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[basedb-cvs] basedb/www array.inc.php,1.37,1.38 bioassay.inc.php,1.39,1.40 bioassayset.inc.php,1.28,1.29 genelist.inc.php,1.23,1.24 misc.inc.php,1.39,1.40 molecule.inc.php,1.34,1.35 plate.inc.php,1.35,1.36 probe_search.phtml,1.4,1.5 search.inc.php,1.42,1.43 searchhtml.inc.php,1.41,1.42
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From: <tr...@us...> - 2002-09-30 21:13:14
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Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv24108
Modified Files:
array.inc.php bioassay.inc.php bioassayset.inc.php
genelist.inc.php misc.inc.php molecule.inc.php plate.inc.php
probe_search.phtml search.inc.php searchhtml.inc.php
Log Message:
Removed 1-byte length prefix from Molecule.cloneId
Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** array.inc.php 10 Sep 2002 23:04:36 -0000 1.37
--- array.inc.php 30 Sep 2002 21:13:09 -0000 1.38
***************
*** 487,492 ****
$y = (int)$y;
! $query = "SELECT e.id, p.molecule, ".
! "SUBSTRING(m.`cloneId`, 2) AS `cloneId` ".
"FROM Element e, Well w, Probe p, Molecule m ".
"WHERE e.`arrayType` = $arrayType AND e.block = $block ".
--- 487,491 ----
$y = (int)$y;
! $query = "SELECT e.id, p.molecule, m.`cloneId` ".
"FROM Element e, Well w, Probe p, Molecule m ".
"WHERE e.`arrayType` = $arrayType AND e.block = $block ".
***************
*** 504,509 ****
$arrayType = (int)$arrayType;
! $query = "SELECT e.block, e.x, e.y, ".
! "SUBSTRING(m.`cloneId`, 2) AS `cloneId`, m.`geneName` ".
"FROM Element e, Well w, Probe p, Molecule m ".
"WHERE e.`arrayType` = $arrayType AND w.id = e.well AND ".
--- 503,507 ----
$arrayType = (int)$arrayType;
! $query = "SELECT e.block, e.x, e.y, m.`cloneId`, m.`geneName` ".
"FROM Element e, Well w, Probe p, Molecule m ".
"WHERE e.`arrayType` = $arrayType AND w.id = e.well AND ".
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassay.inc.php,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** bioassay.inc.php 12 Sep 2002 11:45:25 -0000 1.39
--- bioassay.inc.php 30 Sep 2002 21:13:10 -0000 1.40
***************
*** 445,449 ****
$ecol = $search->getExtraColumnExpressions();
! $query = "SELECT SUBSTRING(m.`cloneId`, 2) AS `cloneId`, m.`geneName`, ".
"bad.intensity1 AS i1, bad.intensity2 AS i2, bad.ratio, ".
"m.species, m.`clusterId`, bad.molecule, bad.position AS position, ".
--- 445,449 ----
$ecol = $search->getExtraColumnExpressions();
! $query = "SELECT m.`cloneId`, m.`geneName`, ".
"bad.intensity1 AS i1, bad.intensity2 AS i2, bad.ratio, ".
"m.species, m.`clusterId`, bad.molecule, bad.position AS position, ".
***************
*** 684,688 ****
"intensity1" => "AVG(bad.intensity1) AS intensity1",
"intensity2" => "AVG(bad.intensity2) AS intensity2",
! "cloneId" => "SUBSTRING(m.`cloneId`, 2) AS `cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
--- 684,688 ----
"intensity1" => "AVG(bad.intensity1) AS intensity1",
"intensity2" => "AVG(bad.intensity2) AS intensity2",
! "cloneId" => "m.`cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
***************
*** 710,714 ****
"intensity1" => "bad.intensity1",
"intensity2" => "bad.intensity2",
! "cloneId" => "SUBSTRING(m.`cloneId`, 2) AS `cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
--- 710,714 ----
"intensity1" => "bad.intensity1",
"intensity2" => "bad.intensity2",
! "cloneId" => "m.`cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassayset.inc.php,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** bioassayset.inc.php 10 Sep 2002 23:04:54 -0000 1.28
--- bioassayset.inc.php 30 Sep 2002 21:13:10 -0000 1.29
***************
*** 395,399 ****
$fieldsql = array(
"position" => "0 AS position",
! "cloneId" => "SUBSTRING(m.`cloneId`, 2) AS `cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
--- 395,399 ----
$fieldsql = array(
"position" => "0 AS position",
! "cloneId" => "m.`cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
***************
*** 408,412 ****
$fieldsql = array(
"position" => "sg.position",
! "cloneId" => "SUBSTRING(m.`cloneId`, 2) AS `cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
--- 408,412 ----
$fieldsql = array(
"position" => "sg.position",
! "cloneId" => "m.`cloneId`",
"clusterId" => "m.`clusterId`",
"species" => "m.species",
***************
*** 548,554 ****
$ob = BioAssaySet::geneSearchSortOrder($search, true);
$ecol = $search->getExtraColumnExpressions();
! $sel = "m.id, SUBSTRING(m.`cloneId`, 2) AS `cloneId`, ".
! "m.`geneName`, m.`clusterId`, m.species, sg.cnt";
! if(!$average) $sel .= ", sg.position";
$table = $average ? "$config[dbDynamic]BioAssaySetGene" :
--- 548,555 ----
$ob = BioAssaySet::geneSearchSortOrder($search, true);
$ecol = $search->getExtraColumnExpressions();
! $sel = "m.id, m.`cloneId`, m.`geneName`, m.`clusterId`, ".
! "m.species, sg.cnt";
! if(!$average)
! $sel .= ", sg.position";
$table = $average ? "$config[dbDynamic]BioAssaySetGene" :
Index: genelist.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/genelist.inc.php,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** genelist.inc.php 11 Sep 2002 09:02:04 -0000 1.23
--- genelist.inc.php 30 Sep 2002 21:13:10 -0000 1.24
***************
*** 342,347 ****
function getGenesBrief()
{
! $query = "SELECT SUBSTRING(m.`cloneId`, 2) AS `cloneId`, ".
! "glg.score, m.`geneName` ".
"FROM GeneListGene glg, Molecule m ".
"WHERE glg.`geneList` = $this->id AND m.id = glg.molecule ".
--- 342,346 ----
function getGenesBrief()
{
! $query = "SELECT m.`cloneId`, glg.score, m.`geneName` ".
"FROM GeneListGene glg, Molecule m ".
"WHERE glg.`geneList` = $this->id AND m.id = glg.molecule ".
Index: misc.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/misc.inc.php,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** misc.inc.php 30 Sep 2002 08:26:44 -0000 1.39
--- misc.inc.php 30 Sep 2002 21:13:10 -0000 1.40
***************
*** 43,47 ****
{
if(strlen($txt) > $len)
! return substr($txt, 0, $len).$etc;
else
return $txt;
--- 43,47 ----
{
if(strlen($txt) > $len)
! return substr($txt, 0, $len - strlen($etc)).$etc;
else
return $txt;
Index: molecule.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/molecule.inc.php,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** molecule.inc.php 30 Sep 2002 08:26:44 -0000 1.34
--- molecule.inc.php 30 Sep 2002 21:13:10 -0000 1.35
***************
*** 27,43 ****
require_once("genelist.inc.php");
! // The maximum cloneId length requires a bit of explanation:
! // To get a reasonable sort order for both numbers and strings,
! // the cloneId has its length prepended when it's stored in the
! // database. This length is stored in the simplest possible way -
! // as the ascii value of a single character. Because we want
! // case insensitivity in the cloneId, there will be problems with
! // the sort order if the character gets into the range of lowercase
! // letters, and since 'a' has ascii value 97, we limit the cloneId
[...258 lines suppressed...]
return $arr;
}
--- 626,631 ----
$res = query($query);
$arr = array();
! while($row =& db_fetch_row($res))
! $arr[] = (int)$row[0];
return $arr;
}
***************
*** 689,696 ****
if(!($res = query($query))) return $arr;
while($row =& db_fetch_assoc($res))
- {
- $row["cloneId"] = substr($row["cloneId"], 1);
$arr[] = $row;
- }
return $arr;
}
--- 679,683 ----
Index: plate.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plate.inc.php,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** plate.inc.php 22 Sep 2002 23:37:35 -0000 1.35
--- plate.inc.php 30 Sep 2002 21:13:10 -0000 1.36
***************
*** 373,377 ****
}
! $query = "SELECT w.*, SUBSTRING(s.`cloneId`, 2) AS `cloneId`, ".
"s.species, s.`clusterId`, s.`geneName`, s.`geneSymbol` ".
"FROM Well w, Probe p, Molecule s ".
--- 373,377 ----
}
! $query = "SELECT w.*, s.`cloneId`, ".
"s.species, s.`clusterId`, s.`geneName`, s.`geneSymbol` ".
"FROM Well w, Probe p, Molecule s ".
Index: probe_search.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/probe_search.phtml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** probe_search.phtml 12 Sep 2002 13:53:29 -0000 1.4
--- probe_search.phtml 30 Sep 2002 21:13:10 -0000 1.5
***************
*** 80,84 ****
</script>
<?
! Molecule::prepareSearch($search, 30);
makeSearchHeader($search, $headerfields, $sortorder, $defsort, "",
--- 80,84 ----
</script>
<?
! Molecule::prepareSearch($search, 25);
makeSearchHeader($search, $headerfields, $sortorder, $defsort, "",
***************
*** 105,109 ****
$s["cloneId"])."</td>".
"<td>".html($s["geneSymbol"])."</td>".
! "<td>".html(maxlen($s["geneName"], 40, "..."))."</td>".
"</tr>\n";
}
--- 105,110 ----
$s["cloneId"])."</td>".
"<td>".html($s["geneSymbol"])."</td>".
! "<td>".html($oneHit ? $s["geneName"] :
! maxlen($s["geneName"], 60, "..."))."</td>".
"</tr>\n";
}
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.42
retrieving revision 1.43
diff -C2 -d -r1.42 -r1.43
*** search.inc.php 12 Sep 2002 22:37:56 -0000 1.42
--- search.inc.php 30 Sep 2002 21:13:10 -0000 1.43
***************
*** 92,97 ****
// Defined fieldtypes: 0 = string, 1 = date, 2 = int, 3 = float,
! // 4 = boolean, 5 = string%, 6 = %string%, 7 = genelist, 8 = 2^float,
! // 9 = cloneId, array(0=>0, n => option) = SELECT
define("SEARCH_STRING", 0);
--- 92,98 ----
// Defined fieldtypes: 0 = string, 1 = date, 2 = int, 3 = float,
! // 4 = boolean, 5 = string% (deprected), 6 = %string% (depr),
! // 7 = genelist, 8 = 2^float, 9 = cloneId(obsolete),
! // array(0=>0, n => option) = SELECT
define("SEARCH_STRING", 0);
***************
*** 967,970 ****
--- 968,978 ----
}
+ if($type == SEARCH_CLONEID)
+ {
+ // The SEARCH_CLONEID type was a design error which I'm now removing.
+ // Recall that $type is a reference to $fieldtypes[$this->field].
+ $type = SEARCH_STRING;
+ }
+
if($type == SEARCH_GENELIST) // Genelists are a bit special
{
***************
*** 1024,1030 ****
else if($type == SEARCH_CLONEID)
{
! $s = (string)$arr[$j];
! $arr[$j] = chr(strlen($s)).$s;
! $view[] = $s;
}
else
--- 1032,1039 ----
else if($type == SEARCH_CLONEID)
{
! $arr[$j] = (string)$arr[$j];
! // $s = (string)$arr[$j];
! // $arr[$j] = chr(strlen($s)).$s;
! // $view[] = $s;
}
else
Index: searchhtml.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/searchhtml.inc.php,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** searchhtml.inc.php 12 Sep 2002 11:45:26 -0000 1.41
--- searchhtml.inc.php 30 Sep 2002 21:13:10 -0000 1.42
***************
*** 32,36 ****
// Defined fieldtypes: 0 = string, 1 = date, 2 = int, 3 = float,
// 4 = boolean, 5 = string%, 6 = %string%, 7 = genelist, 8 = 2^float,
! // 9 = cloneId, array(0, ... ) = enum
//
// $userid - ID of the user for which the table is shown
--- 32,36 ----
// Defined fieldtypes: 0 = string, 1 = date, 2 = int, 3 = float,
// 4 = boolean, 5 = string%, 6 = %string%, 7 = genelist, 8 = 2^float,
! // 9 = cloneId(obsolete), array(0, ... ) = enum
//
// $userid - ID of the user for which the table is shown
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