[basedb-cvs] basedb/www array.inc.php,1.41,1.42 array_popup.phtml,1.11,1.12 hyb.inc.php,1.24,1.25 hy

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Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv413

Modified Files:
	array.inc.php array_popup.phtml hyb.inc.php hyb_common.inc.php 
	hyb_edit.phtml hyb_list.phtml hyb_result.phtml 
	links_common.inc.php 
Log Message:
Re-made it possible to pick array for hyb

Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** array.inc.php	2 Oct 2002 17:50:56 -0000	1.41
--- array.inc.php	3 Oct 2002 18:00:07 -0000	1.42
***************
*** 191,195 ****
  	}

! 	// Returns an array of arrays with id,name,batches,arrays
  	function getWithSharedBatch($ownerId)
  	{
--- 191,195 ----
  	}

! /*	// Returns an array of arrays with id,name,batches,arrays
  	function getWithSharedBatch($ownerId)
[...112 lines suppressed...]

! 		$query = "SELECT a.id, a.name, a.removed, a.batch, ".
! 			Item::whereshared("a", $user)." AS arrayRead, ".
! 			"ab.name AS `batchName`, ab.removed AS `batchRemoved`, ".
! 			Item::whereshared("ab", $user)." AS batchRead, ".
! 			"ab.name AS `batchName`, ab.removed AS `batchRemoved`, ".
! 			"ab.`arrayType`, ".
! 			Item::whereshared("ab", $user)." AS batchRead, ".
! 			"at.name AS `designName`, at.removed AS `designRemoved`, ".
! 			Item::whereshared("at", $user)." AS designRead ".
! 			"FROM ArraySlide a, ArrayBatch ab, ArrayType at ".
! 			"WHERE a.hybridization = $hyb AND ab.id = a.batch ".
! 			"AND at.id = ab.`arrayType`";
  		$res = query($query);
  		if($row =& db_fetch_assoc($res))
  			return $row;
  		return false;
! 	}

  	function getNameFromId($id)

Index: array_popup.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array_popup.phtml,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** array_popup.phtml	5 Aug 2002 11:29:31 -0000	1.11
--- array_popup.phtml	3 Oct 2002 18:00:07 -0000	1.12
***************
*** 59,63 ****
  <tr><th>Name</th><th>Date</th><th>Arrays</th><th>Design</th></tr>
  <?
! 		$arrs = ArrayBatch::getWithUnusedArray(0, $curUser->getId());

  		for($i = 0; $i < count($arrs); $i++)
--- 59,63 ----
  <tr><th>Name</th><th>Date</th><th>Arrays</th><th>Design</th></tr>
  <?
! 		$arrs = ArrayBatch::getWithUnusedArray(0, $curUser);

  		for($i = 0; $i < count($arrs); $i++)
***************
*** 66,70 ****
  <tr><td><a href="array_popup.phtml?i_batch=<?= $arrs[$i]["id"] ?>"
  	><?= html($arrs[$i]["name"]) ?></td>
! 	<td><?= htmldate($arrs[$i]["date"]) ?></td>
  	<td><?= $arrs[$i]["arrays"] ?></td>
  	<td><?= html($arrs[$i]["designName"]) ?></td></tr>
--- 66,70 ----
  <tr><td><a href="array_popup.phtml?i_batch=<?= $arrs[$i]["id"] ?>"
  	><?= html($arrs[$i]["name"]) ?></td>
! 	<td><?= htmldate($arrs[$i]["addedDate"]) ?></td>
  	<td><?= $arrs[$i]["arrays"] ?></td>
  	<td><?= html($arrs[$i]["designName"]) ?></td></tr>
***************
*** 84,88 ****
  <tr><th>#</th><th>Barcode</th></tr>
  <?
! 		$arrs = ArrayBatch::getUnusedArrays($i_batch);
  		for(reset($arrs); list($pos, $bc) = each($arrs); )
  		{
--- 84,88 ----
  <tr><th>#</th><th>Barcode</th></tr>
  <?
! 		$arrs = ArraySlide::getUnusedForBatch($i_batch, $curUser);
  		for(reset($arrs); list($pos, $bc) = each($arrs); )
  		{

Index: hyb.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb.inc.php,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** hyb.inc.php	30 Sep 2002 16:57:05 -0000	1.24
--- hyb.inc.php	3 Oct 2002 18:00:08 -0000	1.25
***************
*** 79,83 ****
  			"WHERE hybridization IN (".implode(",", $del).")";
  		$ok = $ok && query($query);
! 		$query = "UPDATE Array SET hybridization = NULL ".
  			"WHERE hybridization IN (".implode(",", $del).")";
  		$ok = $ok && query($query);
--- 79,83 ----
  			"WHERE hybridization IN (".implode(",", $del).")";
  		$ok = $ok && query($query);
! 		$query = "UPDATE ArraySlide SET hybridization = NULL ".
  			"WHERE hybridization IN (".implode(",", $del).")";
  		$ok = $ok && query($query);
***************
*** 154,160 ****
  	{
  		// Add more fields here
! 		$sortfields = array("name", 0, "barcode", "`hybridizationDate`",
  			"`userName`", 0, 0, 0,
! 			"`protocolName`", "scans", "images", "raws");

  		$ob = $search->makeOrderBy($sortfields);
--- 154,161 ----
  	{
  		// Add more fields here
! 		$sortfields = array("name", 0,
  			"`userName`", 0, 0, 0,
! 			"`hybridizationDate`", "barcode", "`protocolName`",
! 			"scans", "images", "raws");

  		$ob = $search->makeOrderBy($sortfields);
***************
*** 172,185 ****

  		$query = "SELECT h.*, $ss1 p.name AS `protocolName`, ".
! 			"ug.name AS `userName`, ".
  			Item::whereShared("p", $user)." AS `protocolRead`, ".
  			"COUNT(DISTINCT ia.id) AS scans, ".
  			"COUNT(DISTINCT i.id) AS images, ".
! 			"COUNT(DISTINCT rba.id) AS raws, a.barcode ".
  			"FROM UserGroup ug, Protocol p, Hybridization h ".
  			"LEFT JOIN ImageAcquisition ia ON ia.hybridization = h.id ".
  			"LEFT JOIN Image i ON i.`imageAcquisition` = ia.id ".
  			"LEFT JOIN RawBioAssay rba ON rba.`imageAcquisition` = ia.id ".
! 			"LEFT JOIN Array a ON a.hybridization = h.id ".
  			"WHERE p.id = h.protocol AND ug.id = h.owner ".
  			$search->getExtraWhere()." ".$search->getWhere()." ".
--- 173,186 ----

  		$query = "SELECT h.*, $ss1 p.name AS `protocolName`, ".
! 			"ug.name AS `userName`, a.name AS barcode, ".
  			Item::whereShared("p", $user)." AS `protocolRead`, ".
  			"COUNT(DISTINCT ia.id) AS scans, ".
  			"COUNT(DISTINCT i.id) AS images, ".
! 			"COUNT(DISTINCT rba.id) AS raws ".
  			"FROM UserGroup ug, Protocol p, Hybridization h ".
  			"LEFT JOIN ImageAcquisition ia ON ia.hybridization = h.id ".
  			"LEFT JOIN Image i ON i.`imageAcquisition` = ia.id ".
  			"LEFT JOIN RawBioAssay rba ON rba.`imageAcquisition` = ia.id ".
! 			"LEFT JOIN ArraySlide a ON a.hybridization = h.id ".
  			"WHERE p.id = h.protocol AND ug.id = h.owner ".
  			$search->getExtraWhere()." ".$search->getWhere()." ".

Index: hyb_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_common.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** hyb_common.inc.php	30 Sep 2002 16:57:05 -0000	1.10
--- hyb_common.inc.php	3 Oct 2002 18:00:09 -0000	1.11
***************
*** 39,66 ****
  	<td><?= html($hyb->getName()).remMark($hyb) ?></td></tr>
  <?
! 		$ai = ArrayBatch::getArrayInfo($hyb->getId(), $curUser->getId());
  		if($ai)
  		{
- 			$blink = html($ai["batchName"]);
- 			if(!$ai["private"] && acc(BUA_ARRAY_READ))
- 			{
- 				$blink = "<a ".
- 					href("array_batch.phtml?i_ab=$ai[batchId]", 2).">$blink</a>";
- 			}
- 
- 			$tlink = html($ai["typeName"]);
- 			if(acc(BUA_ARRAY_READ))
- 			{
- 				$tlink = "<a ".
- 					href("array_edit.phtml?i_at=$ai[typeId]", 2).">$tlink</a>";
- 			}
  ?>
! <tr><th>Array slide</th>
! 	<td><?= html($ai["barcode"]) ?></td></tr>
! <tr><th>Array print</th><td><?= $blink ?></td></tr>
! <tr><th>Array design</th><td><?= $tlink ?></td></tr>
  <?
  		}
! 		else echo "<tr><th>Array slide</th><td>-</td></tr>\n";

  		$used = LabeledExtract::getBriefForHyb($hybid, $curUser);
--- 39,53 ----
  	<td><?= html($hyb->getName()).remMark($hyb) ?></td></tr>
  <?
! 		$ai = ArraySlide::getBriefForHyb($hyb->getId(), $curUser);
  		if($ai)
  		{
  ?>
! <tr><th>Array slide</th><td><?= ArraySlideArrLink($ai) ?></td></tr>
! <tr><th>Array print</th><td><?= ArrayBatchArrLink($ai) ?></td></tr>
! <tr><th>Array design</th><td><?= ArrayTypeArrLink($ai) ?></td></tr>
  <?
  		}
! 		else
! 			echo "<tr><th>Array slide</th><td>".html(NULL)."</td></tr>\n";

  		$used = LabeledExtract::getBriefForHyb($hybid, $curUser);

Index: hyb_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_edit.phtml,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** hyb_edit.phtml	2 Oct 2002 17:50:56 -0000	1.37
--- hyb_edit.phtml	3 Oct 2002 18:00:10 -0000	1.38
***************
*** 87,103 ****

  	$ai = 0;
! 	if(isset($i_array) && $i_array != "" && $err == "")
  	{
  		$as = new ArraySlide();
! 		if(!$as->readShared($i_array, $curUser))
  			$err = "No such array slide or access denied";
  		else if($as->getHybridization())
- 			$err = "That array slide has already been used";
- 		$ai = ArrayBatch::getArrayId($i_array);
[...144 lines suppressed...]
! 				"(ARRAY_READ)</td></tr>\n";
  		}
  ?>
--- 380,395 ----
  <?
  			}
! 			else if($ainfo)
  			{
! 				echo "<tr><th>Array slide</th><td>".arraySlideArrLink($ainfo)." ";
  				if(acc(BUA_ARRAY_READ))
  					echo "<input type=submit name=i_charray value='Change'>";
  				echo "</td></tr>\n";
  			}
! 			else
! 			{
! 				echo "<tr><th>Array slide</th><td class=help>".
! 					"Access denied (ARRAY_READ)</td></tr>\n";
! 			}
  		}
  ?>

Index: hyb_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_list.phtml,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** hyb_list.phtml	30 Sep 2002 16:57:05 -0000	1.16
--- hyb_list.phtml	3 Oct 2002 18:00:12 -0000	1.17
***************
*** 43,52 ****
  		"Hybridization date", "Protocol");
  	$fieldtype = array(0, 0, 0, 1, 1, 0);
! 	$headerfields = array("Name", "Labeled extracts", "Array",
! 		"Hyb date",
  		"Owner", "[<a href=javascript:selAll(1)>A</a> ".
  		"<a href=javascript:selAll(0)>N</a>]", "Group", "World",
! 		"Protocol", "Img sets", "Images", "Result files");
! 	$sortorder = array(1, 0, 1, -1, 1, 0, 0, 0, 1, -1, -1, -1);
  	$defsort = 0;

--- 43,52 ----
  		"Hybridization date", "Protocol");
  	$fieldtype = array(0, 0, 0, 1, 1, 0);
! 	$headerfields = array("Name", "Labeled extracts",
  		"Owner", "[<a href=javascript:selAll(1)>A</a> ".
  		"<a href=javascript:selAll(0)>N</a>]", "Group", "World",
! 		 "Hyb date", "Array", "Protocol", "Img sets", "Images",
! 		 "Result files");
! 	$sortorder = array(1, 0, 1, 0, 0, 0, -1, 1, 1, -1, -1, -1);
  	$defsort = 0;

***************
*** 101,130 ****
  			$llink[] = html("");

- /*		$samps = Sample::getBriefForHyb($id, $curUser);
- 		$slink = array();
- 		for($j = 0; $j < count($samps); $j++)
- 		{
- 			$slink[] = html($samps[$j]["name"]);
- 			if($samps[$j]["public"])
- 			{
- 				$slink[$j] = "<a href='sample_edit.phtml?i_samp=".
- 					$samps[$j]["id"]."'>$slink[$j]</a>".
- 					remMark($samps[$j]["removed"]);
- 			}
- 		}
- 		if(!count($slink))
- 			$slink[] = "&nbsp;";
- */
- 
  		echo "<tr bgcolor=$tdbg[$odd]>".
  			"<td><a href='hyb_edit.phtml?i_hyb=$s[id]'>".html($s["name"]).
  				"</a>".remMark($s["removed"])."</td>".
  			"<td>".implode(",\n", $llink)."</td>".
- 			"<td>".html($s["barcode"])."</td>".
- 			"<td>".htmldate($s["hybridizationDate"])."</td>".
  			"<td>".html($s["userName"])."</td>".
  			"<td>".groupAccessCheckbox($s["id"])."</td>".
  			"<td>".groupInfo($s, $users)."</td>".
  			"<td>".worldInfo($s)."</td>".
  			"<td>".protocolArrLink($s)."</td>".
  			"<td>".html($s["scans"])."</td>".
--- 101,114 ----
  			$llink[] = html("");

  		echo "<tr bgcolor=$tdbg[$odd]>".
  			"<td><a href='hyb_edit.phtml?i_hyb=$s[id]'>".html($s["name"]).
  				"</a>".remMark($s["removed"])."</td>".
  			"<td>".implode(",\n", $llink)."</td>".
  			"<td>".html($s["userName"])."</td>".
  			"<td>".groupAccessCheckbox($s["id"])."</td>".
  			"<td>".groupInfo($s, $users)."</td>".
  			"<td>".worldInfo($s)."</td>".
+ 			"<td>".htmldate($s["hybridizationDate"])."</td>".
+ 			"<td>".html($s["barcode"])."</td>".
  			"<td>".protocolArrLink($s)."</td>".
  			"<td>".html($s["scans"])."</td>".

Index: hyb_result.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_result.phtml,v
retrieving revision 1.55
retrieving revision 1.56
diff -C2 -d -r1.55 -r1.56
*** hyb_result.phtml	22 Sep 2002 23:37:34 -0000	1.55
--- hyb_result.phtml	3 Oct 2002 18:00:14 -0000	1.56
***************
*** 36,39 ****
--- 36,40 ----
  	require_once("wizzzard.inc.php");
  	require_once("item_common.inc.php");
+ 	require_once("upload_common.inc.php");

  	verifyAccess(BUA_BIO_EDIT);
***************
*** 41,46 ****

  	$upl = new Upload();
! 	$err = $upl->handleUpload("i_file", "i_fileid",
! 		isset($i_descr) ? $i_descr : "");
  	$fileid = $upl->getId();

--- 42,46 ----

  	$upl = new Upload();
! 	$err = handleUpload($upl, $curUser);
  	$fileid = $upl->getId();

***************
*** 404,426 ****
  <input type=hidden name=location value="<?= html($location, 0) ?>">
  <?
! 		$ups = Upload::getAll($curUser->getId());
! 		if(count($ups))
! 		{
! 			echo "<tr><th>Select an uploaded file</th>".
! 				"<td><select name=i_fileid><option value=0>- none -\n";
! 			for($i = 0; $i < count($ups); $i++)
! 			{
! 				$sel = $fileid == $ups[$i]->getId() ? "selected" : "";
! 				echo "<option $sel value=".$ups[$i]->getId().">".
! 					html($ups[$i]->getName())." (".$ups[$i]->getFileSize()." B)\n";
! 			}
! 			echo "</select></td></tr>\n";
! 			echo "<tr><th>Or pick a file to upload</th>";
! 		}
! 		else echo "<tr><th>Pick a file to upload</th>";
  ?>
- <td><input type=file name=i_file></td></tr>
- <tr><th>File description</th>
- 	<td><input type=text name=i_descr size=30></td></tr>
  <tr><td colspan=2><input type=submit value='Continue'></td></tr>
  </table>
--- 404,409 ----
  <input type=hidden name=location value="<?= html($location, 0) ?>">
  <?
! 		uploadInput($curUser);
  ?>
  <tr><td colspan=2><input type=submit value='Continue'></td></tr>
  </table>

Index: links_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/links_common.inc.php,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** links_common.inc.php	2 Oct 2002 17:50:56 -0000	1.3
--- links_common.inc.php	3 Oct 2002 18:00:15 -0000	1.4
***************
*** 134,137 ****
--- 134,146 ----
  }

+ function arraySlideArrLink(&$arr)
+ {
+ 	if(!$arr["arrayRead"])
+ 		return html($arr["name"]).remMark($arr["removed"]);
+ 	return "<a ".href("arrayslide_edit.phtml?i_as=".
+ 		(int)$arr["id"], 2).">".
+ 		html($arr["name"])."</a>".remMark($arr["removed"]);
+ }
+ 

  ?>

[basedb-cvs] basedb/www array.inc.php,1.41,1.42 array_popup.phtml,1.11,1.12 hyb.inc.php,1.24,1.25 hy

[basedb-cvs] basedb/www array.inc.php,1.41,1.42 array_popup.phtml,1.11,1.12 hyb.inc.php,1.24,1.25 hyb_common.inc.php,1.10,1.11 hyb_edit.phtml,1.37,1.38 hyb_list.phtml,1.16,1.17 hyb_result.phtml,1.55,1.56 links_common.inc.php,1.3,1.4