basedb-cvs Mailing List for BASE (Page 37)

Brought to you by: kurri, troein

basedb-cvs — CVS commit messages

You can subscribe to this list here.

2002	_Jan	_Feb	_Mar	_Apr	_May	_Jun	_Jul	_Aug (14)	_Sep (76)	_Oct (65)	_Nov (177)	_Dec (147)
2003	_Jan (257)	_Feb (313)	_Mar	_Apr	_May	_Jun	_Jul	_Aug	_Sep	_Oct	_Nov	_Dec

Flat | Threaded

<< < 1 .. 35 36 37 38 39 .. 42 > >> (Page 37 of 42)

[basedb-cvs] basedb/www mysql.inc.php,1.19,1.20

From: <mat...@us...> - 2002-10-30 09:27:01

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv4358

Modified Files:
	mysql.inc.php 
Log Message:
Removed query logging


Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** mysql.inc.php	29 Oct 2002 16:33:48 -0000	1.19
--- mysql.inc.php	30 Oct 2002 09:26:57 -0000	1.20
***************
*** 75,85 ****
  }
  
- function tmp_ful_log($s) {
-     $filename ="/home/shakespeare/mats/log.txt";
-     $handle= fopen($filename,'a');
-     fputs($handle, $s);
-     fclose($handle);
- }
- 
  function query(&$query, $quiet = 0)
  {
--- 75,78 ----
***************
*** 88,93 ****
  //		error_log("Q: $query");
  //	error_log("Q: $query");
- 
-     tmp_ful_log("$query\n");
  
  	$res = mysql_query($query);
--- 81,84 ----

[basedb-cvs] basedb/www label.inc.php,NONE,1.1 label_edit.phtml,NONE,1.1 label_list.phtml,NONE,1.1 bio.inc.php,1.29,1.30 item.inc.php,1.36,1.37 labeled_edit.phtml,1.20,1.21 labeled_list.phtml,1.17,1.18 left.phtml,1.50,1.51 mysql.inc.php,1.18,1.19 raw_common.inc.php,1.19,1.20 raw_edit.phtml,1.16,1.17 raw_plotter.phtml,1.15,1.16

From: <mat...@us...> - 2002-10-29 16:33:54

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv19159

Modified Files:
	bio.inc.php item.inc.php labeled_edit.phtml labeled_list.phtml 
	left.phtml mysql.inc.php raw_common.inc.php raw_edit.phtml 
	raw_plotter.phtml 
Added Files:
	label.inc.php label_edit.phtml label_list.phtml 
Log Message:
Labels getting their own table

--- NEW FILE: label.inc.php ---
<?
// $Id: label.inc.php,v 1.1 2002/10/29 16:33:46 matsattnas Exp $
//
// BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
// Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson,
//    David Martin
//
// 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
[...115 lines suppressed...]
		return parent::getNameFromId("Label", $id);
	}
	function getBasicFromId($id)
	{
		return parent::getBasicFromId("Label", $id);
	}

	function getSharersForId($id)
	{
		return parent::getSharersForId("Label", $id);
	}

	function isSharedId($id, &$user, $write = 0)
	{
		return parent::isSharedId("Label", $id, $user, $write);
	}

}

?>
--- NEW FILE: label_edit.phtml ---
<?
// $Id: label_edit.phtml,v 1.1 2002/10/29 16:33:47 matsattnas 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
[...118 lines suppressed...]
					"confirm('Really delete this label?')\" ".
					href("label_edit.phtml?i_lbl=$lblid&i_delete=1", 1).
					">Delete label</a></td></tr>\n";
			}
		}
		if($lbl->mayEdit($curUser, BUA_BIO_EDIT))
		{
			echo "<tr><td colspan=2><a ".
				href("label_edit.phtml?i_lbl=$lblid&i_edit=1", 1).
				">Edit label</a></td></tr>\n";
		}

?>
<tr><th>Name</th><td><?= html($lbl->getName()).remMark($lbl) ?></td></tr>
<tr><th>Description</th><td><?= html($lbl->getDescr()) ?></td></tr>
<?
	}
?>
</body>
</html>
--- NEW FILE: label_list.phtml ---
<?
// $Id: label_list.phtml,v 1.1 2002/10/29 16:33:47 matsattnas 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
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
//
	require_once("init.inc.php");
	require_once("search.inc.php");
	require_once("searchhtml.inc.php");
	require_once("item_common.inc.php");
	require_once("links_common.inc.php");
	require_once("label.inc.php");

	verifyAccess(BUA_BIO_READ);
	showDelPrep();

	// Sharing
	$users = UserGroup::getBrief();
	groupAccessHandle("Label", $curUser);

	$searchfields = array("Name", "Description", "Owner");
	$fieldtype = array(0, 0, 0);
	$headerfields = array("Name", "Owner", "[<a href=javascript:selAll(1)>A</a> ".
		"<a href=javascript:selAll(0)>N</a>]", "Group", "World");
	$sortorder = array(1, 1, 0, 0, 0);
	$defsort = 0;
	$userid = $curUser->getId();

	$pageTitle="$config[codename] - Labels";
	require_once("htmlinit.phtml");
?>
<table <?= $cellpad ?>>
<form name=ff method=post action="label_list.phtml">
<tr><th class=pagehead>Labels <?= webHelp(73, 1) ?></th></tr>
</table>
<?
	$search = makeSearchTable($userid, "label", "User", $userid,
		"label", $searchfields, $fieldtype, 2, "", true);
	echo "<p>\n";

	Label::prepareSearch($search, $curUser, 30, showDelValue());

	groupAccessScripts();

	if(!acc(BUA_BIO_EDIT))
		$addlink = "";
	else
		$addlink = "<a class=large href='label_edit.phtml'>Add label</a>";
	makeSearchHeader($search, $headerfields, $sortorder, $defsort, "",
		"document.ff.submit();", "", "", array($addlink));

	$labels = Label::search($search, $curUser);

	for($i = 0, $odd = 1; $i < count($labels); $i++, $odd ^= 1)
	{
		$s =& $labels[$i];

		echo "<tr bgcolor=$tdbg[$odd]>".
			"<td><a href='label_edit.phtml?i_lbl=$s[id]'>".
				html($s["name"])."</a>".remMark($s["removed"])."</td>".
			"<td>".html($s["userName"])."</td>".
			"<td>".groupAccessCheckbox($s["id"])."</td>".
			"<td>".groupInfo($s, $users)."</td>".
			"<td>".worldInfo($s)."</td></tr>\n";
	}
	$cols = count($headerfields);
	if($addlink != "")
		echo "<tr><td colspan=$cols>$addlink</td></tr>\n";

	groupAccessFooter($cols, $curUser);
	showDelLinks($cols);
?>
</form>
</table>

</body>
</html>

Index: bio.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bio.inc.php,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** bio.inc.php	8 Oct 2002 09:05:13 -0000	1.29
--- bio.inc.php	29 Oct 2002 16:33:44 -0000	1.30
***************
*** 503,507 ****
  	function LabeledExtract($name = "", $descr = "", $owner = 0,
  		$addedDate = "", $extract = 0, $protocol = 0, $labelingDate = "",
! 		$quantity = 0, $quantityLeft = "", $label = "", $id = 0,
  		$removed = 0)
  	{
--- 503,507 ----
  	function LabeledExtract($name = "", $descr = "", $owner = 0,
  		$addedDate = "", $extract = 0, $protocol = 0, $labelingDate = "",
! 		$quantity = 0, $quantityLeft = "", $label = 0, $id = 0,
  		$removed = 0)
[...137 lines suppressed...]
  			"WHERE e.id = le.extract AND s.id = e.sample ".
  			"AND ug.id = le.owner AND p.id = le.protocol ".
  			$search->getWhere()." ".$search->getExtraWhere().
--- 742,757 ----
  
  		$query = "SELECT le.*, ug.name AS `userName`, ".
+ 			Item::whereShared("l", $user)." AS `labelRead`, ".
  			Item::whereShared("s", $user)." AS `sampleRead`, ".
  			Item::whereShared("e", $user)." AS `extractRead`, ".
  			Item::whereShared("p", $user)." AS `protocolRead`, ".
+ 			"l.name AS `labelName`, l.removed AS `labelRemoved`, ".
  			"p.name AS `protocolName`, p.removed AS `protocolRemoved`, ".
  			"e.name AS `extractName`, e.removed AS `extractRemoved`, ".
  			"e.sample, s.name AS `sampleName`, s.removed AS `sampleRemoved` ".
! 			"FROM LabeledExtract le, Extract e, Label l, ".
  			"Sample s, Protocol p, UserGroup ug ".
  			"WHERE e.id = le.extract AND s.id = e.sample ".
+             "AND le.label = l.id ".
  			"AND ug.id = le.owner AND p.id = le.protocol ".
  			$search->getWhere()." ".$search->getExtraWhere().

Index: item.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/item.inc.php,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** item.inc.php	8 Oct 2002 09:05:13 -0000	1.36
--- item.inc.php	29 Oct 2002 16:33:44 -0000	1.37
***************
*** 267,275 ****
  	function getBrief($type, &$user, $removed = NULL)
  	{
- 		$owner = (int)$owner;
  		$arr = array();
  		$query = "SELECT i.id, i.name FROM $type i ".
! 			"WHERE ".$this->whereShared("i", $user)." ".
! 			$this->whereRemovedAnd("i", $removed);
  		$res = query($query);
  		while($row =& db_fetch_row($res))
--- 267,274 ----
  	function getBrief($type, &$user, $removed = NULL)
  	{
  		$arr = array();
  		$query = "SELECT i.id, i.name FROM $type i ".
! 			"WHERE ".Item::whereShared("i", $user)." ".
! 			Item::whereRemovedAnd("i", $removed);
  		$res = query($query);
  		while($row =& db_fetch_row($res))

Index: labeled_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_edit.phtml,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** labeled_edit.phtml	1 Oct 2002 21:53:20 -0000	1.20
--- labeled_edit.phtml	29 Oct 2002 16:33:47 -0000	1.21
***************
*** 216,224 ****
  <tr><th>Label</th><td><select name=i_label>
  <?
! 		$labels = LabeledExtract::getLabels();
! 		for($i = 0; $i < count($labels); $i++)
  		{
! 			$sel = ($labels[$i] == $lext->getLabel()) ? "selected" : "";
! 			echo "<option $sel value='$labels[$i]'>".html($labels[$i], 0)."\n";
  		}
  ?>
--- 216,224 ----
  <tr><th>Label</th><td><select name=i_label>
  <?
! 		$labels = LabeledExtract::getLabels($curUser);
! 		while (list($key, $value) = each($labels))
  		{
! 		  $sel = ($key == $lext->getLabel()) ? "selected" : "";
! 		  echo "<option $sel value='$key'>".html($value["name"], 0)."\n";
  		}
  ?>
***************
*** 313,317 ****
  	protocolIdLink($lext->getProtocol(), $curUser) ?></td></tr>
  <tr><th>Description</th><td><?= html($lext->getDescr()) ?></td></tr>
! <tr><th>Label</th><td><?= html($lext->getLabel()) ?></td></tr>
  <tr><th>Quantity of extract labeled (µg)</th><td><?=
  	html($lext->getQuantity()) ?></td></tr>
--- 313,320 ----
  	protocolIdLink($lext->getProtocol(), $curUser) ?></td></tr>
  <tr><th>Description</th><td><?= html($lext->getDescr()) ?></td></tr>
! <?
!                $labels = LabeledExtract::getLabels($curUser);
! ?>
! <tr><th>Label</th><td><?= html($labels[$lext->getLabel()]["name"]) ?></td></tr>
  <tr><th>Quantity of extract labeled (µg)</th><td><?=
  	html($lext->getQuantity()) ?></td></tr>

Index: labeled_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_list.phtml,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** labeled_list.phtml	30 Sep 2002 16:57:05 -0000	1.17
--- labeled_list.phtml	29 Oct 2002 16:33:48 -0000	1.18
***************
*** 40,46 ****
  	groupAccessHandle("LabeledExtract", $curUser);
  
! 	$searchfields = array("Name", "Description", "Extract", "Sample",
  		"Date added", "Labeling date", "Protocol", "Quantity left");
! 	$fieldtype = array(0, 0, 0, 0, 1, 1, 0, 2);
  	$headerfields = array("Labeled extract", "Label",
  		"Extract", "Sample", "Labeled",
--- 40,46 ----
  	groupAccessHandle("LabeledExtract", $curUser);
  
! 	$searchfields = array("Name", "Description", "Extract", "Label", "Sample",
  		"Date added", "Labeling date", "Protocol", "Quantity left");
! 	$fieldtype = array(0, 0, 0, 0, 0, 1, 1, 0, 2);
  	$headerfields = array("Labeled extract", "Label",
  		"Extract", "Sample", "Labeled",
***************
*** 84,88 ****
  	{
  		$s =& $lexts[$i];
! 
  		if($s["sampleRead"])
  		{
--- 84,94 ----
  	{
  		$s =& $lexts[$i];
! 		
! 		if($s["labelRead"])
! 		{
! 			$llink = "<a href='label_edit.phtml?i_lbl=$s[label]'>".
! 				html($s["labelName"])."</a>".remMark($s["labelRemoved"]);
! 		} else
! 			$llink = html($s["labelName"]);
  		if($s["sampleRead"])
  		{
***************
*** 115,119 ****
  			"<td><a href='labeled_edit.phtml?i_lext=$s[id]'>".
  				html($s["name"])."</a>".remMark($s["removed"])."</td>".
! 			"<td>".html($s["label"])."</td>".
  			"<td>$elink</td>".
  			"<td>$slink</td>".
--- 121,125 ----
  			"<td><a href='labeled_edit.phtml?i_lext=$s[id]'>".
  				html($s["name"])."</a>".remMark($s["removed"])."</td>".
! 			"<td>$llink</td>".
  			"<td>$elink</td>".
  			"<td>$slink</td>".

Index: left.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/left.phtml,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** left.phtml	21 Oct 2002 16:16:26 -0000	1.50
--- left.phtml	29 Oct 2002 16:33:48 -0000	1.51
***************
*** 210,213 ****
--- 210,214 ----
  <tr><td><a target=main href="sample_list.phtml">Samples</a></td></tr>
  <tr><td><a target=main href="extract_list.phtml">Extracts</a></td></tr>
+ <tr><td><a target=main href="label_list.phtml">Labels</a></td></tr>
  <tr><td><a target=main href="labeled_list.phtml">Labeled extracts</a></td></tr>
  <tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>

Index: mysql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/mysql.inc.php,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** mysql.inc.php	3 Oct 2002 16:45:06 -0000	1.18
--- mysql.inc.php	29 Oct 2002 16:33:48 -0000	1.19
***************
*** 75,78 ****
--- 75,85 ----
  }
  
+ function tmp_ful_log($s) {
+     $filename ="/home/shakespeare/mats/log.txt";
+     $handle= fopen($filename,'a');
+     fputs($handle, $s);
+     fclose($handle);
+ }
+ 
  function query(&$query, $quiet = 0)
  {
***************
*** 81,84 ****
--- 88,93 ----
  //		error_log("Q: $query");
  //	error_log("Q: $query");
+ 
+     tmp_ful_log("$query\n");
  
  	$res = mysql_query($query);

Index: raw_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_common.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** raw_common.inc.php	12 Sep 2002 22:37:56 -0000	1.19
--- raw_common.inc.php	29 Oct 2002 16:33:49 -0000	1.20
***************
*** 133,136 ****
--- 133,142 ----
  		'scrollbars=yes,resizable=yes,toolbar=1');
  }
+ function rawPlotter2(raw)
+ {
+ 	window.open('raw_plotter2.phtml?i_r='+raw, 'rawPlotter_'+raw,
+ 		'location=1,menubar=1,personalbar=0,width=1250,height=820,'+
+ 		'scrollbars=yes,resizable=yes,toolbar=1');
+ }
  </script>
  <?
***************
*** 211,215 ****
  				"Overview&nbsp;plot</a>] ".
  				"[<a class=popup href='javascript:rawPlotter($id)'>".
! 				"Plot&nbsp;tool</a>]</td>".
  				"</tr>\n";
  		}
--- 217,223 ----
  				"Overview&nbsp;plot</a>] ".
  				"[<a class=popup href='javascript:rawPlotter($id)'>".
! 				"Plot&nbsp;tool&nbsp;(classic)</a>] ".
! 				"[<a class=popup href='javascript:rawPlotter2($id)'>".
! 				"Plot&nbsp;tool&nbsp;(beta)</a>]</td>".
  				"</tr>\n";
  		}

Index: raw_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_edit.phtml,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** raw_edit.phtml	10 Sep 2002 23:06:28 -0000	1.16
--- raw_edit.phtml	29 Oct 2002 16:33:49 -0000	1.17
***************
*** 172,176 ****
  			"Overview plot</a>]".
  			" [<a class=popup href='javascript:rawPlotter($rawid)'>".
! 			"Plot tool</a>]".
  			"</td></tr>\n".
  			"<tr><th>Molecule IDs</th>".
--- 172,178 ----
  			"Overview plot</a>]".
  			" [<a class=popup href='javascript:rawPlotter($rawid)'>".
! 			"Plot tool (classic)</a>]".
! 			" [<a class=popup href='javascript:rawPlotter2($rawid)'>".
! 			"Plot tool (beta)</a>]".
  			"</td></tr>\n".
  			"<tr><th>Molecule IDs</th>".

Index: raw_plotter.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_plotter.phtml,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** raw_plotter.phtml	29 Aug 2002 16:51:34 -0000	1.15
--- raw_plotter.phtml	29 Oct 2002 16:33:49 -0000	1.16
***************
*** 120,123 ****
--- 120,124 ----
  		include("htmlinit.phtml");
  ?>
+ 
  <table <?= $cellpad ?> width=100%>
  <tr><th class=pagehead><?= $plotType ?> plot</th>
***************
*** 222,229 ****
  ?>
  	</select></td></tr>
! <tr><td colspan=5 rowspan=8><img name=thePlot
! 	src="img/baseplotlogo.png" width=<?= $plotSize[0] ?>
! 	height=<?= $plotSize[1] ?>></td>
! 	<th>Format</th></tr>
  <tr><td valign=top><select name=i_fmt>
  <?
--- 223,230 ----
  ?>
  	</select></td></tr>
!  <tr><td colspan=5 rowspan=8><img name=thePlot
!  	src="img/baseplotlogo.png" width=<?= $plotSize[0] ?>
!  	height=<?= $plotSize[1] ?>></td>
!  	<th>Format</th></tr>
  <tr><td valign=top><select name=i_fmt>
  <?
***************
*** 245,248 ****
--- 246,250 ----
  	<input type=button value="View" onClick="subm(2)"></td></tr>
  </table>
+ 
  </body>
  </html>

[basedb-cvs] basedb/www extracols.inc.php,NONE,1.1 reporter_columns.inc.php,NONE,1.1 extract_list.phtml,1.17,1.18 molecule.inc.php,1.35,1.36 raw_columns.inc.php,1.1,1.2 sample_annotate.phtml,1.12,1.13

From: <tr...@us...> - 2002-10-28 14:39:48

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv18430

Modified Files:
	extract_list.phtml molecule.inc.php raw_columns.inc.php 
	sample_annotate.phtml 
Added Files:
	extracols.inc.php reporter_columns.inc.php 
Log Message:
Admin-defined column stuff

--- NEW FILE: extracols.inc.php ---
<?
// $Id: extracols.inc.php,v 1.1 2002/10/28 14:39:33 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
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
//

require_once("search.inc.php");

define("XCOL_FLOAT",			1);	// 32 or 64 bits
define("XCOL_BOOLEAN",		2);	// 0 or 1 (not pgsql's boolean type)
define("XCOL_TINYINT",		3);	// 8 bits
define("XCOL_SMALLINT",		4);	// 16 bits
define("XCOL_INT",			5);	// 32 bits
define("XCOL_STRING",		6);	// 255 chars
define("XCOL_LONGSTRING",	7);	// 65535 chars
define("XCOL_DATETIME",		8);	// well, duh

function xcolTypecast(&$var, $type)
{
	switch($type)
	{
		case XCOL_FLOAT:
			set_type($var, "float");
			break;
		case XCOL_BOOLEAN:
			$var = $var ? 1 : 0;
			break;
		case XCOL_TINYINT:
			$var = max(-128, min(127, (int)$var));
			break;
		case XCOL_SMALLINT:
			$var = max(-32768, min(32767, (int)$var));
			break;
		case XCOL_INT:
			set_type($var, "int");
			break;
		case XCOL_STRING:
			set_type($var, "string");
			if(strlen($var) > 255)
				$var = substr($var, 0, 255);
			break;
		case XCOL_LONGSTRING:
			set_type($var, "string");
			if(strlen($var) > 65535)
				$var = substr($var, 0, 65535);
			break;
		default:
			error_log("Invalid extra column type $type (value=$var)");
	}
}

?>
--- NEW FILE: reporter_columns.inc.php ---
<?
// $Id: reporter_columns.inc.php,v 1.1 2002/10/28 14:39:38 troein Exp $
//
// This file is part of BASE.
// BioArray Software Environment (BASE) - http://base.thep.lu.se/
// Copyright (C) 2002 Carl Troein
//
// BASE is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public License
// as published by the Free Software Foundation; either version 2
// of the License, or (at your option) any later version.
//
// BASE is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
[...103 lines suppressed...]
		return array(
			array("reporterId",	XCOL_STRING,	"Reporter ID"),
			array("species",		XCOL_STRING,	"Species"),
			array("clusterId",	XCOL_INT,		"UniGene cluster ID"),
			array("geneName",		XCOL_STRING,	"Gene name"),
			array("geneSymbol",	XCOL_STRING,	"Gene symbol"),
		);
	}
	
	function getAllColumns()
	{
		return array_merge(MoleculeColumn::getBasicColumns(),
			MoleculeColumn::getColumns());
	}
}




?>
Index: extract_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/extract_list.phtml,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** extract_list.phtml	1 Oct 2002 17:35:10 -0000	1.17
--- extract_list.phtml	28 Oct 2002 14:39:34 -0000	1.18
***************
*** 94,98 ****
  				html($arr["name"])."</a>".remMark($arr["removed"]);
  		}
! 		$hybs = implode(", ", $hybs);
  		if($hybs == "")
  			$hybs = html("");
--- 94,98 ----
  				html($arr["name"])."</a>".remMark($arr["removed"]);
  		}
! 		$hybs = implode(",\n", $hybs);
  		if($hybs == "")
  			$hybs = html("");
***************
*** 107,111 ****
  		if(!$s["removed"] && acc(BUA_BIO_EDIT))
  			$labs[] = "<a href='labeled_edit.phtml?i_ext=$s[id]'>[new]</a>";
! 		$labs = implode(", ", $labs);
  		if($labs == "")
  			$labs = html("");
--- 107,111 ----
  		if(!$s["removed"] && acc(BUA_BIO_EDIT))
  			$labs[] = "<a href='labeled_edit.phtml?i_ext=$s[id]'>[new]</a>";
! 		$labs = implode(",\n", $labs);
  		if($labs == "")
  			$labs = html("");

Index: molecule.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/molecule.inc.php,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** molecule.inc.php	30 Sep 2002 21:13:10 -0000	1.35
--- molecule.inc.php	28 Oct 2002 14:39:35 -0000	1.36
***************
*** 25,108 ****
  //
  require_once("db.inc.php");
  require_once("genelist.inc.php");
  
! define("CLEN_MOLECULE_CLONEID", 255);
! define("CLEN_MOLECULE_SPECIES", 2);
! define("CLEN_MOLECULE_ACCESSION", 20);
! define("CLEN_MOLECULE_NID", 20);
! define("CLEN_MOLECULE_CHROMOSOME", 3);
! define("CLEN_MOLECULE_CYTOBAND", 30);
[...824 lines suppressed...]
  			"markers", "locusLink", "omim", "accession", "nid", "antibiotics",
--- 516,520 ----
  	function searchIntoGeneList(&$search, $genelist)
  	{
! 		$sortfields = array("reporterId", array("species", "clusterId"),
  			"geneSymbol", "geneName", "chromosome", "cytoBand",
  			"markers", "locusLink", "omim", "accession", "nid", "antibiotics",
***************
*** 708,712 ****
  
  		$query = "SELECT m.id ".
! 			"FROM Molecule m ".$search->getExtraTables()." ".
  			"WHERE ".db_true()." ".$search->getWhere()." ".
  			$search->getExtraWhere()." $ob";
--- 539,543 ----
  
  		$query = "SELECT m.id ".
! 			"FROM Reporter m ".$search->getExtraTables()." ".
  			"WHERE ".db_true()." ".$search->getWhere()." ".
  			$search->getExtraWhere()." $ob";

Index: raw_columns.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_columns.inc.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** raw_columns.inc.php	8 Oct 2002 09:05:13 -0000	1.1
--- raw_columns.inc.php	28 Oct 2002 14:39:36 -0000	1.2
***************
*** 21,25 ****
  //
  
! require_once("search.inc.php");
  
  class RawBioAssayData
--- 21,25 ----
  //
  
! require_once("extracols.inc.php");
  
[...107 lines suppressed...]
! 			array("y", XCOL_FLOAT, ""),
  		);
  	}
***************
*** 87,93 ****
  	{
  		return array(
! 			array("reporter", "s", "Reporter ID"),
! 			array("x", "f", "Physical x coord."),
! 			array("y", "f", "Physical y coord."),
  		);
  	}
--- 85,91 ----
  	{
  		return array(
! 			array("reporter", XCOL_STRING, "Reporter ID"),
! 			array("x", XCOL_FLOAT, "Physical x coord."),
! 			array("y", XCOL_FLOAT, "Physical y coord."),
  		);
  	}

Index: sample_annotate.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sample_annotate.phtml,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** sample_annotate.phtml	16 Sep 2002 14:20:57 -0000	1.12
--- sample_annotate.phtml	28 Oct 2002 14:39:38 -0000	1.13
***************
*** 31,44 ****
  	setLocation("sample_list.phtml");
  
! 	$annottypes = SampleAnnotationType::getAllById();
  	$types = SampleAnnotationType::getValueTypeNames();
! 	if(!isset($i_use)) $i_use = array();
! 	if(!isset($i_annot)) $i_annot = array();
  
  	$err = "";
  	$samp = new Sample();
! 	if(!isset($i_samp)) $err = "No sample specified";
! 	else if(!$samp->readOwned($i_samp, $curUser->getId()))
  		$err = "No such sample";
  	if(isset($i_ok) || isset($i_more))
  	{
--- 31,49 ----
  	setLocation("sample_list.phtml");
  
! 	$annottypes = SampleAnnotationType::getAllById($curUser);
  	$types = SampleAnnotationType::getValueTypeNames();
! 	if(!isset($i_use))
! 		$i_use = array();
! 	if(!isset($i_annot))
! 		$i_annot = array();
  
  	$err = "";
  	$samp = new Sample();
! 	if(!isset($i_samp))
! 		$err = "No sample specified";
! 	else if(!$samp->readShared($i_samp, $curUser))
  		$err = "No such sample";
+ 	else if(!$samp->mayEdit($curUser, BUA_BIO_EDIT))
+ 		$err = "Write access denied";
  	if(isset($i_ok) || isset($i_more))
  	{

[basedb-cvs] basedb/www/img lu.gif,1.1,NONE

From: <tr...@us...> - 2002-10-28 14:39:45

Update of /cvsroot/basedb/basedb/www/img
In directory usw-pr-cvs1:/tmp/cvs-serv18430/img

Removed Files:
	lu.gif 
Log Message:
Admin-defined column stuff

--- lu.gif DELETED ---

[basedb-cvs] basedb/www labeled_edit.phtml,1.12,1.12.2.1

From: <tr...@us...> - 2002-10-25 05:27:08

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv25913

Modified Files:
      Tag: stable_1_0_6
	labeled_edit.phtml 
Log Message:
Fixed getName that should be getDescr (from Mark Wilkinson)

Index: labeled_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_edit.phtml,v
retrieving revision 1.12
retrieving revision 1.12.2.1
diff -C2 -d -r1.12 -r1.12.2.1
*** labeled_edit.phtml	5 Aug 2002 11:29:34 -0000	1.12
--- labeled_edit.phtml	24 Oct 2002 20:38:22 -0000	1.12.2.1
***************
*** 320,324 ****
  <tr><th>Extract</th><td><?= $ename ?></td></tr>
  <tr><th>Protocol</th><td><?= html($pname) ?></td></tr>
! <tr><th>Description</th><td><?= html($lext->getName()) ?></td></tr>
  <tr><th>Label</th><td><?= html($lext->getLabel()) ?></td></tr>
  <tr><th>Quantity of extract labeled (µg)</th><td><?=
--- 320,324 ----
  <tr><th>Extract</th><td><?= $ename ?></td></tr>
  <tr><th>Protocol</th><td><?= html($pname) ?></td></tr>
! <tr><th>Description</th><td><?= html($lext->getDescr()) ?></td></tr>
  <tr><th>Label</th><td><?= html($lext->getLabel()) ?></td></tr>
  <tr><th>Quantity of extract labeled (µg)</th><td><?=

[basedb-cvs] basedb/documentation/development baseschema.fig,NONE,1.1 baseschema.ps,NONE,1.1 plugins.txt,NONE,1.1

From: <tr...@us...> - 2002-10-21 16:21:44

Update of /cvsroot/basedb/basedb/documentation/development
In directory usw-pr-cvs1:/tmp/cvs-serv12085

Added Files:
	baseschema.fig baseschema.ps plugins.txt 
Log Message:
A bit of documentation

--- NEW FILE: baseschema.fig ---
#FIG 3.2
Landscape
Center
Metric
A4      
100.00
Single
-2
1200 2
0 32 #ff5900
0 33 #000000
6 630 4815 3240 5355
2 2 0 2 23 7 50 0 -1 0.000 0 0 -1 0 0 5
	 675 4860 3195 4860 3195 5310 675 5310 675 4860
4 0 0 50 0 18 16 0.0000 4 240 2385 765 5175 BioAssaySetExplore\001
-6
6 8955 7515 10575 8055
2 2 0 2 11 7 50 0 -1 0.000 0 0 -1 0 0 5
	 9000 7560 10530 7560 10530 8010 9000 8010 9000 7560
[...500 lines suppressed...]
4 0 0 50 0 18 16 0.0000 4 180 1755 4275 8550 JobFileSection\001
4 0 0 50 0 18 16 0.0000 4 180 1905 1800 8550 BaseFileSection\001
4 0 0 50 0 18 16 0.0000 4 180 1575 10800 9225 WizzzardUser\001
4 0 0 50 0 18 16 0.0000 4 180 1020 9000 9225 Wizzzard\001
4 0 0 50 0 18 16 0.0000 4 240 1575 2475 9225 ProtocolType\001
4 0 0 50 0 18 16 0.0000 4 180 990 675 9225 Protocol\001
4 0 0 50 0 18 16 0.0000 4 180 660 4950 9225 News\001
4 0 0 50 0 18 16 0.0000 4 240 825 6525 9225 Upload\001
4 0 0 50 0 18 16 0.0000 4 180 1845 6750 8550 SchemaVersion\001
4 0 0 50 0 18 16 0.0000 4 240 1860 11295 1125 PlateEventType\001
4 0 0 50 0 18 16 0.0000 4 180 2610 6525 7200 TransformationSearch\001
4 0 0 50 0 18 16 0.0000 4 180 1770 675 450 LabeledExtract\001
4 0 0 50 0 18 10 0.0000 4 120 270 6075 7245 0..2\001
4 0 0 50 0 18 16 0.0000 4 240 2460 5220 2475 RawBioAssayHeader\001
4 0 0 50 0 18 10 0.0000 4 120 270 2520 675 1..2\001
4 0 0 50 0 18 10 0.0000 4 120 270 2565 225 1..2\001
4 0 0 50 0 18 16 0.0000 4 240 1125 6570 7875 EventLog\001
4 0 0 50 0 18 10 0.0000 4 120 270 2430 2790 1..2\001
4 0 0 50 0 18 16 0.0000 4 240 870 1440 2880 Sample\001
4 0 0 50 0 18 16 0.0000 4 240 1650 315 1800 SampleTissue\001

--- NEW FILE: baseschema.ps ---
%!PS-Adobe-2.0
%%Title: baseschema.ps
%%Creator: fig2dev Version 3.2 Patchlevel 3c
%%CreationDate: Thu Oct  3 16:55:36 2002
%%For: carl@blixen (Carl Troein,,,)
%%Orientation: Landscape
%%Pages: 1
%%BoundingBox: 0 0 595 842
%%BeginSetup
%%IncludeFeature: *PageSize A4
%%EndSetup
%%Magnification: 1.0000
%%EndComments
/$F2psDict 200 dict def
$F2psDict begin
$F2psDict /mtrx matrix put
/col-1 {0 setgray} bind def
/col0 {0.000 0.000 0.000 srgb} bind def
/col1 {0.000 0.000 1.000 srgb} bind def
[...1038 lines suppressed...]
n 4320 2655 45 45 0 360 DrawEllipse gs 0.00 setgray ef gr gs col0 s gr

% Ellipse
n 9180 2385 45 45 0 360 DrawEllipse gs 0.00 setgray ef gr gs col0 s gr

% Ellipse
n 6390 6435 45 45 0 360 DrawEllipse gs 0.00 setgray ef gr gs col0 s gr

% Ellipse
n 6390 7110 45 45 0 360 DrawEllipse gs 0.00 setgray ef gr gs col0 s gr

% Ellipse
n 11565 8865 45 45 0 360 DrawEllipse gs 0.00 setgray ef gr gs col0 s gr

% Ellipse
n 495 6165 45 45 0 360 DrawEllipse gs 0.00 setgray ef gr gs col0 s gr

$F2psEnd
rs
showpage

--- NEW FILE: plugins.txt ---
J C writes:

> Thinking of writting a plug_in for BASE, but
> unfortunatly there isn't a whole lot written about
> this in the mannual.  What I have gathered so far is
> some of the plug_ins are using the 'jobs' directory to
> read and write files from, but it is not quite clear
> as to what should a plug_in expect as input and what
> kind of information does BASE expect at the end of a
> process.  Any information on the subject is greatly
> appreciated.

What a plugin needs to know is this: It's run in a directory
where it's allowed to create files. Things written to stdout
will end up in a file called stdout.txt (in the current
directory). Errors and other information can be written to
stderr. On stdin the plugin will get the data to be processed,
in the rather badly documented BASEfile format.
When the plugin has terminated, jobController.php will scan the
[...84 lines suppressed...]
BASEfile with one 'assays' section per assay in the input, have
only one assay per such section (that it, make it the 'serial'
version of this format), and put the same id for the assay as
you got in the input. You need to pass the position and molecule
columns through unchanged, and output the normalized values
in columns called 'intensity1' and 'intensity2'. Have a look at
a stdout.txt from lowess to see what I mean.

To have a genelist(reporter list) created by jobController.php,
output a section 'genelist' with columns 'cloneId' and 'value',
where the cloneId is passed through from the input BASEfile and
'value' is a value to be associated with the gene. If there is
no such value or you just want the rank of the gene (the position
in the genelist), leave out the 'value' column altogether.

The BaseFileReader class:
In exec/source there is a C++ class called BaseFileReader.
This class is used by the plugins provided with BASE, and in
the source for those you can see how it can be used to parse
BASEfiles.

[basedb-cvs] basedb/documentation/development - New directory

From: <tr...@us...> - 2002-10-21 16:21:00

Update of /cvsroot/basedb/basedb/documentation/development
In directory usw-pr-cvs1:/tmp/cvs-serv11552/development

Log Message:
Directory /cvsroot/basedb/basedb/documentation/development added to the repository

[basedb-cvs] basedb/exec/source README.basefile,1.1,NONE

From: <tr...@us...> - 2002-10-21 16:20:14

Update of /cvsroot/basedb/basedb/exec/source
In directory usw-pr-cvs1:/tmp/cvs-serv11014

Removed Files:
	README.basefile 
Log Message:
Moved to /documentation/development/plugins.txt

--- README.basefile DELETED ---

[basedb-cvs] basedb example_config.inc.php,1.6,1.7

From: <tr...@us...> - 2002-10-21 16:16:51

Update of /cvsroot/basedb/basedb
In directory usw-pr-cvs1:/tmp/cvs-serv8743

Modified Files:
	example_config.inc.php 
Log Message:
Removed unused config parameter

Index: example_config.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/example_config.inc.php,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** example_config.inc.php	26 Sep 2002 19:36:47 -0000	1.6
--- example_config.inc.php	21 Oct 2002 16:16:48 -0000	1.7
***************
*** 90,103 ****
  	$config["mime.types"]		= "/usr/local/apache/conf/mime.types";
  
- 	// The access system uses a set of columns called readAccessN where
- 	// N is in (1, ..., $config[accessColumns]). These columns exist
- 	// in tables representing all sharable subclasses of Item.
- 	// The maximum number of users+groups is this number times 64.
- 	// Note that to alter this value you need to create the required
- 	// columns in the database first. In the future there will be a
- 	// script for doing this.
- 	$config["accessColumns"]	= 2;
- 
  	require_once("$config[webDir]/common.inc.php");
  
  ?>
--- 90,97 ----
  	$config["mime.types"]		= "/usr/local/apache/conf/mime.types";
  
  	require_once("$config[webDir]/common.inc.php");
  
+ 	// Make sure that there are no empty lines after the closing PHP tag
+ 	// here (a single linefeed is OK), or everything will break. The same
+ 	// goes for any *.inc.php.
  ?>

[basedb-cvs] basedb/www/misc welcome.html,1.9,1.10 BASEbetaInstructions.pdf,1.1,NONE contact.html,1.3,NONE specs.html,1.1,NONE

From: <tr...@us...> - 2002-10-21 16:16:29

Update of /cvsroot/basedb/basedb/www/misc
In directory usw-pr-cvs1:/tmp/cvs-serv8486/misc

Modified Files:
	welcome.html 
Removed Files:
	BASEbetaInstructions.pdf contact.html specs.html 
Log Message:
Cleaned up main page

Index: welcome.html
===================================================================
RCS file: /cvsroot/basedb/basedb/www/misc/welcome.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** welcome.html	9 Aug 2002 16:59:57 -0000	1.9
--- welcome.html	21 Oct 2002 16:16:26 -0000	1.10
***************
*** 1,88 ****
! <tr><th class=pagehead><center>BioArray Software Environment - BASE</center></th></tr>
! <tr><td align=center class=special>Version
! 	<span class=red>1.0.6</span> is now available for download.</td></tr>
! <tr><td>
! <p><span class=subhead>What is BASE?</span>
! 
! <p>BASE is a comprehensive database server to manage the massive amounts of 
! data generated by microarray analysis.  In short, it manages biomaterial 
! information, raw data and images, and provides integrated and 
! "plug-in"-able normalization, data viewing and analysis 
[...105 lines suppressed...]
! If you have any other special issue, you may contact us directly: Lao Saal
! <a href="mailto:lao...@on...">&lt;lao...@on...&gt;</a>,
! Carl Troein <a href="mailto:ca...@th...">&lt;ca...@th...&gt;</a>,
! or Johan Vallon-Christersson
! <a href="mailto:joh...@on..."
! >&lt;joh...@on...&gt;</a>.
!  
! <p><a target=_top href="http://sourceforge.net/"><img
! width="88" height="31"
  src="http://sourceforge.net/sflogo.php?group_id=54527&amp;type=1"
  border="0" alt="SourceForge.net Logo" align=left></a>
  BASE development is coordinated through SourceForge.net. From the
  <a target=_top href="http://sourceforge.net/projects/basedb/"
! >sf.net BASE project page</a> you can e.g. access the CVS repository
! and subscribe to the development mailing list.
! If you're interested in helping out with the development of BASE,
! get the latest version off the CVS and come talk to us on the mailing
! list.<br clear=all>
!  
  <p><p><hr>

--- BASEbetaInstructions.pdf DELETED ---

--- contact.html DELETED ---

--- specs.html DELETED ---

[basedb-cvs] basedb/www news_old.phtml,NONE,1.1 main_main.phtml,1.27,1.28 left.phtml,1.49,1.50

From: <tr...@us...> - 2002-10-21 16:16:29

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv8486

Modified Files:
	main_main.phtml left.phtml 
Added Files:
	news_old.phtml 
Log Message:
Cleaned up main page

--- NEW FILE: news_old.phtml ---
<?
// $Id: news_old.phtml,v 1.1 2002/10/21 16:16:26 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
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
//
	require_once("newinit.inc.php");
	require_once("news.inc.php");

	$loggedIn = checkLogin(false);

	unset($pageTitle);
	include("htmlinit.phtml");

?>
<table <?= $cellpad ?>>
<tr><th class=pagehead>Site news archive</th></tr>
<tr><td>&nbsp;</td></tr>
<?		
	$from = isset($i_nfrom) ? (int)$i_nfrom : 0;
	$count = 100;
	$news = News::getLatest($count, $from);
	if(!$news)
	{
		if($from == 0)
			echo "<tr><td>No news items are available.</td></tr>\n";
		else echo "<tr><td>No such news items exist.</td></tr>\n";
	}
	else
	{
		for($i = 0, $odd = 0; $i < count($news); $i++, $odd ^= 1)
		{
			$n =& $news[$i];
			if($i)
			{
?>
<tr><td><table border=0 cellpadding=0 cellspacing=0 width=100%>
<tr><td height=3><img src="img/1.gif" width=1 height=3></td></tr>
<tr><td height=1 bgcolor=Black><img src="img/1.gif" width=1 height=1></td></tr>
<tr><td height=8><img src="img/1.gif" width=1 height=8></td></tr>
</table></td></tr>
<?
			}
?>
<tr><td><?= htmldate(substr($n->getAddedDate(), 0, 10))
	?>: &nbsp <span class=subhead><?= html($n->getName()) ?></span></td></tr>
	<tr><td><?= nl2br(trim($n->getDescr())) ?></td></tr>
<?
		}
		unset($n);
	}
?>
</table>
</body>
</html>

Index: main_main.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/main_main.phtml,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** main_main.phtml	9 Aug 2002 16:59:57 -0000	1.27
--- main_main.phtml	21 Oct 2002 16:16:25 -0000	1.28
***************
*** 29,46 ****
  	$loggedIn = checkLogin(false);
  
- 	if($loggedIn)
- 	{
- 		$pageTitle = "$config[codename] - Main page";
- 		include("htmlinit.phtml");
- ?>
- <table <?= $cellpad ?>>
- <tr><td>Select something in the menu to the left</td></tr>
- </table>
[...135 lines suppressed...]
! 		unset($n);
  ?>
  <p><hr><p><i>
--- 49,54 ----
  	<?= nl2br(trim($n->getDescr())) ?><br>
  <?
! 	}
! 	unset($n);
  ?>
  <p><hr><p><i>
***************
*** 167,173 ****
  by Lund University.</i>
  </td></tr>
- <?
- 	}
- ?>
  </table>
  
--- 57,60 ----

Index: left.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/left.phtml,v
retrieving revision 1.49
retrieving revision 1.50
diff -C2 -d -r1.49 -r1.50
*** left.phtml	30 Sep 2002 16:57:05 -0000	1.49
--- left.phtml	21 Oct 2002 16:16:26 -0000	1.50
***************
*** 112,116 ****
  	if($loggedIn)
  	{
! 		$loggedin = $curSession->countLoggedIn();
  ?>
  <tr><td class=tiny>Logged in as
--- 112,116 ----
  	if($loggedIn)
  	{
! 		$users = $curSession->countLoggedIn();
  ?>
[...391 lines suppressed...]
  
! 	echo "<tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>\n";
! 
! 	$arr = array("main_main" => "Site info",
! 		"news_old" => "Old news",
! 		"settings" => "GUI settings");
! 	for(reset($arr); list($k, $v) = each($arr); )
  	{
! 		$class = $k == $l ? "subheadact" : "subhead";
! 		echo "<tr><th class=$class><a target=_top ".
! 			"href='index.phtml?l=$k&m=".urlencode("$k.phtml")."'>$v</a>".
! 			"</td></tr>\n";
  	}
  
  ?>
  <tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>
! <tr><th class=subhead><a target=_blank href='http://base.thep.lu.se/'
! 	>BASE project site</a></th></tr>
  
  <?

[basedb-cvs] basedb/www index.phtml,1.18,1.19 lleft.phtml,1.4,NONE

From: <tr...@us...> - 2002-10-21 16:15:46

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv7314

Modified Files:
	index.phtml 
Removed Files:
	lleft.phtml 
Log Message:
removed lleft logo

Index: index.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/index.phtml,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** index.phtml	16 Sep 2002 14:20:57 -0000	1.18
--- index.phtml	21 Oct 2002 16:15:41 -0000	1.19
***************
*** 92,102 ****
  	if(!isset($_REQUEST["l"])) $l = "";
  	else $l = ereg_replace("[^[:print:]]|[:/]", "", $_REQUEST["l"]);
- 
- 	// The download and mailing list pages are not mirrored by each
- 	// BASE installation.
- 	if($m == "main_main.phtml?l=download")
- 		$m = "http://base.thep.lu.se/download/";
- 	else if($m == "main_main.phtml?l=mlist")
- 		$m = "http://www.thep.lu.se/~carl/ezmlm.cgi";
  ?>
  <html>
--- 92,95 ----
***************
*** 109,119 ****
  
  <frameset cols="<?= $width ?>,*" border=0>
! 	<frameset rows="*,150" border=0>
! 		<frame name="left" src="left.phtml?l=<?= html($l, 0)
! 			?>&i_err=<?= $err ?>&i_un=<?= urlencode($i_un) ?>" frameborder=0
! 			marginheight=0 marginwidth=2>
! 		<frame name="lleft" src="lleft.phtml" frameborder=0 marginheight=0
! 			marginwidth=3 scrolling=no>
! 	</frameset>
  	<frame name="main" src="<?= html($m, 0) ?>" frameborder=0 marginheight=6
  		marginwidth=3>
--- 102,108 ----
  
  <frameset cols="<?= $width ?>,*" border=0>
! 	<frame name="left" src="left.phtml?l=<?= html($l, 0)
! 		?>&i_err=<?= $err ?>&i_un=<?= urlencode($i_un) ?>" frameborder=0
! 		marginheight=0 marginwidth=2>
  	<frame name="main" src="<?= html($m, 0) ?>" frameborder=0 marginheight=6
  		marginwidth=3>

--- lleft.phtml DELETED ---

[basedb-cvs] basedb/www common.inc.php,1.21,1.22

From: <tr...@us...> - 2002-10-21 16:14:56

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv6803

Modified Files:
	common.inc.php 
Log Message:
Removed unused config parameter

Index: common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/common.inc.php,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** common.inc.php	30 Sep 2002 08:26:43 -0000	1.21
--- common.inc.php	21 Oct 2002 16:14:49 -0000	1.22
***************
*** 38,42 ****
  		"adminEmail", "uploadDir", "tempDir", "jobDir", "rawFileDir",
  		"rawImageDir", "printMapDir", "execDir", "webDir", "gnuplot",
! 		"mime.types", "displayCookie", "accessColumns", "protocolDir");
  	foreach($cfgvars as $v)
  	{
--- 38,42 ----
  		"adminEmail", "uploadDir", "tempDir", "jobDir", "rawFileDir",
  		"rawImageDir", "printMapDir", "execDir", "webDir", "gnuplot",
! 		"mime.types", "displayCookie", "protocolDir");
  	foreach($cfgvars as $v)
  	{

[basedb-cvs] basedb/www/img/sshot/thumb t_BASE-MGED4-Poster.jpg,1.1,NONE t_BASE-MGED4-Poster.png,1.1,NONE t_BASEaddNewSample.jpg,1.1,NONE t_BASEannotateSample.jpg,1.1,NONE t_BASEcreate384wPlate.jpg,1.1,NONE t_BASEcreateArrayType.jpg,1.1,NONE t_BASEfileUploads.jpg,1.1,NONE t_BASEgeneExplorer.jpg,1.1,NONE t_BASEgeneListExample.jpg,1.1,NONE t_BASEgeneLists.jpg,1.1,NONE t_BASEjobhandler.jpg,1.1,NONE t_BASElistArrayTypes.jpg,1.1,NONE t_BASElistSamples.jpg,1.1,NONE t_BASElistplateTypes.jpg,1.1,NONE t_BASEmdsPlot.jpg,1.1,NONE t_BASEnewAnnotationType.jpg,1.1,NONE t_BASEnewHybridization.jpg,1.1,NONE t_BASEplugIn.jpg,1.1,NONE t_BASEplugInNormalizers.jpg,1.1,NONE t_BASEprojectHypox.jpg,1.1,NONE t_BASEprojectNormalizations.jpg,1.1,NONE t_BASEsampleOriginOntology.jpg,1.1,NONE t_BASEviewArrayType.jpg,1.1,NONE t_BASEviewPlateType.jpg,1.1,NONE t_BASEviewplate384w.jpg,1.1,NONE t_BASEviewplate96w.jpg,1.1,NONE t_ClusterBetaPlug-In.png,1.1,NONE

From: <tr...@us...> - 2002-10-21 15:05:50

Update of /cvsroot/basedb/basedb/www/img/sshot/thumb
In directory usw-pr-cvs1:/tmp/cvs-serv15433/sshot/thumb

Removed Files:
	t_BASE-MGED4-Poster.jpg t_BASE-MGED4-Poster.png 
	t_BASEaddNewSample.jpg t_BASEannotateSample.jpg 
	t_BASEcreate384wPlate.jpg t_BASEcreateArrayType.jpg 
	t_BASEfileUploads.jpg t_BASEgeneExplorer.jpg 
	t_BASEgeneListExample.jpg t_BASEgeneLists.jpg 
	t_BASEjobhandler.jpg t_BASElistArrayTypes.jpg 
	t_BASElistSamples.jpg t_BASElistplateTypes.jpg 
	t_BASEmdsPlot.jpg t_BASEnewAnnotationType.jpg 
	t_BASEnewHybridization.jpg t_BASEplugIn.jpg 
	t_BASEplugInNormalizers.jpg t_BASEprojectHypox.jpg 
	t_BASEprojectNormalizations.jpg t_BASEsampleOriginOntology.jpg 
	t_BASEviewArrayType.jpg t_BASEviewPlateType.jpg 
	t_BASEviewplate384w.jpg t_BASEviewplate96w.jpg 
	t_ClusterBetaPlug-In.png 
Log Message:
Removed screen shots and unused images

--- t_BASE-MGED4-Poster.jpg DELETED ---

--- t_BASE-MGED4-Poster.png DELETED ---

--- t_BASEaddNewSample.jpg DELETED ---

--- t_BASEannotateSample.jpg DELETED ---

--- t_BASEcreate384wPlate.jpg DELETED ---

--- t_BASEcreateArrayType.jpg DELETED ---

--- t_BASEfileUploads.jpg DELETED ---

--- t_BASEgeneExplorer.jpg DELETED ---

--- t_BASEgeneListExample.jpg DELETED ---

--- t_BASEgeneLists.jpg DELETED ---

--- t_BASEjobhandler.jpg DELETED ---

--- t_BASElistArrayTypes.jpg DELETED ---

--- t_BASElistSamples.jpg DELETED ---

--- t_BASElistplateTypes.jpg DELETED ---

--- t_BASEmdsPlot.jpg DELETED ---

--- t_BASEnewAnnotationType.jpg DELETED ---

--- t_BASEnewHybridization.jpg DELETED ---

--- t_BASEplugIn.jpg DELETED ---

--- t_BASEplugInNormalizers.jpg DELETED ---

--- t_BASEprojectHypox.jpg DELETED ---

--- t_BASEprojectNormalizations.jpg DELETED ---

--- t_BASEsampleOriginOntology.jpg DELETED ---

--- t_BASEviewArrayType.jpg DELETED ---

--- t_BASEviewPlateType.jpg DELETED ---

--- t_BASEviewplate384w.jpg DELETED ---

--- t_BASEviewplate96w.jpg DELETED ---

--- t_ClusterBetaPlug-In.png DELETED ---

[basedb-cvs] basedb/www/img/sshot BASE-MGED4-Poster.PDF,1.1,NONE BASE-Oncogenomics-Poster.PDF,1.1,NONE BASE-TableDefinitions.pdf,1.1,NONE BASEaddNewSample.jpg,1.1,NONE BASEannotateSample.jpg,1.1,NONE BASEcreate384wPlate.jpg,1.1,NONE BASEcreateArrayType.jpg,1.1,NONE BASEfileUploads.jpg,1.1,NONE BASEgeneExplorer.jpg,1.1,NONE BASEgeneListExample.jpg,1.1,NONE BASEgeneLists.jpg,1.1,NONE BASEjobhandler.jpg,1.1,NONE BASElistArrayTypes.jpg,1.1,NONE BASElistSamples.jpg,1.1,NONE BASElistplateTypes.jpg,1.1,NONE BASEmdsPlot.jpg,1.1,NONE BASEnewAnnotationType.jpg,1.1,NONE BASEnewHybridization.jpg,1.1,NONE BASEplugIn.jpg,1.1,NONE BASEplugInNormalizers.jpg,1.1,NONE BASEprojectHypox.jpg,1.1,NONE BASEprojectNormalizations.jpg,1.1,NONE BASEsampleOriginOntology.jpg,1.1,NONE BASEschema.png,1.1,NONE BASEviewArrayType.jpg,1.1,NONE BASEviewPlateType.jpg,1.1,NONE BASEviewplate384w.jpg,1.1,NONE BASEviewplate96w.jpg,1.1,NONE ClusterBetaPlug-In.png,1.1,NONE NSLwelcome.png,1.1,NONE

From: <tr...@us...> - 2002-10-21 15:05:50

Update of /cvsroot/basedb/basedb/www/img/sshot
In directory usw-pr-cvs1:/tmp/cvs-serv15433/sshot

Removed Files:
	BASE-MGED4-Poster.PDF BASE-Oncogenomics-Poster.PDF 
	BASE-TableDefinitions.pdf BASEaddNewSample.jpg 
	BASEannotateSample.jpg BASEcreate384wPlate.jpg 
	BASEcreateArrayType.jpg BASEfileUploads.jpg 
	BASEgeneExplorer.jpg BASEgeneListExample.jpg BASEgeneLists.jpg 
	BASEjobhandler.jpg BASElistArrayTypes.jpg BASElistSamples.jpg 
	BASElistplateTypes.jpg BASEmdsPlot.jpg 
	BASEnewAnnotationType.jpg BASEnewHybridization.jpg 
	BASEplugIn.jpg BASEplugInNormalizers.jpg BASEprojectHypox.jpg 
	BASEprojectNormalizations.jpg BASEsampleOriginOntology.jpg 
	BASEschema.png BASEviewArrayType.jpg BASEviewPlateType.jpg 
	BASEviewplate384w.jpg BASEviewplate96w.jpg 
	ClusterBetaPlug-In.png NSLwelcome.png 
Log Message:
Removed screen shots and unused images

--- BASE-MGED4-Poster.PDF DELETED ---

--- BASE-Oncogenomics-Poster.PDF DELETED ---

--- BASE-TableDefinitions.pdf DELETED ---

--- BASEaddNewSample.jpg DELETED ---

--- BASEannotateSample.jpg DELETED ---

--- BASEcreate384wPlate.jpg DELETED ---

--- BASEcreateArrayType.jpg DELETED ---

--- BASEfileUploads.jpg DELETED ---

--- BASEgeneExplorer.jpg DELETED ---

--- BASEgeneListExample.jpg DELETED ---

--- BASEgeneLists.jpg DELETED ---

--- BASEjobhandler.jpg DELETED ---

--- BASElistArrayTypes.jpg DELETED ---

--- BASElistSamples.jpg DELETED ---

--- BASElistplateTypes.jpg DELETED ---

--- BASEmdsPlot.jpg DELETED ---

--- BASEnewAnnotationType.jpg DELETED ---

--- BASEnewHybridization.jpg DELETED ---

--- BASEplugIn.jpg DELETED ---

--- BASEplugInNormalizers.jpg DELETED ---

--- BASEprojectHypox.jpg DELETED ---

--- BASEprojectNormalizations.jpg DELETED ---

--- BASEsampleOriginOntology.jpg DELETED ---

--- BASEschema.png DELETED ---

--- BASEviewArrayType.jpg DELETED ---

--- BASEviewPlateType.jpg DELETED ---

--- BASEviewplate384w.jpg DELETED ---

--- BASEviewplate96w.jpg DELETED ---

--- ClusterBetaPlug-In.png DELETED ---

--- NSLwelcome.png DELETED ---

[basedb-cvs] basedb/www/img lulogo.jpg,1.1,NONE lusealbg.png,1.1,NONE onc.gif,1.1,NONE thep.gif,1.1,NONE

From: <tr...@us...> - 2002-10-21 15:05:45

Update of /cvsroot/basedb/basedb/www/img
In directory usw-pr-cvs1:/tmp/cvs-serv15433

Removed Files:
	lulogo.jpg lusealbg.png onc.gif thep.gif 
Log Message:
Removed screen shots and unused images

--- lulogo.jpg DELETED ---

--- lusealbg.png DELETED ---

--- onc.gif DELETED ---

--- thep.gif DELETED ---

[basedb-cvs] basedb/documentation/todo 1_2.tex,NONE,1.1 1_4.tex,NONE,1.1 Makefile,NONE,1.1 commands.tex,NONE,1.1 firstpage.tex,NONE,1.1 introduction.tex,NONE,1.1 later.tex,NONE,1.1 legend.tex,NONE,1.1 new.tex,NONE,1.1 todo.tex,NONE,1.1

From: <ku...@us...> - 2002-10-18 15:53:52

Update of /cvsroot/basedb/basedb/documentation/todo
In directory usw-pr-cvs1:/tmp/cvs-serv2149

Added Files:
	1_2.tex 1_4.tex Makefile commands.tex firstpage.tex 
	introduction.tex later.tex legend.tex new.tex todo.tex 
Log Message:



--- NEW FILE: 1_2.tex ---
% $Id: 1_2.tex,v 1.1 2002/10/18 15:53:46 kurri Exp $

\setcounter{section}{1}
\setcounter{subsection}{1}
\subsection{Features to fix for release 1.2 of BASE}
\verb:$Revision: 1.1 $ $Date: 2002/10/18 15:53:46 $:

Estimated time of arrival: n/a

\begin{htmlonly}
\subsubsection*{Colour Legend}
\input{legend}
\end{htmlonly}


\entry[progress]
{Installation documentation}
{Darrin Taylor}
{Darrin Taylor}
[...1488 lines suppressed...]
  \myditem[Mark] I wrote a parser that would create a BASE-happy file
    from my QuantArray files, but it still complains that the
    combination of block/row/column does not match the associated
    array.
  \end{description}
}
{}



\entry[progress]
{ Quantities as doubles, please }
{ Harm van Bakel, H.H...@me... }
{ Carl Troein, ca...@th... }
{
  In BASE 1.0 some fields are integers, and this is not appropriate
  for all users.
}
{ The appropriate tables should support floats or double. }
{}

--- NEW FILE: 1_4.tex ---
% $Id: 1_4.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

\setcounter{section}{1}
\setcounter{subsection}{3}
\subsection{Features for release 1.4 of BASE}
\verb:$Revision: 1.1 $ $Date: 2002/10/18 15:53:47 $:

Estimated time of arrival: n/a

\begin{htmlonly}
\subsubsection*{Colour Legend}
\input{legend}
\end{htmlonly}

--- NEW FILE: Makefile ---
# $Id: Makefile,v 1.1 2002/10/18 15:53:47 kurri Exp $

MAIN	= todo

DVI	= $(MAIN).dvi
PS	= $(MAIN).ps
PDF	= $(MAIN).pdf

SRC	= $(MAIN).tex 1_2.tex 1_4.tex commands.tex firstpage.tex \
		introduction.tex later.tex legend.tex new.tex

default: dvi

all:	dvi pdf ps html

clean:
	@rm -rf *.aux *.dvi *.log *.out *.toc *.flc *~ \
		$(MAIN) $(MAIN).pdf $(MAIN).ps

disk:	clean
	@(cd .. ; tar zcf /tmp/$(MAIN).tgz $(MAIN) \
		; mcopy $(MAIN).tgz a: ; rm /tmp/$(MAIN).tgz )

dvi:	$(DVI)

$(DVI):	$(SRC)
	@(latex $(MAIN) ; latex $(MAIN) ; latex $(MAIN))

html:	pdf ps
	@(rm -rf $(MAIN) ; latex2html  -local_icons -split +2 $(MAIN) ; \
		mv $(MAIN).pdf $(MAIN)/base_$(MAIN).pdf ; \
		mv $(MAIN).ps $(MAIN)/base_$(MAIN).ps)

pdf:	$(PDF)

$(PDF):	$(DVI)
	dvipdfm -p a4 $(MAIN)

ps:	$(PS)

$(PS):	$(DVI)
	dvips $(MAIN)

publish: html
	@(scp -rp $(MAIN) ja...@ba...:documents)

undisk:
	@(cd .. ; mcopy a:$(MAIN).tgz /tmp ; tar zxpf /tmp/$(MAIN).tgz \
		; rm /tmp/$(MAIN).tgz ; cd $(MAIN) )

--- NEW FILE: commands.tex ---
% $Id: commands.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

% this file contains defintions of non-standard latex commands

% special \item for description environment
\newcommand{\myditem}[1][someone]{\item[{\mdseries \emph{#1}}]}


% start definition of \entry ---------------------------------------------

% \entry and \entrylater template
\begin{comment}
  % option can be one of {cancel,close,open,partly,pending}.
  % Defaults to {open}.
  \entry[option]
      {title}
      {suggester, email}
      {volunteer, email}
      {current situation}
      {description}
      {status}
\end{comment}

\definecolor{open}{rgb}{0.9,0.1,0.1}
\definecolor{limbo}{rgb}{1,0.5,0.1}
\definecolor{progress}{rgb}{0.8,0.8,0.3}
\definecolor{pending}{rgb}{0.5,0.5,0.2}
\definecolor{close}{rgb}{0,0.7,0}

\newcommand{\entrybase}[5]{
\begin{description}
\myditem[Status] #5
\myditem[Volunteer] #2
\myditem[Proposed by] #1
\myditem[Current situation] \mbox{} \\ #3
\myditem[Discussion] \mbox{} \\ #4
\end{description}
}

\newcommand{\entry}[7][open]{
\subsubsection{\textcolor{#1}{#2}}
\entrybase{#3}{#4}{#5}{#6}{#7}
}

\newcommand{\entrylater}[7][open]{
\subsubsection*{\textcolor{#1}{#2}}
\entrybase{#3}{#4}{#5}{#6}{#7}
}

% end definition of \entry ---------------------------------------------

--- NEW FILE: firstpage.tex ---
% $Id: firstpage.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

\begin{htmlonly}
\begin{verbatim}
$Revision: 1.1 $ $Date: 2002/10/18 15:53:47 $
\end{verbatim}
\end{htmlonly}


Created \today.

\begin{htmlonly}
\input{legend}

This document is also available in \htmladdnormallink{postscript
format}{base_todo.ps} or \htmladdnormallink{portable document format
(pdf)}{base_todo.pdf}.
\end{htmlonly}

--- NEW FILE: introduction.tex ---
% $Id: introduction.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

\section*{BASE Todo List}
\verb:$Revision: 1.1 $ $Date: 2002/10/18 15:53:47 $:

This is the BASE todo list. This list contains an account of issues
regarding features in BASE. The items can be suggestions for
improvements, addition, removal, ... of features in BASE.

We have divided the list of wanted/needed features into three groups
\begin{itemize}
\item items that are to be included into the next release (BASE
  1.2). The implementation of these items must be done before the next
  version is released.
\item Items that are not considered for inclusions into next
  release. Some of these items will be included, whereas others will
  have to wait for later releses.
\item These items are under consideration for inclusion into this
  list.
\end{itemize}
The list is always changing but the features accepted to the next
release are expected to be fixed.

There is a lot to do before release 1.2 of BASE. Almost all of the
items in Section 1.2 will affect the database schema, whereas the
items in the After Next Release grouping are not expected to create
changes in the schema. In consequence, the main focus will be on the
items affected the database structure.

If you want to contribute, please send a message to the
\htmladdnormallinkfoot{BASE mailing list}{mailto:ba...@th...} explaining
what you want to do and start working.

The todo list is moderated, and all items in the list have a {\em
Status}, {\emph Volunteer}, {\emph Proposer}, {\emph Current
Situation} and {\emph Discussion} field describing the state of the
todo item.

The current list is compiled from the discussion in the BASE mailing
list. If you think something is wrong or missing (or disagree on who
is working on what) please send a message to the
\htmladdnormallink{BASE mailing list}{mailto:ba...@th...}.

\begin{latexonly}
\textbf{Colour Legend}
\input{legend}
\end{latexonly}

--- NEW FILE: later.tex ---
% $Id: later.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

\subsection*{After next release}
\verb:$Revision: 1.1 $ $Date: 2002/10/18 15:53:47 $:

Estimated time of arrival: n/a

\begin{htmlonly}
\subsubsection*{Colour Legend}
\input{legend}
\end{htmlonly}


\entrylater[open]
{ File format export/import }
{ Carl Troein, ca...@th... }
{}
{}
{
[...793 lines suppressed...]
    follow, and the data could be easily stored in BASE, in the exact
    same format so that later transformations, filterings and plug-ins
    could be performed without any special handling.  The major issues
    will be how to name the resultant BioAssays (ie if you average 5
    BioAssays into 1; and then how/if to refer them back to the
    original raw data sets [not only to the original values that were
    averaged, but also to the array LIMS]).  I think it should be
    flexible to handle any number of replicates, and multiple
    replicate sets within a single BioAssaySet.

    A practical limitation that I think we should have to impose is
    that all replicates be on identical arrays, so there won't be any
    reporter position issues to deal with.  Anything more than that
    could be a real nightmare.  If we have this limitation, it should
    be possible that the plug-in default to average on reporter
    position, and then have another option to average then on
    reporterID if desired.
  \end{description}
}
{}

--- NEW FILE: legend.tex ---
% $Id: legend.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

We have put together a colouring scheme for the state of the items in
the todo list. The possible states are
\begin{center}
\begin{description}
\item[\mdseries \textcolor{open}{Open}] \mbox{} \\ A feature that has
  been accepted and added to the list, but no one has been assigned,
  or volunteered, for the implementation of the feature.
\item[\mdseries \textcolor{limbo}{Limbo}] \mbox{} \\ Some parts of the
  requests have been done, while others are still awaiting action. The
  item is in a undecided state.
\item[\mdseries \textcolor{progress}{Progress}] \mbox{} \\ The issue
  is being worked on.
\item[\mdseries \textcolor{pending}{Pending}] \mbox{} \\ This item has
  been fixed, but is waiting for being accepted and thus included into
  the CVS repository. Mainly used when non-developers makes
  contributions.
\item[\mdseries \textcolor{close}{Done}] \mbox{} \\ The feature has
  been implemented into BASE and added to CVS.
\end{description}
\end{center}

--- NEW FILE: new.tex ---
% $Id: new.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

\subsection*{Add to list?}
\verb:$Revision: 1.1 $ $Date: 2002/10/18 15:53:47 $:


\entrylater
{ Reporter updates }
{ Carl Troein, ca...@th... }
{}
{}
{
  Update reporters from a simple tab-delimited file. Update reporters
  from a unigene file. Make it possible to edit individual reporters.

  \begin{description}
  \myditem[Vegard Nygaard] How do we change information about the
    reporters? We first uploaded plate information files with just
    cloneid, and when we later tried with more information, the new
[...297 lines suppressed...]
Tables and users were created according to InstallationREADME.

Apache
The standard Apache packages from the linux distribution were used. The
configuration file was changed in /etc/httpd/conf/httpd.conf (mad-peter)
and /etc/httpd/httpd.conf (regulome)to map the URL http://host/base/ to
/usr/local/base/www/:
Alias /base "/usr/local/base/www"

Base compilation
First, gsl was installed (gsl-1.1.1-1.i386.rpm and
gsl-devel-1.1.1-1.i386.rpm).

On regulome, a copy of the g++ library sstream had to be copied to
/usr/include/g++ in order to get MDS to compile.

Somehow, after make install, on regulome the file clusteringscript
couldn't be found, since this is only a text file, it was copied from
mad-peter to the /app directory of Base.
\end{comment}

--- NEW FILE: todo.tex ---
% $Id: todo.tex,v 1.1 2002/10/18 15:53:47 kurri Exp $

\documentclass[10pt]{article}

\usepackage{alltt}
\usepackage{color}
\usepackage{html}

\evensidemargin 0pt
\flushbottom
\footskip 10mm
\oddsidemargin 0pt
\parindent 0pt
\parskip 1ex
\textheight 235mm
\textwidth 165mm
\topmargin -5mm

\input{commands.tex}

\begin{document}

\bodytext{bgcolor=#f0f4f4 text=black}

\input{firstpage}
\input{introduction}
\input{1_2}
\input{later}
\input{1_4}
\input{new}
\end{document}

\entry
{}
{}
{}
{}
{}
{}
{?}

[basedb-cvs] basedb/www sample_list.phtml,1.20,1.21

From: <tr...@us...> - 2002-10-17 16:11:00

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv23275

Modified Files:
	sample_list.phtml 
Log Message:
Fixed annotation type id mess

Index: sample_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sample_list.phtml,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** sample_list.phtml	30 Sep 2002 16:57:05 -0000	1.20
--- sample_list.phtml	17 Oct 2002 16:10:54 -0000	1.21
***************
*** 169,174 ****
  				html($s["name"])."</a>".remMark($s["removed"]).
  				"</td>";
! 			for(reset($annottypes); list($aid) = each($annottypes); )
  			{
  				if(isset($anns[$aid]))
  					echo "<td>".html($anns[$aid])."</td>";
--- 169,175 ----
  				html($s["name"])."</a>".remMark($s["removed"]).
  				"</td>";
! 			for(reset($annottypes); list(, $a) = each($annottypes); )
  			{
+ 				$aid = $a["id"];
  				if(isset($anns[$aid]))
  					echo "<td>".html($anns[$aid])."</td>";

[basedb-cvs] basedb/www oldnews.phtml,NONE,1.1.2.1 index.phtml,1.16,1.16.2.1 left.phtml,1.42,1.42.2.1 main_main.phtml,1.27,1.27.2.1 raw_common.inc.php,1.16,1.16.2.1 raw_edit.phtml,1.14,1.14.2.1 lleft.phtml,1.4,NONE

From: <tr...@us...> - 2002-10-17 16:02:53

Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv19875

Modified Files:
      Tag: stable_1_0_6
	index.phtml left.phtml main_main.phtml raw_common.inc.php 
	raw_edit.phtml 
Added Files:
      Tag: stable_1_0_6
	oldnews.phtml 
Removed Files:
      Tag: stable_1_0_6
	lleft.phtml 
Log Message:
Removed information about BASE and added links to project site

--- NEW FILE: oldnews.phtml ---
<?
// $Id: oldnews.phtml,v 1.1.2.1 2002/10/17 16:02:15 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
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
//
	require_once("newinit.inc.php");
	require_once("news.inc.php");

	$loggedIn = checkLogin(false);

	unset($pageTitle);
	include("htmlinit.phtml");

	if(!isset($_REQUEST["l"])) $l = "";
	else $l = $_REQUEST["l"];
?>
<table <?= $cellpad ?>>
<tr><th class=pagehead>Site news archive</th></tr>
<tr><td>&nbsp;</td></tr>
<?		
	$from = isset($i_nfrom) ? (int)$i_nfrom : 0;
	$count = 100;
	$news = News::getLatest($count, $from);
	if(!$news)
	{
		if($from == 0)
			echo "<tr><td>No news items are available.</td></tr>\n";
		else echo "<tr><td>No such news items exist.</td></tr>\n";
	}
	else
	{
		for($i = 0, $odd = 0; $i < count($news); $i++, $odd ^= 1)
		{
			$n =& $news[$i];
			if($i)
			{
?>
<tr><td><table border=0 cellpadding=0 cellspacing=0 width=100%>
<tr><td height=3><img src="img/1.gif" width=1 height=3></td></tr>
<tr><td height=1 bgcolor=Black><img src="img/1.gif" width=1 height=1></td></tr>
<tr><td height=8><img src="img/1.gif" width=1 height=8></td></tr>
</table></td></tr>
<?
			}
?>
<tr><td><?= htmldate(substr($n->getAddedDate(), 0, 10))
	?>: &nbsp <span class=subhead><?= html($n->getName()) ?></span></td></tr>
	<tr><td><?= nl2br(trim($n->getDescr())) ?></td></tr>
<?
		}
		unset($n);
	}
?>
</table>
</body>
</html>

Index: index.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/index.phtml,v
retrieving revision 1.16
retrieving revision 1.16.2.1
diff -C2 -d -r1.16 -r1.16.2.1
*** index.phtml	5 Aug 2002 11:29:34 -0000	1.16
--- index.phtml	17 Oct 2002 16:02:09 -0000	1.16.2.1
***************
*** 93,103 ****
  	if(!isset($_REQUEST["l"])) $l = "";
  	else $l = ereg_replace("[^[:print:]]|[:/]", "", $_REQUEST["l"]);
- 
- 	// The download and mailing list pages are not mirrored by each
- 	// BASE installation.
- 	if($m == "main_main.phtml?l=download")
- 		$m = "http://base.thep.lu.se/download/";
- 	else if($m == "main_main.phtml?l=mlist")
- 		$m = "http://www.thep.lu.se/~carl/ezmlm.cgi";
  ?>
  <html>
--- 93,96 ----
***************
*** 110,120 ****
  
  <frameset cols="<?= $width ?>,*" border=0>
! 	<frameset rows="*,150" border=0>
! 		<frame name="left" src="left.phtml?l=<?= html($l, 0)
! 			?>&i_err=<?= $err ?>&i_un=<?= urlencode($i_un) ?>" frameborder=0
! 			marginheight=0 marginwidth=2>
! 		<frame name="lleft" src="lleft.phtml" frameborder=0 marginheight=0
! 			marginwidth=3 scrolling=no>
! 	</frameset>
  	<frame name="main" src="<?= html($m, 0) ?>" frameborder=0 marginheight=6
  		marginwidth=3>
--- 103,109 ----
  
  <frameset cols="<?= $width ?>,*" border=0>
! 	<frame name="left" src="left.phtml?l=<?= html($l, 0)
! 		?>&i_err=<?= $err ?>&i_un=<?= urlencode($i_un) ?>" frameborder=0
! 		marginheight=0 marginwidth=2>
  	<frame name="main" src="<?= html($m, 0) ?>" frameborder=0 marginheight=6
  		marginwidth=3>

Index: left.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/left.phtml,v
retrieving revision 1.42
retrieving revision 1.42.2.1
diff -C2 -d -r1.42 -r1.42.2.1
*** left.phtml	5 Aug 2002 11:29:34 -0000	1.42
--- left.phtml	17 Oct 2002 16:02:10 -0000	1.42.2.1
***************
*** 337,362 ****
  			"?l=news&m=news_list.phtml'>News</a></td></tr>\n";
  	}
! 
! 	if(!$loggedIn)
  	{
! 		$arr = array("overview" => "Overview", "spec" => "Specifications",
! 			"contact" => "Contact", "news" => "News",
! 			"screen" => "Screenshots", "download" => "Download",
! 			"mlist" => "List archive");
! 		if(!isset($arr[$l])) $l = "overview";
! 		for(reset($arr); list($k, $v) = each($arr); )
! 		{
! 			$class = $k == $l ? "subheadact" : "subhead";
! 			echo "<tr><th class=$class><a target=_top ".
! 				"href='index.phtml?l=$k&m=".
! 				urlencode("main_main.phtml?l=$k")."'>$v</a>".
! 				"</td></tr>\n";
! 		}
  	}
- 
  ?>
! <tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>
! <tr><th class=subhead><a target=main href='settings.phtml'
! 	>GUI settings</a></th></tr>
  
  <?
--- 337,358 ----
  			"?l=news&m=news_list.phtml'>News</a></td></tr>\n";
  	}
! ?>
! <tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>
! <?
! 	$arr = array("main_main" => "Site info",
! 		"oldnews" => "Old news",
! 		"settings" => "GUI settings");
! 	for(reset($arr); list($k, $v) = each($arr); )
  	{
! 		$class = $k == $l ? "subheadact" : "subhead";
! 		echo "<tr><th class=$class><a target=_top ".
! 			"href='index.phtml?l=$k&m=".
! 			urlencode("$k.phtml")."'>$v</a>".
! 			"</td></tr>\n";
  	}
  ?>
! <tr><td><img src='img/1.gif' alt='' width=1 height=5></td></tr>
! <tr><th class=subhead><a target=_blank href='http://base.thep.lu.se/'
! 	>BASE project site</a></th></tr>
  
  <?

Index: main_main.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/main_main.phtml,v
retrieving revision 1.27
retrieving revision 1.27.2.1
diff -C2 -d -r1.27 -r1.27.2.1
*** main_main.phtml	9 Aug 2002 16:59:57 -0000	1.27
--- main_main.phtml	17 Oct 2002 16:02:11 -0000	1.27.2.1
***************
*** 29,46 ****
  	$loggedIn = checkLogin(false);
  
- 	if($loggedIn)
- 	{
- 		$pageTitle = "$config[codename] - Main page";
- 		include("htmlinit.phtml");
- ?>
- <table <?= $cellpad ?>>
- <tr><td>Select something in the menu to the left</td></tr>
- </table>
[...135 lines suppressed...]
! 		unset($n);
  ?>
  <p><hr><p><i>
--- 49,54 ----
  	<?= nl2br(trim($n->getDescr())) ?><br>
  <?
! 	}
! 	unset($n);
  ?>
  <p><hr><p><i>
***************
*** 167,173 ****
  by Lund University.</i>
  </td></tr>
- <?
- 	}
- ?>
  </table>
  
--- 57,60 ----

Index: raw_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_common.inc.php,v
retrieving revision 1.16
retrieving revision 1.16.2.1
diff -C2 -d -r1.16 -r1.16.2.1
*** raw_common.inc.php	5 Aug 2002 11:29:35 -0000	1.16
--- raw_common.inc.php	17 Oct 2002 16:02:15 -0000	1.16.2.1
***************
*** 133,136 ****
--- 133,142 ----
  		'scrollbars=yes,resizable=yes,toolbar=1');
  }
+ function rawPlotter2(raw)
+ {
+ 	window.open('plotapplet_raw.phtml?i_r='+raw, 'rawPlotter2_'+raw,
+ 		'location=1,menubar=1,personalbar=0,width=680,height=520,'+
+ 		'scrollbars=yes,resizable=yes,toolbar=1');
+ }
  </script>
  <?
***************
*** 210,214 ****
  				"Overview&nbsp;plot</a>] ".
  				"[<a class=popup href='javascript:rawPlotter($id)'>".
! 				"Plot&nbsp;tool</a>]</td>".
  				"</tr>\n";
  		}
--- 216,222 ----
  				"Overview&nbsp;plot</a>] ".
  				"[<a class=popup href='javascript:rawPlotter($id)'>".
! 				"Plot&nbsp;tool&nbsp;(classic)</a>] ".
! 				"[<a class=popup href='javascript:rawPlotter2($id)'>".
! 				"Plot&nbsp;tool&nbsp;(Java)</a>]</td>".
  				"</tr>\n";
  		}

Index: raw_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_edit.phtml,v
retrieving revision 1.14
retrieving revision 1.14.2.1
diff -C2 -d -r1.14 -r1.14.2.1
*** raw_edit.phtml	5 Aug 2002 11:29:35 -0000	1.14
--- raw_edit.phtml	17 Oct 2002 16:02:16 -0000	1.14.2.1
***************
*** 170,174 ****
  			"Overview plot</a>]".
  			" [<a class=popup href='javascript:rawPlotter($rawid)'>".
! 			"Plot tool</a>]".
  			"</td></tr>\n".
  			"<tr><th>Molecule IDs</th>".
--- 170,176 ----
  			"Overview plot</a>]".
  			" [<a class=popup href='javascript:rawPlotter($rawid)'>".
! 			"Plot tool (classic)</a>]".
! 			" [<a class=popup href='javascript:rawPlotter2($rawid)'>".
! 			"Plot tool (Java)</a>]".
  			"</td></tr>\n".
  			"<tr><th>Molecule IDs</th>".

--- lleft.phtml DELETED ---

[basedb-cvs] basedb/www/misc welcome.html,1.9.2.3,1.9.2.4 BASEbetaInstructions.pdf,1.1,NONE contact.html,1.3,NONE specs.html,1.1.2.1,NONE

From: <tr...@us...> - 2002-10-17 16:02:23

Update of /cvsroot/basedb/basedb/www/misc
In directory usw-pr-cvs1:/tmp/cvs-serv19875/misc

Modified Files:
      Tag: stable_1_0_6
	welcome.html 
Removed Files:
      Tag: stable_1_0_6
	BASEbetaInstructions.pdf contact.html specs.html 
Log Message:
Removed information about BASE and added links to project site

Index: welcome.html
===================================================================
RCS file: /cvsroot/basedb/basedb/www/misc/welcome.html,v
retrieving revision 1.9.2.3
retrieving revision 1.9.2.4
diff -C2 -d -r1.9.2.3 -r1.9.2.4
*** welcome.html	10 Oct 2002 10:41:50 -0000	1.9.2.3
--- welcome.html	17 Oct 2002 16:02:18 -0000	1.9.2.4
***************
*** 7,32 ****
  <p>BASE is an open source web-based comprehensive database server to 
  manage the massive amounts of data generated by microarray analysis.  
! Further details about BASE can be found by following the links to the 
! left or by reading the BASE manuscript (see below).
  
! <p>If you are interested, a graphic of the BASE database table schema can be 
! viewed  <a href="img/sshot/BASEschema.png" target=_new2>here (95kB)</a>, 
! along with a 
! <a href="img/sshot/BASE-TableDefinitions.pdf" target=_new3>textual 
! description (28kB)</a>
! of the table definitions.  A PDF file of our poster presentation at the 
! AACR/NHGRI/Nature Genetics 
! sponsored <a href="http://www.nhgri.nih.gov/CONF/Oncogenomics2002/" 
! target=_new4>
! Oncogenomics Meeting</a>, May 1-5, 2002, in Dublin is available
! <a href="img/sshot/BASE-Oncogenomics-Poster.PDF" target=_new5>here 
! (705kB)</a>. A PDF file of our poster presentation at the
! <a href="http://www.mged.org/" target=_new6>MGED 
! IV Meeting</a>, February 13-16, 2002, in Boston is available
! <a href="img/sshot/BASE-MGED4-Poster.PDF" target=_new7>here (540kB)</a>.
  
! <p>There is a BASE mailing list which you can subscribe to by sending a 
! blank email to <a 
! href="mailto:bas...@th...">bas...@th...</a>.
  
  <p><a target=_top href="http://sourceforge.net/"><img 
--- 7,33 ----
  <p>BASE is an open source web-based comprehensive database server to 
  manage the massive amounts of data generated by microarray analysis.  
! <p>For more information about BASE, visit the
! <a href="http://base.thep.lu.se/">BASE project site</a>
  
! For all questions regarding your local BASE installation, please
! contact your local administrator.
! <p>
  
! Please direct all general and technical questions regarding BASE
! to the public mailing list, but only after having read the FAQ.
! You can find the FAQ and additional documentation on the
! <a href="http://base.thep.lu.se/" target=_blank>BASE project site</a>.
! It might also be a good idea to check the list archive before you send a
! mail, as the answers to the most common issues have probably been
! discussed there already.
! You can subscribe to the mailing list by sending a blank email to
! <a href="mailto:bas...@th...">bas...@th...</a>.
! <p>
! If you have any other special issue, you may contact us directly: Lao Saal
! <a href="mailto:lao...@on...">&lt;lao...@on...&gt;</a>,
! Carl Troein <a href="mailto:ca...@th...">&lt;ca...@th...&gt;</a>,
! or Johan Vallon-Christersson
! <a href="mailto:joh...@on..."
! >&lt;joh...@on...&gt;</a>.
  
  <p><a target=_top href="http://sourceforge.net/"><img 
***************
*** 36,57 ****
  BASE development is coordinated through SourceForge.net. From the
  <a target=_top href="http://sourceforge.net/projects/basedb/"
! >BASE project page</a> you can e.g. access the CVS repository. If you're
! interested in helping out with its development, get a SourceForge
! account and tell a project admin.<br clear=all>
! 
! <p><span class=subhead>How to cite BASE?</span>
! <ul>
! <li>
! Lao H. Saal, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, 
! &Aring;ke Borg and Carsten Peterson<br>
! <strong>BioArray Software Environment: A Platform for Comprehensive Management 
! <br>and Analysis of Microarray Data</strong><br>
! <i>Genome Biology</i> 2002 <b>3</b>(8): software0003.1-0003.6<br> 
! [<a href="http://www.thep.lu.se/pub/Preprints/02/lu_tp_02_11_abs.html">abs</a>]
! [<a href="http://www.genomebiology.com/2002/3/8/software/0003/" 
! target=_new8>html</a>] 
! [<a target=_new9
! href="http://www.genomebiology.com/content/pdf/gb-2002-3-8-software0003.pdf">pdf</a>]
! </ul>
  
  <p><p><hr>
--- 37,44 ----
  BASE development is coordinated through SourceForge.net. From the
  <a target=_top href="http://sourceforge.net/projects/basedb/"
! >sf.net BASE project page</a> you can e.g. access the CVS repository.
! If you're interested in helping out with the development of BASE,
! get the latest version off the CVS and come talk to us on the mailing list.
! <br clear=all>
  
  <p><p><hr>

--- BASEbetaInstructions.pdf DELETED ---

--- contact.html DELETED ---

--- specs.html DELETED ---

From: <tr...@us...> - 2002-10-17 13:12:38

Update of /cvsroot/basedb/basedb/www/img/sshot/thumb
In directory usw-pr-cvs1:/tmp/cvs-serv6648/sshot/thumb

Removed Files:
      Tag: stable_1_0_6
	t_BASE-MGED4-Poster.jpg t_BASE-MGED4-Poster.png 
	t_BASEaddNewSample.jpg t_BASEannotateSample.jpg 
	t_BASEcreate384wPlate.jpg t_BASEcreateArrayType.jpg 
	t_BASEfileUploads.jpg t_BASEgeneExplorer.jpg 
	t_BASEgeneListExample.jpg t_BASEgeneLists.jpg 
	t_BASEjobhandler.jpg t_BASElistArrayTypes.jpg 
	t_BASElistSamples.jpg t_BASElistplateTypes.jpg 
	t_BASEmdsPlot.jpg t_BASEnewAnnotationType.jpg 
	t_BASEnewHybridization.jpg t_BASEplugIn.jpg 
	t_BASEplugInNormalizers.jpg t_BASEprojectHypox.jpg 
	t_BASEprojectNormalizations.jpg t_BASEsampleOriginOntology.jpg 
	t_BASEviewArrayType.jpg t_BASEviewPlateType.jpg 
	t_BASEviewplate384w.jpg t_BASEviewplate96w.jpg 
	t_ClusterBetaPlug-In.png 
Log Message:
Screenshots and unused images should not be in the distribution

--- t_BASE-MGED4-Poster.jpg DELETED ---

--- t_BASE-MGED4-Poster.png DELETED ---

--- t_BASEaddNewSample.jpg DELETED ---

--- t_BASEannotateSample.jpg DELETED ---

--- t_BASEcreate384wPlate.jpg DELETED ---

--- t_BASEcreateArrayType.jpg DELETED ---

--- t_BASEfileUploads.jpg DELETED ---

--- t_BASEgeneExplorer.jpg DELETED ---

--- t_BASEgeneListExample.jpg DELETED ---

--- t_BASEgeneLists.jpg DELETED ---

--- t_BASEjobhandler.jpg DELETED ---

--- t_BASElistArrayTypes.jpg DELETED ---

--- t_BASElistSamples.jpg DELETED ---

--- t_BASElistplateTypes.jpg DELETED ---

--- t_BASEmdsPlot.jpg DELETED ---

--- t_BASEnewAnnotationType.jpg DELETED ---

--- t_BASEnewHybridization.jpg DELETED ---

--- t_BASEplugIn.jpg DELETED ---

--- t_BASEplugInNormalizers.jpg DELETED ---

--- t_BASEprojectHypox.jpg DELETED ---

--- t_BASEprojectNormalizations.jpg DELETED ---

--- t_BASEsampleOriginOntology.jpg DELETED ---

--- t_BASEviewArrayType.jpg DELETED ---

--- t_BASEviewPlateType.jpg DELETED ---

--- t_BASEviewplate384w.jpg DELETED ---

--- t_BASEviewplate96w.jpg DELETED ---

--- t_ClusterBetaPlug-In.png DELETED ---

From: <tr...@us...> - 2002-10-17 13:12:35

Update of /cvsroot/basedb/basedb/www/img/sshot
In directory usw-pr-cvs1:/tmp/cvs-serv6648/sshot

Removed Files:
      Tag: stable_1_0_6
	BASE-MGED4-Poster.PDF BASE-Oncogenomics-Poster.PDF 
	BASE-TableDefinitions.pdf BASEaddNewSample.jpg 
	BASEannotateSample.jpg BASEcreate384wPlate.jpg 
	BASEcreateArrayType.jpg BASEfileUploads.jpg 
	BASEgeneExplorer.jpg BASEgeneListExample.jpg BASEgeneLists.jpg 
	BASEjobhandler.jpg BASElistArrayTypes.jpg BASElistSamples.jpg 
	BASElistplateTypes.jpg BASEmdsPlot.jpg 
	BASEnewAnnotationType.jpg BASEnewHybridization.jpg 
	BASEplugIn.jpg BASEplugInNormalizers.jpg BASEprojectHypox.jpg 
	BASEprojectNormalizations.jpg BASEsampleOriginOntology.jpg 
	BASEschema.png BASEviewArrayType.jpg BASEviewPlateType.jpg 
	BASEviewplate384w.jpg BASEviewplate96w.jpg 
	ClusterBetaPlug-In.png NSLwelcome.png 
Log Message:
Screenshots and unused images should not be in the distribution

--- BASE-MGED4-Poster.PDF DELETED ---

--- BASE-Oncogenomics-Poster.PDF DELETED ---

--- BASE-TableDefinitions.pdf DELETED ---

--- BASEaddNewSample.jpg DELETED ---

--- BASEannotateSample.jpg DELETED ---

--- BASEcreate384wPlate.jpg DELETED ---

--- BASEcreateArrayType.jpg DELETED ---

--- BASEfileUploads.jpg DELETED ---

--- BASEgeneExplorer.jpg DELETED ---

--- BASEgeneListExample.jpg DELETED ---

--- BASEgeneLists.jpg DELETED ---

--- BASEjobhandler.jpg DELETED ---

--- BASElistArrayTypes.jpg DELETED ---

--- BASElistSamples.jpg DELETED ---

--- BASElistplateTypes.jpg DELETED ---

--- BASEmdsPlot.jpg DELETED ---

--- BASEnewAnnotationType.jpg DELETED ---

--- BASEnewHybridization.jpg DELETED ---

--- BASEplugIn.jpg DELETED ---

--- BASEplugInNormalizers.jpg DELETED ---

--- BASEprojectHypox.jpg DELETED ---

--- BASEprojectNormalizations.jpg DELETED ---

--- BASEsampleOriginOntology.jpg DELETED ---

--- BASEschema.png DELETED ---

--- BASEviewArrayType.jpg DELETED ---

--- BASEviewPlateType.jpg DELETED ---

--- BASEviewplate384w.jpg DELETED ---

--- BASEviewplate96w.jpg DELETED ---

--- ClusterBetaPlug-In.png DELETED ---

--- NSLwelcome.png DELETED ---

[basedb-cvs] basedb/www/img lu.gif,1.1,NONE lulogo.jpg,1.1,NONE lusealbg.png,1.1,NONE onc.gif,1.1,NONE thep.gif,1.1,NONE

From: <tr...@us...> - 2002-10-17 13:12:32

Update of /cvsroot/basedb/basedb/www/img
In directory usw-pr-cvs1:/tmp/cvs-serv6648

Removed Files:
      Tag: stable_1_0_6
	lu.gif lulogo.jpg lusealbg.png onc.gif thep.gif 
Log Message:
Screenshots and unused images should not be in the distribution

--- lu.gif DELETED ---

--- lulogo.jpg DELETED ---

--- lusealbg.png DELETED ---

--- onc.gif DELETED ---

--- thep.gif DELETED ---

[basedb-cvs] basedb/contrib/plotapplet/plotapplet plot.jar,NONE,1.1.2.1 show_tmp.phtml,NONE,1.1.2.1 store_tmp.phtml,NONE,1.1.2.1

From: <tr...@us...> - 2002-10-17 12:51:16

Update of /cvsroot/basedb/basedb/contrib/plotapplet/plotapplet
In directory usw-pr-cvs1:/tmp/cvs-serv31391/plotapplet/plotapplet

Added Files:
      Tag: stable_1_0_6
	plot.jar show_tmp.phtml store_tmp.phtml 
Log Message:
Added plotapplet beta version

--- NEW FILE: plot.jar ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: show_tmp.phtml ---
<?
require_once("../getconfig.inc.php");

header("Content-Type: " . $_REQUEST["type"] .
       "; filename=\"" . $_REQUEST["name"] . "\"");
header("Content-Disposition: filename=\"" . $_REQUEST["name"] . "\"");
$id = $_REQUEST["id"];
if (count_chars($id) >= 50) {
   $file = $config["tempDir"] ."/" . $id;
   readfile($file);
   unlink($file);
}
?>
--- NEW FILE: store_tmp.phtml ---
<?
require_once("../init.inc.php");
require_once("../misc.inc.php");
require_once("../getconfig.inc.php");
require_once("../raw.inc.php");

verifyAccess(BUA_ANALYZE);

$tmpFile = $config["tempDir"] . "/" . $_REQUEST["id"];

if (strcmp($_REQUEST["in"], "application/postscript") == 0 &&
    strcmp($_REQUEST["out"], "application/pdf") == 0) {
  $psFile = tempFileName();

  $fd = fopen($psFile, "w");
  if(!$fd) return "Unable to open temporary output file";
  fwrite($fd, $_REQUEST["data"]);
  fclose($fd);

  passthru("/usr/bin/ps2pdf $psFile $tmpFile");

  unlink($psFile);

} else {
  $fd = fopen($tmpFile, "w");
  if(!$fd) return "Unable to open temporary output file";
  fwrite($fd, $_REQUEST["data"]);
  fclose($fd);
}

?>

[basedb-cvs] basedb/contrib/plotapplet README,NONE,1.1.2.1 plotapplet_assay.phtml,NONE,1.1.2.1 plotapplet_data.phtml,NONE,1.1.2.1 plotapplet_raw.phtml,NONE,1.1.2.1 www.patch,NONE,1.1.2.1

From: <tr...@us...> - 2002-10-17 12:51:16

Update of /cvsroot/basedb/basedb/contrib/plotapplet
In directory usw-pr-cvs1:/tmp/cvs-serv31391/plotapplet

Added Files:
      Tag: stable_1_0_6
	README plotapplet_assay.phtml plotapplet_data.phtml 
	plotapplet_raw.phtml www.patch 
Log Message:
Added plotapplet beta version

--- NEW FILE: README ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: plotapplet_assay.phtml ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: plotapplet_data.phtml ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: plotapplet_raw.phtml ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: www.patch ---
? clean
? getconfig.inc.php
? mage
? phpMyAdmin
? plotapplet
? plotapplet_assay.phtml
? plotapplet_data.phtml
? plotapplet_raw.phtml
Index: raw_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_common.inc.php,v
retrieving revision 1.16
diff -C2 -r1.16 raw_common.inc.php
*** raw_common.inc.php	5 Aug 2002 11:29:35 -0000	1.16
--- raw_common.inc.php	17 Oct 2002 12:44:06 -0000
***************
*** 133,136 ****
--- 133,142 ----
  		'scrollbars=yes,resizable=yes,toolbar=1');
  }
+ function rawPlotter2(raw)
+ {
+ 	window.open('plotapplet_raw.phtml?i_r='+raw, 'rawPlotter2_'+raw,
+ 		'location=1,menubar=1,personalbar=0,width=680,height=520,'+
+ 		'scrollbars=yes,resizable=yes,toolbar=1');
+ }
  </script>
  <?
***************
*** 210,214 ****
  				"Overview&nbsp;plot</a>] ".
  				"[<a class=popup href='javascript:rawPlotter($id)'>".
! 				"Plot&nbsp;tool</a>]</td>".
  				"</tr>\n";
  		}
--- 216,222 ----
  				"Overview&nbsp;plot</a>] ".
  				"[<a class=popup href='javascript:rawPlotter($id)'>".
! 				"Plot&nbsp;tool&nbsp;(classic)</a>] ".
! 				"[<a class=popup href='javascript:rawPlotter2($id)'>".
! 				"Plot&nbsp;tool&nbsp;(Java)</a>]</td>".
  				"</tr>\n";
  		}
Index: raw_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_edit.phtml,v
retrieving revision 1.14
diff -C2 -r1.14 raw_edit.phtml
*** raw_edit.phtml	5 Aug 2002 11:29:35 -0000	1.14
--- raw_edit.phtml	17 Oct 2002 12:44:06 -0000
***************
*** 170,174 ****
  			"Overview plot</a>]".
  			" [<a class=popup href='javascript:rawPlotter($rawid)'>".
! 			"Plot tool</a>]".
  			"</td></tr>\n".
  			"<tr><th>Molecule IDs</th>".
--- 170,176 ----
  			"Overview plot</a>]".
  			" [<a class=popup href='javascript:rawPlotter($rawid)'>".
! 			"Plot tool (classic)</a>]".
! 			" [<a class=popup href='javascript:rawPlotter2($rawid)'>".
! 			"Plot tool (Java)</a>]".
  			"</td></tr>\n".
  			"<tr><th>Molecule IDs</th>".

Flat | Threaded

<< < 1 .. 35 36 37 38 39 .. 42 > >> (Page 37 of 42)

2002	Jan	Feb	Mar	Apr	May	Jun	Jul	Aug (14)	Sep (76)	Oct (65)	Nov (177)	Dec (147)
2003	Jan (257)	Feb (313)	Mar	Apr	May	Jun	Jul	Aug	Sep	Oct	Nov	Dec