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From: <tr...@us...> - 2003-02-03 13:38:16
|
Update of /cvsroot/basedb/basedb In directory sc8-pr-cvs1:/tmp/cvs-serv4933 Modified Files: ChangeLog Removed Files: CHANGES Log Message: merged old CHANGES with ChangeLog Index: ChangeLog =================================================================== RCS file: /cvsroot/basedb/basedb/ChangeLog,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** ChangeLog 13 Dec 2002 21:59:15 -0000 1.7 --- ChangeLog 3 Feb 2003 13:38:13 -0000 1.8 *************** *** 1,2 **** --- 1,15 ---- + *** 2003-02-03 + * A large number of changes, including: + * Extensible BioAssay columns (not yet fully implemented) + * Restructured directory tree + * Added backup script + * Added default group for users, upload quotas. + * Added reporter maps as alternative to print maps + * Improved and unified plotters + * Added list of raw spots, made it possible to choose what to display in + spot lists (and eexplorer) + * Added option to use INSERT rather than LOCAL INFILE with MySQL. + * Added jobRunner to allow for better security around plugins + *** 2002-12-13 * Added spot image stuff. *************** *** 50,51 **** --- 63,86 ---- * Changed SearchCriterion fields to strings. * A large number of minor or major fixes and changes. + + + Changes between 1.0.2 and 1.0.6: + + undocumented + + + Changes in 1.0.2: + + Multitudes of bug fixes. + Improved plugin management a bit, addded export/import of definitions. + Fixed the ftpd + Added hierarchical clustering plugin and visualizer + Improved uploads page + Added some Affy support - result files with only one channel will have + ratio = channel 1 intensity. + + contributions in 'contrib': + GeneSpring/SpotFire export (Nick DeLong/Ron Hart) + backup scripts (Greg Voronin/Ron Hart) + + And probably a whole lot of things I don't remember anymore. --- CHANGES DELETED --- |
|
From: <tr...@us...> - 2003-02-03 13:29:10
|
Update of /cvsroot/basedb/basedb/documentation/development
In directory sc8-pr-cvs1:/tmp/cvs-serv2119/documentation/development
Added Files:
security.txt
Log Message:
moved README.contributing to documentation/development/security.txt
--- NEW FILE: security.txt ---
This document will eventually describe code standard and such things,
but for now it just contains a reminder:
Never ever trust the user.
If you're supposed to get an int in an input variable, make sure it really
is an int:
$i_var = (int)$i_var;
or
settype($i_var, "int");
When printing something user-input on a web page, always escape any html
entities using the html() function from misc.inc.php:
echo "<b>".html($something)."</b>";
html() turns empty strings into a single to avoid problems with
empty hyperlinks (and Netscape's table parser). Also, line breaks are
turned into <br> tags. Inside other tags' attibutes you should turn off
that stuff:
echo "<input type=text value=\"".html($foo, 0)."\">";
The same goes for the text strings associated with OPTION tags:
echo "<option value=0>".html($foo, 0)."<option value=2>blabla";
Something even more complicated is outputting user-input strings
into javascript. For a link to a javascript function you need to this:
<a href="javascript:foo('bar', '<?= html(addslashes($baz), 0) ?>')">
which with echo looks like this:
echo "<a href=\"javascript:foo('bar', '".html(addslashes($baz), 0)."')\">";
Note that double quotes are used around the href's value and single
quotes are used for the javascript string. The reason that it doesn't work
the other way around is that htmlentities() doesn't escape single quotes
by default. This also implies that you should always use double quotes
around attribute values which might contain single quotes, e.g. all user-
input strings.
An even more complicated matter is passing user input to external
programs. Escaping for the shell (the exec() function) is trivial,
but escaping input to for instance gnuplot is easily forgotten. If
the user is allowed to control the text printed to gnuplot's control
stream, he/she can make gnuplot overwrite files and do all sorts
of nasty things. So if you use user input as the title of a plot,
be sure to remove all unprintable characters and run the string
through addslashes() first. Enclose it in _double_ quotes, or gnuplot
will output \' as \' rather than as ' etc.
|
|
From: <tr...@us...> - 2003-02-03 13:29:09
|
Update of /cvsroot/basedb/basedb In directory sc8-pr-cvs1:/tmp/cvs-serv2119 Removed Files: README.contributing Log Message: moved README.contributing to documentation/development/security.txt --- README.contributing DELETED --- |
|
From: <tr...@us...> - 2003-02-03 13:15:34
|
Update of /cvsroot/basedb/basedb/bin In directory sc8-pr-cvs1:/tmp/cvs-serv29328 Added Files: backup.sh Log Message: A working but not very elegant backup script --- NEW FILE: backup.sh --- #!/bin/bash # A script for backing up the data of a BASE installation running against # MySQL. This file should be readable only by the base user. # We're passing the password to the mysql tool as an argument. This is a # potential security risk, although mysql will only be running for a very # short time. If you're paranoid, create a user with the RELOAD privilege # and nothing else, and use that user for this task. Or prompt the user # for the password. rootpass="" # MySQL's data directory dbdir="/usr/local/var" # The names of the 'base' and 'basedynamic' databases. dbname="base" dyndbname="basedynamic" # The BASE data directory. datadir="/usr/local/base/data" # The backup destination directory. Will be created if it doesn't exist. # (That is, the last part will.) backupdir="/backups/base/`date '+%Y-%m-%d'`" ##### basedbdir="$dbdir/$dbname" basedyndbdir="$dbdir/$dyndbname" progdir="`dirname \"$0\"`" getopts -- "v" "verbose" if [ "$verbose" == v ]; then echo "Starting BASE backup process at `date`" time="time -p" else time="" fi if "$progdir/stopBase.php" "Shut down for backups at `date`" && \ mysql -uroot --password="$rootpass" -B <<-DELIM FLUSH TABLES DELIM then mkdir -p "$backupdir" if [ "$verbose" == v ]; then echo "Copying database '$dbname'"; fi $time cp -R -p -L "$basedbdir" "$backupdir/base" if [ "$verbose" == v ]; then echo "Copying database '$dyndbname'"; fi $time cp -R -p -L "$basedyndbdir" "$backupdir/basedynamic" if [ "$verbose" == v ]; then echo "Copying data files"; fi $time cp -R -p -L "$datadir" "$backupdir/data" "$progdir/startBase.php" fi # Generate report if [ "$verbose" == v ]; then echo "BASE backup process ended at `date`" # We allow for the possibility that all three are on different disks echo -e "\nDisk usage summary:" echo "$dbdir:" df -h "$dbdir" echo "$datadir:" df -h "$datadir" echo "$backupdir:" df -h "$backupdir" echo -e "\nBASE installation size:" echo -n "$backupdir/base: " du -sh "$backupdir/base" |cut -f1 echo -n "$backupdir/basedynamic: " du -sh "$backupdir/basedynamic" |cut -f1 echo -n "$backupdir/data: " du -sh "$backupdir/data" |cut -f1 fi |
|
From: <tr...@us...> - 2003-02-03 13:11:58
|
Update of /cvsroot/basedb/basedb/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv27888
Modified Files:
startBase.php stopBase.php
Log Message:
Better error logging
Index: startBase.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/startBase.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** startBase.php 1 Feb 2003 12:52:50 -0000 1.1
--- startBase.php 3 Feb 2003 13:11:55 -0000 1.2
***************
*** 31,35 ****
if(isset($_SERVER["argv"][1]))
! mydie("Usage: restart.php\n");
$BC = new BaseControl();
--- 31,35 ----
if(isset($_SERVER["argv"][1]))
! mydie("Usage: ".$_SERVER["argv"][0]."\n");
[...88 lines suppressed...]
if($ok)
return 1;
! fwrite(STDERR, "Please read the documentation and correct the error(s)\n");
return 0;
}
***************
*** 122,127 ****
if($sv != "1.2.2")
{
! echo "Error: The database schema version is $sv, but this\n".
! "version of BASE requires schema version 1.2.2\n";
return 0;
}
--- 117,122 ----
if($sv != "1.2.2")
{
! fwrite(STDERR, "Error: The database schema version is $sv,\n".
! "but this version of BASE requires schema version 1.2.2\n");
return 0;
}
Index: stopBase.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/stopBase.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** stopBase.php 1 Feb 2003 12:52:50 -0000 1.1
--- stopBase.php 3 Feb 2003 13:11:55 -0000 1.2
***************
*** 31,35 ****
if(!isset($_SERVER["argv"][1]) || isset($_SERVER["argv"][2]))
! die("Usage: ".$_SERVER["argv"][0]." \"message\"\n");
return shutdownBase($_SERVER["argv"][1]) ? 0 : 1;
--- 31,35 ----
if(!isset($_SERVER["argv"][1]) || isset($_SERVER["argv"][2]))
! mydie("Usage: ".$_SERVER["argv"][0]." \"message\"\n");
return shutdownBase($_SERVER["argv"][1]) ? 0 : 1;
***************
*** 41,48 ****
$BC = new BaseControl();
if(!$BC->mayRun())
! {
! echo "BASE is already shut down\n";
! return false;
! }
// Open database connection
--- 41,45 ----
$BC = new BaseControl();
if(!$BC->mayRun())
! mydie("BASE is already shut down\n");
// Open database connection
***************
*** 52,59 ****
if(!$BC->beginShutdown($msg))
! {
! echo "Unable to initiate shutdown\n";
! return false;
! }
ob_implicit_flush(1);
--- 49,53 ----
if(!$BC->beginShutdown($msg))
! mydie("Unable to initiate shutdown\n");
ob_implicit_flush(1);
***************
*** 69,79 ****
if(!$down)
{
! echo "Timed out after 30 minutes. ".
! "Manual intervention will be needed.\n";
! return false;
}
echo "BASE was successfully shut down.\n";
return true;
}
?>
--- 63,79 ----
if(!$down)
{
! mydie("Timed out after 30 minutes. ".
! "Manual intervention will be needed.\n");
}
echo "BASE was successfully shut down.\n";
return true;
}
+
+ function mydie($msg)
+ {
+ fwrite(STDERR, $msg);
+ exit(1);
+ }
+
?>
|
|
From: <tr...@us...> - 2003-02-03 08:56:14
|
Update of /cvsroot/basedb/basedb/include/local_distr
In directory sc8-pr-cvs1:/tmp/cvs-serv2263/include/local_distr
Modified Files:
raw_columns.inc.php
Log Message:
renamed position to rawPosition in expressions
Index: raw_columns.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/local_distr/raw_columns.inc.php,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** raw_columns.inc.php 1 Feb 2003 23:04:14 -0000 1.14
--- raw_columns.inc.php 3 Feb 2003 08:56:10 -0000 1.15
***************
*** 164,168 ****
array("x", SEARCH_FLOAT, "%%.`x`", "X coordinate"),
array("y", SEARCH_FLOAT, "%%.`y`", "Y coordinate"),
! array("position", SEARCH_INTNOAVG, "%%.`position`", "Position")
);
--- 164,168 ----
array("x", SEARCH_FLOAT, "%%.`x`", "X coordinate"),
array("y", SEARCH_FLOAT, "%%.`y`", "Y coordinate"),
! array("rawPosition", SEARCH_INTNOAVG, "%%.`position`", "Position")
);
|
|
From: <tr...@us...> - 2003-02-03 08:55:51
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv2073/www
Modified Files:
raw_table.phtml
Log Message:
renamed position to rawPosition in expressions
Index: raw_table.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_table.phtml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** raw_table.phtml 23 Jan 2003 16:53:18 -0000 1.2
--- raw_table.phtml 3 Feb 2003 08:55:47 -0000 1.3
***************
*** 126,130 ****
$headerfields = $search->getHeadersFromExtraColumns();
$sortorder = $search->getSortFromExtraColumns();
! $defsort = "position";
makeSearchHeader($search, $headerfields, $sortorder, $defsort,
true, "document.ff.submit();", "");
--- 126,130 ----
$headerfields = $search->getHeadersFromExtraColumns();
$sortorder = $search->getSortFromExtraColumns();
! $defsort = "rawPosition";
makeSearchHeader($search, $headerfields, $sortorder, $defsort,
true, "document.ff.submit();", "");
***************
*** 152,156 ****
$gshow = $show && $repLevel < 5 ? 1 : 0;
$cols = array(
! array("position", false, "Pos", 1, "renderExplorePosition", $show),
array("reporterId", false, "Reporter", 1, 3, $show)
);
--- 152,156 ----
$gshow = $show && $repLevel < 5 ? 1 : 0;
$cols = array(
! array("rawPosition", false, "Pos", 1, "renderExplorePosition", $show),
array("reporterId", false, "Reporter", 1, 3, $show)
);
***************
*** 189,193 ****
{
$cols[] = array("geneName", false, "Reporter name", 1,
! 1, $show);
}
--- 189,193 ----
{
$cols[] = array("geneName", false, "Reporter name", 1,
! "renderGeneName", $show);
}
***************
*** 209,213 ****
global $cbRaw;
! $pos = $row["position"];
$s *= 1;
echo "<td><img width=$s height=$s ".
--- 209,213 ----
global $cbRaw;
! $pos = $row["rawPosition"];
$s *= 1;
echo "<td><img width=$s height=$s ".
|
|
From: <tr...@us...> - 2003-02-03 08:54:15
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv1517/www
Modified Files:
assay_table.phtml gene_explore.phtml label_edit.phtml
left.phtml
Log Message:
minor changes
Index: assay_table.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/assay_table.phtml,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** assay_table.phtml 23 Jan 2003 16:53:18 -0000 1.23
--- assay_table.phtml 3 Feb 2003 08:54:11 -0000 1.24
***************
*** 105,109 ****
?>
<table <?= $cellpad ?>>
! <tr><th class=pagehead>Expression value table</th></tr>
<tr><td class=large><a href="<?= html($location, 0)
?>">Return</a></td></tr>
--- 105,110 ----
?>
<table <?= $cellpad ?>>
! <tr><th class=pagehead>Expression value table, BioAssay <?=
! html($ass->getName()) ?></th></tr>
<tr><td class=large><a href="<?= html($location, 0)
?>">Return</a></td></tr>
Index: gene_explore.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/gene_explore.phtml,v
retrieving revision 1.69
retrieving revision 1.70
diff -C2 -d -r1.69 -r1.70
*** gene_explore.phtml 2 Feb 2003 15:31:52 -0000 1.69
--- gene_explore.phtml 3 Feb 2003 08:54:11 -0000 1.70
***************
*** 870,874 ****
array("geneSymbol", false, "Gene", 1, 1, $forshow),
array("geneName", false, "Reporter name", 1,
! "renderGeneName", $forshow),
array("inAssays", false, "In assays", 1, 1, $forshow)
);
--- 870,874 ----
array("geneSymbol", false, "Gene", 1, 1, $forshow),
array("geneName", false, "Reporter name", 1,
! "renderGeneNameExpl", $forshow),
array("inAssays", false, "In assays", 1, 1, $forshow)
);
***************
*** 891,895 ****
echo "<td>$GLOBALS[cbNumRow]</td>";
}
! function renderGeneName(&$n)
{
// Used to wordwrap, but that looks ugly if the lines are broken
--- 891,895 ----
echo "<td>$GLOBALS[cbNumRow]</td>";
}
! function renderGeneNameExpl(&$n)
{
// Used to wordwrap, but that looks ugly if the lines are broken
Index: label_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/label_edit.phtml,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** label_edit.phtml 2 Feb 2003 15:31:52 -0000 1.11
--- label_edit.phtml 3 Feb 2003 08:54:12 -0000 1.12
***************
*** 126,131 ****
dateAndOwnerTable($lbl, $curUser, true);
?>
! <tr><td colspan=2><input type=submit value="Accept" name=i_ok
! onClick="return chk(this.form)">
</form>
<?
--- 126,130 ----
dateAndOwnerTable($lbl, $curUser, true);
?>
! <tr><td colspan=2><input type=submit value="Accept" name=i_ok></td></tr>
</form>
<?
Index: left.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/left.phtml,v
retrieving revision 1.66
retrieving revision 1.67
diff -C2 -d -r1.66 -r1.67
*** left.phtml 2 Feb 2003 14:53:26 -0000 1.66
--- left.phtml 3 Feb 2003 08:54:12 -0000 1.67
***************
*** 199,203 ****
?>
<tr><th class=subheadact><a target=_top
! href="index.phtml?l=hyb&m=bio_main.phtml">Hybridizations</a></td></tr>
<tr><td><a target=main href="hyb_list.phtml">Hybridizations</a></td></tr>
<tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>
--- 199,203 ----
?>
<tr><th class=subheadact><a target=_top
! href="index.phtml?l=hyb&m=hyb_list.phtml">Hybridizations</a></td></tr>
<tr><td><a target=main href="hyb_list.phtml">Hybridizations</a></td></tr>
<tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>
***************
*** 213,217 ****
}
else echo "<tr><th class=subhead><a target=_top href='index.phtml".
! "?l=hyb&m=bio_main.phtml'>Hybridizations</a></td></tr>\n";
if($l == "upl")
--- 213,217 ----
}
else echo "<tr><th class=subhead><a target=_top href='index.phtml".
! "?l=hyb&m=hyb_list.phtml'>Hybridizations</a></td></tr>\n";
if($l == "upl")
|
|
From: <tr...@us...> - 2003-02-03 08:54:14
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv1517/include/web
Modified Files:
links_common.inc.php
Log Message:
minor changes
Index: links_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/links_common.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** links_common.inc.php 22 Jan 2003 08:01:40 -0000 1.12
--- links_common.inc.php 3 Feb 2003 08:54:11 -0000 1.13
***************
*** 201,205 ****
}
! function imageAcquistionArrLink(&$arr)
{
if(!isset($arr["id"]))
--- 201,205 ----
}
! function imageAcquisitionArrLink(&$arr)
{
if(!isset($arr["id"]))
***************
*** 208,211 ****
--- 208,224 ----
return html($arr["name"]).remMark($arr["removed"]);
return "<a ".href("hyb_image.phtml?i_acq=".(int)$arr["id"], 2).">".
+ html($arr["name"])."</a>".remMark($arr["removed"]);
+ }
+
+ function imageAcquisitionIdLink($id, &$user)
+ {
+ $id = (int)$id;
+ $arr = ImageAcquisition::getBasicFromId($id);
+ if(!$user->access(ImageAcquisition::globalRead()) ||
+ !ImageAcquisition::isSharedArray($arr, $user))
+ {
+ return html($arr["name"]).remMark($arr["removed"]);
+ }
+ return "<a ".href("hyb_image.phtml?i_acq=$id", 2).">".
html($arr["name"])."</a>".remMark($arr["removed"]);
}
|
|
From: <tr...@us...> - 2003-02-03 08:52:59
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv442/include/web
Modified Files:
gene_common.inc.php
Log Message:
renderGeneName cuts at 30-40 chars
Index: gene_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/gene_common.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** gene_common.inc.php 2 Feb 2003 18:02:09 -0000 1.7
--- gene_common.inc.php 3 Feb 2003 08:52:56 -0000 1.8
***************
*** 140,143 ****
--- 140,147 ----
}
+ function renderGeneName(&$name)
+ {
+ echo "<td>".maxlenPopup($name, 30, 40, "Reporter name")."</td>\n";
+ }
|
|
From: <tr...@us...> - 2003-02-03 08:52:19
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv32319/include/classes
Modified Files:
spotimage.inc.php
Log Message:
cleaned up error messages/logging
Index: spotimage.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/spotimage.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** spotimage.inc.php 1 Feb 2003 23:03:38 -0000 1.7
--- spotimage.inc.php 3 Feb 2003 08:52:15 -0000 1.8
***************
*** 121,125 ****
$chopper = escapeshellarg("$config[rootDir]/bin/spotImageChopper");
- $res = array();
$rc = 0;
--- 121,124 ----
***************
*** 138,142 ****
Image::getRepositoryFilenameById($imgBoth));
$tiffsplit = "tiffsplit";
! exec("$tiffsplit 2>&1 $fileBoth", $res, $rc);
$fileR = "xaa.tif";
$fileG = "xab.tif";
--- 137,141 ----
Image::getRepositoryFilenameById($imgBoth));
$tiffsplit = "tiffsplit";
! passthru("$tiffsplit 2>&1 $fileBoth", $rc);
$fileR = "xaa.tif";
$fileG = "xab.tif";
***************
*** 154,158 ****
passthru("$tifftopnm $fileR | { $tifftopnm $fileG | { $chopper ".
"2>&1 <$fileS $ss $xoff $yoff $scale $qual; } 4<&0 ; } 5<&0 ".
! "2>>".escapeshellarg("$config[logDir]/spotimage.log"),
$rc);
}
--- 153,157 ----
passthru("$tifftopnm $fileR | { $tifftopnm $fileG | { $chopper ".
"2>&1 <$fileS $ss $xoff $yoff $scale $qual; } 4<&0 ; } 5<&0 ".
! "2>&1", /* .escapeshellarg("$config[logDir]/spotimage.log"),*/
$rc);
}
***************
*** 170,174 ****
if(!$rc)
return "";
! return "Failed to process images (rc=$rc):\n".implode("\n", $res);
}
--- 169,173 ----
if(!$rc)
return "";
! return "Failed to process images (rc=$rc).\n";
}
|
|
From: <tr...@us...> - 2003-02-03 08:51:41
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv31702/include/classes
Modified Files:
bioassay.inc.php
Log Message:
added reporter list to valueSearch
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassay.inc.php,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** bioassay.inc.php 2 Feb 2003 18:02:34 -0000 1.29
--- bioassay.inc.php 3 Feb 2003 08:51:37 -0000 1.30
***************
*** 505,508 ****
--- 505,511 ----
}
+ $arr[] = array("repList", SEARCH_REPORTERLIST,
+ "%%.reporter", "Reporter list");
+
Search::bindExpressionsToTable($arr, "bad");
***************
*** 549,552 ****
--- 552,556 ----
Search::bindExpressionsToTable($raw, "rbad", "[Raw]");
$rep = ReporterColumn::getExpressions();
+
Search::bindExpressionsToTable($rep, "m", "[Rep]");
$lims = RawBioAssay::boundLimsExpressions();
|
|
From: <tr...@us...> - 2003-02-03 08:51:18
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv31445/include/web
Modified Files:
hyb_common.inc.php
Log Message:
reworked image channel stuff
Index: hyb_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/hyb_common.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** hyb_common.inc.php 22 Jan 2003 08:01:36 -0000 1.9
--- hyb_common.inc.php 3 Feb 2003 08:51:13 -0000 1.10
***************
*** 23,26 ****
--- 23,27 ----
require_once("protocol.inc.php");
require_once("labeled.inc.php");
+ require_once("label.inc.php");
require_once("array.inc.php");
require_once("item_common.inc.php");
***************
*** 134,138 ****
if(!$img->readShared($i_imgjpeg, $user))
return "Unable to use image for JPEG: image not found";
! else if($img->getChannels() < 1 || $img->getChannels() > 3)
return "Unable to use image for JPEG: can't handle its channel(s)";
else if(!$img->takeOverUseForJpeg())
--- 135,140 ----
if(!$img->readShared($i_imgjpeg, $user))
return "Unable to use image for JPEG: image not found";
! $ch = $img->getChannels();
! if($ch != -1 && $ch != 1 && $ch != 2)
return "Unable to use image for JPEG: can't handle its channel(s)";
else if(!$img->takeOverUseForJpeg())
***************
*** 142,145 ****
--- 144,162 ----
}
+ function imageChannelName($ch, $acqid, &$user)
+ {
+ static $chnames = false, $lab = array();
+ if(!$chnames)
+ $chnames = Image::getChannelNames();
+ if(!isset($lab[$acqid]))
+ $lab[$acqid] = ImageAcquisition::getChannelLabelsForId($acqid);
+ $l =& $lab[$acqid];
+
+ $clink = isset($chnames[$ch]) ? html($chnames[$ch]) : "unknown";
+ if(isset($l[$ch]))
+ $clink .= " (label ".labelIdLink($l[$ch], $user).")";
+ return $clink;
+ }
+
// Image list for an imageacquisition. Makes its own table, wants to be
// in a form called ff.
***************
*** 204,208 ****
"<td><a ".href("image_edit.phtml?i_img=$a[id]", 2).">".
html($a["name"])."</a>".remMark($a["removed"])."</td>".
! "<td>".html($acq->getChannelsTitle($ch))."</td>".
"<td>".html($a["userName"])."</td>".
"<td>".htmldate($a["addedDate"])."</td>".
--- 221,225 ----
"<td><a ".href("image_edit.phtml?i_img=$a[id]", 2).">".
html($a["name"])."</a>".remMark($a["removed"])."</td>".
! "<td>".imageChannelName($ch, $acqid, $user)."</td>".
"<td>".html($a["userName"])."</td>".
"<td>".htmldate($a["addedDate"])."</td>".
|
|
From: <tr...@us...> - 2003-02-03 08:51:18
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv31445/include/classes
Modified Files:
acquisition.inc.php image.inc.php
Log Message:
reworked image channel stuff
Index: acquisition.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/acquisition.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** acquisition.inc.php 22 Jan 2003 08:00:46 -0000 1.11
--- acquisition.inc.php 3 Feb 2003 08:51:13 -0000 1.12
***************
*** 225,340 ****
}
! function getChannelsTitle($channels, $label = NULL)
! {
! $name = "";
! if ($channels == -2)
! {
! $name = "Other";
! }
! else if ($channels == -1)
[...107 lines suppressed...]
}
! // Returns array channel => label
! function getChannelLabelsForId($acqid)
{
+ $query = "SELECT hl.channel, le.label ".
+ "FROM ImageAcquisition ia, HybridizedLabeled hl, ".
+ "LabeledExtract le ".
+ "WHERE ia.id = ".(int)$acqid." ".
+ "AND hl.hybridization = ia.hybridization ".
+ "AND le.id = hl.labeled";
$arr = array();
$res = query($query);
while($row =& db_fetch_row($res))
! $arr[$row[0]] = $row[1];
return $arr;
}
+
}
Index: image.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/image.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** image.inc.php 22 Jan 2003 08:00:53 -0000 1.12
--- image.inc.php 3 Feb 2003 08:51:13 -0000 1.13
***************
*** 91,95 ****
function setChannels($val)
{
! $this->channels = $val;
}
function setFileSize($val)
--- 91,95 ----
function setChannels($val)
{
! $this->channels = (int)$val;
}
function setFileSize($val)
***************
*** 208,211 ****
--- 208,219 ----
$this->useForJpeg = 1;
return true;
+ }
+
+ function getChannelNames()
+ {
+ $names = array(-1 => "All", 0 => "None", 2 => "Other");
+ for($i = 1; $i < 9; $i++)
+ $names[$i] = "Ch $i";
+ return $names;
}
|
|
From: <tr...@us...> - 2003-02-03 08:51:18
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv31445/www
Modified Files:
image_edit.phtml
Log Message:
reworked image channel stuff
Index: image_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/image_edit.phtml,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** image_edit.phtml 2 Feb 2003 15:31:52 -0000 1.3
--- image_edit.phtml 3 Feb 2003 08:51:13 -0000 1.4
***************
*** 24,27 ****
--- 24,28 ----
require_once("init.inc.php");
require_once("item_common.inc.php");
+ require_once("hyb_common.inc.php");
require_once("links_common.inc.php");
require_once("image.inc.php");
***************
*** 36,77 ****
$img = new Image();
[...192 lines suppressed...]
! {
! echo " (<a ".href("label_edit.phtml?i_lbl=".$channelLabel["id"]).">";
! echo $channelLabel["name"]."</a>)";
! }
! ?></td></tr>
<?
dateAndOwnerTableNoAccess($img, $curUser);
--- 158,169 ----
">Edit image</a></td></tr>\n";
}
+
?>
<tr><th>Name</th><td><?= html($img->getName()).remMark($img) ?></td></tr>
<tr><th>Description</th><td><?= html($img->getDescr()) ?></td></tr>
! <tr><th>Image set</th><td><?= imageAcquisitionIdLink($acqid, $curUser)
! ?></td></tr>
! <tr><th>Channel(s)</th><td><?=
! imageChannelName($img->getChannels(), $acqid, $curUser) ?></td></tr>
<?
dateAndOwnerTableNoAccess($img, $curUser);
|
|
From: <tr...@us...> - 2003-02-02 18:17:32
|
Update of /cvsroot/basedb/basedb/sql
In directory sc8-pr-cvs1:/tmp/cvs-serv14211
Modified Files:
base_pgsql.sql
Log Message:
Regenerated from latest mysql schema
Index: base_pgsql.sql
===================================================================
RCS file: /cvsroot/basedb/basedb/sql/base_pgsql.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** base_pgsql.sql 1 Feb 2003 12:50:47 -0000 1.1
--- base_pgsql.sql 2 Feb 2003 18:17:29 -0000 1.2
***************
*** 1137,1141 ****
"lastExploredSet" int NOT NULL default '0',
"lastPlateType" int NOT NULL default '0',
! "lastPlateTypeCreated" int NOT NULL default '0'
, CONSTRAINT UserAccount_pkey PRIMARY KEY ("userGroup")
);
--- 1137,1144 ----
"lastExploredSet" int NOT NULL default '0',
"lastPlateType" int NOT NULL default '0',
! "lastPlateTypeCreated" int NOT NULL default '0',
! "defaultGid" int NOT NULL default '0',
[...122 lines suppressed...]
CREATE SEQUENCE Software_id_seq start 1 increment 1 maxvalue 9223372036854775807 minvalue 1 cache 1;
- SELECT setval ('software_id_seq', MAX("id")+1, true) FROM Software;
-
CREATE SEQUENCE Transformation_id_seq start 1 increment 1 maxvalue 9223372036854775807 minvalue 1 cache 1;
- SELECT setval ('transformation_id_seq', MAX("id")+1, true) FROM Transformation;
-
CREATE SEQUENCE Upload_id_seq start 1 increment 1 maxvalue 9223372036854775807 minvalue 1 cache 1;
- SELECT setval ('upload_id_seq', MAX("id")+1, true) FROM Upload;
-
CREATE SEQUENCE UserGroup_id_seq start 1 increment 1 maxvalue 9223372036854775807 minvalue 1 cache 1;
SELECT setval ('usergroup_id_seq', MAX("id")+1, true) FROM UserGroup;
CREATE SEQUENCE Well_id_seq start 1 increment 1 maxvalue 9223372036854775807 minvalue 1 cache 1;
- SELECT setval ('well_id_seq', MAX("id")+1, true) FROM Well;
-
CREATE SEQUENCE Wizzzard_id_seq start 1 increment 1 maxvalue 9223372036854775807 minvalue 1 cache 1;
- SELECT setval ('wizzzard_id_seq', MAX("id")+1, true) FROM Wizzzard;
-
- CREATE FUNCTION "ifnull"(smallint, integer) RETURNS smallint AS 'select CASE WHEN $1 IS NULL THEN $2 ELSE $1 END' LANGUAGE 'sql';
--- 1447,1465 ----
|
|
From: <tr...@us...> - 2003-02-02 18:17:11
|
Update of /cvsroot/basedb/basedb/sql In directory sc8-pr-cvs1:/tmp/cvs-serv14151 Modified Files: base_mysql_data.sql Log Message: removed linefeed which confused porting script Index: base_mysql_data.sql =================================================================== RCS file: /cvsroot/basedb/basedb/sql/base_mysql_data.sql,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** base_mysql_data.sql 1 Feb 2003 12:50:47 -0000 1.1 --- base_mysql_data.sql 2 Feb 2003 18:17:08 -0000 1.2 *************** *** 1,12 **** ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES ! (1,'medianratio','This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant but the median of their ratios (i1/i2) is shifted to 1.\r\n\r\nThe normalizer lets you exclude a percentage of the highest and lowest intensities as well as all spots with at least one intensity below a fixed value.\r\n','2002-08-31',1,'Normalization: Global median ratio','position reporter','intensity1 intensity2',1,'',1,'','','','',1,2,0,0); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES ! (2,'lowess','This is an efficient C++ implementation by Björn Samuelsson <bj...@th...> of the LOWESS algorithm.\r\nIt provides intensity-based normalization.\r\n\r\nThe window size is the only smoothness parameter available in this implementation. The higher it is, the smoother the function will be.\r\nTweaking the other two parameters allows you to gain performance at the price of a small precision loss. The default values are usually good.\r\n\r\nFor more info on LOWESS:\r\nCleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 1988, 83:596-610.\r\n\r\nYang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.\r\n','2002-08-31',1,'Normalization: Lowess','position reporter','intensity1 intensity2',1,'',1,'','','','','1',2,0,0); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES ! (3,'mds','Multi-dimensional scaling (MDS) is a non-linear way to reduce the dimensionality of a data set. This implementation uses the Pearson correlations between assays as a distance metric.\r\n\r\nMDS info:\r\nKhan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS: Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 1998, 58:5009-5013.\r\n','0000-00-00',1,'Analysis: MDS','position','ratio',1,1,'','','','','','1',1,0,1); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES ! (4,'clusteringscript','Hierarchical clustering, bottom-up.\r\nThe two closest points are merged and the new cluster is represented by an unweighted(median) or weighted(center of mass) average of the two points in gene expression space.\r\n\r\nImplemented by Cecilia Ritz <ce...@th...>.\r\n','2002-05-31',1,'Analysis: Hierarchical clustering','reporterId','ratio',1,1,'','','','','','1',1,1,0); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES ! (5,'pca','This program calculates the PCA of the sample variance-covariance matrix of your data set:\r\n a) Data is parsed from a lowess transformed data set in serial BASE file format.\r\n b) The natural logarithm of the ratio of expression intensity 1 to expression intensity 2 is then calculated.\r\n c) The data matrix of the ln transformed date is then created. Rows correspond to genes and columns correspond to experimental variates.\r\n d) The average value of each column is calcuated and a second matrix, called the average matrix is then created. For each column of the average matrix, the row value is equal to the column average of the corresponding column.\r\n e) The average matrix is then subtracted from the data matrix. This produces the difference matrix.\r\n f) The variance-covariance matrix is calcuated from the product of the transpose of the difference matrix times the difference matrix itself. The resulting marix is a symmetric matrix with all positive real values. Multiplying the entire matrix by ( 1/rows -1 ) yields the final sample variance-covariance matrix.\r\n g) The eigenvalues and eigenvectors of the sample variance-covariance matrix are then calculated. The combination of eigenvalues and eigenvectors for a given matrix can be termed the eignensytem of that matrix. The eigensystem is then sorted by the value of the eigenvalue of the system.\r\n h) The variance-covariance matrix and the eigensystem( which is stored in a linked list) are used to generate the output files, currently: covariance.html, eigensystem.html, Scree.png and CoeffieicentPlot.png. \r\n\r\n','2002-08-31',1,'Analysis: PCA','position reporter','intensity1 intensity2',1,'',1,'http://www.ngelab.org/','','','','1',1,0,0); INSERT INTO ProgramParameter VALUES (1,1,'min_I','Use elements with both int >','f','5','100',''); --- 1,7 ---- ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES (1,'medianratio','This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant but the median of their ratios (i1/i2) is shifted to 1.\r\n\r\nThe normalizer lets you exclude a percentage of the highest and lowest intensities as well as all spots with at least one intensity below a fixed value.\r\n','2002-08-31',1,'Normalization: Global median ratio','position reporter','intensity1 intensity2',1,'',1,'','','','',1,2,0,0); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES (2,'lowess','This is an efficient C++ implementation by Björn Samuelsson <bj...@th...> of the LOWESS algorithm.\r\nIt provides intensity-based normalization.\r\n\r\nThe window size is the only smoothness parameter available in this implementation. The higher it is, the smoother the function will be.\r\nTweaking the other two parameters allows you to gain performance at the price of a small precision loss. The default values are usually good.\r\n\r\nFor more info on LOWESS:\r\nCleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 1988, 83:596-610.\r\n\r\nYang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.\r\n','2002-08-31',1,'Normalization: Lowess','position reporter','intensity1 intensity2',1,'',1,'','','','','1',2,0,0); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES (3,'mds','Multi-dimensional scaling (MDS) is a non-linear way to reduce the dimensionality of a data set. This implementation uses the Pearson correlations between assays as a distance metric.\r\n\r\nMDS info:\r\nKhan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS: Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 1998, 58:5009-5013.\r\n','0000-00-00',1,'Analysis: MDS','position','ratio',1,1,'','','','','','1',1,0,1); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES (4,'clusteringscript','Hierarchical clustering, bottom-up.\r\nThe two closest points are merged and the new cluster is represented by an unweighted(median) or weighted(center of mass) average of the two points in gene expression space.\r\n\r\nImplemented by Cecilia Ritz <ce...@th...>.\r\n','2002-05-31',1,'Analysis: Hierarchical clustering','reporterId','ratio',1,1,'','','','','','1',1,1,0); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess,minChannels,leaveStdin,leaveStdout) VALUES (5,'pca','This program calculates the PCA of the sample variance-covariance matrix of your data set:\r\n a) Data is parsed from a lowess transformed data set in serial BASE file format.\r\n b) The natural logarithm of the ratio of expression intensity 1 to expression intensity 2 is then calculated.\r\n c) The data matrix of the ln transformed date is then created. Rows correspond to genes and columns correspond to experimental variates.\r\n d) The average value of each column is calcuated and a second matrix, called the average matrix is then created. For each column of the average matrix, the row value is equal to the column average of the corresponding column.\r\n e) The average matrix is then subtracted from the data matrix. This produces the difference matrix.\r\n f) The variance-covariance matrix is calcuated from the product of the transpose of the difference matrix times the difference matrix itself. The resulting marix is a symmetric matrix with all positive real values. Multiplying the entire matrix by ( 1/rows -1 ) yields the final sample variance-covariance matrix.\r\n g) The eigenvalues and eigenvectors of the sample variance-covariance matrix are then calculated. The combination of eigenvalues and eigenvectors for a given matrix can be termed the eignensytem of that matrix. The eigensystem is then sorted by the value of the eigenvalue of the system.\r\n h) The variance-covariance matrix and the eigensystem( which is stored in a linked list) are used to generate the output files, currently: covariance.html, eigensystem.html, Scree.png and CoeffieicentPlot.png. \r\n\r\n','2002-08-31',1,'Analysis: PCA','position reporter','intensity1 intensity2',1,'',1,'http://www.ngelab.org/','','','','1',1,0,0); INSERT INTO ProgramParameter VALUES (1,1,'min_I','Use elements with both int >','f','5','100',''); |
|
From: <tr...@us...> - 2003-02-02 18:16:47
|
Update of /cvsroot/basedb/basedb/sql
In directory sc8-pr-cvs1:/tmp/cvs-serv14017
Modified Files:
base_mysql.sql
Log Message:
added default group etc to UserAccount
Index: base_mysql.sql
===================================================================
RCS file: /cvsroot/basedb/basedb/sql/base_mysql.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** base_mysql.sql 1 Feb 2003 12:50:47 -0000 1.1
--- base_mysql.sql 2 Feb 2003 18:16:45 -0000 1.2
***************
*** 1188,1191 ****
--- 1188,1194 ----
lastPlateType int(11) NOT NULL default '0',
lastPlateTypeCreated int(11) NOT NULL default '0',
+ defaultGid int(11) NOT NULL default '0',
+ defaultGroupAccess tinyint(1) NOT NULL default '0',
+ defaultWorldAccess tinyint(1) NOT NULL default '0',
PRIMARY KEY (userGroup)
) TYPE=MyISAM;
***************
*** 1197,1201 ****
CREATE TABLE UserGroup (
id int(11) NOT NULL auto_increment,
! name varchar(30) NOT NULL default '',
descr text NOT NULL,
owner int(11) NOT NULL default '0',
--- 1200,1204 ----
CREATE TABLE UserGroup (
id int(11) NOT NULL auto_increment,
! name varchar(30) default NULL,
descr text NOT NULL,
owner int(11) NOT NULL default '0',
|
|
From: <tr...@us...> - 2003-02-02 18:03:06
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv9019/include/classes
Modified Files:
search.inc.php
Log Message:
Fixes for NULL/NOT NULL criteria
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/search.inc.php,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** search.inc.php 1 Feb 2003 23:04:14 -0000 1.29
--- search.inc.php 2 Feb 2003 18:03:03 -0000 1.30
***************
*** 968,971 ****
--- 968,976 ----
else if($op < 13) // Unary IS NULL and IS NOT NULL
{
+ // Undo the smartness of SEARCH_FLOATEXP to get the right
+ // definedness. That is, we want negative and undefined
+ // values to be seen as NULL.
+ if($arr[0] == SEARCH_FLOATEXP)
+ $fname = db_func_log($fname);
$where .= " AND $fname $ops[$op]";
}
***************
*** 1324,1327 ****
--- 1329,1340 ----
}
return false;
+ }
+
+ // IN "" / NOT IN "" translate to IS [NOT] NULL.
+ if($this->op >= 7 && $this->op <= 8 && $this->searchString === "")
+ {
+ $this->translated = array($type); // For internal use only
+ $this->viewable = array("NULL");
+ return true;
}
|
|
From: <tr...@us...> - 2003-02-02 18:02:37
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv8819/include/classes
Modified Files:
bioassay.inc.php
Log Message:
Fixed 'A' to be log10
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassay.inc.php,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** bioassay.inc.php 1 Feb 2003 23:04:14 -0000 1.28
--- bioassay.inc.php 2 Feb 2003 18:02:34 -0000 1.29
***************
*** 447,453 ****
db_func_div("%%.intensity1", "%%.intensity2"),
"M, log2(Ratio)"),
! array("l2intgmean1_2", SEARCH_FLOAT,
! ".5*".db_func_log("%%.intensity1*%%.intensity2", 2),
! "A, log2(sqrt(Ch1*Ch2))"),
array("l2intsum1_2", SEARCH_FLOATEXP,
"%%.intensity1+%%.intensity2", "log2(Ch1+Ch2)")
--- 447,453 ----
db_func_div("%%.intensity1", "%%.intensity2"),
"M, log2(Ratio)"),
! array("l10intgmean1_2", SEARCH_FLOAT,
! ".5*".db_func_log("%%.intensity1*%%.intensity2", 10),
! "A, log10(sqrt(Ch1*Ch2))"),
array("l2intsum1_2", SEARCH_FLOATEXP,
"%%.intensity1+%%.intensity2", "log2(Ch1+Ch2)")
***************
*** 485,491 ****
$name[] = "Ch$ch1";
}
! $arr[] = array("l2intgmean1__$channels", SEARCH_FLOAT,
! db_func_log(implode("*", $sql), 2)."/$channels.",
! "log2(sqrt(".implode("+", $name)."))");
$arr[] = array("l2intsum1__$channels", SEARCH_FLOATEXP,
implode("+", $sql), "log2(".implode("+", $name).")");
--- 485,491 ----
$name[] = "Ch$ch1";
}
! $arr[] = array("l10intgmean1__$channels", SEARCH_FLOAT,
! db_func_log(implode("*", $sql), 10)."/$channels.",
! "log10(sqrt(".implode("+", $name)."))");
$arr[] = array("l2intsum1__$channels", SEARCH_FLOATEXP,
implode("+", $sql), "log2(".implode("+", $name).")");
***************
*** 679,685 ****
$tables = array();
$tables["bad"] = array("$config[dbDynamic]BioAssayData$expid bad");
- $tables["m"] = array("Reporter m", "m.id = bad.reporter",
- array(), "bad");
// We include bao by LEFT JOIN because there could be assays
--- 679,687 ----
$tables = array();
+ // Since the order here is significant (it's used to help the search
+ // class order the tables in the FROM clause), we start with the
+ // heaviest tables and end with the ones most easy to join in after
+ // any WHEREs have done their job.
$tables["bad"] = array("$config[dbDynamic]BioAssayData$expid bad");
// We include bao by LEFT JOIN because there could be assays
***************
*** 697,707 ****
"bao");
- // Get tables for LIMS from RawBioAssay
- $tables = array_merge($tables, RawBioAssay::limsSearchTables());
-
- // bad.bioAssay will always be there, so we use that to join with.
- $tables["ba"] = array("BioAssay ba", "ba.id = bad.`bioAssay`",
- array(), "bad");
-
$xc = ExtraDataColumn::getBriefForSet($setid);
$xctables = ExtraDataColumn::getValueTypeTables();
--- 699,702 ----
***************
*** 716,719 ****
--- 711,724 ----
"$tn.`extraDataColumn` = $xid"));
}
+
+ $tables["m"] = array("Reporter m", "m.id = bad.reporter",
+ array(), "bad");
+
+ // Get tables for LIMS from RawBioAssay
+ $tables = array_merge($tables, RawBioAssay::limsSearchTables());
+
+ // bad.bioAssay will always be there, so we use that to join with.
+ $tables["ba"] = array("BioAssay ba", "ba.id = bad.`bioAssay`",
+ array(), "bad");
return $tables;
|
|
From: <tr...@us...> - 2003-02-02 18:02:14
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv8628/include/web
Modified Files:
gene_common.inc.php
Log Message:
show undef. ratio as NaN
Index: gene_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/gene_common.inc.php,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** gene_common.inc.php 23 Jan 2003 09:05:05 -0000 1.6
--- gene_common.inc.php 2 Feb 2003 18:02:09 -0000 1.7
***************
*** 90,94 ****
function renderExploreRatio(&$r)
{
! echo "<td>".sprintf("%.2f", $r)."</td>".
"<td bgcolor=".ratioColor($r).">".
"<img src='img/1.gif' width=10 height=1 alt=''></td>";
--- 90,94 ----
function renderExploreRatio(&$r)
{
! echo "<td>".(isset($r) ? sprintf("%.2f", $r) : "NaN")."</td>".
"<td bgcolor=".ratioColor($r).">".
"<img src='img/1.gif' width=10 height=1 alt=''></td>";
|
|
From: <tr...@us...> - 2003-02-02 15:53:41
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv30655/www
Modified Files:
user_edit.phtml
Log Message:
Added interface for setting default group and group/world access
Index: user_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user_edit.phtml,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** user_edit.phtml 2 Feb 2003 15:31:52 -0000 1.27
--- user_edit.phtml 2 Feb 2003 15:53:37 -0000 1.28
***************
*** 350,360 ****
echo "</table>\n";
userPrivilegeTable($user, false);
?>
! <table <?= $cellpad ?>>
<tr><th colspan=2 class=subhead>Change password</th></tr>
<?
- if($uid == $curUser->getId())
- {
- echo "<tr><td colspan=2> </td></tr>\n";
$msg = "";
[...71 lines suppressed...]
! </table>
!
! <p><table <?= $cellpad ?>>
<tr><th colspan=2 class=subhead>Change password</th></tr>
<?
$msg = "";
if(isset($i_updatepass))
***************
*** 375,379 ****
$msg = "<span class=red>Error: $err</span>";
else
! $msg = "Updated password successfully";
}
if($msg != "")
--- 440,444 ----
$msg = "<span class=red>Error: $err</span>";
else
! $msg = "Password successfully updated";
}
if($msg != "")
|
|
From: <tr...@us...> - 2003-02-02 15:53:40
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv30655/include/classes
Modified Files:
user.inc.php
Log Message:
Added interface for setting default group and group/world access
Index: user.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/user.inc.php,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** user.inc.php 2 Feb 2003 15:31:51 -0000 1.22
--- user.inc.php 2 Feb 2003 15:53:36 -0000 1.23
***************
*** 450,458 ****
function updateColumn($name, $value)
{
- $this->{$name} = $value;
$query = "UPDATE UserAccount ".
"SET `$name` = '".addslashes($value)."' ".
"WHERE `userGroup` = $this->id";
! return (bool)query($query);
}
function updatePassword($val)
--- 450,460 ----
function updateColumn($name, $value)
{
$query = "UPDATE UserAccount ".
"SET `$name` = '".addslashes($value)."' ".
"WHERE `userGroup` = $this->id";
! if(!query($query))
! return false;
! $this->{$name} = $value;
! return true;
}
function updatePassword($val)
***************
*** 476,490 ****
return $this->updateColumn("lastPlateTypeCreated", (int)$val);
}
! function updateDefaultGid($val)
! {
! return $this->updateColumn("defaultGid", (int)$val);
! }
! function updateDefaultGroupAccess($val)
! {
! return $this->updateColumn("defaultGroupAccess", max(0, min(2, $val)));
! }
! function updateDefaultWorldAccess($val)
{
! return $this->updateColumn("defaultWorldAccess", max(0, min(1, $val)));
}
--- 478,500 ----
return $this->updateColumn("lastPlateTypeCreated", (int)$val);
}
! function updateDefaultAccess($gid, $gacc, $wacc)
{
! $gid = (int)$gid;
! if(!isset($this->groups[$gid]))
! $gid = 0;
! $gacc = max(0, min(2, (int)$gacc));
! $wacc = max(0, min(2, (int)$wacc));
!
! $query = "UPDATE UserAccount ".
! "SET `defaultGid` = $gid, ".
! "`defaultGroupAccess` = $gacc, ".
! "`defaultWorldAccess` = $wacc ".
! "WHERE `userGroup` = $this->id";
! if(!query($query))
! return false;
! $this->defaultGid = $gid;
! $this->defaultGroupAccess = $gacc;
! $this->defaultWorldAccess = $wacc;
! return true;
}
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv22560/www
Modified Files:
arraybatch_edit.phtml arraytype_edit.phtml
experiment_edit.phtml extract_edit.phtml gene_explore.phtml
hyb_edit.phtml hyb_image.phtml hyb_result.phtml
image_edit.phtml label_edit.phtml labeled_edit.phtml
news_edit.phtml plate_arrange.phtml plate_edit.phtml
plate_upload.phtml platetype_edit.phtml program_edit.phtml
protocol_edit.phtml reporterlist_edit.phtml sample_edit.phtml
sampleannot_edit.phtml sampletissue_tree.phtml
trans_create.phtml user_edit.phtml usergroup_edit.phtml
ware_edit.phtml wizzzard_edit.phtml
Log Message:
Added default group/access to UserAccount and changed setOwner calls
Index: arraybatch_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/arraybatch_edit.phtml,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** arraybatch_edit.phtml 2 Feb 2003 13:44:00 -0000 1.10
--- arraybatch_edit.phtml 2 Feb 2003 15:31:51 -0000 1.11
***************
*** 64,68 ****
{
$ab->setArrayType($at->getId());
! $ab->setOwner($curUser->getId());
if(!acc(ArrayBatch::globalEdit()))
$err = "Access denied (".accessName(ArrayBatch::globalEdit()).")";
--- 64,68 ----
{
$ab->setArrayType($at->getId());
! $ab->makeOwned($curUser);
if(!acc(ArrayBatch::globalEdit()))
$err = "Access denied (".accessName(ArrayBatch::globalEdit()).")";
Index: arraytype_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/arraytype_edit.phtml,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** arraytype_edit.phtml 2 Feb 2003 13:44:01 -0000 1.16
--- arraytype_edit.phtml 2 Feb 2003 15:31:51 -0000 1.17
***************
*** 56,60 ****
else
{
! $at->setOwner($curUser->getId());
$at->setPlatform("cDNA");
if(!acc($at->globalEdit()))
--- 56,60 ----
else
{
! $at->makeOwned($curUser);
$at->setPlatform("cDNA");
if(!acc($at->globalEdit()))
Index: experiment_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/experiment_edit.phtml,v
retrieving revision 1.45
retrieving revision 1.46
diff -C2 -d -r1.45 -r1.46
*** experiment_edit.phtml 23 Jan 2003 22:16:54 -0000 1.45
--- experiment_edit.phtml 2 Feb 2003 15:31:51 -0000 1.46
***************
*** 79,83 ****
else
{
! $exp->setOwner($curUser->getId());
if(!acc($exp->globalEdit()))
$err = "Access denied (".accessName($exp->globalEdit()).")";
--- 79,83 ----
else
{
! $exp->makeOwned($curUser);
if(!acc($exp->globalEdit()))
$err = "Access denied (".accessName($exp->globalEdit()).")";
Index: extract_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/extract_edit.phtml,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** extract_edit.phtml 22 Jan 2003 08:01:54 -0000 1.33
--- extract_edit.phtml 2 Feb 2003 15:31:52 -0000 1.34
***************
*** 66,70 ****
(Extract::countForSample($samp->getId()) + 1));
}
! $ext->setOwner($curUser->getId());
$edit = true;
}
--- 66,70 ----
(Extract::countForSample($samp->getId()) + 1));
}
! $ext->makeOwned($curUser);
$edit = true;
}
Index: gene_explore.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/gene_explore.phtml,v
retrieving revision 1.68
retrieving revision 1.69
diff -C2 -d -r1.68 -r1.69
*** gene_explore.phtml 23 Jan 2003 16:53:18 -0000 1.68
--- gene_explore.phtml 2 Feb 2003 15:31:52 -0000 1.69
***************
*** 185,189 ****
$rlist = new ReporterList();
$rlist->setName($i_replistname);
! $rlist->setOwner($curUser->getId());
$rlist->setExperiment($expid);
$bctrans = true;
--- 185,189 ----
$rlist = new ReporterList();
$rlist->setName($i_replistname);
! $rlist->makeOwned($curUser);
$rlist->setExperiment($expid);
$bctrans = true;
Index: hyb_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_edit.phtml,v
retrieving revision 1.51
retrieving revision 1.52
diff -C2 -d -r1.51 -r1.52
*** hyb_edit.phtml 22 Jan 2003 08:02:00 -0000 1.51
--- hyb_edit.phtml 2 Feb 2003 15:31:52 -0000 1.52
***************
*** 66,70 ****
else
{
! $hyb->setOwner($curUser->getId());
if(!acc($hyb->globalEdit()))
$err = "Access denied (".accessName($hyb->globalEdit()).")";
--- 66,70 ----
else
{
! $hyb->makeOwned($curUser);
if(!acc($hyb->globalEdit()))
$err = "Access denied (".accessName($hyb->globalEdit()).")";
Index: hyb_image.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_image.phtml,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** hyb_image.phtml 22 Jan 2003 08:02:02 -0000 1.40
--- hyb_image.phtml 2 Feb 2003 15:31:52 -0000 1.41
***************
*** 91,95 ****
{
$edit = true;
! $acq->setOwner($curUser->getId());
$acq->setHybridization($hyb->getId());
$acq->setName($hyb->getName()." image set ".
--- 91,95 ----
{
$edit = true;
! $acq->makeOwned($curUser);
$acq->setHybridization($hyb->getId());
$acq->setName($hyb->getName()." image set ".
***************
*** 148,152 ****
$image->setName($u->getName());
$image->setDescr($u->getDescr());
! $image->setOwner($curUser->getId());
$image->setImageAcquisition($acqid);
$image->setChannels($i_imgchan[$img]);
--- 148,152 ----
$image->setName($u->getName());
$image->setDescr($u->getDescr());
! $image->makeOwned($curUser);
$image->setImageAcquisition($acqid);
$image->setChannels($i_imgchan[$img]);
Index: hyb_result.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_result.phtml,v
retrieving revision 1.72
retrieving revision 1.73
diff -C2 -d -r1.72 -r1.73
*** hyb_result.phtml 2 Feb 2003 13:44:01 -0000 1.72
--- hyb_result.phtml 2 Feb 2003 15:31:52 -0000 1.73
***************
*** 68,72 ****
{
$raw->setImageAcquisition($acq->getId());
! $raw->setOwner($curUser->getId());
if(isset($i_name))
$raw->setName($i_name);
--- 68,72 ----
{
$raw->setImageAcquisition($acq->getId());
! $raw->makeOwned($curUser);
if(isset($i_name))
$raw->setName($i_name);
Index: image_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/image_edit.phtml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** image_edit.phtml 22 Jan 2003 08:02:07 -0000 1.2
--- image_edit.phtml 2 Feb 2003 15:31:52 -0000 1.3
***************
*** 67,71 ****
else
{
! $img->setOwner($curUser->getId());
if(!acc($img->globalEdit()))
$err = "Access denied (".accessName($img->globalEdit()).")";
--- 67,71 ----
else
{
! $img->makeOwned($curUser);
if(!acc($img->globalEdit()))
$err = "Access denied (".accessName($img->globalEdit()).")";
Index: label_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/label_edit.phtml,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** label_edit.phtml 22 Jan 2003 08:02:07 -0000 1.10
--- label_edit.phtml 2 Feb 2003 15:31:52 -0000 1.11
***************
*** 51,55 ****
else
{
! $lbl->setOwner($curUser->getId());
if(!acc($lbl->globalEdit()))
$err = "Access denied (".accessName($lbl->globalEdit()).")";
--- 51,55 ----
else
{
! $lbl->makeOwned($curUser);
if(!acc($lbl->globalEdit()))
$err = "Access denied (".accessName($lbl->globalEdit()).")";
Index: labeled_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_edit.phtml,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** labeled_edit.phtml 22 Jan 2003 08:02:08 -0000 1.33
--- labeled_edit.phtml 2 Feb 2003 15:31:52 -0000 1.34
***************
*** 60,64 ****
else
{
! $lext->setOwner($curUser->getId());
$edit = true;
if(isset($i_ext))
--- 60,64 ----
else
{
! $lext->makeOwned($curUser);
$edit = true;
if(isset($i_ext))
Index: news_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/news_edit.phtml,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** news_edit.phtml 22 Jan 2003 08:02:12 -0000 1.16
--- news_edit.phtml 2 Feb 2003 15:31:52 -0000 1.17
***************
*** 41,45 ****
else
{
! $news->setOwner($curUser->getId());
}
$news->setName($i_name);
--- 41,45 ----
else
{
! $news->makeOwned($curUser);
}
$news->setName($i_name);
***************
*** 66,70 ****
else
{
! $news->setOwner($curUser->getId());
}
if(isset($i_name)) $news->setName($i_name);
--- 66,70 ----
else
{
! $news->makeOwned($curUser);
}
if(isset($i_name)) $news->setName($i_name);
Index: plate_arrange.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_arrange.phtml,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** plate_arrange.phtml 22 Jan 2003 08:02:12 -0000 1.25
--- plate_arrange.phtml 2 Feb 2003 15:31:52 -0000 1.26
***************
*** 150,154 ****
$p = new Plate();
$p->setName($p384name[$pos]);
! $p->setOwner($userid);
$p->setPlateType($ptype384id);
if(!$p->write())
--- 150,154 ----
$p = new Plate();
$p->setName($p384name[$pos]);
! $p->makeOwned($curUser);
$p->setPlateType($ptype384id);
if(!$p->write())
Index: plate_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_edit.phtml,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -d -r1.47 -r1.48
*** plate_edit.phtml 25 Jan 2003 00:46:52 -0000 1.47
--- plate_edit.phtml 2 Feb 2003 15:31:52 -0000 1.48
***************
*** 63,67 ****
$plate->resetId();
$plate->setPlateType($ptype->getId());
! $plate->setOwner($curUser->getId());
$plate->setAddedDate(today());
$curUser->updateLastPlateTypeCreated($ptype->getId());
--- 63,67 ----
$plate->resetId();
$plate->setPlateType($ptype->getId());
! $plate->makeOwned($curUser);
$plate->setAddedDate(today());
$curUser->updateLastPlateTypeCreated($ptype->getId());
Index: plate_upload.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_upload.phtml,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** plate_upload.phtml 2 Feb 2003 13:44:01 -0000 1.40
--- plate_upload.phtml 2 Feb 2003 15:31:52 -0000 1.41
***************
*** 574,578 ****
$plate = new Plate();
$plate->setName($pname);
! $plate->setOwner($curUser->getId());
$plate->setPlateType($ptypeid);
$plate->setBarcode($barcode);
--- 574,578 ----
$plate = new Plate();
$plate->setName($pname);
! $plate->makeOwned($curUser);
$plate->setPlateType($ptypeid);
$plate->setBarcode($barcode);
Index: platetype_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/platetype_edit.phtml,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** platetype_edit.phtml 22 Jan 2003 08:02:16 -0000 1.24
--- platetype_edit.phtml 2 Feb 2003 15:31:52 -0000 1.25
***************
*** 55,59 ****
else
{
! $ptype->setOwner($curUser->getId());
if(!acc($ptype->globalEdit()))
$err = "Access denied (".accessName($ptype->globalEdit()).")";
--- 55,59 ----
else
{
! $ptype->makeOwned($curUser);
if(!acc($ptype->globalEdit()))
$err = "Access denied (".accessName($ptype->globalEdit()).")";
***************
*** 173,177 ****
if($pet->getName() == "") // Nothing entered?
continue;
! $pet->setOwner($curUser->getId());
$pet->setPlateType($typeid);
}
--- 173,177 ----
if($pet->getName() == "") // Nothing entered?
continue;
! $pet->makeOwned($curUser);
$pet->setPlateType($typeid);
}
Index: program_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/program_edit.phtml,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** program_edit.phtml 1 Feb 2003 08:21:56 -0000 1.30
--- program_edit.phtml 2 Feb 2003 15:31:52 -0000 1.31
***************
*** 3,7 ****
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
--- 3,7 ----
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
***************
*** 58,62 ****
else
{
! $prog->setOwner($curUser->getId());
$err = handleUpload($upl, $curUser);
--- 58,62 ----
else
{
! $prog->makeOwned($curUser);
$err = handleUpload($upl, $curUser);
Index: protocol_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/protocol_edit.phtml,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** protocol_edit.phtml 22 Jan 2003 08:02:19 -0000 1.19
--- protocol_edit.phtml 2 Feb 2003 15:31:52 -0000 1.20
***************
*** 57,61 ****
if(!$protoid)
{
! $proto->setOwner($curUser->getId());
if(!acc($proto->globalEdit()))
$err = "Access denied (".accessName($proto->globalEdit()).")";
--- 57,61 ----
if(!$protoid)
{
! $proto->makeOwned($curUser);
if(!acc($proto->globalEdit()))
$err = "Access denied (".accessName($proto->globalEdit()).")";
Index: reporterlist_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/reporterlist_edit.phtml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** reporterlist_edit.phtml 23 Dec 2002 12:26:44 -0000 1.2
--- reporterlist_edit.phtml 2 Feb 2003 15:31:52 -0000 1.3
***************
*** 3,7 ****
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
--- 3,7 ----
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
***************
*** 83,87 ****
{
$edit = true;
! $rlist->setOwner($curUser->getId());
$rlist->setExperiment($exp->getId());
}
--- 83,87 ----
{
$edit = true;
! $rlist->makeOwned($curUser);
$rlist->setExperiment($exp->getId());
}
Index: sample_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sample_edit.phtml,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** sample_edit.phtml 13 Dec 2002 19:48:36 -0000 1.33
--- sample_edit.phtml 2 Feb 2003 15:31:52 -0000 1.34
***************
*** 3,7 ****
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
--- 3,7 ----
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
***************
*** 56,60 ****
else
{
! $samp->setOwner($curUser->getId());
if(!acc($samp->globalEdit()))
$err = "Access denied (".accessName($samp->globalEdit()).")";
--- 56,60 ----
else
{
! $samp->makeOwned($curUser);
if(!acc($samp->globalEdit()))
$err = "Access denied (".accessName($samp->globalEdit()).")";
Index: sampleannot_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sampleannot_edit.phtml,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** sampleannot_edit.phtml 13 Dec 2002 19:48:36 -0000 1.17
--- sampleannot_edit.phtml 2 Feb 2003 15:31:52 -0000 1.18
***************
*** 61,65 ****
{
$sat->setOptions(10);
! $sat->setOwner($curUser->getId());
}
if($edit)
--- 61,65 ----
{
$sat->setOptions(10);
! $sat->makeOwned($curUser);
}
if($edit)
Index: sampletissue_tree.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sampletissue_tree.phtml,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** sampletissue_tree.phtml 24 Jan 2003 22:10:25 -0000 1.15
--- sampletissue_tree.phtml 2 Feb 2003 15:31:52 -0000 1.16
***************
*** 61,65 ****
if(!isset($i_neworg) || !$i_neworg)
$t2->setParent($tissue->getId());
! $t2->setOwner($curUser->getId());
if(!$t2->write())
{
--- 61,65 ----
if(!isset($i_neworg) || !$i_neworg)
$t2->setParent($tissue->getId());
! $t2->makeOwned($curUser);
if(!$t2->write())
{
Index: trans_create.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/trans_create.phtml,v
retrieving revision 1.42
retrieving revision 1.43
diff -C2 -d -r1.42 -r1.43
*** trans_create.phtml 1 Feb 2003 17:18:51 -0000 1.42
--- trans_create.phtml 2 Feb 2003 15:31:52 -0000 1.43
***************
*** 162,166 ****
$tran = new Transformation();
! $tran->setOwner($userid);
$tran->setBioAssaySet($setid);
$tran->setIsFilter(isset($i_filt) && $i_filt);
--- 162,166 ----
$tran = new Transformation();
! $tran->makeOwned($curUser);
$tran->setBioAssaySet($setid);
$tran->setIsFilter(isset($i_filt) && $i_filt);
Index: user_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user_edit.phtml,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** user_edit.phtml 1 Feb 2003 08:44:09 -0000 1.26
--- user_edit.phtml 2 Feb 2003 15:31:52 -0000 1.27
***************
*** 51,55 ****
{
// Set creator
! $user->setOwner($curUser->getId());
if(!acc($user->globalEdit()))
$err = "Access denied (".accessName($user->globalEdit()).")";
--- 51,55 ----
{
// Set creator
! $user->makeOwned($curUser);
if(!acc($user->globalEdit()))
$err = "Access denied (".accessName($user->globalEdit()).")";
***************
*** 258,262 ****
">Undelete user</a></td></tr>\n";
}
! else
{
echo "<tr><td colspan=2><a onClick=\"return ".
--- 258,262 ----
">Undelete user</a></td></tr>\n";
}
! else if($user->getId() != $curUser->getId())
{
echo "<tr><td colspan=2><a onClick=\"return ".
***************
*** 350,360 ****
echo "</table>\n";
userPrivilegeTable($user, false);
! echo "<table $cellpad>\n";
!
if($uid == $curUser->getId())
{
echo "<tr><td colspan=2> </td></tr>\n";
$msg = "";
! if(isset($i_updatepass) && $i_updatepass)
{
$err = "";
--- 350,362 ----
echo "</table>\n";
userPrivilegeTable($user, false);
! ?>
! <table <?= $cellpad ?>>
! <tr><th colspan=2 class=subhead>Change password</th></tr>
! <?
if($uid == $curUser->getId())
{
echo "<tr><td colspan=2> </td></tr>\n";
$msg = "";
! if(isset($i_updatepass))
{
$err = "";
***************
*** 380,391 ****
<form method=post action='user_edit.phtml?i_u=<?= $uid ?>'>
<input type=hidden name=location value="<?= html($location, 0) ?>">
- <input type=hidden name=i_updatepass value=1>
<tr><th>Old password</th><td><input type=password size=15 name=i_oldpass
value=""></td></tr>
<tr><th>New password</th><td><input type=password size=15 name=i_newpass1
value=""></td></tr>
! <tr><th>Retype</th><td><input type=password size=15 name=i_newpass2
! value=""></td></tr>
! <tr><td colspan=2><input type=submit value='Update'></td></tr>
</form>
<?
--- 382,392 ----
<form method=post action='user_edit.phtml?i_u=<?= $uid ?>'>
<input type=hidden name=location value="<?= html($location, 0) ?>">
<tr><th>Old password</th><td><input type=password size=15 name=i_oldpass
value=""></td></tr>
<tr><th>New password</th><td><input type=password size=15 name=i_newpass1
value=""></td></tr>
! <tr><th>Retype new password</th><td><input type=password size=15 name=i_newpass2
! value="">
! <input type=submit name=i_updatepass value='Update'></td></tr>
</form>
<?
Index: usergroup_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/usergroup_edit.phtml,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** usergroup_edit.phtml 28 Jan 2003 17:22:55 -0000 1.9
--- usergroup_edit.phtml 2 Feb 2003 15:31:52 -0000 1.10
***************
*** 52,56 ****
{
// Set creator
! $group->setOwner($curUser->getId());
if(!acc($group->globalEdit()))
$err = "Access denied (".accessName($group->globalEdit()).")";
--- 52,56 ----
{
// Set creator
! $group->makeOwned($curUser);
if(!acc($group->globalEdit()))
$err = "Access denied (".accessName($group->globalEdit()).")";
Index: ware_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/ware_edit.phtml,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** ware_edit.phtml 13 Dec 2002 19:48:36 -0000 1.17
--- ware_edit.phtml 2 Feb 2003 15:31:52 -0000 1.18
***************
*** 3,7 ****
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
--- 3,7 ----
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson
//
// This file is part of BASE.
***************
*** 70,74 ****
else
{
! $ware->setOwner($curUser->getId());
if(!acc($ware->globalEdit()))
$err = "Access denied (".accessName($ware->globalEdit()).")";
--- 70,74 ----
else
{
! $ware->makeOwned($curUser);
if(!acc($ware->globalEdit()))
$err = "Access denied (".accessName($ware->globalEdit()).")";
Index: wizzzard_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/wizzzard_edit.phtml,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** wizzzard_edit.phtml 2 Feb 2003 13:44:01 -0000 1.8
--- wizzzard_edit.phtml 2 Feb 2003 15:31:52 -0000 1.9
***************
*** 48,52 ****
$wiz->resetId();
$wiz->setAddedDate(now());
! $wiz->setOwner($curUser->getId());
}
else if(!$wiz->mayEdit($curUser))
--- 48,52 ----
$wiz->resetId();
$wiz->setAddedDate(now());
! $wiz->makeOwned($curUser);
}
else if(!$wiz->mayEdit($curUser))
***************
*** 60,64 ****
else
{
! $wiz->setOwner($curUser->getId());
$wiz->setFormatType($i_type);
if($fileid && $err == "")
--- 60,64 ----
else
{
! $wiz->makeOwned($curUser)
$wiz->setFormatType($i_type);
if($fileid && $err == "")
|
|
From: <tr...@us...> - 2003-02-02 15:31:54
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv22560/include/web
Modified Files:
array_common.inc.php experiment_common.inc.php
reporterlist_common.inc.php upload_common.inc.php
Log Message:
Added default group/access to UserAccount and changed setOwner calls
Index: array_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/array_common.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** array_common.inc.php 2 Feb 2003 13:44:00 -0000 1.10
--- array_common.inc.php 2 Feb 2003 15:31:51 -0000 1.11
***************
*** 215,219 ****
$as->setOrderNumber($on);
$as->setBatch($abid);
! $as->setOwner($user->getId());
if(isset($i_adescr[$on]))
$as->setDescr($i_adescr[$on]);
--- 215,219 ----
$as->setOrderNumber($on);
$as->setBatch($abid);
! $as->makeOwned($user);
if(isset($i_adescr[$on]))
$as->setDescr($i_adescr[$on]);
Index: experiment_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/experiment_common.inc.php,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** experiment_common.inc.php 23 Jan 2003 11:33:38 -0000 1.21
--- experiment_common.inc.php 2 Feb 2003 15:31:51 -0000 1.22
***************
*** 58,62 ****
if($set->getName() == "")
return "The BioAssaySet must have a name";
! $set->setOwner($user->getId());
$set->setExperiment($exp->getId());
$set->setIntensityMeasure($measure);
--- 58,62 ----
if($set->getName() == "")
return "The BioAssaySet must have a name";
! $set->makeOwned($user);
$set->setExperiment($exp->getId());
$set->setIntensityMeasure($measure);
***************
*** 91,95 ****
$ba->setExperiment($exp->getId());
$ba->setChannels($exp->getChannels());
! $ba->setOwner($user->getId());
$ba->setName(RawBioAssay::getNameFromId($r));
--- 91,95 ----
$ba->setExperiment($exp->getId());
$ba->setChannels($exp->getChannels());
! $ba->makeOwned($user);
$ba->setName(RawBioAssay::getNameFromId($r));
Index: reporterlist_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/reporterlist_common.inc.php,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** reporterlist_common.inc.php 22 Jan 2003 08:01:44 -0000 1.6
--- reporterlist_common.inc.php 2 Feb 2003 15:31:51 -0000 1.7
***************
*** 45,49 ****
$rlist = new ReporterList();
$rlist->setName($i_replistname);
! $rlist->setOwner($user->getId());
$rlist->setExperiment($expid);
if($err != "") {}
--- 45,49 ----
$rlist = new ReporterList();
$rlist->setName($i_replistname);
! $rlist->makeOwned($user);
$rlist->setExperiment($expid);
if($err != "") {}
Index: upload_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/upload_common.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** upload_common.inc.php 22 Jan 2003 08:01:45 -0000 1.12
--- upload_common.inc.php 2 Feb 2003 15:31:51 -0000 1.13
***************
*** 181,185 ****
if(isset($_REQUEST[$descrVar]))
$upload->setDescr($_REQUEST[$descrVar]);
! $upload->setOwner($user->getId());
$upload->setAddedDate(now());
$upload->setFileSize($f["size"]);
--- 181,185 ----
if(isset($_REQUEST[$descrVar]))
$upload->setDescr($_REQUEST[$descrVar]);
! $upload->makeOwned($user);
$upload->setAddedDate(now());
$upload->setFileSize($f["size"]);
|
