002 15:02:23 -0000 1.1.2.12
--- edit_atree1.html 17 Dec 2002 21:33:32 -0000 1.1.2.13
***************
*** 15,19 ****
</tr>
</table>
! <form action="edit_atree2.pl" method=POST>
Analysis tree name: {tree_name}
<input type="text" name="tree_name" value="{tree_name}"> <input type="submit" name="Update" value="Update Name">
--- 15,19 ----
</tr>
</table>
! <form action="edit_atree2.pl" method=GET>
Analysis tree name: {tree_name}
<input type="text" name="tree_name" value="{tree_name}"> <input type="submit" name="Update" value="Update Name">
Index: edit_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree2.pl,v
retrieving revision 1.1.2.12
retrieving revision 1.1.2.13
diff -C2 -d -r1.1.2.12 -r1.1.2.13
*** edit_atree2.pl 17 Dec 2002 15:02:21 -0000 1.1.2.12
--- edit_atree2.pl 17 Dec 2002 21:33:32 -0000 1.1.2.13
***************
*** 16,19 ****
--- 16,21 ----
my $us_fk = get_us_fk($dbh);
+
+
my %tree = read_tree($q);
***************
*** 55,58 ****
--- 57,65 ----
my %tree;
+ foreach my $key (keys(%ENV))
+ {
+ write_log("$key: $ENV{$key}");
+ }
+
foreach my $key (keys(%ch))
{
***************
*** 76,79 ****
--- 83,87 ----
{
$tree{$key} = $ch{$key};
+ # write_log("$key: $ch{$key}");
}
}
|
|
From: <td...@us...> - 2002-12-17 21:56:22
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis/test
In directory sc8-pr-cvs1:/tmp/cvs-serv25184
Modified Files:
Tag: Rel-1_0_1-branch
populate depopulate
Log Message:
added new cfgs
Index: populate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/populate,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** populate 17 Dec 2002 21:34:33 -0000 1.1.2.4
--- populate 17 Dec 2002 21:52:41 -0000 1.1.2.5
***************
*** 1,9 ****
../../add_analysis.pl --configfile ../qualityControl.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
--- 1,18 ----
+ ../../add_analysis.pl --configfile ../statAnalysis.cfg --action insert
+ ../../add_analysis.pl --configfile ../foldChange.cfg --action insert
+ ../../add_analysis.pl --configfile ../cluster.cfg --action insert
+ ../../add_analysis.pl --configfile ../genBank.cfg --action insert
+ ../../add_analysis.pl --configfile ../geneOnt.cfg --action insert
+ ../../add_analysis.pl --configfile ../locusLink.cfg --action insert
+ ../../add_analysis.pl --configfile ../lowessNorm.cfg --action insert
+ ../../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 ../qualityControl.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
Index: depopulate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/depopulate,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** depopulate 17 Dec 2002 21:34:33 -0000 1.1.2.4
--- depopulate 17 Dec 2002 21:52:41 -0000 1.1.2.5
***************
*** 1,10 ****
- #./test_tree.pl --action remove
./test_quality.pl --action remove
../../add_analysis.pl --configfile ../qualityControl.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
--- 1,24 ----
./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
! ../../add_analysis.pl --configfile ../locusLink.cfg --action remove
! ../../add_analysis.pl --configfile ../lowessNorm.cfg --action remove
! ../../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
|
|
From: <td...@us...> - 2002-12-17 21:49:59
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv24172
Added Files:
Tag: Rel-1_0_1-branch
cluster.cfg foldChange.cfg genBank.cfg geneOnt.cfg
locusLink.cfg lowessNorm.cfg ttest.cfg unigene.cfg
Log Message:
For demo purposes
--- NEW FILE: cluster.cfg ---
## filetypes
filetype = name=clusterin
filetype = comment=Input file for clusering
filetype = arg_name=--infile
filetype = name=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=clusterin
extension = ext=lnin
extension = filetype=clusterout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = clusering
cmdstr = ./analysis/Rwrapper.pl --kind cluster
#analysis_filetypes_link
analysisfile = filetype=clusterin
analysisfile = input =1
analysisfile = filetype=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: foldChange.cfg ---
## filetypes
filetype = name=foldin
filetype = comment=Input file for fold change
filetype = arg_name=--infile
filetype = name=foldout
filetype = comment=Data output for fold change
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=foldin
extension = ext=lnin
extension = filetype=foldout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = fold change
cmdstr = ./analysis/Rwrapper.pl --kind foldChange
#analysis_filetypes_link
analysisfile = filetype=foldin
analysisfile = input =1
analysisfile = filetype=foldout
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: genBank.cfg ---
## filetypes
filetype = name=genBankin
filetype = comment=Input file for NCBI GenBank
filetype = arg_name=--infile
filetype = name=genBankout
filetype = comment=Data output for NCBI GenBank
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=genBankin
extension = ext=lnin
extension = filetype=genBankout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = NCBI GenBank
cmdstr = ./analysis/Rwrapper.pl --kind genBank
#analysis_filetypes_link
analysisfile = filetype=genBankin
analysisfile = input =1
analysisfile = filetype=genBankout
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: geneOnt.cfg ---
## filetypes
filetype = name=geneOntin
filetype = comment=Input file for Gene Ontology
filetype = arg_name=--infile
filetype = name=geneOntout
filetype = comment=Data output for Gene Ontology
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=geneOntin
extension = ext=lnin
extension = filetype=geneOntout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = Gene Ontology
cmdstr = ./analysis/Rwrapper.pl --kind geneOnt
#analysis_filetypes_link
analysisfile = filetype=geneOntin
analysisfile = input =1
analysisfile = filetype=geneOntout
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: locusLink.cfg ---
## filetypes
filetype = name=locusin
filetype = comment=Input file for locus link
filetype = arg_name=--infile
filetype = name=locusout
filetype = comment=Data output for locus link
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=locusin
extension = ext=lnin
extension = filetype=locusout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = locus link
cmdstr = ./analysis/Rwrapper.pl --kind locus
#analysis_filetypes_link
analysisfile = filetype=locusin
analysisfile = input =1
analysisfile = filetype=locusout
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: lowessNorm.cfg ---
## filetypes
filetype = name=lowessin
filetype = comment=Input file for lowess normalization
filetype = arg_name=--infile
filetype = name=lowessout
filetype = comment=Data output for lowess normalization
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=lowessin
extension = ext=lnin
extension = filetype=lowessout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = lowess normalization
cmdstr = ./analysis/Rwrapper.pl --kind lowessNorm
#analysis_filetypes_link
analysisfile = filetype=lowessin
analysisfile = input =1
analysisfile = filetype=lowessout
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: ttest.cfg ---
## filetypes
filetype = name=ttestin
filetype = comment=Input file for t-test
filetype = arg_name=--infile
filetype = name=ttestout
filetype = comment=Data output for t-test
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=ttestin
extension = ext=lnin
extension = filetype=ttestout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = t-test
cmdstr = ./analysis/Rwrapper.pl --kind ttest
#analysis_filetypes_link
analysisfile = filetype=ttestin
analysisfile = input =1
analysisfile = filetype=ttestout
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: unigene.cfg ---
## filetypes
filetype = name=unigenein
filetype = comment=Input file for UniGene
filetype = arg_name=--infile
filetype = name=unigeneout
filetype = comment=Data output for UniGene
filetype = arg_name=--outfile
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=unigenein
extension = ext=lnin
extension = filetype=unigeneout
extension = ext=lnout
extension = filetype=log
extension = ext=txt
# analysis
name = UniGene
cmdstr = ./analysis/Rwrapper.pl --kind unigene
#analysis_filetypes_link
analysisfile = filetype=unigenein
analysisfile = input =1
analysisfile = filetype=unigeneout
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
|
|
From: <tw...@us...> - 2002-12-17 21:38:37
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv19857
Added Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
New.
--- NEW FILE: makefile ---
all : rw_files ssc_files cfg_files pl_files
NOOP = $(SHELL) -c true
DEST = /var/www/html/genex/webtools
pl_srcs := $(patsubst %.pl,$(DEST)/%.pl,$(wildcard *.pl))
pl_files: $(pl_srcs)
$(DEST)/%.pl : ./%.pl
./config.pl $<
rw_srcs := $(patsubst %.rw,$(DEST)/%.rw,$(wildcard *.rw))
rw_files : $(rw_srcs)
$(DEST)/%.rw : ./%.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)
cfg_srcs := $(patsubst %.cfg,$(DEST)/%.cfg,$(wildcard *.cfg))
cfg_files : $(cfg_srcs)
$(DEST)/%.cfg : ./%.cfg
cp -f $< $(DEST)
|
|
From: <tw...@us...> - 2002-12-17 21:34:37
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis/test
In directory sc8-pr-cvs1:/tmp/cvs-serv18132
Modified Files:
Tag: Rel-1_0_1-branch
populate depopulate
Log Message:
fixes for qc
Index: populate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/populate,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** populate 17 Dec 2002 14:01:47 -0000 1.1.2.3
--- populate 17 Dec 2002 21:34:33 -0000 1.1.2.4
***************
*** 1,9 ****
! ../../add_analysis.pl --configfile ./qualityControl.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
cat > /tmp/initial_in << EOF
This is the
--- 1,10 ----
! ../../add_analysis.pl --configfile ../qualityControl.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
Index: depopulate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/depopulate,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** depopulate 17 Dec 2002 14:01:47 -0000 1.1.2.3
--- depopulate 17 Dec 2002 21:34:33 -0000 1.1.2.4
***************
*** 1,9 ****
! ./test_tree.pl --action remove
! ../../add_analysis.pl --configfile ./qualityControl.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
--- 1,10 ----
! #./test_tree.pl --action remove
! ./test_quality.pl --action remove
! ../../add_analysis.pl --configfile ../qualityControl.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
|
|
From: <tw...@us...> - 2002-12-17 20:53:40
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv2019
Modified Files:
Tag: Rel-1_0_1-branch
qualityControl.cfg
Log Message:
remove space in "= test" to make it "=test"
Index: qualityControl.cfg
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/Attic/qualityControl.cfg,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** qualityControl.cfg 17 Dec 2002 18:24:23 -0000 1.1.2.2
--- qualityControl.cfg 17 Dec 2002 20:53:35 -0000 1.1.2.3
***************
*** 71,87 ****
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
up = name=--settings outgph
up = display_name = Graphical output filename
! up = type= text
up = name=--settings outtxt
up = display_name = Statistical output filename
! up = type= text
--- 71,87 ----
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
up = name=--settings outgph
up = display_name = Graphical output filename
! up = type=text
up = name=--settings outtxt
up = display_name = Statistical output filename
! up = type=text
|
|
From: <jas...@us...> - 2002-12-17 19:55:59
|
Update of /cvsroot/genex/genex-server/DB/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv10362/DB/scripts
Added Files:
fix-array-mas5.pl tab2AD-mas5.pl
Log Message:
new files for MAS5
--- NEW FILE: fix-array-mas5.pl ---
#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
my %OPTIONS;
my $rc = GetOptions(\%OPTIONS,
'infile=s',
'design=s',
'help',
);
my $USAGE = <<"EOU";
usage: $0 [required flags] file1 ...
required flags:
--infile=file : the file to read
--design=file : the array design file to create
optional flags:
--help : print this message
EOU
die "Bad option\n$USAGE" unless $rc;
die $USAGE if exists $OPTIONS{help};
die "Must specify --infile\n$USAGE"
unless exists $OPTIONS{infile};
die "Must specify --design\n$USAGE"
unless exists $OPTIONS{design};
open(IN,"$OPTIONS{infile}")
or die "Couldn't open $OPTIONS{infile} for reading";
open(DESIGN,">$OPTIONS{design}")
or die "Couldn't open $OPTIONS{design} for writing";
print DESIGN "# id\tname\n";
# 0) Line Num
# 1) Analysis Name
# 2) Probe Set Name
# 3) Stat Pairs
# 4) Stat Pairs Used
# 5) Signal
# 6) Detection
# 7) Detection p-value
# 8) Stat Common Pairs
# 9) Signal Log Ratio
# 10) Signal Log Ratio Low
# 11) Signal Log Ratio High
# 12) Change
# 13) Change p-value
# 14) Positive
# 15) Negative
# 16) Pairs
# 17) Pairs Used
# 18) Pairs InAvg
# 19) Pos Fraction
# 20) Log Avg
# 21) Pos/Neg
# 22) Avg Diff
# 23) Abs Call
# 24) Inc
# 25) Dec
# 26) Inc Ratio
# 27) Dec Ratio
# 28) Pos Change
# 29) Neg Change
# 30) Inc/Dec
# 31) DPos-DNeg Ratio
# 32) Log Avg Ratio Change
# 33) Diff Call
# 34) Avg Diff Change
# 35) B=A
# 36) Fold Change
# 37) Sort Score
# all we need are:
# 0) Line Num
# 2) Probe Set Name
my @INDICES = qw(0 2);
my $in_data;
my $data_start_regexp = qr/^Expression\s+Analysis/o;
my $reading_data;
my $reading_data_regexp = qr/^\tAnalysis/;
my @spots;
my $count = 0;
my %REPS;
my %IDS;
while (<IN>) {
# see if we've found the Data section already
unless ($in_data or /$data_start_regexp/) {
next;
}
# check if this is the beginning of the Data section
if (/$data_start_regexp/) {
$in_data = 1;
next;
}
# don't proceed unless we've past the Data section header line
next unless $reading_data or /$reading_data_regexp/;
# check if this is the header line of the Data section
if (/$reading_data_regexp/) {
$reading_data = 1;
next;
}
# when we reach the end of the Data section, we're done
last if /^End/;
my @data = split /\t/;
my ($num,$name) = @data[@INDICES];
# commence error checking
die "No line number"
unless defined $num;
die "Bad line number: $num"
if exists $IDS{$num};
die "Bad reporter: $name"
if exists $REPS{$name};
if (exists $OPTIONS{design}) {
print DESIGN "$num\t$name\n";
}
}
print STDERR "Finished\n";
--- NEW FILE: tab2AD-mas5.pl ---
#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
use Bio::MAGE 20020902.3 qw(:ALL);
use Bio::MAGE::XMLUtils;
use Benchmark;
my %OPTIONS;
my $rc = GetOptions(\%OPTIONS,
'infile=s',
'outfile=s',
'ad_identifier=s',
'fg_identifier=s',
'rg_identifier=s',
'help',
);
my $USAGE = <<"EOU";
usage: $0 [required flags] file1 ...
required flags:
--infile=file : the tab-delimited file to read
--outfile=file : the array design XML file to create
--ad_identifier=id : the identifier to use for the ArrayDesign
optional flags:
--fg_identifier=id : the identifier to use for the FeatureGroup
--rg_identifier=id : the identifier to use for the ReporterGroup
--help : print this message
EOU
die "Bad option\n$USAGE" unless $rc;
die $USAGE if exists $OPTIONS{help};
die "Must specify --infile\n$USAGE"
unless exists $OPTIONS{infile};
die "Must specify --outfile\n$USAGE"
unless exists $OPTIONS{outfile};
die "Must specify --identifier\n$USAGE"
unless exists $OPTIONS{ad_identifier};
unless (exists $OPTIONS{fg_identifier}) {
$OPTIONS{fg_identifier} = $OPTIONS{ad_identifier};
$OPTIONS{fg_identifier} =~ s/ArrayDesign/FeatureGroup/;
}
unless (exists $OPTIONS{rg_identifier}) {
$OPTIONS{rg_identifier} = $OPTIONS{ad_identifier};
$OPTIONS{rg_identifier} =~ s/ArrayDesign/ReporterGroup/;
}
open(IN,"$OPTIONS{infile}")
or die "Couldn't open $OPTIONS{infile} for reading";
open(OUT,">$OPTIONS{outfile}")
or die "Couldn't open $OPTIONS{outfile} for writing";
my %reporters;
my $num_features;
my $start = new Benchmark;
my $fg = Bio::MAGE::ArrayDesign::FeatureGroup->new(identifier=>"$OPTIONS{fg_identifier}",
name=>"$OPTIONS{fg_identifier}"
);
my $rg = Bio::MAGE::ArrayDesign::ReporterGroup->new(identifier=>"$OPTIONS{rg_identifier}",
name=>"$OPTIONS{rg_identifier}"
);
my $zone;
while (<IN>) {
next if /^\#/; # skip comment lines
chomp;
my ($id, $name) = split /\t/;
my $feature = Bio::MAGE::DesignElement::Feature->new(identifier=>"$id",
name=>$id,
);
$fg->addFeatures($feature);
# create a Reporter if necessary
my $reporter = $reporters{$name};
unless (defined $reporter) {
$reporter = Bio::MAGE::DesignElement::Reporter->new(identifier=>"Reporter:$name",
name=>$name,
);
$rg->addReporters($reporter);
$reporters{$name} = $reporter;
}
# create a FeatureReporterMap if necessary
unless (defined $reporter->getFeatureReporterMaps()) {
my $map = Bio::MAGE::DesignElement::FeatureReporterMap->new(identifier=>"FeatureReporterMap:$name",
name=>"FeatureReporterMap:$name");
$map->setReporter($reporter);
$reporter->addFeatureReporterMaps($map);
}
# map the Feature to the Reporter
my $map_ref = $reporter->getFeatureReporterMaps();
my $info = Bio::MAGE::DesignElement::FeatureInformation->new(feature=>$feature,
);
$map_ref->[0]->addFeatureInformationSources($info);
$num_features++;
print "Completed $num_features\n" if $num_features % 1000 == 0;
}
print STDERR "Found $num_features features\n";
my $stop = new Benchmark;
my $diff = timediff($stop,$start);
print STDERR "Parsing took:", timestr($diff),"\n";
print STDERR "Found $num_features features\n";
my $ad = Bio::MAGE::ArrayDesign::PhysicalArrayDesign->new(identifier=>$OPTIONS{ad_identifier},
numberOfFeatures=>$num_features,
featureGroups=>[$fg],
reporterGroups=>[$rg],
);
print STDERR "Creating the MAGE object\n";
$start = new Benchmark;
my $mage = Bio::MAGE->new(identifier=>"MAGE-$OPTIONS{ad_identifier}",
objects=>[$ad]
);
$stop = new Benchmark;
$diff = timediff($stop,$start);
print STDERR "MAGE creation took:", timestr($diff),"\n";
print STDERR "Writing MAGE-ML\n";
$start = new Benchmark;
my $writer = Bio::MAGE::XML::Writer->new(fh=>\*OUT);
$writer->write($mage);
$stop = new Benchmark;
$diff = timediff($stop,$start);
print STDERR "Writing XML took:", timestr($diff),"\n";
print STDERR "Finished\n";
|
|
From: <jas...@us...> - 2002-12-17 19:53:33
|
Update of /cvsroot/genex/genex-server/Genex/Connect
In directory sc8-pr-cvs1:/tmp/cvs-serv9405/Genex/Connect
Modified Files:
Connect.pm.in
Log Message:
* Connect/Connect.pm.in (Repository):
added some more string types to ontology_type2sql_type()
Index: Connect.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Connect/Connect.pm.in,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Connect.pm.in 9 Nov 2002 00:32:04 -0000 1.9
--- Connect.pm.in 17 Dec 2002 19:53:28 -0000 1.10
***************
*** 1453,1456 ****
--- 1453,1460 ----
} elsif ($type eq 'char24') {
$data_type = 'varchar(24)';
+ } elsif ($type eq 'char128') {
+ $data_type = 'varchar(128)';
+ } elsif ($type eq 'text') {
+ $data_type = 'text';
} else {
$dbh->error(@error_args,
|
|
From: <tw...@us...> - 2002-12-17 19:01:09
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv22312
Modified Files:
Tag: Rel-1_0_1-branch
chgrp_order1.html chgrp_study1.html choose_order.html
choose_study.html edit_am1.html edit_sample1.html index.html
view_orders.html
Log Message:
html format fix
Index: chgrp_order1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp_order1.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
*** chgrp_order1.html 26 Nov 2002 21:36:12 -0000 1.1.2.1
--- chgrp_order1.html 17 Dec 2002 19:00:42 -0000 1.1.2.2
***************
*** 1,18 ****
<html><head><title>Manage Order group ownership and permissions</title></head>
<body bgcolor="#FFFFFF">
! <table width="600" border=0 cellpadding=0 cellspacing=0>
! <tr>
! <td align=top><img src="../graphics/genex_logo.jpg" align="left">Change Order
! group, permissions<br>
! <br>
<a href="./">Return to Genex Member Home</a>
- <br><br clear=all><br>
- Change the group and/or read-write permissions of your orders.<br>
- Samples and hybridizations within a given order will be given the same permissions
- as the order.<br>
- <font color="#FF0000">{message}</font>
</td>
</tr>
</table>
<br>
<form action="chgrp_order2.pl" method="post">
--- 1,13 ----
<html><head><title>Manage Order group ownership and permissions</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">Change Order group, permissions<br><br>
<a href="./">Return to Genex Member Home</a>
</td>
</tr>
</table>
+ <font color="#FF0000">{message}</font>
<br>
<form action="chgrp_order2.pl" method="post">
Index: chgrp_study1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/chgrp_study1.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
*** chgrp_study1.html 26 Nov 2002 21:36:12 -0000 1.1.2.2
--- chgrp_study1.html 17 Dec 2002 19:00:44 -0000 1.1.2.3
***************
*** 2,8 ****
<body bgcolor="#FFFFFF">
<table width="600" border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">Change Study group, permissions<br><br>
<a href="./">Return to Genex Member Home</a>
! <br><br clear=all><br>
Change the group ownership and/or group read-write permissions.<br>
The experimental conditions for each study will be changed to reflect study
--- 2,10 ----
<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>Change Study group, permissions<br><br>
<a href="./">Return to Genex Member Home</a>
! <br><br><br>
Change the group ownership and/or group read-write permissions.<br>
The experimental conditions for each study will be changed to reflect study
Index: choose_order.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_order.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.html 27 Nov 2002 14:29:49 -0000 1.1.2.2
--- choose_order.html 17 Dec 2002 19:00:46 -0000 1.1.2.3
***************
*** 1,7 ****
<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">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><br><br></td>
! <td> </td>
! <td valign="top">GeneX Account Update<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
Index: choose_study.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_study.html,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** choose_study.html 27 Nov 2002 14:29:49 -0000 1.1.2.3
--- choose_study.html 17 Dec 2002 19:00:46 -0000 1.1.2.4
***************
*** 1,7 ****
<html><head><title>Choose a Study</title></head>
<body bgcolor="#FFFFFF">
! <table border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Study Selection<br><br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
--- 1,9 ----
<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 Study Selection<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
Index: edit_am1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_am1.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
*** edit_am1.html 21 Nov 2002 18:48:48 -0000 1.1.2.2
--- edit_am1.html 17 Dec 2002 19:00:48 -0000 1.1.2.3
***************
*** 1,10 ****
<html><head><title>Edit hybridizations</title></head>
<body bgcolor="#FFFFFF">
! <table border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Hybridizations Update<br><br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
</table>
<br>
Please choose the Affymetrix chip for each hybridization of the following samples.
--- 1,13 ----
<html><head><title>Edit 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 Hybridizations Update<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
</table>
+
<br>
Please choose the Affymetrix chip for each hybridization of the following samples.
Index: edit_sample1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_sample1.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
*** edit_sample1.html 15 Nov 2002 15:16:28 -0000 1.1.2.2
--- edit_sample1.html 17 Dec 2002 19:00:49 -0000 1.1.2.3
***************
*** 1,10 ****
<html><head><title>Edit/update sample information</title></head>
<body bgcolor="#FFFFFF">
! <table border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Sample Info Update<br><br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
</table>
<br>
<font color="#FF0000"><b>{message}</b></font>
--- 1,13 ----
<html><head><title>Edit/update sample information</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 Sample Info Update<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
</table>
+
<br>
<font color="#FF0000"><b>{message}</b></font>
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/index.html,v
retrieving revision 1.1.2.5
retrieving revision 1.1.2.6
diff -C2 -d -r1.1.2.5 -r1.1.2.6
*** index.html 27 Nov 2002 14:49:42 -0000 1.1.2.5
--- index.html 17 Dec 2002 19:00:50 -0000 1.1.2.6
***************
*** 2,9 ****
<head><title>GeneX Members</title></head>
<body bgcolor="#FFFFFF">
! <img src="../graphics/genex_logo.jpg" align="left"><font size="+1">Genex Member Home Page</font>
! <br><br>
! Return to <a href="../">local Genex Home Page</a>
! <br><br clear=all>
<table width="600" border="0" cellpadding="3" cellspacing="0">
<tr>
--- 2,14 ----
<head><title>GeneX Members</title></head>
<body bgcolor="#FFFFFF">
! <table width=600 border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top width=207><a href="./"><img src="../graphics/genex_logo.jpg" border=0 width=207 height=87></a><br><br></td>
! <td> </td>
! <td valign="top">Genex Member Home Page<br><br>
! Return to <a href="../">local Genex Home Page</a>
! </td>
! </tr>
! </table>
!
<table width="600" border="0" cellpadding="3" cellspacing="0">
<tr>
Index: view_orders.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/view_orders.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
*** view_orders.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- view_orders.html 17 Dec 2002 19:00:52 -0000 1.1.2.2
***************
*** 1,7 ****
<html><head><title>View all your orders</title></head>
<body bgcolor="#FFFFFF">
! <table border=0 cellpadding=0 cellspacing=0>
! <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Report of all Orders<br><br>
! <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
</td>
</tr>
--- 1,9 ----
<html><head><title>View all your orders</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><br><br></td>
! <td> </td>
! <td valign="top">GeneX Report of all Orders<br><br>
! <a href="./">Return to Genex Member Home</a>
</td>
</tr>
|
|
From: <jl...@us...> - 2002-12-17 18:26:29
|
Update of /cvsroot/genex/genex-server/site/graphics
In directory sc8-pr-cvs1:/tmp/cvs-serv8912
Modified Files:
Tag: Rel-1_0_1-branch
genex_logo.jpg
Log Message:
cropped
Index: genex_logo.jpg
===================================================================
RCS file: /cvsroot/genex/genex-server/site/graphics/Attic/genex_logo.jpg,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
Binary files /tmp/cvsVVCLhx and /tmp/cvsiJWKhU differ
|
|
From: <td...@us...> - 2002-12-17 18:25:32
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv8600
Modified Files:
Tag: Rel-1_0_1-branch
runtree.pl
Log Message:
Updated
Index: runtree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/runtree.pl,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** runtree.pl 16 Dec 2002 21:16:58 -0000 1.1.2.3
--- runtree.pl 17 Dec 2002 18:25:27 -0000 1.1.2.4
***************
*** 10,14 ****
=head1 SYNOPSIS
! ./runtree.pl --treeName <tree_name> --treeOwner <owner>
=head1 DESCRIPTION
--- 10,14 ----
=head1 SYNOPSIS
! ./runtree.pl --treeName <tree_name> --owner <owner>
=head1 DESCRIPTION
***************
*** 58,62 ****
# determine log name
! $stm="select file_name from file_info,tree where fi_pk = fi_log_fk";
$sth=$dbh->prepare($stm);
$sth->execute;
--- 58,62 ----
# determine log name
! $stm="select file_name from file_info,tree where fi_pk = fi_log_fk and tree_pk = $tree_pk";
$sth=$dbh->prepare($stm);
$sth->execute;
***************
*** 230,234 ****
}
! $userParams .= $up_name . " '$up_value' ";
# TODO - do I need to use default or does Tom set?
}
--- 230,234 ----
}
! $userParams .= $up_name . "$up_value ";
# TODO - do I need to use default or does Tom set?
}
***************
*** 258,266 ****
}
! $sysParams .= $sp_name . " '$sp_value' ";
# TODO - do I need to use default or does Tom set?
}
! # excute the command
my $cmd = $cmdStr . $userParams . $sysParams ;
print $logfile "Running cmd:\n$cmd\n";
--- 258,266 ----
}
! $sysParams .= $sp_name . "$sp_value ";
# TODO - do I need to use default or does Tom set?
}
! # execute the command
my $cmd = $cmdStr . $userParams . $sysParams ;
print $logfile "Running cmd:\n$cmd\n";
***************
*** 279,283 ****
while (my ($fileprefix) = $sth2->fetchrow_array)
{
! $userParams =~ /$fileprefix\s*'+([\S]+)'+\s/;
my $filename = $1;
insertFile($dbh, $node_pk, $filename);
--- 279,283 ----
while (my ($fileprefix) = $sth2->fetchrow_array)
{
! $userParams =~ /$fileprefix\s*'?([\S]+)'?\s/;
my $filename = $1;
insertFile($dbh, $node_pk, $filename);
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv8084
Modified Files:
Tag: Rel-1_0_1-branch
Rwrapper.pl statAnalysis.rw qualityControl.cfg
qualityControl.rw
Added Files:
Tag: Rel-1_0_1-branch
statAnalysis.cfg
Log Message:
Updated
--- NEW FILE: statAnalysis.cfg ---
## filetypes
filetype = name=statin
filetype = comment=Input file for statistical analysis
filetype = arg_name=--infile
filetype = name=statout
filetype = comment=Data output for statistical analysis
filetype = arg_name=--outfile
filetype = name=stattxt
filetype = comment=Text output for quality control
filetype = arg_name=--outtxt
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=statin
extension = ext=qcout
extension = filetype=statout
extension = ext=statout
extension = filetype=stattxt
extension = ext=txt
# analysis
name = statAnalysis
cmdstr = ./analysis/Rwrapper.pl --kind statAnalysis
#analysis_filetypes_link
analysisfile = filetype=statin
analysisfile = input =1
analysisfile = filetype=statout
analysisfile = input =0
analysisfile = filetype=stattxt
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=--settings outfile
up = display_name=Data output for use by other analyses
up = type=text
up = name=--settings logfile
up = display_name=Log filename
up = type=text
up = name=--settings outtxt
up = display_name=Statistical data output
up = type=text
#sys_parameter_names
sp = name=--email
sp = name=--fileURI
sp = name=--settings conds
sp = name=--settings path
sp = name=--settings infile
Index: Rwrapper.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/Attic/Rwrapper.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
*** Rwrapper.pl 15 Nov 2002 20:43:48 -0000 1.1.2.1
--- Rwrapper.pl 17 Dec 2002 18:24:21 -0000 1.1.2.2
***************
*** 11,29 ****
=head1 SYNOPSIS
! ./Rwrapper --kind <qualityControl|statAnalysis> --email <addy to notify>
! --settings <name=arg>
Multiple settings are possible and represent values in the script
that should be changed--essentially a command line arg hack.
- Current settings include: conds, inputDataFile, outputFile,
- path, graphFormat.
./Rwrapper --kind qualityControl
--email "tdj\@virginia.edu"
--settings conds="2,4,5"
--settings condLabels='"min10","min10","hr4"'
! --settings inputDataFile="dChipAfter.txt"
! --settings outputFile="custom"
! --settings fileURI="http://www.somelink.net"
--settings graphFormat="pdf"
--settings path="/home/tdj"
--- 11,28 ----
=head1 SYNOPSIS
! ./Rwrapper --kind <qualityControl|statAnalysis> --email <addy to notify>
! --infile <filename> --outfile <filename> --logfile <filename>
! --settings <name=arg>
Multiple settings are possible and represent values in the script
that should be changed--essentially a command line arg hack.
./Rwrapper --kind qualityControl
--email "tdj\@virginia.edu"
+ --fileURI="http://www.somelink.net"
--settings conds="2,4,5"
--settings condLabels='"min10","min10","hr4"'
! --settings infile="dChipAfter.txt"
! --settings outfile="custom"
--settings graphFormat="pdf"
--settings path="/home/tdj"
***************
*** 40,43 ****
--- 39,51 ----
R environment before the analysis function is called.
+ infile - the name of the file containing signal data. Should
+ correspond to the condition structure as specified above. Currently
+ expects tab separated data.
+
+ outfile - basename of the file to store output in. Each analysis
+ will output a text file named "basename.txt". If other output files
+ are generated (i.e. graphical) they will take the form "basename.jpg"
+ or "basename.pdf"
+
Definition of settings parameters:
***************
*** 57,68 ****
with a number and will prefix such labels with an X
- inputDataFile - the name of the file containing signal data. Should
- correspond to the condition structure as specified above. Currently
- expects tab separated data.
-
- outputFile - basename of the file to store output in. Each analysis
- will output a text file named "basename.txt". If other output files
- are generated (i.e. graphical) they will take the form "basename.jpg"
- or "basename.pdf"
graphFormat - preferred format for graphical output. Accepts jpg or
--- 65,68 ----
***************
*** 79,88 ****
--- 79,95 ----
my $kind = "" ;
my $email = "";
+ my $infile = "";
+ my $outfile = "";
+ my $logfile = "";
my %settings;
my @fileURI=();
#main
+ my @cmdline = @ARGV;
getOptions();
+ open(LOG, "> $logfile") || die "Unable to open $logfile:$!\n";
+ print LOG "Running Rwrapper as: \n @cmdline \n\n";
+
# check for lock file
***************
*** 111,119 ****
}
foreach my $temp (@kindList)
{
$kind = $temp;
parseSettings($lockFile);
! initiateAnalysis($lockFile);
}
--- 118,130 ----
}
+
+ # outscript could be overwritten here TODO
+ # eliminate the loop - no one uses it
+ my $outscript;
foreach my $temp (@kindList)
{
$kind = $temp;
parseSettings($lockFile);
! $outscript = initiateAnalysis($lockFile);
}
***************
*** 123,126 ****
--- 134,141 ----
clearLock($lockFile);
+ print LOG "\n Complete - appending R session\n";
+ close(LOG);
+ `cat $outscript >> $logfile`;
+
# end main
***************
*** 136,139 ****
--- 151,157 ----
'email=s' => \$email,
'settings=s' => \%settings,
+ 'infile=s' => \$infile,
+ 'outfile=s' => \$outfile,
+ 'logfile=s' => \$logfile,
'fileURI=s' => \@fileURI,
'help|?' => \$help);
***************
*** 149,155 ****
print "./Rwrapper.pl \n --kind [qualityControl | statAnalysis | westfallYoung] \n";
print "--email <email address - escape the \@ sign> \n";
! print "--fileURI <value> --fileURI <value>\n";
print "--settings <name>=<value>\n";
! print " setting names: inputDataFile conds condLabels outputFile";
print " path graphFormat\n";
exit;
--- 167,174 ----
print "./Rwrapper.pl \n --kind [qualityControl | statAnalysis | westfallYoung] \n";
print "--email <email address - escape the \@ sign> \n";
! print "--infile <value> --outfile <value>\n";
! print "--logfile <value> --fileURI <value>\n";
print "--settings <name>=<value>\n";
! print " setting names: conds condLabels ";
print " path graphFormat\n";
exit;
***************
*** 169,172 ****
--- 188,198 ----
$settings{path} .= "/" if ($lastchar ne "/");
+ die "Must specify an input file\n" if ($infile eq "");
+ die "Must specify an output file\n" if ($outfile eq "");
+ die "Must specify a log file\n" if ($logfile eq "");
+
+ $settings{inputDataFile} = $infile;
+ $settings{outdata} = $outfile;
+
# where is inputFile - user might give us complete path to input file
# or may give us name and assume we will prepend path
***************
*** 182,190 ****
#what about output file - if they don't supply specific path info
#then prepend settings path
! if (exists($settings{outputFile}))
{
! if ($settings{outputFile} !~ /\//)
{
! $settings{outputFile} = $settings{path} . $settings{outputFile};
}
}
--- 208,216 ----
#what about output file - if they don't supply specific path info
#then prepend settings path
! if (exists($settings{outdata}))
{
! if ($settings{outdata} !~ /\//)
{
! $settings{outdata} = $settings{path} . $settings{outdata};
}
}
***************
*** 198,202 ****
my $lockFile = shift;
! open(INFILE, "$kind.rw") || die "Couldn't open $kind.rw: $!\n";
open(OUTFILE, "> $settings{path}/$kind.r") ||
((clearLock($lockFile)) &&
--- 224,228 ----
my $lockFile = shift;
! open(INFILE, "analysis/$kind.rw") || die "Couldn't open analysis/$kind.rw: $!\n";
open(OUTFILE, "> $settings{path}/$kind.r") ||
((clearLock($lockFile)) &&
***************
*** 250,258 ****
if ((!exists $settings{conds}) ||
(!exists $settings{inputDataFile}) ||
! (!exists $settings{outputFile}) ||
(!exists $settings{graphFormat}))
{
clearLock($lockFile);
! die "Settings conditions, inputDataFile, and outputFile must have data for a quality control analysis\n";
}
--- 276,284 ----
if ((!exists $settings{conds}) ||
(!exists $settings{inputDataFile}) ||
! (!exists $settings{outdata}) ||
(!exists $settings{graphFormat}))
{
clearLock($lockFile);
! die "Settings conditions, inputDataFile, and outdata must have data for a quality control analysis\n";
}
***************
*** 271,278 ****
if ((!exists $settings{conds}) ||
(!exists $settings{inputDataFile}) ||
! (!exists $settings{outputFile}))
{
clearLock($lockFile);
! die "Settings conditions, inputDataFile, and outputFile must have data for stat analysis\n";
}
}
--- 297,304 ----
if ((!exists $settings{conds}) ||
(!exists $settings{inputDataFile}) ||
! (!exists $settings{outdata}))
{
clearLock($lockFile);
! die "Settings conditions, inputDataFile, and outdata must have data for stat analysis\n";
}
}
***************
*** 283,290 ****
if ((!exists $settings{conds}) ||
(!exists $settings{inputDataFile}) ||
! (!exists $settings{outputFile}))
{
clearLock($lockFile);
! die "Settings conditions, inputDataFile, and outputFile must have data for stat analysis\n";
}
}
--- 309,316 ----
if ((!exists $settings{conds}) ||
(!exists $settings{inputDataFile}) ||
! (!exists $settings{outdata}))
{
clearLock($lockFile);
! die "Settings conditions, inputDataFile, and outdata must have data for stat analysis\n";
}
}
***************
*** 293,296 ****
--- 319,324 ----
my $outScript = $settings{path} . $kind . ".Rout";
my $done = `R CMD BATCH $script $outScript`;
+
+ return($outScript);
} #initiateAnalysis
Index: statAnalysis.rw
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/Attic/statAnalysis.rw,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** statAnalysis.rw 15 Nov 2002 20:43:47 -0000 1.1.2.1
--- statAnalysis.rw 17 Dec 2002 18:24:22 -0000 1.1.2.2
***************
*** 211,225 ****
conditions <- c(conds)
### REPLACE outputFile
! outFile <- "outputFile.txt"
### REPLACE condLabels
labels <- c(condLabels)
# prepare data
! source("sourceSPLUSbioinfo.ssc")
! geneData <- geneData[substring(geneData$Probe.Set,1,4)!='AFFX',]
! geneSigs <- as.matrix(geneData[,-1])
! geneSigs.N <- btwn.norm(geneSigs)
! geneSigs.N[geneSigs.N<1] <- 1
--- 211,228 ----
conditions <- c(conds)
### REPLACE outputFile
! outFile <- "outputFile"
### REPLACE condLabels
labels <- c(condLabels)
+
+ # No longer necessary - we're planning on getting the data in this
+ # form from a qc outfile
# prepare data
! #source("sourceSPLUSbioinfo.ssc")
! #geneData <- geneData[substring(geneData$Probe.Set,1,4)!='AFFX',]
! #geneSigs <- as.matrix(geneData[,-1])
! # geneSigs.N <- btwn.norm(geneSigs)
! #geneSigs.N[geneSigs.N<1] <- 1
Index: qualityControl.cfg
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/Attic/qualityControl.cfg,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** qualityControl.cfg 7 Nov 2002 19:23:18 -0000 1.1.2.1
--- qualityControl.cfg 17 Dec 2002 18:24:23 -0000 1.1.2.2
***************
*** 2,24 ****
filetype = name=qcin
filetype = comment=Input file for quality control
! filetype = passin=--settings inputDataFile=
! filetype = name=qcouttxt
filetype = comment=Text output for quality control
! filetype = passin=--settings outputTxt=
filetype = name=qcoutgph
- filetype = extension=pdf png jpg
filetype = comment=Graphic output for quality control
filetype = name=log
- filetype = extension=txt
filetype = comment=Log file
#extension
extension = filetype=qcin
! extension = ext=txt
! extension = filetype=qcouttxt
extension = ext=txt
--- 2,31 ----
filetype = name=qcin
filetype = comment=Input file for quality control
! filetype = arg_name=--infile
! filetype = name=qcout
! filetype = comment=Data output for quality control
! filetype = arg_name=--outfile
!
! filetype = name=qctxt
filetype = comment=Text output for quality control
! filetype = arg_name=--outtxt
filetype = name=qcoutgph
filetype = comment=Graphic output for quality control
+ filetype = arg_name=--outgph
filetype = name=log
filetype = comment=Log file
+ filetype = arg_name=--logfile
#extension
extension = filetype=qcin
! extension = ext=qcin
! extension = filetype=qcout
! extension = ext=qcout
!
! extension = filetype=qctxt
extension = ext=txt
***************
*** 34,68 ****
# analysis
name = qualityControl
! cmdstr = ./Rwrapper --kind qualityControl
! #analysis_ft_input_link
! inputfile = qcin
! #analysis_ft_ouput_link
! outputfile = qcouttxt
! outputfile = qcoutgph
#user_parameter_names
! up = name = graphFormat
up = display_name = File type of graphical output
up = type=radio png pdf jpg
up = default=jpg
! up = name=condLabels
up = display_name=Labels for each of the conditions
up = type=text
! up = name=outputFile
! up = display_name=Basename for analysis output files
! up = type=text
! up = default=qcout
#sys_parameter_names
! sp = name=conds
! sp = name=inputDataFile
! sp = name=fileURI
! sp = name=path
--- 41,98 ----
# analysis
name = qualityControl
! cmdstr = ./analysis/Rwrapper.pl --kind qualityControl
! #analysis_filetypes_link
! analysisfile = filetype=qcin
! analysisfile = input =1
! analysisfile = filetype=qcout
! analysisfile = input =0
!
! analysisfile = filetype=qctxt
! analysisfile = input =0
!
! analysisfile = filetype=qcoutgph
! analysisfile = input =0
!
! analysisfile = filetype=log
! analysisfile = input =0
#user_parameter_names
! up = name =--settings graphFormat
up = display_name = File type of graphical output
up = type=radio png pdf jpg
up = default=jpg
! 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
!
! up = name=--settings outgph
! up = display_name = Graphical output filename
! up = type= text
!
! up = name=--settings outtxt
! up = display_name = Statistical output filename
! up = type= text
!
#sys_parameter_names
! sp = name=--email
! sp = name=--fileURI
! sp = name=--settings conds
! sp = name=--settings path
!
! sp = name=--infile
Index: qualityControl.rw
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/Attic/qualityControl.rw,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** qualityControl.rw 15 Nov 2002 20:43:47 -0000 1.1.2.1
--- qualityControl.rw 17 Dec 2002 18:24:23 -0000 1.1.2.2
***************
*** 4,9 ****
#
# INPUT: dataframe with Probe.Set.Name and signals for all chips
! # outFile - output filename for text output
! # outFileJpeg - output filename for graphical output
# conditions - a vector describing experiment set
# length is the number of conditions
--- 4,8 ----
#
# INPUT: dataframe with Probe.Set.Name and signals for all chips
! # outdata, outtxt, outgph - output filenames
# conditions - a vector describing experiment set
# length is the number of conditions
***************
*** 11,16 ****
#
# OUTPUT: sensitivity and specificity
! # outFile.out - text analysis info
! # outFile.jpeg - graphical analysis
#
# FUNCTIONALITY: The function will prompt for two output filenames.
--- 10,16 ----
#
# OUTPUT: sensitivity and specificity
! # outdata - data file that can be read by subsequent analyses
! # outtxt - text analysis info
! # outgph - graphical analysis
#
# FUNCTIONALITY: The function will prompt for two output filenames.
***************
*** 23,27 ****
#
! qualityControl <- function(geneData, outFileBase, conditions)
{
# include necessary functions
--- 23,27 ----
#
! qualityControl <- function(geneData, outdata, outtxt, outgph, conditions)
{
# include necessary functions
***************
*** 43,61 ****
-apply(geneSigs.N,2,quantile,0.25,na.rm=T))
# output data after normalization
! outFile <- paste(outFileBase, ".txt", sep="")
! write("Adjusted data values:", outFile, append=FALSE)
! write(t(normData), outFile, ncolumns=4, append=TRUE)
! write("\n\n", outFile, append=TRUE)
#Threshold and log adjusted avg difference
- geneSigs.N[geneSigs.N<1] <- 1
geneSigs.N <- data.frame(logb(geneSigs.N,base=2))
# output graph data
- outFileGph <- paste(outFileBase, ".", gphFormat, sep="")
if (gphFormat == "jpg")
{
! bitmap(file=outFileGph, type="jpeg")
pairs(geneSigs.N,pch=".")
graphics.off()
--- 43,59 ----
-apply(geneSigs.N,2,quantile,0.25,na.rm=T))
+ geneSigs.N[geneSigs.N<1] <- 1
+
# output data after normalization
! write(t(geneSigs.N), outdata, ncolumns=4, append=TRUE)
! write(t(normData), outtxt, ncolumns=4, append=TRUE)
#Threshold and log adjusted avg difference
geneSigs.N <- data.frame(logb(geneSigs.N,base=2))
# output graph data
if (gphFormat == "jpg")
{
! bitmap(file=outgph, type="jpeg")
pairs(geneSigs.N,pch=".")
graphics.off()
***************
*** 63,67 ****
if (gphFormat == "pdf")
{
! pdf(file=outFileGph)
pairs(geneSigs.N, pch=".")
dev.off()
--- 61,65 ----
if (gphFormat == "pdf")
{
! pdf(file=outgph)
pairs(geneSigs.N, pch=".")
dev.off()
***************
*** 71,77 ****
tmp.cor <- cor(geneSigs.N,use="complete.obs")
! write("Correlation: ", outFile, append=TRUE)
! write(t(tmp.cor), outFile, ncolumns=9, append=TRUE)
! write("\n", outFile, append=TRUE)
--- 69,75 ----
tmp.cor <- cor(geneSigs.N,use="complete.obs")
! write("Correlation: ", outtxt, append=TRUE)
! write(t(tmp.cor), outtxt, ncolumns=9, append=TRUE)
! write("\n", outtxt, append=TRUE)
***************
*** 104,115 ****
#output sensitivity and specificity values
! write("Specificity: ", outFile, append=TRUE)
! write(specificity, outFile, append=TRUE)
! write("\n", outFile, append=TRUE)
! write("Sensitivity: ", outFile, append=TRUE)
! write(sensitivity, outFile, append=TRUE)
! write("\n", outFile, append=TRUE)
! lowess.nor.mult(geneSigs.N, outFile)
return(sensitivity, specificity)
--- 102,113 ----
#output sensitivity and specificity values
! write("Specificity: ", outtxt, append=TRUE)
! write(specificity, outtxt, append=TRUE)
! write("\n", outtxt, append=TRUE)
! write("Sensitivity: ", outtxt, append=TRUE)
! write(sensitivity, outtxt, append=TRUE)
! write("\n", outtxt, append=TRUE)
! lowess.nor.mult(geneSigs.N, outtxt)
return(sensitivity, specificity)
***************
*** 133,137 ****
# for each column.
#
! lowess.nor.mult <- function(datacols, outFile)
{
out <- c()
--- 131,135 ----
# for each column.
#
! lowess.nor.mult <- function(datacols, outtxt)
{
out <- c()
***************
*** 151,157 ****
outData <- cbind(x, out)
! write("Lowess norm values: ", outFile, append=TRUE)
! write(outData, outFile, ncolumns=numCols, append=TRUE)
! write("\n", outFile, append=TRUE)
return(out)
--- 149,155 ----
outData <- cbind(x, out)
! write("Lowess norm values: ", outtxt, append=TRUE)
! write(outData, outtxt, ncolumns=numCols, append=TRUE)
! write("\n", outtxt, append=TRUE)
return(out)
***************
*** 165,168 ****
### REPLACE graphFormat
gphFormat <- "graphFormat"
! ### REPLACE outputFile ###
! qualityControl(geneData, "outputFile", conditions)
--- 163,170 ----
### REPLACE graphFormat
gphFormat <- "graphFormat"
! ### REPLACE outdata ###
! qualityControl(geneData, "outdata",
! ### REPLACE outtxt ###
! "outtxt",
! ### REPLACE outgph ###
! "outgph", conditions)
|
|
From: <td...@us...> - 2002-12-17 18:22:51
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis/test
In directory sc8-pr-cvs1:/tmp/cvs-serv7100
Removed Files:
Tag: Rel-1_0_1-branch
qualityControl.cfg
Log Message:
Obsolete
--- qualityControl.cfg DELETED ---
|
|
From: <td...@us...> - 2002-12-17 18:20:57
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis/test
In directory sc8-pr-cvs1:/tmp/cvs-serv5641
Added Files:
Tag: Rel-1_0_1-branch
test_quality.pl
Log Message:
Added to test qc node
--- NEW FILE: test_quality.pl ---
#!/usr/bin/perl -w
use DBI;
require "sessionlib.pl";
use Getopt::Long 2.13;
#command line options
my $action = '';
getOptions();
my $dbh = new_connection();
if ($action eq "insert")
{
act_file_info($dbh, $action);
act_tree($dbh, $action);
act_nodes($dbh, $action);
act_user_parameter_values($dbh, $action);
act_sys_parameter_values($dbh, $action);
}
elsif ($action eq "remove")
{
act_sys_parameter_values($dbh, $action);
act_user_parameter_values($dbh, $action);
act_file_info($dbh, $action);
act_nodes($dbh, $action);
act_tree($dbh, $action);
}
$dbh->disconnect();
sub act_file_info
{
my ($dbh, $action) = @_;
if ($action eq "insert")
{
# insert initial input file values
$stm = "insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
. "values (NULL, '/tmp/in.qcin', 't', 'initial input file for qualityControl');";
$stm .="insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
. "values (NULL, '/tmp/qctreelog.txt', 'f', 'logfile for qualityControl');";
my $sth = $dbh->prepare($stm);
$sth->execute();
$dbh->commit();
}
else
{
$stm = "select fi_input_fk, fi_log_fk from tree where tree_name = 'qcTree'";
my $sth = $dbh->prepare($stm);
$sth->execute();
while (my ($fi_ifk, $fi_lfk) = $sth->fetchrow_array)
{
$stm = "delete from file_info where fi_pk = $fi_ifk;";
$stm .= "delete from file_info where fi_pk = $fi_lfk;";
my $sth = $dbh->prepare($stm);
$sth->execute();
$dbh->commit();
}
}
}
# insert tree
sub act_tree
{
my ($dbh, $action) = @_;
my ($stm, $sth);
if ($action eq "insert")
{
$stm = "select fi_pk from file_info where file_name like '%qctreelog%'";
$sth = $dbh->prepare($stm);
$sth->execute();
my $fi_lfk = $sth->fetchrow_array;
$stm = "select fi_pk from file_info where file_name like '%in.qcin%'";
$sth = $dbh->prepare($stm);
$sth->execute();
my $fi_ifk = $sth->fetchrow_array;
$stm = "insert into tree (tree_name, fi_input_fk, fi_log_fk) values ('qcTree', $fi_ifk, $fi_lfk)";
}
else
{
$stm = "delete from tree where tree_name = 'qcTree'";
}
$sth = $dbh->prepare($stm);
$sth->execute();
$dbh->commit();
}
# insert node
sub act_nodes
{
my ($dbh, $action) = @_;
my ($stm, $sth);
$stm = "select tree_pk from tree where tree_name = 'qcTree'";
$sth = $dbh->prepare($stm);
$sth->execute();
my $tree_fk = $sth->fetchrow_array;
if ($action eq "insert")
{
$stm = "select an_pk from analysis where an_name = 'qualityControl'";
$sth = $dbh->prepare($stm);
$sth->execute();
my $an_fk_qc = $sth->fetchrow_array;
$stm = "insert into node (tree_fk, an_fk, parent_key) values " .
"($tree_fk, $an_fk_qc, -1)";
$sth = $dbh->prepare($stm);
$sth->execute();
$dbh->commit();
$stm = "select node_pk from node where an_fk = $an_fk_qc";
$sth = $dbh->prepare($stm);
$sth->execute();
my $node_pk_qc = $sth->fetchrow_array;
}
else
{
$stm = "delete from node where tree_fk = $tree_fk";
}
$sth = $dbh->prepare($stm);
$sth->execute();
$dbh->commit();
}
#insert into user_parameter_values
sub act_user_parameter_values
{
my ($dbh, $action) = @_;
my ($stm, $sth);
if ($action eq "insert")
{
# qc - params
# --outfile
# --logfile
# --settings outgph
# --settings graphFormat
# --settings condLabels
$stm = "select node_pk, an_pk from node,analysis " .
" where an_fk = an_pk and an_name = 'qualityControl'";
$sth = $dbh->prepare($stm);
$sth->execute();
my ($node_fk, $an_key) = $sth->fetchrow_array;
$stm = "select upn_pk from user_parameter_names " .
"where up_name like '%graphFormat%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
my $upn_fk = $sth->fetchrow_array;
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
" values ($node_fk, '=jpg', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select upn_pk from user_parameter_names " .
"where up_name like '%condLabels%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$upn_fk = $sth->fetchrow_array;
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
" values ($node_fk, '=\\'\"min10\",\"min10\",\"hr4\"\\'', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select upn_pk from user_parameter_names " .
"where up_name like '%outfile%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$upn_fk = $sth->fetchrow_array;
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
" values ($node_fk, '=/tmp/out.qcout', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select upn_pk from user_parameter_names " .
"where up_name like '%logfile%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$upn_fk = $sth->fetchrow_array;
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
" values ($node_fk, '=/tmp/qclog.log', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select upn_pk from user_parameter_names " .
"where up_name like '%outtxt%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$upn_fk = $sth->fetchrow_array;
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
" values ($node_fk, '=/tmp/qc.txt', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select upn_pk from user_parameter_names " .
"where up_name like '%outgph%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$upn_fk = $sth->fetchrow_array;
$stm = "insert into user_parameter_values (node_fk, up_value, upn_fk)" .
" values ($node_fk, '=/tmp/qc.jpg', $upn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
}
elsif ($action eq "remove")
{
$stm = "select node_pk from node, tree where tree_fk = tree_pk and ".
" tree_name = 'qcTree'";
my $node_fk;
my $sth2 = $dbh->prepare($stm);
$sth2->execute();
while (($node_fk) = $sth2->fetchrow_array)
{
$stm = "delete from user_parameter_values where node_fk = $node_fk";
$sth = $dbh->prepare($stm);
$sth->execute();
}
}
$dbh->commit();
}
#insert into sys_parameter_values
sub act_sys_parameter_values
{
my ($dbh, $action) = @_;
my ($stm, $sth);
if ($action eq "insert")
{
#-qc params:
# --email
# --fileURI
# --infile
# --settings conds
# --settings path
# --settings outtxt
$stm = "select node_pk, an_pk from node,analysis " .
" where an_fk = an_pk and an_name = 'qualityControl'";
$sth = $dbh->prepare($stm);
$sth->execute();
my ($node_fk, $an_key) = $sth->fetchrow_array;
$stm = "select spn_pk from sys_parameter_names " .
"where sp_name like '%email%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
my $spn_fk = $sth->fetchrow_array;
my $email = "=tdj4mvirginia.edu";
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
" values ($node_fk, '$email', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select spn_pk from sys_parameter_names " .
"where sp_name like '%conds%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$spn_fk = $sth->fetchrow_array;
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
" values ($node_fk, '=\"3,3,3\"', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select spn_pk from sys_parameter_names " .
"where sp_name like '%fileURI%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$spn_fk = $sth->fetchrow_array;
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
" values ($node_fk, '=/tmp', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
$stm = "select spn_pk from sys_parameter_names " .
"where sp_name like '%path%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$spn_fk = $sth->fetchrow_array;
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
" values ($node_fk, '=/tmp', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
# --settings infile
$stm = "select spn_pk from sys_parameter_names " .
"where sp_name like '%infile%' and an_fk = $an_key";
$sth = $dbh->prepare($stm);
$sth->execute();
$spn_fk = $sth->fetchrow_array;
$stm = "insert into sys_parameter_values (node_fk, sp_value, spn_fk)" .
" values ($node_fk, '=/tmp/in.qcin', $spn_fk);";
$sth = $dbh->prepare($stm);
$sth->execute();
}
elsif ($action eq "remove")
{
$stm = "select node_pk from node, tree where tree_fk = tree_pk and ".
" tree_name = 'qcTree'";
my $sth2 = $dbh->prepare($stm);
$sth2->execute();
while (my ($node_fk) = $sth2->fetchrow_array)
{
$stm = "delete from sys_parameter_values where node_fk = $node_fk";
$sth = $dbh->prepare($stm);
$sth->execute();
}
}
$dbh->commit();
}
sub getOptions
{
my $help;
if (@ARGV > 0 )
{
# format
# string : 'var=s' => \$var,
# boolean : 'var!' => \$var,
GetOptions(
'action=s' => \$action,
'help|?' => \$help,
);
} #have command line args
usage() if $help;
if (($action ne "insert") && ($action ne "remove"))
{
print "Must specify a valid action.\n";
usage();
}
} # getOptions
sub usage
{
print "Usage: \n";
print " ./test_quality.pl --action=<insert|remove> \n";
exit;
}
|
|
From: <tw...@us...> - 2002-12-17 17:30:43
|
Update of /cvsroot/genex/genex-server/site/graphics
In directory sc8-pr-cvs1:/tmp/cvs-serv6001
Modified Files:
Tag: Rel-1_0_1-branch
genex_logo.jpg
Log Message:
new logo
Index: genex_logo.jpg
===================================================================
RCS file: /cvsroot/genex/genex-server/site/graphics/Attic/genex_logo.jpg,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
Binary files /tmp/cvskS4BiA and /tmp/cvseS20j0 differ
|
|
From: <tw...@us...> - 2002-12-17 17:24:26
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv560
Modified Files:
Tag: Rel-1_0_1-branch
makefile
Log Message:
fix .htaccess %% resolution
move *.rw, *.ssc *.cfg to analysis makefile
Index: makefile
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/makefile,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** makefile 24 Oct 2002 19:19:27 -0000 1.1.2.2
--- makefile 17 Dec 2002 17:24:23 -0000 1.1.2.3
***************
*** 1,6 ****
--- 1,8 ----
all: pl_files pm_files html_files htaccess_src rw_files ssc_files options
+ # Dec 17 2002 analysis stuff is in ./analysis
NOOP = $(SHELL) -c true
DEST = /var/www/html/genex/webtools
+ ANA = ./analysis
pl_srcs := $(patsubst %.pl,$(DEST)/%.pl,$(wildcard *.pl))
***************
*** 21,30 ****
# aug 1 2002 tom change from .R to .rw files
! rw_srcs := $(patsubst %.rw,$(DEST)/%.rw,$(wildcard *.rw))
rw_files : $(rw_srcs)
! $(DEST)/%.rw : ./%.rw
cp -f $< $(DEST)
ssc_srcs := $(patsubst %.ssc,$(DEST)/%.ssc,$(wildcard *.ssc))
--- 23,37 ----
# aug 1 2002 tom change from .R to .rw files
+ # 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))
***************
*** 36,44 ****
# Oct 24, 2002 Tom: it is too easy to loose the .htaccess source file,
# so remove the dot from the source file
htaccess_src : $(DEST)/.htaccess
$(DEST)/.htaccess : htaccess
@echo "making $<"
! cp -f htaccess $(DEST)/.htaccess
#
--- 43,54 ----
# Oct 24, 2002 Tom: it is too easy to loose the .htaccess source file,
# so remove the dot from the source file
+ # call install_lib.pl to resolve the host name
+ # put the dot back on with a cp
htaccess_src : $(DEST)/.htaccess
$(DEST)/.htaccess : htaccess
@echo "making $<"
! cd ../../; ./install_lib.pl $< ./site/webtools $(DEST)
! mv $(DEST)/$< $(DEST)/.htaccess
#
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv15500
Modified Files:
Tag: Rel-1_0_1-branch
edit_atree1.pl sql_lib.pl analysis_tree_lib.pl edit_atree2.pl
edit_atree1.html
Log Message:
Analysis tree GUI writes upv to db.
Reset button added to properties (upv).
Index: edit_atree1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.pl,v
retrieving revision 1.1.2.8
retrieving revision 1.1.2.9
diff -C2 -d -r1.1.2.8 -r1.1.2.9
*** edit_atree1.pl 16 Dec 2002 14:50:29 -0000 1.1.2.8
--- edit_atree1.pl 17 Dec 2002 15:02:05 -0000 1.1.2.9
***************
*** 15,27 ****
my %ch = $q->Vars();
my $dbh = new_connection();
-
my %tree = read_db($dbh, $tree_pk);
- my $atree = render_at();
- my $select_node = select_node($dbh);
-
if (! exists($ch{node_pk}))
{
$ch{node_pk} = $tree{root};
}
$properties = build_properties($dbh, $ch{node_pk});
--- 15,25 ----
my %ch = $q->Vars();
my $dbh = new_connection();
my %tree = read_db($dbh, $tree_pk);
if (! exists($ch{node_pk}))
{
$ch{node_pk} = $tree{root};
}
+ my $atree = render_at($ch{node_pk});
+ my $select_node = select_node($dbh);
$properties = build_properties($dbh, $ch{node_pk});
***************
*** 50,54 ****
$sth->execute($node_pk) || die "Query execute get_upn fails.\n$DBI::errstr\n";
$results = "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n";
! $results .= "<td>($node_pk)</td><td></td>\n";
my $hr; # hashref
while( $hr = $sth->fetchrow_hashref())
--- 48,52 ----
$sth->execute($node_pk) || die "Query execute get_upn fails.\n$DBI::errstr\n";
$results = "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n";
! $results .= "<td>($node_pk)<input type=\"hidden\" name=\"properties_node_pk\" value=\"$node_pk\"></td><td><input type=\"reset\" name=\"reset\" value=\"Reset Values\"><br><br></td>\n";
my $hr; # hashref
while( $hr = $sth->fetchrow_hashref())
***************
*** 56,60 ****
if ($hr->{up_type} eq "text")
{
! $results .= "<tr><td valign=\"top\">$hr->{up_display_name} <br><br></td><td valign=\"top\"><input type=\"text\" name=\"$hr->{up_name}\" value=\"$hr->{up_value}\" size=\"30\" maxlength=\"128\"></td></tr>\n";
}
elsif ($hr->{up_type} =~ m/^radio/)
--- 54,58 ----
if ($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";
}
elsif ($hr->{up_type} =~ m/^radio/)
***************
*** 65,71 ****
foreach my $label (@radio_buttons)
{
! $results .= "<tr><td valign=\"top\">$label <br><br></td><td valign=\"top\"><input type=\"radio\" name=\"$hr->{up_name}\" value=\"$label\"></td></tr>\n";
}
! $results = fixradiocheck($hr->{up_name}, $hr->{up_value}, "radio", $results);
}
}
--- 63,69 ----
foreach my $label (@radio_buttons)
{
! $results .= "<tr><td valign=\"top\">$label <br><br></td><td valign=\"top\"><input type=\"radio\" name=\"upv_pk_$hr->{upv_pk}\" value=\"$label\"></td></tr>\n";
}
! $results = fixradiocheck("upv_pk_$hr->{upv_pk}", $hr->{up_value}, "radio", $results);
}
}
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.24
retrieving revision 1.1.2.25
diff -C2 -d -r1.1.2.24 -r1.1.2.25
*** sql_lib.pl 16 Dec 2002 14:50:20 -0000 1.1.2.24
--- sql_lib.pl 17 Dec 2002 15:02:08 -0000 1.1.2.25
***************
*** 300,304 ****
$sql = "select * from sys_parameter_names,sys_parameter_values where node_fk=? and spn_pk=spn_fk";
}
!
# write_log("sql: $sql");
--- 300,307 ----
$sql = "select * from sys_parameter_names,sys_parameter_values where node_fk=? and spn_pk=spn_fk";
}
! elsif ($q_name eq "update_upv")
! {
! $sql = "update user_parameter_values set up_value=? where upv_pk=?";
! }
# write_log("sql: $sql");
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.37
retrieving revision 1.1.2.38
diff -C2 -d -r1.1.2.37 -r1.1.2.38
*** analysis_tree_lib.pl 16 Dec 2002 14:50:13 -0000 1.1.2.37
--- analysis_tree_lib.pl 17 Dec 2002 15:02:14 -0000 1.1.2.38
***************
*** 36,40 ****
$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;
--- 36,39 ----
***************
*** 220,223 ****
--- 219,223 ----
sub render_at
{
+ my $selected_node_pk = $_[0];
# print_tree_info();
# print_children_info();
***************
*** 228,232 ****
tile_color(); # reads @table, creates @colors
tile_connect(); # modifies @table adding img tags, reads @loc
! my $html = render_html(); # reads @table, @colors
# print_ascii_tree();
--- 228,232 ----
tile_color(); # reads @table, creates @colors
tile_connect(); # modifies @table adding img tags, reads @loc
! my $html = render_html($selected_node_pk); # reads @table, @colors
# print_ascii_tree();
***************
*** 247,250 ****
--- 247,267 ----
$sth->execute($tree{tree_name}, $tree{tree_pk});
+ # This better exist!
+ if (exists($tree{properties_node_pk}))
+ {
+ $sth = getq("update_upv", $dbh);
+ #
+ # It is crude but simple to crawl through all the keys
+ # looking for upv_pk_nnn
+ #
+ foreach my $key (keys(%tree))
+ {
+ if ($key =~ m/upv_pk_(\d+)$/)
+ {
+ $sth->execute($tree{$key}, $1);
+ }
+ }
+ }
+
if (exists($tree{add_an_fk}))
{
***************
*** 383,386 ****
--- 400,405 ----
sub render_html
{
+ my $selected_node_pk = $_[0];
+ my $node_select;
# @table is a global
***************
*** 415,420 ****
else
{
#
! # If any of these change, then corresponding changes have to be made
# to edit_atree1.pl and edit_atree2.pl
#
--- 434,444 ----
else
{
+ $node_select = "";
+ if ($node == $selected_node_pk)
+ {
+ $node_select ="<font color=\"#FF0000\">*</font>";
+ }
#
! # If any of these hidden fields change, then corresponding changes have to be made
# to edit_atree1.pl and edit_atree2.pl
#
***************
*** 429,433 ****
}
$html .= "<table border=\"0\" width=\"100%\"><tr><td width=\"50%\"><div align=\"left\">$del_string</div></td><td width\"50%\"><div align=\"right\"><input type=\"image\" border=\"0\" name=\"edit_$node\" src=\"../graphics/pencil.gif\" width=\"25\" height=\"25\"></div></td></tr></table>\n";
! $html .= "<div align=\"center\"><font size=\"-1\">$tree{$node}[0]<br>($node)<input type=\"radio\" name=\"node_pk\" value=\"$node\">\n";
$html .= "</font></div></td>\n";
}
--- 453,457 ----
}
$html .= "<table border=\"0\" width=\"100%\"><tr><td width=\"50%\"><div align=\"left\">$del_string</div></td><td width\"50%\"><div align=\"right\"><input type=\"image\" border=\"0\" name=\"edit_$node\" src=\"../graphics/pencil.gif\" width=\"25\" height=\"25\"></div></td></tr></table>\n";
! $html .= "<div align=\"center\"><font size=\"-1\">$tree{$node}[0]<br>($node)$node_select<input type=\"radio\" name=\"node_pk\" value=\"$node\">\n";
$html .= "</font></div></td>\n";
}
Index: edit_atree2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree2.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_atree2.pl 13 Dec 2002 21:51:59 -0000 1.1.2.11
--- edit_atree2.pl 17 Dec 2002 15:02:21 -0000 1.1.2.12
***************
*** 21,32 ****
my $url = index_url(); # see sessionlib.pl
! $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";
! }
else
{
! print "Location: $url?tree_pk=$ch{tree_pk}\n\n";
}
$dbh->commit();
--- 21,47 ----
my $url = index_url(); # see sessionlib.pl
!
! if ($ch{run})
{
! # It is easier (and maybe better) to call this with $tree_pk and $us_pk
! my $sth = getq("select_tree", $dbh);
! $sth->execute();
! (my $tree_name, my $tree_pk) = $sth->fetchrow_array();
! $sth->finish();
! `./runtree.pl --treeName $tree_name --treeOwner $ENV{REMOTE_USER}`;
! $url =~ s/(.*)\/.*/$1\/files.pl/;
! print "Location: $url\n\n";
! 2 }
else
{
! $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";
! }
! else
! {
! print "Location: $url?tree_pk=$ch{tree_pk}\n\n";
! }
}
$dbh->commit();
***************
*** 43,46 ****
--- 58,65 ----
{
# write_log("parse CGI key:$key");
+ #
+ # Capture name_nnn fields where nnn is an integer starting with zero
+ # These are not sparse: zero through nnn max should exist.
+ #
if ($key =~ m/name_(\d+)$/) # force full match!
{
***************
*** 48,51 ****
--- 67,80 ----
$tree{$1}[1] = $ch{"parent_$1"};
}
+ #
+ # Capture upv_pk's and values for fields we will update
+ # see properties_node_pk below.
+ # These are sparse. There will only be a few fields, and the
+ # pk's could be any integer.
+ #
+ if ($key =~ m/upv_pk_\d+/) # force full match!
+ {
+ $tree{$key} = $ch{$key};
+ }
}
my $active_node;
***************
*** 71,74 ****
--- 100,104 ----
$tree{delete_node_pk} = $active_node;
}
+ $tree{properties_node_pk} = $ch{properties_node_pk};
$tree{tree_pk} = $ch{tree_pk};
$tree{root} = $ch{root};
Index: edit_atree1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.html,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.html 13 Dec 2002 21:51:59 -0000 1.1.2.11
--- edit_atree1.html 17 Dec 2002 15:02:23 -0000 1.1.2.12
***************
*** 20,23 ****
--- 20,25 ----
<input type="hidden" name="tree_pk" value="{tree_pk}">
<input type="hidden" name="root" value="{root}">
+
+ <input type="submit" name="run" value="Run Analysis">
<table width="760" border="0" cellpadding="0" cellspacing="4">
<tr>
|
Update of /cvsroot/genex/genex-server/site/webtools/analysis/test
In directory sc8-pr-cvs1:/tmp/cvs-serv24586
Modified Files:
Tag: Rel-1_0_1-branch
depopulate populate test_tree.pl
Added Files:
Tag: Rel-1_0_1-branch
qualityControl.cfg
Log Message:
Added qualityControl.cfg to populate and depopulate.
Fixed file_info table management by using fi_update().
--- NEW FILE: qualityControl.cfg ---
## filetypes
filetype = name=qcin
filetype = comment=Input file for quality control
filetype = arg_name=--infile
filetype = name=qcout
filetype = comment=Text output for quality control
filetype = arg_name=--outfile
filetype = name=qcoutgph
filetype = comment=Graphic output for quality control
filetype = arg_name=--outfilegph
filetype = name=log
filetype = comment=Log file
filetype = arg_name=--logfile
#extension
extension = filetype=qcin
extension = ext=txt
extension = filetype=qcout
extension = ext=txt
extension = filetype=qcoutgph
extension = ext=pdf
extension = filetype=qcoutgph
extension = ext=png
extension = filetype=qcoutgph
extension = ext=jpg
# analysis
name = qualityControl
cmdstr = ./analysis/Rwrapper.pl --kind qualityControl
#analysis_filetypes_link
analysisfile = filetype=qcin
analysisfile = input =1
analysisfile = filetype=qcout
analysisfile = input =0
analysisfile = filetype=qcoutgph
analysisfile = input =0
analysisfile = filetype=log
analysisfile = input =0
#user_parameter_names
up = name =--settings graphFormat
up = display_name = File type of graphical output
up = type=radio png pdf jpg
up = default=jpg
up = name=--settings condLabels
up = display_name=Labels for each of the conditions
up = type=text
#sys_parameter_names
sp = name=--email
sp = name=--fileURI
sp = name=--settings conds
sp = name=--settings path
sp = name=--settings infile
sp = name=--settings outfile
sp = name=--settings logfile
sp = name=--settings outfilegph
Index: depopulate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/depopulate,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** depopulate 15 Nov 2002 21:54:32 -0000 1.1.2.2
--- depopulate 17 Dec 2002 14:01:47 -0000 1.1.2.3
***************
*** 1,3 ****
--- 1,4 ----
./test_tree.pl --action remove
+ ../../add_analysis.pl --configfile ./qualityControl.cfg --action remove
../../add_analysis.pl --configfile demo4.cfg --action remove
../../add_analysis.pl --configfile demo3.cfg --action remove
Index: populate
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/populate,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** populate 15 Nov 2002 21:54:32 -0000 1.1.2.2
--- populate 17 Dec 2002 14:01:47 -0000 1.1.2.3
***************
*** 1,2 ****
--- 1,3 ----
+ ../../add_analysis.pl --configfile ./qualityControl.cfg --action insert
../../add_analysis.pl --configfile ./demo.cfg --action insert
../../add_analysis.pl --configfile ./demo1.cfg --action insert
Index: test_tree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/analysis/test/Attic/test_tree.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
*** test_tree.pl 15 Nov 2002 21:54:32 -0000 1.1.2.2
--- test_tree.pl 17 Dec 2002 14:01:48 -0000 1.1.2.3
***************
*** 38,44 ****
# insert initial input file values
$stm = "insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (NULL, '/tmp/initial_in', 't', 'initial input file for demo');";
$stm .="insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (NULL, '/tmp/treelog.txt', 'f', 'logfile for demo');";
my $sth = $dbh->prepare($stm);
$sth->execute();
--- 38,44 ----
# insert initial input file values
$stm = "insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (-1, '/tmp/initial_in', 't', 'initial input file for demo');";
$stm .="insert into file_info (node_fk, file_name, use_as_input, fi_comments)"
! . "values (-1, '/tmp/treelog.txt', 'f', 'logfile for demo');";
my $sth = $dbh->prepare($stm);
$sth->execute();
***************
*** 92,95 ****
--- 92,97 ----
$sth = $dbh->prepare($stm);
$sth->execute();
+ my $us_fk = get_us_fk($dbh);
+ insert_security($dbh, $us_fk, $us_fk, 0);
$dbh->commit();
***************
*** 138,142 ****
$stm = "insert into node (tree_fk, an_fk, parent_key) values " .
! "($tree_fk, $an_fk_demo, NULL)";
$sth = $dbh->prepare($stm);
$sth->execute();
--- 140,144 ----
$stm = "insert into node (tree_fk, an_fk, parent_key) values " .
! "($tree_fk, $an_fk_demo, -1)";
$sth = $dbh->prepare($stm);
$sth->execute();
|
|
From: <tw...@us...> - 2002-12-16 21:17:02
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv19831
Modified Files:
Tag: Rel-1_0_1-branch
runtree.pl
Log Message:
fixed fi_update and cured some file conflicts.
Index: runtree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/runtree.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
*** runtree.pl 15 Nov 2002 21:54:53 -0000 1.1.2.2
--- runtree.pl 16 Dec 2002 21:16:58 -0000 1.1.2.3
***************
*** 2,6 ****
#TODO - change to accomodate version number as part of name
!
=head1 NAME
--- 2,6 ----
#TODO - change to accomodate version number as part of name
! # use strict;
=head1 NAME
***************
*** 84,88 ****
$stm="select node_pk, an_fk from node" .
! " where tree_fk = $tree_pk and parent_key is NULL";
$sth=$dbh->prepare($stm);
$sth->execute();
--- 84,88 ----
$stm="select node_pk, an_fk from node" .
! " where tree_fk = $tree_pk and parent_key=-1"; # old: is NULL
$sth=$dbh->prepare($stm);
$sth->execute();
***************
*** 121,128 ****
$sth= $dbh->prepare($stm);
$sth->execute();
-
! # is this necessary - we should check files existence when we run the
! #child
while (my ($child_node_pk, $child_an_fk) = $sth->fetchrow_array )
{
--- 121,129 ----
$sth= $dbh->prepare($stm);
$sth->execute();
! #
! # is this necessary - we should check files existence
! # when we run the child
! #
while (my ($child_node_pk, $child_an_fk) = $sth->fetchrow_array )
{
***************
*** 152,161 ****
$infile =~ /.*\.(.*)/;
my $file_ext = $1;
-
if ($ext eq $file_ext)
{
if ($found == 1)
{
! warn "Great trauma! There are two appropriate input files";
}
$found = 1;
--- 153,161 ----
$infile =~ /.*\.(.*)/;
my $file_ext = $1;
if ($ext eq $file_ext)
{
if ($found == 1)
{
! warn "Great trauma! There are two appropriate input files. infile:$infile";
}
$found = 1;
***************
*** 178,182 ****
if ($found == 0)
{
! warn "No input file with type: $ext for node: $child_node_pk\n";
$have_all_inputs = 0;
}
--- 178,182 ----
if ($found == 0)
{
! warn "No input file with type: $ext for node: $child_node_pk an_pk: $child_an_fk\n";
$have_all_inputs = 0;
}
***************
*** 274,278 ****
" ft_pk=ft_fk and analysis_filetypes_link.an_fk = an_pk ".
" and an_pk=node.an_fk and node_pk = $node_pk";
! $sth2 = $dbh->prepare($stm);
$sth2->execute();
--- 274,278 ----
" ft_pk=ft_fk and analysis_filetypes_link.an_fk = an_pk ".
" and an_pk=node.an_fk and node_pk = $node_pk";
! my $sth2 = $dbh->prepare($stm);
$sth2->execute();
***************
*** 295,304 ****
my $comments="Output from node $node_fk";
my $checksum="check:-)";
- my $stm = "insert into file_info (node_fk, file_name, timestamp," .
- " use_as_input, fi_comments, fi_checksum) values ($node_fk," .
- " '$file', $timestamp, '$uai', '$comments', '$checksum')";
- my $sth= $dbh->prepare($stm);
- $sth->execute();
$dbh->commit();
}
--- 295,314 ----
my $comments="Output from node $node_fk";
my $checksum="check:-)";
+ my $us_fk = get_us_fk($dbh);
+
+ # my $stm = "insert into file_info (node_fk, file_name, timestamp," .
+ # " use_as_input, fi_comments, fi_checksum) values ($node_fk," .
+ # " '$file', $timestamp, '$uai', '$comments', '$checksum')";
+ # my $sth= $dbh->prepare($stm);
+ # $sth->execute();
+
+ my $fi_pk = fi_update($dbh, $us_fk, $us_fk, $file, $comments);
+ #
+ # Someday modify fi_update() to know about use_as_input and node_fk
+ #
+ my $sql = "update file_info set use_as_input='t',node_fk=$node_fk where fi_pk=$fi_pk";
+ my $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
+ $sth->execute() || die "$sql\n$DBI::errstr\n";
$dbh->commit();
}
|
|
From: <tw...@us...> - 2002-12-16 15:53:37
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv6009
Modified Files:
Tag: Rel-1_0_1-branch
sessionlib.pl
Log Message:
comments to document fi_update() and get_us_fk()
Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.18
retrieving revision 1.1.2.19
diff -C2 -d -r1.1.2.18 -r1.1.2.19
*** sessionlib.pl 13 Dec 2002 18:37:42 -0000 1.1.2.18
--- sessionlib.pl 16 Dec 2002 15:53:16 -0000 1.1.2.19
***************
*** 654,658 ****
}
!
sub fi_update
{
--- 654,671 ----
}
! #
! # fi_update() Does both insert and update for file_info.
! #
! # Just like most Linux systems, where uid==gid, GeneX us_pk==gs_pk. In GeneX is it easy to
! # get the us_pk (us_fk) with get_us_fk() which you can find elsewhere in sessionlib.pl. Normally,
! # fi_update() is called with us_fk for both user and group foreign keys.
! #
! # $file_name is the full path to the file
! # To get the full name where the file name is $fn
! # my %opts = read_optionsdotreminders();
! # $fn = "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/$fn";
! #
! # Comments are passed in from the UI
! #
sub fi_update
{
***************
*** 1181,1184 ****
--- 1194,1203 ----
}
+ #
+ # Pass in a valid database handle.
+ # get_us_fk() reads the user name from the REMOTE_USER environment variable
+ # which is set by Apache when there is a valid user logged in.
+ # From the user name we look up the us_pk (us_fk).
+ #
sub get_us_fk
{
|
|
From: <tw...@us...> - 2002-12-16 14:50:56
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv14426
Modified Files:
Tag: Rel-1_0_1-branch
analysis_tree_lib.pl sql_lib.pl edit_atree1.pl
Log Message:
insert default sys_parameters when making new tree or new node.
display sys_parameter_values
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.36
retrieving revision 1.1.2.37
diff -C2 -d -r1.1.2.36 -r1.1.2.37
*** analysis_tree_lib.pl 13 Dec 2002 21:51:59 -0000 1.1.2.36
--- analysis_tree_lib.pl 16 Dec 2002 14:50:13 -0000 1.1.2.37
***************
*** 45,48 ****
--- 45,58 ----
$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";
+ }
$dbh->commit;
***************
*** 239,242 ****
--- 249,253 ----
if (exists($tree{add_an_fk}))
{
+ # 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
***************
*** 246,250 ****
$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;
--- 257,260 ----
***************
*** 255,261 ****
--- 265,283 ----
$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", $dbh);
# ana_fk, node_pk
***************
*** 264,267 ****
--- 286,290 ----
elsif (exists($tree{delete_node_pk}))
{
+ # delete node
my $s_node;
my @nstack;
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.23
retrieving revision 1.1.2.24
diff -C2 -d -r1.1.2.23 -r1.1.2.24
*** sql_lib.pl 13 Dec 2002 17:12:35 -0000 1.1.2.23
--- sql_lib.pl 16 Dec 2002 14:50:20 -0000 1.1.2.24
***************
*** 284,290 ****
--- 284,302 ----
$sql = "insert into user_parameter_values (node_fk, up_value, upn_fk) values (?,?,?)";
}
+ elsif ($q_name eq "default_spv")
+ {
+ $sql = "select spn_pk,sp_default from sys_parameter_names where an_fk=?";
+ }
+ elsif ($q_name eq "insert_spv")
+ {
+ $sql = "insert into sys_parameter_values (node_fk, sp_value, spn_fk) values (?,?,?)";
+ }
elsif ($q_name eq "get_upn")
{
$sql = "select * from user_parameter_names,user_parameter_values where node_fk=? and upn_pk=upn_fk";
+ }
+ elsif ($q_name eq "get_spn")
+ {
+ $sql = "select * from sys_parameter_names,sys_parameter_values where node_fk=? and spn_pk=spn_fk";
}
Index: edit_atree1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_atree1.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
*** edit_atree1.pl 13 Dec 2002 21:51:59 -0000 1.1.2.7
--- edit_atree1.pl 16 Dec 2002 14:50:29 -0000 1.1.2.8
***************
*** 58,61 ****
--- 58,82 ----
$results .= "<tr><td valign=\"top\">$hr->{up_display_name} <br><br></td><td valign=\"top\"><input type=\"text\" name=\"$hr->{up_name}\" value=\"$hr->{up_value}\" size=\"30\" maxlength=\"128\"></td></tr>\n";
}
+ elsif ($hr->{up_type} =~ m/^radio/)
+ {
+ $results .= "<tr><td valign=\"top\">$hr->{up_display_name}<br></td><td valign=\"top\"> </td></tr>\n";
+ my @radio_buttons = split(" ", $hr->{up_type});
+ shift(@radio_buttons); # the first value is the type of input
+ foreach my $label (@radio_buttons)
+ {
+ $results .= "<tr><td valign=\"top\">$label <br><br></td><td valign=\"top\"><input type=\"radio\" name=\"$hr->{up_name}\" value=\"$label\"></td></tr>\n";
+ }
+ $results = fixradiocheck($hr->{up_name}, $hr->{up_value}, "radio", $results);
+ }
+ }
+ $results .= "</table>\n";
+
+ $sth = getq("get_spn", $dbh); # get names and values
+ $sth->execute($node_pk) || die "Query execute get_spn fails.\n$DBI::errstr\n";
+ $results .= "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n";
+ $results .= "<td>($node_pk)</td><td></td>\n";
+ 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";
|
