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[basedb-cvs] basedb/www array.inc.php,1.39,1.40 array_batchlist.phtml,1.13,1.14 array_common.inc.php,1.12,1.13 array_edit.phtml,1.23,1.24 extract_edit.phtml,1.20,1.21 hyb_edit.phtml,1.35,1.36 labeled_edit.phtml,1.19,1.20 plate_edit.phtml,1.32,1.33 platetype_edit.phtml,1.15,1.16 protocol_common.inc.php,1.2,1.3 protocol_edit.phtml,1.10,1.11 protocol_list.phtml,1.12,1.13
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From: <tr...@us...> - 2002-10-01 21:53:23
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Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv28083
Modified Files:
array.inc.php array_batchlist.phtml array_common.inc.php
array_edit.phtml extract_edit.phtml hyb_edit.phtml
labeled_edit.phtml plate_edit.phtml platetype_edit.phtml
protocol_common.inc.php protocol_edit.phtml
protocol_list.phtml
Log Message:
Protocol fixes, mostly
Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** array.inc.php 1 Oct 2002 17:35:10 -0000 1.39
--- array.inc.php 1 Oct 2002 21:53:19 -0000 1.40
***************
*** 764,784 ****
// Counts the number of hits and sets up the search object
! function prepareSearch(&$search, $hpp, $arrayType = 0)
{
- // Add more fields and operators here
$fields = array();
$search->makeWhere($fields);
$arrayType = (int)$arrayType;
if($arrayType) $search->addExtraWhere("ab.`arrayType` = $arrayType");
[...74 lines suppressed...]
--- 799,817 ----
{
$ss1 = "t.* FROM ArrayBatch ab, (SELECT ab.id,";
! $ss2 = ",`designName`, `userName`, `arrayTypeRead`, ".
! "`arrayTypeRemoved`) AS t";
}
else
$ss1 = $ss2 = "";
! $query = "SELECT ab.*, $ss1 at.name AS `designName`, ".
! "ug.name AS `userName`, ".
"COUNT(a.id) AS arrays, COUNT(a.hybridization) AS hybs, ".
! "SUM(a.destroyed) AS destroyed, ".
! Item::whereShared("at", $user)." AS `arrayTypeRead`, ".
! "at.removed AS `arrayTypeRemoved` ".
! "FROM ArrayType at, UserGroup ug, ArrayBatch ab ".
"LEFT JOIN Array a ON a.batch = ab.id ".
! "WHERE at.id = ab.`arrayType` AND ug.id = ab.owner ".
$search->getWhere()." ".$search->getExtraWhere()." ".
"GROUP BY ab.id $ss2 $ob ".$search->makeLimit();
Index: array_batchlist.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array_batchlist.phtml,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** array_batchlist.phtml 5 Aug 2002 11:29:31 -0000 1.13
--- array_batchlist.phtml 1 Oct 2002 21:53:19 -0000 1.14
***************
*** 31,50 ****
verifyAccess(BUA_ARRAY_READ);
- $users = Submitter::getBrief();
- $userid = $curUser->getId();
-
- batchSharing($users);
-
$pageTitle="$config[codename] - Array prints";
require_once("htmlinit.phtml");
?>
<table <?= $cellpad ?>>
<tr><th class=pagehead>Array prints <?= webHelp(29, 1) ?></th></tr>
<tr><td class=help>To create new prints, start from the array design
! pages.</td></tr>
! <form method=post name=ff action='array_batchlist.phtml'>
</table>
<?
! batchList($users, 0);
?>
</form>
--- 31,45 ----
verifyAccess(BUA_ARRAY_READ);
$pageTitle="$config[codename] - Array prints";
require_once("htmlinit.phtml");
?>
<table <?= $cellpad ?>>
+ <form method=post name=ff action='array_batchlist.phtml'>
<tr><th class=pagehead>Array prints <?= webHelp(29, 1) ?></th></tr>
<tr><td class=help>To create new prints, start from the array design
! page.</td></tr>
</table>
<?
! batchList($curUser, 0);
?>
</form>
Index: array_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array_common.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** array_common.inc.php 1 Oct 2002 17:35:10 -0000 1.12
--- array_common.inc.php 1 Oct 2002 21:53:19 -0000 1.13
***************
*** 24,114 ****
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
! require_once("array.inc.php");
! require_once("hyb.inc.php");
! require_once("search.inc.php");
! require_once("searchhtml.inc.php");
!
! function batchSharing(&$users)
! {
! global $i_sh, $i_unsh, $i_shuser, $i_user, $curUser;
[...171 lines suppressed...]
!
! echo "<tr bgcolor=$tdbg[$odd]>".
! "<td><a ".href("array_batch.phtml?i_ab=$id", 2).">".
! html($b["name"])."</a>".remMark($b["removed"])."</td>".
! "<td>".$atlink."</td>\n".
! "<td>".htmldatetime($b["printStartDate"])."</td>".
"<td>".html($b["userName"])."</td>\n".
+ "<td>".groupAccessCheckbox($b["id"])."</td>".
+ "<td>".groupInfo($b, $users)."</td>".
+ "<td>".worldInfo($b)."</td>".
"<td>$b[arrays] ($b[hybs] used, $b[destroyed] destr, ".
! ($b["arrays"]-$b["hybs"]-$b["destroyed"])." free)</td>".
! "</tr>\n";
}
unset($b);
+ $cols = count($headerfields);
+ groupAccessFooter($cols, $user);
+ showDelLinks($cols);
echo "</table>\n";
}
Index: array_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array_edit.phtml,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** array_edit.phtml 1 Oct 2002 17:35:10 -0000 1.23
--- array_edit.phtml 1 Oct 2002 21:53:19 -0000 1.24
***************
*** 74,80 ****
if(isset($i_plat))
$at->setPlatform($i_plat);
! if(isset($i_proto) && $i_proto)
! $at->setProtocol($i_proto);
! dateAndOwnerInputHandle($samp, $curUser);
}
$atid = $at->getId();
--- 74,83 ----
if(isset($i_plat))
$at->setPlatform($i_plat);
! $p = $at->getProtocol();
! $e = protocolValidate($p, "Configuration", $curUser);
! if($err == "")
! $err = $e;
! $at->setProtocol($p);
! dateAndOwnerInputHandle($at, $curUser);
}
$atid = $at->getId();
***************
*** 92,100 ****
else if($at->getName() == "")
$err = "The array design must have a name";
! else if(!Protocol::isSharedAndType($at->getProtocol(),
! $curUser, "Configuration"))
! {
! $err = "Invalid protocol";
! }
else if(!$at->write())
{
--- 95,100 ----
else if($at->getName() == "")
$err = "The array design must have a name";
! else if(!$at->getProtocol())
! $err = "No protocol selected";
else if(!$at->write())
{
***************
*** 531,543 ****
arrayPlateList($at, $curUser);
! /* // Only show batches for printed array designs
if($printed)
{
?>
<form method=post name=ff action="array_edit.phtml?i_at=<?= $atid ?>">
<?
! batchList($users, $atid);
echo "</form>\n";
! }*/
}
?>
--- 531,544 ----
arrayPlateList($at, $curUser);
! // Only show batches for printed array designs
if($printed)
{
?>
<form method=post name=ff action="array_edit.phtml?i_at=<?= $atid ?>">
+ <input type=hidden name=location value="<?= html($location, 0) ?>">
<?
! batchList($curUser, $atid);
echo "</form>\n";
! }
}
?>
Index: extract_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/extract_edit.phtml,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** extract_edit.phtml 30 Sep 2002 16:57:05 -0000 1.20
--- extract_edit.phtml 1 Oct 2002 21:53:20 -0000 1.21
***************
*** 65,70 ****
if(isset($i_name))
$ext->setName($i_name);
- if(isset($i_proto) && $i_proto)
- $ext->setProtocol($i_proto);
if(isset($i_descr))
$ext->setDescr($i_descr);
--- 65,68 ----
***************
*** 74,77 ****
--- 72,81 ----
$ext->setExtractionDate("$i_ey-$i_em-$i_ed");
dateAndOwnerInputHandle($ext, $curUser);
+
+ $p = $ext->getProtocol();
+ $e = protocolValidate($p, "Extraction", $curUser);
+ if($err == "")
+ $err = $e;
+ $ext->setProtocol($p);
}
***************
*** 98,107 ****
else if($ext->getName() == "")
$err = "The extract must have a name";
! else if(!Protocol::isSharedAndType($ext->getProtocol(),
! $curUser, "Extraction"))
! {
! // Removed protocols will pass the test above.
! $err = "Invalid protocol";
! }
else if(!$ext->write())
{
--- 102,107 ----
else if($ext->getName() == "")
$err = "The extract must have a name";
! else if(!$ext->getProtocol())
! $err = "No protocol selected";
else if(!$ext->write())
{
Index: hyb_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_edit.phtml,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** hyb_edit.phtml 30 Sep 2002 16:57:05 -0000 1.35
--- hyb_edit.phtml 1 Oct 2002 21:53:20 -0000 1.36
***************
*** 77,83 ****
if(isset($i_ey) && isset($i_em) && isset($i_ed))
$hyb->setHybridizationDate("$i_ey-$i_em-$i_ed");
- if(isset($i_proto) && $i_proto)
- $hyb->setProtocol($i_proto);
dateAndOwnerInputHandle($hyb, $curUser);
}
--- 77,87 ----
if(isset($i_ey) && isset($i_em) && isset($i_ed))
$hyb->setHybridizationDate("$i_ey-$i_em-$i_ed");
dateAndOwnerInputHandle($hyb, $curUser);
+
+ $p = $hyb->getProtocol();
+ $e = protocolValidate($p, "Hybridization", $curUser);
+ if($err == "")
+ $err = $e;
+ $hyb->setProtocol($p);
}
***************
*** 107,115 ****
else if($hyb->getName() == "")
$err = "The hybridization must have a name";
! else if(!Protocol::isSharedAndType($hyb->getProtocol(),
! $curUser, "Hybridization"))
! {
! $err = "Invalid protocol";
! }
else if(!$hyb->write())
{
--- 111,116 ----
else if($hyb->getName() == "")
$err = "The hybridization must have a name";
! else if(!$hyb->getProtocol())
! $err = "No protocol selected";
else if(!$hyb->write())
{
Index: labeled_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_edit.phtml,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** labeled_edit.phtml 30 Sep 2002 16:57:05 -0000 1.19
--- labeled_edit.phtml 1 Oct 2002 21:53:20 -0000 1.20
***************
*** 69,74 ****
if(isset($i_ey) && isset($i_em) && isset($i_ed))
$lext->setLabelingDate("$i_ey-$i_em-$i_ed");
- if(isset($i_proto) && $i_proto)
- $lext->setProtocol($i_proto);
if(isset($i_label))
$lext->setLabel($i_label);
--- 69,72 ----
***************
*** 76,79 ****
--- 74,83 ----
$lext->setQuantity($i_origqty);
dateAndOwnerInputHandle($lext, $curUser);
+
+ $p = $lext->getProtocol();
+ $e = protocolValidate($p, "Labeling", $curUser);
+ if($err == "")
+ $err = $e;
+ $lext->setProtocol($p);
}
***************
*** 99,108 ****
else if($lext->getName() == "")
$err = "The labeled extract must have a name";
! else if(!Protocol::isSharedAndType($lext->getProtocol(),
! $curUser, "Labeling"))
! {
! // Removed protocols will pass the test above.
! $err = "Invalid protocol";
! }
else if(!$lext->write())
{
--- 103,108 ----
else if($lext->getName() == "")
$err = "The labeled extract must have a name";
! else if(!$lext->getProtocol())
! $err = "No protocol selected";
else if(!$lext->write())
{
Index: plate_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate_edit.phtml,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** plate_edit.phtml 1 Oct 2002 17:35:10 -0000 1.32
--- plate_edit.phtml 1 Oct 2002 21:53:20 -0000 1.33
***************
*** 38,41 ****
--- 38,43 ----
setLocation("plate_list.phtml");
+ $protocolTypes = ProtocolType::getBrief();
+
$edit = false; // Default to false
$clone = 0;
***************
*** 121,127 ****
$ev =& $events[$eid];
[...68 lines suppressed...]
"value='$ed'></td>".
"<td>".html($prototypename)."</td>\n".
! "<td>".protocolSelect($events[$eid]["protocol"],
! $prototypename, $curUser, "i_proto$eid")."</td>".
! "</tr>\n";
}
unset($e);
***************
*** 484,488 ****
{
echo "<tr><td colspan=2><a ".
! href("plate_edit.phtml?i_p=$plateid&i_edit=1", 1).
">Edit plate</a></td></tr>\n";
}
--- 486,490 ----
{
echo "<tr><td colspan=2><a ".
! href("plate_edit.phtml?i_p=$plateid&i_edit=1", 2).
">Edit plate</a></td></tr>\n";
}
Index: platetype_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/platetype_edit.phtml,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** platetype_edit.phtml 22 Sep 2002 23:37:35 -0000 1.15
--- platetype_edit.phtml 1 Oct 2002 21:53:20 -0000 1.16
***************
*** 34,38 ****
setLocation("platetype_list.phtml");
! $protoTypes = Protocol::getTypes();
$edit = true;
--- 34,38 ----
setLocation("platetype_list.phtml");
! $protoTypes = ProtocolType::getBrief();
$edit = true;
Index: protocol_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/protocol_common.inc.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** protocol_common.inc.php 1 Oct 2002 17:35:10 -0000 1.2
--- protocol_common.inc.php 1 Oct 2002 21:53:20 -0000 1.3
***************
*** 29,48 ****
function protocolSelect($oldid, $typename, &$user, $varname = "i_proto")
{
- echo "<select name=$varname>";
$protos = Protocol::getBriefByType(
ProtocolType::getIdFromName($typename), $user, 0);
for(reset($protos); list($id, $arr) = each($protos); )
{
$sel = $id == $oldid ? "selected" : "";
! echo "<option $sel value=$id>".html($arr["name"], 0).
remMark($arr["removed"], 0)."\n";
}
! if(!isset($protos[$oldid]))
{
$arr = Protocol::getBasicFromId($oldid);
! echo "<option selected value=0>".html($arr["name"], 0).
remMark($arr["removed"], 0)."\n";
}
! echo "</select>";
}
--- 29,64 ----
function protocolSelect($oldid, $typename, &$user, $varname = "i_proto")
{
$protos = Protocol::getBriefByType(
ProtocolType::getIdFromName($typename), $user, 0);
+ if(!$protos && !$oldid)
+ {
+ return "<span class=red>None defined</span>";
+ }
+ $str = "<select name=$varname>";
for(reset($protos); list($id, $arr) = each($protos); )
{
$sel = $id == $oldid ? "selected" : "";
! $str .= "<option $sel value=$id>".html($arr["name"], 0).
remMark($arr["removed"], 0)."\n";
}
! if($oldid && !isset($protos[$oldid]))
{
$arr = Protocol::getBasicFromId($oldid);
! $str .= "<option selected value=0>".html($arr["name"], 0).
remMark($arr["removed"], 0)."\n";
}
! return $str."</select>";
! }
!
! // Returns "" if the protocol id is valid, and an error message otherwise.
! function protocolValidate(&$id, $typename, &$user, $varname = "i_proto")
! {
! if(!isset($GLOBALS[$varname]) || !$GLOBALS[$varname])
! return "";
! $newid = (int)$GLOBALS[$varname];
! if(!Protocol::isSharedAndType($newid, $user, $typename))
! return "Invalid $typename protocol (id = $newid)";
! $id = $newid;
! return "";
}
Index: protocol_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/protocol_edit.phtml,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** protocol_edit.phtml 26 Sep 2002 19:35:05 -0000 1.10
--- protocol_edit.phtml 1 Oct 2002 21:53:20 -0000 1.11
***************
*** 129,133 ****
<form method=post enctype="multipart/form-data"
action="protocol_edit.phtml?i_p=<?= $protoid ?>">
- <input type=hidden name=i_type value=<?= $proto->getProtocolType() ?>>
<input type=hidden name=i_edit value=1>
<input type=hidden name=location value="<?= html($location, 0) ?>">
--- 129,132 ----
***************
*** 137,145 ****
value="<?= html($proto->getName(), 0) ?>"></td></tr>
! <tr><th>Protocol type</th><td><select name=i_type>
<?
for(reset($types); list($tid, $tn) = each($types); )
{
! $sel = $tid == $proto->getType() ? "selected" : "";
echo "<option $sel value=$tid>".html($tn, 0)."\n";
}
--- 136,144 ----
value="<?= html($proto->getName(), 0) ?>"></td></tr>
! <tr><th>Protocol type</th><td><select name=i_ptype>
<?
for(reset($types); list($tid, $tn) = each($types); )
{
! $sel = $tid == $proto->getProtocolType() ? "selected" : "";
echo "<option $sel value=$tid>".html($tn, 0)."\n";
}
Index: protocol_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/protocol_list.phtml,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** protocol_list.phtml 30 Sep 2002 16:57:05 -0000 1.12
--- protocol_list.phtml 1 Oct 2002 21:53:20 -0000 1.13
***************
*** 54,59 ****
$typeid = $rev[$i_typename];
}
! else if(isset($i_type))
! $typeid = isset($types[$i_type]) ? $i_type : 0;
else
$typeid = 0;
--- 54,59 ----
$typeid = $rev[$i_typename];
}
! else if(isset($i_ptype))
! $typeid = isset($types[$i_ptype]) ? $i_ptype : 0;
else
$typeid = 0;
***************
*** 67,78 ****
if(s.selectedIndex < 0) return;
f=s.form;
! f.action="protocol_list.phtml?i_type="+s.options[s.selectedIndex].value;
f.submit();
}
</script>
<table <?= $cellpad ?>>
! <form name=ff method=post action="protocol_list.phtml?i_type=<?= $typeid ?>">
<tr><th class=pagehead>Protocols for
! <select name=i_type onChange="changePType(this)">
<option value=0>Everything
<?
--- 67,78 ----
if(s.selectedIndex < 0) return;
f=s.form;
! f.action="protocol_list.phtml?i_ptype="+s.options[s.selectedIndex].value;
f.submit();
}
</script>
<table <?= $cellpad ?>>
! <form name=ff method=post action="protocol_list.phtml?i_ptype=<?= $typeid ?>">
<tr><th class=pagehead>Protocols for
! <select name=i_ptype onChange="changePType(this)">
<option value=0>Everything
<?
***************
*** 100,104 ****
{
$addlink = "<a class=large href='protocol_edit.phtml".
! "?i_type=$typeid'>Add protocol</a>";
}
makeSearchHeader($search, $headerfields, $sortorder, $defsort, "",
--- 100,104 ----
{
$addlink = "<a class=large href='protocol_edit.phtml".
! "?i_ptype=$typeid'>Add protocol</a>";
}
makeSearchHeader($search, $headerfields, $sortorder, $defsort, "",
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