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From: <tr...@us...> - 2002-09-09 08:17:25
|
Update of /cvsroot/basedb/basedb In directory usw-pr-cvs1:/tmp/cvs-serv17115 Modified Files: README Log Message: Corrected tpyo, clarified shebang part Index: README =================================================================== RCS file: /cvsroot/basedb/basedb/README,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** README 21 Aug 2002 12:56:57 -0000 1.6 --- README 9 Sep 2002 08:17:21 -0000 1.7 *************** *** 7,18 **** Here's what you need to do to get BASE running: ! Download, install, and configure Apache, MySQL, and PHP. ! Version requirements: ! Apache 1.3.x has been tested. Apache 2 might be tricky to get to ! work with PHP, but it has been done. ! MySQL 3.23.x (x > 40 or so) is know to work with BASE. We don't know ! if anyone has tested MySQL 4, but it's likely that it works. PHP 4.2.1 works, and 4.2.0 probably works too. Note that there is a security ! issue with 4.2.1. PHP compilation: --- 7,18 ---- Here's what you need to do to get BASE running: ! Download, install, and configure Apache, MySQL, and PHP. Version ! requirements: Apache 1.3.x has been tested. Apache 2 might be tricky to get ! to work with PHP, but it has been done. ! MySQL 3.23.x (x > 40 or so) is know to work with BASE. We don't know if ! anyone has tested MySQL 4, but it's likely that it works. PHP 4.2.1 works, and 4.2.0 probably works too. Note that there is a security ! issue with 4.2.1, and you should use 4.2.2. At the moment of writing, PHP 4.3 ! hasn't been released yet, adn we haven't tested BASE with it. PHP compilation: *************** *** 23,28 **** PHP) to upload files to BASE, you'll need socket support in the standalone version of PHP. The scripts helpParser.php, jobController.php and ! updateGenes.php (in subdir exec/), exspect standalone interpreter to be found ! as #!/usr/local/bin/php. If it is elsewhere, adjust their first lines. PHP configuration: --- 23,29 ---- PHP) to upload files to BASE, you'll need socket support in the standalone version of PHP. The scripts helpParser.php, jobController.php and ! updateGenes.php (in subdir exec/) expect the standalone interpreter to be ! found as #!/usr/local/bin/php. If it is elsewhere, adjust their first ! line of those php files. PHP configuration: |
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv8628
Modified Files:
misc.inc.php mysql.inc.php pgsql.inc.php plate_edit.phtml
user_edit.phtml user_list.phtml
Log Message:
Added db_date_never to deal with 0001-01-01 vs. 0000-00-00
Index: misc.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/misc.inc.php,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** misc.inc.php 5 Aug 2002 11:29:34 -0000 1.34
--- misc.inc.php 9 Sep 2002 06:39:01 -0000 1.35
***************
*** 25,28 ****
--- 25,30 ----
//
+ require_once("db.inc.php");
+
function html($txt, $nbsp = true)
{
***************
*** 46,52 ****
function strtodate($txt)
{
! if($txt == "") return "0000-00-00";
$t = @strtotime($txt);
! if($t < 0) return "0000-00-00";
return date("Y-m-d", $t);
}
--- 48,54 ----
function strtodate($txt)
{
! if($txt == "") return db_date_never();
$t = @strtotime($txt);
! if($t < 0) return db_date_never();
return date("Y-m-d", $t);
}
***************
*** 54,60 ****
function strtodatetime($txt)
{
! if($txt == "") return "0000-00-00 00:00:00";
$t = @strtotime($txt);
! if($t < 0) return "0000-00-00 00:00:00";
return date("Y-m-d H:i:s", $t);
}
--- 56,62 ----
function strtodatetime($txt)
{
! if($txt == "") return db_date_never()." 00:00:00";
$t = @strtotime($txt);
! if($t < 0) return db_date_never()." 00:00:00";
return date("Y-m-d H:i:s", $t);
}
***************
*** 62,66 ****
function htmldate($txt, $nbsp = true)
{
! if(substr($txt, 0, 10) == "0000-00-00")
return ($nbsp ? "-" : "");
return $txt;
--- 64,68 ----
function htmldate($txt, $nbsp = true)
{
! if(substr($txt, 0, 10) == db_date_never())
return ($nbsp ? "-" : "");
return $txt;
***************
*** 69,73 ****
function htmldatetime($txt)
{
! if(substr($txt, 0, 10) == "0000-00-00")
return "-";
return substr($txt, 0, 16);
--- 71,75 ----
function htmldatetime($txt)
{
! if(substr($txt, 0, 10) == db_date_never())
return "-";
return substr($txt, 0, 16);
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** mysql.inc.php 9 Sep 2002 06:29:34 -0000 1.10
--- mysql.inc.php 9 Sep 2002 06:39:01 -0000 1.11
***************
*** 270,272 ****
--- 270,277 ----
}
+ function db_date_never()
+ {
+ return "0000-00-00";
+ }
+
?>
Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** pgsql.inc.php 9 Sep 2002 06:29:34 -0000 1.6
--- pgsql.inc.php 9 Sep 2002 06:39:01 -0000 1.7
***************
*** 334,336 ****
--- 334,341 ----
}
+ function db_date_never()
+ {
+ return "0001-01-01";
+ }
+
?>
Index: plate_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_edit.phtml,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** plate_edit.phtml 29 Aug 2002 16:51:34 -0000 1.26
--- plate_edit.phtml 9 Sep 2002 06:39:01 -0000 1.27
***************
*** 335,339 ****
$protos = Protocol::getBriefer($e["protocolType"]);
if(isset($events[$eid]["eventDate"]) &&
! $events[$eid]["eventDate"] != "0000-00-00")
$ed = $events[$eid]["eventDate"];
else $ed = "";
--- 335,339 ----
$protos = Protocol::getBriefer($e["protocolType"]);
if(isset($events[$eid]["eventDate"]) &&
! $events[$eid]["eventDate"] != db_date_never())
$ed = $events[$eid]["eventDate"];
else $ed = "";
Index: user_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user_edit.phtml,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** user_edit.phtml 5 Aug 2002 11:29:35 -0000 1.13
--- user_edit.phtml 9 Sep 2002 06:39:01 -0000 1.14
***************
*** 183,187 ****
{
$nev = "";
! if($actu == "0000-00-00")
$actu = "";
}
--- 183,187 ----
{
$nev = "";
! if($actu == db_date_never())
$actu = "";
}
***************
*** 228,232 ****
if($actu == "9999-12-31")
$actu = "never";
! else if($actu == "0000-00-00")
$actu = "inactive account";
?>
--- 228,232 ----
if($actu == "9999-12-31")
$actu = "never";
! else if($actu == db_date_never())
$actu = "inactive account";
?>
Index: user_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user_list.phtml,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** user_list.phtml 29 Aug 2002 16:51:34 -0000 1.12
--- user_list.phtml 9 Sep 2002 06:39:01 -0000 1.13
***************
*** 120,124 ****
if($date == "9999-12-31")
return "<span class=active_0>forever</span>";
! if($date == "0000-00-00")
return "<span class=active_5>-</span>";
if($daysLeft > 30)
--- 120,124 ----
if($date == "9999-12-31")
return "<span class=active_0>forever</span>";
! if($date == db_date_never())
return "<span class=active_5>-</span>";
if($daysLeft > 30)
|
|
From: <tr...@us...> - 2002-09-09 06:33:53
|
Update of /cvsroot/basedb/basedb/www In directory usw-pr-cvs1:/tmp/cvs-serv6959 Modified Files: experiment.inc.php Log Message: added a missing strtodate Index: experiment.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/experiment.inc.php,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -d -r1.47 -r1.48 *** experiment.inc.php 9 Sep 2002 06:30:50 -0000 1.47 --- experiment.inc.php 9 Sep 2002 06:33:50 -0000 1.48 *************** *** 51,55 **** $this->abstract = $abstract; $this->pubMedId = $pubMedId; ! $this->publicationDate = $publicationDate; } --- 51,55 ---- $this->abstract = $abstract; $this->pubMedId = $pubMedId; ! $this->publicationDate = strtodate($publicationDate); } |
|
From: <tr...@us...> - 2002-09-09 06:30:53
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv5866
Modified Files:
experiment.inc.php
Log Message:
Moved misplaced comma
Index: experiment.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/experiment.inc.php,v
retrieving revision 1.46
retrieving revision 1.47
diff -C2 -d -r1.46 -r1.47
*** experiment.inc.php 9 Sep 2002 06:29:34 -0000 1.46
--- experiment.inc.php 9 Sep 2002 06:30:50 -0000 1.47
***************
*** 304,308 ****
if(db_has_subselects())
{
! $ss1 = ", t.raws, t.sets, t.assays FROM Experiment e, ".
"(SELECT e.id,";
$ss2 = ") AS t WHERE e.id = t.id";
--- 304,308 ----
if(db_has_subselects())
{
! $ss1 = "t.raws, t.sets, t.assays FROM Experiment e, ".
"(SELECT e.id,";
$ss2 = ") AS t WHERE e.id = t.id";
***************
*** 311,315 ****
$ss1 = $ss2 = "";
! $query = "SELECT e.* $ss1 ".
"COUNT(DISTINCT erb.`rawBioAssay`) AS raws, ".
"COUNT(DISTINCT bas.id) AS sets, ".
--- 311,315 ----
$ss1 = $ss2 = "";
! $query = "SELECT e.*, $ss1 ".
"COUNT(DISTINCT erb.`rawBioAssay`) AS raws, ".
"COUNT(DISTINCT bas.id) AS sets, ".
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv5308
Modified Files:
acquisition.inc.php array.inc.php bio.inc.php bioassay.inc.php
experiment.inc.php genelist.inc.php image.inc.php job.inc.php
molecule.inc.php mysql.inc.php news.inc.php pgsql.inc.php
plate.inc.php program.inc.php raw.inc.php user.inc.php
ware.inc.php
Log Message:
Replaced TRUE with db_true because of missing TRUE/FALSE in mysql
Index: acquisition.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/acquisition.inc.php,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** acquisition.inc.php 9 Sep 2002 06:21:19 -0000 1.13
--- acquisition.inc.php 9 Sep 2002 06:29:33 -0000 1.14
***************
*** 159,163 ****
$query = "SELECT COUNT(*) FROM ImageAcquisition ia ".
"LEFT JOIN Image im ON im.imageAcquisition = ia.id ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 159,163 ----
$query = "SELECT COUNT(*) FROM ImageAcquisition ia ".
"LEFT JOIN Image im ON im.imageAcquisition = ia.id ".
! "WHERE ".db_true()." ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** array.inc.php 9 Sep 2002 06:21:19 -0000 1.34
--- array.inc.php 9 Sep 2002 06:29:34 -0000 1.35
***************
*** 863,867 ****
$query = "SELECT COUNT(*) FROM ArrayBatch ab ".
! "WHERE TRUE ".$search->getWhere()." ".
$search->getExtraWhere();
--- 863,867 ----
$query = "SELECT COUNT(*) FROM ArrayBatch ab ".
! "WHERE ".db_true()." ".$search->getWhere()." ".
$search->getExtraWhere();
Index: bio.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bio.inc.php,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** bio.inc.php 9 Sep 2002 06:21:19 -0000 1.21
--- bio.inc.php 9 Sep 2002 06:29:34 -0000 1.22
***************
*** 161,165 ****
{
$owner = (int)$owner;
! $query = "SELECT * FROM Sample WHERE TRUE";
if($owner >= 0)
$query .= " AND owner = $owner";
--- 161,165 ----
{
$owner = (int)$owner;
! $query = "SELECT * FROM Sample WHERE ".db_true();
if($owner >= 0)
$query .= " AND owner = $owner";
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassay.inc.php,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** bioassay.inc.php 9 Sep 2002 06:21:19 -0000 1.32
--- bioassay.inc.php 9 Sep 2002 06:29:34 -0000 1.33
***************
*** 384,388 ****
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res))
--- 384,389 ----
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE ".db_true()." ".
! $search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res))
***************
*** 434,438 ****
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
" $ob ".$search->makeLimit();
$arr = array();
--- 435,440 ----
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE ".db_true()." ".
! $search->getWhere()." ".$search->getExtraWhere().
" $ob ".$search->makeLimit();
$arr = array();
***************
*** 475,480 ****
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
! " $ob";
return $genelist->populateFromQuery($query);
}
--- 477,482 ----
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE ".db_true()." ".$search->getWhere()." ".
! $search->getExtraWhere()." $ob";
return $genelist->populateFromQuery($query);
}
***************
*** 499,503 ****
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
return (bool)query($query);
}
--- 501,506 ----
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE ".db_true()." ".$search->getWhere()." ".
! $search->getExtraWhere();
return (bool)query($query);
}
Index: experiment.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/experiment.inc.php,v
retrieving revision 1.45
retrieving revision 1.46
diff -C2 -d -r1.45 -r1.46
*** experiment.inc.php 9 Sep 2002 06:20:40 -0000 1.45
--- experiment.inc.php 9 Sep 2002 06:29:34 -0000 1.46
***************
*** 285,289 ****
$query = "SELECT COUNT(*) FROM Experiment e ".
! "WHERE TRUE ".$search->getExtraWhere()." ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 285,290 ----
$query = "SELECT COUNT(*) FROM Experiment e ".
! "WHERE ".db_true()." ".$search->getExtraWhere()." ".
! $search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
***************
*** 318,322 ****
"LEFT JOIN BioAssaySet bas ON bas.experiment = e.id ".
"LEFT JOIN BioAssay ba ON ba.`bioAssaySet` = bas.id ".
! "WHERE TRUE ".$search->getExtraWhere()." ".$search->getWhere()." ".
"GROUP BY e.id $ss2 $ob ".$search->makeLimit();
--- 319,324 ----
"LEFT JOIN BioAssaySet bas ON bas.experiment = e.id ".
"LEFT JOIN BioAssay ba ON ba.`bioAssaySet` = bas.id ".
! "WHERE ".db_true()." ".$search->getExtraWhere()." ".
! $search->getWhere()." ".
"GROUP BY e.id $ss2 $ob ".$search->makeLimit();
Index: genelist.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/genelist.inc.php,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** genelist.inc.php 9 Sep 2002 06:21:19 -0000 1.20
--- genelist.inc.php 9 Sep 2002 06:29:34 -0000 1.21
***************
*** 115,119 ****
$query = "SELECT COUNT(*) FROM GeneList gl ".
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
--- 115,119 ----
$query = "SELECT COUNT(*) FROM GeneList gl ".
! "WHERE ".db_true()." ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
***************
*** 135,139 ****
$query = "SELECT gl.* ".
"FROM GeneList gl ".
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere()." ".
"GROUP BY id $ob ".$search->makeLimit();
--- 135,139 ----
$query = "SELECT gl.* ".
"FROM GeneList gl ".
! "WHERE ".db_true()." ".$search->getExtraWhere()." ".
$search->getWhere()." ".
"GROUP BY id $ob ".$search->makeLimit();
Index: image.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/image.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** image.inc.php 9 Sep 2002 06:21:19 -0000 1.11
--- image.inc.php 9 Sep 2002 06:29:34 -0000 1.12
***************
*** 134,138 ****
$query = "SELECT COUNT(*) FROM Image im ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 134,138 ----
$query = "SELECT COUNT(*) FROM Image im ".
! "WHERE ".db_true()." ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
***************
*** 152,156 ****
$query = "SELECT im.* ".
! "FROM Image im WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere()." ".
"$ob ".$search->makeLimit();
--- 152,156 ----
$query = "SELECT im.* ".
! "FROM Image im WHERE ".db_true()." ".
$search->getWhere()." ".$search->getExtraWhere()." ".
"$ob ".$search->makeLimit();
Index: job.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/job.inc.php,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** job.inc.php 9 Sep 2002 06:21:20 -0000 1.35
--- job.inc.php 9 Sep 2002 06:29:34 -0000 1.36
***************
*** 273,277 ****
$query = "SELECT COUNT(*) FROM Job j ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 273,277 ----
$query = "SELECT COUNT(*) FROM Job j ".
! "WHERE ".db_true()." ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
Index: molecule.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/molecule.inc.php,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** molecule.inc.php 9 Sep 2002 06:21:20 -0000 1.29
--- molecule.inc.php 9 Sep 2002 06:29:34 -0000 1.30
***************
*** 628,632 ****
$query = "SELECT COUNT(*) FROM Molecule m ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 628,633 ----
$query = "SELECT COUNT(*) FROM Molecule m ".
$search->getExtraTables()." ".
! "WHERE ".db_true()." ".$search->getWhere()." ".
! $search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
***************
*** 652,656 ****
"l.name AS `libraryName` ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
" $ob ".$search->makeLimit();
--- 653,658 ----
"l.name AS `libraryName` ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE ".db_true()." ".$search->getWhere()." ".
! $search->getExtraWhere().
" $ob ".$search->makeLimit();
***************
*** 691,696 ****
$query = "SELECT m.id ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
! " $ob";
return $genelist->populateFromQuery($query);
--- 693,698 ----
$query = "SELECT m.id ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE ".db_true()." ".$search->getWhere()." ".
! $search->getExtraWhere()." $ob";
return $genelist->populateFromQuery($query);
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** mysql.inc.php 9 Sep 2002 06:21:00 -0000 1.9
--- mysql.inc.php 9 Sep 2002 06:29:34 -0000 1.10
***************
*** 265,267 ****
--- 265,272 ----
}
+ function db_true()
+ {
+ return "1";
+ }
+
?>
Index: news.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/news.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** news.inc.php 9 Sep 2002 06:21:20 -0000 1.7
--- news.inc.php 9 Sep 2002 06:29:34 -0000 1.8
***************
*** 66,70 ****
$query = "SELECT COUNT(*) FROM News n ".
! "WHERE TRUE ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 66,70 ----
$query = "SELECT COUNT(*) FROM News n ".
! "WHERE ".db_true()." ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** pgsql.inc.php 9 Sep 2002 06:21:00 -0000 1.5
--- pgsql.inc.php 9 Sep 2002 06:29:34 -0000 1.6
***************
*** 329,331 ****
--- 329,336 ----
}
+ function db_true()
+ {
+ return "TRUE";
+ }
+
?>
Index: plate.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate.inc.php,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** plate.inc.php 9 Sep 2002 06:21:20 -0000 1.30
--- plate.inc.php 9 Sep 2002 06:29:34 -0000 1.31
***************
*** 253,257 ****
$query = "SELECT COUNT(*) FROM PlateType pt ".
! "WHERE TRUE ".$search->getWhere();
$res = query($query);
--- 253,257 ----
$query = "SELECT COUNT(*) FROM PlateType pt ".
! "WHERE ".db_true()." ".$search->getWhere();
$res = query($query);
***************
*** 272,276 ****
$query = "SELECT pt.* ".
"FROM PlateType pt ".
! "WHERE TRUE ".$search->getWhere()." $ob ".$search->makeLimit();
$arr = array();
--- 272,277 ----
$query = "SELECT pt.* ".
"FROM PlateType pt ".
! "WHERE ".db_true()." ".
! $search->getWhere()." $ob ".$search->makeLimit();
$arr = array();
***************
*** 652,656 ****
$query = "SELECT COUNT(*) FROM Plate p ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
--- 653,657 ----
$query = "SELECT COUNT(*) FROM Plate p ".
$search->getExtraTables()." ".
! "WHERE ".db_true()." ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
***************
*** 678,682 ****
$query = "SELECT p.* $selectfields ".
"FROM Plate p ".$search->getExtraTables().
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere()." $ob ".$search->makeLimit();
--- 679,683 ----
$query = "SELECT p.* $selectfields ".
"FROM Plate p ".$search->getExtraTables().
! "WHERE ".db_true()." ".$search->getExtraWhere()." ".
$search->getWhere()." $ob ".$search->makeLimit();
Index: program.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/program.inc.php,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** program.inc.php 9 Sep 2002 06:21:20 -0000 1.21
--- program.inc.php 9 Sep 2002 06:29:34 -0000 1.22
***************
*** 260,264 ****
$query = "SELECT COUNT(*) FROM Program p ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 260,265 ----
$query = "SELECT COUNT(*) FROM Program p ".
! "WHERE ".db_true()." ".
! $search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
Index: raw.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw.inc.php,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** raw.inc.php 9 Sep 2002 06:21:20 -0000 1.33
--- raw.inc.php 9 Sep 2002 06:29:34 -0000 1.34
***************
*** 266,270 ****
$query = "SELECT COUNT(*) ".
"FROM RawBioAssay r ".
! "WHERE TRUE ".
$search->getExtraWhere()." ".$search->getWhere();
--- 266,270 ----
$query = "SELECT COUNT(*) ".
"FROM RawBioAssay r ".
! "WHERE ".db_true()." ".
$search->getExtraWhere()." ".$search->getWhere();
Index: user.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** user.inc.php 9 Sep 2002 06:21:20 -0000 1.7
--- user.inc.php 9 Sep 2002 06:29:34 -0000 1.8
***************
*** 359,363 ****
$query = "SELECT COUNT(*) FROM Submitter u ".
! "WHERE TRUE ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res))
--- 359,363 ----
$query = "SELECT COUNT(*) FROM Submitter u ".
! "WHERE ".db_true()." ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res))
***************
*** 381,385 ****
"TO_DAYS(`activeUntil`) - TO_DAYS(NOW()) AS `daysLeft`, ".
"(u.`accessMask` & (".BUA_SUPERUSER.")) AS `superUser` ".
! "FROM Submitter u WHERE TRUE ".$search->getWhere().
" $ob ".$search->makeLimit();
--- 381,385 ----
"TO_DAYS(`activeUntil`) - TO_DAYS(NOW()) AS `daysLeft`, ".
"(u.`accessMask` & (".BUA_SUPERUSER.")) AS `superUser` ".
! "FROM Submitter u WHERE ".db_true()." ".$search->getWhere().
" $ob ".$search->makeLimit();
Index: ware.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/ware.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** ware.inc.php 9 Sep 2002 06:21:20 -0000 1.10
--- ware.inc.php 9 Sep 2002 06:29:34 -0000 1.11
***************
*** 91,95 ****
$query = "SELECT COUNT(*) FROM $type w ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 91,95 ----
$query = "SELECT COUNT(*) FROM $type w ".
! "WHERE ".db_true()." ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv2356
Modified Files:
acquisition.inc.php array.inc.php bio.inc.php bioassay.inc.php
genelist.inc.php image.inc.php item.inc.php job.inc.php
molecule.inc.php news.inc.php plate.inc.php program.inc.php
raw.inc.php search.inc.php user.inc.php ware.inc.php
Log Message:
Changed WHERE 1 to WHERE TRUE
Index: acquisition.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/acquisition.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** acquisition.inc.php 7 Sep 2002 11:36:31 -0000 1.12
--- acquisition.inc.php 9 Sep 2002 06:21:19 -0000 1.13
***************
*** 159,163 ****
$query = "SELECT COUNT(*) FROM ImageAcquisition ia ".
"LEFT JOIN Image im ON im.imageAcquisition = ia.id ".
! "WHERE 1 ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 159,163 ----
$query = "SELECT COUNT(*) FROM ImageAcquisition ia ".
"LEFT JOIN Image im ON im.imageAcquisition = ia.id ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** array.inc.php 8 Sep 2002 22:38:08 -0000 1.33
--- array.inc.php 9 Sep 2002 06:21:19 -0000 1.34
***************
*** 863,867 ****
$query = "SELECT COUNT(*) FROM ArrayBatch ab ".
! "WHERE 1 ".$search->getWhere()." ".
$search->getExtraWhere();
--- 863,867 ----
$query = "SELECT COUNT(*) FROM ArrayBatch ab ".
! "WHERE TRUE ".$search->getWhere()." ".
$search->getExtraWhere();
Index: bio.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bio.inc.php,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** bio.inc.php 8 Sep 2002 23:13:56 -0000 1.20
--- bio.inc.php 9 Sep 2002 06:21:19 -0000 1.21
***************
*** 161,165 ****
{
$owner = (int)$owner;
! $query = "SELECT * FROM Sample WHERE 1";
if($owner >= 0)
$query .= " AND owner = $owner";
--- 161,165 ----
{
$owner = (int)$owner;
! $query = "SELECT * FROM Sample WHERE TRUE";
if($owner >= 0)
$query .= " AND owner = $owner";
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassay.inc.php,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** bioassay.inc.php 8 Sep 2002 22:38:08 -0000 1.31
--- bioassay.inc.php 9 Sep 2002 06:21:19 -0000 1.32
***************
*** 384,388 ****
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res))
--- 384,388 ----
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res))
***************
*** 434,438 ****
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere().
" $ob ".$search->makeLimit();
$arr = array();
--- 434,438 ----
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
" $ob ".$search->makeLimit();
$arr = array();
***************
*** 475,479 ****
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere().
" $ob";
return $genelist->populateFromQuery($query);
--- 475,479 ----
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$search->getExtraTables()." $ljoin ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
" $ob";
return $genelist->populateFromQuery($query);
***************
*** 499,503 ****
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere();
return (bool)query($query);
}
--- 499,503 ----
"FROM $config[dbDynamic].BioAssayData$expid bad ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
return (bool)query($query);
}
Index: genelist.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/genelist.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** genelist.inc.php 8 Sep 2002 22:38:08 -0000 1.19
--- genelist.inc.php 9 Sep 2002 06:21:19 -0000 1.20
***************
*** 115,119 ****
$query = "SELECT COUNT(*) FROM GeneList gl ".
! "WHERE 1 ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
--- 115,119 ----
$query = "SELECT COUNT(*) FROM GeneList gl ".
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
***************
*** 135,139 ****
$query = "SELECT gl.* ".
"FROM GeneList gl ".
! "WHERE 1 ".$search->getExtraWhere()." ".
$search->getWhere()." ".
"GROUP BY id $ob ".$search->makeLimit();
--- 135,139 ----
$query = "SELECT gl.* ".
"FROM GeneList gl ".
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere()." ".
"GROUP BY id $ob ".$search->makeLimit();
Index: image.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/image.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** image.inc.php 8 Sep 2002 22:38:08 -0000 1.10
--- image.inc.php 9 Sep 2002 06:21:19 -0000 1.11
***************
*** 134,138 ****
$query = "SELECT COUNT(*) FROM Image im ".
! "WHERE 1 ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 134,138 ----
$query = "SELECT COUNT(*) FROM Image im ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
***************
*** 152,156 ****
$query = "SELECT im.* ".
! "FROM Image im WHERE 1 ".
$search->getWhere()." ".$search->getExtraWhere()." ".
"$ob ".$search->makeLimit();
--- 152,156 ----
$query = "SELECT im.* ".
! "FROM Image im WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere()." ".
"$ob ".$search->makeLimit();
Index: item.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/item.inc.php,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** item.inc.php 8 Sep 2002 23:13:56 -0000 1.25
--- item.inc.php 9 Sep 2002 06:21:19 -0000 1.26
***************
*** 269,273 ****
function getSharers()
{
! $query = "SELECT si.owner, u.`userName` FROM Shared$this->type si ".
"LEFT JOIN Submitter u ON u.id = si.owner ".
"WHERE si.item = $this->id ORDER BY u.`userName`";
--- 269,274 ----
function getSharers()
{
! $query = "SELECT si.owner, u.`userName` ".
! "FROM Shared$this->type si ".
"LEFT JOIN Submitter u ON u.id = si.owner ".
"WHERE si.item = $this->id ORDER BY u.`userName`";
Index: job.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/job.inc.php,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** job.inc.php 8 Sep 2002 22:38:08 -0000 1.34
--- job.inc.php 9 Sep 2002 06:21:20 -0000 1.35
***************
*** 273,277 ****
$query = "SELECT COUNT(*) FROM Job j ".
! "WHERE 1 ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 273,277 ----
$query = "SELECT COUNT(*) FROM Job j ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
Index: molecule.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/molecule.inc.php,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** molecule.inc.php 8 Sep 2002 22:38:08 -0000 1.28
--- molecule.inc.php 9 Sep 2002 06:21:20 -0000 1.29
***************
*** 628,632 ****
$query = "SELECT COUNT(*) FROM Molecule m ".
$search->getExtraTables()." ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 628,632 ----
$query = "SELECT COUNT(*) FROM Molecule m ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
***************
*** 652,656 ****
"l.name AS `libraryName` ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere().
" $ob ".$search->makeLimit();
--- 652,656 ----
"l.name AS `libraryName` ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
" $ob ".$search->makeLimit();
***************
*** 691,695 ****
$query = "SELECT m.id ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere().
" $ob";
--- 691,695 ----
$query = "SELECT m.id ".
"FROM Molecule m ".$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere().
" $ob";
Index: news.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/news.inc.php,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** news.inc.php 8 Sep 2002 22:38:08 -0000 1.6
--- news.inc.php 9 Sep 2002 06:21:20 -0000 1.7
***************
*** 66,70 ****
$query = "SELECT COUNT(*) FROM News n ".
! "WHERE 1 ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 66,70 ----
$query = "SELECT COUNT(*) FROM News n ".
! "WHERE TRUE ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
Index: plate.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate.inc.php,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** plate.inc.php 8 Sep 2002 22:38:08 -0000 1.29
--- plate.inc.php 9 Sep 2002 06:21:20 -0000 1.30
***************
*** 253,257 ****
$query = "SELECT COUNT(*) FROM PlateType pt ".
! "WHERE 1 ".$search->getWhere();
$res = query($query);
--- 253,257 ----
$query = "SELECT COUNT(*) FROM PlateType pt ".
! "WHERE TRUE ".$search->getWhere();
$res = query($query);
***************
*** 272,276 ****
$query = "SELECT pt.* ".
"FROM PlateType pt ".
! "WHERE 1 ".$search->getWhere()." $ob ".$search->makeLimit();
$arr = array();
--- 272,276 ----
$query = "SELECT pt.* ".
"FROM PlateType pt ".
! "WHERE TRUE ".$search->getWhere()." $ob ".$search->makeLimit();
$arr = array();
***************
*** 652,656 ****
$query = "SELECT COUNT(*) FROM Plate p ".
$search->getExtraTables()." ".
! "WHERE 1 ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
--- 652,656 ----
$query = "SELECT COUNT(*) FROM Plate p ".
$search->getExtraTables()." ".
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere();
$res = query($query);
***************
*** 678,682 ****
$query = "SELECT p.* $selectfields ".
"FROM Plate p ".$search->getExtraTables().
! "WHERE 1 ".$search->getExtraWhere()." ".
$search->getWhere()." $ob ".$search->makeLimit();
--- 678,682 ----
$query = "SELECT p.* $selectfields ".
"FROM Plate p ".$search->getExtraTables().
! "WHERE TRUE ".$search->getExtraWhere()." ".
$search->getWhere()." $ob ".$search->makeLimit();
Index: program.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/program.inc.php,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** program.inc.php 8 Sep 2002 22:38:08 -0000 1.20
--- program.inc.php 9 Sep 2002 06:21:20 -0000 1.21
***************
*** 260,264 ****
$query = "SELECT COUNT(*) FROM Program p ".
! "WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 260,264 ----
$query = "SELECT COUNT(*) FROM Program p ".
! "WHERE TRUE ".$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
Index: raw.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw.inc.php,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** raw.inc.php 8 Sep 2002 22:38:08 -0000 1.32
--- raw.inc.php 9 Sep 2002 06:21:20 -0000 1.33
***************
*** 266,270 ****
$query = "SELECT COUNT(*) ".
"FROM RawBioAssay r ".
! "WHERE 1 ".
$search->getExtraWhere()." ".$search->getWhere();
--- 266,270 ----
$query = "SELECT COUNT(*) ".
"FROM RawBioAssay r ".
! "WHERE TRUE ".
$search->getExtraWhere()." ".$search->getWhere();
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** search.inc.php 8 Sep 2002 23:13:56 -0000 1.37
--- search.inc.php 9 Sep 2002 06:21:20 -0000 1.38
***************
*** 719,725 ****
for(reset($textra); list($fid) = each($textra); )
{
! if(isset($tables[$fid][0])) $this->addExtraTable($tables[$fid][0]);
! if(isset($tables[$fid][1])) $this->addExtraWhere($tables[$fid][1]);
! if(isset($tables[$fid][2])) $this->addLeftJoin($tables[$fid][2]);
}
$this->where = $where;
--- 719,728 ----
for(reset($textra); list($fid) = each($textra); )
{
! if(isset($tables[$fid][0]))
! $this->addExtraTable($tables[$fid][0]);
! if(isset($tables[$fid][1]))
! $this->addExtraWhere($tables[$fid][1]);
! if(isset($tables[$fid][2]))
! $this->addLeftJoin($tables[$fid][2]);
}
$this->where = $where;
Index: user.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user.inc.php,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** user.inc.php 8 Sep 2002 22:38:08 -0000 1.6
--- user.inc.php 9 Sep 2002 06:21:20 -0000 1.7
***************
*** 359,363 ****
$query = "SELECT COUNT(*) FROM Submitter u ".
! "WHERE 1 ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res))
--- 359,363 ----
$query = "SELECT COUNT(*) FROM Submitter u ".
! "WHERE TRUE ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res))
***************
*** 381,385 ****
"TO_DAYS(`activeUntil`) - TO_DAYS(NOW()) AS `daysLeft`, ".
"(u.`accessMask` & (".BUA_SUPERUSER.")) AS `superUser` ".
! "FROM Submitter u WHERE 1 ".$search->getWhere().
" $ob ".$search->makeLimit();
--- 381,385 ----
"TO_DAYS(`activeUntil`) - TO_DAYS(NOW()) AS `daysLeft`, ".
"(u.`accessMask` & (".BUA_SUPERUSER.")) AS `superUser` ".
! "FROM Submitter u WHERE TRUE ".$search->getWhere().
" $ob ".$search->makeLimit();
Index: ware.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/ware.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** ware.inc.php 8 Sep 2002 22:38:08 -0000 1.9
--- ware.inc.php 9 Sep 2002 06:21:20 -0000 1.10
***************
*** 91,95 ****
$query = "SELECT COUNT(*) FROM $type w ".
! "WHERE 1 ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
--- 91,95 ----
$query = "SELECT COUNT(*) FROM $type w ".
! "WHERE TRUE ".
$search->getWhere()." ".$search->getExtraWhere();
$res = query($query);
|
|
From: <tr...@us...> - 2002-09-09 06:21:02
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv2226
Modified Files:
pgsql.inc.php mysql.inc.php
Log Message:
Aded db_has_subselect
Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** pgsql.inc.php 8 Sep 2002 22:37:25 -0000 1.4
--- pgsql.inc.php 9 Sep 2002 06:21:00 -0000 1.5
***************
*** 324,326 ****
--- 324,331 ----
}
+ function db_has_subselects()
+ {
+ return true;
+ }
+
?>
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** mysql.inc.php 8 Sep 2002 22:37:25 -0000 1.8
--- mysql.inc.php 9 Sep 2002 06:21:00 -0000 1.9
***************
*** 260,262 ****
--- 260,267 ----
}
+ function db_has_subselects()
+ {
+ return false;
+ }
+
?>
|
|
From: <tr...@us...> - 2002-09-09 06:20:45
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv2148
Modified Files:
experiment.inc.php
Log Message:
Added subselect to deal with MySQL's GROUP BY/'first encountered value' feature
Index: experiment.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/experiment.inc.php,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** experiment.inc.php 8 Sep 2002 22:38:08 -0000 1.44
--- experiment.inc.php 9 Sep 2002 06:20:40 -0000 1.45
***************
*** 285,289 ****
$query = "SELECT COUNT(*) FROM Experiment e ".
! "WHERE 1 ".$search->getExtraWhere()." ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
--- 285,289 ----
$query = "SELECT COUNT(*) FROM Experiment e ".
! "WHERE TRUE ".$search->getExtraWhere()." ".$search->getWhere();
$res = query($query);
if($row =& db_fetch_row($res)) $cnt = $row[0];
***************
*** 301,305 ****
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT e.*, COUNT(DISTINCT erb.`rawBioAssay`) AS raws, ".
"COUNT(DISTINCT bas.id) AS sets, ".
"COUNT(DISTINCT ba.id) AS assays ".
--- 301,315 ----
$ob = $search->makeOrderBy($sortfields);
! if(db_has_subselects())
! {
! $ss1 = ", t.raws, t.sets, t.assays FROM Experiment e, ".
! "(SELECT e.id,";
! $ss2 = ") AS t WHERE e.id = t.id";
! }
! else
! $ss1 = $ss2 = "";
!
! $query = "SELECT e.* $ss1 ".
! "COUNT(DISTINCT erb.`rawBioAssay`) AS raws, ".
"COUNT(DISTINCT bas.id) AS sets, ".
"COUNT(DISTINCT ba.id) AS assays ".
***************
*** 308,313 ****
"LEFT JOIN BioAssaySet bas ON bas.experiment = e.id ".
"LEFT JOIN BioAssay ba ON ba.`bioAssaySet` = bas.id ".
! "WHERE 1 ".$search->getExtraWhere()." ".$search->getWhere()." ".
! "GROUP BY e.id $ob ".$search->makeLimit();
$arr = array();
--- 318,323 ----
"LEFT JOIN BioAssaySet bas ON bas.experiment = e.id ".
"LEFT JOIN BioAssay ba ON ba.`bioAssaySet` = bas.id ".
! "WHERE TRUE ".$search->getExtraWhere()." ".$search->getWhere()." ".
! "GROUP BY e.id $ss2 $ob ".$search->makeLimit();
$arr = array();
|
|
From: <tr...@us...> - 2002-09-08 23:14:00
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv1867
Modified Files:
bio.inc.php hyb.inc.php item.inc.php search.inc.php
Log Message:
Fixed mysql-ism: implicit cast of numbers to booleans
Index: bio.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bio.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** bio.inc.php 8 Sep 2002 22:38:08 -0000 1.19
--- bio.inc.php 8 Sep 2002 23:13:56 -0000 1.20
***************
*** 119,123 ****
$search->makeWhere($fields);
if($visible)
! $search->addExtraWhere("s.`isVisible`");
$query = "SELECT COUNT(*) FROM Sample s, Submitter u, SharedSample ss ".
--- 119,123 ----
$search->makeWhere($fields);
if($visible)
! $search->addExtraWhere("s.`isVisible` <> 0");
$query = "SELECT COUNT(*) FROM Sample s, Submitter u, SharedSample ss ".
***************
*** 165,169 ****
$query .= " AND owner = $owner";
if($visible)
! $query .= " AND `isVisible`";
$arr = array();
$res = query($query);
--- 165,169 ----
$query .= " AND owner = $owner";
if($visible)
! $query .= " AND `isVisible` <> 0";
$arr = array();
$res = query($query);
***************
*** 206,211 ****
if($visible)
{
! $query .= " AND s.`isVisibl`e AND e.`isVisible` AND le.`isVisible` ".
! "AND h`.isVisible`";
}
$res = query($query);
--- 206,211 ----
if($visible)
{
! $query .= " AND s.`isVisible` <> 0 AND e.`isVisible` <> 0 ".
! "AND le.`isVisible` <> 0 AND h`.isVisible` <> 0";
}
$res = query($query);
***************
*** 227,231 ****
"WHERE le.id = $labeled AND e.id = le.extract AND s.id = e.sample";
if($visible)
! $query .= " AND s.`isVisible` AND e.`isVisible` AND le.`isVisible`";
$res = query($query);
if($row =& db_fetch_assoc($res))
--- 227,232 ----
"WHERE le.id = $labeled AND e.id = le.extract AND s.id = e.sample";
if($visible)
! $query .= " AND s.`isVisible` <> 0 AND e.`isVisible` <> 0 ".
! "AND le.`isVisible` <> 0";
$res = query($query);
if($row =& db_fetch_assoc($res))
Index: hyb.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb.inc.php,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** hyb.inc.php 8 Sep 2002 22:38:08 -0000 1.18
--- hyb.inc.php 8 Sep 2002 23:13:56 -0000 1.19
***************
*** 145,153 ****
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT h.*, p.name AS `protocolName`, u.`userName,` ".
"COUNT(DISTINCT ia.id) AS scans, COUNT(DISTINCT i.id) AS images, ".
"COUNT(DISTINCT rba.id) AS raws, a.barcode ".
! "FROM Hybridization h, SharedHybridization sh, Submitter u, ".
! "Protocol p ".
"LEFT JOIN ImageAcquisition ia ON ia.hybridization = h.id ".
"LEFT JOIN Image i ON i.`imageAcquisition` = ia.id ".
--- 145,153 ----
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT h.*, p.name AS `protocolName`, u.`userName`, ".
"COUNT(DISTINCT ia.id) AS scans, COUNT(DISTINCT i.id) AS images, ".
"COUNT(DISTINCT rba.id) AS raws, a.barcode ".
! "FROM SharedHybridization sh, Submitter u, ".
! "Protocol p, Hybridization h ".
"LEFT JOIN ImageAcquisition ia ON ia.hybridization = h.id ".
"LEFT JOIN Image i ON i.`imageAcquisition` = ia.id ".
Index: item.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/item.inc.php,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** item.inc.php 8 Sep 2002 22:38:08 -0000 1.24
--- item.inc.php 8 Sep 2002 23:13:56 -0000 1.25
***************
*** 70,74 ****
}
if($visible)
! $query .= " AND i.`isVisible`";
return $this->readQuery($query);
}
--- 70,74 ----
}
if($visible)
! $query .= " AND i.`isVisible` <> 0";
return $this->readQuery($query);
}
***************
*** 172,176 ****
"WHERE si.item = i.id AND si.owner = $owner";
if($visible)
! $query .= " AND i.`isVisible`";
$res = query($query);
while($row =& db_fetch_row($res))
--- 172,176 ----
"WHERE si.item = i.id AND si.owner = $owner";
if($visible)
! $query .= " AND i.`isVisible` <> 0";
$res = query($query);
while($row =& db_fetch_row($res))
***************
*** 181,185 ****
" WHERE si.item = i.id AND si.owner = 0";
if($visible)
! $query .= " AND i.`isVisible`";
$res = query($query);
while($row =& db_fetch_row($res))
--- 181,185 ----
" WHERE si.item = i.id AND si.owner = 0";
if($visible)
! $query .= " AND i.`isVisible` <> 0";
$res = query($query);
while($row =& db_fetch_row($res))
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** search.inc.php 8 Sep 2002 22:38:08 -0000 1.36
--- search.inc.php 8 Sep 2002 23:13:56 -0000 1.37
***************
*** 831,835 ****
{
for($i = 0; $i < count($vars); $i++)
! $vars[$i] = "$vars[$i] = '".addslashes($this->{$vars[$i]})."'";
$query = "UPDATE SearchCriterion SET ".implode(", ", $vars)." ".
"WHERE search = $this->search AND position = $this->position";
--- 831,835 ----
{
for($i = 0; $i < count($vars); $i++)
! $vars[$i] = "`$vars[$i]` = '".addslashes($this->{$vars[$i]})."'";
$query = "UPDATE SearchCriterion SET ".implode(", ", $vars)." ".
"WHERE search = $this->search AND position = $this->position";
|
|
From: <tr...@us...> - 2002-09-08 23:12:42
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv1630
Modified Files:
protocol.inc.php
Log Message:
Fixed join order to work with postgresql (LEFT JOIN)
Index: protocol.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/protocol.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** protocol.inc.php 8 Sep 2002 22:38:08 -0000 1.8
--- protocol.inc.php 8 Sep 2002 23:12:40 -0000 1.9
***************
*** 178,182 ****
// Returns an array with lots of fields (id,etype,name,descr,submitter,
! // fileid,fname,fileSize,date,sname).
function getBrief($type = 0)
{
--- 178,182 ----
// Returns an array with lots of fields (id,etype,name,descr,submitter,
! // fileId,fname,fileSize,date,sname).
function getBrief($type = 0)
{
***************
*** 184,189 ****
$query = "SELECT p.*, u.name AS fname, u.`fileSize`, ".
"u.`addedDate` AS fdate, s.`userName` AS sname ".
! "FROM Protocol p, Submitter s ".
! "LEFT JOIN Upload u ON u.id = p.fileid ".
"WHERE s.id = p.submitter ";
if($type) $query .= "AND p.etype = $type ORDER BY p.id";
--- 184,189 ----
$query = "SELECT p.*, u.name AS fname, u.`fileSize`, ".
"u.`addedDate` AS fdate, s.`userName` AS sname ".
! "FROM Submitter s, Protocol p ".
! "LEFT JOIN Upload u ON u.id = p.`fileId` ".
"WHERE s.id = p.submitter ";
if($type) $query .= "AND p.etype = $type ORDER BY p.id";
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv25478
Modified Files:
array.inc.php bio.inc.php bioassay.inc.php bioassayset.inc.php
eventlog.inc.php experiment.inc.php genelist.inc.php
hyb.inc.php image.inc.php item.inc.php job.inc.php left.phtml
molecule.inc.php news.inc.php plate.inc.php plot.inc.php
program.inc.php protocol.inc.php raw.inc.php
sampleannotation.inc.php sampletissue.inc.php search.inc.php
session.inc.php transformation.inc.php upload.inc.php
user.inc.php ware.inc.php wizzzard.inc.php
Log Message:
Added backticks around all mixed/upper case column names
Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** array.inc.php 7 Sep 2002 11:36:31 -0000 1.32
--- array.inc.php 8 Sep 2002 22:38:08 -0000 1.33
***************
*** 78,86 ****
if(!query($query) || db_affected_rows() < 1)
return false;
! $query = "DELETE FROM ArrayTypePlate WHERE arrayType = $this->id";
query($query);
! $query = "DELETE FROM Element WHERE arrayType = $this->id";
query($query);
! $query = "DELETE FROM ArrayBlock WHERE arrayType = $this->id";
query($query);
@unlink($this->getRepositoryFilename());
--- 78,86 ----
[...560 lines suppressed...]
$search->getWhere()." ".$search->getExtraWhere()." ".
--- 936,953 ----
{
// Add more fields here
! $sortfields = array("barcode", array("`batchName`", "`orderNumber`"),
! "`orderNumber`", "`userName`", array("`designName`", "`batchName`",
! "`orderNumber`"), "`printStartDate`", "destroyed", "comment",
! "`hybName`", "`hybUserName`");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT a.*, ab.name AS `batchName`, ab.`arrayType`, ".
! "ab.`printStartDate`, at.name AS `designName`, u.`userName`, ".
! "h.name AS `hybName`, hu.`userName` AS `hybUserName` ".
"FROM Array a, ArrayBatch ab, ArrayType at, Submitter u ".
$search->getExtraTables()." ".
"LEFT JOIN Hybridization h ON h.id = a.hybridization ".
"LEFT JOIN Submitter hu ON hu.id = h.owner ".
! "WHERE a.batch = ab.id AND ab.`arrayType` = at.id ".
"AND u.id = ab.owner ".
$search->getWhere()." ".$search->getExtraWhere()." ".
Index: bio.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bio.inc.php,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** bio.inc.php 7 Sep 2002 11:59:40 -0000 1.18
--- bio.inc.php 8 Sep 2002 22:38:08 -0000 1.19
***************
*** 115,123 ****
$ownerId = (int)$ownerId;
// Add more fields and operators here
! $fields = array("s.name", "s.descr", "u.userName", "s.addedDate");
$search->makeWhere($fields);
if($visible)
! $search->addExtraWhere("s.isVisible");
$query = "SELECT COUNT(*) FROM Sample s, Submitter u, SharedSample ss ".
--- 115,123 ----
[...233 lines suppressed...]
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT le.*, se.owner AS extractPublic, ".
! "ss.owner AS samplePublic, p.name AS protocolName, ".
! "e.name AS extractName, e.sample, s.name AS sampleName ".
"FROM LabeledExtract le, Extract e, SharedLabeledExtract sle, ".
"Sample s, Protocol p ".
--- 699,710 ----
// Add more fields here
! $sortfields = array("name", "label", "`extractName`", "`sampleName`",
! "`labelingDate`", "`protocolName`", "`quantityLeft`", 0);
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT le.*, se.owner AS `extractPublic`, ".
! "ss.owner AS `samplePublic`, p.name AS `protocolName`, ".
! "e.name AS `extractName`, e.sample, s.name AS `sampleName` ".
"FROM LabeledExtract le, Extract e, SharedLabeledExtract sle, ".
"Sample s, Protocol p ".
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassay.inc.php,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** bioassay.inc.php 7 Sep 2002 11:36:31 -0000 1.30
--- bioassay.inc.php 8 Sep 2002 22:38:08 -0000 1.31
***************
*** 76,80 ****
$query = "DELETE FROM $config[dbDynamic].BioAssayData$this->experiment ".
! "WHERE bioAssay = $this->id";
query($query);
--- 76,80 ----
$query = "DELETE FROM $config[dbDynamic].BioAssayData$this->experiment ".
! "WHERE `bioAssay` = $this->id";
query($query);
[...705 lines suppressed...]
! else $extra .= " 0 AS C";
! $query = "SELECT $xc AS A, $yc AS B, $extra ".
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$sea->getExtraTables()." ".
! "WHERE bad.bioAssay = $this->id ".$sea->getExtraWhere()." ".
"$groupby";
$res = query($query);
--- 1046,1056 ----
}
else if($third >= 0)
! $extra .= " $groups[$third] AS `C`";
! else $extra .= " 0 AS `C`";
! $query = "SELECT $xc AS `A`, $yc AS `B`, $extra ".
"FROM $config[dbDynamic].BioAssayData$this->experiment bad ".
$sea->getExtraTables()." ".
! "WHERE bad.`bioAssay` = $this->id ".$sea->getExtraWhere()." ".
"$groupby";
$res = query($query);
Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassayset.inc.php,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** bioassayset.inc.php 7 Sep 2002 11:36:31 -0000 1.24
--- bioassayset.inc.php 8 Sep 2002 22:38:08 -0000 1.25
***************
*** 65,70 ****
function write()
{
! if($this->id) return parent::write(array());
! else return parent::write(array("experiment", "transformation"));
}
--- 65,72 ----
function write()
{
! if($this->id)
[...413 lines suppressed...]
if($row =& db_fetch_assoc($res)) return $row;
--- 652,656 ----
{
$query = "SELECT * FROM BioAssaySetExplore ".
! "WHERE `bioAssaySet` = $this->id";
$res = query($query);
if($row =& db_fetch_assoc($res)) return $row;
***************
*** 696,700 ****
{
$query = "SELECT * FROM BioAssaySetCreation ".
! "WHERE bioAssaySet = $this->id";
$res = query($query);
return db_fetch_assoc($res);
--- 706,710 ----
{
$query = "SELECT * FROM BioAssaySetCreation ".
! "WHERE `bioAssaySet` = $this->id";
$res = query($query);
return db_fetch_assoc($res);
Index: eventlog.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/eventlog.inc.php,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** eventlog.inc.php 7 Sep 2002 11:36:32 -0000 1.4
--- eventlog.inc.php 8 Sep 2002 22:38:08 -0000 1.5
***************
*** 30,44 ****
function log($type, $message)
{
! $query = "INSERT INTO EventLog (eventDate, eventType, message) ".
! "VALUES (NOW(), '".addslashes($type)."', '".addslashes($message)."')";
return (bool)query($query);
}
! // Returns array(array(date,type,message))
function getLast($cnt)
{
! $query = "SELECT eventDate AS date, eventType AS type, message ".
! "FROM EventLog WHERE eventType='broadcast' ".
! "ORDER BY eventDate DESC ".db_limit(0, (int)$cnt);
$res = query($query);
$arr = array();
--- 30,45 ----
function log($type, $message)
{
! $query = "INSERT INTO EventLog ".
! "(`eventDate`, `eventType`, message) VALUES ".
! "(NOW(), '".addslashes($type)."', '".addslashes($message)."')";
return (bool)query($query);
}
! // Returns array(array(eventDate,eventType,message))
function getLast($cnt)
{
! $query = "SELECT `eventDate`, `eventType`, message ".
! "FROM EventLog WHERE `eventType` = 'broadcast' ".
! "ORDER BY `eventDate` DESC ".db_limit(0, (int)$cnt);
$res = query($query);
$arr = array();
Index: experiment.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/experiment.inc.php,v
retrieving revision 1.43
retrieving revision 1.44
diff -C2 -d -r1.43 -r1.44
*** experiment.inc.php 7 Sep 2002 11:36:32 -0000 1.43
--- experiment.inc.php 8 Sep 2002 22:38:08 -0000 1.44
***************
*** 111,115 ****
$query = "DELETE FROM Experiment WHERE id = $id";
! if(!query($query)) return false;
db_table_drop("$config[dbDynamic].BioAssayData$id");
--- 111,116 ----
$query = "DELETE FROM Experiment WHERE id = $id";
! if(!query($query))
! return false;
[...209 lines suppressed...]
--- 399,403 ----
$rc = false;
$query = "DELETE FROM ExperimentRawBioAssay ".
! "WHERE experiment = $expid AND `rawBioAssay` = $rawid";
if(query($query) && db_affected_rows() == 1)
{
***************
*** 405,409 ****
"WHERE experiment = $this->id";
$res = query($query);
! if($row =& db_fetch_row($res)) return $row[0];
else return false;
}
--- 415,420 ----
"WHERE experiment = $this->id";
$res = query($query);
! if($row =& db_fetch_row($res))
! return $row[0];
else return false;
}
Index: genelist.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/genelist.inc.php,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** genelist.inc.php 8 Sep 2002 14:02:42 -0000 1.18
--- genelist.inc.php 8 Sep 2002 22:38:08 -0000 1.19
***************
*** 55,59 ****
if(query($query))
{
! $query = "DELETE FROM GeneListGene WHERE geneList = $this->id";
query($query);
}
--- 55,59 ----
if(query($query))
{
! $query = "DELETE FROM GeneListGene WHERE `geneList` = $this->id";
query($query);
[...152 lines suppressed...]
$query = "SELECT glg.molecule, glg.score ".
"FROM GeneListGene glg ".
! "WHERE glg.geneList = $this->id ".
"ORDER BY score";
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res)) $arr[$row[0]] = $row[1];
return $arr;
}
--- 323,332 ----
$query = "SELECT glg.molecule, glg.score ".
"FROM GeneListGene glg ".
! "WHERE glg.`geneList` = $this->id ".
"ORDER BY score";
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res))
! $arr[$row[0]] = $row[1];
return $arr;
}
Index: hyb.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb.inc.php,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** hyb.inc.php 7 Sep 2002 11:36:32 -0000 1.17
--- hyb.inc.php 8 Sep 2002 22:38:08 -0000 1.18
***************
*** 118,123 ****
// Add more fields and operators here
! $fields = array("h.name", "h.descr", "u.userName",
! "h.addedDate", "h.hybridizationDate", "p.name");
$search->addExtraWhere("sh.owner IN (0, $ownerId)");
--- 118,123 ----
// Add more fields and operators here
! $fields = array("h.name", "h.descr", "u.`userName`",
[...122 lines suppressed...]
}
***************
*** 261,267 ****
{
$query = "SELECT COUNT(*) FROM ImageAcquisition ia, RawBioAssay r ".
! "WHERE ia.hybridization = $this->id AND r.imageAcquisition = ia.id";
$res = query($query);
! if($row =& db_fetch_row($res)) return($row[0]);
return 0;
}
--- 269,277 ----
{
$query = "SELECT COUNT(*) FROM ImageAcquisition ia, RawBioAssay r ".
! "WHERE ia.hybridization = $this->id ".
! "AND r.`imageAcquisition` = ia.id";
$res = query($query);
! if($row =& db_fetch_row($res))
! return($row[0]);
return 0;
}
Index: image.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/image.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** image.inc.php 7 Sep 2002 11:36:32 -0000 1.9
--- image.inc.php 8 Sep 2002 22:38:08 -0000 1.10
***************
*** 51,60 ****
$id = (int)$id;
$owner = (int)$owner;
! if($owner < 0) $query = "SELECT * FROM $this->type WHERE id = $id";
else
{
$query = "SELECT i.* FROM Image i, ImageAcquisition ia, ".
"SharedHybridization sh ".
! "WHERE ia.id = i.imageAcquisition AND sh.item = ia.hybridization ".
"AND sh.owner IN (0, $owner) AND i.id = $id";
}
--- 51,62 ----
$id = (int)$id;
$owner = (int)$owner;
! if($owner < 0)
! $query = "SELECT * FROM $this->type WHERE id = $id";
else
{
$query = "SELECT i.* FROM Image i, ImageAcquisition ia, ".
"SharedHybridization sh ".
! "WHERE ia.id = i.`imageAcquisition` ".
! "AND sh.item = ia.hybridization ".
"AND sh.owner IN (0, $owner) AND i.id = $id";
}
***************
*** 64,68 ****
function write()
{
! return parent::write(array("imageAcquisition", "channels", "fileSize"));
}
--- 66,71 ----
function write()
{
! return parent::write(array("`imageAcquisition`", "channels",
! "`fileSize`"));
}
***************
*** 127,131 ****
$fields = array();
! $search->addExtraWhere("im.imageAcquisition = ".(int)$acq);
$search->makeWhere($fields);
--- 130,134 ----
$fields = array();
! $search->addExtraWhere("im.`imageAcquisition` = ".(int)$acq);
$search->makeWhere($fields);
***************
*** 144,148 ****
{
// Add more fields here
! $sortfields = array("name", "channels", "fileSize", "descr");
$ob = $search->makeOrderBy($sortfields);
--- 147,151 ----
{
// Add more fields here
! $sortfields = array("name", "channels", "`fileSize`", "descr");
$ob = $search->makeOrderBy($sortfields);
***************
*** 153,158 ****
"$ob ".$search->makeLimit();
$arr = array();
! if(!($res = query($query))) return $arr;
! while($row =& db_fetch_assoc($res)) $arr[] = $row;
return $arr;
}
--- 156,163 ----
"$ob ".$search->makeLimit();
$arr = array();
! if(!($res = query($query)))
! return $arr;
! while($row =& db_fetch_assoc($res))
! $arr[] = $row;
return $arr;
}
Index: item.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/item.inc.php,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** item.inc.php 7 Sep 2002 11:36:32 -0000 1.23
--- item.inc.php 8 Sep 2002 22:38:08 -0000 1.24
***************
*** 70,74 ****
}
if($visible)
! $query .= " AND i.isVisible";
return $this->readQuery($query);
}
--- 70,74 ----
}
if($visible)
! $query .= " AND i.`isVisible`";
return $this->readQuery($query);
[...201 lines suppressed...]
! "WHERE id = $id AND `useCount` = -1";
return query($query) && db_affected_rows() == 1;
}
! $query = "UPDATE $type SET `useCount` = `useCount` - 1 ".
! "WHERE id = $id AND `useCount` > 0";
return query($query) && db_affected_rows() == 1;
}
***************
*** 446,450 ****
function getUseCount()
{
! $query = "SELECT useCount FROM $this->type WHERE id = $this->id";
$res = query($query);
if($row =& db_fetch_row($res))
--- 452,456 ----
function getUseCount()
{
! $query = "SELECT `useCount` FROM $this->type WHERE id = $this->id";
$res = query($query);
if($row =& db_fetch_row($res))
Index: job.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/job.inc.php,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** job.inc.php 7 Sep 2002 11:36:32 -0000 1.33
--- job.inc.php 8 Sep 2002 22:38:08 -0000 1.34
***************
*** 91,95 ****
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] = "'".addslashes($this->{$vars[$i]})."'";
$id = db_insert("Job", $vars, $vals);
if(!$id)
--- 91,95 ----
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] =& $this->{$vars[$i]};
$id = db_insert("Job", $vars, $vals);
[...144 lines suppressed...]
// worst thing that can happen isn't all that horrible.
$query = "INSERT INTO JobFileSection ".
! "(`jobFile`, `fileSection`, `sectionCount`) ".
"VALUES ($this->id, $section, $count)";
return (bool)query($query);
***************
*** 651,656 ****
function sectionCount($section)
{
! $query = "SELECT sectionCount FROM JobFileSection ".
! "WHERE jobFile = $this->id AND fileSection = ".(int)$section;
$res = query($query);
if($row =& db_fetch_row($res))
--- 652,657 ----
function sectionCount($section)
{
! $query = "SELECT `sectionCount` FROM JobFileSection ".
! "WHERE `jobFile` = $this->id AND `fileSection` = ".(int)$section;
$res = query($query);
if($row =& db_fetch_row($res))
Index: left.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/left.phtml,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** left.phtml 7 Sep 2002 11:36:32 -0000 1.44
--- left.phtml 8 Sep 2002 22:38:08 -0000 1.45
***************
*** 376,383 ****
for($i = count($events) - 1; $i >= 0; $i--)
{
! $txt = sprintf($et[$events[$i]["type"]],
html($events[$i]["message"]));
! $date = (int)substr($events[$i]["date"], 8, 2).". ".
! substr($events[$i]["date"], 11, 5);
echo "$date $txt<br>\n";
}
--- 376,383 ----
for($i = count($events) - 1; $i >= 0; $i--)
{
! $txt = sprintf($et[$events[$i]["eventType"]],
html($events[$i]["message"]));
! $date = (int)substr($events[$i]["eventDate"], 8, 2).". ".
! substr($events[$i]["eventDate"], 11, 5);
echo "$date $txt<br>\n";
}
Index: molecule.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/molecule.inc.php,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** molecule.inc.php 8 Sep 2002 14:46:57 -0000 1.27
--- molecule.inc.php 8 Sep 2002 22:38:08 -0000 1.28
***************
*** 125,129 ****
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] = "'".addslashes($this->{$vars[$i]})."'";
$vals[] = chr(strlen($this->cloneId)).$this->cloneId;
$id = db_insert("Molecule", $vars, $vals);
--- 125,129 ----
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] =& $this->{$vars[$i]};
$vals[] = chr(strlen($this->cloneId)).$this->cloneId;
[...101 lines suppressed...]
! "tissueName", "vectorName", "libraryName", "lastUpdate");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT m.*, v.name AS vectorName, t.name AS tissueName, ".
! "l.name AS libraryName ".
"FROM Molecule m ".$search->getExtraTables()." ".
"WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere().
--- 643,654 ----
"l.id = m.library"));
! $sortfields = array("`cloneId`", array("species", "`clusterId`"),
! "`geneSymbol`", "`geneName`", "chromosome", "`cytoBand`",
! "markers", "`locusLink`", "omim", "accession", "nid", "antibiotics",
! "`tissueName`", "`vectorName`", "`libraryName`", "`lastUpdate`");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT m.*, v.name AS `vectorName`, t.name AS `tissueName`, ".
! "l.name AS `libraryName` ".
"FROM Molecule m ".$search->getExtraTables()." ".
"WHERE 1 ".$search->getWhere()." ".$search->getExtraWhere().
Index: news.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/news.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** news.inc.php 7 Sep 2002 11:36:32 -0000 1.5
--- news.inc.php 8 Sep 2002 22:38:08 -0000 1.6
***************
*** 44,48 ****
function getLatest($count, $from = 0)
{
! $query = "SELECT * FROM News ORDER BY addedDate DESC ".
db_limit((int)$from, (int)$count);
$res = query($query);
--- 44,48 ----
function getLatest($count, $from = 0)
{
! $query = "SELECT * FROM News ORDER BY `addedDate` DESC ".
db_limit((int)$from, (int)$count);
$res = query($query);
***************
*** 82,86 ****
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT n.*, u.userName ".
"FROM News n, Submitter u WHERE n.owner = u.id ".
$search->getWhere()." $ob ".$search->makeLimit();
--- 82,86 ----
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT n.*, u.`userName` ".
"FROM News n, Submitter u WHERE n.owner = u.id ".
$search->getWhere()." $ob ".$search->makeLimit();
Index: plate.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate.inc.php,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** plate.inc.php 7 Sep 2002 11:36:32 -0000 1.28
--- plate.inc.php 8 Sep 2002 22:38:08 -0000 1.29
***************
*** 59,63 ****
{
$query = "SELECT pt.* FROM PlateType pt, Plate p ".
! "WHERE p.id = ".(int)$plate." AND pt.id = p.plateType";
return $this->readQuery($query);
}
--- 59,63 ----
{
$query = "SELECT pt.* FROM PlateType pt, Plate p ".
! "WHERE p.id = ".(int)$plate." AND pt.id = p.`plateType`";
return $this->readQuery($query);
[...638 lines suppressed...]
$arr[1][$row[0]] = $row[1];
! $query = "SELECT `bacterialGrowth`, COUNT(*) ".
! "FROM Well WHERE `bacterialGrowth` <> '' AND probe = $probe ".
! "GROUP BY `bacterialGrowth`";
$res = query($query);
while($row =& db_fetch_row($res))
***************
*** 962,966 ****
{
$probe = (int)$probe;
! $query = "SELECT w.*, p.plateType, p.name ".
"FROM Well w, Plate p WHERE p.id = w.plate AND w.probe = $probe";
$res = query($query);
--- 964,968 ----
{
$probe = (int)$probe;
! $query = "SELECT w.*, p.`plateType`, p.name ".
"FROM Well w, Plate p WHERE p.id = w.plate AND w.probe = $probe";
$res = query($query);
Index: plot.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plot.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** plot.inc.php 7 Sep 2002 11:36:32 -0000 1.19
--- plot.inc.php 8 Sep 2002 22:38:08 -0000 1.20
***************
*** 112,121 ****
}
else $mn = "Median";
! if($this->item == 0) $s = "$table.FCh1$mn-$table.BCh1$mn";
! else if($this->item == 1) $s = "$table.FCh2$mn-$table.BCh2$mn";
! else if($this->item == 2) $s = "($table.FCh1$mn-$table.BCh1$mn)/".
! "($table.FCh2$mn-$table.BCh2$mn)";
! else $s = "($table.FCh1$mn-$table.BCh1$mn)*".
! "($table.FCh2$mn-$table.BCh2$mn)";
if($log) $s = "LOG($s)/LOG($log)";
if($this->item == 3)
--- 112,121 ----
}
else $mn = "Median";
! if($this->item == 0) $s = "$table.`FCh1$mn`-$table.`BCh1$mn`";
! else if($this->item == 1) $s = "$table.`FCh2$mn`-$table.`BCh2$mn`";
! else if($this->item == 2) $s = "($table.`FCh1$mn`-$table.`BCh1$mn`)/".
! "($table.`FCh2$mn`-$table.`BCh2$mn`)";
! else $s = "($table.`FCh1$mn`-$table.`BCh1$mn`)*".
! "($table.`FCh2$mn`-$table.`BCh2$mn`)";
if($log) $s = "LOG($s)/LOG($log)";
if($this->item == 3)
***************
*** 444,449 ****
"), AVG(".$a2->getExpression("t1", $ylog).
") FROM $table1 ".
! "WHERE t1.".($a1->type == "v" ? "bioAssay" : "rawBioAssay").
! " = $a1->id";
}
else
--- 444,449 ----
"), AVG(".$a2->getExpression("t1", $ylog).
") FROM $table1 ".
! "WHERE t1.`".($a1->type == "v" ? "bioAssay" : "rawBioAssay").
! "` = $a1->id";
}
else
***************
*** 451,456 ****
$query = "SELECT ".$a1->getExpression("t1", $xlog).", ".
$a2->getExpression("t1", $ylog)." FROM $table1 ".
! "WHERE t1.".($a1->type == "v" ? "bioAssay" : "rawBioAssay").
! " = $a1->id";
}
if($excluded && $a1->type == "v")
--- 451,456 ----
$query = "SELECT ".$a1->getExpression("t1", $xlog).", ".
$a2->getExpression("t1", $ylog)." FROM $table1 ".
! "WHERE t1.`".($a1->type == "v" ? "bioAssay" : "rawBioAssay").
! "` = $a1->id";
}
if($excluded && $a1->type == "v")
***************
*** 488,494 ****
"WHERE t1.position = t2.position";
}
! $query .= " AND t1.".($a1->type == "v" ? "bioAssay" : "rawBioAssay").
! " = $a1->id AND t2.".
! ($a2->type == "v" ? "bioAssay" : "rawBioAssay")." = $a2->id";
if($excluded)
{
--- 488,494 ----
"WHERE t1.position = t2.position";
}
! $query .= " AND t1.`".($a1->type == "v" ? "bioAssay" : "rawBioAssay").
! "` = $a1->id AND t2.`".
! ($a2->type == "v" ? "bioAssay" : "rawBioAssay")."` = $a2->id";
if($excluded)
{
Index: program.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/program.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** program.inc.php 7 Sep 2002 11:36:32 -0000 1.19
--- program.inc.php 8 Sep 2002 22:38:08 -0000 1.20
***************
*** 167,174 ****
{
$query = "SELECT id, name FROM Program ".
! "WHERE onServer ORDER BY name";
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res)) $arr[$row[0]] = $row[1];
return $arr;
}
--- 167,175 ----
{
$query = "SELECT id, name FROM Program ".
! "WHERE `onServer` ORDER BY name";
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res))
! $arr[$row[0]] = $row[1];
return $arr;
}
***************
*** 207,212 ****
{
$query = "REPLACE INTO ProgramParameter ".
! "(program, position, name, commonName, valueType, options, ".
! "defaultValue, enumOptions) VALUES ".
"($this->id, ".(int)$pos.", ".
"'".addslashes($name)."', ".
--- 208,213 ----
{
$query = "REPLACE INTO ProgramParameter ".
! "(program, position, name, `commonName`, `valueType`, options, ".
! "`defaultValue`, `enumOptions`) VALUES ".
"($this->id, ".(int)$pos.", ".
"'".addslashes($name)."', ".
***************
*** 271,280 ****
{
// Add more fields here
! $sortfields = array("name", "execName", array("addedDate", "p.id"),
! "userName", "onServer", "geneAverages", "serialFormat", "url");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT p.*, u.userName ".
"FROM Program p, Submitter u ".
"WHERE u.id = p.owner ".$search->getWhere()." ".
--- 272,282 ----
{
// Add more fields here
! $sortfields = array("name", "`execName`", array("`addedDate`", "p.id"),
! "`userName`", "`onServer`", "`geneAverages`", "`serialFormat`",
! "url");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT p.*, u.`userName` ".
"FROM Program p, Submitter u ".
"WHERE u.id = p.owner ".$search->getWhere()." ".
Index: protocol.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/protocol.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** protocol.inc.php 7 Sep 2002 11:36:32 -0000 1.7
--- protocol.inc.php 8 Sep 2002 22:38:08 -0000 1.8
***************
*** 82,86 ****
"descr = '".addslashes($this->descr)."', ".
"submitter = ".$this->submitter.", ".
! "fileId = ".$this->fileId." ".
"WHERE id = $this->id";
return query($query);
--- 82,86 ----
"descr = '".addslashes($this->descr)."', ".
"submitter = ".$this->submitter.", ".
! "`fileId` = ".$this->fileId." ".
"WHERE id = $this->id";
return query($query);
***************
*** 182,187 ****
{
$type = (int)$type;
! $query = "SELECT p.*, u.name AS fname, u.fileSize, ".
! "u.addedDate AS fdate, s.userName AS sname ".
"FROM Protocol p, Submitter s ".
"LEFT JOIN Upload u ON u.id = p.fileid ".
--- 182,187 ----
{
$type = (int)$type;
! $query = "SELECT p.*, u.name AS fname, u.`fileSize`, ".
! "u.`addedDate` AS fdate, s.`userName` AS sname ".
"FROM Protocol p, Submitter s ".
"LEFT JOIN Upload u ON u.id = p.fileid ".
***************
*** 203,207 ****
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res)) $arr[$row[0]] = $row[1];
return $arr;
}
--- 203,208 ----
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res))
! $arr[$row[0]] = $row[1];
return $arr;
}
Index: raw.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw.inc.php,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** raw.inc.php 7 Sep 2002 11:36:32 -0000 1.31
--- raw.inc.php 8 Sep 2002 22:38:08 -0000 1.32
***************
*** 87,99 ****
query($query);
$query = "DELETE FROM RawBioAssayData ".
! "WHERE rawBioAssay = $this->id";
query($query);
$query = "DELETE FROM RawBioAssayHeader ".
! "WHERE rawBioAssay = $this->id";
query($query);
// This is silly and will be deleted.
$query = "DELETE FROM ExperimentRawBioAssay ".
[...629 lines suppressed...]
$res2 = query($query);
! if($row2 =& db_fetch_row($res2)) $row[3] = $row2[0];
! else $row[3] = false;
}
$arr[] = $row;
--- 754,767 ----
else if($grouping == 2)
{
! $query = "SELECT h.`hybridizationDate` FROM RawBioAssay r, ".
"ImageAcquisition ia, Hybridization h ".
! "WHERE r.id = $row[3] AND ia.id = r.`imageAcquisition` ".
"AND h.id = ia.hybridization";
}
$res2 = query($query);
! if($row2 =& db_fetch_row($res2))
! $row[3] = $row2[0];
! else
! $row[3] = false;
}
$arr[] = $row;
Index: sampleannotation.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sampleannotation.inc.php,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** sampleannotation.inc.php 7 Sep 2002 11:36:32 -0000 1.15
--- sampleannotation.inc.php 8 Sep 2002 22:38:08 -0000 1.16
***************
*** 65,69 ****
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] = "'".addslashes($this->{$vars[$i]})."'";
$id = db_insert("SampleAnnotationType", $vars, $vals);
if(!$id)
--- 65,69 ----
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] =& $this->{$vars[$i]};
$id = db_insert("SampleAnnotationType", $vars, $vals);
[...108 lines suppressed...]
function getBrieferForSample($sample)
{
! $query = "SELECT sa.`annotationType`, sa.annotation ".
"FROM SampleAnnotation sa ".
! "WHERE sa.sample = ".(int)$sample." ORDER BY sa.`annotationType`";
$arr = array();
$res = query($query);
***************
*** 289,293 ****
$annotationType = (int)$annotationType;
$query = "DELETE FROM SampleAnnotation ".
! "WHERE sample = $sample AND annotationType = $annotationType";
query($query);
}
--- 293,297 ----
$annotationType = (int)$annotationType;
$query = "DELETE FROM SampleAnnotation ".
! "WHERE sample = $sample AND `annotationType` = $annotationType";
query($query);
}
Index: sampletissue.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sampletissue.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** sampletissue.inc.php 7 Sep 2002 11:36:32 -0000 1.7
--- sampletissue.inc.php 8 Sep 2002 22:38:08 -0000 1.8
***************
*** 80,84 ****
query($query);
if(db_affected_rows() <= 0) return false;
! $query = "UPDATE Sample SET tissue = $this->parent WHERE tissue = $this->id";
query($query);
return true;
--- 80,85 ----
query($query);
if(db_affected_rows() <= 0) return false;
! $query = "UPDATE Sample SET tissue = $this->parent ".
! "WHERE tissue = $this->id";
query($query);
return true;
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** search.inc.php 8 Sep 2002 13:18:04 -0000 1.35
--- search.inc.php 8 Sep 2002 22:38:08 -0000 1.36
***************
*** 140,144 ****
$search = (int)$search;
$query = "SELECT * FROM Preset ".
! "WHERE search = $search AND searchType = $searchType ".
"AND owner = ".(int)$owner;
return $this->readQuery($query);
--- 140,144 ----
$search = (int)$search;
$query = "SELECT * FROM Preset ".
! "WHERE search = $search AND `searchType` = $searchType ".
"AND owner = ".(int)$owner;
[...179 lines suppressed...]
$this->search = (int)$search;
$this->position = (int)$position;
! $query = "SELECT * FROM SearchCriterion ".
! "WHERE search = $this->search ".
"AND position = $this->position";
$res = query($query);
***************
*** 887,891 ****
{
$search = (int)$search;
! $query = "SELECT * FROM SearchCriterion WHERE search = $search ORDER BY position";
$res = query($query);
$arr = array();
--- 898,903 ----
{
$search = (int)$search;
! $query = "SELECT * FROM SearchCriterion ".
! "WHERE search = $search ORDER BY position";
$res = query($query);
$arr = array();
Index: session.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/session.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** session.inc.php 8 Sep 2002 14:46:58 -0000 1.5
--- session.inc.php 8 Sep 2002 22:38:08 -0000 1.6
***************
*** 44,49 ****
if($cookie != "") $this->cookie = $cookie;
! $query = "SELECT * FROM Cookie WHERE cookie = '".addslashes($this->cookie)."' ";
! if($ip != "") $query .= "AND IP = '".addslashes($ip)."'";
$res = query($query);
if($row =& db_fetch_assoc($res))
--- 44,51 ----
if($cookie != "") $this->cookie = $cookie;
! $query = "SELECT * FROM Cookie ".
[...91 lines suppressed...]
function justLoggedIn()
{
! $query = "SELECT u.userName FROM Cookie c, Submitter u ".
! "WHERE c.owner = u.id AND c.loginDate > NOW() - ".db_interval(200);
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res)) $arr[] = $row[0];
return $arr;
}
--- 215,224 ----
function justLoggedIn()
{
! $query = "SELECT u.`userName` FROM Cookie c, Submitter u ".
! "WHERE c.owner = u.id AND c.`loginDate` > NOW() - ".db_interval(200);
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res))
! $arr[] = $row[0];
return $arr;
}
Index: transformation.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/transformation.inc.php,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** transformation.inc.php 7 Sep 2002 12:04:26 -0000 1.14
--- transformation.inc.php 8 Sep 2002 22:38:08 -0000 1.15
***************
*** 139,144 ****
$query = "SELECT tr.* ".
"FROM Transformation tr, BioAssaySet bas ".
! "WHERE bas.experiment = $expid AND tr.bioAssaySet = bas.id ".
! "ORDER BY addedDate, id";
$res = query($query);
$arr = array();
--- 139,144 ----
$query = "SELECT tr.* ".
"FROM Transformation tr, BioAssaySet bas ".
! "WHERE bas.experiment = $expid AND tr.`bioAssaySet` = bas.id ".
[...118 lines suppressed...]
"AND bas.experiment = $expid";
$res = query($query);
! if($row =& db_fetch_row($res))
! return true;
return false;
}
***************
*** 226,230 ****
"WHERE p.id = j.program AND j.transformation = ".(int)$id;
$res = query($query);
! if($row =& db_fetch_row($res)) return $row[0];
return "";
}
--- 232,237 ----
"WHERE p.id = j.program AND j.transformation = ".(int)$id;
$res = query($query);
! if($row =& db_fetch_row($res))
! return $row[0];
return "";
}
Index: upload.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/upload.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** upload.inc.php 7 Sep 2002 11:36:32 -0000 1.19
--- upload.inc.php 8 Sep 2002 22:38:08 -0000 1.20
***************
*** 138,142 ****
$owner = (int)$owner;
$query = "SELECT * FROM Upload WHERE owner = $owner ".
! "AND !hidden ORDER BY addedDate";
$res = query($query);
$arr = array();
--- 138,142 ----
$owner = (int)$owner;
$query = "SELECT * FROM Upload WHERE owner = $owner ".
! "AND hidden = 0 ORDER BY `addedDate`";
$res = query($query);
[...116 lines suppressed...]
{
// Add more fields here
! $sortfields = array("name", "`fileSize`", "`addedDate`",
! "descr", "`userName`");
if($search->getSortField() == 4)
{
***************
*** 313,317 ****
$query = "SELECT up.* ".
"FROM Upload up". $search->getExtraTables()." ".
! "WHERE !up.hidden ".$search->getExtraWhere()." ".$search->getWhere().
" $ob ".$search->makeLimit();
--- 315,320 ----
$query = "SELECT up.* ".
"FROM Upload up". $search->getExtraTables()." ".
! "WHERE up.hidden = 0 ".$search->getExtraWhere()." ".
! $search->getWhere().
" $ob ".$search->makeLimit();
Index: user.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** user.inc.php 7 Sep 2002 11:36:32 -0000 1.5
--- user.inc.php 8 Sep 2002 22:38:08 -0000 1.6
***************
*** 94,100 ****
if($pass != "") $this->setPassword($pass);
$query = "SELECT * FROM Submitter ".
! "WHERE userName = '".addslashes($this->userName)."' ".
! "AND md5Pass = '".addslashes($this->md5Pass)."' ".
! "AND activeUntil >= NOW()";
return $this->readQuery($query);
}
--- 94,100 ----
if($pass != "") $this->setPassword($pass);
$query = "SELECT * FROM Submitter ".
[...183 lines suppressed...]
$ob = $search->makeOrderBy($sortfields);
$query = "SELECT u.*, ".
! "TO_DAYS(activeUntil) - TO_DAYS(NOW()) AS daysLeft, ".
! "(u.accessMask & (".BUA_SUPERUSER.")) AS superUser ".
"FROM Submitter u WHERE 1 ".$search->getWhere().
" $ob ".$search->makeLimit();
--- 373,384 ----
{
// Add more fields here
! $sortfields = array("`userName`", "name", "phone", "email",
! "`activeUntil`", "`superUser`", "`accessMask`");
$ob = $search->makeOrderBy($sortfields);
$query = "SELECT u.*, ".
! "TO_DAYS(`activeUntil`) - TO_DAYS(NOW()) AS `daysLeft`, ".
! "(u.`accessMask` & (".BUA_SUPERUSER.")) AS `superUser` ".
"FROM Submitter u WHERE 1 ".$search->getWhere().
" $ob ".$search->makeLimit();
Index: ware.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/ware.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** ware.inc.php 7 Sep 2002 11:36:32 -0000 1.8
--- ware.inc.php 8 Sep 2002 22:38:08 -0000 1.9
***************
*** 105,113 ****
// Add more fields here
$sortfields = array("shown", array("name", "version"),
! array("version", "name"), "addedDate", "userName");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT w.*, u.userName ".
"FROM $type w, Submitter u ".
"WHERE u.id = w.owner ".
--- 105,113 ----
// Add more fields here
$sortfields = array("shown", array("name", "version"),
! array("version", "name"), "`addedDate`", "`userName`");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT w.*, u.`userName` ".
"FROM $type w, Submitter u ".
"WHERE u.id = w.owner ".
***************
*** 115,120 ****
"$ob ".$search->makeLimit();
$arr = array();
! if(!($res = query($query))) return $arr;
! while($row =& db_fetch_assoc($res)) $arr[] = $row;
return $arr;
}
--- 115,122 ----
"$ob ".$search->makeLimit();
$arr = array();
! if(!($res = query($query)))
! return $arr;
! while($row =& db_fetch_assoc($res))
! $arr[] = $row;
return $arr;
}
***************
*** 169,173 ****
$res = query($query);
$arr = array();
! while($row =& db_fetch_assoc($res)) $arr[$row["id"]] = $row;
return $arr;
}
--- 171,176 ----
$res = query($query);
$arr = array();
! while($row =& db_fetch_assoc($res))
! $arr[$row["id"]] = $row;
return $arr;
}
***************
*** 236,240 ****
$res = query($query);
$arr = array();
! while($row =& db_fetch_assoc($res)) $arr[$row["id"]] = $row;
return $arr;
}
--- 239,244 ----
$res = query($query);
$arr = array();
! while($row =& db_fetch_assoc($res))
! $arr[$row["id"]] = $row;
return $arr;
}
Index: wizzzard.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/wizzzard.inc.php,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** wizzzard.inc.php 7 Sep 2002 11:36:32 -0000 1.24
--- wizzzard.inc.php 8 Sep 2002 22:38:08 -0000 1.25
***************
*** 63,67 ****
{
$vars = array("id", "owner", "etype", "name", "numCols",
! "extraCols", "dataHeader", "typeHeader", "typeHeaderLine", "mapping");
for($i = 0; $i < count($vars); $i++)
$this->$vars[$i] = $row[$vars[$i]];
--- 63,68 ----
{
$vars = array("id", "owner", "etype", "name", "numCols",
! "extraCols", "dataHeader", "typeHeader", "typeHeaderLine",
! "mapping");
for($i = 0; $i < count($vars); $i++)
$this->$vars[$i] = $row[$vars[$i]];
***************
*** 83,87 ****
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] = "'".addslashes($this->{$vars[$i]})."'";
$id = db_insert("Wizzzard", $vars, $vals);
if(!$id)
--- 84,88 ----
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] =& $this->{$vars[$i]};
$id = db_insert("Wizzzard", $vars, $vals);
if(!$id)
***************
*** 93,97 ****
{
for($i = 0; $i < count($vars); $i++)
! $vars[$i] = "$vars[$i] = '".addslashes($this->{$vars[$i]})."'";
$query = "UPDATE Wizzzard SET ".implode(", ", $vars)." ".
"WHERE id = $this->id";
--- 94,98 ----
{
for($i = 0; $i < count($vars); $i++)
! $vars[$i] = "`$vars[$i]` = '".addslashes($this->{$vars[$i]})."'";
$query = "UPDATE Wizzzard SET ".implode(", ", $vars)." ".
"WHERE id = $this->id";
***************
*** 671,679 ****
$ownerId = (int)$ownerId;
// Add more fields here
! $sortfields = array("name", "userName", "extraCols", "useWiz");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT w.*, u.userName, (wu.owner IS NOT NULL) AS useWiz ".
"FROM Wizzzard w, Submitter u ".
"LEFT JOIN WizzzardUser wu ON wu.wizzzard = w.id ".
--- 672,681 ----
$ownerId = (int)$ownerId;
// Add more fields here
! $sortfields = array("name", "`userName`", "`extraCols`", "`useWiz`");
$ob = $search->makeOrderBy($sortfields);
! $query = "SELECT w.*, u.`userName`, ".
! "(wu.owner IS NOT NULL) AS `useWiz` ".
"FROM Wizzzard w, Submitter u ".
"LEFT JOIN WizzzardUser wu ON wu.wizzzard = w.id ".
***************
*** 713,717 ****
$query = "SELECT owner FROM Wizzzard WHERE id = ".(int)$id;
$res = query($query);
! if($row =& db_fetch_row($res)) return $row[0] == (int)$owner;
return false;
}
--- 715,720 ----
$query = "SELECT owner FROM Wizzzard WHERE id = ".(int)$id;
$res = query($query);
! if($row =& db_fetch_row($res))
! return $row[0] == (int)$owner;
return false;
}
|
|
From: <tr...@us...> - 2002-09-08 22:37:29
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv25321
Modified Files:
mysql.inc.php pgsql.inc.php
Log Message:
re-added multiinsert
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** mysql.inc.php 8 Sep 2002 18:05:24 -0000 1.7
--- mysql.inc.php 8 Sep 2002 22:37:25 -0000 1.8
***************
*** 180,184 ****
}
! /*function db_multiinsert_begin($table, $columns)
{
$res = array($table, $columns, array());
--- 180,184 ----
}
! function db_multiinsert_begin($table, $columns)
{
$res = array($table, $columns, array());
***************
*** 205,209 ****
return -1;
return mysql_affected_rows();
! }*/
function db_tabfile_load($filename, $table, $columns)
--- 205,209 ----
return -1;
return mysql_affected_rows();
! }
function db_tabfile_load($filename, $table, $columns)
Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** pgsql.inc.php 8 Sep 2002 14:50:02 -0000 1.3
--- pgsql.inc.php 8 Sep 2002 22:37:25 -0000 1.4
***************
*** 36,40 ****
"dbname = '".addslashes($database)."'";
$this->serv = pg_pconnect($cstring)
! or die("pg_pconnect() failed: ".pg_last_error()."\n");
}
--- 36,40 ----
"dbname = '".addslashes($database)."'";
$this->serv = pg_pconnect($cstring)
! or die("pg_pconnect() failed: ".pg_last_error());
}
[...220 lines suppressed...]
+ }
+ else if($s == 1)
+ {
+ if($c == "'") $s = 0;
+ else if($c == "\\") $s = 2;
+ $q2 .= $c;
+ }
+ else
+ {
+ $s = 1;
+ $q2 .= $c;
+ }
+ }
+ if($s != 0)
+ {
+ error_log("db_pgsql_requote: error in query string (final state: ".
+ ($s == 1 ? "quoted" : "backslashed").")");
+ }
}
|
|
From: <tr...@us...> - 2002-09-08 18:05:28
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv22821
Modified Files:
mysql.inc.php
Log Message:
Added forgotten escaping in db_insert
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** mysql.inc.php 8 Sep 2002 14:50:02 -0000 1.6
--- mysql.inc.php 8 Sep 2002 18:05:24 -0000 1.7
***************
*** 93,99 ****
function db_insert($table, &$columns, &$values)
{
$query = "INSERT INTO $table (".implode(", ", $columns).") ".
! "VALUES (".implode(", ", $values).")";
! if(!query($query)) return false;
return mysql_insert_id();
}
--- 93,104 ----
function db_insert($table, &$columns, &$values)
{
+ $arr = array();
+ for(reset($values); list(, $v) = each($values); )
+ $arr[] = "'".addslashes($v)."'";
+
$query = "INSERT INTO $table (".implode(", ", $columns).") ".
! "VALUES (".implode(", ", $arr).")";
! if(!query($query))
! return false;
return mysql_insert_id();
}
|
|
From: <tr...@us...> - 2002-09-08 14:50:05
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv11433
Modified Files:
mysql.inc.php pgsql.inc.php
Log Message:
Added missing 'function' keyword
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** mysql.inc.php 8 Sep 2002 14:46:58 -0000 1.5
--- mysql.inc.php 8 Sep 2002 14:50:02 -0000 1.6
***************
*** 250,254 ****
// Return a representation of a time interval
! db_interval($secs)
{
return "INTERVAL ".(int)$secs." SECOND";
--- 250,254 ----
// Return a representation of a time interval
! function db_interval($secs)
{
return "INTERVAL ".(int)$secs." SECOND";
Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** pgsql.inc.php 8 Sep 2002 14:46:58 -0000 1.2
--- pgsql.inc.php 8 Sep 2002 14:50:02 -0000 1.3
***************
*** 249,253 ****
// Return a representation of a time interval
! db_interval($secs)
{
return "INTERVAL '".(int)$secs." s'";
--- 249,253 ----
// Return a representation of a time interval
! function db_interval($secs)
{
return "INTERVAL '".(int)$secs." s'";
|
|
From: <tr...@us...> - 2002-09-08 14:48:03
|
Update of /cvsroot/basedb/basedb
In directory usw-pr-cvs1:/tmp/cvs-serv10876
Added Files:
base_pg.sql
Log Message:
Structure and data for postgresql
--- NEW FILE: base_pg.sql ---
--
-- Selected TOC Entries:
--
\connect base base
--
-- TOC Entry ID 2 (OID 1099523)
--
-- Name: array_id_seq Type: SEQUENCE Owner: postgres
--
CREATE SEQUENCE array_id_seq start 1 increment 1 maxvalue 9223372036854775807 minvalue 1 cache 1;
--
-- TOC Entry ID 98 (OID 1099525)
--
-- Name: Array Type: TABLE Owner: postgres
--
[...2221 lines suppressed...]
--
-- TOC Entry ID 247 (OID 1100079)
--
-- Name: name_sample_index Type: INDEX Owner: postgres
--
CREATE UNIQUE INDEX name_sample_index ON Sample USING btree (name);
SELECT setval ('program_id_seq', 5, true);
SELECT setval ('protocol_id_seq', 13, true);
SELECT setval ('protocoltype_id_seq', 15, true);
SELECT setval ('submitter_id_seq', 2, true);
SELECT setval ('sampletissue_id_seq', 2, true);
|
|
From: <tr...@us...> - 2002-09-08 14:47:04
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv10601
Modified Files:
molecule.inc.php mysql.inc.php pgsql.inc.php session.inc.php
Log Message:
Added db_interval function to deal with different time interval representations
Index: molecule.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/molecule.inc.php,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** molecule.inc.php 7 Sep 2002 11:36:32 -0000 1.26
--- molecule.inc.php 8 Sep 2002 14:46:57 -0000 1.27
***************
*** 603,607 ****
$secs = (int)$secs;
$query = "SELECT id FROM Molecule ".
! "WHERE lastUpdate < NOW() - INTERVAL $secs SECOND ".
"ORDER BY lastUpdate";
$res = query($query);
--- 603,607 ----
$secs = (int)$secs;
$query = "SELECT id FROM Molecule ".
! "WHERE lastUpdate < NOW() - ".db_interval($secs)." ".
"ORDER BY lastUpdate";
$res = query($query);
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** mysql.inc.php 8 Sep 2002 13:17:08 -0000 1.4
--- mysql.inc.php 8 Sep 2002 14:46:58 -0000 1.5
***************
*** 249,251 ****
--- 249,257 ----
}
+ // Return a representation of a time interval
+ db_interval($secs)
+ {
+ return "INTERVAL ".(int)$secs." SECOND";
+ }
+
?>
Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/pgsql.inc.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** pgsql.inc.php 8 Sep 2002 13:15:59 -0000 1.1
--- pgsql.inc.php 8 Sep 2002 14:46:58 -0000 1.2
***************
*** 60,64 ****
function &db_fetch_assoc(&$r)
{
! return pg_fetch_array($GLOBALS["curDb"]->serv, $r, PGSQL_ASSOC);
}
function db_num_rows(&$r)
--- 60,66 ----
function &db_fetch_assoc(&$r)
{
! // print_r(get_defined_vars());
! // return pg_fetch_array($GLOBALS["curDb"]->serv, $r, PGSQL_ASSOC);
! return pg_fetch_array($r);
}
function db_num_rows(&$r)
***************
*** 73,82 ****
function query(&$query, $quiet = 0)
{
! // error_log("Q: $query");
$res = pg_query($query);
if(!$res && !$quiet)
error_log("PostgresSQL query failed: \"".$query."\" : ".pg_last_error());
! $GLOBALS["curDb"]->affected = pg_affected_rows($res);
return $res;
}
--- 75,87 ----
function query(&$query, $quiet = 0)
{
! error_log("Q: $query");
$res = pg_query($query);
if(!$res && !$quiet)
error_log("PostgresSQL query failed: \"".$query."\" : ".pg_last_error());
! if($res)
! $GLOBALS["curDb"]->affected = pg_affected_rows($res);
! else
! $GLOBALS["curDb"]->affected = -1;
return $res;
}
***************
*** 114,118 ****
$arr = array();
for($i = 0; $i < count($keycolumns) - 1; $i++)
! $arr[] = "$keycolumns[$i] = '".addslashes($keyvalues[$i])."'"
$query = "SELECT MAX($lastcol) FROM $table ".
--- 119,123 ----
$arr = array();
for($i = 0; $i < count($keycolumns) - 1; $i++)
! $arr[] = "$keycolumns[$i] = '".addslashes($keyvalues[$i])."'";
$query = "SELECT MAX($lastcol) FROM $table ".
***************
*** 241,244 ****
--- 246,255 ----
}
return true;
+ }
+
+ // Return a representation of a time interval
+ db_interval($secs)
+ {
+ return "INTERVAL '".(int)$secs." s'";
}
Index: session.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/session.inc.php,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** session.inc.php 7 Sep 2002 11:36:32 -0000 1.4
--- session.inc.php 8 Sep 2002 14:46:58 -0000 1.5
***************
*** 195,199 ****
$secsToLive = (int)$secsToLive;
$query = "DELETE FROM Cookie ".
! "WHERE lastseen < NOW() - INTERVAL $secsToLive SECOND";
query($query);
}
--- 195,199 ----
$secsToLive = (int)$secsToLive;
$query = "DELETE FROM Cookie ".
! "WHERE lastseen < NOW() - ".db_interval($secsToLive);
query($query);
}
***************
*** 210,214 ****
{
$query = "SELECT u.userName FROM Cookie c, Submitter u ".
! "WHERE c.owner = u.id AND c.loginDate > NOW() - INTERVAL 200 SECOND";
$res = query($query);
$arr = array();
--- 210,214 ----
{
$query = "SELECT u.userName FROM Cookie c, Submitter u ".
! "WHERE c.owner = u.id AND c.loginDate > NOW() - ".db_interval(200);
$res = query($query);
$arr = array();
|
|
From: <tr...@us...> - 2002-09-08 14:02:45
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv636
Modified Files:
genelist.inc.php
Log Message:
ugly fix for auto_increment in temp table
Index: genelist.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/genelist.inc.php,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** genelist.inc.php 7 Sep 2002 13:12:13 -0000 1.17
--- genelist.inc.php 8 Sep 2002 14:02:42 -0000 1.18
***************
*** 237,240 ****
--- 237,242 ----
function populateFromQuery($moleculequery)
{
+ global $config;
+
// Previously it was possible to select directly into GeneListGene
// if no genelist was used in the select, but with the new 'score'
***************
*** 249,259 ****
return -1;
}
$res = -1;
$moleculequery = "INSERT INTO GeneListTemp (molecule) ".$moleculequery;
! if(query($moleculequery))
{
$query = "INSERT INTO GeneListGene (geneList, molecule, score) ".
"SELECT $this->id, molecule, score FROM GeneListTemp";
! if(query($query)) $res = db_affected_rows();
}
db_table_drop("GeneListTemp");
--- 251,273 ----
return -1;
}
+ if($config["RDBMS"] != "mysql")
+ {
+ $query = "CREATE TEMPORARY SEQUENCE genelisttemp_score_seq";
+ query($query);
+ }
$res = -1;
$moleculequery = "INSERT INTO GeneListTemp (molecule) ".$moleculequery;
! $tmp = query($moleculequery);
! if($config["RDBMS"] != "mysql")
! {
! $query = "DROP SEQUENCE genelisttemp_score_seq";
! query($query);
! }
! if($tmp)
{
$query = "INSERT INTO GeneListGene (geneList, molecule, score) ".
"SELECT $this->id, molecule, score FROM GeneListTemp";
! if(query($query))
! $res = db_affected_rows();
}
db_table_drop("GeneListTemp");
|
|
From: <tr...@us...> - 2002-09-08 13:19:03
|
Update of /cvsroot/basedb/basedb In directory usw-pr-cvs1:/tmp/cvs-serv20157 Modified Files: example_config.inc.php Log Message: Added config item 'RDBMS' Index: example_config.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/example_config.inc.php,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** example_config.inc.php 30 Jul 2002 16:57:34 -0000 1.4 --- example_config.inc.php 8 Sep 2002 13:19:00 -0000 1.5 *************** *** 30,34 **** $config["sessionTimeout"] = 900; ! // MySQL details: Host, user, password, main database, database for // dynamic tables (can be the same as the main database, but it's not // recommended as it'll get awfully cluttered). --- 30,38 ---- $config["sessionTimeout"] = 900; ! // What relational database management system to use. ! // Possible values: mysql, pgsql ! $config["RDBMS"] = "mysql"; ! ! // Database settings: Host, user, password, main database, database for // dynamic tables (can be the same as the main database, but it's not // recommended as it'll get awfully cluttered). |
|
From: <tr...@us...> - 2002-09-08 13:18:36
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv20077
Modified Files:
common.inc.php db.inc.php
Log Message:
Added config item 'RDBMS'
Index: common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/common.inc.php,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** common.inc.php 23 Aug 2002 13:13:58 -0000 1.17
--- common.inc.php 8 Sep 2002 13:18:33 -0000 1.18
***************
*** 33,40 ****
die("Configuration error - see log for details");
}
! $cfgvars = array("sessionTimeout", "dbHost", "dbUser", "dbPassword",
! "dbDatabase", "dbDynamic", "cookieName", "adminName", "adminEmail",
! "uploadDir", "tempDir", "jobDir", "rawFileDir", "rawImageDir",
! "printMapDir", "execDir", "webDir", "gnuplot", "mime.types");
foreach($cfgvars as $v)
{
--- 33,41 ----
die("Configuration error - see log for details");
}
! $cfgvars = array("sessionTimeout", "RDBMS", "dbHost", "dbUser",
! "dbPassword", "dbDatabase", "dbDynamic", "cookieName", "adminName",
! "adminEmail", "uploadDir", "tempDir", "jobDir", "rawFileDir",
! "rawImageDir", "printMapDir", "execDir", "webDir", "gnuplot",
! "mime.types");
foreach($cfgvars as $v)
{
***************
*** 49,53 ****
unset($v);
! // This appeared before we had chosen the name 'BASE'.
$config["codename"] = "BASE 1.1dev";
--- 50,56 ----
unset($v);
! // This appeared before we had chosen the name 'BASE'. It used to be in
! // the config file but then it wasn't updated with each new version and
! // that was... well, not a Good Thing.
$config["codename"] = "BASE 1.1dev";
Index: db.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/db.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** db.inc.php 7 Sep 2002 11:36:32 -0000 1.10
--- db.inc.php 8 Sep 2002 13:18:33 -0000 1.11
***************
*** 25,29 ****
//
! require_once("mysql.inc.php");
?>
--- 25,29 ----
//
! require_once("$config[RDBMS].inc.php");
?>
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From: <tr...@us...> - 2002-09-08 13:18:06
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv19979
Modified Files:
search.inc.php
Log Message:
moved some escaping to db_insert_multicol
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** search.inc.php 7 Sep 2002 11:36:32 -0000 1.34
--- search.inc.php 8 Sep 2002 13:18:04 -0000 1.35
***************
*** 805,814 ****
if($this->position < 1)
{
- $vars[] = "search";
$keycols = array("search", "position");
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] = "'".addslashes($this->{$vars[$i]})."'";
! $pos = db_insert_multicol("SearchCriterion", $keycols, $vars, $vals);
if(!$pos)
return false;
--- 805,815 ----
if($this->position < 1)
{
$keycols = array("search", "position");
+ $keyvals = array($this->search);
$vals = array();
for($i = 0; $i < count($vars); $i++)
! $vals[] =& $this->{$vars[$i]};
! $pos = db_insert_multicol("SearchCriterion",
! $keycols, $keyvals, $vars, $vals);
if(!$pos)
return false;
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From: <tr...@us...> - 2002-09-08 13:17:11
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv19778
Modified Files:
mysql.inc.php
Log Message:
Fixed missing escaping
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** mysql.inc.php 7 Sep 2002 13:12:13 -0000 1.3
--- mysql.inc.php 8 Sep 2002 13:17:08 -0000 1.4
***************
*** 91,97 ****
// a column called 'id' as its primary key. The id of the newly inserted
// row is returned.
! function db_insert($table, &$names, &$values)
{
! $query = "INSERT INTO $table (".implode(", ", $names).") ".
"VALUES (".implode(", ", $values).")";
if(!query($query)) return false;
--- 91,97 ----
// a column called 'id' as its primary key. The id of the newly inserted
// row is returned.
! function db_insert($table, &$columns, &$values)
{
! $query = "INSERT INTO $table (".implode(", ", $columns).") ".
"VALUES (".implode(", ", $values).")";
if(!query($query)) return false;
***************
*** 106,114 ****
// This is the behavior you get with auto_increment on the non-first
// column of a primary key in MySQL.
! function db_insert_multicol($table, &$keycolumns, &$names, &$values)
{
! $query = "INSERT INTO $table (".implode(", ", $names).") ".
! "VALUES (".implode(", ", $values).")";
! if(!query($query)) return false;
return mysql_insert_id();
}
--- 106,123 ----
// This is the behavior you get with auto_increment on the non-first
// column of a primary key in MySQL.
! function db_insert_multicol($table, &$keycolumns, &$keyvalues,
! &$columns, &$values)
{
! $arr = array();
! for(reset($keyvalues); list(, $v) = each($keyvalues); )
! $arr[] = "'".addslashes($v)."'";
! for(reset($values); list(, $v) = each($values); )
! $arr[] = "'".addslashes($v)."'";
! $allcols = array_merge($keycolumns, $columns);
!
! $query = "INSERT INTO $table (".implode(", ", $allcols).") ".
! "VALUES (".implode(", ", $arr).")";
! if(!query($query))
! return false;
return mysql_insert_id();
}
***************
*** 147,154 ****
$arr[] = "'".addslashes($v)."'";
$query = "INSERT INTO $table ".
! "(".implode(",", $keys).",".implode(",", $columns).") ".
"VALUES (".implode(",", $arr).")";
! return query($query) && mysql_affected_rows() > 0;
}
--- 156,164 ----
$arr[] = "'".addslashes($v)."'";
+ $allcols = array_merge($keys, $columns);
$query = "INSERT INTO $table ".
! "(".implode(",", $allcols).") ".
"VALUES (".implode(",", $arr).")";
! return (bool)query($query);
}
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From: <tr...@us...> - 2002-09-08 13:16:02
|
Update of /cvsroot/basedb/basedb/www In directory usw-pr-cvs1:/tmp/cvs-serv19569 Added Files: pgsql.inc.php Log Message: First untested attempt at postgresql compatibility --- NEW FILE: pgsql.inc.php --- <? // $Id: pgsql.inc.php,v 1.1 2002/09/08 13:15:59 troein Exp $ // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson (LSCTJVC) // // Write to LSCTJVC, Dept. of Oncology, Lund University Hospital, // Klinikgatan 7, SE-22185, Lund, Sweden. // // 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 [...206 lines suppressed...] $query = "CREATE $tmp TABLE $to () INHERITS ($from)"; return (bool)query($query); } // This function drops a table quietly. It exists because we want to use // persistent connections and we might come across temporary tables that // haven't been deleted because of script errors. function db_table_drop($table) { $query = "DROP TABLE $table"; if(!pg_query($query) && pg_last_error() != "ERROR: table \"$table\" does not exist") { error_log("PostgresSQL query failed: \"".$query."\" : ".pg_last_error()); return false; } return true; } ?> |
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From: <tr...@us...> - 2002-09-07 13:12:16
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv10570
Modified Files:
genelist.inc.php mysql.inc.php
Log Message:
made the multiinsert functions unnecessary
Index: genelist.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/genelist.inc.php,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** genelist.inc.php 7 Sep 2002 11:36:32 -0000 1.16
--- genelist.inc.php 7 Sep 2002 13:12:13 -0000 1.17
***************
*** 191,199 ****
--- 191,203 ----
function populate(&$genes, $append = false)
{
+ $iua = ignore_user_abort(1);
if(!$append)
{
$query = "DELETE FROM GeneListGene WHERE geneList = $this->id";
if(!query($query))
+ {
+ ignore_user_abort($iua);
return false;
+ }
}
else
***************
*** 203,220 ****
"AND molecule IN (".implode(",", array_keys($genes)).")";
if(!query($query))
return false;
}
! $mi = db_multiinsert_begin("GeneListGene",
! array("geneList", "molecule", "score"));
! for(reset($genes); list($i,$v) = each($genes);)
{
! $arr = array($this->id, (int)$i, (float)$v);
! db_multiinsert_row($mi, $arr);
}
! unset($arr);
! $added = db_multiinsert_finish($mi);
$this->updateGeneCount();
return $added;
}
--- 207,232 ----
"AND molecule IN (".implode(",", array_keys($genes)).")";
if(!query($query))
+ {
+ ignore_user_abort($iua);
return false;
+ }
}
! $fname = tempFileName();
! $fd = fopen($fname, "wb");
! if(!$fd)
{
! ignore_user_abort($iua);
! return false;
}
! for(reset($genes); list($i,$v) = each($genes);)
! fwrite($fd, $this->id."\t".(int)$i."\t".(float)$v."\n");
! fclose($fd);
+ $added = db_tabfile_load($fname, "GeneListGene",
+ array("geneList", "molecule", "score"));
+ unlink($fname);
$this->updateGeneCount();
+ ignore_user_abort($iua);
return $added;
}
Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** mysql.inc.php 7 Sep 2002 12:04:05 -0000 1.2
--- mysql.inc.php 7 Sep 2002 13:12:13 -0000 1.3
***************
*** 165,169 ****
}
! function db_multiinsert_begin($table, $columns)
{
$res = array($table, $columns, array());
--- 165,169 ----
}
! /*function db_multiinsert_begin($table, $columns)
{
$res = array($table, $columns, array());
***************
*** 190,194 ****
return -1;
return mysql_affected_rows();
! }
function db_tabfile_load($filename, $table, $columns)
--- 190,194 ----
return -1;
return mysql_affected_rows();
! }*/
function db_tabfile_load($filename, $table, $columns)
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From: <tr...@us...> - 2002-09-07 13:11:48
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv10476
Modified Files:
genelist_edit.phtml
Log Message:
improved how the form retains values on failure
Index: genelist_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/genelist_edit.phtml,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** genelist_edit.phtml 29 Aug 2002 16:51:33 -0000 1.13
--- genelist_edit.phtml 7 Sep 2002 13:11:44 -0000 1.14
***************
*** 185,192 ****
<tr><th colspan=4>Alter the reporter list</th></tr>
<tr><th>Mode of operation</th><td colspan=3><select name=i_append>
- <option value=0>Replace the entire list
- <option value=1>Append reporters to list
- </select></td></tr>
<?
}
--- 185,196 ----
<tr><th colspan=4>Alter the reporter list</th></tr>
<tr><th>Mode of operation</th><td colspan=3><select name=i_append>
<?
+ $modes = array("Replace the entire list", "Append/update reporters");
+ for(reset($modes); list($i, $n) = each($modes); )
+ {
+ $sel = (isset($i_append) && $i_append == $i) ? "selected" : "";
+ echo "<option value=$i $sel>".html($n, 0)."\n";
+ }
+ echo "</select></td></tr>\n";
}
***************
*** 220,227 ****
isset($i_col) ? (int)$i_col : "" ?>" size=5></td></tr>
<tr><th>Value column</th>
! <td><input type=text name=i_vcol value="<?=
! isset($i_vcol) ? (int)$i_vcol : "" ?>" size=5></td>
! <td class=help colspan=2>Leave this blank to get values from 1
! and up</td></tr>
<tr><td colspan=4><input type=submit value="Accept"></td></tr>
--- 224,231 ----
isset($i_col) ? (int)$i_col : "" ?>" size=5></td></tr>
<tr><th>Value column</th>
! <td colspan=3><input type=text name=i_vcol value="<?=
! (isset($i_vcol) && $i_vcol > 0) ? (int)$i_vcol : "" ?>" size=5>
! <span class=help>Leave this blank to get values from 1
! and up</span></td></tr>
<tr><td colspan=4><input type=submit value="Accept"></td></tr>
|
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From: <tr...@us...> - 2002-09-07 12:04:30
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv28493
Modified Files:
transformation.inc.php
Log Message:
removed debug info
Index: transformation.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/transformation.inc.php,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** transformation.inc.php 7 Sep 2002 11:36:32 -0000 1.13
--- transformation.inc.php 7 Sep 2002 12:04:26 -0000 1.14
***************
*** 50,56 ****
{
$n = $this->id;
! $r = parent::write(array("bioAssaySet", "isFilter"));
! error_log(($n ? "Updated" : "Created") . "Transformation $this->id");
! return $r;
}
--- 50,54 ----
{
$n = $this->id;
! return parent::write(array("bioAssaySet", "isFilter"));
}
***************
*** 61,65 ****
{
$id = $this->id;
- error_log("Removing Transformation $id");
Search::removeAllForTransformation($id);
--- 59,62 ----
***************
*** 235,260 ****
function lockId($id, $exclusive)
{
! $r = parent::lockItem("Transformation", $id, $exclusive);
! error_log("Transformation $id lockId (".(int)$exclusive."): ".(int)$r);
! return $r;
}
function unlockId($id, $exclusive)
{
! $r = parent::unlockItem("Transformation", $id, $exclusive);
! error_log("Transformation $id unlockId (".(int)$exclusive."): ".(int)$r);
! return $r;
! }
!
! function lock($exclusive)
! {
! $r = parent::lock($exclusive);
! error_log("Transformation $this->id lock (".(int)$exclusive."): ".(int)$r);
! return $r;
! }
! function unlock($exclusive)
! {
! $r = parent::unlock($exclusive);
! error_log("Transformation $this->id unlock (".(int)$exclusive."): ".(int)$r);
! return $r;
}
--- 232,240 ----
function lockId($id, $exclusive)
{
! return parent::lockItem("Transformation", $id, $exclusive);
}
function unlockId($id, $exclusive)
{
! return parent::unlockItem("Transformation", $id, $exclusive);
}
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