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August 2008
- 8 participants
- 31 discussions
1
0
[hg] galaxy 1471: Fix for interval2maf.py when metadata missing ...
by greg＠scofield.bx.psu.edu 12 Aug '08
by greg＠scofield.bx.psu.edu 12 Aug '08
12 Aug '08
details: http://www.bx.psu.edu/hg/galaxy/rev/1958657d8f8d
changeset: 1471:1958657d8f8d
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Tue Aug 12 10:04:28 2008 -0400
description:
Fix for interval2maf.py when metadata missing strand column value.
1 file(s) affected in this change:
tools/maf/interval2maf.py
diffs (31 lines):
diff -r 78e84936b7a3 -r 1958657d8f8d tools/maf/interval2maf.py
--- a/tools/maf/interval2maf.py Tue Aug 12 09:18:47 2008 -0400
+++ b/tools/maf/interval2maf.py Tue Aug 12 10:04:28 2008 -0400
@@ -54,23 +54,22 @@
if options.chromCol: chromCol = int( options.chromCol ) - 1
else:
- print >>sys.stderr, "Chromosome column has not been specified."
+ print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
sys.exit()
if options.startCol: startCol = int( options.startCol ) - 1
else:
- print >>sys.stderr, "Start column has not been specified."
+ print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes."
sys.exit()
if options.endCol: endCol = int( options.endCol ) - 1
else:
- print >>sys.stderr, "End column has not been specified."
+ print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes."
sys.exit()
if options.strandCol: strandCol = int( options.strandCol ) - 1
else:
- print >>sys.stderr, "Strand column has not been specified."
- sys.exit()
+ strandCol = -1
if options.interval_file: interval_file = options.interval_file
else:
1
0
1
0
12 Aug '08
details: http://www.bx.psu.edu/hg/galaxy/rev/b9142bbae4ad
changeset: 1469:b9142bbae4ad
user: Nate Coraor <nate(a)bx.psu.edu>
date: Fri Aug 08 13:42:32 2008 -0400
description:
Reports: Wrap the stderr and traceback in pre tags so they display nicely.
6 file(s) affected in this change:
lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css
lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako
lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako
lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako
lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako
lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako
diffs (105 lines):
diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css
--- a/lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css Thu Aug 07 19:28:42 2008 -0400
+++ b/lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css Fri Aug 08 13:42:32 2008 -0400
@@ -322,3 +322,6 @@
display: none;
}
+pre {
+ font-size: 80%;
+}
diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako Thu Aug 07 19:28:42 2008 -0400
+++ b/lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako Fri Aug 08 13:42:32 2008 -0400
@@ -60,13 +60,13 @@
<td colspan="5">Stderr</td>
</tr>
<tr>
- <td colspan="5">${job[9]}</td>
+ <td colspan="5"><pre>${job[9]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Stack Trace</td>
</tr>
<tr>
- <td colspan="5">${job[10]}</td>
+ <td colspan="5"><pre>${job[10]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Info</td>
diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako Thu Aug 07 19:28:42 2008 -0400
+++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako Fri Aug 08 13:42:32 2008 -0400
@@ -64,13 +64,13 @@
<td colspan="5">Stderr</td>
</tr>
<tr>
- <td colspan="5">${job[9]}</td>
+ <td colspan="5"><pre>${job[9]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Stack Trace</td>
</tr>
<tr>
- <td colspan="5">${job[10]}</td>
+ <td colspan="5"><pre>${job[10]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Info</td>
diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Thu Aug 07 19:28:42 2008 -0400
+++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Fri Aug 08 13:42:32 2008 -0400
@@ -51,13 +51,13 @@
<td colspan="5">Stderr</td>
</tr>
<tr>
- <td colspan="5">${job[9]}</td>
+ <td colspan="5"><pre>${job[9]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Stack Trace</td>
</tr>
<tr>
- <td colspan="5">${job[10]}</td>
+ <td colspan="5"><pre>${job[10]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Info</td>
diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako Thu Aug 07 19:28:42 2008 -0400
+++ b/lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako Fri Aug 08 13:42:32 2008 -0400
@@ -64,13 +64,13 @@
<td colspan="5">Stderr</td>
</tr>
<tr>
- <td colspan="5">${job[9]}</td>
+ <td colspan="5"><pre>${job[9]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Stack Trace</td>
</tr>
<tr>
- <td colspan="5">${job[10]}</td>
+ <td colspan="5"><pre>${job[10]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Info</td>
diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako Thu Aug 07 19:28:42 2008 -0400
+++ b/lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako Fri Aug 08 13:42:32 2008 -0400
@@ -64,13 +64,13 @@
<td colspan="5">Stderr</td>
</tr>
<tr>
- <td colspan="5">${job[9]}</td>
+ <td colspan="5"><pre>${job[9]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Stack Trace</td>
</tr>
<tr>
- <td colspan="5">${job[10]}</td>
+ <td colspan="5"><pre>${job[10]}</pre></td>
</tr>
<tr class="header">
<td colspan="5">Info</td>
1
0
12 Aug '08
details: http://www.bx.psu.edu/hg/galaxy/rev/78e84936b7a3
changeset: 1470:78e84936b7a3
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Tue Aug 12 09:18:47 2008 -0400
description:
Fix for Extract Genomic DNA when input file metadata missing strand column value.
2 file(s) affected in this change:
tools/extract/extract_genomic_dna.py
tools/extract/extract_genomic_dna.xml
diffs (79 lines):
diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.py
--- a/tools/extract/extract_genomic_dna.py Fri Aug 08 13:42:32 2008 -0400
+++ b/tools/extract/extract_genomic_dna.py Tue Aug 12 09:18:47 2008 -0400
@@ -1,7 +1,10 @@
#!/usr/bin/env python
"""
-usage: extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format GALAXY_DATA_INDEX_DIR
-by Wen-Yu Chung
+usage: %prog $input $out_file1
+ -1, --cols=N,N,N,N: Columns for start, end, strand in input file
+ -d, --dbkey=N: Genome build of input file
+ -o, --output_format=N: the data type of the output file
+ -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc and twobit.loc
"""
from galaxy import eggs
import pkg_resources
@@ -10,6 +13,7 @@
from bx.cookbook import doc_optparse
import bx.seq.nib
import bx.seq.twobit
+from galaxy.tools.util.galaxyops import *
assert sys.version_info[:2] >= ( 2, 4 )
@@ -54,32 +58,18 @@
return twobit_path
def __main__():
- input_filename = sys.argv[1]
- output_filename = sys.argv[2]
- includes_strand_col = False
+ options, args = doc_optparse.parse( __doc__ )
+ try:
+ chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
+ dbkey = options.dbkey
+ output_format = options.output_format
+ GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
+ input_filename, output_filename = args
+ except:
+ doc_optparse.exception()
+
+ includes_strand_col = strand_col >= 0
strand = None
- # If any of the following exceptions are thrown, we need to improve the metadata validator.
- try:
- chrom_col = int( sys.argv[3] ) - 1
- except:
- stop_err( "Chrom column not properly set, click the pencil icon in your history item to set it." )
- try:
- start_col = int( sys.argv[4] ) - 1
- except:
- stop_err( "Start column not properly set, click the pencil icon in your history item to set it." )
- try:
- end_col = int( sys.argv[5] ) - 1
- except:
- stop_err( "End column not properly set, click the pencil icon in your history item to set it." )
- try:
- strand_col = int( sys.argv[6] ) - 1
- if strand_col >= 0:
- includes_strand_col = True
- except:
- pass
- dbkey = sys.argv[7]
- output_format = sys.argv[8]
- GALAXY_DATA_INDEX_DIR = sys.argv[9]
nibs = {}
twobits = {}
nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR )
diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.xml
--- a/tools/extract/extract_genomic_dna.xml Fri Aug 08 13:42:32 2008 -0400
+++ b/tools/extract/extract_genomic_dna.xml Tue Aug 12 09:18:47 2008 -0400
@@ -1,6 +1,6 @@
<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.1.0">
<description>using coordinates from assembled/unassembled genomes</description>
- <command interpreter="python">extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format ${GALAXY_DATA_INDEX_DIR}</command>
+ <command interpreter="python">extract_genomic_dna.py $input $out_file1 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command>
<inputs>
<param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query">
<validator type="unspecified_build" />
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/c17db2e5f334
changeset: 1468:c17db2e5f334
user: James Taylor <james(a)jamestaylor.org>
date: Thu Aug 07 19:28:42 2008 -0400
description:
Updating packed versions of javascripts.
12 file(s) affected in this change:
static/scripts/packed/IE7.js
static/scripts/packed/IE8.js
static/scripts/packed/cookie_set.js
static/scripts/packed/galaxy.base.js
static/scripts/packed/galaxy.panels.js
static/scripts/packed/galaxy.ui.scrollPanel.js
static/scripts/packed/galaxy.workflow_editor.canvas.js
static/scripts/packed/ie7-recalc.js
static/scripts/packed/jquery.cookie.js
static/scripts/packed/jquery.form.js
static/scripts/packed/jquery.hoverIntent.js
static/scripts/packed/jquery.json.js
diffs (99 lines):
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/IE7.js
--- a/static/scripts/packed/IE7.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/IE7.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,2 +1,1 @@
-/* IE7/IE8.js - copyright 2004-2008, Dean Edwards */
-(function(){IE7={toString:function(){return"IE7 version 2.0 (beta3)"}};var k=IE7.appVersion=navigator.appVersion.match(/MSIE (\d\.\d)/)[1];if(/ie7_off/.test(top.location.search)||k<5)return;var Q=bG();var C=document.compatMode!="CSS1Compat";var bm=document.documentElement,v,s;var bA="!";var G=":link{ie7-link:link}:visited{ie7-link:visited}";var cj=/^[\w\.]+[^:]*$/;function W(a,b){if(cj.test(a))a=(b||"")+a;return a};function bn(a,b){a=W(a,b);return a.slice(0,a.lastIndexOf("/")+1)};var bB=document.scripts[document.scripts.length-1];var ck=bn(bB.src);try{var H=new ActiveXObject("Microsoft.XMLHTTP")}catch(e){}var X={};function cl(a,b){try{a=W(a,b);if(!X[a]){H.open("GET",a,false);H.send();if(H.status==0||H.status==200){X[a]=H.responseText}}}catch(e){}finally{return X[a]||""}};if(k<5.5){undefined=Q();bA="HTML:!";var cm=/(g|gi)$/;var cn=String.prototype.replace;String.prototype.replace=function(a,b){if(typeof b=="function"){if(a&&a.constructor==RegExp){var c=a;var d=c.global;if(d==
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ar style=element.style.left;var runtimeStyle=element.runtimeStyle.left;element.runtimeStyle.left=element.currentStyle.left;element.style.left=value||0;value=element.style.pixelLeft;element.style.left=style;element.runtimeStyle.left=runtimeStyle;return value};var $IE7="ie7-";var Fix=Base.extend({constructor:function(){this.fixes=[];this.recalcs=[]},init:Undefined});var recalcs=[];function addRecalc(recalc){recalcs.push(recalc)}IE7.recalc=function(){IE7.HTML.recalc();IE7.CSS.recalc();for(var i=0;i<recalcs.length;i++){recalcs[i]()}};function isFixed(element){return element.currentStyle["ie7-position"]=="fixed"}function getDefinedStyle(element,propertyName){return element.currentStyle[$IE7+propertyName]||element.currentStyle[propertyName]}function setOverrideStyle(element,propertyName,value){if(element.currentStyle[$IE7+propertyName]==null){element.runtimeStyle[$IE7+propertyName]=element.currentStyle[propertyName]}element.runtimeStyle[propertyName]=value}function createTempEleme
nt(tagName){var element=document.createElement(tagName||"object");element.style.cssText="position:absolute;padding:0;display:block;border:none;clip:rect(0 0 0 0);left:-9999";element.ie7_anon=true;return element}function cssQuery(selector,context,single){if(!_cache[selector]){reg=[];var fn="";var selectors=cssParser.escape(selector).split(",");for(var i=0;i<selectors.length;i++){_wild=_index=_list=0;_duplicate=selectors.length>1?2:0;var block=cssParser.exec(selectors[i])||"if(0){";if(_wild){block+=format("if(e%1.nodeName!='!'){",_index)}var store=_duplicate>1?_TEST:"";block+=format(store+_STORE,_index);block+=Array(match(block,/\{/g).length+1).join("}");fn+=block}eval(format(_FN,reg)+cssParser.unescape(fn)+"return s?null:r}");_cache[selector]=_selectorFunction}return _cache[selector](context||document,single)}var _MSIE5=appVersion<6;var _EVALUATED=/^(href|src)$/;var _ATTRIBUTES={"class":"className","for":"htmlFor"};IE7._indexed=1;IE7._byId=function(document,id){var result=doc
ument.all[id]||null;if(!result||result.id==id){return result}for(var i=0;i<result.length;i++){if(result[i].id==id){return result[i]}}return null};IE7._getAttribute=function(element,name){if(name=="src"&&element.pngSrc){return element.pngSrc}var attribute=_MSIE5?(element.attributes[name]||element.attributes[_ATTRIBUTES[name.toLowerCase()]]):element.getAttributeNode(name);if(attribute&&(attribute.specified||name=="value")){if(_EVALUATED.test(name)){return element.getAttribute(name,2)}else{if(name=="class"){return element.className.replace(/\sie7_\w+/g,"")}else{if(name=="style"){return element.style.cssText}else{return attribute.nodeValue}}}}return null};var names="colSpan,rowSpan,vAlign,dateTime,accessKey,tabIndex,encType,maxLength,readOnly,longDesc";extend(_ATTRIBUTES,combine(names.toLowerCase().split(","),names.split(",")));IE7._getNextElementSibling=function(node){while(node&&(node=node.nextSibling)&&(node.nodeType!=1||node.nodeName=="!")){continue}return node};IE7._getPrev
iousElementSibling=function(node){while(node&&(node=node.previousSibling)&&(node.nodeType!=1||node.nodeName=="!")){continue}return node};var IMPLIED_ASTERISK=/([\s>+~,]|[^(]\+|^)([#.:\[])/g,IMPLIED_SPACE=/(^|,)([^\s>+~])/g,WHITESPACE=/\s*([\s>+~(),]|^|$)\s*/g,WILD_CARD=/\s\*\s/g;var CSSParser=RegGrp.extend({constructor:function(items){this.base(items);this.sorter=new RegGrp;this.sorter.add(/:not\([^)]*\)/,RegGrp.IGNORE);this.sorter.add(/([ >](\*|[\w-]+))([^: >+~]*)(:\w+-child(\([^)]+\))?)([^: >+~]*)/,"$1$3$6$4")},ignoreCase:true,escape:function(selector){return this.optimise(this.format(selector))},format:function(selector){return selector.replace(WHITESPACE,"$1").replace(IMPLIED_SPACE,"$1 $2").replace(IMPLIED_ASTERISK,"$1*$2")},optimise:function(selector){return this.sorter.exec(selector.replace(WILD_CARD,">* "))},unescape:function(selector){return decode(selector)}});var _OPERATORS={"":"%1!=null","=":"%1=='%2'","~=":/(^| )%1( |$)/,"|=":/^%1(-|$)/,"^=":/^%1/,"$=":/%1$/,"*="
:/%1/};var _PSEUDO_CLASSES={"first-child":"!IE7._getPreviousElementSibling(e%1)",link:"e%1.currentStyle['ie7-link']=='link'",visited:"e%1.currentStyle['ie7-link']=='visited'"};var _VAR="var p%2=0,i%2,e%2,n%2=e%1.";var _ID="e%1.sourceIndex";var _TEST="var g="+_ID+";if(!p[g]){p[g]=1;";var _STORE="r[r.length]=e%1;if(s)return e%1;";var _FN="var _selectorFunction=function(e0,s){IE7._indexed++;var r=[],p={},reg=[%1],d=document;";var reg;var _index;var _wild;var _list;var _duplicate;var _cache={};var cssParser=new CSSParser({" (\\*|[\\w-]+)#([\\w-]+)":function(match,tagName,id){_wild=false;var replacement="var e%2=IE7._byId(d,'%4');if(e%2&&";if(tagName!="*"){replacement+="e%2.nodeName=='%3'&&"}replacement+="(e%1==d||e%1.contains(e%2))){";if(_list){replacement+=format("i%1=n%1.length;",_list)}return format(replacement,_index++,_index,tagName.toUpperCase(),id)}," (\\*|[\\w-]+)":function(match,tagName){_duplicate++;_wild=tagName=="*";var replacement=_VAR;replacement+=(_wild&&_MSIE5)?"
all":"getElementsByTagName('%3')";replacement+=";for(i%2=0;(e%2=n%2[i%2]);i%2++){";return format(replacement,_index++,_list=_index,tagName.toUpperCase())},">(\\*|[\\w-]+)":function(match,tagName){var children=_list;_wild=tagName=="*";var replacement=_VAR;replacement+=children?"children":"childNodes";if(!_wild&&children){replacement+=".tags('%3')"}replacement+=";for(i%2=0;(e%2=n%2[i%2]);i%2++){";if(_wild){replacement+="if(e%2.nodeType==1){";_wild=_MSIE5}else{if(!children){replacement+="if(e%2.nodeName=='%3'){"}}return format(replacement,_index++,_list=_index,tagName.toUpperCase())},"\\+(\\*|[\\w-]+)":function(match,tagName){var replacement="";if(_wild){replacement+="if(e%1.nodeName!='!'){"}_wild=false;replacement+="e%1=IE7._getNextElementSibling(e%1);if(e%1";if(tagName!="*"){replacement+="&&e%1.nodeName=='%2'"}replacement+="){";return format(replacement,_index,tagName.toUpperCase())},"~(\\*|[\\w-]+)":function(match,tagName){var replacement="";if(_wild){replacement+="if(e%1.no
deName!='!'){"}_wild=false;_duplicate=2;replacement+="while(e%1=e%1.nextSibling){if(e%1.ie7_adjacent==IE7._indexed)break;if(";if(tagName=="*"){replacement+="e%1.nodeType==1";if(_MSIE5){replacement+="&&e%1.nodeName!='!'"}}else{replacement+="e%1.nodeName=='%2'"}replacement+="){e%1.ie7_adjacent=IE7._indexed;";return format(replacement,_index,tagName.toUpperCase())},"#([\\w-]+)":function(match,id){_wild=false;var replacement="if(e%1.id=='%2'){";if(_list){replacement+=format("i%1=n%1.length;",_list)}return format(replacement,_index,id)},"\\.([\\w-]+)":function(match,className){_wild=false;reg.push(new RegExp("(^|\\s)"+rescape(className)+"(\\s|$)"));return format("if(e%1.className&®[%2].test(e%1.className)){",_index,reg.length-1)},"\\[([\\w-]+)\\s*([^=]?=)?\\s*([^\\]]*)\\]":function(match,attr,operator,value){var alias=_ATTRIBUTES[attr]||attr;if(operator){var getAttribute="e%1.getAttribute('%2',2)";if(!_EVALUATED.test(attr)){getAttribute="e%1.%3||"+getAttribute}attr=format("("+
getAttribute+")",_index,attr,alias)}else{attr=format("IE7._getAttribute(e%1,'%2')",_index,attr)}var replacement=_OPERATORS[operator||""]||"0";if(replacement&&replacement.source){reg.push(new RegExp(format(replacement.source,rescape(cssParser.unescape(value)))));replacement="reg[%2].test(%1)";value=reg.length-1}return"if("+format(replacement,attr,value)+"){"},":+([\\w-]+)(\\(([^)]+)\\))?":function(match,pseudoClass,$2,args){pseudoClass=_PSEUDO_CLASSES[pseudoClass];return"if("+(pseudoClass?format(pseudoClass,_index,args||""):"0")+"){"}});var HYPERLINK=/a(#[\w-]+)?(\.[\w-]+)?:(hover|active)/i;var BRACE1=/\s*\{\s*/,BRACE2=/\s*\}\s*/,COMMA=/\s*\,\s*/;var FIRST_LINE_LETTER=/(.*)(:first-(line|letter))/;var styleSheets=document.styleSheets;IE7.CSS=new (Fix.extend({parser:new Parser,screen:"",print:"",styles:[],rules:[],pseudoClasses:appVersion<7?"first\\-child":"",dynamicPseudoClasses:{toString:function(){var strings=[];for(var pseudoClass in this){strings.push(pseudoClass)}return s
trings.join("|")}},init:function(){var NONE="^\x01$";var CLASS="\\[class=?[^\\]]*\\]";var pseudoClasses=[];if(this.pseudoClasses){pseudoClasses.push(this.pseudoClasses)}var dynamicPseudoClasses=this.dynamicPseudoClasses.toString();if(dynamicPseudoClasses){pseudoClasses.push(dynamicPseudoClasses)}pseudoClasses=pseudoClasses.join("|");var unknown=appVersion<7?["[>+~[(]|([:.])\\w+\\1"]:[CLASS];if(pseudoClasses){unknown.push(":("+pseudoClasses+")")}this.UNKNOWN=new RegExp(unknown.join("|")||NONE,"i");var complex=appVersion<7?["\\[[^\\]]+\\]|[^\\s(\\[]+\\s*[+~]"]:[CLASS];var complexRule=complex.concat();if(pseudoClasses){complexRule.push(":("+pseudoClasses+")")}Rule.COMPLEX=new RegExp(complexRule.join("|")||NONE,"ig");if(this.pseudoClasses){complex.push(":("+this.pseudoClasses+")")}DynamicRule.COMPLEX=new RegExp(complex.join("|")||NONE,"i");DynamicRule.MATCH=new RegExp(dynamicPseudoClasses?"(.*):("+dynamicPseudoClasses+")(.*)":NONE,"i");this.createStyleSheet();this.refresh()},add
EventHandler:function(){addEventHandler.apply(null,arguments)},addFix:function(expression,replacement){this.parser.add(expression,replacement)},addRecalc:function(propertyName,test,handler,replacement){test=new RegExp("([{;\\s])"+propertyName+"\\s*:\\s*"+test+"[^;}]*");var id=this.recalcs.length;if(replacement){replacement=propertyName+":"+replacement}this.addFix(test,function(match,$1){return(replacement?$1+replacement:match)+";ie7-"+match.slice(1)+";ie7_recalc"+id+":1"});this.recalcs.push(arguments);return id},apply:function(){this.getInlineStyles();new StyleSheet("screen");this.trash()},createStyleSheet:function(){this.styleSheet=document.createStyleSheet();this.styleSheet.ie7=true;this.styleSheet.owningElement.ie7=true;this.styleSheet.cssText=HEADER},getInlineStyles:function(){var styleSheets=document.getElementsByTagName("style"),styleSheet;for(var i=styleSheets.length-1;(styleSheet=styleSheets[i]);i--){if(!styleSheet.disabled&&!styleSheet.ie7){this.styles.push(styleShe
et.innerHTML)}}},getText:function(styleSheet,path){try{var cssText=styleSheet.cssText}catch(e){cssText=""}if(httpRequest){cssText=loadFile(styleSheet.href,path)||cssText}return cssText},recalc:function(){this.screen.recalc();var RECALCS=/ie7_recalc\d+/g;var start=HEADER.match(/[{,]/g).length;var stop=start+(this.screen.cssText.match(/\{/g)||"").length;var rules=this.styleSheet.rules,rule;var calcs,calc,elements,element,i,j,k,id;for(i=start;i<stop;i++){rule=rules[i];var cssText=rule.style.cssText;if(rule&&(calcs=cssText.match(RECALCS))){elements=cssQuery(rule.selectorText);if(elements.length){for(j=0;j<calcs.length;j++){id=calcs[j];calc=IE7.CSS.recalcs[id.slice(10)][2];for(k=0;(element=elements[k]);k++){if(element.currentStyle[id]){calc(element,cssText)}}}}}}},refresh:function(){this.styleSheet.cssText=HEADER+this.screen+this.print},trash:function(){for(var i=0;i<styleSheets.length;i++){if(!styleSheets[i].ie7){try{var cssText=styleSheets[i].cssText}catch(e){cssText=""}if(cssT
ext){styleSheets[i].cssText=""}}}}}));var StyleSheet=Base.extend({constructor:function(media){this.media=media;this.load();IE7.CSS[media]=this;IE7.CSS.refresh()},createRule:function(selector,cssText){if(IE7.CSS.UNKNOWN.test(selector)){var match;if(PseudoElement&&(match=selector.match(PseudoElement.MATCH))){return new PseudoElement(match[1],match[2],cssText)}else{if(match=selector.match(DynamicRule.MATCH)){if(!HYPERLINK.test(match[0])||DynamicRule.COMPLEX.test(match[0])){return new DynamicRule(selector,match[1],match[2],match[3],cssText)}}else{return new Rule(selector,cssText)}}}return selector+" {"+cssText+"}"},getText:function(){var _inlineStyles=[].concat(IE7.CSS.styles);var MEDIA=/@media\s+([^{]*)\{([^@]+\})\s*\}/gi;var ALL=/\ball\b|^$/i,SCREEN=/\bscreen\b/i,PRINT=/\bprint\b/i;function _parseMedia(cssText,media){_filterMedia.value=media;return cssText.replace(MEDIA,_filterMedia)}function _filterMedia(match,media,cssText){media=_simpleMedia(media);switch(media){case"screen
":case"print":if(media!=_filterMedia.value){return""}case"all":return cssText}return""}function _simpleMedia(media){if(ALL.test(media)){return"all"}else{if(SCREEN.test(media)){return(PRINT.test(media))?"all":"screen"}else{if(PRINT.test(media)){return"print"}}}}var self=this;function _getCSSText(styleSheet,path,media,level){var cssText="";if(!level){media=_simpleMedia(styleSheet.media);level=0}if(media=="all"||media==self.media){if(level<3){for(var i=0;i<styleSheet.imports.length;i++){cssText+=_getCSSText(styleSheet.imports[i],getPath(styleSheet.href,path),media,level+1)}}cssText+=encode(styleSheet.href?_loadStyleSheet(styleSheet,path):_inlineStyles.pop()||"");cssText=_parseMedia(cssText,self.media)}return cssText}var fileCache={};function _loadStyleSheet(styleSheet,path){var url=makePath(styleSheet.href,path);if(fileCache[url]){return""}fileCache[url]=(styleSheet.disabled)?"":_fixUrls(IE7.CSS.getText(styleSheet,path),getPath(styleSheet.href,path));return fileCache[url]}var U
RL=/(url\s*\(\s*['"]?)([\w\.]+[^:\)]*['"]?\))/gi;function _fixUrls(cssText,pathname){return cssText.replace(URL,"$1"+pathname.slice(0,pathname.lastIndexOf("/")+1)+"$2")}for(var i=0;i<styleSheets.length;i++){if(!styleSheets[i].disabled&&!styleSheets[i].ie7){this.cssText+=_getCSSText(styleSheets[i])}}},load:function(){this.cssText="";this.getText();this.parse();this.cssText=decode(this.cssText);fileCache={}},parse:function(){this.cssText=IE7.CSS.parser.exec(this.cssText);var offset=IE7.CSS.rules.length;var rules=this.cssText.split(BRACE2),rule;var selectors,cssText,i,j;for(i=0;i<rules.length;i++){rule=rules[i].split(BRACE1);selectors=rule[0].split(COMMA);cssText=rule[1];for(j=0;j<selectors.length;j++){selectors[j]=cssText?this.createRule(selectors[j],cssText):""}rules[i]=selectors.join("\n")}this.cssText=rules.join("\n");this.rules=IE7.CSS.rules.slice(offset)},recalc:function(){var rule,i;for(i=0;(rule=this.rules[i]);i++){rule.recalc()}},toString:function(){return"@media "+thi
s.media+"{"+this.cssText+"}"}});var PseudoElement;var Rule=IE7.Rule=Base.extend({constructor:function(selector,cssText){this.id=IE7.CSS.rules.length;this.className=Rule.PREFIX+this.id;selector=selector.match(FIRST_LINE_LETTER)||selector||"*";this.selector=selector[1]||selector;this.selectorText=this.parse(this.selector)+(selector[2]||"");this.cssText=cssText;this.MATCH=new RegExp("\\s"+this.className+"(\\s|$)","g");IE7.CSS.rules.push(this);this.init()},init:Undefined,add:function(element){element.className+=" "+this.className},recalc:function(){var match=cssQuery(this.selector);for(var i=0;i<match.length;i++){this.add(match[i])}},parse:function(selector){var simple=selector.replace(Rule.CHILD," ").replace(Rule.COMPLEX,"");if(appVersion<7){simple=simple.replace(Rule.MULTI,"")}var tags=match(simple,Rule.TAGS).length-match(selector,Rule.TAGS).length;var classes=match(simple,Rule.CLASSES).length-match(selector,Rule.CLASSES).length+1;while(classes>0&&Rule.CLASS.test(simple)){simp
le=simple.replace(Rule.CLASS,"");classes--}while(tags>0&&Rule.TAG.test(simple)){simple=simple.replace(Rule.TAG,"$1*");tags--}simple+="."+this.className;classes=Math.min(classes,2);tags=Math.min(tags,2);var score=-10*classes-tags;if(score>0){simple=simple+","+Rule.MAP[score]+" "+simple}return simple},remove:function(element){element.className=element.className.replace(this.MATCH,"$1")},toString:function(){return format("%1 {%2}",this.selectorText,this.cssText)}},{CHILD:/>/g,CLASS:/\.[\w-]+/,CLASSES:/[.:\[]/g,MULTI:/(\.[\w-]+)+/g,PREFIX:"ie7_class",TAG:/^\w+|([\s>+~])\w+/,TAGS:/^\w|[\s>+~]\w/g,MAP:{1:"html",2:"html body",10:".ie7_html",11:"html.ie7_html",12:"html.ie7_html body",20:".ie7_html .ie7_body",21:"html.ie7_html .ie7_body",22:"html.ie7_html body.ie7_body"}});var DynamicRule=Rule.extend({constructor:function(selector,attach,dynamicPseudoClass,target,cssText){this.attach=attach||"*";this.dynamicPseudoClass=IE7.CSS.dynamicPseudoClasses[dynamicPseudoClass];this.target=targ
et;this.base(selector,cssText)},recalc:function(){var attaches=cssQuery(this.attach),attach;for(var i=0;attach=attaches[i];i++){var target=this.target?cssQuery(this.target,attach):[attach];if(target.length){this.dynamicPseudoClass.apply(attach,target,this)}}}});var DynamicPseudoClass=Base.extend({constructor:function(name,apply){this.name=name;this.apply=apply;this.instances={};IE7.CSS.dynamicPseudoClasses[name]=this},register:function(instance){var _class=instance[2];instance.id=_class.id+instance[0].uniqueID;if(!this.instances[instance.id]){var target=instance[1],j;for(j=0;j<target.length;j++){_class.add(target[j])}this.instances[instance.id]=instance}},unregister:function(instance){if(this.instances[instance.id]){var _class=instance[2];var target=instance[1],j;for(j=0;j<target.length;j++){_class.remove(target[j])}delete this.instances[instance.id]}}});if(appVersion<7){var Hover=new DynamicPseudoClass("hover",function(element){var instance=arguments;IE7.CSS.addEventHandler
(element,appVersion<5.5?"onmouseover":"onmouseenter",function(){Hover.register(instance)});IE7.CSS.addEventHandler(element,appVersion<5.5?"onmouseout":"onmouseleave",function(){Hover.unregister(instance)})});addEventHandler(document,"onmouseup",function(){var instances=Hover.instances;for(var i in instances){if(!instances[i][0].contains(event.srcElement)){Hover.unregister(instances[i])}}})}IE7.CSS.addRecalc("[\\w-]+","inherit",function(element,cssText){var inherited=cssText.match(/[\w-]+\s*:\s*inherit/g);for(var i=0;i<inherited.length;i++){var propertyName=inherited[i].replace(/ie7\-|\s*:\s*inherit/g,"").replace(/\-([a-z])/g,function(match,chr){return chr.toUpperCase()});element.runtimeStyle[propertyName]=element.parentElement.currentStyle[propertyName]}});IE7.HTML=new (Fix.extend({fixed:{},init:Undefined,addFix:function(){this.fixes.push(arguments)},apply:function(){for(var i=0;i<this.fixes.length;i++){var match=cssQuery(this.fixes[i][0]);var fix=this.fixes[i][1];for(var j=
0;j<match.length;j++){fix(match[j])}}},addRecalc:function(){this.recalcs.push(arguments)},recalc:function(){for(var i=0;i<this.recalcs.length;i++){var match=cssQuery(this.recalcs[i][0]);var recalc=this.recalcs[i][1],element;var key=Math.pow(2,i);for(var j=0;(element=match[j]);j++){var uniqueID=element.uniqueID;if((this.fixed[uniqueID]&key)==0){element=recalc(element)||element;this.fixed[uniqueID]|=key}}}}}));if(appVersion<7){document.createElement("abbr");IE7.HTML.addRecalc("label",function(label){if(!label.htmlFor){var firstChildControl=cssQuery("input,textarea",label,true);if(firstChildControl){addEventHandler(label,"onclick",function(){firstChildControl.click()})}}})}var NUMERIC="[.\\d]";new function(_){var layout=IE7.Layout=this;HEADER+="*{boxSizing:content-box}";IE7.hasLayout=appVersion<5.5?function(element){return element.clientWidth}:function(element){return element.currentStyle.hasLayout};layout.boxSizing=function(element){if(!IE7.hasLayout(element)){element.style.he
ight="0cm";if(element.currentStyle.verticalAlign=="auto"){element.runtimeStyle.verticalAlign="top"}collapseMargins(element)}};function collapseMargins(element){if(element!=viewport&&element.currentStyle.position!="absolute"){collapseMargin(element,"marginTop");collapseMargin(element,"marginBottom")}}function collapseMargin(element,type){if(!element.runtimeStyle[type]){var parentElement=element.parentElement;if(parentElement&&IE7.hasLayout(parentElement)&&!IE7[type=="marginTop"?"_getPreviousElementSibling":"_getNextElementSibling"](element)){return }var child=cssQuery(">*:"+(type=="marginTop"?"first":"last")+"-child",element,true);if(child&&child.currentStyle.styleFloat=="none"&&IE7.hasLayout(child)){collapseMargin(child,type);margin=_getMargin(element,element.currentStyle[type]);childMargin=_getMargin(child,child.currentStyle[type]);if(margin<0||childMargin<0){element.runtimeStyle[type]=margin+childMargin}else{element.runtimeStyle[type]=Math.max(childMargin,margin)}child.run
timeStyle[type]="0px"}}}function _getMargin(element,value){return value=="auto"?0:getPixelValue(element,value)}var UNIT=/^[.\d][\w%]*$/,AUTO=/^(auto|0cm)$/;var applyWidth,applyHeight;IE7.Layout.borderBox=function(element){applyWidth(element);applyHeight(element)};var fixWidth=function(HEIGHT){applyWidth=function(element){if(!PERCENT.test(element.currentStyle.width)){fixWidth(element)}collapseMargins(element)};function fixWidth(element,value){if(!element.runtimeStyle.fixedWidth){if(!value){value=element.currentStyle.width}element.runtimeStyle.fixedWidth=(UNIT.test(value))?Math.max(0,getFixedWidth(element,value)):value;setOverrideStyle(element,"width",element.runtimeStyle.fixedWidth)}}function layoutWidth(element){if(!isFixed(element)){var layoutParent=element.offsetParent;while(layoutParent&&!IE7.hasLayout(layoutParent)){layoutParent=layoutParent.offsetParent}}return(layoutParent||viewport).clientWidth}function getPixelWidth(element,value){if(PERCENT.test(value)){return parse
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0);setOverrideStyle(element,"width",width);return width}}}eval(rotate(clipWidth));function positionLeft(element,recalc){if(!recalc&&PERCENT.test(element.currentStyle.width)){element.runtimeStyle.fixWidth=element.currentStyle.width}if(element.runtimeStyle.fixWidth){element.runtimeStyle.width=getPixelWidth(element,element.runtimeStyle.fixWidth)}element.runtimeStyle.shiftLeft=0;element.runtimeStyle._left=element.currentStyle.left;element.runtimeStyle.autoLeft=element.currentStyle.right!="auto"&&element.currentStyle.left=="auto";element.runtimeStyle.left="";element.runtimeStyle.screenLeft=getScreenLeft(element);element.runtimeStyle.pixelLeft=element.runtimeStyle.screenLeft;if(!recalc&&!_isFixed(element.offsetParent)){_setExpression(element,"pixelLeft","runtimeStyle.screenLeft+runtimeStyle.shiftLeft+document."+$viewport+".scrollLeft")}}eval(rotate(positionLeft));function getScreenLeft(element){var screenLeft=element.offsetLeft,nested=1;if(element.runtimeStyle.autoLeft){screenLeft
=viewport.clientWidth-element.offsetWidth-getPixelWidth(element,element.currentStyle.right)}if(element.currentStyle.marginLeft!="auto"){screenLeft-=getPixelWidth(element,element.currentStyle.marginLeft)}while(element=element.offsetParent){if(element.currentStyle.position!="static"){nested=-1}screenLeft+=element.offsetLeft*nested}return screenLeft}eval(rotate(getScreenLeft));function getPixelWidth(element,value){return PERCENT.test(value)?parseInt(parseFloat(value)/100*viewport.clientWidth):getPixelValue(element,value)}eval(rotate(getPixelWidth));function _resize(){var elements=_backgroundFixed.elements;for(var i in elements){_backgroundPosition(elements[i])}elements=_positionFixed.elements;for(i in elements){_foregroundPosition(elements[i],true);_foregroundPosition(elements[i],true)}_timer=0}var _timer;addResize(function(){if(!_timer){_timer=setTimeout(_resize,0)}})};var WRAPPER_STYLE={backgroundColor:"transparent",backgroundImage:"none",backgroundPositionX:null,backgroundPo
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ute";element.parentNode.insertBefore(wrapper,element);wrapper.appendChild(element)});function ie7Quirks(){var FONT_SIZES="xx-small,x-small,small,medium,large,x-large,xx-large".split(",");for(var i=0;i<FONT_SIZES.length;i++){FONT_SIZES[FONT_SIZES[i]]=FONT_SIZES[i-1]||"0.67em"}IE7.CSS.addFix(/(font(-size)?\s*:\s*)([\w.-]+)/,function(match,label,size,value){return label+(FONT_SIZES[value]||value)});if(appVersion<6){var NEGATIVE=/^\-/,LENGTH=/(em|ex)$/i;var EM=/em$/i,EX=/ex$/i;getPixelValue=function(element,value){if(PIXEL.test(value)){return parseInt(value)||0}var scale=NEGATIVE.test(value)?-1:1;if(LENGTH.test(value)){scale*=getFontScale(element)}temp.style.width=(scale<0)?value.slice(1):value;body.appendChild(temp);value=scale*temp.offsetWidth;temp.removeNode();return parseInt(value)};var temp=createTempElement();function getFontScale(element){var scale=1;temp.style.fontFamily=element.currentStyle.fontFamily;temp.style.lineHeight=element.currentStyle.lineHeight;while(element!=
body){var fontSize=element.currentStyle["ie7-font-size"];if(fontSize){if(EM.test(fontSize)){scale*=parseFloat(fontSize)}else{if(PERCENT.test(fontSize)){scale*=(parseFloat(fontSize)/100)}else{if(EX.test(fontSize)){scale*=(parseFloat(fontSize)/2)}else{temp.style.fontSize=fontSize;return 1}}}}element=element.parentElement}return scale}IE7.CSS.addFix(/cursor\s*:\s*pointer/,"cursor:hand");IE7.CSS.addFix(/display\s*:\s*list-item/,"display:block")}function fixMargin(element){if(appVersion<5.5){IE7.Layout.boxSizing(element.parentElement)}var parent=element.parentElement;var margin=parent.offsetWidth-element.offsetWidth-getPaddingWidth(parent);var autoRight=(element.currentStyle["ie7-margin"]&&element.currentStyle.marginRight=="auto")||element.currentStyle["ie7-margin-right"]=="auto";switch(parent.currentStyle.textAlign){case"right":margin=autoRight?parseInt(margin/2):0;element.runtimeStyle.marginRight=margin+"px";break;case"center":if(autoRight){margin=0}default:if(autoRight){margin
/=2}element.runtimeStyle.marginLeft=parseInt(margin)+"px"}}function getPaddingWidth(element){return getPixelValue(element,element.currentStyle.paddingLeft)+getPixelValue(element,element.currentStyle.paddingRight)}IE7.CSS.addRecalc("margin(-left|-right)?","[^};]*auto",function(element){if(register(fixMargin,element,element.parentElement&&element.currentStyle.display=="block"&&element.currentStyle.marginLeft=="auto"&&element.currentStyle.position!="absolute")){fixMargin(element)}});addResize(function(){for(var i in fixMargin.elements){var element=fixMargin.elements[i];element.runtimeStyle.marginLeft=element.runtimeStyle.marginRight="";fixMargin(element)}})}IE7.loaded=true;(function(){try{documentElement.doScroll("left")}catch(e){setTimeout(arguments.callee,1);return }try{eval(script.innerHTML)}catch(e){}PNG=new RegExp(rescape(typeof IE7_PNG_SUFFIX=="string"?IE7_PNG_SUFFIX:"-trans.png")+"$","i");body=document.body;viewport=quirksMode?body:documentElement;body.className+=" ie7_b
ody";documentElement.className+=" ie7_html";if(quirksMode){ie7Quirks()}IE7.CSS.init();IE7.HTML.init();IE7.HTML.apply();IE7.CSS.apply();IE7.recalc()})()})();
\ No newline at end of file
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/IE8.js
--- a/static/scripts/packed/IE8.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/IE8.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,2 +1,1 @@
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ext){styleSheets[i].cssText=""}}}}}));var StyleSheet=Base.extend({constructor:function(media){this.media=media;this.load();IE7.CSS[media]=this;IE7.CSS.refresh()},createRule:function(selector,cssText){if(IE7.CSS.UNKNOWN.test(selector)){var match;if(PseudoElement&&(match=selector.match(PseudoElement.MATCH))){return new PseudoElement(match[1],match[2],cssText)}else{if(match=selector.match(DynamicRule.MATCH)){if(!HYPERLINK.test(match[0])||DynamicRule.COMPLEX.test(match[0])){return new DynamicRule(selector,match[1],match[2],match[3],cssText)}}else{return new Rule(selector,cssText)}}}return selector+" {"+cssText+"}"},getText:function(){var _inlineStyles=[].concat(IE7.CSS.styles);var MEDIA=/@media\s+([^{]*)\{([^@]+\})\s*\}/gi;var ALL=/\ball\b|^$/i,SCREEN=/\bscreen\b/i,PRINT=/\bprint\b/i;function _parseMedia(cssText,media){_filterMedia.value=media;return cssText.replace(MEDIA,_filterMedia)}function _filterMedia(match,media,cssText){media=_simpleMedia(media);switch(media){case"screen
":case"print":if(media!=_filterMedia.value){return""}case"all":return cssText}return""}function _simpleMedia(media){if(ALL.test(media)){return"all"}else{if(SCREEN.test(media)){return(PRINT.test(media))?"all":"screen"}else{if(PRINT.test(media)){return"print"}}}}var self=this;function _getCSSText(styleSheet,path,media,level){var cssText="";if(!level){media=_simpleMedia(styleSheet.media);level=0}if(media=="all"||media==self.media){if(level<3){for(var i=0;i<styleSheet.imports.length;i++){cssText+=_getCSSText(styleSheet.imports[i],getPath(styleSheet.href,path),media,level+1)}}cssText+=encode(styleSheet.href?_loadStyleSheet(styleSheet,path):_inlineStyles.pop()||"");cssText=_parseMedia(cssText,self.media)}return cssText}var fileCache={};function _loadStyleSheet(styleSheet,path){var url=makePath(styleSheet.href,path);if(fileCache[url]){return""}fileCache[url]=(styleSheet.disabled)?"":_fixUrls(IE7.CSS.getText(styleSheet,path),getPath(styleSheet.href,path));return fileCache[url]}var U
RL=/(url\s*\(\s*['"]?)([\w\.]+[^:\)]*['"]?\))/gi;function _fixUrls(cssText,pathname){return cssText.replace(URL,"$1"+pathname.slice(0,pathname.lastIndexOf("/")+1)+"$2")}for(var i=0;i<styleSheets.length;i++){if(!styleSheets[i].disabled&&!styleSheets[i].ie7){this.cssText+=_getCSSText(styleSheets[i])}}},load:function(){this.cssText="";this.getText();this.parse();this.cssText=decode(this.cssText);fileCache={}},parse:function(){this.cssText=IE7.CSS.parser.exec(this.cssText);var offset=IE7.CSS.rules.length;var rules=this.cssText.split(BRACE2),rule;var selectors,cssText,i,j;for(i=0;i<rules.length;i++){rule=rules[i].split(BRACE1);selectors=rule[0].split(COMMA);cssText=rule[1];for(j=0;j<selectors.length;j++){selectors[j]=cssText?this.createRule(selectors[j],cssText):""}rules[i]=selectors.join("\n")}this.cssText=rules.join("\n");this.rules=IE7.CSS.rules.slice(offset)},recalc:function(){var rule,i;for(i=0;(rule=this.rules[i]);i++){rule.recalc()}},toString:function(){return"@media "+thi
s.media+"{"+this.cssText+"}"}});var PseudoElement;var Rule=IE7.Rule=Base.extend({constructor:function(selector,cssText){this.id=IE7.CSS.rules.length;this.className=Rule.PREFIX+this.id;selector=selector.match(FIRST_LINE_LETTER)||selector||"*";this.selector=selector[1]||selector;this.selectorText=this.parse(this.selector)+(selector[2]||"");this.cssText=cssText;this.MATCH=new RegExp("\\s"+this.className+"(\\s|$)","g");IE7.CSS.rules.push(this);this.init()},init:Undefined,add:function(element){element.className+=" "+this.className},recalc:function(){var match=cssQuery(this.selector);for(var i=0;i<match.length;i++){this.add(match[i])}},parse:function(selector){var simple=selector.replace(Rule.CHILD," ").replace(Rule.COMPLEX,"");if(appVersion<7){simple=simple.replace(Rule.MULTI,"")}var tags=match(simple,Rule.TAGS).length-match(selector,Rule.TAGS).length;var classes=match(simple,Rule.CLASSES).length-match(selector,Rule.CLASSES).length+1;while(classes>0&&Rule.CLASS.test(simple)){simp
le=simple.replace(Rule.CLASS,"");classes--}while(tags>0&&Rule.TAG.test(simple)){simple=simple.replace(Rule.TAG,"$1*");tags--}simple+="."+this.className;classes=Math.min(classes,2);tags=Math.min(tags,2);var score=-10*classes-tags;if(score>0){simple=simple+","+Rule.MAP[score]+" "+simple}return simple},remove:function(element){element.className=element.className.replace(this.MATCH,"$1")},toString:function(){return format("%1 {%2}",this.selectorText,this.cssText)}},{CHILD:/>/g,CLASS:/\.[\w-]+/,CLASSES:/[.:\[]/g,MULTI:/(\.[\w-]+)+/g,PREFIX:"ie7_class",TAG:/^\w+|([\s>+~])\w+/,TAGS:/^\w|[\s>+~]\w/g,MAP:{1:"html",2:"html body",10:".ie7_html",11:"html.ie7_html",12:"html.ie7_html body",20:".ie7_html .ie7_body",21:"html.ie7_html .ie7_body",22:"html.ie7_html body.ie7_body"}});var DynamicRule=Rule.extend({constructor:function(selector,attach,dynamicPseudoClass,target,cssText){this.attach=attach||"*";this.dynamicPseudoClass=IE7.CSS.dynamicPseudoClasses[dynamicPseudoClass];this.target=targ
et;this.base(selector,cssText)},recalc:function(){var attaches=cssQuery(this.attach),attach;for(var i=0;attach=attaches[i];i++){var target=this.target?cssQuery(this.target,attach):[attach];if(target.length){this.dynamicPseudoClass.apply(attach,target,this)}}}});var DynamicPseudoClass=Base.extend({constructor:function(name,apply){this.name=name;this.apply=apply;this.instances={};IE7.CSS.dynamicPseudoClasses[name]=this},register:function(instance){var _class=instance[2];instance.id=_class.id+instance[0].uniqueID;if(!this.instances[instance.id]){var target=instance[1],j;for(j=0;j<target.length;j++){_class.add(target[j])}this.instances[instance.id]=instance}},unregister:function(instance){if(this.instances[instance.id]){var _class=instance[2];var target=instance[1],j;for(j=0;j<target.length;j++){_class.remove(target[j])}delete this.instances[instance.id]}}});if(appVersion<7){var Hover=new DynamicPseudoClass("hover",function(element){var instance=arguments;IE7.CSS.addEventHandler
(element,appVersion<5.5?"onmouseover":"onmouseenter",function(){Hover.register(instance)});IE7.CSS.addEventHandler(element,appVersion<5.5?"onmouseout":"onmouseleave",function(){Hover.unregister(instance)})});addEventHandler(document,"onmouseup",function(){var instances=Hover.instances;for(var i in instances){if(!instances[i][0].contains(event.srcElement)){Hover.unregister(instances[i])}}})}IE7.CSS.addRecalc("[\\w-]+","inherit",function(element,cssText){var inherited=cssText.match(/[\w-]+\s*:\s*inherit/g);for(var i=0;i<inherited.length;i++){var propertyName=inherited[i].replace(/ie7\-|\s*:\s*inherit/g,"").replace(/\-([a-z])/g,function(match,chr){return chr.toUpperCase()});element.runtimeStyle[propertyName]=element.parentElement.currentStyle[propertyName]}});IE7.HTML=new (Fix.extend({fixed:{},init:Undefined,addFix:function(){this.fixes.push(arguments)},apply:function(){for(var i=0;i<this.fixes.length;i++){var match=cssQuery(this.fixes[i][0]);var fix=this.fixes[i][1];for(var j=
0;j<match.length;j++){fix(match[j])}}},addRecalc:function(){this.recalcs.push(arguments)},recalc:function(){for(var i=0;i<this.recalcs.length;i++){var match=cssQuery(this.recalcs[i][0]);var recalc=this.recalcs[i][1],element;var key=Math.pow(2,i);for(var j=0;(element=match[j]);j++){var uniqueID=element.uniqueID;if((this.fixed[uniqueID]&key)==0){element=recalc(element)||element;this.fixed[uniqueID]|=key}}}}}));if(appVersion<7){document.createElement("abbr");IE7.HTML.addRecalc("label",function(label){if(!label.htmlFor){var firstChildControl=cssQuery("input,textarea",label,true);if(firstChildControl){addEventHandler(label,"onclick",function(){firstChildControl.click()})}}})}var NUMERIC="[.\\d]";new function(_){var layout=IE7.Layout=this;HEADER+="*{boxSizing:content-box}";IE7.hasLayout=appVersion<5.5?function(element){return element.clientWidth}:function(element){return element.currentStyle.hasLayout};layout.boxSizing=function(element){if(!IE7.hasLayout(element)){element.style.he
ight="0cm";if(element.currentStyle.verticalAlign=="auto"){element.runtimeStyle.verticalAlign="top"}collapseMargins(element)}};function collapseMargins(element){if(element!=viewport&&element.currentStyle.position!="absolute"){collapseMargin(element,"marginTop");collapseMargin(element,"marginBottom")}}function collapseMargin(element,type){if(!element.runtimeStyle[type]){var parentElement=element.parentElement;if(parentElement&&IE7.hasLayout(parentElement)&&!IE7[type=="marginTop"?"_getPreviousElementSibling":"_getNextElementSibling"](element)){return }var child=cssQuery(">*:"+(type=="marginTop"?"first":"last")+"-child",element,true);if(child&&child.currentStyle.styleFloat=="none"&&IE7.hasLayout(child)){collapseMargin(child,type);margin=_getMargin(element,element.currentStyle[type]);childMargin=_getMargin(child,child.currentStyle[type]);if(margin<0||childMargin<0){element.runtimeStyle[type]=margin+childMargin}else{element.runtimeStyle[type]=Math.max(childMargin,margin)}child.run
timeStyle[type]="0px"}}}function _getMargin(element,value){return value=="auto"?0:getPixelValue(element,value)}var UNIT=/^[.\d][\w%]*$/,AUTO=/^(auto|0cm)$/;var applyWidth,applyHeight;IE7.Layout.borderBox=function(element){applyWidth(element);applyHeight(element)};var fixWidth=function(HEIGHT){applyWidth=function(element){if(!PERCENT.test(element.currentStyle.width)){fixWidth(element)}collapseMargins(element)};function fixWidth(element,value){if(!element.runtimeStyle.fixedWidth){if(!value){value=element.currentStyle.width}element.runtimeStyle.fixedWidth=(UNIT.test(value))?Math.max(0,getFixedWidth(element,value)):value;setOverrideStyle(element,"width",element.runtimeStyle.fixedWidth)}}function layoutWidth(element){if(!isFixed(element)){var layoutParent=element.offsetParent;while(layoutParent&&!IE7.hasLayout(layoutParent)){layoutParent=layoutParent.offsetParent}}return(layoutParent||viewport).clientWidth}function getPixelWidth(element,value){if(PERCENT.test(value)){return parse
Int(parseFloat(value)/100*layoutWidth(element))}return getPixelValue(element,value)}var getFixedWidth=function(element,value){var borderBox=element.currentStyle["box-sizing"]=="border-box";var adjustment=0;if(quirksMode&&!borderBox){adjustment+=getBorderWidth(element)+getWidth(element,"padding")}else{if(!quirksMode&&borderBox){adjustment-=getBorderWidth(element)+getWidth(element,"padding")}}return getPixelWidth(element,value)+adjustment};function getBorderWidth(element){return element.offsetWidth-element.clientWidth}function getWidth(element,type){return getPixelWidth(element,element.currentStyle[type+"Left"])+getPixelWidth(element,element.currentStyle[type+"Right"])}HEADER+="*{minWidth:none;maxWidth:none;min-width:none;max-width:none}";layout.minWidth=function(element){if(element.currentStyle["min-width"]!=null){element.style.minWidth=element.currentStyle["min-width"]}if(register(arguments.callee,element,element.currentStyle.minWidth!="none")){layout.boxSizing(element);fixW
idth(element);resizeWidth(element)}};eval("IE7.Layout.maxWidth="+String(layout.minWidth).replace(/min/g,"max"));function resizeWidth(element){var rect=element.getBoundingClientRect();var width=rect.right-rect.left;if(element.currentStyle.minWidth!="none"&&width<=getFixedWidth(element,element.currentStyle.minWidth)){element.runtimeStyle.width=element.currentStyle.minWidth}else{if(element.currentStyle.maxWidth!="none"&&width>=getFixedWidth(element,element.currentStyle.maxWidth)){element.runtimeStyle.width=element.currentStyle.maxWidth}else{element.runtimeStyle.width=element.runtimeStyle.fixedWidth}}}function fixRight(element){if(register(fixRight,element,/^(fixed|absolute)$/.test(element.currentStyle.position)&&getDefinedStyle(element,"left")!="auto"&&getDefinedStyle(element,"right")!="auto"&&AUTO.test(getDefinedStyle(element,"width")))){resizeRight(element);IE7.Layout.boxSizing(element)}}IE7.Layout.fixRight=fixRight;function resizeRight(element){var left=getPixelWidth(element
,element.runtimeStyle._left||element.currentStyle.left);var width=layoutWidth(element)-getPixelWidth(element,element.currentStyle.right)-left-getWidth(element,"margin");if(parseInt(element.runtimeStyle.width)==width){return }element.runtimeStyle.width="";if(isFixed(element)||HEIGHT||element.offsetWidth<width){if(!quirksMode){width-=getBorderWidth(element)+getWidth(element,"padding")}if(width<0){width=0}element.runtimeStyle.fixedWidth=width;setOverrideStyle(element,"width",width)}}var clientWidth=0;addResize(function(){if(!viewport){return }var i,wider=(clientWidth<viewport.clientWidth);clientWidth=viewport.clientWidth;var elements=layout.minWidth.elements;for(i in elements){var element=elements[i];var fixedWidth=(parseInt(element.runtimeStyle.width)==getFixedWidth(element,element.currentStyle.minWidth));if(wider&&fixedWidth){element.runtimeStyle.width=""}if(wider==fixedWidth){resizeWidth(element)}}var elements=layout.maxWidth.elements;for(i in elements){var element=elements[
i];var fixedWidth=(parseInt(element.runtimeStyle.width)==getFixedWidth(element,element.currentStyle.maxWidth));if(!wider&&fixedWidth){element.runtimeStyle.width=""}if(wider!=fixedWidth){resizeWidth(element)}}for(i in fixRight.elements){resizeRight(fixRight.elements[i])}});if(quirksMode){IE7.CSS.addRecalc("width",NUMERIC,applyWidth)}if(appVersion<7){IE7.CSS.addRecalc("min-width",NUMERIC,layout.minWidth);IE7.CSS.addRecalc("max-width",NUMERIC,layout.maxWidth);IE7.CSS.addRecalc("right",NUMERIC,fixRight)}};eval("var fixHeight="+rotate(fixWidth));fixWidth();fixHeight(true)};var BLANK_GIF=makePath("blank.gif",path);var ALPHA_IMAGE_LOADER="DXImageTransform.Microsoft.AlphaImageLoader";var PNG_FILTER="progid:"+ALPHA_IMAGE_LOADER+"(src='%1',sizingMethod='%2')";var PNG;var filtered=[];function fixImage(element){if(PNG.test(element.src)){var image=new Image(element.width,element.height);image.onload=function(){element.width=image.width;element.height=image.height;image=null};image.src=el
ement.src;element.pngSrc=element.src;addFilter(element)}}if(appVersion>=5.5&&appVersion<7){IE7.CSS.addFix(/background(-image)?\s*:\s*([^};]*)?url\(([^\)]+)\)([^;}]*)?/,function(match,$1,$2,url,$4){url=getString(url);return PNG.test(url)?"filter:"+format(PNG_FILTER,url,"crop")+";zoom:1;background"+($1||"")+":"+($2||"")+"none"+($4||""):match});IE7.HTML.addRecalc("img,input",function(element){if(element.tagName=="INPUT"&&element.type!="image"){return }fixImage(element);addEventHandler(element,"onpropertychange",function(){if(!printing&&event.propertyName=="src"&&element.src.indexOf(BLANK_GIF)==-1){fixImage(element)}})});var printing=false;addEventHandler(window,"onbeforeprint",function(){printing=true;for(var i=0;i<filtered.length;i++){removeFilter(filtered[i])}});addEventHandler(window,"onafterprint",function(){for(var i=0;i<filtered.length;i++){addFilter(filtered[i])}printing=false})}function addFilter(element,sizingMethod){var filter=element.filters[ALPHA_IMAGE_LOADER];if(fi
lter){filter.src=element.src;filter.enabled=true}else{element.runtimeStyle.filter=format(PNG_FILTER,element.src,sizingMethod||"scale");filtered.push(element)}element.src=BLANK_GIF}function removeFilter(element){element.src=element.pngSrc;element.filters[ALPHA_IMAGE_LOADER].enabled=false}new function(_){if(appVersion>=7){return }IE7.CSS.addRecalc("position","fixed",_positionFixed,"absolute");IE7.CSS.addRecalc("background(-attachment)?","[^};]*fixed",_backgroundFixed);var $viewport=quirksMode?"body":"documentElement";function _fixBackground(){if(body.currentStyle.backgroundAttachment!="fixed"){if(body.currentStyle.backgroundImage=="none"){body.runtimeStyle.backgroundRepeat="no-repeat";body.runtimeStyle.backgroundImage="url("+BLANK_GIF+")"}body.runtimeStyle.backgroundAttachment="fixed"}_fixBackground=Undefined}var _tmp=createTempElement("img");function _isFixed(element){return element?isFixed(element)||_isFixed(element.parentElement):false}function _setExpression(element,proper
tyName,expression){setTimeout("document.all."+element.uniqueID+".runtimeStyle.setExpression('"+propertyName+"','"+expression+"')",0)}function _backgroundFixed(element){if(register(_backgroundFixed,element,element.currentStyle.backgroundAttachment=="fixed"&&!element.contains(body))){_fixBackground();bgLeft(element);bgTop(element);_backgroundPosition(element)}}function _backgroundPosition(element){_tmp.src=element.currentStyle.backgroundImage.slice(5,-2);var parentElement=element.canHaveChildren?element:element.parentElement;parentElement.appendChild(_tmp);setOffsetLeft(element);setOffsetTop(element);parentElement.removeChild(_tmp)}function bgLeft(element){element.style.backgroundPositionX=element.currentStyle.backgroundPositionX;if(!_isFixed(element)){_setExpression(element,"backgroundPositionX","(parseInt(runtimeStyle.offsetLeft)+document."+$viewport+".scrollLeft)||0")}}eval(rotate(bgLeft));function setOffsetLeft(element){var propertyName=_isFixed(element)?"backgroundPositio
nX":"offsetLeft";element.runtimeStyle[propertyName]=getOffsetLeft(element,element.style.backgroundPositionX)-element.getBoundingClientRect().left-element.clientLeft+2}eval(rotate(setOffsetLeft));function getOffsetLeft(element,position){switch(position){case"left":case"top":return 0;case"right":case"bottom":return viewport.clientWidth-_tmp.offsetWidth;case"center":return(viewport.clientWidth-_tmp.offsetWidth)/2;default:if(PERCENT.test(position)){return parseInt((viewport.clientWidth-_tmp.offsetWidth)*parseFloat(position)/100)}_tmp.style.left=position;return _tmp.offsetLeft}}eval(rotate(getOffsetLeft));function _positionFixed(element){if(register(_positionFixed,element,isFixed(element))){setOverrideStyle(element,"position","absolute");setOverrideStyle(element,"left",element.currentStyle.left);setOverrideStyle(element,"top",element.currentStyle.top);_fixBackground();IE7.Layout.fixRight(element);_foregroundPosition(element)}}function _foregroundPosition(element,recalc){positionT
op(element,recalc);positionLeft(element,recalc,true);if(!element.runtimeStyle.autoLeft&&element.currentStyle.marginLeft=="auto"&&element.currentStyle.right!="auto"){var left=viewport.clientWidth-getPixelWidth(element,element.currentStyle.right)-getPixelWidth(element,element.runtimeStyle._left)-element.clientWidth;if(element.currentStyle.marginRight=="auto"){left=parseInt(left/2)}if(_isFixed(element.offsetParent)){element.runtimeStyle.pixelLeft+=left}else{element.runtimeStyle.shiftLeft=left}}clipWidth(element);clipHeight(element)}function clipWidth(element){var fixWidth=element.runtimeStyle.fixWidth;element.runtimeStyle.borderRightWidth="";element.runtimeStyle.width=fixWidth?getPixelWidth(element,fixWidth):"";if(element.currentStyle.width!="auto"){var rect=element.getBoundingClientRect();var width=element.offsetWidth-viewport.clientWidth+rect.left-2;if(width>=0){element.runtimeStyle.borderRightWidth="0px";width=Math.max(getPixelValue(element,element.currentStyle.width)-width,
0);setOverrideStyle(element,"width",width);return width}}}eval(rotate(clipWidth));function positionLeft(element,recalc){if(!recalc&&PERCENT.test(element.currentStyle.width)){element.runtimeStyle.fixWidth=element.currentStyle.width}if(element.runtimeStyle.fixWidth){element.runtimeStyle.width=getPixelWidth(element,element.runtimeStyle.fixWidth)}element.runtimeStyle.shiftLeft=0;element.runtimeStyle._left=element.currentStyle.left;element.runtimeStyle.autoLeft=element.currentStyle.right!="auto"&&element.currentStyle.left=="auto";element.runtimeStyle.left="";element.runtimeStyle.screenLeft=getScreenLeft(element);element.runtimeStyle.pixelLeft=element.runtimeStyle.screenLeft;if(!recalc&&!_isFixed(element.offsetParent)){_setExpression(element,"pixelLeft","runtimeStyle.screenLeft+runtimeStyle.shiftLeft+document."+$viewport+".scrollLeft")}}eval(rotate(positionLeft));function getScreenLeft(element){var screenLeft=element.offsetLeft,nested=1;if(element.runtimeStyle.autoLeft){screenLeft
=viewport.clientWidth-element.offsetWidth-getPixelWidth(element,element.currentStyle.right)}if(element.currentStyle.marginLeft!="auto"){screenLeft-=getPixelWidth(element,element.currentStyle.marginLeft)}while(element=element.offsetParent){if(element.currentStyle.position!="static"){nested=-1}screenLeft+=element.offsetLeft*nested}return screenLeft}eval(rotate(getScreenLeft));function getPixelWidth(element,value){return PERCENT.test(value)?parseInt(parseFloat(value)/100*viewport.clientWidth):getPixelValue(element,value)}eval(rotate(getPixelWidth));function _resize(){var elements=_backgroundFixed.elements;for(var i in elements){_backgroundPosition(elements[i])}elements=_positionFixed.elements;for(i in elements){_foregroundPosition(elements[i],true);_foregroundPosition(elements[i],true)}_timer=0}var _timer;addResize(function(){if(!_timer){_timer=setTimeout(_resize,0)}})};var WRAPPER_STYLE={backgroundColor:"transparent",backgroundImage:"none",backgroundPositionX:null,backgroundPo
sitionY:null,backgroundRepeat:null,borderTopWidth:0,borderRightWidth:0,borderBottomWidth:0,borderLeftStyle:"none",borderTopStyle:"none",borderRightStyle:"none",borderBottomStyle:"none",borderLeftWidth:0,height:null,marginTop:0,marginBottom:0,marginRight:0,marginLeft:0,width:"100%"};IE7.CSS.addRecalc("overflow","visible",function(element){if(element.parentNode.ie7_wrapped){return }if(IE7.Layout&&element.currentStyle["max-height"]!="auto"){IE7.Layout.maxHeight(element)}if(element.currentStyle.marginLeft=="auto"){element.style.marginLeft=0}if(element.currentStyle.marginRight=="auto"){element.style.marginRight=0}var wrapper=document.createElement(ANON);wrapper.ie7_wrapped=element;for(var propertyName in WRAPPER_STYLE){wrapper.style[propertyName]=element.currentStyle[propertyName];if(WRAPPER_STYLE[propertyName]!=null){element.runtimeStyle[propertyName]=WRAPPER_STYLE[propertyName]}}wrapper.style.display="block";wrapper.style.position="relative";element.runtimeStyle.position="absol
ute";element.parentNode.insertBefore(wrapper,element);wrapper.appendChild(element)});function ie7Quirks(){var FONT_SIZES="xx-small,x-small,small,medium,large,x-large,xx-large".split(",");for(var i=0;i<FONT_SIZES.length;i++){FONT_SIZES[FONT_SIZES[i]]=FONT_SIZES[i-1]||"0.67em"}IE7.CSS.addFix(/(font(-size)?\s*:\s*)([\w.-]+)/,function(match,label,size,value){return label+(FONT_SIZES[value]||value)});if(appVersion<6){var NEGATIVE=/^\-/,LENGTH=/(em|ex)$/i;var EM=/em$/i,EX=/ex$/i;getPixelValue=function(element,value){if(PIXEL.test(value)){return parseInt(value)||0}var scale=NEGATIVE.test(value)?-1:1;if(LENGTH.test(value)){scale*=getFontScale(element)}temp.style.width=(scale<0)?value.slice(1):value;body.appendChild(temp);value=scale*temp.offsetWidth;temp.removeNode();return parseInt(value)};var temp=createTempElement();function getFontScale(element){var scale=1;temp.style.fontFamily=element.currentStyle.fontFamily;temp.style.lineHeight=element.currentStyle.lineHeight;while(element!=
body){var fontSize=element.currentStyle["ie7-font-size"];if(fontSize){if(EM.test(fontSize)){scale*=parseFloat(fontSize)}else{if(PERCENT.test(fontSize)){scale*=(parseFloat(fontSize)/100)}else{if(EX.test(fontSize)){scale*=(parseFloat(fontSize)/2)}else{temp.style.fontSize=fontSize;return 1}}}}element=element.parentElement}return scale}IE7.CSS.addFix(/cursor\s*:\s*pointer/,"cursor:hand");IE7.CSS.addFix(/display\s*:\s*list-item/,"display:block")}function fixMargin(element){if(appVersion<5.5){IE7.Layout.boxSizing(element.parentElement)}var parent=element.parentElement;var margin=parent.offsetWidth-element.offsetWidth-getPaddingWidth(parent);var autoRight=(element.currentStyle["ie7-margin"]&&element.currentStyle.marginRight=="auto")||element.currentStyle["ie7-margin-right"]=="auto";switch(parent.currentStyle.textAlign){case"right":margin=autoRight?parseInt(margin/2):0;element.runtimeStyle.marginRight=margin+"px";break;case"center":if(autoRight){margin=0}default:if(autoRight){margin
/=2}element.runtimeStyle.marginLeft=parseInt(margin)+"px"}}function getPaddingWidth(element){return getPixelValue(element,element.currentStyle.paddingLeft)+getPixelValue(element,element.currentStyle.paddingRight)}IE7.CSS.addRecalc("margin(-left|-right)?","[^};]*auto",function(element){if(register(fixMargin,element,element.parentElement&&element.currentStyle.display=="block"&&element.currentStyle.marginLeft=="auto"&&element.currentStyle.position!="absolute")){fixMargin(element)}});addResize(function(){for(var i in fixMargin.elements){var element=fixMargin.elements[i];element.runtimeStyle.marginLeft=element.runtimeStyle.marginRight="";fixMargin(element)}})}IE7._isEmpty=function(element){element=element.firstChild;while(element){if(element.nodeType==3||(element.nodeType==1&&element.nodeName!="!")){return false}element=element.nextSibling}return true};IE7._isLang=function(element,code){while(element&&!element.getAttribute("lang")){element=element.parentNode}return element&&new R
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udoClass("active",function(element){var instance=arguments;IE7.CSS.addEventHandler(element,"onmousedown",function(){Active.register(instance)})});addEventHandler(document,"onmouseup",function(){var instances=Active.instances;for(var i in instances){Active.unregister(instances[i])}});var Checked=new DynamicPseudoClass("checked",function(element){if(typeof element.checked!="boolean"){return }var instance=arguments;IE7.CSS.addEventHandler(element,"onpropertychange",function(){if(event.propertyName=="checked"){if(element.checked){Checked.register(instance)}else{Checked.unregister(instance)}}});if(element.checked){Checked.register(instance)}});var Enabled=new DynamicPseudoClass("enabled",function(element){if(typeof element.disabled!="boolean"){return }var instance=arguments;IE7.CSS.addEventHandler(element,"onpropertychange",function(){if(event.propertyName=="disabled"){if(!element.isDisabled){Enabled.register(instance)}else{Enabled.unregister(instance)}}});if(!element.isDisabled)
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dEventHandler(document,"onpropertychange",function(){if(event.propertyName=="activeElement"){if(element.id&&element.id==location.hash.slice(1)){Target.register(instance)}else{Target.unregister(instance)}}});if(element.id&&element.id==location.hash.slice(1)){Target.register(instance)}});var ATTR=/^attr/;var URL=/^url\s*\(\s*([^)]*)\)$/;var POSITION_MAP={before0:"beforeBegin",before1:"afterBegin",after0:"afterEnd",after1:"beforeEnd"};var PseudoElement=IE7.PseudoElement=Rule.extend({constructor:function(selector,position,cssText){this.position=position;var content=cssText.match(PseudoElement.CONTENT),match,entity;if(content){content=content[1];match=content.split(/\s+/);for(var i=0;(entity=match[i]);i++){match[i]=ATTR.test(entity)?{attr:entity.slice(5,-1)}:(entity.charAt(0)=="'")?getString(entity):decode(entity)}content=match}this.content=content;this.base(selector,decode(cssText))},init:function(){this.match=cssQuery(this.selector);for(var i=0;i<this.match.length;i++){var runt
imeStyle=this.match[i].runtimeStyle;if(!runtimeStyle[this.position]){runtimeStyle[this.position]={cssText:""}}runtimeStyle[this.position].cssText+=";"+this.cssText;if(this.content!=null){runtimeStyle[this.position].content=this.content}}},create:function(target){var generated=target.runtimeStyle[this.position];if(generated){var content=[].concat(generated.content||"");for(var j=0;j<content.length;j++){if(typeof content[j]=="object"){content[j]=target.getAttribute(content[j].attr)}}content=content.join("");var url=content.match(URL);var cssText="overflow:hidden;"+generated.cssText.replace(/'/g,'"');if(target.currentStyle.styleFloat!="none"){}var position=POSITION_MAP[this.position+Number(target.canHaveChildren)];var id="ie7_pseudo"+PseudoElement.count++;target.insertAdjacentHTML(position,format(PseudoElement.ANON,this.className,id,cssText,url?"":content));if(url){var pseudoElement=document.getElementById(id);pseudoElement.src=getString(url[1]);addFilter(pseudoElement,"crop")}
target.runtimeStyle[this.position]=null}},recalc:function(){if(this.content==null){return }for(var i=0;i<this.match.length;i++){this.create(this.match[i])}},toString:function(){return"."+this.className+"{display:inline}"}},{CONTENT:/content\s*:\s*([^;]*)(;|$)/,ANON:"<ie7:! class='ie7_anon %1' id=%2 style='%3'>%4</ie7:!>",MATCH:/(.*):(before|after).*/,count:0});var UNSUCCESSFUL=/^(submit|reset|button)$/;IE7.HTML.addRecalc("button,input",function(button){if(button.tagName=="BUTTON"){var match=button.outerHTML.match(/ value="([^"]*)"/i);button.runtimeStyle.value=(match)?match[1]:""}if(button.type=="submit"){addEventHandler(button,"onclick",function(){button.runtimeStyle.clicked=true;setTimeout("document.all."+button.uniqueID+".runtimeStyle.clicked=false",1)})}});IE7.HTML.addRecalc("form",function(form){addEventHandler(form,"onsubmit",function(){for(var element,i=0;element=form[i];i++){if(UNSUCCESSFUL.test(element.type)&&!element.disabled&&!element.runtimeStyle.clicked){element.
disabled=true;setTimeout("document.all."+element.uniqueID+".disabled=false",1)}else{if(element.tagName=="BUTTON"&&element.type=="submit"){setTimeout("document.all."+element.uniqueID+".value='"+element.value+"'",1);element.value=element.runtimeStyle.value}}}})});IE7.HTML.addRecalc("img",function(img){if(img.alt&&!img.title){img.title=""}});IE7.CSS.addRecalc("border-spacing",NUMERIC,function(element){if(element.currentStyle.borderCollapse!="collapse"){element.cellSpacing=getPixelValue(element,element.currentStyle["border-spacing"])}});IE7.CSS.addRecalc("box-sizing","content-box",IE7.Layout.boxSizing);IE7.CSS.addRecalc("box-sizing","border-box",IE7.Layout.borderBox);IE7.CSS.addFix(/opacity\s*:\s*([\d.]+)/,function(match,value){return"zoom:1;filter:Alpha(opacity="+((value*100)||1)+")"});var IMAGE=/^image/i;IE7.HTML.addRecalc("object",function(element){if(IMAGE.test(element.type)){element.body.style.cssText="margin:0;padding:0;border:none;overflow:hidden";return element}});IE7.lo
aded=true;(function(){try{documentElement.doScroll("left")}catch(e){setTimeout(arguments.callee,1);return }try{eval(script.innerHTML)}catch(e){}PNG=new RegExp(rescape(typeof IE7_PNG_SUFFIX=="string"?IE7_PNG_SUFFIX:"-trans.png")+"$","i");body=document.body;viewport=quirksMode?body:documentElement;body.className+=" ie7_body";documentElement.className+=" ie7_html";if(quirksMode){ie7Quirks()}IE7.CSS.init();IE7.HTML.init();IE7.HTML.apply();IE7.CSS.apply();IE7.recalc()})()})();
\ No newline at end of file
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/cookie_set.js
--- a/static/scripts/packed/cookie_set.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/cookie_set.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
-function CookieSet(A){this.cookie_name=A;this.store=store={};q.each((q.cookie(A)||"").split("|"),function(C,B){store[B]=true})}CookieSet.prototype.add=function(A){this.store[A]=true;return this};CookieSet.prototype.remove=function(A){delete this.store[A];return this};CookieSet.prototype.removeAll=function(A){this.store={};return this};CookieSet.prototype.contains=function(A){return(A in this.store)};CookieSet.prototype.save=function(){t=[];for(key in this.store){if(key!=""){t.push(key)}}q.cookie(this.cookie_name,t.join("|"));return this}
\ No newline at end of file
+function CookieSet(A){this.cookie_name=A;this.store=store={};q.each((q.cookie(A)||"").split("|"),function(C,B){store[B]=true})}CookieSet.prototype.add=function(A){this.store[A]=true;return this};CookieSet.prototype.remove=function(A){delete this.store[A];return this};CookieSet.prototype.removeAll=function(A){this.store={};return this};CookieSet.prototype.contains=function(A){return(A in this.store)};CookieSet.prototype.save=function(){t=[];for(key in this.store){if(key!=""){t.push(key)}}q.cookie(this.cookie_name,t.join("|"));return this};
\ No newline at end of file
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/galaxy.base.js
--- a/static/scripts/packed/galaxy.base.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/galaxy.base.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
-jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))})})
\ No newline at end of file
+jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[@popupmenu]").each(function(){var B={};$(this).find("a").each(function(){var C=$(this).attr("confirm"),D=$(this).attr("href"),E=$(this).attr("target");B[$(this).text()]=function(){if(!C||confirm(C)){var F=window;if(E=="_parent"){F=window.parent}F.location=D}}});var A=$("#"+$(this).attr("popupmenu"));make_popupmenu(A,B);$(this).remove();A.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){var A=$("<div id='popup-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 15000;'></div>");if($.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}}function make_popupmenu(D,B){ensure_popup_helper();var A=$("<div class='popupmenu'></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=functi
on(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(F){var G=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.pageY-2,left:F.pageX-2});return false};$(D).click(E)};
\ No newline at end of file
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/galaxy.panels.js
--- a/static/scripts/packed/galaxy.panels.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/galaxy.panels.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
-var hidden_width=7;var border_tweak=9;var jq=jQuery;function ensure_dd_helper(){if(jq("#DD-helper").length==0){var A=jq("<div id='DD-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 9000;'></div>");if(jq.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}if(jq("#popup-helper").length==0){var A=jq("<div id='popup-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 15000;'></div>");if(jq.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}}function make_left_panel(E,A,B){var D=false;var C=null;resize=function(F){var G=F;if(F<0){F=0}jq(E).css("width",F);jq(B).css("left",G);jq(A).css("left",F+7);if(document.recalc){document.recalc()}};toggle=function(){if(D){jq(B).removeClass("hover");jq(B).animate({left:C},"fast");jq(E).css("left",-C).show().animate({left:0},"fast",function(){resize(C);jq(B).removeClass("hidden")});D
=false}else{C=jq(B).position().left;jq(A).css("left",hidden_width);if(document.recalc){document.recalc()}jq(B).removeClass("hover");jq(E).animate({left:-C},"fast");jq(B).animate({left:-1},"fast",function(){jq(this).addClass("hidden")});D=true}};jq(B).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(F,G){jq("#DD-helper").show()},stop:function(F,G){jq("#DD-helper").hide();return false},drag:function(F,G){x=G.position.left;x=Math.min(400,Math.max(100,x));if(D){jq(E).css("left",0);jq(B).removeClass("hidden");D=false}resize(x);G.position.left=x;G.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show()}function make_right_panel(A,E,G){var I=false;var F=false;var C=null;var D=function(J){jq(A).css("width",J);jq(E).css("right",J+9);jq(G).css("right",J).css("left","");if(document.recalc){document.recalc()}};var H=function(){if(I){jq(G).removeClass("hover");jq(G).anima
te({right:C},"fast");jq(A).css("right",-C).show().animate({right:0},"fast",function(){D(C);jq(G).removeClass("hidden")});I=false}else{C=jq(document).width()-jq(G).position().left-border_tweak;jq(E).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq(G).removeClass("hover");jq(A).animate({right:-C},"fast");jq(G).animate({right:-1},"fast",function(){jq(this).addClass("hidden")});I=true}F=false};var B=function(J){var K=jq(E).width()-(I?C:0);if(K<J){if(!I){H();F=true}}else{if(F){H();F=false}}};jq(G).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(J,K){jq("#DD-helper").show()},stop:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);D(w-x-border_tweak);jq("#DD-helper").hide();return false},click:function(){H()},drag:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(I){jq(A).css("right",0);jq(G).removeClass("hidde
n");I=false}D(w-x-border_tweak);K.position.left=x;K.position.top=$(this).data("draggable").originalPosition.top}}).find("div").show();return{handle_minwidth_hint:B}}function make_popupmenu(D,B){var A=$("<div class='popupmenu'><div class='popupmenu-top'><div class='popupmenu-top-inner'/></div></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)};
\ No newline at end of file
+var hidden_width=7;var border_tweak=9;var jq=jQuery;function ensure_dd_helper(){if(jq("#DD-helper").length==0){var A=jq("<div id='DD-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 9000;'></div>");if(jq.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}}function make_left_panel(E,A,B){var D=false;var C=null;resize=function(F){var G=F;if(F<0){F=0}jq(E).css("width",F);jq(B).css("left",G);jq(A).css("left",F+7);if(document.recalc){document.recalc()}};toggle=function(){if(D){jq(B).removeClass("hover");jq(B).animate({left:C},"fast");jq(E).css("left",-C).show().animate({left:0},"fast",function(){resize(C);jq(B).removeClass("hidden")});D=false}else{C=jq(B).position().left;jq(A).css("left",hidden_width);if(document.recalc){document.recalc()}jq(B).removeClass("hover");jq(E).animate({left:-C},"fast");jq(B).animate({left:-1},"fast",function(){jq(this).addClass("hidden")});D=true}};jq(B).hover(function(
){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(F,G){jq("#DD-helper").show()},stop:function(F,G){jq("#DD-helper").hide();return false},drag:function(F,G){x=G.position.left;x=Math.min(400,Math.max(100,x));if(D){jq(E).css("left",0);jq(B).removeClass("hidden");D=false}resize(x);G.position.left=x;G.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show()}function make_right_panel(A,E,G){var I=false;var F=false;var C=null;var D=function(J){jq(A).css("width",J);jq(E).css("right",J+9);jq(G).css("right",J).css("left","");if(document.recalc){document.recalc()}};var H=function(){if(I){jq(G).removeClass("hover");jq(G).animate({right:C},"fast");jq(A).css("right",-C).show().animate({right:0},"fast",function(){D(C);jq(G).removeClass("hidden")});I=false}else{C=jq(document).width()-jq(G).position().left-border_tweak;jq(E).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq
(G).removeClass("hover");jq(A).animate({right:-C},"fast");jq(G).animate({right:-1},"fast",function(){jq(this).addClass("hidden")});I=true}F=false};var B=function(J){var K=jq(E).width()-(I?C:0);if(K<J){if(!I){H();F=true}}else{if(F){H();F=false}}};jq(G).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(J,K){jq("#DD-helper").show()},stop:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);D(w-x-border_tweak);jq("#DD-helper").hide();return false},click:function(){H()},drag:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(I){jq(A).css("right",0);jq(G).removeClass("hidden");I=false}D(w-x-border_tweak);K.position.left=x;K.position.top=$(this).data("draggable").originalPosition.top}}).find("div").show();return{handle_minwidth_hint:B}}function make_popupmenu(D,B){var A=$("<div class='popupmenu'><div class='popupmenu-top'><div class='p
opupmenu-top-inner'/></div></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)};
\ No newline at end of file
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/galaxy.ui.scrollPanel.js
--- a/static/scripts/packed/galaxy.ui.scrollPanel.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/galaxy.ui.scrollPanel.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
-$.ui.plugin.add("draggable","scrollPanel",{drag:function(G,H){var J=$(this).data("draggable");clearTimeout(J.timeout);var B=H.options,D=J.element,A=B.panel,C=A.position(),I=A.width(),E=A.height();viewport=A.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),element_w=D.width(),element_h=D.height(),moved=false,close=5,nudge=23,p_min_x=-(I-viewport_w),p_min_y=-(E-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-C.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-C.top,max_vis_y=min_vis_y+viewport_h,mouse_x=H.position.left+J.offset.click.left;mouse_y=H.position.top+J.offset.click.top;if((C.left<p_max_x)&&(mouse_x-close<min_vis_x)){var K=Math.min(nudge,p_max_x-C.left);A.css("left",C.left+K);moved=true;J.offset.parent.left+=K;H.position.left-=K}if((!moved)&&(C.left>p_min_x)&&(mouse_x+close>max_vis_x)){var K=Math.min(nudge,C.left-p_min_x);A.css("left",C.left-K);moved=true;J.offset.parent.left-=K;H.position.left+=K}if((!moved)&&(C.top<p_max_y)&&(mouse_y-close<min_vis_y)){var
K=Math.min(nudge,p_max_y-C.top);A.css("top",C.top+K);var F=A.position().top-C.top;J.offset.parent.top+=F;H.position.top-=F;moved=true}if((!moved)&&(C.top>p_min_y)&&(mouse_y+close>max_vis_y)){var K=Math.min(nudge,C.top-p_min_x);A.css("top",(C.top-K)+"px");var F=C.top-A.position().top;J.offset.parent.top-=F;H.position.top+=F;moved=true}if(moved){$.ui.ddmanager.prepareOffsets(J,G)}H.position.left=Math.max(H.position.left,0);H.position.top=Math.max(H.position.top,0);H.position.left=Math.min(H.position.left,I-element_w);H.position.top=Math.min(H.position.top,E-element_h);if(moved){J.old_e=G;J.timeout=setTimeout(function(){J.mouseMove(G)},50)}}});
\ No newline at end of file
+$.ui.plugin.add("draggable","scrollPanel",{drag:function(G,H){var J=$(this).data("draggable");clearTimeout(J.timeout);var B=H.options,D=J.element,A=B.panel,C=A.position(),I=A.width(),E=A.height();viewport=A.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),element_w=D.width(),element_h=D.height(),moved=false,close=5,nudge=23,p_min_x=-(I-viewport_w),p_min_y=-(E-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-C.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-C.top,max_vis_y=min_vis_y+viewport_h,mouse_x=H.position.left+J.offset.click.left;mouse_y=H.position.top+J.offset.click.top;if((C.left<p_max_x)&&(mouse_x-close<min_vis_x)){var K=Math.min(nudge,p_max_x-C.left);A.css("left",C.left+K);moved=true;J.offset.parent.left+=K;H.position.left-=K}if((!moved)&&(C.left>p_min_x)&&(mouse_x+close>max_vis_x)){var K=Math.min(nudge,C.left-p_min_x);A.css("left",C.left-K);moved=true;J.offset.parent.left-=K;H.position.left+=K}if((!moved)&&(C.top<p_max_y)&&(mouse_y-close<min_vis_y)){var
K=Math.min(nudge,p_max_y-C.top);A.css("top",C.top+K);var F=A.position().top-C.top;J.offset.parent.top+=F;H.position.top-=F;moved=true}if((!moved)&&(C.top>p_min_y)&&(mouse_y+close>max_vis_y)){var K=Math.min(nudge,C.top-p_min_x);A.css("top",(C.top-K)+"px");var F=C.top-A.position().top;J.offset.parent.top-=F;H.position.top+=F;moved=true}H.position.left=Math.max(H.position.left,0);H.position.top=Math.max(H.position.top,0);H.position.left=Math.min(H.position.left,I-element_w);H.position.top=Math.min(H.position.top,E-element_h);if(moved){$.ui.ddmanager.prepareOffsets(J,G)}if(moved){J.old_e=G;J.timeout=setTimeout(function(){J.mouseMove(G)},50)}},stop:function(C,B){var A=$(this).data("draggable");clearTimeout(A.timeout)}});
\ No newline at end of file
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/galaxy.workflow_editor.canvas.js
--- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
-function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype.__proto__=Terminal.prototype;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype={__proto__:Terminal.prototype,can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}};function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototype
,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.style.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("h
eight",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=
E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).fadeOut("fast",function(){$(this).remove()})});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).fadeIn("fast")}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);E.terminal=new OutputTerm
inal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_error
s){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'/>").appendTo(A);$.each(D.data_inputs,function(G,F){t=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(t,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(t))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(D){var B=$(this.element),C=this;this.tool_state=D.state;this.form_html=D.form_html;this.tool_errors=D.tool_errors;if(this.tool_errors){B.a
ddClass("tool-node-error")}else{B.removeClass("tool-node-error")}var E=B.find("div.inputs");var A=$("<div class='inputs'/>");old=E.find("div.input-data-row");$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");C.enable_input_terminal(G,F.name,F.extensions);E.find("div[name="+F.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var I=this.terminal.connectors[0];if(I){G[0].terminal.connectors[0]=I;I.handle2=G[0].terminal}});$(this).remove()});A.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(G))});E.replaceWith(A);E.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_changed(this)},changed:function(){workflow.node
_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,function(E,D){var C=prebuild_node("tool",D.name,
D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectable'>"+F+"</div>");E.append(J);E.css("left
",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10,scrollSpeed:20,click:function(L,N){var M=$(this).data("draggable").element.get(0);(function(O){O.removeChild(M);O.appendChild(M)})(M.parentNode);workflow.activate_node
(C)},start:function(){workflow.activate_node(C);$(this).css("z-index","1000")},drag:function(){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(L,N){var M=$(this).data("draggable").element.get(0);(function(O){O.removeChild(M);O.appendChild(M)})(M.parentNode);$(this).css("z-index","100");$(this).find(".terminal").each(function(){this.terminal.redraw()})}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes};
\ No newline at end of file
+function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype.__proto__=Terminal.prototype;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype={__proto__:Terminal.prototype,can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}};function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototype
,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.style.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("h
eight",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=
E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).fadeOut("fast",function(){$(this).remove()})});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).fadeIn("fast")}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);E.terminal=new OutputTerm
inal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_error
s){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'/>").appendTo(A);$.each(D.data_inputs,function(G,F){t=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(t,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(t))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(D){var B=$(this.element),C=this;this.tool_state=D.tool_state;this.form_html=D.form_html;this.tool_errors=D.tool_errors;if(this.tool_errors
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diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/ie7-recalc.js
--- a/static/scripts/packed/ie7-recalc.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/ie7-recalc.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,2 +1,1 @@
-/* IE7/IE8.js - copyright 2004-2008, Dean Edwards */
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\ No newline at end of file
+(function(){if(!IE7.loaded){return }CLASSES=/\sie7_class\d+/g;IE7.CSS.extend({elements:{},handlers:[],reset:function(){this.removeEventHandlers();var elements=this.elements;for(var i in elements){elements[i].runtimeStyle.cssText=""}this.elements={};var elements=IE7.Rule.elements;for(var i in elements){with(elements[i]){className=className.replace(CLASSES,"")}}IE7.Rule.elements={}},reload:function(){this.rules=[];this.getInlineStyles();this.screen.load();if(this.print){this.print.load()}this.refresh();this.trash()},addRecalc:function(propertyName,test,handler,replacement){this.base(propertyName,test,function(element){handler(element);IE7.CSS.elements[element.uniqueID]=element},replacement)},recalc:function(){this.reset();this.base()},addEventHandler:function(element,type,handler){element.attachEvent(type,handler);this.handlers.push(arguments)},removeEventHandlers:function(){var handler;while(handler=this.handlers.pop()){handler[0].detachEvent(handler[1],handler[2])}},getInlin
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\ No newline at end of file
diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/jquery.cookie.js
--- a/static/scripts/packed/jquery.cookie.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/jquery.cookie.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
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\ No newline at end of file
+jQuery.cookie=function(B,I,L){if(typeof I!="undefined"){L=L||{};if(I===null){I="";L.expires=-1}var E="";if(L.expires&&(typeof L.expires=="number"||L.expires.toUTCString)){var F;if(typeof L.expires=="number"){F=new Date();F.setTime(F.getTime()+(L.expires*24*60*60*1000))}else{F=L.expires}E="; expires="+F.toUTCString()}var K=L.path?"; path="+L.path:"";var G=L.domain?"; domain="+L.domain:"";var A=L.secure?"; secure":"";document.cookie=[B,"=",encodeURIComponent(I),E,K,G,A].join("")}else{var D=null;if(document.cookie&&document.cookie!=""){var J=document.cookie.split(";");for(var H=0;H<J.length;H++){var C=jQuery.trim(J[H]);if(C.substring(0,B.length+1)==(B+"=")){D=decodeURIComponent(C.substring(B.length+1));break}}}return D}};
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diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/jquery.form.js
--- a/static/scripts/packed/jquery.form.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/jquery.form.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
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diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/jquery.hoverIntent.js
--- a/static/scripts/packed/jquery.hoverIntent.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/jquery.hoverIntent.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
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e",E);if(M.hoverIntent_s==1){M.hoverIntent_t=setTimeout(function(){G(N,M)},J.timeout)}}};return this.mouseover(B).mouseout(B)}})(jQuery)
\ No newline at end of file
+(function(A){A.fn.hoverIntent=function(I,H){var J={sensitivity:7,interval:100,timeout:0};J=A.extend(J,H?{over:I,out:H}:I);var L,K,F,D;var E=function(M){L=M.pageX;K=M.pageY};var C=function(N,M){M.hoverIntent_t=clearTimeout(M.hoverIntent_t);if((Math.abs(F-L)+Math.abs(D-K))<J.sensitivity){A(M).unbind("mousemove",E);M.hoverIntent_s=1;return J.over.apply(M,[N])}else{F=L;D=K;M.hoverIntent_t=setTimeout(function(){C(N,M)},J.interval)}};var G=function(N,M){M.hoverIntent_t=clearTimeout(M.hoverIntent_t);M.hoverIntent_s=0;return J.out.apply(M,[N])};var B=function(P){var O=(P.type=="mouseover"?P.fromElement:P.toElement)||P.relatedTarget;while(O&&O!=this){try{O=O.parentNode}catch(P){O=this}}if(O==this){return false}var N=A.extend({},P);var M=this;if(M.hoverIntent_t){M.hoverIntent_t=clearTimeout(M.hoverIntent_t)}if(P.type=="mouseover"){F=N.pageX;D=N.pageY;A(M).bind("mousemove",E);if(M.hoverIntent_s!=1){M.hoverIntent_t=setTimeout(function(){C(N,M)},J.interval)}}else{A(M).unbind("mousemov
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diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/jquery.json.js
--- a/static/scripts/packed/jquery.json.js Thu Aug 07 11:41:59 2008 -0400
+++ b/static/scripts/packed/jquery.json.js Thu Aug 07 19:28:42 2008 -0400
@@ -1,1 +1,1 @@
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\ No newline at end of file
1
0
07 Aug '08
details: http://www.bx.psu.edu/hg/galaxy/rev/95e3285790d1
changeset: 1467:95e3285790d1
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Thu Aug 07 11:41:59 2008 -0400
description:
Fix for dynamic select lists generated from contents of input file when no valid datasets exist in the history.
1 file(s) affected in this change:
lib/galaxy/tools/parameters/dynamic_options.py
diffs (11 lines):
diff -r 91c63a82359a -r 95e3285790d1 lib/galaxy/tools/parameters/dynamic_options.py
--- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Aug 04 10:20:23 2008 -0400
+++ b/lib/galaxy/tools/parameters/dynamic_options.py Thu Aug 07 11:41:59 2008 -0400
@@ -363,6 +363,7 @@
if self.dataset_ref_name:
dataset = other_values.get( self.dataset_ref_name, None )
assert dataset is not None, "Required dataset '%s' missing from input" % self.dataset_ref_name
+ if not dataset: return [] #no valid dataset in history
options = self.parse_file_fields( open( dataset.file_name ) )
else:
options = list( self.file_fields )
1
0
With Workflows enabled.
1
0
06 Aug '08
details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ…
changeset: 1460:837f8b7698c4
user: James Taylor <james(a)jamestaylor.org>
date: Thu Jul 31 17:55:41 2008 -0400
description:
Fix for preserving values of parameters after a repeat/conditional in
Tool.update_state. This should fix the problem reported by Dan with the
subject "Re: [galaxy-bugs] Galaxy tool error report from cathy(a)bx.psu.edu".
Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1461: Compensatory bug in conditional parameters that was revealed by previous
details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ…
changeset: 1461:6bbf70be8b03
user: James Taylor <james(a)jamestaylor.org>
date: Thu Jul 31 20:49:06 2008 -0400
description:
Compensatory bug in conditional parameters that was revealed by previous
commit.
Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1462: Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed.
details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ…
changeset: 1462:777d9bdfd7d3
user: greg
date: Fri Aug 01 14:25:42 2008 -0400
description:
Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed.
Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1463: Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params.
details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ…
changeset: 1463:66be239241bc
user: greg
date: Fri Aug 01 14:34:16 2008 -0400
description:
Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params.
Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1464: Fix for the creation of workflows from shared histories.
details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ…
changeset: 1464:c7acaa1bb88f
user: dan(a)scofield.bx.psu.edu
date: Fri Aug 01 15:05:54 2008 -0400
description:
Fix for the creation of workflows from shared histories.
Added a column 'copied_from_history_dataset_association' to history_dataset_association. This requires a db change.
Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1465: Remove a couple templates that I missed in the rollback.
details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ…
changeset: 1465:3b35cdf1689a
user: Nate Coraor <nate(a)bx.psu.edu>
date: Fri Aug 01 15:26:02 2008 -0400
description:
Remove a couple templates that I missed in the rollback.
Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1466: Better fix for gops command line parser, now properly handles no strand column.
details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ…
changeset: 1466:91c63a82359a
user: greg
date: Mon Aug 04 10:20:23 2008 -0400
description:
Better fix for gops command line parser, now properly handles no strand column.
diffs (371 lines):
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Mon Aug 04 10:20:23 2008 -0400
@@ -1,5 +1,5 @@
<tool id="CONVERTER_fastqsolexa_to_qual_0" name="Convert Fastqsolexa to Qual">
- <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 $input1.extension</command>
+ <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 ${input1.extension}</command>
<inputs>
<param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/>
</inputs>
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Aug 04 10:20:23 2008 -0400
@@ -1,7 +1,7 @@
<tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<!-- Used on the metadata edit page. -->
- <command interpreter="python">interval_to_bed_converter.py $output1 $input1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol</command>
+ <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command>
<inputs>
<page>
<param format="interval" name="input1" type="data" label="Choose intervals"/>
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
--- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Mon Aug 04 10:20:23 2008 -0400
@@ -1,6 +1,6 @@
<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
- <command interpreter="python">maf_to_interval_converter.py $output1 $input1 $input1_dbkey</command>
+ <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command>
<inputs>
<page>
<param format="maf" name="input1" type="data" label="Choose MAF file"/>
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/jobs/__init__.py Mon Aug 04 10:20:23 2008 -0400
@@ -400,11 +400,6 @@
else:
job.state = 'ok'
for dataset_assoc in job.output_datasets:
- if stderr:
- dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
- else:
- dataset_assoc.dataset.dataset.state = model.Dataset.states.OK
- dataset_assoc.dataset.dataset.flush()
for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running
dataset.blurb = 'done'
dataset.peek = 'no peek'
@@ -424,6 +419,11 @@
else:
dataset.blurb = "empty"
dataset.flush()
+ if stderr:
+ dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
+ else:
+ dataset_assoc.dataset.dataset.state = model.Dataset.states.OK
+ dataset_assoc.dataset.dataset.flush()
# Save stdout and stderr
if len( stdout ) > 32768:
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/model/__init__.py Mon Aug 04 10:20:23 2008 -0400
@@ -104,7 +104,7 @@
class HistoryDatasetAssociation( object ):
def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None,
dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None,
- parent_id=None, validation_errors=None, visible=True, create_dataset = False ):
+ parent_id=None, copied_from_history_dataset_association = None, validation_errors=None, visible=True, create_dataset = False ):
self.name = name or "Unnamed dataset"
self.id = id
self.hid = hid
@@ -125,6 +125,7 @@
self.dataset = dataset
self.parent_id = parent_id
self.validation_errors = validation_errors
+ self.copied_from_history_dataset_association = copied_from_history_dataset_association
@property
def ext( self ):
@@ -252,7 +253,7 @@
return self.datatype.get_converter_types( self, datatypes_registry)
def copy( self, copy_children = False, parent_id = None ):
- des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id )
+ des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self )
des.flush()
if copy_children:
for child in self.children:
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/model/mapping.py Mon Aug 04 10:20:23 2008 -0400
@@ -72,6 +72,7 @@
Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ),
Column( "hid", Integer ),
Column( "name", TrimmedString( 255 ) ),
Column( "info", TrimmedString( 255 ) ),
@@ -250,13 +251,17 @@
history=relation(
History,
primaryjoin=( History.table.c.id == HistoryDatasetAssociation.table.c.history_id ) ),
+ copied_to_history_dataset_associations=relation(
+ HistoryDatasetAssociation,
+ primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ),
+ backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) ),
implicitly_converted_datasets=relation(
ImplicitlyConvertedDatasetAssociation,
primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ),
children=relation(
HistoryDatasetAssociation,
primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ),
- backref=backref( "parent", remote_side=[HistoryDatasetAssociation.table.c.id] ) )
+ backref=backref( "parent", primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) )
) )
assign_mapper( context, Dataset, Dataset.table,
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/tools/__init__.py Mon Aug 04 10:20:23 2008 -0400
@@ -731,7 +731,7 @@
for i, rep_state in enumerate( group_state ):
rep_index = rep_state['__index__']
max_index = max( max_index, rep_index )
- prefix = "%s_%d|" % ( key, rep_index )
+ rep_prefix = "%s_%d|" % ( key, rep_index )
if group_old_errors:
rep_old_errors = group_old_errors[i]
else:
@@ -740,7 +740,7 @@
input.inputs,
rep_state,
incoming,
- prefix=prefix,
+ prefix=rep_prefix,
context=context,
update_only=update_only,
old_errors=rep_old_errors,
@@ -765,9 +765,9 @@
group_state = state[input.name]
group_old_errors = old_errors.get( input.name, {} )
old_current_case = group_state['__current_case__']
- prefix = "%s|" % ( key )
+ group_prefix = "%s|" % ( key )
# Deal with the 'test' element and see if it's value changed
- test_param_key = prefix + input.test_param.name
+ test_param_key = group_prefix + input.test_param.name
test_param_error = None
test_incoming = incoming.get( test_param_key, None )
if test_param_key not in incoming \
@@ -797,7 +797,7 @@
input.cases[current_case].inputs,
group_state,
incoming,
- prefix=prefix,
+ prefix=group_prefix,
context=context,
update_only=update_only,
old_errors=group_old_errors,
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/tools/util/galaxyops/__init__.py
--- a/lib/galaxy/tools/util/galaxyops/__init__.py Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/tools/util/galaxyops/__init__.py Mon Aug 04 10:20:23 2008 -0400
@@ -13,13 +13,18 @@
print >> sys.stderr, msg
sys.exit( 1 )
-# Default chrom, start, end, stran cols for a bed file
+# Default chrom, start, end, strand cols for a bed file
BED_DEFAULT_COLS = 0, 1, 2, 5
def parse_cols_arg( cols ):
"""Parse a columns command line argument into a four-tuple"""
if cols:
- return map( lambda x: int( x ) - 1, cols.split(",") )
+ # Handle case where no strand column included - in this case, cols
+ # looks something like 1,2,3,
+ if cols.endswith( ',' ):
+ cols += '0'
+ col_list = map( lambda x: int( x ) - 1, cols.split(",") )
+ return col_list
else:
return BED_DEFAULT_COLS
diff -r b301cae30997 -r 91c63a82359a lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py Wed Jul 30 17:15:40 2008 -0400
+++ b/lib/galaxy/web/controllers/workflow.py Mon Aug 04 10:20:23 2008 -0400
@@ -676,9 +676,16 @@
if dataset.state in ( 'new', 'running', 'queued' ):
warnings.add( "Some datasets still queued or running were ignored" )
continue
- if not dataset.creating_job_associations:
- jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
- for assoc in dataset.creating_job_associations:
+
+ #if this hda was copied from another, we need to find the job that created the origial hda
+ job_hda = dataset
+ while job_hda.copied_from_history_dataset_association:
+ job_hda = job_hda.copied_from_history_dataset_association
+
+ if not job_hda.creating_job_associations:
+ jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
+
+ for assoc in job_hda.creating_job_associations:
job = assoc.job
if job in jobs:
jobs[ job ].append( ( assoc.name, dataset ) )
diff -r b301cae30997 -r 91c63a82359a templates/history/permissions.mako
--- a/templates/history/permissions.mako Wed Jul 30 17:15:40 2008 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-<%inherit file="/base.mako"/>
-<%def name="title()">Change Default History Permissions</%def>
-
-%if trans.user:
- <div class="toolForm">
- <div class="toolFormTitle">Change Default History Permissions</div>
- <div class="toolFormBody">
- <form name="set_permissions" method="post">
- <div class="form-row">
- <% user_groups = [ assoc.group for assoc in trans.user.groups ] %>
- <% cur_groups = [ assoc.group for assoc in trans.get_history().default_groups ] %>
- <div style="float: left; width: 250px; margin-right: 10px;">
- <table>
- <tr><th>Group</th><th>In</th><th>Out</th></tr>
- %for group in user_groups:
- <tr><td>${group.name}</td><td><input type="radio" name="group_${group.id}" value="in"
- %if group in cur_groups:
- checked
- %endif
- ></td><td><input type="radio" name="group_${group.id}" value="out"
- %if group not in cur_groups:
- checked
- %endif
- ></td></tr>
- %endfor
- </table>
- </div>
-
- <div style="clear: both"></div>
-
- <div class="toolParamHelp" style="clear: both;">
- This will change the default permissions assigned to new datasets for your current history.
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="set_permissions" value="Save">
- </div>
- </form>
- </div>
- </div>
-%endif
\ No newline at end of file
diff -r b301cae30997 -r 91c63a82359a templates/tool_form.tmpl
--- a/templates/tool_form.tmpl Wed Jul 30 17:15:40 2008 -0400
+++ b/templates/tool_form.tmpl Mon Aug 04 10:20:23 2008 -0400
@@ -57,9 +57,9 @@
#set group_state = $tool_state[$input.name]
#set group_errors = $errors.get( $input.name, {} )
#set current_case = $group_state['__current_case__']
- #set prefix = $prefix + $input.name + "|"
- $row_for_param( $prefix, $input.test_param, $group_state, $group_errors, $context )
- $do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $prefix, $context )
+ #set group_prefix = $prefix + $input.name + "|"
+ $row_for_param( $group_prefix, $input.test_param, $group_state, $group_errors, $context )
+ $do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $group_prefix, $context )
#else
$row_for_param( $prefix, $input, $tool_state, $errors, $context )
#end if
diff -r b301cae30997 -r 91c63a82359a templates/user/permissions.mako
--- a/templates/user/permissions.mako Wed Jul 30 17:15:40 2008 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-<%inherit file="/base.mako"/>
-<%def name="title()">Change Default History Permissions</%def>
-
-%if trans.user:
- <div class="toolForm">
- <div class="toolFormTitle">Change Default Permissions for new Histories </div>
- <div class="toolFormBody">
- <form name="set_permissions" method="post">
- <div class="form-row">
- <% user_groups = [ assoc.group for assoc in trans.user.groups ] %>
- <% cur_groups = [ assoc.group for assoc in trans.user.default_groups ] %>
- <div style="float: left; width: 250px; margin-right: 10px;">
- <table>
- <tr><th>Group</th><th>In</th><th>Out</th></tr>
- %for group in user_groups:
- <tr><td>${group.name}</td><td><input type="radio" name="group_${group.id}" value="in"
- %if group in cur_groups:
- checked
- %endif
- ></td><td><input type="radio" name="group_${group.id}" value="out"
- %if group not in cur_groups:
- checked
- %endif
- ></td></tr>
- %endfor
- </table>
- </div>
-
- <div style="clear: both"></div>
-
- <div class="toolParamHelp" style="clear: both;">
- This will change the default permissions assigned to new datasets for new histories.
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="set_permissions" value="Save">
- </div>
- </form>
- </div>
- </div>
-%endif
\ No newline at end of file
diff -r b301cae30997 -r 91c63a82359a templates/workflow/editor_tool_form.mako
--- a/templates/workflow/editor_tool_form.mako Wed Jul 30 17:15:40 2008 -0400
+++ b/templates/workflow/editor_tool_form.mako Mon Aug 04 10:20:23 2008 -0400
@@ -23,10 +23,10 @@
%elif input.type == "conditional":
<% group_values = values[input.name] %>
<% current_case = group_values['__current_case__'] %>
- <% prefix = prefix + input.name + "|" %>
+ <% group_prefix = prefix + input.name + "|" %>
<% group_errors = errors.get( input.name, {} ) %>
- ${row_for_param( input.test_param, group_values[ input.test_param.name ], group_errors, prefix )}
- ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, prefix )}
+ ${row_for_param( input.test_param, group_values[ input.test_param.name ], group_errors, group_prefix )}
+ ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, group_prefix )}
%else:
${row_for_param( input, values[ input.name ], errors, prefix )}
%endif
diff -r b301cae30997 -r 91c63a82359a test-data/12.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/12.bed Mon Aug 04 10:20:23 2008 -0400
@@ -0,0 +1,10 @@
+chr1 147962192 147962580
+chr1 115468538 115468624
+chr1 115483024 115483277
+chr1 115484165 115484501
+chr1 115485764 115485980
+chr1 115486322 115486481
+chr1 115491298 115491487
+chr1 115468538 115468624
+chr1 115483024 115483277
+chr1 115484165 115484501
diff -r b301cae30997 -r 91c63a82359a test-data/gops_intersect_no_strand_out.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gops_intersect_no_strand_out.bed Mon Aug 04 10:20:23 2008 -0400
@@ -0,0 +1,1 @@
+chr1 147962192 147962580
diff -r b301cae30997 -r 91c63a82359a tools/new_operations/intersect.xml
--- a/tools/new_operations/intersect.xml Wed Jul 30 17:15:40 2008 -0400
+++ b/tools/new_operations/intersect.xml Mon Aug 04 10:20:23 2008 -0400
@@ -50,6 +50,13 @@
<param name="returntype" value="" />
<output name="output" file="gops_intersect_bigint_out.interval" />
</test>
+ <test>
+ <param name="input1" value="12.bed" ftype="bed" />
+ <param name="input2" value="1.bed" ftype="bed" />
+ <param name="min" value="1" />
+ <param name="returntype" value="" />
+ <output name="output" file="gops_intersect_no_strand_out.bed" />
+ </test>
</tests>
<help>
1
0
I cannot run cfrun from thumper with my account, so we'll have to wait
until it runs automatically...
1
0