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[basedb-cvs] basedb/www array.inc.php,1.38,1.39 array_common.inc.php,1.11,1.12 array_edit.phtml,1.22,1.23 array_list.phtml,1.15,1.16 extract_list.phtml,1.16,1.17 item_common.inc.php,1.5,1.6 plate.inc.php,1.36,1.37 plate_common.inc.php,1.3,1.4 plate_edit.phtml,1.31,1.32 plate_list.phtml,1.28,1.29 platetype.inc.php,1.1,1.2 probe_search.phtml,1.5,1.6 protocol_common.inc.php,1.1,1.2 sample_edit.phtml,1.24,1.25 test.phtml,1.50,1.51
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv18528
Modified Files:
array.inc.php array_common.inc.php array_edit.phtml
array_list.phtml extract_list.phtml item_common.inc.php
plate.inc.php plate_common.inc.php plate_edit.phtml
plate_list.phtml platetype.inc.php probe_search.phtml
protocol_common.inc.php sample_edit.phtml test.phtml
Log Message:
Mostly getting LIMS stuff back in working condition
Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** array.inc.php 30 Sep 2002 21:13:09 -0000 1.38
--- array.inc.php 1 Oct 2002 17:35:10 -0000 1.39
***************
*** 27,33 ****
require_once("item.inc.php");
! define("CLEN_ARRAYTYPE_NAME", CLEN_ITEM_NAME);
define("CLEN_ARRAYTYPE_PLATFORM", 255);
! define("CLEN_ARRAYBATCH_NAME", CLEN_ITEM_NAME);
define("CLEN_ARRAYBATCH_SURFACETYPE", 40);
define("CLEN_ARRAY_BARCODE", 20);
--- 27,33 ----
require_once("item.inc.php");
[...347 lines suppressed...]
$this->notes = $val;
+ }
+
+ // Returns array (id,name,removed)
+ function getBriefForArrayType($atid, &$user, $removed = 0)
+ {
+ $atid = (int)$atid;
+ $query = "SELECT ab.id, ab.name, ab.removed ".
+ "FROM ArrayBatch ab ".
+ "WHERE ab.`arrayType` = $atid ".
+ "AND ".Item::whereShared("ab", $user)." ".
+ Item::whereRemovedAnd("ab", $removed)." ".
+ "ORDER BY ab.name";
+ $res = query($query);
+ $arr = array();
+ while($row =& db_fetch_assoc($res))
+ $arr[] = $row;
+ return $arr;
}
Index: array_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array_common.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** array_common.inc.php 10 Sep 2002 23:04:40 -0000 1.11
--- array_common.inc.php 1 Oct 2002 17:35:10 -0000 1.12
***************
*** 62,68 ****
! function batchList(&$users, $arrayType)
{
! global $i_sh, $curUser, $tdbg;
$userid = $curUser->getId();
--- 62,68 ----
! function batchList(&$user, $arrayType)
{
! global $$tdbg;
$userid = $curUser->getId();
***************
*** 365,368 ****
--- 365,396 ----
</table>
<?
+ }
+
+ function arrayPlateList(&$at, &$user)
+ {
+ global $cellpad, $tdbg;
+ ?>
+ <table <?= $cellpad ?>>
+ <tr><th colspan=2 class=subhead>Plates</th></tr>
+ <tr><th>Position</th><th>Plate</th></tr>
+ <?
+ $used = $at->findPlates($user);
+ if(!$used)
+ echo "<tr><td colspan=2>None</td></tr>\n";
+ for(reset($used), $odd = 0; list(, $s) = each($used); $odd ^= 1)
+ {
+ if($s["plateRead"])
+ {
+ $plink = "<a href='plate_edit.phtml?i_p=$s[id]'>".
+ html($s["name"])."</a>".remMark($s["removed"]);
+ }
+ else
+ $plink = html($s["name"]).remMark($s["removed"]);
+ echo "<tr bgcolor=$tdbg[$odd]>".
+ "<td>".$s["position"]."</td>".
+ "<td>".$plink."</td>".
+ "</tr>\n";
+ }
+ echo "</table>\n";
}
Index: array_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array_edit.phtml,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** array_edit.phtml 10 Sep 2002 23:04:45 -0000 1.22
--- array_edit.phtml 1 Oct 2002 17:35:10 -0000 1.23
***************
*** 31,34 ****
--- 31,37 ----
require_once("search.inc.php");
require_once("searchhtml.inc.php");
+ require_once("item_common.inc.php");
+ require_once("links_common.inc.php");
+ require_once("protocol_common.inc.php");
verifyAccess(BUA_ARRAY_READ);
***************
*** 40,51 ****
[...576 lines suppressed...]
</table><br>
<?
! arrayPlateList($at, $curUser);
! /* // Only show batches for printed array designs
if($printed)
{
***************
*** 509,513 ****
batchList($users, $atid);
echo "</form>\n";
! }
}
?>
--- 539,543 ----
batchList($users, $atid);
echo "</form>\n";
! }*/
}
?>
Index: array_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array_list.phtml,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** array_list.phtml 29 Aug 2002 16:51:33 -0000 1.15
--- array_list.phtml 1 Oct 2002 17:35:10 -0000 1.16
***************
*** 29,58 ****
require_once("search.inc.php");
require_once("searchhtml.inc.php");
verifyAccess(BUA_ARRAY_READ);
! $searchfields = array("Design name", "User", "Date added");
! $searchtypes = array(0, 0, 1);
! $headerfields = array("Design name", "Blocks", "Protocol", "Description",
! "Date added", "Prints", "Owner");
! $sortorder = array(1, 1, 1, 1, -1, 0, 1);
[...152 lines suppressed...]
"<td>".$blk."</td>".
"<td>".html($s["addedDate"])."</td>".
+ "<td>".html($s["userName"])."</td>".
+ "<td>".groupAccessCheckbox($s["id"])."</td>".
+ "<td>".groupInfo($s, $users)."</td>".
+ "<td>".worldInfo($s)."</td>".
+ "<td>".protocolArrLink($s)."</td>".
"<td>".implode(", ", $blink)."</td>".
! "</tr>\n";
}
+ $cols = count($headerfields);
+ if($addlink != "")
+ echo "<tr><td colspan=$cols>$addlink</td></tr>\n";
+
+ groupAccessFooter($cols, $curUser);
+ showDelLinks($cols);
?>
! </form>
</table>
Index: extract_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/extract_list.phtml,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** extract_list.phtml 30 Sep 2002 16:57:05 -0000 1.16
--- extract_list.phtml 1 Oct 2002 17:35:10 -0000 1.17
***************
*** 44,49 ****
$fieldtype = array(0, 0, 0, 0, 1, 1, 0, 2);
$headerfields = array("Name", "Sample", "Extracted",
! "Owner",
! "[<a href=javascript:selAll(1)>A</a> ".
"<a href=javascript:selAll(0)>N</a>]", "Group", "World",
"Protocol", "µg left", "Labelings", "Hybridizations");
--- 44,48 ----
$fieldtype = array(0, 0, 0, 0, 1, 1, 0, 2);
$headerfields = array("Name", "Sample", "Extracted",
! "Owner", "[<a href=javascript:selAll(1)>A</a> ".
"<a href=javascript:selAll(0)>N</a>]", "Group", "World",
"Protocol", "µg left", "Labelings", "Hybridizations");
Index: item_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/item_common.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** item_common.inc.php 30 Sep 2002 16:57:05 -0000 1.5
--- item_common.inc.php 1 Oct 2002 17:35:10 -0000 1.6
***************
*** 231,235 ****
{
// Only the owner may do these things.
! if(!Item::isOwner($subclass, $sh, $user->getId()))
continue;
--- 231,235 ----
{
// Only the owner may do these things.
! if(!Item::isSharedId($subclass, $sh, $user, 2))
continue;
***************
*** 424,429 ****
for(reset($i_sh); list($sh) = each($i_sh); )
{
! // Only the owner may do these things.
! if(!Item::isOwner($subclass, $sh, $user->getId()))
continue;
Item::updateRemovedId($subclass, $sh, $del);
--- 424,429 ----
for(reset($i_sh); list($sh) = each($i_sh); )
{
! // Only the owner/SU may do these things.
! if(!Item::isSharedId($subclass, $sh, $user, 2))
continue;
Item::updateRemovedId($subclass, $sh, $del);
Index: plate.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate.inc.php,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** plate.inc.php 30 Sep 2002 21:13:10 -0000 1.36
--- plate.inc.php 1 Oct 2002 17:35:10 -0000 1.37
***************
*** 94,114 ****
! // Returns array eventType=>(protocol,eventDate)
! function getEvents()
! {
! $query = "SELECT pe.etype, pe.protocol, pe.`eventDate` ".
! "FROM PlateEvent pe, Protocol p ".
! "WHERE pe.plate = $this->id AND p.id = pe.protocol";
! $res = query($query);
! $arr = array();
! while($row =& db_fetch_assoc($res))
! $arr[$row[0]] = $row;
! return $arr;
! }
!
! // Returns array eventType=>array(eventDate,name)
function getEventsBrief()
{
! $query = "SELECT pe.etype, pe.`eventDate`, p.name ".
"FROM PlateEvent pe, Protocol p ".
"WHERE pe.plate = $this->id AND p.id = pe.protocol";
--- 94,101 ----
! // Returns array eventType=>array(eventDate,name,protocol)
function getEventsBrief()
{
! $query = "SELECT pe.etype, pe.`eventDate`, p.name, pe.protocol ".
"FROM PlateEvent pe, Protocol p ".
"WHERE pe.plate = $this->id AND p.id = pe.protocol";
***************
*** 116,120 ****
$arr = array();
while($row =& db_fetch_assoc($res))
! $arr[$row[0]] = $row;
return $arr;
}
--- 103,107 ----
$arr = array();
while($row =& db_fetch_assoc($res))
! $arr[$row["etype"]] = $row;
return $arr;
}
***************
*** 471,477 ****
function getNameAndDate($id)
{
! $query = "SELECT name, `addedDate` FROM Plate WHERE id = ".(int)$id;
$res = query($query);
! if($row =& db_fetch_row($res)) return $row;
return false;
}
--- 458,466 ----
function getNameAndDate($id)
{
! $query = "SELECT id, name, `addedDate` ".
! "FROM Plate WHERE id = ".(int)$id;
$res = query($query);
! if($row =& db_fetch_assoc($res))
! return $row;
return false;
}
***************
*** 487,490 ****
--- 476,484 ----
{
return parent::exists("Plate", $id);
+ }
+
+ function isSharedId($id, &$user, $write = 0)
+ {
+ return parent::isSharedId("Plate", $id, $user, $write);
}
}
Index: plate_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_common.inc.php,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** plate_common.inc.php 5 Aug 2002 11:29:34 -0000 1.3
--- plate_common.inc.php 1 Oct 2002 17:35:10 -0000 1.4
***************
*** 25,59 ****
//
! function plateFamilyList($plateid)
{
! $parents = Plate::getParentsBrief($plateid);
! for(reset($parents); list(, $a) = each($parents); )
{
! echo "<tr><th>Parent plate</th>".
! "<td><a ".href("plate_edit.phtml?i_p=$a[id]", 2).">".
! html($a["name"])."</a>";
! if($a["position"]) echo " : $a[position] <img width=11 height=11 ".
"src='img/p384_$a[position].gif'>";
- echo " (".html($a["typeName"], 0).")</td></tr>\n";
}
! $children = Plate::getChildrenBrief($plateid, 1);
for(reset($children); list(, $a) = each($children); )
{
! echo "<tr><th>Plate used on</th>".
! "<td><a ".href("plate_edit.phtml?i_p=$a[id]", 2).">".
! html($a["name"])."</a>";
! if($a["position"]) echo " : $a[position] <img width=11 height=11 ".
! "src='img/p384_$a[position].gif'>";
! echo " (".html($a["typeName"], 0).")</td></tr>\n";
}
! $children = Plate::getChildrenBrief($plateid, 0);
for(reset($children); list(, $a) = each($children); )
{
! echo "<tr><th>Child plate</th>".
! "<td><a ".href("plate_edit.phtml?i_p=$a[id]", 2).">".
! html($a["name"])."</a>";
! if($a["position"]) echo " : $a[position] <img width=11 height=11 ".
! "src='img/p384_$a[position].gif'>";
! echo " (".html($a["typeName"], 0).")</td></tr>\n";
}
}
--- 25,64 ----
//
! function plateArrLink($a)
{
! if(!$a["readAccess"])
! $lnk = html($a["name"]).remMark($a["removed"]);
! else
{
! $lnk = "<a ".href("plate_edit.phtml?i_p=$a[id]", 2).">".
! html($a["name"])."</a>".remMark($a["removed"]);
! }
! if($a["position"])
! {
! $lnk .= " : $a[position] <img width=11 height=11 ".
"src='img/p384_$a[position].gif'>";
}
! return $lnk ." (".html($a["typeName"], 0).")";
! }
!
! function plateFamilyList($plateid, &$user)
! {
! $parents = Plate::getParentsBrief($plateid, $user);
! for(reset($parents); list(, $a) = each($parents); )
! {
! echo "<tr><th>Parent plate</th><td>".
! plateArrLink($a)."</td></tr>\n";
! }
! $children = Plate::getChildrenBrief($plateid, 1, $user);
for(reset($children); list(, $a) = each($children); )
{
! echo "<tr><th>Plate used on</th><td>".
! plateArrLink($a)."</td></tr>\n";
}
! $children = Plate::getChildrenBrief($plateid, 0, $user);
for(reset($children); list(, $a) = each($children); )
{
! echo "<tr><th>Child plate</th><td>".
! plateArrLink($a)."</td></tr>\n";
}
}
Index: plate_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_edit.phtml,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** plate_edit.phtml 30 Sep 2002 08:26:44 -0000 1.31
--- plate_edit.phtml 1 Oct 2002 17:35:10 -0000 1.32
***************
*** 32,35 ****
--- 32,37 ----
require_once("searchhtml.inc.php");
require_once("item_common.inc.php");
+ require_once("links_common.inc.php");
+ require_once("protocol_common.inc.php");
verifyAccess(BUA_ARRAY_READ);
***************
*** 46,50 ****
if(isset($i_clone) && $i_clone)
[...755 lines suppressed...]
! $plate->prepareWellSearch($search, 96);
?>
<form name=ff method=post action="plate_edit.phtml?i_p=<?=
! $plate->getId() ?>">
<input type=hidden name=location value="<?= html($location, 0) ?>">
<?
makeSearchHeader($search, $headerfields, $sortorder, $defsort,
"", "document.ff.submit();", "Wells");
! $wells = $plate->wellSearch($search);
for($i = 0, $odd = 0; $i < count($wells); $i++, $odd ^= 1)
{
$a =& $wells[$i];
echo "<tr bgcolor=$tdbg[$odd]>".
! "<td>".chr($a["y"]+64)."</td>".
! "<td>$a[x]</td>".
"<td>".Molecule::cloneLink($a["cloneId"])."</td>".
"<td>".Molecule::clusterLink($a["species"], $a["clusterId"],
Index: plate_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_list.phtml,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** plate_list.phtml 22 Sep 2002 23:37:35 -0000 1.28
--- plate_list.phtml 1 Oct 2002 17:35:10 -0000 1.29
***************
*** 42,46 ****
$err = "";
! $types = PlateType::getBrief();
if($types)
{
--- 42,46 ----
$err = "";
! $types = PlateType::getBrief($curUser);
if($types)
{
***************
*** 58,62 ****
if($ptypeid)
{
! $eventTypes = PlateEventType::getBriefForPlateType($ptypeid, $curUser);
}
else
--- 58,63 ----
if($ptypeid)
{
! $eventTypes = PlateEventType::getBriefForPlateType($ptypeid,
! showDelSublist());
}
else
Index: platetype.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/platetype.inc.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** platetype.inc.php 22 Sep 2002 23:37:35 -0000 1.1
--- platetype.inc.php 1 Oct 2002 17:35:10 -0000 1.2
***************
*** 260,269 ****
// Returns array id=>name
! function getBrief($wells = -1, $removed = 0)
{
if($wells < 0)
{
$query = "SELECT pt.id, pt.name FROM PlateType pt ".
! "WHERE ".db_true()." ".
Item::whereRemovedAnd("pt", $removed)." ".
"ORDER BY name";
--- 260,269 ----
// Returns array id=>name
! function getBrief(&$user, $wells = -1, $removed = 0)
{
if($wells < 0)
{
$query = "SELECT pt.id, pt.name FROM PlateType pt ".
! "WHERE ".Item::whereShared("pt", $user)." ".
Item::whereRemovedAnd("pt", $removed)." ".
"ORDER BY name";
***************
*** 273,276 ****
--- 273,277 ----
$query = "SELECT id, name FROM PlateType ".
"WHERE wells = ".(int)$wells." ".
+ "AND ".Item::whereShared("pt", $user)." ".
Item::whereRemovedAnd("pt", $removed)." ".
"ORDER BY name";
Index: probe_search.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/probe_search.phtml,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** probe_search.phtml 30 Sep 2002 21:13:10 -0000 1.5
--- probe_search.phtml 1 Oct 2002 17:35:10 -0000 1.6
***************
*** 115,119 ****
if($oneHit)
{
! $ptypes = PlateType::getBrief();
?>
--- 115,119 ----
if($oneHit)
{
! $ptypes = PlateType::getBrief($curUser);
?>
Index: protocol_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/protocol_common.inc.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** protocol_common.inc.php 30 Sep 2002 16:57:05 -0000 1.1
--- protocol_common.inc.php 1 Oct 2002 17:35:10 -0000 1.2
***************
*** 27,33 ****
! function protocolSelect($oldid, $typename, &$user)
{
! echo "<select name=i_proto>";
$protos = Protocol::getBriefByType(
ProtocolType::getIdFromName($typename), $user, 0);
--- 27,33 ----
! function protocolSelect($oldid, $typename, &$user, $varname = "i_proto")
{
! echo "<select name=$varname>";
$protos = Protocol::getBriefByType(
ProtocolType::getIdFromName($typename), $user, 0);
Index: sample_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/sample_edit.phtml,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** sample_edit.phtml 30 Sep 2002 16:57:05 -0000 1.24
--- sample_edit.phtml 1 Oct 2002 17:35:10 -0000 1.25
***************
*** 96,100 ****
if($curDb->dupKey())
$err = "There is already a sample with that name";
! else $err = "Unable to save sample";
}
--- 96,101 ----
if($curDb->dupKey())
$err = "There is already a sample with that name";
! else
! $err = "Unable to save sample";
}
Index: test.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/test.phtml,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** test.phtml 30 Sep 2002 08:26:44 -0000 1.50
--- test.phtml 1 Oct 2002 17:35:10 -0000 1.51
***************
*** 26,29 ****
--- 26,42 ----
header("content-type: text/plain");
+
+ echo "aaa\n";
+
+ eval("echo(\"bbb\\n\");");
+
+ echo "ccc\n";
+
+ eval("function foo(){echo \"ddd\\n\";}");
+
+ foo();
+
+ exit;
+ /*
print_r($GLOBALS);
***************
*** 47,51 ****
echo "$s / max : ".foo($s, "ffffffff")."\n";
}
!
//require_once("init.inc.php");
--- 60,64 ----
echo "$s / max : ".foo($s, "ffffffff")."\n";
}
! */
//require_once("init.inc.php");
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