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From: <jas...@us...> - 2002-11-22 00:40:34
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv25433/Mason/workspace
Modified Files:
autohandler.in
Log Message:
* Mason/workspace/autohandler.in (Repository):
removed seperate call to authenticate.mason
Index: autohandler.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/autohandler.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** autohandler.in 20 Nov 2002 22:25:38 -0000 1.2
--- autohandler.in 22 Nov 2002 00:40:31 -0000 1.3
***************
*** 34,39 ****
unless (defined $session and exists $session->{username}) {
! my $path = $comp->attr('path');
! $m->comp('comps/authenticate.mason', caller=>$path);
}
--- 34,45 ----
unless (defined $session and exists $session->{username}) {
! $m->clear_buffer();
! # $r is the global variable for the Apache request object
! # $m is the global variable for the Mason request object
! Bio::Genex::HTMLUtils::call_page($r,
! '%%GENEX_WORKSPACE_URL%%/authenticate.html',
! $comp->attr('path'),
! );
! $m->abort(301);
}
|
|
From: <jas...@us...> - 2002-11-22 00:39:30
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv25180/Mason/workspace
Modified Files:
check-login.html
Log Message:
* Mason/workspace/check-login.html (Repository):
localized $session and limited its scope
Index: check-login.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/check-login.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** check-login.html 20 Nov 2002 22:27:43 -0000 1.2
--- check-login.html 22 Nov 2002 00:39:27 -0000 1.3
***************
*** 20,30 ****
my $name = $m->current_comp->attr('name');
my $login;
! my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
! if (defined $session) {
! warn "check: retrieving session";
! foreach my $arg (keys %{$session}) {
! warn "check: session arg: $arg: $session->{$arg}";
}
- $login = $session->{username};
}
</%init>
--- 20,32 ----
my $name = $m->current_comp->attr('name');
my $login;
! {
! local $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
! if (defined $session) {
! warn "check: retrieving session";
! foreach my $arg (keys %{$session}) {
! warn "check: session arg: $arg: $session->{$arg}";
! }
! $login = $session->{username};
}
}
</%init>
|
|
From: <jas...@us...> - 2002-11-22 00:38:42
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv25004/Mason/workspace
Modified Files:
experimentset-create.html.in
Log Message:
* Mason/workspace/experimentset-create.html.in (Repository):
added commented out debugging info
Index: experimentset-create.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/experimentset-create.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** experimentset-create.html.in 20 Nov 2002 22:33:51 -0000 1.2
--- experimentset-create.html.in 22 Nov 2002 00:38:37 -0000 1.3
***************
*** 182,185 ****
--- 182,186 ----
use Bio::Genex::ExperimentSet;
use Bio::Genex::ControlledVocab;
+ # use Apache::DB ();
</%once>
***************
*** 188,191 ****
--- 189,195 ----
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
+
+ # Apache::DB->init;
+ # Apache::DB->handler;
$dbh->assert_table_defined('GroupSec');
|
|
From: <jas...@us...> - 2002-11-22 00:37:53
|
Update of /cvsroot/genex/genex-server/apache
In directory sc8-pr-cvs1:/tmp/cvs-serv24851/apache
Modified Files:
genex-2.conf.in
Log Message:
* apache/genex-2.conf.in (Repository):
added some commented out debugging info
added some modules to be loaded during server init
Index: genex-2.conf.in
===================================================================
RCS file: /cvsroot/genex/genex-server/apache/genex-2.conf.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** genex-2.conf.in 20 Nov 2002 21:23:05 -0000 1.3
--- genex-2.conf.in 22 Nov 2002 00:37:50 -0000 1.4
***************
*** 4,7 ****
--- 4,9 ----
PerlModule HTML::Mason::ApacheHandler
+ PerlModule Bio::Genex::Connect
+ PerlModule XML::Xerces
PerlSetVar MasonAllowGlobals $dbh
***************
*** 10,13 ****
--- 12,16 ----
<Directory %%GENEX_WORKSPACE_DIR%%>
+ # PerlFixupHandler +Apache::DB
SetHandler perl-script
PerlHandler HTML::Mason::ApacheHandler
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv12812
Modified Files:
Tag: Rel-1_0_1-branch
loadam_spots.pl sql_lib.pl qc.pl choose_hybs.html
choose_hybs.pl
Added Files:
Tag: Rel-1_0_1-branch
get_data1.html
Log Message:
more field name fixes
improve the format for data export chooser
--- NEW FILE: get_data1.html ---
<html><head><title>Choose MAS5 hybridizations to analyze.</title></head>
<body bgcolor="#FFFFFF">
<table width="600" border=0 cellpadding=0 cellspacing=0>
<tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX MAS5 Hybridization Analysis<br><br>
<a href="./">Return to Genex Member Home</a>
<br><br clear=all><br>
Choose hybridizations to analyze, and change the grouping as necessary.<br>
<font color="#FF0000">{message}</font>
</td>
</tr>
</table>
<br>
<form action="get_data2.pl" method="post">
<input type="submit" name="submit" value="Next">
<br>
Comments:<br>
<input type="text" name="comments" value="{comments}" size=50>
<br>
<br>
<table width="800" border=1 cellspacing=0 cellpadding=3>
<tr bgcolor="#ccccff">
<td valign=top width="84"> </td>
<td valign=top width="84"> </td>
<td valign=top width="84"> Hybridization Comments </td>
<td valign=top width="72"> Experiment Notes </td>
<td valign=top width="105"> Short Exp. Name </td>
<td valign=top width="102"> Exp. Cond. Description </td>
<td valign=top width="126"> Hybridization Name </td>
<td valign=top width="110"> Owner </td>
<td valign=top width="51"> UserID </td>
</tr>
<loop>
<tr>
<td valign=top width="84">
<input type="checkbox" name="am_pk" value="{am_pk}">
</td>
<td valign=top width="84">{select_exp}</td>
<td valign=top width="84"> {comments} </td>
<td valign=top width="72"> {notes} </td>
<td valign=top width="105"> {abbrev_name} </td>
<td valign=top width="102"> {description} </td>
<td valign=top width="126"> {hybridization_name} </td>
<td valign=top width="110"> {contact_fname} {contact_lname} </td>
<td valign=top width="51"> {login} </td>
</tr>
</loop>
</table>
<br>
<input type="submit" name="submit" value="Next">
</form>
</body>
</html>
Index: loadam_spots.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/loadam_spots.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
*** loadam_spots.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- loadam_spots.pl 21 Nov 2002 21:48:47 -0000 1.1.2.2
***************
*** 141,148 ****
# have spot data.
#
# At this point, the associated records in other tables have been created.
! # The usf_fk field in am_spots will get used as als_fk, pointing to
! # al_spots as it will for the next schema.
! # instance_code set to "als" in arraymeasurement will be used to flag
# that this key is reserved for the new link.
#
--- 141,148 ----
# have spot data.
#
+ # Nov 21, 2002 Tom:
+ # usf_fk has been renamed to als_fk since that is what it is used for.
# At this point, the associated records in other tables have been created.
! # Instance_code set to "als" in arraymeasurement will be used to flag
# that this key is reserved for the new link.
#
***************
*** 181,185 ****
my $total_rows=0;
my $spot_key;
! my $ams_sql = "insert into am_spots_mas5 (usf_fk, am_fk, statpairs, statpairsused, signal, detection, detectionp) values (?,?,?,?,?,?,?)";
my $ams_sth = $dbh->prepare($ams_sql) || die "$ams_sql\n$DBI::errstr\n";
--- 181,185 ----
my $total_rows=0;
my $spot_key;
! my $ams_sql = "insert into am_spots_mas5 (als_fk, am_fk, statpairs, statpairsused, signal, detection, detectionp) values (?,?,?,?,?,?,?)";
my $ams_sth = $dbh->prepare($ams_sql) || die "$ams_sql\n$DBI::errstr\n";
***************
*** 194,201 ****
$spot_key = $skh{$refRow->{ProbeSet}};
#
! # This use of the usf_fk is Affymetrix specific.
! # When adding other types of array technologies, fix this.
#
! $am_spot{usf_fk} = $spot_key;
$am_spot{am_fk} = $options{am_pk};
$am_spot{statpairs} = $refRow->{StatPairs};
--- 194,202 ----
$spot_key = $skh{$refRow->{ProbeSet}};
#
! # When we used the usf_fk and a view instead of the als_fk
! # this use of the als_fk is Affymetrix specific. Maybe that is
! # no longer true. When adding other types of array technologies, consider this.
#
! $am_spot{als_fk} = $spot_key;
$am_spot{am_fk} = $options{am_pk};
$am_spot{statpairs} = $refRow->{StatPairs};
***************
*** 205,209 ****
$am_spot{detectionp} = $refRow->{DetectionP};
! $ams_sth->execute($am_spot{usf_fk},
$am_spot{am_fk},
$am_spot{statpairs},
--- 206,210 ----
$am_spot{detectionp} = $refRow->{DetectionP};
! $ams_sth->execute($am_spot{als_fk},
$am_spot{am_fk},
$am_spot{statpairs},
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.10
retrieving revision 1.1.2.11
diff -C2 -d -r1.1.2.10 -r1.1.2.11
*** sql_lib.pl 21 Nov 2002 18:48:48 -0000 1.1.2.10
--- sql_lib.pl 21 Nov 2002 21:48:47 -0000 1.1.2.11
***************
*** 71,75 ****
my $us_fk = get_us_fk($dbh);
(my $fclause, my $wclause) = read_where_clause("arraymeasurement", "am_pk", $us_fk);
! $sql = "select am_pk, smp_fk, comments, hybridization_name from arraymeasurement, $fclause where $wclause";
}
elsif ($q_name eq "hyb_owner_info")
--- 71,75 ----
my $us_fk = get_us_fk($dbh);
(my $fclause, my $wclause) = read_where_clause("arraymeasurement", "am_pk", $us_fk);
! $sql = "select am_pk, smp_fk, am_comments, hybridization_name from arraymeasurement, $fclause where $wclause";
}
elsif ($q_name eq "hyb_owner_info")
Index: qc.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/qc.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
*** qc.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- qc.pl 21 Nov 2002 21:48:47 -0000 1.1.2.2
***************
*** 1,5 ****
#!/usr/bin/perl
use strict;
- # use HTTP::Request::Common qw(POST);
use CGI;
use CGI::Carp qw(fatalsToBrowser);
--- 1,4 ----
***************
*** 20,24 ****
$message = "6m";
}
! if (length($ch{comments}) == 0)
{
$message .= "7m";
--- 19,23 ----
$message = "6m";
}
! if (length($ch{fi_comments}) == 0)
{
$message .= "7m";
***************
*** 32,36 ****
# This isn't fool proof. It is a somewhat simpleminded escape, not true URL-encoding.
# $::findme_encoded = CGI::escape($::findme);
! $ch{comments} = CGI::escape($ch{comments});
delete($ch{submit});
my $params;
--- 31,35 ----
# This isn't fool proof. It is a somewhat simpleminded escape, not true URL-encoding.
# $::findme_encoded = CGI::escape($::findme);
! $ch{fi_comments} = CGI::escape($ch{fi_comments});
delete($ch{submit});
my $params;
***************
*** 175,179 ****
# see sessionlib.pl for fi_update()
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_temp.txt", "$ch{comments} - qc data");
#
--- 174,178 ----
# see sessionlib.pl for fi_update()
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_temp.txt", "$ch{fi_comments} - qc data");
#
***************
*** 187,192 ****
{
`./Rwrapper.pl --kind="qualityControl" --settings inputDataFile="qc_temp.txt" --settings conds=$cond_args --settings outputFile="qc_out" --settings graphFormat="jpg" --settings path="$esc_path"`;
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_out.txt", "$ch{comments} - Quality Control");
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_out.jpg", "$ch{comments} - Quality Control graph");
}
--- 186,191 ----
{
`./Rwrapper.pl --kind="qualityControl" --settings inputDataFile="qc_temp.txt" --settings conds=$cond_args --settings outputFile="qc_out" --settings graphFormat="jpg" --settings path="$esc_path"`;
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_out.txt", "$ch{fi_comments} - Quality Control");
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_out.jpg", "$ch{fi_comments} - Quality Control graph");
}
***************
*** 194,198 ****
{
`./Rwrapper.pl --kind="statAnalysis" --settings inputDataFile="qc_temp.txt" --settings conds=$cond_args --settings condLabels=$cond_labels --settings outputFile="sa_out" --settings graphFormat="jpg" --settings path="$esc_path"`;
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/sa_out.txt", "$ch{comments} - Stat Analysis");
}
--- 193,197 ----
{
`./Rwrapper.pl --kind="statAnalysis" --settings inputDataFile="qc_temp.txt" --settings conds=$cond_args --settings condLabels=$cond_labels --settings outputFile="sa_out" --settings graphFormat="jpg" --settings path="$esc_path"`;
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/sa_out.txt", "$ch{fi_comments} - Stat Analysis");
}
***************
*** 200,207 ****
{
`./Rwrapper.pl --kind="westfallYoung" --settings inputDataFile="qc_temp.txt" --settings conds=$cond_args --settings condLabels=$cond_labels --settings outputFile="wy_out" --settings graphFormat="jpg" --settings path="$esc_path"`;
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/wy_out.txt", "$ch{comments} - Westfall & Young");
}
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_error.txt", "$ch{comments} - qc run log");
$dbh->commit();
--- 199,206 ----
{
`./Rwrapper.pl --kind="westfallYoung" --settings inputDataFile="qc_temp.txt" --settings conds=$cond_args --settings condLabels=$cond_labels --settings outputFile="wy_out" --settings graphFormat="jpg" --settings path="$esc_path"`;
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/wy_out.txt", "$ch{fi_comments} - Westfall & Young");
}
! fi_update($dbh, $us_fk, $us_fk, "$opts{USER_DATA_DIR}/$ENV{REMOTE_USER}/qc_error.txt", "$ch{fi_comments} - qc run log");
$dbh->commit();
Index: choose_hybs.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_hybs.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
*** choose_hybs.html 29 Oct 2002 15:13:54 -0000 1.1.2.5
--- choose_hybs.html 21 Nov 2002 21:48:47 -0000 1.1.2.6
***************
*** 15,19 ****
<br>
Comments:<br>
! <input type="text" name="comments" value="{comments}" size=50>
<br>
<br>
--- 15,19 ----
<br>
Comments:<br>
! <input type="text" name="fi_comments" value="{fi_comments}" size=50>
<br>
<br>
***************
*** 43,47 ****
<tr>
! <td valign=top width="84"> {comments} </td>
<td valign=top width="72"> {notes} </td>
<td valign=top width="105"> {abbrev_name} </td>
--- 43,47 ----
<tr>
! <td valign=top width="84"> {am_comments} </td>
<td valign=top width="72"> {notes} </td>
<td valign=top width="105"> {abbrev_name} </td>
Index: choose_hybs.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_hybs.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
*** choose_hybs.pl 29 Oct 2002 14:59:33 -0000 1.1.2.2
--- choose_hybs.pl 21 Nov 2002 21:48:47 -0000 1.1.2.3
***************
*** 26,30 ****
#
(my $fclause, my $wclause) = read_where_clause("arraymeasurement", "am_pk", $us_fk);
! my $sql = "select am_pk, smp_fk, comments, hybridization_name from arraymeasurement, $fclause where $wclause";
my $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
$sth->execute() || die "$sql\n$DBI::errstr\n";
--- 26,30 ----
#
(my $fclause, my $wclause) = read_where_clause("arraymeasurement", "am_pk", $us_fk);
! my $sql = "select am_pk, smp_fk, am_comments, hybridization_name from arraymeasurement, $fclause where $wclause";
my $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
$sth->execute() || die "$sql\n$DBI::errstr\n";
|
|
From: <tw...@us...> - 2002-11-21 18:48:51
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv29600
Modified Files:
Tag: Rel-1_0_1-branch
edit_am1.pl edit_am1.html edit_am2.pl choose_study.html
edit_study2.pl edit_study1.html edit_study1.pl insert_study.pl
sql_lib.pl
Log Message:
change some fields named 'comments' to be unique across all tables.
Index: edit_am1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_am1.pl,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** edit_am1.pl 18 Nov 2002 19:10:51 -0000 1.1.2.3
--- edit_am1.pl 21 Nov 2002 18:48:48 -0000 1.1.2.4
***************
*** 78,82 ****
($fclause, $wclause) = read_where_clause("sample", "smp_pk", $us_fk );
! $sql = "select oi_pk,hybridization_name,am_pk,al_fk,arraymeasurement.comments,smp_pk,ec_pk,abbrev_name,order_number,order_date,exp_condition.name,study.study_name,timestamp from arraymeasurement,sample,exp_condition,order_info,study,$fclause where $wclause and sample.oi_fk=$ch{oi_pk} and sample.smp_pk=arraymeasurement.smp_fk and sample.ec_fk=exp_condition.ec_pk and order_info.oi_pk=sample.oi_fk and sty_pk=sty_fk order by smp_pk,am_pk;";
my $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
--- 78,82 ----
($fclause, $wclause) = read_where_clause("sample", "smp_pk", $us_fk );
! $sql = "select oi_pk,hybridization_name,am_pk,al_fk,arraymeasurement.am_comments,smp_pk,ec_pk,abbrev_name,order_number,order_date,exp_condition.name,study.study_name,timestamp from arraymeasurement,sample,exp_condition,order_info,study,$fclause where $wclause and sample.oi_fk=$ch{oi_pk} and sample.smp_pk=arraymeasurement.smp_fk and sample.ec_fk=exp_condition.ec_pk and order_info.oi_pk=sample.oi_fk and sty_pk=sty_fk order by smp_pk,am_pk;";
my $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
Index: edit_am1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_am1.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
*** edit_am1.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- edit_am1.html 21 Nov 2002 18:48:48 -0000 1.1.2.2
***************
*** 10,13 ****
--- 10,14 ----
Please choose the Affymetrix chip for each hybridization of the following samples.
<br>
+ <font color="#FF0000"><b>{message}</b></font>
<form action="edit_am2.pl" method=POST>
<input type=submit name="Finish" value="Finish"> <a href="./">Cancel</a>
***************
*** 63,67 ****
<tr>
<td valign="top">Comments</td>
! <td><input type=text name="comments" value="{comments}"><br><br></td>
</tr>
--- 64,68 ----
<tr>
<td valign="top">Comments</td>
! <td><input type=text name="am_comments" value="{am_comments}"><br><br></td>
</tr>
Index: edit_am2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_am2.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
*** edit_am2.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- edit_am2.pl 21 Nov 2002 18:48:48 -0000 1.1.2.2
***************
*** 6,9 ****
--- 6,10 ----
require "sessionlib.pl";
+ my $message;
main:
***************
*** 45,52 ****
}
$dbh->commit;
$dbh->disconnect;
! my $url = index_url(); # see sessionlib.pl
! print "Location: $url\n\n";
}
--- 46,65 ----
}
+
+
$dbh->commit;
$dbh->disconnect;
! if ((length($message) > 0))
! {
! my $url = index_url(); # see sessionlib.pl
! $url =~ s/(.*)\/.*/$1\/edit_am1.pl/;
! print "Location: $url?&oi_pk=$ch{oi_pk}&message=$message\n\n";
! exit();
! }
! else
! {
! my $url = index_url(); # see sessionlib.pl
! print "Location: $url\n\n";
! }
}
***************
*** 166,171 ****
die "$sql\nReturned $row_count rows, but only 1 row was expected\n";
}
! $sql = "update arraymeasurement set al_fk='$ch{al_fk}', comments=trim('$ch{comments}') where am_pk=$ch{am_pk}";
$dbh->do($sql) || die "$sql\n$DBI::errstr\n";
}
--- 179,189 ----
die "$sql\nReturned $row_count rows, but only 1 row was expected\n";
}
! $sql = "update arraymeasurement set al_fk='$ch{al_fk}', am_comments=trim('$ch{am_comments}') where am_pk=$ch{am_pk}";
$dbh->do($sql) || die "$sql\n$DBI::errstr\n";
+ my $temp = verify_hyb($dbh, $ch{am_pk});
+ if ($message !~ m/^$temp|m$temp/)
+ {
+ $message .= $temp;
+ }
}
Index: choose_study.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_study.html,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** choose_study.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- choose_study.html 21 Nov 2002 18:48:48 -0000 1.1.2.2
***************
*** 20,24 ****
Study name: {study_name}<br>
Date started: {start_date}<br>
! Comments: {comments}<br>
Number of conditions: {number_of_conditions}
</form>
--- 20,24 ----
Study name: {study_name}<br>
Date started: {start_date}<br>
! Comments: {sty_comments}<br>
Number of conditions: {number_of_conditions}
</form>
Index: edit_study2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_study2.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
*** edit_study2.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- edit_study2.pl 21 Nov 2002 18:48:48 -0000 1.1.2.2
***************
*** 80,87 ****
$ch{start_date} = date2sql($ch{start_date});
! my $sql = "update study set study_name=trim(?), comments=trim(?), start_date=? where sty_pk=$ch{sty_pk}";
my $sth = $dbh->prepare($sql) || die "edit_study2 write_study: $sql\n$DBI::errstr\n";
$sth->execute($ch{study_name},
! $ch{comments},
$ch{start_date}) || die "$sql\n$DBI::errstr\n";
$sth->finish();
--- 80,87 ----
$ch{start_date} = date2sql($ch{start_date});
! my $sql = "update study set study_name=trim(?), sty_comments=trim(?), start_date=? where sty_pk=$ch{sty_pk}";
my $sth = $dbh->prepare($sql) || die "edit_study2 write_study: $sql\n$DBI::errstr\n";
$sth->execute($ch{study_name},
! $ch{sty_comments},
$ch{start_date}) || die "$sql\n$DBI::errstr\n";
$sth->finish();
Index: edit_study1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_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
*** edit_study1.html 14 Nov 2002 21:55:29 -0000 1.1.2.2
--- edit_study1.html 21 Nov 2002 18:48:48 -0000 1.1.2.3
***************
*** 25,29 ****
</td></tr>
<tr><td>
! <div align="right">Study Comments </div></td><td> <textarea name="comments" rows=5 cols=40 wrap="virtual">{comments}</textarea>
</td></tr>
--- 25,29 ----
</td></tr>
<tr><td>
! <div align="right">Study Comments </div></td><td> <textarea name="sty_comments" rows=5 cols=40 wrap="virtual">{sty_comments}</textarea>
</td></tr>
Index: edit_study1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/edit_study1.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
*** edit_study1.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- edit_study1.pl 21 Nov 2002 18:48:48 -0000 1.1.2.2
***************
*** 56,61 ****
(my $fclause, my $wclause) = write_where_clause("study", "sty_pk", $us_fk );
! my $sql = "select study_name,comments,start_date from study, $fclause where sty_pk=$ch{sty_pk} and $wclause";
! (($ch{study_name}, $ch{comments}, $ch{start_date}) = $dbh->selectrow_array($sql)) || die "$sql\n$DBI::errstr\n" ;
$ch{start_date} = sql2date($ch{start_date});
--- 56,61 ----
(my $fclause, my $wclause) = write_where_clause("study", "sty_pk", $us_fk );
! my $sql = "select study_name,sty_comments,start_date from study, $fclause where sty_pk=$ch{sty_pk} and $wclause";
! (($ch{study_name}, $ch{sty_comments}, $ch{start_date}) = $dbh->selectrow_array($sql)) || die "$sql\n$DBI::errstr\n" ;
$ch{start_date} = sql2date($ch{start_date});
Index: insert_study.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/insert_study.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
*** insert_study.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- insert_study.pl 21 Nov 2002 18:48:48 -0000 1.1.2.2
***************
*** 23,27 ****
my $sql = "select study_name from study,$from where $where";
! my $sth = $dbh->prepare($sql) || die "insert_study: $sql\n$DBI::errstr\n";
$sth->execute();
my %sn_hash;
--- 23,27 ----
my $sql = "select study_name from study,$from where $where";
! my $sth = $dbh->prepare($sql) || die "insert_study.pl: $sql\n$DBI::errstr\n";
$sth->execute();
my %sn_hash;
***************
*** 41,52 ****
}
}
-
! $sql = "insert into study (study_name, comments) values (trim('$new_name'), trim('comments'))";
!
! if (! $dbh->do($sql))
! {
! die "Insert failed: $sql\n$DBI::errstr\n";
! }
my $sty_pk = insert_security($dbh, $us_fk, $us_fk, 0);
--- 41,47 ----
}
}
! my $sth = getq("insert_study", $dbh);
! $sth->execute($new_name) || die "Query insert_study execute fails.\n$DBI::errstr\n";
my $sty_pk = insert_security($dbh, $us_fk, $us_fk, 0);
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.9
retrieving revision 1.1.2.10
diff -C2 -d -r1.1.2.9 -r1.1.2.10
*** sql_lib.pl 18 Nov 2002 21:20:53 -0000 1.1.2.9
--- sql_lib.pl 21 Nov 2002 18:48:48 -0000 1.1.2.10
***************
*** 117,121 ****
groupref.us_fk=usersec.us_pk";
}
!
if (defined($sql))
{
--- 117,124 ----
groupref.us_fk=usersec.us_pk";
}
! elsif ($q_name eq "insert_study")
! {
! $sql = "insert into study (study_name, sty_comments) values (trim(?), trim('Enter comments here.'))";
! }
if (defined($sql))
{
|
|
From: <tw...@us...> - 2002-11-21 16:10:57
|
Update of /cvsroot/genex/genex-server/archive
In directory sc8-pr-cvs1:/tmp/cvs-serv30495
Removed Files:
Tag: Rel-1_0_1-branch
old_genex.tar
Log Message:
removing a munged tar file
--- old_genex.tar DELETED ---
|
|
From: <tw...@us...> - 2002-11-21 15:57:32
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv25676
Added Files:
Tag: Rel-1_0_1-branch
layout.pl
Log Message:
script to automate loading the layouts
--- NEW FILE: layout.pl ---
#!/usr/bin/perl
use strict;
my $uid;
if ($ARGV[0])
{
$uid = $ARGV[0];
}
else
{
print "Usage: layout.pl user_name\nFor example\nlayout.pl mst3k\n";
exit(1);
}
my $wdir = `./install_lib.pl -W`;
chomp($wdir);
my $ldir = `./install_lib.pl -L`;
chomp($ldir);
# To run loadaffylayout.pl in test mode, call it with --nocommit
`$wdir/loadaffylayout.pl --name=RT-U34 --input=$ldir/rt-u34.txt --speciesid=53 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=RN-U34 --input=$ldir/rn-u34.txt --speciesid=53 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=RG-U34A --input=$ldir/RG-U34A.xls --speciesid=53 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=RG-U34B --input=$ldir/RG-U34B.xls --speciesid=53 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=RG-U34C --input=$ldir/RG-U34C.xls --speciesid=53 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=MG-U74Av2 --input=$ldir/mg-u74av2.txt --speciesid=41 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=MG-U74Bv2 --input=$ldir/mg-u74bv2.txt --speciesid=41 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=MG-U74Cv2 --input=$ldir/mg-u74cv2.txt --speciesid=41 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=Mu11KA --input=$ldir/Mu11KA.xls --speciesid=41 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=Mu11KB --input=$ldir/Mu11KB.xls --speciesid=41 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HG-U133B --input=$ldir/HG-U133b.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HG-U133A --input=$ldir/HG-U133a.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HUFL --input=$ldir/HUFL.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HG-U95Av2 --input=$ldir/HgU95Av2.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HG-U95B --input=$ldir/HG-U95B.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HG-U95C --input=$ldir/HG-U95C.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HG-U95D --input=$ldir/HG-U95D.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=HG-U95E --input=$ldir/HG-U95E.xls --speciesid=50 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=YG-S98 --input=$ldir/YG-S98.xls --speciesid=5 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=E_coli --input=$ldir/E_coli.xls --speciesid=4 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=DROSOPHILA --input=$ldir/drosophila.txt --speciesid=44 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name="P.AERUGINOSA" --input=$ldir/p-aeruginosa.txt --speciesid=108 --login=$uid --dbname=genex >> layout.log`;
`$wdir/loadaffylayout.pl --name=Arabidopsis --input=$ldir/Arabidopsis.xls --speciesid=6 --login=$uid --dbname=genex >> layout.log`;
|
|
From: <jas...@us...> - 2002-11-21 12:46:15
|
Update of /cvsroot/genex/genex-server/Genex/Reporter
In directory sc8-pr-cvs1:/tmp/cvs-serv18044/Reporter
Modified Files:
Reporter.pm
Log Message:
added count output for insert_matrix
Index: Reporter.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Reporter/Reporter.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Reporter.pm 21 Nov 2002 12:28:48 -0000 1.7
--- Reporter.pm 21 Nov 2002 12:46:12 -0000 1.8
***************
*** 28,32 ****
! use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $FKEYS $COLUMN2NAME $NAME2COLUMN $COLUMN_NAMES %_CACHE $USE_CACHE $LIMIT $FKEY_OBJ2RAW $TABLE2PKEY $UNIQUE_COLUMNS $SUPER_CLASSES $TABLE_TYPE $PKEY_NAME $TABLE_NAME $DEBUG $TABLE_NAME_VIEW);
require Exporter;
--- 28,32 ----
! use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $FKEYS $COLUMN2NAME $NAME2COLUMN $COLUMN_NAMES %_CACHE $USE_CACHE $LIMIT $FKEY_OBJ2RAW $TABLE2PKEY $UNIQUE_COLUMNS $SUPER_CLASSES $TABLE_TYPE $PKEY_NAME $TABLE_NAME $DEBUG $TABLE_NAME_VIEW $COUNT);
require Exporter;
***************
*** 1242,1246 ****
--- 1242,1249 ----
message=>"Couldn't prepare insert sql",
sql=>$sql);
+
+ my $count;
foreach my $row (@{$matrix}) {
+ $count++;
$seq_sth->execute()
or $dbh->error(@error_args,
***************
*** 1266,1269 ****
--- 1269,1275 ----
+ print STDERR "Handled $count Bio::Genex::Reporter objects
+ "
+ if $DEBUG and $COUNT and ($count % $COUNT == 0);
}
my $ga_db = Bio::Genex::GenexAdmin->new();
|
|
From: <jas...@us...> - 2002-11-21 12:38:41
|
Update of /cvsroot/genex/genex-server/Genex In directory sc8-pr-cvs1:/tmp/cvs-serv14628 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.121 retrieving revision 1.122 diff -C2 -d -r1.121 -r1.122 *** ChangeLog 21 Nov 2002 09:56:44 -0000 1.121 --- ChangeLog 21 Nov 2002 12:38:39 -0000 1.122 *************** *** 1,4 **** --- 1,11 ---- 2002-11-21 Jason E. Stewart <ja...@op...> + * scripts/create_genex_class.pl.in (Repository): + added insert_matrix() to all classes + added $COUNT for loop verbosity + + * scripts/array-design-insert.pl.in (Repository): + uses Reporter::insert_matrix() + * Genex.pm.in (Repository): new version (2.7.20021121) |
|
From: <jas...@us...> - 2002-11-21 12:38:26
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv14512/scripts
Modified Files:
array-design-insert.pl.in
Log Message:
added count output
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** array-design-insert.pl.in 21 Nov 2002 12:29:45 -0000 1.10
--- array-design-insert.pl.in 21 Nov 2002 12:38:23 -0000 1.11
***************
*** 167,172 ****
push(@names,$name);
! push(@matrix,[$name,$type,$con_fk,$OPTIONS{ro_group},$OPTIONS{rw_group}])
!
}
if (exists $OPTIONS{reporters_only}) {
--- 167,177 ----
push(@names,$name);
! push(@matrix,[$name,$type,$con_fk,$OPTIONS{ro_group},$OPTIONS{rw_group}]);
! print STDERR "Added $count Reporters to matrix\n"
! if exists $OPTIONS{count} and ($count % $OPTIONS{count} == 0);
! }
! if ($OPTIONS{count}) {
! $Bio::Genex::Reporter::DEBUG = 1;
! $Bio::Genex::Reporter::COUNT = $OPTIONS{count};
}
if (exists $OPTIONS{reporters_only}) {
|
|
From: <jas...@us...> - 2002-11-21 12:37:33
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv14122/scripts
Modified Files:
create_genex_class.pl.in
Log Message:
* scripts/create_genex_class.pl.in (Repository):
added insert_matrix() to all classes
added $COUNT for loop verbosity
Index: create_genex_class.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_class.pl.in,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** create_genex_class.pl.in 15 Nov 2002 22:00:38 -0000 1.19
--- create_genex_class.pl.in 21 Nov 2002 12:37:29 -0000 1.20
***************
*** 528,537 ****
print_get_objects();
}
-
print_get_all_objects();
if ($HAS_LT_FKEY) {
! # Lookup table classes need to return and insert a matrix of values
! print_insert_matrix();
print_get_matrix();
}
--- 528,537 ----
print_get_objects();
}
print_get_all_objects();
+ # we now allow all classes to insert by matrix
+ print_insert_matrix();
if ($HAS_LT_FKEY) {
! # Lookup table classes need to return a matrix of values
print_get_matrix();
}
***************
*** 606,610 ****
$use_modules
! use vars qw(\$VERSION \@ISA \@EXPORT \@EXPORT_OK \$FKEYS \$COLUMN2NAME \$NAME2COLUMN \$COLUMN_NAMES \%_CACHE \$USE_CACHE \$LIMIT \$FKEY_OBJ2RAW \$TABLE2PKEY \$UNIQUE_COLUMNS \$SUPER_CLASSES \$TABLE_TYPE \$PKEY_NAME \$TABLE_NAME \$DEBUG \$TABLE_NAME_VIEW);
require Exporter;
--- 606,610 ----
$use_modules
! use vars qw(\$VERSION \@ISA \@EXPORT \@EXPORT_OK \$FKEYS \$COLUMN2NAME \$NAME2COLUMN \$COLUMN_NAMES \%_CACHE \$USE_CACHE \$LIMIT \$FKEY_OBJ2RAW \$TABLE2PKEY \$UNIQUE_COLUMNS \$SUPER_CLASSES \$TABLE_TYPE \$PKEY_NAME \$TABLE_NAME \$DEBUG \$TABLE_NAME_VIEW \$COUNT);
require Exporter;
***************
*** 1189,1203 ****
# begin print_insert_matrix()
! my $lt_fkey_class = $lt_fkeys[0]->table_name();
! my $lt_fkey_class_full = "Bio::Genex::$lt_fkey_class";
! my $lt_fkey_pkey = $lt_fkeys[0]->pkey_name();
! my $lt_fkey = $FKEY_OBJ2RAW{$lt_fkeys[0]->fkey_name};
! my $lt_fkey_class_lc = lc($lt_fkey_class);
! # start a section with variable expansion *enabled*
! print OUT <<"EOT";
!
! =item insert_matrix(\$class,\%args)
!
! This method inserts the data for the object into the database
specified by the DB handle \$dbh. To use this method, create a blank
container object with C<new()> (for class C<$full_module_name> the
--- 1189,1206 ----
# begin print_insert_matrix()
! my $POD;
! my $fkey_pod = '';
! my $warning_pod = '';
! my $push_header;
! my $execute;
! my $check_lt_pkey = '';
! if (scalar @lt_fkeys) {
! my $lt_fkey_class = $lt_fkeys[0]->table_name();
! my $lt_fkey_class_full = "Bio::Genex::$lt_fkey_class";
! my $lt_fkey_pkey = $lt_fkeys[0]->pkey_name();
! my $lt_fkey = $FKEY_OBJ2RAW{$lt_fkeys[0]->fkey_name};
! my $lt_fkey_class_lc = lc($lt_fkey_class);
! $POD = <<POD;
! This method inserts a matrix of data into the database
specified by the DB handle \$dbh. To use this method, create a blank
container object with C<new()> (for class C<$full_module_name> the
***************
*** 1213,1216 ****
--- 1216,1293 ----
\$$lt_fkey_class_lc->$ {module_name_lc}_obj(\@matrix);
\$$lt_fkey_class_lc->insert_db(\$dbh);
+ POD
+ $fkey_pod = <<'POD';
+ =item * fkey
+
+ the container objects primary key that will be entered in the foreign
+ key slot for each matrix row
+ POD
+ $warning_pod = <<'POD';
+ B<NOTE:> As indicated above, you do not want to call
+ C<insert_matrix()> directly, as it needs information about its
+ container object.
+ POD
+
+ $check_lt_pkey = <<EOT;
+ my \$lt_pkey = \$args{fkey};
+ # first we ensure that the container instance is really in the DB
+ \$sql = \$dbh->create_select_sql( COLUMNS=>['$lt_fkey_pkey'],
+ FROM=>[$lt_fkey_class_full->table_or_viewname(\$dbh)],
+ WHERE=>qq[$lt_fkey_pkey='\$lt_pkey'],
+ );
+ my \$ref = \$dbh->selectall_arrayref(\$sql);
+ \$dbh->error(\@error_args,
+ message=>"Couldn't fetch container class",
+ sql=>\$sql)
+ if not defined \$ref or not scalar \@{\$ref};
+ EOT
+
+ $push_header = <<EOT;
+ # ok to proceed with insert
+ # add lookup table fkey and primary key to each row
+ push(\@{\$header},'$lt_fkey','$PKEY');
+ EOT
+
+ $execute = <<EOT;
+ \$sth->execute(\@{\$row},\$lt_pkey,\$pkey->[0])
+ or \$dbh->error(\@error_args,
+ message=>"Couldn't execute insert sql with args: "
+ . join(',',\@{\$row},\$lt_pkey,\$pkey->[0]),
+ sth=>\$sth,
+ sql=>\$sql);
+ EOT
+ } else {
+ $POD = <<POD;
+
+ This method inserts a matrix of data into the database specified by
+ the DB handle \$dbh. Class C<$full_module_name> has no foreign keys of
+ type 'lookup table', so C<insert_matrix> may be invoked as a ordinary
+ class method.
+
+ my \$matrix = some_method_returning_data();
+ $full_module_name->insert_matrix(dbh=>\$dbh,matrix=>\$matrix);
+
+ POD
+
+ $push_header = <<EOT;
+ # add primary key to each row
+ push(\@{\$header},'$PKEY');
+ EOT
+ $execute = <<EOT;
+ \$sth->execute(\@{\$row},\$pkey->[0])
+ or \$dbh->error(\@error_args,
+ message=>"Couldn't execute insert sql with args: "
+ . join(',',\@{\$row},\$pkey->[0]),
+ sth=>\$sth,
+ sql=>\$sql);
+ EOT
+ }
+
+ # start a section with variable expansion *enabled*
+ print OUT <<"EOT";
+
+ =item insert_matrix(\$class,\%args)
+
+ $POD
Supported \%args
***************
*** 1222,1237 ****
an active database handle
- =item * fkey
-
- the container objects primary key that will be entered in the foreign
- key slot for each matrix row
-
=item * matrix
an array ref holding the matrix
! =item * name
!
! the person responisible for the insertion
=back
--- 1299,1307 ----
an active database handle
=item * matrix
an array ref holding the matrix
! $fkey_pod
=back
***************
*** 1240,1246 ****
priveleges in the DB, otherwise you will get a DBI error.
! B<NOTE:> As indicated above, you do not want to call
! C<insert_matrix()> directly, as it needs information about its
! container object.
=cut
--- 1310,1314 ----
priveleges in the DB, otherwise you will get a DBI error.
! $warning_pod
=cut
***************
*** 1255,1275 ****
my (\$pack,\$file,\$line,\$sub) = caller(0);
push(\@error_args, caller=>"\$pack:\$file:\$line:\$sub");
-
- my \$lt_pkey = \$args{fkey};
my \$matrix = \$args{matrix};
- # first we ensure that the container instance is really in the DB
- my \$sql = \$dbh->create_select_sql( COLUMNS=>['$lt_fkey_pkey'],
- FROM=>[$lt_fkey_class_full->table_or_viewname(\$dbh)],
- WHERE=>qq[$lt_fkey_pkey='\$lt_pkey'],
- );
- my \$ref = \$dbh->selectall_arrayref(\$sql);
\$dbh->error(\@error_args,
! message=>"Couldn't fetch container class",
! sql=>\$sql)
! if not defined \$ref or not scalar \@{\$ref};
!
! # ok to proceed with insert
my \$header = shift \@{\$matrix};
! push(\@{\$header},'$lt_fkey','$PKEY');
# pre-fetch the next value of the sequence
--- 1323,1338 ----
my (\$pack,\$file,\$line,\$sub) = caller(0);
push(\@error_args, caller=>"\$pack:\$file:\$line:\$sub");
my \$matrix = \$args{matrix};
\$dbh->error(\@error_args,
! message=>"Must supply array reference for 'matrix'",
! no_errstr=>1,
! )
! unless ref(\$matrix) eq 'ARRAY';
my \$header = shift \@{\$matrix};
! my \$sql;
!
! $check_lt_pkey
!
! $push_header
# pre-fetch the next value of the sequence
***************
*** 1289,1293 ****
--- 1352,1359 ----
message=>"Couldn't prepare insert sql",
sql=>\$sql);
+
+ my \$count;
foreach my \$row (\@{\$matrix}) {
+ \$count++;
\$seq_sth->execute()
or \$dbh->error(\@error_args,
***************
*** 1304,1313 ****
# DBI won't re-run the SQL until we finish
\$seq_sth->finish();
! \$sth->execute(\@{\$row},\$lt_pkey,\$pkey->[0])
! or \$dbh->error(\@error_args,
! message=>"Couldn't execute insert sql with args: "
! . join(',',\@{\$row},\$pkey->[0]),
! sth=>\$sth,
! sql=>\$sql);
}
my \$ga_db = Bio::Genex::GenexAdmin->new();
--- 1370,1378 ----
# DBI won't re-run the SQL until we finish
\$seq_sth->finish();
!
! $execute
!
! print STDERR "Handled \$count $full_module_name objects\n"
! if \$DEBUG and \$COUNT and (\$count % \$COUNT == 0);
}
my \$ga_db = Bio::Genex::GenexAdmin->new();
|
|
From: <jas...@us...> - 2002-11-21 12:29:48
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv9955/scripts
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Repository):
uses Reporter::insert_matrix()
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** array-design-insert.pl.in 21 Nov 2002 09:55:11 -0000 1.9
--- array-design-insert.pl.in 21 Nov 2002 12:29:45 -0000 1.10
***************
*** 153,156 ****
--- 153,160 ----
$start = new Benchmark;
my $count;
+ my @header = qw(rep_name rep_type provider_con_fk ro_groupname rw_groupname);
+ my @matrix = (\@header);
+ my @names;
+ my $con_fk = $CONTACT_GENEX->con_pk();
foreach my $mage_reporter (@mage_reporters) {
$count++;
***************
*** 162,181 ****
my $type = 'clone_name'; # FIXME
! # we should figure out how to enable a contact for the reporters FIXME
! my $rep_db = Bio::Genex::Reporter->new(rep_name=>$name,
! rep_type=>$type,
! provider_con_obj=>$CONTACT_GENEX,
! ro_groupname=>$OPTIONS{ro_group},
! rw_groupname=>$OPTIONS{rw_group},
! );
! my $rep_pk = $rep_db->insert_db(dbh=>$dbh,no_genex_admin=>1);
! $dbh->error(@error_args,
! message=>"couldn't insert record for reporter: $name")
! if $dbh->err;
! $REPORTERS{$name} = $rep_pk
! unless exists $OPTIONS{reporters_only};
! print STDERR "Handled $count Reporters",
! if exists $OPTIONS{count} and ($count % $OPTIONS{count} == 0);
}
$stop = new Benchmark;
$diff = timediff($stop,$start);
--- 166,181 ----
my $type = 'clone_name'; # FIXME
! push(@names,$name);
! push(@matrix,[$name,$type,$con_fk,$OPTIONS{ro_group},$OPTIONS{rw_group}])
!
}
+ if (exists $OPTIONS{reporters_only}) {
+ Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,
+ matrix=>\@matrix);
+ } else {
+ $REPORTERS{@names} = Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,
+ matrix=>\@matrix);
+ }
+
$stop = new Benchmark;
$diff = timediff($stop,$start);
|
|
From: <jas...@us...> - 2002-11-21 12:28:51
|
Update of /cvsroot/genex/genex-server/Genex/Reporter
In directory sc8-pr-cvs1:/tmp/cvs-serv9614/Reporter
Modified Files:
Reporter.pm
Log Message:
added insert_matrix()
Index: Reporter.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Reporter/Reporter.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Reporter.pm 15 Nov 2002 21:55:17 -0000 1.6
--- Reporter.pm 21 Nov 2002 12:28:48 -0000 1.7
***************
*** 1166,1169 ****
--- 1166,1282 ----
+ =item insert_matrix($class,%args)
+
+
+ This method inserts a matrix of data into the database specified by
+ the DB handle $dbh. Class C<Bio::Genex::Reporter> has no foreign keys of
+ type 'lookup table', so C<insert_matrix> may be invoked as a ordinary
+ class method.
+
+ my $matrix = some_method_returning_data();
+ Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,matrix=>$matrix);
+
+
+
+ Supported %args
+
+ =over
+
+ =item * dbh
+
+ an active database handle
+
+ =item * matrix
+
+ an array ref holding the matrix
+
+
+
+ =back
+
+ B<NOTE:> You must log into the DB with a user/password that has INSERT
+ priveleges in the DB, otherwise you will get a DBI error.
+
+
+
+ =cut
+
+ sub insert_matrix {
+ my ($class,%args) = @_;
+ my $dbh = $args{dbh};
+ assert_dbh($dbh);
+
+ my $table_name = Bio::Genex::Reporter->table_or_viewname($dbh);
+ my @error_args = ();
+ my ($pack,$file,$line,$sub) = caller(0);
+ push(@error_args, caller=>"$pack:$file:$line:$sub");
+ my $matrix = $args{matrix};
+ $dbh->error(@error_args,
+ message=>"Must supply array reference for 'matrix'",
+ no_errstr=>1,
+ )
+ unless ref($matrix) eq 'ARRAY';
+ my $header = shift @{$matrix};
+ my $sql;
+
+
+
+ # add primary key to each row
+ push(@{$header},'rep_pk');
+
+
+ # pre-fetch the next value of the sequence
+ my $seq = 'GENEX_ID_SEQ';
+ my $seq_sql = qq[SELECT nextval('"$seq"'::text)];
+ my $seq_sth = $dbh->prepare($seq_sql)
+ or $dbh->error(@error_args,
+ sql=>$seq_sql,
+ message=>"Couldn't prepare nextval for sequence $seq",
+ );
+
+ $sql = $dbh->create_insert_sql($table_name,
+ $header,
+ );
+ my $sth = $dbh->prepare($sql)
+ or $dbh->error(@error_args,
+ message=>"Couldn't prepare insert sql",
+ sql=>$sql);
+ foreach my $row (@{$matrix}) {
+ $seq_sth->execute()
+ or $dbh->error(@error_args,
+ message=>"Couldn't execute nextval from sequence $seq",
+ sth=>$seq_sth,
+ sql=>$seq_sql);
+ my $pkey = $seq_sth->fetchrow_arrayref();
+ $dbh->error(@error_args,
+ message=>"Couldn't fetch nextval from sequence $seq",
+ sth=>$seq_sth,
+ sql=>$seq_sql)
+ unless defined $pkey && $pkey->[0];
+
+ # DBI won't re-run the SQL until we finish
+ $seq_sth->finish();
+
+ $sth->execute(@{$row},$pkey->[0])
+ or $dbh->error(@error_args,
+ message=>"Couldn't execute insert sql with args: "
+ . join(',',@{$row},$pkey->[0]),
+ sth=>$sth,
+ sql=>$sql);
+
+
+ }
+ my $ga_db = Bio::Genex::GenexAdmin->new();
+ my $description = "inserted " . scalar @{$matrix} . " Bio::Genex::Reporter objects";
+ $ga_db->description($description);
+ $ga_db->insert_db($dbh);
+
+ $dbh->error(@error_args,
+ message=>"Couldn't insert GenexAdmin record")
+ if $dbh->err;
+
+ return 1;
+ }
+
# ObjectTemplate automagically creates a new() method for us
# that method invokes $self->initialize() after first setting all
|
|
From: <jas...@us...> - 2002-11-21 10:05:05
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv21595 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.110 retrieving revision 1.111 diff -C2 -d -r1.110 -r1.111 *** ChangeLog 20 Nov 2002 22:43:04 -0000 1.110 --- ChangeLog 21 Nov 2002 10:05:03 -0000 1.111 *************** *** 1,2 **** --- 1,11 ---- + 2002-11-21 Jason E. Stewart <ja...@op...> + + * Install (Repository): + installation of Config.pm now handled by Perl + + * Configure (Repository): + removed make clean cruft + now copies Config.pm into Genex/Config so that Perl can install it + 2002-11-20 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2002-11-21 10:04:48
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv21519
Modified Files:
Install
Log Message:
* Install (Repository):
installation of Config.pm now handled by Perl
Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Install 15 Nov 2002 22:04:23 -0000 1.15
--- Install 21 Nov 2002 10:04:46 -0000 1.16
***************
*** 504,516 ****
slow() if ($SLOW);
- #
- # Config.pm
- #
- print STDOUT "Installing Config.pm ...\n\n";
- $DIR = "$GENEX_INSTALLSITE/Bio/Genex";
- genex_mkdir($DIR)
- unless -d $DIR;
- genex_system("$VARS{GNUINSTALL} -m 444 $CACHE_FILE_NAME $DIR");
-
my ($PERLPATH) = $START_PERL =~ m/^\#\!(.*)$/;
die "Tried to use $PERLPATH as perl executable and failed"
--- 504,507 ----
|
|
From: <jas...@us...> - 2002-11-21 10:04:06
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv21276
Modified Files:
Configure
Log Message:
* Configure (Repository):
removed make clean cruft
now copies Config.pm into Genex/Config so that Perl can install it
Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Configure 15 Nov 2002 22:03:52 -0000 1.11
--- Configure 21 Nov 2002 10:04:03 -0000 1.12
***************
*** 268,312 ****
init_error();
- if ($CLEAN) {
- print STDOUT "\n\n\n\t About to clean out the subdirs!\n\n\n";
- print STDOUT " if this is what you wanted to do, hit [Enter]; if not, ^C now!\n";
- $tmp = <STDIN>;
- if (-e "$CACHE_FILE_NAME") {
- genex_system("cd $MOTHERDIR; cp $CACHE_FILE_NAME $CACHE_FILE_NAME.old");
- check_sys($?, $!, __LINE__, "copying cache file");
- }
- unlink $CACHE_FILE_NAME;
- unlink <$MOTHERDIR/curation-tool/*.pl>;
-
- unlink <$MOTHERDIR/CyberT-dist/Cyber*.pl>;
- unlink <$MOTHERDIR/CyberT-dist/*.inc>;
- unlink <$MOTHERDIR/CyberT-dist/runa.*o>;
- unlink <$MOTHERDIR/CyberT-dist/xgobi>;
- unlink <$MOTHERDIR/CyberT-dist/munge4R.pl>;
- unlink <$MOTHERDIR/CyberT-dist/hdarray>;
- unlink <$MOTHERDIR/CyberT-dist/CyberT.html>;
-
- unlink <$MOTHERDIR/gxquery/*.pl>;
-
- unlink <$MOTHERDIR/login/*.pl>;
-
- unlink "$MOTHERDIR/CyberT-Demo/Basic_CyberT_Demo.shtml";
-
- unlink "$MOTHERDIR/top_level/genex_info.shtml";
- unlink "$MOTHERDIR/top_level/index.shtml";
- unlink "$MOTHERDIR/top_level/analysis_tools.shtml";
-
- unlink "$MOTHERDIR/xcluster/*.pl";
-
- chdir "$MOTHERDIR/rcluster-1.0";
- genex_system('make clean');
-
- chdir "$MOTHERDIR/Genex";
- if (-e "Makefile") { genex_system('make clean'); }
- chdir $MOTHERDIR;
- check_sys($?, $!, __LINE__, "Cleaning the cruft left over from previous install");
- exit();
- }
-
# skip the whole process if instructed to
goto INSTALL if $SKIP_SUBSTITUTION;
--- 268,271 ----
***************
*** 389,393 ****
}
}
! print STDOUT "\n\nUsing Config file: $ {CACHE_FILE_DIR}$CACHE_FILE_NAME\n";
} else {
print STDOUT "\n\nOK... Proceeding with new installation\n";
--- 348,352 ----
}
}
! print STDOUT "\n\nUsing Config file: $CACHE_FILE_DIR$CACHE_FILE_NAME\n";
} else {
print STDOUT "\n\nOK... Proceeding with new installation\n";
***************
*** 404,408 ****
my $USE_CACHE = 0;
my %SUBST;
! if (-f "$ {CACHE_FILE_DIR}$CACHE_FILE_NAME") {
$USE_CACHE = 1;
--- 363,367 ----
my $USE_CACHE = 0;
my %SUBST;
! if (-f "$CACHE_FILE_DIR$CACHE_FILE_NAME") {
$USE_CACHE = 1;
***************
*** 411,415 ****
print STDOUT <<"EOM";
! I found a GeneX Configuration file at: $ {CACHE_FILE_DIR}$CACHE_FILE_NAME.
You must have installed GeneX before.
EOM
--- 370,374 ----
print STDOUT <<"EOM";
! I found a GeneX Configuration file at: $CACHE_FILE_DIR$CACHE_FILE_NAME.
You must have installed GeneX before.
EOM
***************
*** 1733,1736 ****
--- 1692,1700 ----
print CACHE $d->Dump(), "\n1;\n__END__\n";
close(CACHE);
+
+ # we move a copy of the cache file into the Genex/Config directory so
+ # that when build the Perl API the cache file will be installed along
+ # with the rest of the API
+ genex_system("cp $CACHE_FILE_NAME Genex/Config");
print STDOUT <<"EOM";
|
|
From: <jas...@us...> - 2002-11-21 09:56:47
|
Update of /cvsroot/genex/genex-server/Genex In directory sc8-pr-cvs1:/tmp/cvs-serv18796 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.120 retrieving revision 1.121 diff -C2 -d -r1.120 -r1.121 *** ChangeLog 20 Nov 2002 00:22:15 -0000 1.120 --- ChangeLog 21 Nov 2002 09:56:44 -0000 1.121 *************** *** 1,2 **** --- 1,17 ---- + 2002-11-21 Jason E. Stewart <ja...@op...> + + * Genex.pm.in (Repository): + new version (2.7.20021121) + + * scripts/array-design-insert.pl.in (Repository): + added count output to reporter inserts (for the paranoid) + + 2002-11-20 Jason E. Stewart <ja...@op...> + + * scripts/array-design-insert.pl.in (Repository): + uses 'identifier' for rep_name if 'name' isn't defined + uses BioSequence name/identifier for rep_name if defined + changed exit() to goto + 2002-11-19 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2002-11-21 09:56:35
|
Update of /cvsroot/genex/genex-server/Genex/Config In directory sc8-pr-cvs1:/tmp/cvs-serv18738/Config Added Files: .cvsignore Log Message: usual --- NEW FILE: .cvsignore --- Config.pm Makefile pm_to_blib |
|
From: <jas...@us...> - 2002-11-21 09:55:56
|
Update of /cvsroot/genex/genex-server/Genex
In directory sc8-pr-cvs1:/tmp/cvs-serv18516
Modified Files:
Genex.pm.in
Log Message:
* Genex.pm.in (Repository):
new version (2.7.20021121)
Index: Genex.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Genex.pm.in,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** Genex.pm.in 15 Nov 2002 21:51:27 -0000 1.50
--- Genex.pm.in 21 Nov 2002 09:55:50 -0000 1.51
***************
*** 58,62 ****
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20021108';
# Preloaded methods go here.
--- 58,62 ----
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20021121';
# Preloaded methods go here.
|
|
From: <jas...@us...> - 2002-11-21 09:55:14
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv18300/scripts
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Repository):
added count output to reporter inserts (for the paranoid)
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** array-design-insert.pl.in 20 Nov 2002 23:36:11 -0000 1.8
--- array-design-insert.pl.in 21 Nov 2002 09:55:11 -0000 1.9
***************
*** 152,156 ****
--- 152,158 ----
}
$start = new Benchmark;
+ my $count;
foreach my $mage_reporter (@mage_reporters) {
+ $count++;
my $name = $mage_reporter->getName() || $mage_reporter->getIdentifier();
if (defined $mage_reporter->getImmobilizedCharacteristics()) {
***************
*** 173,176 ****
--- 175,180 ----
$REPORTERS{$name} = $rep_pk
unless exists $OPTIONS{reporters_only};
+ print STDERR "Handled $count Reporters",
+ if exists $OPTIONS{count} and ($count % $OPTIONS{count} == 0);
}
$stop = new Benchmark;
|
|
From: <jas...@us...> - 2002-11-21 09:44:36
|
Update of /cvsroot/genex/genex-server/Genex/Config
In directory sc8-pr-cvs1:/tmp/cvs-serv15406/Config
Added Files:
Makefile.PL
Log Message:
--- NEW FILE: Makefile.PL ---
sub MY::top_targets {
package MY; # so that "SUPER" works right
my $inherited = shift->SUPER::top_targets(@_);
$inherited =~ s/(man|html)ifypods//g;
$inherited;
}
WriteMakefile(
'NAME' => 'Bio::Genex::Config',
'SKIP' => [qw( test makeaperl manifypods htmlifypods xs_o static)],
'VERSION_FROM' => '../Genex.pm', # finds $VERSION
);
|
|
From: <jas...@us...> - 2002-11-21 09:43:57
|
Update of /cvsroot/genex/genex-server/Genex/Config In directory sc8-pr-cvs1:/tmp/cvs-serv15255/Config Log Message: Directory /cvsroot/genex/genex-server/Genex/Config added to the repository |
|
From: <jas...@us...> - 2002-11-20 23:36:14
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv26443
Modified Files:
array-design-insert.pl.in
Log Message:
fixed typo FINISHED => FINISH
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** array-design-insert.pl.in 20 Nov 2002 23:34:26 -0000 1.7
--- array-design-insert.pl.in 20 Nov 2002 23:36:11 -0000 1.8
***************
*** 177,181 ****
$diff = timediff($stop,$start);
print STDERR "Inserting Reporters took:", timestr($diff),"\n";
! goto FINISHED
if $OPTIONS{reporters_only};
}
--- 177,181 ----
$diff = timediff($stop,$start);
print STDERR "Inserting Reporters took:", timestr($diff),"\n";
! goto FINISH
if $OPTIONS{reporters_only};
}
|
|
From: <jas...@us...> - 2002-11-20 23:34:29
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv25875
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Repository):
changed exit() to goto
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** array-design-insert.pl.in 20 Nov 2002 23:23:47 -0000 1.6
--- array-design-insert.pl.in 20 Nov 2002 23:34:26 -0000 1.7
***************
*** 177,181 ****
$diff = timediff($stop,$start);
print STDERR "Inserting Reporters took:", timestr($diff),"\n";
! exit(0) if $OPTIONS{reporters_only};
}
--- 177,182 ----
$diff = timediff($stop,$start);
print STDERR "Inserting Reporters took:", timestr($diff),"\n";
! goto FINISHED
! if $OPTIONS{reporters_only};
}
***************
*** 342,346 ****
}
! print STDERR "Finished\n";
if ($OPTIONS{debug}) {
--- 343,349 ----
}
! FINISH : {
! print STDERR "Finished\n";
! }
if ($OPTIONS{debug}) {
|
