basedb-cvs Mailing List for BASE (Page 40)

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Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv31072

Modified Files:
	bio.inc.php extract_edit.phtml extract_list.phtml 
	htmlinit.phtml hyb.inc.php item.inc.php labeled_edit.phtml 
	labeled_list.phtml misc.inc.php raw_common.inc.php 
	sample_edit.phtml sample_list.phtml search.inc.php 
Added Files:
	item_common.inc.php 
Log Message:
First steps towards data hiding.

--- NEW FILE: item_common.inc.php ---
<?
// $Id: item_common.inc.php,v 1.1 2002/09/12 22:37:56 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.
//

// Input: Item object or scalar. Output: string denoting deleted item.
function remMark(&$obj)
{
	if(is_object($obj))
	{
		if(!$obj->getRemoved())
			return "";
	}
	else if(!$obj)
		return "";
	return " <span class=del>(D)</span>";
}

// Set $showdel from $i_showdel
function showDelPrep()
{
	global $showdel, $i_showdel;
	$showdel = isset($i_showdel) ? max(-1, min(1, (int)$i_showdel)) : 0;
}

// Get value to use for $removed in function call
function showDelValue()
{
	global $showdel;
	return $showdel < 0 ? NULL : $showdel;
}

// Get value for $removed when you want to hide removed items unless
// the user is including removed items in the search.
function showDelSublist()
{
	global $showdel;
	return $showdel === 0 ? 0 : NULL;
}

// Outputs a table row with links to change what to view. Must be in
// a form called "ff". $columns is the number of cols in the table.
function showDelLinks($columns)
{
	global $showdel;
?>
<input type=hidden name=i_showdel value="<?= $showdel ?>">
<script>
function showDel(sd)
{
	document.ff.i_showdel.value=sd;
	document.ff.submit();
}
</script>
<tr><td colspan=<?= $columns ?> align=right>
	<a <?= !$showdel ? "class=special" : "" ?>
		href="javascript:showDel(0)">Undeleted</a> /
	<a <?= $showdel > 0 ? "class=special" : "" ?>
		href="javascript:showDel(1)">Deleted</a> /
	<a <?= $showdel < 0 ? "class=special" : "" ?>
		href="javascript:showDel(-1)">All</a>
</td></tr>
<?
}

?>
Index: bio.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bio.inc.php,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** bio.inc.php	10 Sep 2002 23:04:50 -0000	1.24
--- bio.inc.php	12 Sep 2002 22:37:56 -0000	1.25
***************
*** 34,45 ****
  class Sample extends Item
  {
! 	var $tissue/*, $project*/;
  
  	function Sample($name = "", $descr = "", $owner = 0, $addedDate = "",
! 		$tissue = 0, /*$project = 0,*/ $id = 0, $visible = 0)
  	{
! 		$this->Item("Sample", $name, $descr, $owner, $addedDate, $id, $visible);
  		$this->tissue = (int)$tissue;
! /*		$this->project = (int)$project;*/
[...821 lines suppressed...]
+ 		return parent::getBasicFromId("LabeledExtract", $id);
+ 	}
  
  	function countForExtract($extract)
***************
*** 769,781 ****
  	{
  		parent::changeQuantityLeft("LabeledExtract", $amount, $id);
- 	}
- 
- 	function lockId($id, $exclusive)
- 	{
- 		return parent::lockItem("LabeledExtract", $id, $exclusive);
- 	}
- 	function unlockId($id, $exclusive)
- 	{
- 		return parent::unlockItem("LabeledExtract", $id, $exclusive);
  	}
  
--- 795,798 ----

Index: extract_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/extract_edit.phtml,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** extract_edit.phtml	10 Sep 2002 23:05:02 -0000	1.14
--- extract_edit.phtml	12 Sep 2002 22:37:56 -0000	1.15
***************
*** 27,30 ****
--- 27,31 ----
  	require_once("protocol.inc.php");
  	require_once("bio.inc.php");
+ 	require_once("item_common.inc.php");
  
  	verifyAccess(BUA_BIO_READ);
***************
*** 38,43 ****
  		if($i_ext > 0)
  		{
[...271 lines suppressed...]
- <tr><th>Usecount</th><td><?= $usecount ?></td></tr>
- <tr><td colspan=2><a <?= href("labeled_edit.phtml?i_ext=$extid", 1)
- 	?>>Label extract</a></td></tr>
- </table>
  <?
  	}
  ?>
--- 315,326 ----
  <tr><th>Owner</th><td><?= html($uname) ?></td></tr>
  <tr><th>Public</th><td><?= $ext->isSharedWith(0) ? "Yes" : "No" ?></td></tr>
  <?
+ 		if(!$ext->getRemoved())
+ 		{
+ 			echo "<tr><td colspan=2><a ".
+ 				href("labeled_edit.phtml?i_ext=$extid", 1).">".
+ 				"Label extract</a></td></tr>\n";
+ 		}
+ 		echo "</table>";
  	}
  ?>

Index: extract_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/extract_list.phtml,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** extract_list.phtml	5 Aug 2002 11:29:34 -0000	1.11
--- extract_list.phtml	12 Sep 2002 22:37:56 -0000	1.12
***************
*** 30,37 ****
  	require_once("search.inc.php");
  	require_once("searchhtml.inc.php");
  
  	verifyAccess(BUA_BIO_READ);
  
! 	$searchfields = array("Name", "Description", "Sample", "User",
  		"Date added", "Extraction date", "Protocol", "Quantity left");
  	$fieldtype = array(0, 0, 0, 0, 1, 1, 0, 2);
--- 30,39 ----
  	require_once("search.inc.php");
[...86 lines suppressed...]
  			"<td>".$qty."</td>".
! 			"<td>".LabeledExtract::countForExtract($s["id"]).
! 				"<a href='labeled_edit.phtml?i_ext=$s[id]'> [new]</a></td>".
  			"<td>".$hybs."</td></tr>\n";
  	}
! 	if($addlink != "") echo "<tr><td colspan=9>$addlink</td></tr>\n";
  ?>
  </form>
--- 102,112 ----
  			"<td>".($s["public"] ? "Yes" : "No")."</td>".
  			"<td>".$qty."</td>".
! 			"<td>".$labs."</td>".
  			"<td>".$hybs."</td></tr>\n";
  	}
! 	$cols = 9;
! 	if($addlink != "")
! 		echo "<tr><td colspan=$cols>$addlink</td></tr>\n";
! 	showDelLinks($cols);
  ?>
  </form>

Index: htmlinit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/htmlinit.phtml,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** htmlinit.phtml	5 Aug 2002 11:29:34 -0000	1.24
--- htmlinit.phtml	12 Sep 2002 22:37:56 -0000	1.25
***************
*** 42,59 ****
  	if(isset($pageTitle) && $pageTitle != "")
  		echo "<title>".html($pageTitle, 0)."</title>\n";
  ?>
  <meta name=creator content="Typoed by Círdan">
  <style type="text/css">
! a:active { text-decoration: underline; color: #ff5050; }
  a:link { text-decoration: none; color: #1000d0; }
  a:visited { text-decoration: none; color: #1000d0; }
  
! a.ext:active { text-decoration: underline; color: #ff5050; }
  a.ext:link { text-decoration: none; color: #f00000; }
  a.ext:visited { text-decoration: none; color: #800000; }
  
! body { font-family: Helvetica, sans-serif; background-color: #f0f4f4;
  	font-size: <?= $curDisplay->getTextSize("normal") ?>pt; font-weight: normal }
! div { font-family: Helvetica, sans-serif; background-color: #f0f4f4;
  	font-size: <?= $curDisplay->getTextSize("normal") ?>pt; font-weight: normal }
  td { font-family: Helvetica, sans-serif; font-size: <?=
--- 42,61 ----
  	if(isset($pageTitle) && $pageTitle != "")
  		echo "<title>".html($pageTitle, 0)."</title>\n";
+ 
+ 	$bgColor = "#f0f4f4";
  ?>
  <meta name=creator content="Typoed by Círdan">
  <style type="text/css">
! a:active { text-decoration: none; color: #ff5050; }
  a:link { text-decoration: none; color: #1000d0; }
  a:visited { text-decoration: none; color: #1000d0; }
  
! a.ext:active { text-decoration: none; color: #ff5050; }
  a.ext:link { text-decoration: none; color: #f00000; }
  a.ext:visited { text-decoration: none; color: #800000; }
  
! body { font-family: Helvetica, sans-serif; background-color: <?= $bgColor ?>;
  	font-size: <?= $curDisplay->getTextSize("normal") ?>pt; font-weight: normal }
! div { font-family: Helvetica, sans-serif; background-color: <?= $bgColor ?>;
  	font-size: <?= $curDisplay->getTextSize("normal") ?>pt; font-weight: normal }
  td { font-family: Helvetica, sans-serif; font-size: <?=
***************
*** 74,78 ****
  .help { font-style: italic }
  .special { font-weight: bold }
! .pagehead { text-align: left; background-color: #f0f4f4;
  	font-size: <?=  $curDisplay->getTextSize("pagehead") ?>pt }
  .subhead { text-align: left; font-size: <?=
--- 76,80 ----
  .help { font-style: italic }
  .special { font-weight: bold }
! .pagehead { text-align: left; background-color: <?= $bgColor ?>;
  	font-size: <?=  $curDisplay->getTextSize("pagehead") ?>pt }
  .subhead { text-align: left; font-size: <?=
***************
*** 82,85 ****
--- 84,88 ----
  	font-weight: bold; background-color: #ffe0c0; }
  .red { color: Red; font-size: <?= $curDisplay->getTextSize("large") ?>pt }
+ .del { color: #e00050; font-weight: bold }
  .popup { color: #007010 }
  .tiny { font-size: <?= $curDisplay->getTextSize("tiny") ?>pt }
***************
*** 101,105 ****
  ?>
  </head>
! <body bgcolor=#f0f4f4 text=black>
  <?
  	}
--- 104,108 ----
  ?>
  </head>
! <body bgcolor="<?= $bgColor ?>" text=black>
  <?
  	}

Index: hyb.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb.inc.php,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** hyb.inc.php	10 Sep 2002 23:05:10 -0000	1.21
--- hyb.inc.php	12 Sep 2002 22:37:56 -0000	1.22
***************
*** 33,40 ****
  	var $hybridizationDate, $protocol;
  
! 	function Hybridization($name = "", $descr = "", $owner = 0, $addedDate = "",
! 		$hybridizationDate = "", $protocol = 0, $id = 0)
  	{
! 		$this->Item("Hybridization", $name, $descr, $owner, $addedDate, $id);
  		$this->hybridizationDate = $hybridizationDate;
  		$this->protocol = (int)$protocol;
--- 33,42 ----
  	var $hybridizationDate, $protocol;
[...265 lines suppressed...]
+ 		return parent::getBasicFromId("Hybridization", $id);
+ 	}
  
  	function isOwner($id, $owner)
***************
*** 298,310 ****
  		query($query);
  		return db_affected_rows() > 0;
- 	}
- 
- 	function lockId($id, $exclusive)
- 	{
- 		return parent::lockItem("Hybridization", $id, $exclusive);
- 	}
- 	function unlockId($id, $exclusive)
- 	{
- 		return parent::unlockItem("Hybridization", $id, $exclusive);
  	}
  }
--- 321,324 ----

Index: item.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/item.inc.php,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** item.inc.php	12 Sep 2002 11:45:26 -0000	1.29
--- item.inc.php	12 Sep 2002 22:37:56 -0000	1.30
***************
*** 67,76 ****
  	}
  
! 	function sqlRemoved($table, $removed)
  	{
  		if(isset($removed))
! 			return "AND $table.removed == ".(int)(bool)$removed;
  		return "";
  	}
  
  	function read($id, $owner = -1, $removed = NULL)
[...179 lines suppressed...]
  			$res = query($query);
  			while($row =& db_fetch_row($res))
***************
*** 222,225 ****
--- 244,258 ----
  		else $n = "";
  		return $n;
+ 	}
+ 
+ 	// Returns an array with (name,removed,owner)
+ 	function getBasicFromId($type, $id)
+ 	{
+ 		$query = "SELECT name, removed, owner ".
+ 			"FROM $type WHERE id = ".(int)$id;
+ 		$res = query($query);
+ 		if($row =& db_fetch_assoc($res))
+ 			return $row;
+ 		return false;
  	}
  

Index: labeled_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_edit.phtml,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** labeled_edit.phtml	10 Sep 2002 23:05:53 -0000	1.14
--- labeled_edit.phtml	12 Sep 2002 22:37:56 -0000	1.15
***************
*** 27,30 ****
--- 27,31 ----
  	require_once("protocol.inc.php");
  	require_once("bio.inc.php");
+ 	require_once("item_common.inc.php");
  
  	verifyAccess(BUA_BIO_READ);
***************
*** 47,62 ****
  		{
  			$newlabeled = true;
[...261 lines suppressed...]
- <tr><th>Usecount</th><td><?= $usecount ?></td></tr>
- <tr><td colspan=2><a <?= href("hyb_edit.phtml?i_lext=$lextid", 1)
- 	?>>Hybridize labeled extract</a></td></tr>
- </table>
  <?
  	}
  ?>
--- 337,348 ----
  <tr><th>Owner</th><td><?= html($uname) ?></td></tr>
  <tr><th>Public</th><td><?= $lext->isSharedWith(0) ? "Yes" : "No" ?></td></tr>
  <?
+ 		if(!$lext->getRemoved())
+ 		{
+ 			echo "<tr><td colspan=2><a ".
+ 				href("hyb_edit.phtml?i_lext=$lextid", 1).">".
+ 				"Hybridize labeled extract</a></td></tr>\n";
+ 		}
+ 		echo "</table>";
  	}
  ?>

Index: labeled_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_list.phtml,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** labeled_list.phtml	29 Aug 2002 16:51:34 -0000	1.12
--- labeled_list.phtml	12 Sep 2002 22:37:56 -0000	1.13
***************
*** 30,35 ****
--- 30,37 ----
  	require_once("search.inc.php");
  	require_once("searchhtml.inc.php");
+ 	require_once("item_common.inc.php");
  
  	verifyAccess(BUA_BIO_READ);
+ 	showDelPrep();
  
  	$searchfields = array("Name", "Description", "Extract", "Sample",
***************
[...83 lines suppressed...]
  			"<td><a href='labeled_edit.phtml?i_lext=$s[id]'>".
! 				html($s["name"]).remMark($s["removed"])."</a></td>".
  			"<td>".html($s["label"])."</td>".
  			"<td>$elink</td>".
***************
*** 103,107 ****
  			"<td>".$hybs."</td></tr>\n";
  	}
! 	if($addlink != "") echo "<tr><td colspan=8>$addlink</td></tr>\n";
  ?>
  </form>
--- 110,117 ----
  			"<td>".$hybs."</td></tr>\n";
  	}
! 	$cols = 8;
! 	if($addlink != "")
! 		echo "<tr><td colspan=$cols>$addlink</td></tr>\n";
! 	showDelLinks($cols);
  ?>
  </form>

Index: misc.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/misc.inc.php,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** misc.inc.php	12 Sep 2002 11:45:26 -0000	1.37
--- misc.inc.php	12 Sep 2002 22:37:56 -0000	1.38
***************
*** 376,378 ****
--- 376,379 ----
  			"href=\"javascript:window.close()\">Close</a>]</span>";
  	}
+ 
  ?>

Index: raw_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_common.inc.php,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** raw_common.inc.php	10 Sep 2002 23:06:28 -0000	1.18
--- raw_common.inc.php	12 Sep 2002 22:37:56 -0000	1.19
***************
*** 67,71 ****
  		if(isset($i_expgo))
  		{
! 			$iua = ignore_user_abort();
  			$expid = 0;
  			if(isset($i_expname) && $i_expname != "")
--- 67,71 ----
  		if(isset($i_expgo))
  		{
! 			$iua = ignore_user_abort(1);
  			$expid = 0;
  			if(isset($i_expname) && $i_expname != "")

Index: sample_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sample_edit.phtml,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** sample_edit.phtml	10 Sep 2002 23:06:29 -0000	1.18
--- sample_edit.phtml	12 Sep 2002 22:37:56 -0000	1.19
***************
*** 29,32 ****
--- 29,33 ----
  	require_once("sampletissue.inc.php");
  	require_once("sampleannotation.inc.php");
+ 	require_once("item_common.inc.php");
  
  	verifyAccess(BUA_BIO_READ);
***************
*** 35,53 ****
  	$edit = true;
  	$err = "";
[...305 lines suppressed...]
! <tr><th>Sample date</th><td><?= htmldate($samp->getSampleDate()) ?></td></tr>
! <tr><th>Date added</th><td><?= htmldate($samp->getAddedDate()) ?></td></tr>
  <tr><th>Owner</th><td><?= html($uname) ?></td></tr>
  <tr><th>Public</th><td><?= $samp->isSharedWith(0) ? "Yes" : "No" ?></td></tr>
  <tr><td colspan=2 class=tiny>&nbsp;</td></tr>
  <tr><th colspan=2 class=subhead>Annotations</th></tr>
***************
*** 277,284 ****
--- 298,308 ----
  				"<td>".html($arr["annotation"])."</td></tr>\n";
  		}
+ 		if(!$samp->getRemoved())
+ 		{
  ?>
  <tr><td colspan=2><a <?= href("extract_edit.phtml?i_samp=$sampid", 1)
  	?>>Extract from sample</a></td></tr>
  <?
+ 		}
  	}
  ?>

Index: sample_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sample_list.phtml,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** sample_list.phtml	23 Aug 2002 13:16:11 -0000	1.14
--- sample_list.phtml	12 Sep 2002 22:37:56 -0000	1.15
***************
*** 32,45 ****
  	require_once("search.inc.php");
  	require_once("searchhtml.inc.php");
  
  	verifyAccess(BUA_BIO_READ);
  
  	$view = isset($i_view) && $i_view ? 1 : 0;
  
! 	$searchfields = array("Name", "Description", "User", "Date added");
! 	$searchtypes = array(0, 0, 0, 1);
  	if(!$view)
[...143 lines suppressed...]
  
! 			$anns = SampleAnnotation::getBrieferForSample($s["id"]);
  
! 			echo "<tr bgcolor=$tdbg[$odd]>".
! 				"<td><a href='sample_edit.phtml?i_samp=$s[id]'>".
! 				html($s["name"])."</a></td>";
! 			for(reset($annottypes); list($aid) = each($annottypes); )
! 			{
! 				if(isset($anns[$aid]))
! 					echo "<td>".html($anns[$aid])."</td>";
! 				else echo "<td bgcolor=$tdbg2[$odd]>&nbsp;</td>";
! 			}
! 			echo "</tr>\n";
  		}
  	}
! 	if($addlink != "")
! 		echo "<tr><td colspan=$cols>$addlink</td></tr>\n";
! 	showDelLinks($cols);
  ?>
  </form>

Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** search.inc.php	11 Sep 2002 10:35:51 -0000	1.41
--- search.inc.php	12 Sep 2002 22:37:56 -0000	1.42
***************
*** 603,607 ****
  				$this->extraWhere[$where[$t]] = 1;
  		}
! 		else $this->extraWhere[$where] = 1;
  	}
  	function addLeftJoin($lj)
--- 603,608 ----
  				$this->extraWhere[$where[$t]] = 1;
  		}
! 		else if($where != "")
! 			$this->extraWhere[$where] = 1;
  	}
  	function addLeftJoin($lj)

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basedb-cvs Mailing List for BASE (Page 40)

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