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[basedb-cvs] basedb/include/classes basecontrol.inc.php,1.8,1.9 basefile.inc.php,1.5,1.6 bioassayset.inc.php,1.20,1.21 ftpd.inc.php,1.2,1.3 jobhandler.inc.php,1.8,1.9 upload.inc.php,1.14,1.15
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv29789/include/classes
Modified Files:
basecontrol.inc.php basefile.inc.php bioassayset.inc.php
ftpd.inc.php jobhandler.inc.php upload.inc.php
Log Message:
Work done on laptop in Gothenburg - no time for more detailed message
Index: basecontrol.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/basecontrol.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** basecontrol.inc.php 30 Jan 2003 16:44:38 -0000 1.8
--- basecontrol.inc.php 10 Feb 2003 08:40:42 -0000 1.9
***************
*** 85,102 ****
}
function awaitUp($secs = 3600)
{
! $secs = (int)$secs;
! while($secs >= 0)
{
- if($this->mayRun() && db_verify_connection())
- {
- $query = "SELECT 1 FROM BaseControl WHERE `shutDown` = 0";
[...89 lines suppressed...]
{
$query = "UPDATE BaseControl SET `shutDown` = 0 ".
"WHERE `shutDown` = 1";
+ if(!$ignorePending)
+ $query .= " AND `pendingTransactions` = 0";
if(!query($query) || db_affected_rows() != 1)
return false;
***************
*** 217,221 ****
if(!db_verify_connection())
return false;
! if(!$this->abortShutdown())
return false;
$query = "UPDATE BaseControl SET `startTime` = NOW()";
--- 236,240 ----
if(!db_verify_connection())
return false;
! if(!$this->abortShutdown(false))
return false;
$query = "UPDATE BaseControl SET `startTime` = NOW()";
Index: basefile.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/basefile.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** basefile.inc.php 1 Feb 2003 17:18:50 -0000 1.5
--- basefile.inc.php 10 Feb 2003 08:40:42 -0000 1.6
***************
*** 162,166 ****
// value is the empty string. If the file is not a BASEfile, the special
// string "NOBASE" is returned.
! function countSections($filename, &$sections, &$assays)
{
// Use the external program, which also tracks assays
--- 162,168 ----
// value is the empty string. If the file is not a BASEfile, the special
// string "NOBASE" is returned.
! // $extraFloats is an array which will contain the names of extra data
! // columns (of type float) for the bioassayset (as keys).
[...80 lines suppressed...]
! if($t[1] == "")
! $par = array();
else
! $par = explode("/", $t[1]);
! $assays[$t[0]] = array($par, $t[2]);
}
+ else
+ $assays[$t[0]] = array(array($t[0]), "");
}
}
! else if($mode == 2)
{
! $extraFloats = array_flip(explode("\t", $res[$i]));
! unset($extraFloats[""]);
}
}
+ if($mode != 2)
+ return "Invalid output from sectionCounter (case 2)";
return "";
}
Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassayset.inc.php,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** bioassayset.inc.php 3 Feb 2003 20:13:17 -0000 1.20
--- bioassayset.inc.php 10 Feb 2003 08:40:42 -0000 1.21
***************
*** 636,639 ****
--- 636,642 ----
{
global $config;
+
+ BioAssaySet::makeGeneSearchWhere($search);
+
$query = "INSERT ".
"INTO $config[dbDynamic]BioAssayData$this->experiment ".
Index: ftpd.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/ftpd.inc.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ftpd.inc.php 4 Feb 2003 18:29:48 -0000 1.2
--- ftpd.inc.php 10 Feb 2003 08:40:44 -0000 1.3
***************
*** 25,28 ****
--- 25,29 ----
require_once("user.inc.php");
require_once("upload.inc.php");
+ require_once("search.inc.php");
class ftpd
***************
*** 40,44 ****
var $dirType; // What sort of directory we're in - uploads, printmaps etc.
var $dirUser; // UserAccount object for owner of current dir, or NULL
[...1029 lines suppressed...]
+ }
+
+ if(!$this->mayAlterHere())
+ {
+ echo "550 Access denied\r\n";
+ $this->loadDirState($dirstate);
+ return;
+ }
+
+ $fname = explode("/", $arg);
+ $fname = $fname[count($fname) - 1];
+
+ $func = $this->dirType."DeleteFile";
+ $this->$func($fname);
+
+ $this->loadDirState($dirstate);
+ }
+
function comSYST()
Index: jobhandler.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/jobhandler.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** jobhandler.inc.php 2 Feb 2003 15:31:51 -0000 1.8
--- jobhandler.inc.php 10 Feb 2003 08:40:45 -0000 1.9
***************
*** 277,281 ****
$sects = false;
$assays = false;
! $err = BaseFileInfo::countSections($jf->getName(), $sects, $assays);
if($err != "")
{
--- 277,283 ----
$sects = false;
$assays = false;
! $extraFloats = false;
! $err = BaseFileInfo::countSections($jf->getName(), $sects, $assays,
! $extraFloats);
if($err != "")
{
***************
*** 312,316 ****
if($assays)
{
! $err = $this->createChildSet($jf->getName(), $assays);
if($err != "")
$job->appendResultText($err);
--- 314,318 ----
if($assays)
{
! $err = $this->createChildSet($jf->getName(), $assays, $extraFloats);
if($err != "")
$job->appendResultText($err);
***************
*** 325,329 ****
// $assayids is an array from identifier to array(array(parents),name).
! function createChildSet($fname, &$assayids)
{
// These used to be function arguments
--- 327,331 ----
// $assayids is an array from identifier to array(array(parents),name).
! function createChildSet($fname, &$assayids, &$extraFloats)
{
// These used to be function arguments
Index: upload.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/upload.inc.php,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** upload.inc.php 4 Feb 2003 18:28:59 -0000 1.14
--- upload.inc.php 10 Feb 2003 08:40:46 -0000 1.15
***************
*** 37,41 ****
$this->fileSize = 0;
$this->mimeType = "";
! $this->addedDate = "" ? now() : strtodatetime($addedDate);
}
--- 37,42 ----
$this->fileSize = 0;
$this->mimeType = "";
! $this->addedDate =
! $addedDate == "" ? now() : strtodatetime($addedDate);
[...102 lines suppressed...]
+ function updateFileSize($val)
+ {
+ $this->fileSize = (int)$val;
+ return Item::updateColumn("Upload", $this->id, "fileSize",
+ $this->fileSize);
+ }
+
// Returns all users as an array of (id,name,lastChanged,cnt)
function getUserSummaryList(&$user)
{
$query = "SELECT ug.id, ug.name, ".
! "MAX(u.`addedDate`) AS `lastChanged`, COUNT(u.id) AS cnt ".
"FROM UserGroup ug LEFT JOIN Upload u ".
"ON ug.id = u.owner ".
Item::whereRemovedAnd("u", 0)." ".
"AND ".Item::whereShared("u", $user)." ".
+ "WHERE ".Item::whereRemoved("ug", 0)." ".
+ "AND ug.isAccount = 1 ".
"GROUP BY ug.name, ug.id ORDER BY ug.name";
$res = query($query);
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