January 2010 - galaxy-dev - lists.galaxyproject.org

Suggestion: heartbeat log - show only non sleeping threads
by Assaf Gordon 27 Jan '10

27 Jan '10

Hello all, While looking for possible slowness causes in my galaxy server, I found the heartbeat log to invaluable, but very frustrating to read: it contains everything that the active threads are doing - while most of them aren't relevant at all. I suggest the following patch, that adds a second heartbeat log which is easier to use. This second log has the following properties: 1. Only non-sleeping threads are reported. 2. If all threads are sleeping, the log simply says "All threads are sleeping." 3. For each non-sleeping thread, only the inner-most frame is printed (filename,line,function,text) - if the inner most frame comes from within the "/lib/galaxy" folder (so that deeper frames from eggs aren't printed). 4. for each non-seeping thread, shows a count of how many consecutive hearts-beats this thread is active - meaning the thread is either running for N heartbeats, or is very often waken up. This log makes it much easier to quickly pin-point what galaxy is doing, and then one can go back to the original heartbeat log and see the full stack trace. Example of the heartbeat.log.nonsleeping (showing that the "set_meta" in sequence.py is running for 6 heartbeats = 6x20 seconds = 2 minutes: ======================== ... ... Non-Sleeping threads at Thu Jan 7 23:27:28 2010: Thread 1101138256 <Thread(Thread-2, started)> non-sleeping for 4 heartbeat(s) File /lib/galaxy/datatypes/sequence.py:30 Function "set_meta" for line in file( dataset.file_name ): Non-Sleeping threads at Thu Jan 7 23:27:48 2010: Thread 1101138256 <Thread(Thread-2, started)> non-sleeping for 5 heartbeat(s) File /lib/galaxy/datatypes/sequence.py:30 Function "set_meta" for line in file( dataset.file_name ): Non-Sleeping threads at Thu Jan 7 23:28:08 2010: Thread 1101138256 <Thread(Thread-2, started)> non-sleeping for 6 heartbeat(s) File /lib/galaxy/datatypes/sequence.py:30 Function "set_meta" for line in file( dataset.file_name ): Non-Sleeping threads at Thu Jan 7 23:28:28 2010: All threads are sleeping. ... ... ... ======================== The patch is also available here: http://cancan.cshl.edu/labmembers/gordon/files/nonsleeping_heartbeat.patch Comments are welcomed, -gordon

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uploading files from local directory strangeness
by Chris Cole 27 Jan '10

27 Jan '10

Hi, I'm trying to implement the data upload from a directory as per here: http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles And all seems to be working, in that I can import the datasets into my current history. The problem is that I shouldn't be able to! I set the upload to not copy the files into Galaxy and then I deleted the softlinks and renamed the original files. However, I'm still able to import the files to my current history? How's that possible? I've checked that the files don't exist under <galaxy>/database/files/. Anyone have any suggestions? Thanks, Chris

2 4

Uploading file error
by /fox/ 27 Jan '10

27 Jan '10

Hi list, I'm new to galaxy and I've a problem, when I try to upload any file from my computer I get this error: /home/fox/galaxy-central/lib/galaxy/__init__.py:31: UserWarning: Module pkg_resources was already imported from /home/fox/galaxy-central/lib/pkg_resources.pyc, but /usr/lib64/python2.6/site-packages is being added to sys.path __import__( "pkg_resources" ).declare_namespace( __name__ ) /home/fox/galaxy-central/lib/galaxy/__init__.py:31: UserWarning: Module site was already imported from /usr/lib64/python2.6/site.pyc, but /usr/lib64/python2.6/site-packages is being added to sys.path __import__( "pkg_resources" ).declare_namespace( __name__ ) ...even if i try to upload the test data included in the program tree. I think that maybe there's a problem with my python configuration. Any hint? -- f. "E' in un giorno di pioggia che ti ho conosciuta e il vento dell'ovest rideva gentile..." (Modena City Ramblers) http://fox.noblogs.org/

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Re: [galaxy-dev] Storing Genomic Sequences
by Guruprasad Ananda 27 Jan '10

27 Jan '10

Hi Shaun, Please download hg19.2bit file from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/, and update your tool-data/alignseq.loc file with the following line: seq hg19 PATH_TO_hg19.2bit (tab-separated fields) This will then let the 'fetch sequences' tool to access hg19 sequences. Thanks for using Galaxy, Guru Galaxy team. > From: SHAUN WEBB <swebb1(a)staffmail.ed.ac.uk> > Date: January 27, 2010 9:50:23 AM EST > To: galaxy-dev(a)bx.psu.edu > Subject: [galaxy-dev] Storing Genomic Sequences > > > Hi, we would like to store the new hg19 sequence locally for use with galaxy tools (e.g Fetch Genomic Sequence). I was wondering which files were required to this and where they are located. > > Thanks > Shaun Webb > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev

1 0

Storing Genomic Sequences
by SHAUN WEBB 27 Jan '10

27 Jan '10

Hi, we would like to store the new hg19 sequence locally for use with galaxy tools (e.g Fetch Genomic Sequence). I was wondering which files were required to this and where they are located. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

[hg] galaxy 3279: Update tool_conf.xml.main and the tool conf fo...
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/69a04e6bd513 changeset: 3279:69a04e6bd513 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jan 27 08:51:23 2010 -0500 description: Update tool_conf.xml.main and the tool conf for eupathdb. diffstat: tool_conf.xml.main | 24 +++++++++++++----------- tools/data_source/eupathdb.xml | 2 +- 2 files changed, 14 insertions(+), 12 deletions(-) diffs (75 lines): diff -r e25fbd7cd958 -r 69a04e6bd513 tool_conf.xml.main --- a/tool_conf.xml.main Tue Jan 26 19:52:38 2010 -0500 +++ b/tool_conf.xml.main Wed Jan 27 08:51:23 2010 -0500 @@ -8,8 +8,6 @@ <tool file="data_source/biomart.xml" /> <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/flymine.xml" /> - <tool file="data_source/modmine.xml" /> - <tool file="data_source/ratmine.xml" /> <tool file="data_source/eupathdb.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> @@ -49,7 +47,6 @@ <tool file="maf/maf_to_fasta.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="filters/wiggle_to_simple.xml" /> </section> <section name="FASTA manipulation" id="fasta_manipulation"> <tool file="fasta_tools/fasta_compute_length.xml" /> @@ -98,7 +95,7 @@ <tool file="extract/phastOdds/phastOdds_tool.xml" /> </section> <section name="Operate on Genomic Intervals" id="bxops"> - <tool file="new_operations/intersect.xml" /> + <tool file="new_operations/intersect.xml" /> <tool file="new_operations/subtract.xml" /> <tool file="new_operations/merge.xml" /> <tool file="new_operations/concat.xml" /> @@ -277,16 +274,20 @@ <tool file="metag_tools/short_reads_figure_score.xml" /> <tool file="metag_tools/short_reads_trim_seq.xml" /> <label text="AB-SOLiD data" id="solid" /> - <tool file="next_gen_conversion/solid_to_fastq.xml" /> + <tool file="next_gen_conversion/solid2fastq.xml" /> <tool file="solid_tools/solid_qual_stats.xml" /> <tool file="solid_tools/solid_qual_boxplot.xml" /> </section> - <section name="NGS: Mapping" id="solexa_tools"> - <tool file="sr_mapping/bowtie_wrapper.xml" /> - <tool file="sr_mapping/bwa_wrapper.xml" /> -  - <tool file="metag_tools/megablast_wrapper.xml" /> - <tool file="metag_tools/megablast_xml_parser.xml" /> + <section name="NGS: Mapping" id="ngs_mapping"> + <label text="Illumina" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> + <label text="Roche-454" /> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <label text="AB-SOLiD" /> + <tool file="sr_mapping/bowtie_color_wrapper.xml" /> </section> <section name="NGS: SAM Tools" id="samtools"> <tool file="samtools/sam_bitwise_flag_filter.xml" /> @@ -297,4 +298,5 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> + </toolbox> diff -r e25fbd7cd958 -r 69a04e6bd513 tools/data_source/eupathdb.xml --- a/tools/data_source/eupathdb.xml Tue Jan 26 19:52:38 2010 -0500 +++ b/tools/data_source/eupathdb.xml Wed Jan 27 08:51:23 2010 -0500 @@ -6,7 +6,7 @@ <tool name="EuPathDB" id="eupathdb" tool_type="data_source"> <description>server</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post"> + <inputs action="http://eupathdb.org/eupathdb/queries_tools.jsp" check_values="false" method="post"> <display>go to EuPathDB server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" /> </inputs>

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[hg] galaxy 3278: Small changes to the list of pre-set options i...
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e25fbd7cd958 changeset: 3278:e25fbd7cd958 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Jan 26 19:52:38 2010 -0500 description: Small changes to the list of pre-set options in lastz diffstat: tools/sr_mapping/lastz_wrapper.xml | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (19 lines): diff -r 597a06d4921f -r e25fbd7cd958 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Tue Jan 26 19:42:00 2010 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Tue Jan 26 19:52:38 2010 -0500 @@ -52,13 +52,13 @@ </param> <when value="pre_set"> <param name="pre_set_options" type="select" label="Select mapping mode"> - <option value="yasra95short">Illumina-Solexa/AB-SOLiD 95% identity</option> - <option value="yasra85short">Illumina-Solexa/AB-SOLiD 85% identity</option> <option value="yasra98">Roche-454 98% identity</option> <option value="yasra95">Roche-454 95% identity</option> <option value="yasra90">Roche-454 90% identity</option> <option value="yasra85">Roche-454 85% identity</option> <option value="yasra75">Roche-454 75% identity</option> + <option value="yasra95short">Illumina 95% identity</option> + <option value="yasra85short">Illumina 85% identity</option> </param> </when> <when value="full">

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[hg] galaxy 3277: Fixing typos in bowtie wrappers
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/597a06d4921f changeset: 3277:597a06d4921f user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Jan 26 19:42:00 2010 -0500 description: Fixing typos in bowtie wrappers diffstat: tools/sr_mapping/bowtie_color_wrapper.xml | 2 +- tools/sr_mapping/bowtie_wrapper.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (24 lines): diff -r e95696a14e18 -r 597a06d4921f tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml Tue Jan 26 16:47:06 2010 -0500 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Tue Jan 26 19:42:00 2010 -0500 @@ -283,7 +283,7 @@ <option value="noTryHard">Do not try hard</option> <option value="doTryHard">Try hard</option> </param> - <param name="sValAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" /> + <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> <option value="noAllValAligns">Do not report all valid alignments</option> <option value="doAllValAligns">Report all valid alignments</option> diff -r e95696a14e18 -r 597a06d4921f tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Tue Jan 26 16:47:06 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Tue Jan 26 19:42:00 2010 -0500 @@ -277,7 +277,7 @@ <option value="noTryHard">Do not try hard</option> <option value="doTryHard">Try hard</option> </param> - <param name="sValAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" /> + <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> <option value="noAllValAligns">Do not report all valid alignments</option> <option value="doAllValAligns">Report all valid alignments</option>

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[hg] galaxy 3276: trackster: add jquery ui files
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e95696a14e18 changeset: 3276:e95696a14e18 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 26 16:47:06 2010 -0500 description: trackster: add jquery ui files diffstat: static/scripts/ui.core.js | 519 ++++++++++++++++++++ static/scripts/ui.sortable.js | 1019 +++++++++++++++++++++++++++++++++++++++++ templates/tracks/browser.mako | 1 - 3 files changed, 1538 insertions(+), 1 deletions(-) diffs (1557 lines): diff -r b74b3682e30a -r e95696a14e18 static/scripts/ui.core.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/ui.core.js Tue Jan 26 16:47:06 2010 -0500 @@ -0,0 +1,519 @@ +/* + * jQuery UI 1.7.2 + * + * Copyright (c) 2009 AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT (MIT-LICENSE.txt) + * and GPL (GPL-LICENSE.txt) licenses. + * + * http://docs.jquery.com/UI + */ +;jQuery.ui || (function($) { + +var _remove = $.fn.remove, + isFF2 = $.browser.mozilla && (parseFloat($.browser.version) < 1.9); + +//Helper functions and ui object +$.ui = { + version: "1.7.2", + + // $.ui.plugin is deprecated. Use the proxy pattern instead. + plugin: { + add: function(module, option, set) { + var proto = $.ui[module].prototype; + for(var i in set) { + proto.plugins[i] = proto.plugins[i] || []; + proto.plugins[i].push([option, set[i]]); + } + }, + call: function(instance, name, args) { + var set = instance.plugins[name]; + if(!set || !instance.element[0].parentNode) { return; } + + for (var i = 0; i < set.length; i++) { + if (instance.options[set[i][0]]) { + set[i][1].apply(instance.element, args); + } + } + } + }, + + contains: function(a, b) { + return document.compareDocumentPosition + ? a.compareDocumentPosition(b) & 16 + : a !== b && a.contains(b); + }, + + hasScroll: function(el, a) { + + //If overflow is hidden, the element might have extra content, but the user wants to hide it + if ($(el).css('overflow') == 'hidden') { return false; } + + var scroll = (a && a == 'left') ? 'scrollLeft' : 'scrollTop', + has = false; + + if (el[scroll] > 0) { return true; } + + // TODO: determine which cases actually cause this to happen + // if the element doesn't have the scroll set, see if it's possible to + // set the scroll + el[scroll] = 1; + has = (el[scroll] > 0); + el[scroll] = 0; + return has; + }, + + isOverAxis: function(x, reference, size) { + //Determines when x coordinate is over "b" element axis + return (x > reference) && (x < (reference + size)); + }, + + isOver: function(y, x, top, left, height, width) { + //Determines when x, y coordinates is over "b" element + return $.ui.isOverAxis(y, top, height) && $.ui.isOverAxis(x, left, width); + }, + + keyCode: { + BACKSPACE: 8, + CAPS_LOCK: 20, + COMMA: 188, + CONTROL: 17, + DELETE: 46, + DOWN: 40, + END: 35, + ENTER: 13, + ESCAPE: 27, + HOME: 36, + INSERT: 45, + LEFT: 37, + NUMPAD_ADD: 107, + NUMPAD_DECIMAL: 110, + NUMPAD_DIVIDE: 111, + NUMPAD_ENTER: 108, + NUMPAD_MULTIPLY: 106, + NUMPAD_SUBTRACT: 109, + PAGE_DOWN: 34, + PAGE_UP: 33, + PERIOD: 190, + RIGHT: 39, + SHIFT: 16, + SPACE: 32, + TAB: 9, + UP: 38 + } +}; + +// WAI-ARIA normalization +if (isFF2) { + var attr = $.attr, + removeAttr = $.fn.removeAttr, + ariaNS = "http://www.w3.org/2005/07/aaa", + ariaState = /^aria-/, + ariaRole = /^wairole:/; + + $.attr = function(elem, name, value) { + var set = value !== undefined; + + return (name == 'role' + ? (set + ? attr.call(this, elem, name, "wairole:" + value) + : (attr.apply(this, arguments) || "").replace(ariaRole, "")) + : (ariaState.test(name) + ? (set + ? elem.setAttributeNS(ariaNS, + name.replace(ariaState, "aaa:"), value) + : attr.call(this, elem, name.replace(ariaState, "aaa:"))) + : attr.apply(this, arguments))); + }; + + $.fn.removeAttr = function(name) { + return (ariaState.test(name) + ? this.each(function() { + this.removeAttributeNS(ariaNS, name.replace(ariaState, "")); + }) : removeAttr.call(this, name)); + }; +} + +//jQuery plugins +$.fn.extend({ + remove: function() { + // Safari has a native remove event which actually removes DOM elements, + // so we have to use triggerHandler instead of trigger (#3037). + $("*", this).add(this).each(function() { + $(this).triggerHandler("remove"); + }); + return _remove.apply(this, arguments ); + }, + + enableSelection: function() { + return this + .attr('unselectable', 'off') + .css('MozUserSelect', '') + .unbind('selectstart.ui'); + }, + + disableSelection: function() { + return this + .attr('unselectable', 'on') + .css('MozUserSelect', 'none') + .bind('selectstart.ui', function() { return false; }); + }, + + scrollParent: function() { + var scrollParent; + if(($.browser.msie && (/(static|relative)/).test(this.css('position'))) || (/absolute/).test(this.css('position'))) { + scrollParent = this.parents().filter(function() { + return (/(relative|absolute|fixed)/).test($.curCSS(this,'position',1)) && (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); + }).eq(0); + } else { + scrollParent = this.parents().filter(function() { + return (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); + }).eq(0); + } + + return (/fixed/).test(this.css('position')) || !scrollParent.length ? $(document) : scrollParent; + } +}); + + +//Additional selectors +$.extend($.expr[':'], { + data: function(elem, i, match) { + return !!$.data(elem, match[3]); + }, + + focusable: function(element) { + var nodeName = element.nodeName.toLowerCase(), + tabIndex = $.attr(element, 'tabindex'); + return (/input|select|textarea|button|object/.test(nodeName) + ? !element.disabled + : 'a' == nodeName || 'area' == nodeName + ? element.href || !isNaN(tabIndex) + : !isNaN(tabIndex)) + // the element and all of its ancestors must be visible + // the browser may report that the area is hidden + && !$(element)['area' == nodeName ? 'parents' : 'closest'](':hidden').length; + }, + + tabbable: function(element) { + var tabIndex = $.attr(element, 'tabindex'); + return (isNaN(tabIndex) || tabIndex >= 0) && $(element).is(':focusable'); + } +}); + + +// $.widget is a factory to create jQuery plugins +// taking some boilerplate code out of the plugin code +function getter(namespace, plugin, method, args) { + function getMethods(type) { + var methods = $[namespace][plugin][type] || []; + return (typeof methods == 'string' ? methods.split(/,?\s+/) : methods); + } + + var methods = getMethods('getter'); + if (args.length == 1 && typeof args[0] == 'string') { + methods = methods.concat(getMethods('getterSetter')); + } + return ($.inArray(method, methods) != -1); +} + +$.widget = function(name, prototype) { + var namespace = name.split(".")[0]; + name = name.split(".")[1]; + + // create plugin method + $.fn[name] = function(options) { + var isMethodCall = (typeof options == 'string'), + args = Array.prototype.slice.call(arguments, 1); + + // prevent calls to internal methods + if (isMethodCall && options.substring(0, 1) == '_') { + return this; + } + + // handle getter methods + if (isMethodCall && getter(namespace, name, options, args)) { + var instance = $.data(this[0], name); + return (instance ? instance[options].apply(instance, args) + : undefined); + } + + // handle initialization and non-getter methods + return this.each(function() { + var instance = $.data(this, name); + + // constructor + (!instance && !isMethodCall && + $.data(this, name, new $[namespace][name](this, options))._init()); + + // method call + (instance && isMethodCall && $.isFunction(instance[options]) && + instance[options].apply(instance, args)); + }); + }; + + // create widget constructor + $[namespace] = $[namespace] || {}; + $[namespace][name] = function(element, options) { + var self = this; + + this.namespace = namespace; + this.widgetName = name; + this.widgetEventPrefix = $[namespace][name].eventPrefix || name; + this.widgetBaseClass = namespace + '-' + name; + + this.options = $.extend({}, + $.widget.defaults, + $[namespace][name].defaults, + $.metadata && $.metadata.get(element)[name], + options); + + this.element = $(element) + .bind('setData.' + name, function(event, key, value) { + if (event.target == element) { + return self._setData(key, value); + } + }) + .bind('getData.' + name, function(event, key) { + if (event.target == element) { + return self._getData(key); + } + }) + .bind('remove', function() { + return self.destroy(); + }); + }; + + // add widget prototype + $[namespace][name].prototype = $.extend({}, $.widget.prototype, prototype); + + // TODO: merge getter and getterSetter properties from widget prototype + // and plugin prototype + $[namespace][name].getterSetter = 'option'; +}; + +$.widget.prototype = { + _init: function() {}, + destroy: function() { + this.element.removeData(this.widgetName) + .removeClass(this.widgetBaseClass + '-disabled' + ' ' + this.namespace + '-state-disabled') + .removeAttr('aria-disabled'); + }, + + option: function(key, value) { + var options = key, + self = this; + + if (typeof key == "string") { + if (value === undefined) { + return this._getData(key); + } + options = {}; + options[key] = value; + } + + $.each(options, function(key, value) { + self._setData(key, value); + }); + }, + _getData: function(key) { + return this.options[key]; + }, + _setData: function(key, value) { + this.options[key] = value; + + if (key == 'disabled') { + this.element + [value ? 'addClass' : 'removeClass']( + this.widgetBaseClass + '-disabled' + ' ' + + this.namespace + '-state-disabled') + .attr("aria-disabled", value); + } + }, + + enable: function() { + this._setData('disabled', false); + }, + disable: function() { + this._setData('disabled', true); + }, + + _trigger: function(type, event, data) { + var callback = this.options[type], + eventName = (type == this.widgetEventPrefix + ? type : this.widgetEventPrefix + type); + + event = $.Event(event); + event.type = eventName; + + // copy original event properties over to the new event + // this would happen if we could call $.event.fix instead of $.Event + // but we don't have a way to force an event to be fixed multiple times + if (event.originalEvent) { + for (var i = $.event.props.length, prop; i;) { + prop = $.event.props[--i]; + event[prop] = event.originalEvent[prop]; + } + } + + this.element.trigger(event, data); + + return !($.isFunction(callback) && callback.call(this.element[0], event, data) === false + || event.isDefaultPrevented()); + } +}; + +$.widget.defaults = { + disabled: false +}; + + +/** Mouse Interaction Plugin **/ + +$.ui.mouse = { + _mouseInit: function() { + var self = this; + + this.element + .bind('mousedown.'+this.widgetName, function(event) { + return self._mouseDown(event); + }) + .bind('click.'+this.widgetName, function(event) { + if(self._preventClickEvent) { + self._preventClickEvent = false; + event.stopImmediatePropagation(); + return false; + } + }); + + // Prevent text selection in IE + if ($.browser.msie) { + this._mouseUnselectable = this.element.attr('unselectable'); + this.element.attr('unselectable', 'on'); + } + + this.started = false; + }, + + // TODO: make sure destroying one instance of mouse doesn't mess with + // other instances of mouse + _mouseDestroy: function() { + this.element.unbind('.'+this.widgetName); + + // Restore text selection in IE + ($.browser.msie + && this.element.attr('unselectable', this._mouseUnselectable)); + }, + + _mouseDown: function(event) { + // don't let more than one widget handle mouseStart + // TODO: figure out why we have to use originalEvent + event.originalEvent = event.originalEvent || {}; + if (event.originalEvent.mouseHandled) { return; } + + // we may have missed mouseup (out of window) + (this._mouseStarted && this._mouseUp(event)); + + this._mouseDownEvent = event; + + var self = this, + btnIsLeft = (event.which == 1), + elIsCancel = (typeof this.options.cancel == "string" ? $(event.target).parents().add(event.target).filter(this.options.cancel).length : false); + if (!btnIsLeft || elIsCancel || !this._mouseCapture(event)) { + return true; + } + + this.mouseDelayMet = !this.options.delay; + if (!this.mouseDelayMet) { + this._mouseDelayTimer = setTimeout(function() { + self.mouseDelayMet = true; + }, this.options.delay); + } + + if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { + this._mouseStarted = (this._mouseStart(event) !== false); + if (!this._mouseStarted) { + event.preventDefault(); + return true; + } + } + + // these delegates are required to keep context + this._mouseMoveDelegate = function(event) { + return self._mouseMove(event); + }; + this._mouseUpDelegate = function(event) { + return self._mouseUp(event); + }; + $(document) + .bind('mousemove.'+this.widgetName, this._mouseMoveDelegate) + .bind('mouseup.'+this.widgetName, this._mouseUpDelegate); + + // preventDefault() is used to prevent the selection of text here - + // however, in Safari, this causes select boxes not to be selectable + // anymore, so this fix is needed + ($.browser.safari || event.preventDefault()); + + event.originalEvent.mouseHandled = true; + return true; + }, + + _mouseMove: function(event) { + // IE mouseup check - mouseup happened when mouse was out of window + if ($.browser.msie && !event.button) { + return this._mouseUp(event); + } + + if (this._mouseStarted) { + this._mouseDrag(event); + return event.preventDefault(); + } + + if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { + this._mouseStarted = + (this._mouseStart(this._mouseDownEvent, event) !== false); + (this._mouseStarted ? this._mouseDrag(event) : this._mouseUp(event)); + } + + return !this._mouseStarted; + }, + + _mouseUp: function(event) { + $(document) + .unbind('mousemove.'+this.widgetName, this._mouseMoveDelegate) + .unbind('mouseup.'+this.widgetName, this._mouseUpDelegate); + + if (this._mouseStarted) { + this._mouseStarted = false; + this._preventClickEvent = (event.target == this._mouseDownEvent.target); + this._mouseStop(event); + } + + return false; + }, + + _mouseDistanceMet: function(event) { + return (Math.max( + Math.abs(this._mouseDownEvent.pageX - event.pageX), + Math.abs(this._mouseDownEvent.pageY - event.pageY) + ) >= this.options.distance + ); + }, + + _mouseDelayMet: function(event) { + return this.mouseDelayMet; + }, + + // These are placeholder methods, to be overriden by extending plugin + _mouseStart: function(event) {}, + _mouseDrag: function(event) {}, + _mouseStop: function(event) {}, + _mouseCapture: function(event) { return true; } +}; + +$.ui.mouse.defaults = { + cancel: null, + distance: 1, + delay: 0 +}; + +})(jQuery); diff -r b74b3682e30a -r e95696a14e18 static/scripts/ui.sortable.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/ui.sortable.js Tue Jan 26 16:47:06 2010 -0500 @@ -0,0 +1,1019 @@ +/* + * jQuery UI Sortable 1.7.2 + * + * Copyright (c) 2009 AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT (MIT-LICENSE.txt) + * and GPL (GPL-LICENSE.txt) licenses. + * + * http://docs.jquery.com/UI/Sortables + * + * Depends: + * ui.core.js + */ +(function($) { + +$.widget("ui.sortable", $.extend({}, $.ui.mouse, { + _init: function() { + + var o = this.options; + this.containerCache = {}; + this.element.addClass("ui-sortable"); + + //Get the items + this.refresh(); + + //Let's determine if the items are floating + this.floating = this.items.length ? (/left|right/).test(this.items[0].item.css('float')) : false; + + //Let's determine the parent's offset + this.offset = this.element.offset(); + + //Initialize mouse events for interaction + this._mouseInit(); + + }, + + destroy: function() { + this.element + .removeClass("ui-sortable ui-sortable-disabled") + .removeData("sortable") + .unbind(".sortable"); + this._mouseDestroy(); + + for ( var i = this.items.length - 1; i >= 0; i-- ) + this.items[i].item.removeData("sortable-item"); + }, + + _mouseCapture: function(event, overrideHandle) { + + if (this.reverting) { + return false; + } + + if(this.options.disabled || this.options.type == 'static') return false; + + //We have to refresh the items data once first + this._refreshItems(event); + + //Find out if the clicked node (or one of its parents) is a actual item in this.items + var currentItem = null, self = this, nodes = $(event.target).parents().each(function() { + if($.data(this, 'sortable-item') == self) { + currentItem = $(this); + return false; + } + }); + if($.data(event.target, 'sortable-item') == self) currentItem = $(event.target); + + if(!currentItem) return false; + if(this.options.handle && !overrideHandle) { + var validHandle = false; + + $(this.options.handle, currentItem).find("*").andSelf().each(function() { if(this == event.target) validHandle = true; }); + if(!validHandle) return false; + } + + this.currentItem = currentItem; + this._removeCurrentsFromItems(); + return true; + + }, + + _mouseStart: function(event, overrideHandle, noActivation) { + + var o = this.options, self = this; + this.currentContainer = this; + + //We only need to call refreshPositions, because the refreshItems call has been moved to mouseCapture + this.refreshPositions(); + + //Create and append the visible helper + this.helper = this._createHelper(event); + + //Cache the helper size + this._cacheHelperProportions(); + + /* + * - Position generation - + * This block generates everything position related - it's the core of draggables. + */ + + //Cache the margins of the original element + this._cacheMargins(); + + //Get the next scrolling parent + this.scrollParent = this.helper.scrollParent(); + + //The element's absolute position on the page minus margins + this.offset = this.currentItem.offset(); + this.offset = { + top: this.offset.top - this.margins.top, + left: this.offset.left - this.margins.left + }; + + // Only after we got the offset, we can change the helper's position to absolute + // TODO: Still need to figure out a way to make relative sorting possible + this.helper.css("position", "absolute"); + this.cssPosition = this.helper.css("position"); + + $.extend(this.offset, { + click: { //Where the click happened, relative to the element + left: event.pageX - this.offset.left, + top: event.pageY - this.offset.top + }, + parent: this._getParentOffset(), + relative: this._getRelativeOffset() //This is a relative to absolute position minus the actual position calculation - only used for relative positioned helper + }); + + //Generate the original position + this.originalPosition = this._generatePosition(event); + this.originalPageX = event.pageX; + this.originalPageY = event.pageY; + + //Adjust the mouse offset relative to the helper if 'cursorAt' is supplied + if(o.cursorAt) + this._adjustOffsetFromHelper(o.cursorAt); + + //Cache the former DOM position + this.domPosition = { prev: this.currentItem.prev()[0], parent: this.currentItem.parent()[0] }; + + //If the helper is not the original, hide the original so it's not playing any role during the drag, won't cause anything bad this way + if(this.helper[0] != this.currentItem[0]) { + this.currentItem.hide(); + } + + //Create the placeholder + this._createPlaceholder(); + + //Set a containment if given in the options + if(o.containment) + this._setContainment(); + + if(o.cursor) { // cursor option + if ($('body').css("cursor")) this._storedCursor = $('body').css("cursor"); + $('body').css("cursor", o.cursor); + } + + if(o.opacity) { // opacity option + if (this.helper.css("opacity")) this._storedOpacity = this.helper.css("opacity"); + this.helper.css("opacity", o.opacity); + } + + if(o.zIndex) { // zIndex option + if (this.helper.css("zIndex")) this._storedZIndex = this.helper.css("zIndex"); + this.helper.css("zIndex", o.zIndex); + } + + //Prepare scrolling + if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') + this.overflowOffset = this.scrollParent.offset(); + + //Call callbacks + this._trigger("start", event, this._uiHash()); + + //Recache the helper size + if(!this._preserveHelperProportions) + this._cacheHelperProportions(); + + + //Post 'activate' events to possible containers + if(!noActivation) { + for (var i = this.containers.length - 1; i >= 0; i--) { this.containers[i]._trigger("activate", event, self._uiHash(this)); } + } + + //Prepare possible droppables + if($.ui.ddmanager) + $.ui.ddmanager.current = this; + + if ($.ui.ddmanager && !o.dropBehaviour) + $.ui.ddmanager.prepareOffsets(this, event); + + this.dragging = true; + + this.helper.addClass("ui-sortable-helper"); + this._mouseDrag(event); //Execute the drag once - this causes the helper not to be visible before getting its correct position + return true; + + }, + + _mouseDrag: function(event) { + + //Compute the helpers position + this.position = this._generatePosition(event); + this.positionAbs = this._convertPositionTo("absolute"); + + if (!this.lastPositionAbs) { + this.lastPositionAbs = this.positionAbs; + } + + //Do scrolling + if(this.options.scroll) { + var o = this.options, scrolled = false; + if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') { + + if((this.overflowOffset.top + this.scrollParent[0].offsetHeight) - event.pageY < o.scrollSensitivity) + this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop + o.scrollSpeed; + else if(event.pageY - this.overflowOffset.top < o.scrollSensitivity) + this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop - o.scrollSpeed; + + if((this.overflowOffset.left + this.scrollParent[0].offsetWidth) - event.pageX < o.scrollSensitivity) + this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft + o.scrollSpeed; + else if(event.pageX - this.overflowOffset.left < o.scrollSensitivity) + this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft - o.scrollSpeed; + + } else { + + if(event.pageY - $(document).scrollTop() < o.scrollSensitivity) + scrolled = $(document).scrollTop($(document).scrollTop() - o.scrollSpeed); + else if($(window).height() - (event.pageY - $(document).scrollTop()) < o.scrollSensitivity) + scrolled = $(document).scrollTop($(document).scrollTop() + o.scrollSpeed); + + if(event.pageX - $(document).scrollLeft() < o.scrollSensitivity) + scrolled = $(document).scrollLeft($(document).scrollLeft() - o.scrollSpeed); + else if($(window).width() - (event.pageX - $(document).scrollLeft()) < o.scrollSensitivity) + scrolled = $(document).scrollLeft($(document).scrollLeft() + o.scrollSpeed); + + } + + if(scrolled !== false && $.ui.ddmanager && !o.dropBehaviour) + $.ui.ddmanager.prepareOffsets(this, event); + } + + //Regenerate the absolute position used for position checks + this.positionAbs = this._convertPositionTo("absolute"); + + //Set the helper position + if(!this.options.axis || this.options.axis != "y") this.helper[0].style.left = this.position.left+'px'; + if(!this.options.axis || this.options.axis != "x") this.helper[0].style.top = this.position.top+'px'; + + //Rearrange + for (var i = this.items.length - 1; i >= 0; i--) { + + //Cache variables and intersection, continue if no intersection + var item = this.items[i], itemElement = item.item[0], intersection = this._intersectsWithPointer(item); + if (!intersection) continue; + + if(itemElement != this.currentItem[0] //cannot intersect with itself + && this.placeholder[intersection == 1 ? "next" : "prev"]()[0] != itemElement //no useless actions that have been done before + && !$.ui.contains(this.placeholder[0], itemElement) //no action if the item moved is the parent of the item checked + && (this.options.type == 'semi-dynamic' ? !$.ui.contains(this.element[0], itemElement) : true) + ) { + + this.direction = intersection == 1 ? "down" : "up"; + + if (this.options.tolerance == "pointer" || this._intersectsWithSides(item)) { + this._rearrange(event, item); + } else { + break; + } + + this._trigger("change", event, this._uiHash()); + break; + } + } + + //Post events to containers + this._contactContainers(event); + + //Interconnect with droppables + if($.ui.ddmanager) $.ui.ddmanager.drag(this, event); + + //Call callbacks + this._trigger('sort', event, this._uiHash()); + + this.lastPositionAbs = this.positionAbs; + return false; + + }, + + _mouseStop: function(event, noPropagation) { + + if(!event) return; + + //If we are using droppables, inform the manager about the drop + if ($.ui.ddmanager && !this.options.dropBehaviour) + $.ui.ddmanager.drop(this, event); + + if(this.options.revert) { + var self = this; + var cur = self.placeholder.offset(); + + self.reverting = true; + + $(this.helper).animate({ + left: cur.left - this.offset.parent.left - self.margins.left + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollLeft), + top: cur.top - this.offset.parent.top - self.margins.top + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollTop) + }, parseInt(this.options.revert, 10) || 500, function() { + self._clear(event); + }); + } else { + this._clear(event, noPropagation); + } + + return false; + + }, + + cancel: function() { + + var self = this; + + if(this.dragging) { + + this._mouseUp(); + + if(this.options.helper == "original") + this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); + else + this.currentItem.show(); + + //Post deactivating events to containers + for (var i = this.containers.length - 1; i >= 0; i--){ + this.containers[i]._trigger("deactivate", null, self._uiHash(this)); + if(this.containers[i].containerCache.over) { + this.containers[i]._trigger("out", null, self._uiHash(this)); + this.containers[i].containerCache.over = 0; + } + } + + } + + //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! + if(this.placeholder[0].parentNode) this.placeholder[0].parentNode.removeChild(this.placeholder[0]); + if(this.options.helper != "original" && this.helper && this.helper[0].parentNode) this.helper.remove(); + + $.extend(this, { + helper: null, + dragging: false, + reverting: false, + _noFinalSort: null + }); + + if(this.domPosition.prev) { + $(this.domPosition.prev).after(this.currentItem); + } else { + $(this.domPosition.parent).prepend(this.currentItem); + } + + return true; + + }, + + serialize: function(o) { + + var items = this._getItemsAsjQuery(o && o.connected); + var str = []; o = o || {}; + + $(items).each(function() { + var res = ($(o.item || this).attr(o.attribute || 'id') || '').match(o.expression || (/(.+)[-=_](.+)/)); + if(res) str.push((o.key || res[1]+'[]')+'='+(o.key && o.expression ? res[1] : res[2])); + }); + + return str.join('&'); + + }, + + toArray: function(o) { + + var items = this._getItemsAsjQuery(o && o.connected); + var ret = []; o = o || {}; + + items.each(function() { ret.push($(o.item || this).attr(o.attribute || 'id') || ''); }); + return ret; + + }, + + /* Be careful with the following core functions */ + _intersectsWith: function(item) { + + var x1 = this.positionAbs.left, + x2 = x1 + this.helperProportions.width, + y1 = this.positionAbs.top, + y2 = y1 + this.helperProportions.height; + + var l = item.left, + r = l + item.width, + t = item.top, + b = t + item.height; + + var dyClick = this.offset.click.top, + dxClick = this.offset.click.left; + + var isOverElement = (y1 + dyClick) > t && (y1 + dyClick) < b && (x1 + dxClick) > l && (x1 + dxClick) < r; + + if( this.options.tolerance == "pointer" + || this.options.forcePointerForContainers + || (this.options.tolerance != "pointer" && this.helperProportions[this.floating ? 'width' : 'height'] > item[this.floating ? 'width' : 'height']) + ) { + return isOverElement; + } else { + + return (l < x1 + (this.helperProportions.width / 2) // Right Half + && x2 - (this.helperProportions.width / 2) < r // Left Half + && t < y1 + (this.helperProportions.height / 2) // Bottom Half + && y2 - (this.helperProportions.height / 2) < b ); // Top Half + + } + }, + + _intersectsWithPointer: function(item) { + + var isOverElementHeight = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top, item.height), + isOverElementWidth = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left, item.width), + isOverElement = isOverElementHeight && isOverElementWidth, + verticalDirection = this._getDragVerticalDirection(), + horizontalDirection = this._getDragHorizontalDirection(); + + if (!isOverElement) + return false; + + return this.floating ? + ( ((horizontalDirection && horizontalDirection == "right") || verticalDirection == "down") ? 2 : 1 ) + : ( verticalDirection && (verticalDirection == "down" ? 2 : 1) ); + + }, + + _intersectsWithSides: function(item) { + + var isOverBottomHalf = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top + (item.height/2), item.height), + isOverRightHalf = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left + (item.width/2), item.width), + verticalDirection = this._getDragVerticalDirection(), + horizontalDirection = this._getDragHorizontalDirection(); + + if (this.floating && horizontalDirection) { + return ((horizontalDirection == "right" && isOverRightHalf) || (horizontalDirection == "left" && !isOverRightHalf)); + } else { + return verticalDirection && ((verticalDirection == "down" && isOverBottomHalf) || (verticalDirection == "up" && !isOverBottomHalf)); + } + + }, + + _getDragVerticalDirection: function() { + var delta = this.positionAbs.top - this.lastPositionAbs.top; + return delta != 0 && (delta > 0 ? "down" : "up"); + }, + + _getDragHorizontalDirection: function() { + var delta = this.positionAbs.left - this.lastPositionAbs.left; + return delta != 0 && (delta > 0 ? "right" : "left"); + }, + + refresh: function(event) { + this._refreshItems(event); + this.refreshPositions(); + }, + + _connectWith: function() { + var options = this.options; + return options.connectWith.constructor == String + ? [options.connectWith] + : options.connectWith; + }, + + _getItemsAsjQuery: function(connected) { + + var self = this; + var items = []; + var queries = []; + var connectWith = this._connectWith(); + + if(connectWith && connected) { + for (var i = connectWith.length - 1; i >= 0; i--){ + var cur = $(connectWith[i]); + for (var j = cur.length - 1; j >= 0; j--){ + var inst = $.data(cur[j], 'sortable'); + if(inst && inst != this && !inst.options.disabled) { + queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element) : $(inst.options.items, inst.element).not(".ui-sortable-helper"), inst]); + } + }; + }; + } + + queries.push([$.isFunction(this.options.items) ? this.options.items.call(this.element, null, { options: this.options, item: this.currentItem }) : $(this.options.items, this.element).not(".ui-sortable-helper"), this]); + + for (var i = queries.length - 1; i >= 0; i--){ + queries[i][0].each(function() { + items.push(this); + }); + }; + + return $(items); + + }, + + _removeCurrentsFromItems: function() { + + var list = this.currentItem.find(":data(sortable-item)"); + + for (var i=0; i < this.items.length; i++) { + + for (var j=0; j < list.length; j++) { + if(list[j] == this.items[i].item[0]) + this.items.splice(i,1); + }; + + }; + + }, + + _refreshItems: function(event) { + + this.items = []; + this.containers = [this]; + var items = this.items; + var self = this; + var queries = [[$.isFunction(this.options.items) ? this.options.items.call(this.element[0], event, { item: this.currentItem }) : $(this.options.items, this.element), this]]; + var connectWith = this._connectWith(); + + if(connectWith) { + for (var i = connectWith.length - 1; i >= 0; i--){ + var cur = $(connectWith[i]); + for (var j = cur.length - 1; j >= 0; j--){ + var inst = $.data(cur[j], 'sortable'); + if(inst && inst != this && !inst.options.disabled) { + queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element[0], event, { item: this.currentItem }) : $(inst.options.items, inst.element), inst]); + this.containers.push(inst); + } + }; + }; + } + + for (var i = queries.length - 1; i >= 0; i--) { + var targetData = queries[i][1]; + var _queries = queries[i][0]; + + for (var j=0, queriesLength = _queries.length; j < queriesLength; j++) { + var item = $(_queries[j]); + + item.data('sortable-item', targetData); // Data for target checking (mouse manager) + + items.push({ + item: item, + instance: targetData, + width: 0, height: 0, + left: 0, top: 0 + }); + }; + }; + + }, + + refreshPositions: function(fast) { + + //This has to be redone because due to the item being moved out/into the offsetParent, the offsetParent's position will change + if(this.offsetParent && this.helper) { + this.offset.parent = this._getParentOffset(); + } + + for (var i = this.items.length - 1; i >= 0; i--){ + var item = this.items[i]; + + //We ignore calculating positions of all connected containers when we're not over them + if(item.instance != this.currentContainer && this.currentContainer && item.item[0] != this.currentItem[0]) + continue; + + var t = this.options.toleranceElement ? $(this.options.toleranceElement, item.item) : item.item; + + if (!fast) { + item.width = t.outerWidth(); + item.height = t.outerHeight(); + } + + var p = t.offset(); + item.left = p.left; + item.top = p.top; + }; + + if(this.options.custom && this.options.custom.refreshContainers) { + this.options.custom.refreshContainers.call(this); + } else { + for (var i = this.containers.length - 1; i >= 0; i--){ + var p = this.containers[i].element.offset(); + this.containers[i].containerCache.left = p.left; + this.containers[i].containerCache.top = p.top; + this.containers[i].containerCache.width = this.containers[i].element.outerWidth(); + this.containers[i].containerCache.height = this.containers[i].element.outerHeight(); + }; + } + + }, + + _createPlaceholder: function(that) { + + var self = that || this, o = self.options; + + if(!o.placeholder || o.placeholder.constructor == String) { + var className = o.placeholder; + o.placeholder = { + element: function() { + + var el = $(document.createElement(self.currentItem[0].nodeName)) + .addClass(className || self.currentItem[0].className+" ui-sortable-placeholder") + .removeClass("ui-sortable-helper")[0]; + + if(!className) + el.style.visibility = "hidden"; + + return el; + }, + update: function(container, p) { + + // 1. If a className is set as 'placeholder option, we don't force sizes - the class is responsible for that + // 2. The option 'forcePlaceholderSize can be enabled to force it even if a class name is specified + if(className && !o.forcePlaceholderSize) return; + + //If the element doesn't have a actual height by itself (without styles coming from a stylesheet), it receives the inline height from the dragged item + if(!p.height()) { p.height(self.currentItem.innerHeight() - parseInt(self.currentItem.css('paddingTop')||0, 10) - parseInt(self.currentItem.css('paddingBottom')||0, 10)); }; + if(!p.width()) { p.width(self.currentItem.innerWidth() - parseInt(self.currentItem.css('paddingLeft')||0, 10) - parseInt(self.currentItem.css('paddingRight')||0, 10)); }; + } + }; + } + + //Create the placeholder + self.placeholder = $(o.placeholder.element.call(self.element, self.currentItem)); + + //Append it after the actual current item + self.currentItem.after(self.placeholder); + + //Update the size of the placeholder (TODO: Logic to fuzzy, see line 316/317) + o.placeholder.update(self, self.placeholder); + + }, + + _contactContainers: function(event) { + for (var i = this.containers.length - 1; i >= 0; i--){ + + if(this._intersectsWith(this.containers[i].containerCache)) { + if(!this.containers[i].containerCache.over) { + + if(this.currentContainer != this.containers[i]) { + + //When entering a new container, we will find the item with the least distance and append our item near it + var dist = 10000; var itemWithLeastDistance = null; var base = this.positionAbs[this.containers[i].floating ? 'left' : 'top']; + for (var j = this.items.length - 1; j >= 0; j--) { + if(!$.ui.contains(this.containers[i].element[0], this.items[j].item[0])) continue; + var cur = this.items[j][this.containers[i].floating ? 'left' : 'top']; + if(Math.abs(cur - base) < dist) { + dist = Math.abs(cur - base); itemWithLeastDistance = this.items[j]; + } + } + + if(!itemWithLeastDistance && !this.options.dropOnEmpty) //Check if dropOnEmpty is enabled + continue; + + this.currentContainer = this.containers[i]; + itemWithLeastDistance ? this._rearrange(event, itemWithLeastDistance, null, true) : this._rearrange(event, null, this.containers[i].element, true); + this._trigger("change", event, this._uiHash()); + this.containers[i]._trigger("change", event, this._uiHash(this)); + + //Update the placeholder + this.options.placeholder.update(this.currentContainer, this.placeholder); + + } + + this.containers[i]._trigger("over", event, this._uiHash(this)); + this.containers[i].containerCache.over = 1; + } + } else { + if(this.containers[i].containerCache.over) { + this.containers[i]._trigger("out", event, this._uiHash(this)); + this.containers[i].containerCache.over = 0; + } + } + + }; + }, + + _createHelper: function(event) { + + var o = this.options; + var helper = $.isFunction(o.helper) ? $(o.helper.apply(this.element[0], [event, this.currentItem])) : (o.helper == 'clone' ? this.currentItem.clone() : this.currentItem); + + if(!helper.parents('body').length) //Add the helper to the DOM if that didn't happen already + $(o.appendTo != 'parent' ? o.appendTo : this.currentItem[0].parentNode)[0].appendChild(helper[0]); + + if(helper[0] == this.currentItem[0]) + this._storedCSS = { width: this.currentItem[0].style.width, height: this.currentItem[0].style.height, position: this.currentItem.css("position"), top: this.currentItem.css("top"), left: this.currentItem.css("left") }; + + if(helper[0].style.width == '' || o.forceHelperSize) helper.width(this.currentItem.width()); + if(helper[0].style.height == '' || o.forceHelperSize) helper.height(this.currentItem.height()); + + return helper; + + }, + + _adjustOffsetFromHelper: function(obj) { + if(obj.left != undefined) this.offset.click.left = obj.left + this.margins.left; + if(obj.right != undefined) this.offset.click.left = this.helperProportions.width - obj.right + this.margins.left; + if(obj.top != undefined) this.offset.click.top = obj.top + this.margins.top; + if(obj.bottom != undefined) this.offset.click.top = this.helperProportions.height - obj.bottom + this.margins.top; + }, + + _getParentOffset: function() { + + + //Get the offsetParent and cache its position + this.offsetParent = this.helper.offsetParent(); + var po = this.offsetParent.offset(); + + // This is a special case where we need to modify a offset calculated on start, since the following happened: + // 1. The position of the helper is absolute, so it's position is calculated based on the next positioned parent + // 2. The actual offset parent is a child of the scroll parent, and the scroll parent isn't the document, which means that + // the scroll is included in the initial calculation of the offset of the parent, and never recalculated upon drag + if(this.cssPosition == 'absolute' && this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) { + po.left += this.scrollParent.scrollLeft(); + po.top += this.scrollParent.scrollTop(); + } + + if((this.offsetParent[0] == document.body) //This needs to be actually done for all browsers, since pageX/pageY includes this information + || (this.offsetParent[0].tagName && this.offsetParent[0].tagName.toLowerCase() == 'html' && $.browser.msie)) //Ugly IE fix + po = { top: 0, left: 0 }; + + return { + top: po.top + (parseInt(this.offsetParent.css("borderTopWidth"),10) || 0), + left: po.left + (parseInt(this.offsetParent.css("borderLeftWidth"),10) || 0) + }; + + }, + + _getRelativeOffset: function() { + + if(this.cssPosition == "relative") { + var p = this.currentItem.position(); + return { + top: p.top - (parseInt(this.helper.css("top"),10) || 0) + this.scrollParent.scrollTop(), + left: p.left - (parseInt(this.helper.css("left"),10) || 0) + this.scrollParent.scrollLeft() + }; + } else { + return { top: 0, left: 0 }; + } + + }, + + _cacheMargins: function() { + this.margins = { + left: (parseInt(this.currentItem.css("marginLeft"),10) || 0), + top: (parseInt(this.currentItem.css("marginTop"),10) || 0) + }; + }, + + _cacheHelperProportions: function() { + this.helperProportions = { + width: this.helper.outerWidth(), + height: this.helper.outerHeight() + }; + }, + + _setContainment: function() { + + var o = this.options; + if(o.containment == 'parent') o.containment = this.helper[0].parentNode; + if(o.containment == 'document' || o.containment == 'window') this.containment = [ + 0 - this.offset.relative.left - this.offset.parent.left, + 0 - this.offset.relative.top - this.offset.parent.top, + $(o.containment == 'document' ? document : window).width() - this.helperProportions.width - this.margins.left, + ($(o.containment == 'document' ? document : window).height() || document.body.parentNode.scrollHeight) - this.helperProportions.height - this.margins.top + ]; + + if(!(/^(document|window|parent)$/).test(o.containment)) { + var ce = $(o.containment)[0]; + var co = $(o.containment).offset(); + var over = ($(ce).css("overflow") != 'hidden'); + + this.containment = [ + co.left + (parseInt($(ce).css("borderLeftWidth"),10) || 0) + (parseInt($(ce).css("paddingLeft"),10) || 0) - this.margins.left, + co.top + (parseInt($(ce).css("borderTopWidth"),10) || 0) + (parseInt($(ce).css("paddingTop"),10) || 0) - this.margins.top, + co.left+(over ? Math.max(ce.scrollWidth,ce.offsetWidth) : ce.offsetWidth) - (parseInt($(ce).css("borderLeftWidth"),10) || 0) - (parseInt($(ce).css("paddingRight"),10) || 0) - this.helperProportions.width - this.margins.left, + co.top+(over ? Math.max(ce.scrollHeight,ce.offsetHeight) : ce.offsetHeight) - (parseInt($(ce).css("borderTopWidth"),10) || 0) - (parseInt($(ce).css("paddingBottom"),10) || 0) - this.helperProportions.height - this.margins.top + ]; + } + + }, + + _convertPositionTo: function(d, pos) { + + if(!pos) pos = this.position; + var mod = d == "absolute" ? 1 : -1; + var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); + + return { + top: ( + pos.top // The absolute mouse position + + this.offset.relative.top * mod // Only for relative positioned nodes: Relative offset from element to offset parent + + this.offset.parent.top * mod // The offsetParent's offset without borders (offset + border) + - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) ) * mod) + ), + left: ( + pos.left // The absolute mouse position + + this.offset.relative.left * mod // Only for relative positioned nodes: Relative offset from element to offset parent + + this.offset.parent.left * mod // The offsetParent's offset without borders (offset + border) + - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() ) * mod) + ) + }; + + }, + + _generatePosition: function(event) { + + var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); + + // This is another very weird special case that only happens for relative elements: + // 1. If the css position is relative + // 2. and the scroll parent is the document or similar to the offset parent + // we have to refresh the relative offset during the scroll so there are no jumps + if(this.cssPosition == 'relative' && !(this.scrollParent[0] != document && this.scrollParent[0] != this.offsetParent[0])) { + this.offset.relative = this._getRelativeOffset(); + } + + var pageX = event.pageX; + var pageY = event.pageY; + + /* + * - Position constraining - + * Constrain the position to a mix of grid, containment. + */ + + if(this.originalPosition) { //If we are not dragging yet, we won't check for options + + if(this.containment) { + if(event.pageX - this.offset.click.left < this.containment[0]) pageX = this.containment[0] + this.offset.click.left; + if(event.pageY - this.offset.click.top < this.containment[1]) pageY = this.containment[1] + this.offset.click.top; + if(event.pageX - this.offset.click.left > this.containment[2]) pageX = this.containment[2] + this.offset.click.left; + if(event.pageY - this.offset.click.top > this.containment[3]) pageY = this.containment[3] + this.offset.click.top; + } + + if(o.grid) { + var top = this.originalPageY + Math.round((pageY - this.originalPageY) / o.grid[1]) * o.grid[1]; + pageY = this.containment ? (!(top - this.offset.click.top < this.containment[1] || top - this.offset.click.top > this.containment[3]) ? top : (!(top - this.offset.click.top < this.containment[1]) ? top - o.grid[1] : top + o.grid[1])) : top; + + var left = this.originalPageX + Math.round((pageX - this.originalPageX) / o.grid[0]) * o.grid[0]; + pageX = this.containment ? (!(left - this.offset.click.left < this.containment[0] || left - this.offset.click.left > this.containment[2]) ? left : (!(left - this.offset.click.left < this.containment[0]) ? left - o.grid[0] : left + o.grid[0])) : left; + } + + } + + return { + top: ( + pageY // The absolute mouse position + - this.offset.click.top // Click offset (relative to the element) + - this.offset.relative.top // Only for relative positioned nodes: Relative offset from element to offset parent + - this.offset.parent.top // The offsetParent's offset without borders (offset + border) + + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) )) + ), + left: ( + pageX // The absolute mouse position + - this.offset.click.left // Click offset (relative to the element) + - this.offset.relative.left // Only for relative positioned nodes: Relative offset from element to offset parent + - this.offset.parent.left // The offsetParent's offset without borders (offset + border) + + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() )) + ) + }; + + }, + + _rearrange: function(event, i, a, hardRefresh) { + + a ? a[0].appendChild(this.placeholder[0]) : i.item[0].parentNode.insertBefore(this.placeholder[0], (this.direction == 'down' ? i.item[0] : i.item[0].nextSibling)); + + //Various things done here to improve the performance: + // 1. we create a setTimeout, that calls refreshPositions + // 2. on the instance, we have a counter variable, that get's higher after every append + // 3. on the local scope, we copy the counter variable, and check in the timeout, if it's still the same + // 4. this lets only the last addition to the timeout stack through + this.counter = this.counter ? ++this.counter : 1; + var self = this, counter = this.counter; + + window.setTimeout(function() { + if(counter == self.counter) self.refreshPositions(!hardRefresh); //Precompute after each DOM insertion, NOT on mousemove + },0); + + }, + + _clear: function(event, noPropagation) { + + this.reverting = false; + // We delay all events that have to be triggered to after the point where the placeholder has been removed and + // everything else normalized again + var delayedTriggers = [], self = this; + + // We first have to update the dom position of the actual currentItem + // Note: don't do it if the current item is already removed (by a user), or it gets reappended (see #4088) + if(!this._noFinalSort && this.currentItem[0].parentNode) this.placeholder.before(this.currentItem); + this._noFinalSort = null; + + if(this.helper[0] == this.currentItem[0]) { + for(var i in this._storedCSS) { + if(this._storedCSS[i] == 'auto' || this._storedCSS[i] == 'static') this._storedCSS[i] = ''; + } + this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); + } else { + this.currentItem.show(); + } + + if(this.fromOutside && !noPropagation) delayedTriggers.push(function(event) { this._trigger("receive", event, this._uiHash(this.fromOutside)); }); + if((this.fromOutside || this.domPosition.prev != this.currentItem.prev().not(".ui-sortable-helper")[0] || this.domPosition.parent != this.currentItem.parent()[0]) && !noPropagation) delayedTriggers.push(function(event) { this._trigger("update", event, this._uiHash()); }); //Trigger update callback if the DOM position has changed + if(!$.ui.contains(this.element[0], this.currentItem[0])) { //Node was moved out of the current element + if(!noPropagation) delayedTriggers.push(function(event) { this._trigger("remove", event, this._uiHash()); }); + for (var i = this.containers.length - 1; i >= 0; i--){ + if($.ui.contains(this.containers[i].element[0], this.currentItem[0]) && !noPropagation) { + delayedTriggers.push((function(c) { return function(event) { c._trigger("receive", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + delayedTriggers.push((function(c) { return function(event) { c._trigger("update", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + } + }; + }; + + //Post events to containers + for (var i = this.containers.length - 1; i >= 0; i--){ + if(!noPropagation) delayedTriggers.push((function(c) { return function(event) { c._trigger("deactivate", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + if(this.containers[i].containerCache.over) { + delayedTriggers.push((function(c) { return function(event) { c._trigger("out", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + this.containers[i].containerCache.over = 0; + } + } + + //Do what was originally in plugins + if(this._storedCursor) $('body').css("cursor", this._storedCursor); //Reset cursor + if(this._storedOpacity) this.helper.css("opacity", this._storedOpacity); //Reset cursor + if(this._storedZIndex) this.helper.css("zIndex", this._storedZIndex == 'auto' ? '' : this._storedZIndex); //Reset z-index + + this.dragging = false; + if(this.cancelHelperRemoval) { + if(!noPropagation) { + this._trigger("beforeStop", event, this._uiHash()); + for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events + this._trigger("stop", event, this._uiHash()); + } + return false; + } + + if(!noPropagation) this._trigger("beforeStop", event, this._uiHash()); + + //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! + this.placeholder[0].parentNode.removeChild(this.placeholder[0]); + + if(this.helper[0] != this.currentItem[0]) this.helper.remove(); this.helper = null; + + if(!noPropagation) { + for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events + this._trigger("stop", event, this._uiHash()); + } + + this.fromOutside = false; + return true; + + }, + + _trigger: function() { + if ($.widget.prototype._trigger.apply(this, arguments) === false) { + this.cancel(); + } + }, + + _uiHash: function(inst) { + var self = inst || this; + return { + helper: self.helper, + placeholder: self.placeholder || $([]), + position: self.position, + absolutePosition: self.positionAbs, //deprecated + offset: self.positionAbs, + item: self.currentItem, + sender: inst ? inst.element : null + }; + } + +})); + +$.extend($.ui.sortable, { + getter: "serialize toArray", + version: "1.7.2", + eventPrefix: "sort", + defaults: { + appendTo: "parent", + axis: false, + cancel: ":input,option", + connectWith: false, + containment: false, + cursor: 'auto', + cursorAt: false, + delay: 0, + distance: 1, + dropOnEmpty: true, + forcePlaceholderSize: false, + forceHelperSize: false, + grid: false, + handle: false, + helper: "original", + items: '> *', + opacity: false, + placeholder: false, + revert: false, + scroll: true, + scrollSensitivity: 20, + scrollSpeed: 20, + scope: "default", + tolerance: "intersect", + zIndex: 1000 + } +}); + +})(jQuery); diff -r b74b3682e30a -r e95696a14e18 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Jan 26 16:43:58 2010 -0500 +++ b/templates/tracks/browser.mako Tue Jan 26 16:47:06 2010 -0500 @@ -14,7 +14,6 @@ ${h.css( "history" )} <link rel="stylesheet" type="text/css" href="${h.url_for('/static/trackster.css')}" /> -<link rel="stylesheet" type="text/css" href="${h.url_for('/static/ui.theme.css')}" /> <style type="text/css"> ul#sortable-ul { list-style: none;

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[hg] galaxy 3275: trackster: lighter intron colors
by Greg Von Kuster 27 Jan '10

27 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b74b3682e30a changeset: 3275:b74b3682e30a user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 26 16:43:58 2010 -0500 description: trackster: lighter intron colors diffstat: static/images/visualization/strand_left.png | 0 static/images/visualization/strand_right.png | 0 2 files changed, 0 insertions(+), 0 deletions(-) diffs (4 lines): diff -r c8ef8611841d -r b74b3682e30a static/images/visualization/strand_left.png Binary file static/images/visualization/strand_left.png has changed diff -r c8ef8611841d -r b74b3682e30a static/images/visualization/strand_right.png Binary file static/images/visualization/strand_right.png has changed

1 0