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From: <ku...@us...> - 2003-02-06 00:43:36
|
Update of /cvsroot/basedb/basedb In directory sc8-pr-cvs1:/tmp/cvs-serv4237 Added Files: Makefile.am configure.ac Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:33 kurri Exp $ SUBDIRS = src plugins --- NEW FILE: configure.ac --- # $Id: configure.ac,v 1.1 2003/02/06 00:43:33 kurri Exp $ // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. // // BASE is free software; you can redistribute it and/or // modify it under the terms of the GNU General Public License // as published by the Free Software Foundation; either version 2 // of the License, or (at your option) any later version. // BASE is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program; if not, write to the Free Software // Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. [...303 lines suppressed...] # plugins/src #CLUSTERING_LIBS="-lgsl -lgslcblas -lgd -L$libdir -lcgraph -lpng" #AC_SUBST(CLUSTERING_LIBS) AC_CONFIG_FILES([Makefile plugins/Makefile plugins/src/Makefile plugins/src/clustering/Cgraph/Makefile plugins/src/clustering/Cgraph/source/Makefile plugins/src/clustering/Makefile plugins/src/mds/Makefile plugins/src/merge_bioassays/Makefile plugins/src/normalizers/Makefile plugins/src/pca/Makefile src/Makefile src/assayImporter/Makefile src/jobRunner/Makefile src/lib/Makefile src/sectionCounter/Makefile]) AC_OUTPUT |
|
From: <ku...@us...> - 2003-02-06 00:34:20
|
Update of /cvsroot/basedb/basedb/plugins/src/normalizers In directory sc8-pr-cvs1:/tmp/cvs-serv1079 Modified Files: lowess_test.cc Log Message: Index: lowess_test.cc =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/normalizers/lowess_test.cc,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** lowess_test.cc 1 Feb 2003 12:52:52 -0000 1.1 --- lowess_test.cc 6 Feb 2003 00:34:16 -0000 1.2 *************** *** 22,25 **** --- 22,26 ---- #include <cstdlib> #include <functional> + #include <iostream> #include <vector> #include "lowess.hh" |
|
From: <ku...@us...> - 2003-02-05 21:56:05
|
Update of /cvsroot/basedb/basedb/src/jobRunner In directory sc8-pr-cvs1:/tmp/cvs-serv3600/jobRunner Log Message: Directory /cvsroot/basedb/basedb/src/jobRunner added to the repository |
|
From: <ku...@us...> - 2003-02-05 21:56:05
|
Update of /cvsroot/basedb/basedb/src/sectionCounter In directory sc8-pr-cvs1:/tmp/cvs-serv3600/sectionCounter Log Message: Directory /cvsroot/basedb/basedb/src/sectionCounter added to the repository |
|
From: <ku...@us...> - 2003-02-05 21:56:05
|
Update of /cvsroot/basedb/basedb/src/lib In directory sc8-pr-cvs1:/tmp/cvs-serv3600/lib Log Message: Directory /cvsroot/basedb/basedb/src/lib added to the repository |
|
From: <ku...@us...> - 2003-02-05 21:54:22
|
Update of /cvsroot/basedb/basedb/src/assayImporter In directory sc8-pr-cvs1:/tmp/cvs-serv2973/assayImporter Log Message: Directory /cvsroot/basedb/basedb/src/assayImporter added to the repository |
|
From: <ku...@us...> - 2003-02-05 17:13:57
|
Update of /cvsroot/basedb/basedb In directory sc8-pr-cvs1:/tmp/cvs-serv3102 Added Files: autogen.sh Log Message: --- NEW FILE: autogen.sh --- #!/bin/sh # $Id: autogen.sh,v 1.1 2003/02/05 17:13:53 kurri Exp $ # Run this to generate all auto-generated files needed by the GNU # configure program. This should be run everytime # configure.ac/configure.in is changed. libtoolize --automake aclocal automake --add-missing --gnu autoconf |
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From: <tr...@us...> - 2003-02-04 21:57:15
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv4735
Modified Files:
platetype_edit.phtml
Log Message:
added missing check for 0 id in input
Index: platetype_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/platetype_edit.phtml,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** platetype_edit.phtml 2 Feb 2003 15:31:52 -0000 1.25
--- platetype_edit.phtml 4 Feb 2003 21:57:10 -0000 1.26
***************
*** 39,43 ****
$ptype = new PlateType();
! if(isset($i_pt))
{
if(!$ptype->readShared($i_pt, $curUser))
--- 39,43 ----
$ptype = new PlateType();
! if(isset($i_pt) && $i_pt)
{
if(!$ptype->readShared($i_pt, $curUser))
|
|
From: <tr...@us...> - 2003-02-04 21:51:18
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv2061/www
Modified Files:
gene_explore.phtml
Log Message:
minor bugfix
Index: gene_explore.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/gene_explore.phtml,v
retrieving revision 1.70
retrieving revision 1.71
diff -C2 -d -r1.70 -r1.71
*** gene_explore.phtml 3 Feb 2003 08:54:11 -0000 1.70
--- gene_explore.phtml 4 Feb 2003 21:51:13 -0000 1.71
***************
*** 949,958 ****
$rawcols = RawBioAssayData::getAllShownColumns();
! $rawcols = xcolFilterColumns($rawcols, $rawLevel, 1);
for($i = 0; $i < count($rawcols); $i++)
{
$rc =& $rawcols[$i];
! $cols[] = array($rc[0], false, $rc[2],
! xcolDefaultOrder($rc[1]), 1, 1);
}
unset($rc);
--- 949,959 ----
$rawcols = RawBioAssayData::getAllShownColumns();
! $rawcols = xcolFilterColumns($rawcols, $rawLevel, $average);
for($i = 0; $i < count($rawcols); $i++)
{
$rc =& $rawcols[$i];
! $rnd = xcolTypeIsNumber($rc[1]);
! $cols[] = array($rc[0], false, $rc[2], xcolDefaultOrder($rc[1]),
! $rnd ? "renderExploreIntensity" : 1, 1);
}
unset($rc);
|
|
From: <tr...@us...> - 2003-02-04 21:51:17
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv2061/include/web
Modified Files:
gene_common.inc.php
Log Message:
minor bugfix
Index: gene_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/gene_common.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** gene_common.inc.php 3 Feb 2003 08:52:56 -0000 1.8
--- gene_common.inc.php 4 Feb 2003 21:51:11 -0000 1.9
***************
*** 86,90 ****
function renderExploreIntensity(&$i)
{
! echo "<td>".sprintf("%.2f", $i)."</td>\n";
}
function renderExploreRatio(&$r)
--- 86,103 ----
function renderExploreIntensity(&$i)
{
! $i = (float)$i;
! if($i > 9999 || $i < -9999)
! echo "<td>".sprintf("%.0f", $i)."</td>\n";
! else if($i < 1e-4 && $i > -1e4)
! {
! $s = (string)$i;
! $p = strpos($s, "E");
! if($p > 4)
! $s = substr($s, 0, 4).substr($s, $p);
! echo "<td>$s</td>\n";
! }
! else
! echo "<td>".substr($i, 0, $i > 0 ? 6 : 7)."</td>\n";
! // echo "<td>".sprintf("%.2f", $i)."</td>\n";
}
function renderExploreRatio(&$r)
|
|
From: <tr...@us...> - 2003-02-04 18:29:50
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv5908/include/classes
Modified Files:
ftpd.inc.php
Log Message:
worked on conversion to 1.2, added EPRT/EPSV
Index: ftpd.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/ftpd.inc.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ftpd.inc.php 1 Feb 2003 12:52:50 -0000 1.1
--- ftpd.inc.php 4 Feb 2003 18:29:48 -0000 1.2
***************
*** 22,50 ****
//
class ftpd
{
! var $config, $user, $userName, $commands;
! var $ip, $port, $dirUser, $passive, $socket, $myip, $restPos;
! function ftpd(&$config, $myip, $yourip)
{
$this->commands = array("USER" => 1, "PASS" => 1, "NOOP" => 0,
[...830 lines suppressed...]
}
! function ftpdSYST()
{
! if(!$this->ckUser()) return;
echo "215 UNIX\r\n";
}
--- 707,718 ----
else if(!unlink($this->config["uploadDir"]."/".$upl->getId()))
echo "450 Unable to delete file\r\n";
! else
! echo "200 Deleted\r\n";
}
! function comSYST()
{
! if(!$this->ckUser())
! return;
echo "215 UNIX\r\n";
}
|
|
From: <tr...@us...> - 2003-02-04 18:29:02
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv5464/include/classes
Modified Files:
user.inc.php upload.inc.php
Log Message:
added support func for ftpd
Index: user.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/user.inc.php,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** user.inc.php 2 Feb 2003 15:53:36 -0000 1.23
--- user.inc.php 4 Feb 2003 18:28:59 -0000 1.24
***************
*** 369,372 ****
--- 369,381 ----
}
+ function readByName($name)
+ {
+ $query = "SELECT * FROM UserGroup ug, UserAccount ua ".
+ "WHERE ug.id = ua.`userGroup` ".
+ "AND ug.name = '".addslashes($name)."' ".
+ "AND ug.removed = 0";
+ return $this->readQuery($query);
+ }
+
function write()
Index: upload.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/upload.inc.php,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** upload.inc.php 24 Jan 2003 22:10:22 -0000 1.13
--- upload.inc.php 4 Feb 2003 18:28:59 -0000 1.14
***************
*** 217,220 ****
--- 217,238 ----
return parent::updateRemoved($how);
}
+
+ // Returns all users as an array of (id,name,lastChanged,cnt)
+ function getUserSummaryList(&$user)
+ {
+ $query = "SELECT ug.id, ug.name, ".
+ "MAX(u.`addedDate`) AS `lastChanged`, COUNT(*) AS cnt ".
+ "FROM UserGroup ug LEFT JOIN Upload u ".
+ "ON ug.id = u.owner ".
+ "WHERE ".Item::whereRemoved("ug", 0)." ".
+ Item::whereRemovedAnd("u", 0)." ".
+ "AND ".Item::whereShared("u", $user)." ".
+ "GROUP BY ug.name, ug.id ORDER BY ug.name";
+ $res = query($query);
+ $arr = array();
+ while($row =& db_fetch_assoc($res))
+ $arr[] = $row;
+ return $arr;
+ }
}
|
|
From: <tr...@us...> - 2003-02-04 18:28:36
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv5246/include/classes
Modified Files:
wizzzard.inc.php
Log Message:
Added missing getBasicFromId
Index: wizzzard.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/wizzzard.inc.php,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** wizzzard.inc.php 2 Feb 2003 13:44:00 -0000 1.13
--- wizzzard.inc.php 4 Feb 2003 18:28:33 -0000 1.14
***************
*** 808,811 ****
--- 808,816 ----
return BUA_WIZZZARD_EDIT;
}
+
+ function getBasicFromId($id)
+ {
+ return parent::getBasicFromId("Wizzzard", $id);
+ }
}
|
|
From: <tr...@us...> - 2003-02-04 18:23:18
|
Update of /cvsroot/basedb/basedb/bin In directory sc8-pr-cvs1:/tmp/cvs-serv3208 Modified Files: backup.sh Log Message: Added tarring and gzipping Index: backup.sh =================================================================== RCS file: /cvsroot/basedb/basedb/bin/backup.sh,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** backup.sh 3 Feb 2003 13:15:30 -0000 1.1 --- backup.sh 4 Feb 2003 18:23:15 -0000 1.2 *************** *** 3,6 **** --- 3,11 ---- # A script for backing up the data of a BASE installation running against # MySQL. This file should be readable only by the base user. + # + # Usage: backup.sh [-v] [-t [-z]] + # -v verbose mode + # -t tar backup on the fly + # -z gzip backup after bringing BASE back online # We're passing the password to the mysql tool as an argument. This is a [...146 lines suppressed...] + echo -n "$datadir: " + du -sh "$datadir" |cut -f1 + + echo echo "$dbdir:" df -h "$dbdir" *************** *** 78,88 **** df -h "$backupdir" - echo -e "\nBASE installation size:" - echo -n "$backupdir/base: " - du -sh "$backupdir/base" |cut -f1 - echo -n "$backupdir/basedynamic: " - du -sh "$backupdir/basedynamic" |cut -f1 - echo -n "$backupdir/data: " - du -sh "$backupdir/data" |cut -f1 fi --- 142,145 ---- |
|
From: <tr...@us...> - 2003-02-04 18:22:53
|
Update of /cvsroot/basedb/basedb/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv3044
Modified Files:
baseftpd.php
Log Message:
Updated for 1.2
Index: baseftpd.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/baseftpd.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** baseftpd.php 1 Feb 2003 12:52:49 -0000 1.1
--- baseftpd.php 4 Feb 2003 18:22:50 -0000 1.2
***************
*** 24,29 ****
require_once(dirname($_SERVER["argv"][0])."/../config.inc.php");
- require_once("upload.inc.php");
- require_once("misc.inc.php");
require_once("ftpd.inc.php");
--- 24,27 ----
***************
*** 40,44 ****
mt_srand((int)substr($usec, 1) ^ $sec ^ (getmypid() << 16));
! $ftpd = new ftpd($config, $_SERVER["argv"][1], $_SERVER["argv"][2]);
while(!feof(STDIN))
--- 38,54 ----
mt_srand((int)substr($usec, 1) ^ $sec ^ (getmypid() << 16));
! $BC = new BaseControl();
! if(!$BC->mayRun())
! die("421 BASE has been shut down\n");
!
! // Open database connection
! if(!db_connect($config["dbHost"], $config["dbUser"],
! $config["dbPassword"], $config["dbDatabase"]))
! {
! die("421 Unable to connect to database\n");
! }
! unset($config["dbPassword"]);
!
! $ftpd = new ftpd($_SERVER["argv"][1], $_SERVER["argv"][2]);
while(!feof(STDIN))
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv13698/include/classes
Modified Files:
bioassay.inc.php bioassayset.inc.php extract.inc.php
image.inc.php raw.inc.php spotimage.inc.php
Log Message:
Minor fixes
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassay.inc.php,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** bioassay.inc.php 3 Feb 2003 08:51:37 -0000 1.30
--- bioassay.inc.php 3 Feb 2003 20:13:17 -0000 1.31
***************
*** 1298,1302 ****
if($cols)
return $cols;
! $cols = array(array("histogram", false, "Histogram", 0, 0, 0));
$cols = array_merge(
$cols,
--- 1298,1303 ----
if($cols)
return $cols;
! $cols = array(array("histogram", false, "Histogram", 0, 0, 0,
! "type" => SEARCH_INT));
$cols = array_merge(
$cols,
Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassayset.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** bioassayset.inc.php 23 Jan 2003 09:05:03 -0000 1.19
--- bioassayset.inc.php 3 Feb 2003 20:13:17 -0000 1.20
***************
*** 493,497 ****
$search->addExtraColumns($columns);
! $ob = $search->newMakeOrderBy();
// Find unwanted columns.
--- 493,497 ----
$search->addExtraColumns($columns);
! // $ob = $search->newMakeOrderBy();
// Find unwanted columns.
***************
*** 513,517 ****
"WHERE sg.`bioAssaySet` = $this->id ".
$search->getWhere()." ".
! $search->getExtraWhere()." ".$ob;
$res = query($query);
--- 513,517 ----
"WHERE sg.`bioAssaySet` = $this->id ".
$search->getWhere()." ".
! $search->getExtraWhere(); //." ".$ob;
$res = query($query);
Index: extract.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/extract.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** extract.inc.php 22 Jan 2003 08:00:52 -0000 1.10
--- extract.inc.php 3 Feb 2003 20:13:18 -0000 1.11
***************
*** 304,308 ****
function changeQuantityLeftById($id, $amount)
{
! parent::changeQuantityLeft("Extract", $id, $amount);
}
--- 304,308 ----
function changeQuantityLeftById($id, $amount)
{
! parent::changeQuantityLeftById("Extract", $id, $amount);
}
Index: image.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/image.inc.php,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** image.inc.php 3 Feb 2003 08:51:13 -0000 1.13
--- image.inc.php 3 Feb 2003 20:13:18 -0000 1.14
***************
*** 193,197 ****
function takeOverUseForJpeg()
{
! if($this->channels == 3)
$andchan = "";
else if($this->channels == 1 || $this->channels == 2)
--- 193,197 ----
function takeOverUseForJpeg()
{
! if($this->channels == -3)
$andchan = "";
else if($this->channels == 1 || $this->channels == 2)
***************
*** 212,218 ****
function getChannelNames()
{
! $names = array(-1 => "All", 0 => "None", 2 => "Other");
for($i = 1; $i < 9; $i++)
$names[$i] = "Ch $i";
return $names;
}
--- 212,219 ----
function getChannelNames()
{
! $names = array(-1 => "All", -3 => "Both", 0 => "None");
for($i = 1; $i < 9; $i++)
$names[$i] = "Ch $i";
+ $names[-2] = "Other";
return $names;
}
Index: raw.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/raw.inc.php,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** raw.inc.php 2 Feb 2003 13:44:00 -0000 1.26
--- raw.inc.php 3 Feb 2003 20:13:18 -0000 1.27
***************
*** 1018,1022 ****
if($cols)
return $cols;
! $cols = array(array("histogram", false, "Histogram", 0, 0, 0));
$cols = array_merge(
$cols,
--- 1018,1023 ----
if($cols)
return $cols;
! $cols = array(array("histogram", false, "Histogram", 0, 0, 0,
! "type" => SEARCH_INT));
$cols = array_merge(
$cols,
Index: spotimage.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/spotimage.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** spotimage.inc.php 3 Feb 2003 08:52:15 -0000 1.8
--- spotimage.inc.php 3 Feb 2003 20:13:19 -0000 1.9
***************
*** 97,100 ****
--- 97,102 ----
}
+ // $imgs is an array with either two images (keys 1 and 2) or one image
+ // (key -3).
function runSpotImageChopper($dir, $imgs)
{
***************
*** 133,137 ****
{
echo "Splitting two-channel TIFF image\n";
! $imgBoth = $imgs[3];
$fileBoth = escapeshellarg(
Image::getRepositoryFilenameById($imgBoth));
--- 135,139 ----
{
echo "Splitting two-channel TIFF image\n";
! $imgBoth = $imgs[-3];
$fileBoth = escapeshellarg(
Image::getRepositoryFilenameById($imgBoth));
***************
*** 182,186 ****
return "Spot images already exist or are being processed";
$imgs = Image::getBriefForJpeg($raw->getImageAcquisition());
! if(count($imgs) == 1 && isset($imgs[3]))
;
else if(count($imgs) == 2 && isset($imgs[1]) && isset($imgs[2]))
--- 184,188 ----
return "Spot images already exist or are being processed";
$imgs = Image::getBriefForJpeg($raw->getImageAcquisition());
! if(count($imgs) == 1 && isset($imgs[-3]))
;
else if(count($imgs) == 2 && isset($imgs[1]) && isset($imgs[2]))
|
|
From: <tr...@us...> - 2003-02-03 20:13:25
|
Update of /cvsroot/basedb/basedb/www/plotapplet
In directory sc8-pr-cvs1:/tmp/cvs-serv13698/www/plotapplet
Modified Files:
plot_assay.phtml store_tmp.phtml
Log Message:
Minor fixes
Index: plot_assay.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plotapplet/plot_assay.phtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** plot_assay.phtml 1 Feb 2003 18:19:12 -0000 1.1
--- plot_assay.phtml 3 Feb 2003 20:13:20 -0000 1.2
***************
*** 21,25 ****
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
! require_once("getconfig.inc.php");
require_once("init.inc.php");
require_once("item_common.inc.php");
--- 21,25 ----
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
! require_once("../getconfig.inc.php");
require_once("init.inc.php");
require_once("item_common.inc.php");
Index: store_tmp.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plotapplet/store_tmp.phtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** store_tmp.phtml 30 Jan 2003 13:35:59 -0000 1.1
--- store_tmp.phtml 3 Feb 2003 20:13:21 -0000 1.2
***************
*** 1,7 ****
<?
- require_once("../init.inc.php");
- require_once("../misc.inc.php");
require_once("../getconfig.inc.php");
! require_once("../raw.inc.php");
verifyAccess(BUA_ANALYZE);
--- 1,7 ----
<?
require_once("../getconfig.inc.php");
! require_once("init.inc.php");
! require_once("misc.inc.php");
! require_once("raw.inc.php");
verifyAccess(BUA_ANALYZE);
|
|
From: <tr...@us...> - 2003-02-03 20:13:25
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv13698/www
Modified Files:
hyb_image.phtml wizzzard_edit.phtml
Log Message:
Minor fixes
Index: hyb_image.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_image.phtml,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** hyb_image.phtml 2 Feb 2003 15:31:52 -0000 1.41
--- hyb_image.phtml 3 Feb 2003 20:13:19 -0000 1.42
***************
*** 388,392 ****
<tr><th colspan=2 class=subhead>Add image(s)</th></tr>
<?
! $chans = $acq->getAvailableChannels();
// Ouput a set of image upload/picking thingies
--- 388,392 ----
<tr><th colspan=2 class=subhead>Add image(s)</th></tr>
<?
! $chans = Image::getChannelNames();
// Ouput a set of image upload/picking thingies
***************
*** 397,408 ****
<select name='i_imgchan[<?= $img ?>]'>
<?
!
! // If there was a channel picked for a failed image add, preselect it.
$oldChan = (isset($i_imgchan) &&
! isset($i_imgchan[$img])) ? $i_imgchan[$img] : 0;
! for(reset($chans); list($id, $c) = each($chans); )
{
$sel = ($oldChan == $id) ? "selected" : "";
! echo "<option value=$id $sel>".html($c["name"], 0)."\n";
}
echo "</select></td></tr>\n";
--- 397,407 ----
<select name='i_imgchan[<?= $img ?>]'>
<?
! // If there was a channel picked for a failed add, preselect it.
$oldChan = (isset($i_imgchan) &&
! isset($i_imgchan[$img])) ? (int)$i_imgchan[$img] : 0;
! for(reset($chans); list($id, $n) = each($chans); )
{
$sel = ($oldChan == $id) ? "selected" : "";
! echo "<option value=$id $sel>".html($n, 0)."\n";
}
echo "</select></td></tr>\n";
Index: wizzzard_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/wizzzard_edit.phtml,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** wizzzard_edit.phtml 2 Feb 2003 15:31:52 -0000 1.9
--- wizzzard_edit.phtml 3 Feb 2003 20:13:20 -0000 1.10
***************
*** 60,64 ****
else
{
! $wiz->makeOwned($curUser)
$wiz->setFormatType($i_type);
if($fileid && $err == "")
--- 60,64 ----
else
{
! $wiz->makeOwned($curUser);
$wiz->setFormatType($i_type);
if($fileid && $err == "")
|
|
From: <tr...@us...> - 2003-02-03 20:13:20
|
Update of /cvsroot/basedb/basedb/bin In directory sc8-pr-cvs1:/tmp/cvs-serv13698/bin Added Files: .cvsignore Log Message: Minor fixes --- NEW FILE: .cvsignore --- assayImporter sectionCounter jobRunner spotImageChopper tifftopnm |
|
From: <tr...@us...> - 2003-02-03 20:13:11
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv13588/include/web
Modified Files:
experiment_common.inc.php
Log Message:
moved jobController starting to class Job
Index: experiment_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/experiment_common.inc.php,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** experiment_common.inc.php 2 Feb 2003 15:31:51 -0000 1.22
--- experiment_common.inc.php 3 Feb 2003 20:13:07 -0000 1.23
***************
*** 759,765 ****
if(!$filter && $job->getTransformation())
{
$jobid = $job->getTransformation();
$s = $job->getStatus();
! if($s == "done" || $s == "error")
$ref = "";
else
--- 759,773 ----
if(!$filter && $job->getTransformation())
{
[...74 lines suppressed...]
! <tr><th>Status</th><td><?= $s.$ref.$rest ?></td></tr>
<tr><th>Job started</th><td><?= htmldate($job->getStartTime()) ?></td></tr>
<tr><th>Job ended</th><td><?= htmldate($job->getEndTime()) ?></td></tr>
***************
*** 821,827 ****
else if($params[$pos]["valueType"] == "e")
{
! // Find the long text if it exists. These enums are stored
! // in a rather silly way: short (internal) name with even
! // indices, long names with odd.
$arr = explode("\t", $params[$pos]["enumOptions"]);
for($i = 0; $i < count($arr); $i += 2)
--- 851,857 ----
else if($params[$pos]["valueType"] == "e")
{
! // Find the long text if it exists. These enums are
! // stored in a rather silly way: short (internal) name
! // with even keys, long names with odd.
$arr = explode("\t", $params[$pos]["enumOptions"]);
for($i = 0; $i < count($arr); $i += 2)
|
|
From: <tr...@us...> - 2003-02-03 20:13:10
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv13588/www
Modified Files:
trans_create.phtml
Log Message:
moved jobController starting to class Job
Index: trans_create.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/trans_create.phtml,v
retrieving revision 1.43
retrieving revision 1.44
diff -C2 -d -r1.43 -r1.44
*** trans_create.phtml 2 Feb 2003 15:31:52 -0000 1.43
--- trans_create.phtml 3 Feb 2003 20:13:06 -0000 1.44
***************
*** 710,718 ****
$res = array();
! $rc = 0;
! exec(escapeshellarg("$config[rootDir]/bin/jobController.php").
! " ".$job->getTransformation()." </dev/null ".
! ">>".escapeshellarg("$config[logDir]/jobController.log")." 2>&1 &",
! $res, $rc);
if($rc)
{
--- 710,714 ----
$res = array();
! $rc = $job->runJobController($res);
if($rc)
{
|
|
From: <tr...@us...> - 2003-02-03 20:13:10
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv13588/include/classes
Modified Files:
job.inc.php
Log Message:
moved jobController starting to class Job
Index: job.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/job.inc.php,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** job.inc.php 22 Jan 2003 18:46:07 -0000 1.14
--- job.inc.php 3 Feb 2003 20:13:03 -0000 1.15
***************
*** 494,497 ****
--- 494,510 ----
return $dirName;
}
+
+ function runJobController(&$res)
+ {
+ global $config;
+ $res = array();
+ $rc = 0;
+ // Because we run this in the background, it 'should' never fail.
+ exec(escapeshellarg("$config[rootDir]/bin/jobController.php").
+ " $this->transformation </dev/null ".
+ ">>".escapeshellarg("$config[logDir]/jobController.log")." 2>&1 &",
+ $res, $rc);
+ return $rc;
+ }
}
|
|
From: <tr...@us...> - 2003-02-03 19:30:21
|
Update of /cvsroot/basedb/basedb/documentation/development In directory sc8-pr-cvs1:/tmp/cvs-serv27361 Modified Files: CODING_STANDARDS Log Message: updated Index: CODING_STANDARDS =================================================================== RCS file: /cvsroot/basedb/basedb/documentation/development/CODING_STANDARDS,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** CODING_STANDARDS 2 Nov 2002 17:54:34 -0000 1.1 --- CODING_STANDARDS 3 Feb 2003 19:30:17 -0000 1.2 *************** *** 4,8 **** All communication with the RDBMS should be done by classes, and all classes are defined in .inc.php, whereas all URIs the user might request should be ! .phtml files. Indentation is done with tabs and never with spaces. Tab stops are assumed to be every 3 characters. The maximum width of a line is 80 characters, --- 4,8 ---- All communication with the RDBMS should be done by classes, and all classes are defined in .inc.php, whereas all URIs the user might request should be ! .phtml files resifing in www. Indentation is done with tabs and never with spaces. Tab stops are assumed to be every 3 characters. The maximum width of a line is 80 characters, |
|
From: <tr...@us...> - 2003-02-03 17:39:36
|
Update of /cvsroot/basedb/basedb/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv6953
Modified Files:
dbmigrate_107_to_12.php
Log Message:
Updated image channels
Index: dbmigrate_107_to_12.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/dbmigrate_107_to_12.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** dbmigrate_107_to_12.php 2 Feb 2003 13:40:40 -0000 1.2
--- dbmigrate_107_to_12.php 3 Feb 2003 17:39:29 -0000 1.3
***************
*** 744,747 ****
--- 744,748 ----
$query = "SELECT * FROM $oldDb.Image";
$res = myquery($query, 1);
+ $chanmap = array(0, 1, 2, -3, 1);
while($row =& db_fetch_assoc($res))
{
***************
*** 761,764 ****
--- 762,766 ----
$row["owner"] = $row["user"];
$row["removed"] = 0;
+ $row["channels"] = (int)$chanmap[$row["channels"]];
$vars = array("id", "name", "descr", "owner", "addedDate",
"imageAcquisition", "channels", "fileSize", "removed");
|
|
From: <tr...@us...> - 2003-02-03 17:22:15
|
Update of /cvsroot/basedb/basedb/www In directory sc8-pr-cvs1:/tmp/cvs-serv30509 Modified Files: codesize Log Message: added plotapplet Index: codesize =================================================================== RCS file: /cvsroot/basedb/basedb/www/codesize,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** codesize 1 Feb 2003 23:05:40 -0000 1.7 --- codesize 3 Feb 2003 17:22:05 -0000 1.8 *************** *** 22,25 **** --- 22,26 ---- cntstuff webinc "../include/web/*.php" cntstuff bin "../bin/*.php" + cntstuff plotapp "plotapplet/*.phtml" cntstuff total " *.phtml *************** *** 29,32 **** ../include/local_distr/*.php ../include/web/*.php ! ../bin/*.php" --- 30,34 ---- ../include/local_distr/*.php ../include/web/*.php ! ../bin/*.php ! plotapplet/*.phtml" |
