09 Feb '10
details: http://www.bx.psu.edu/hg/galaxy/rev/aa81684b9275
changeset: 3352:aa81684b9275
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Mon Feb 08 09:03:07 2010 -0500
description:
Bug fixes to slug editing, tooltips, and click-to-edit elements.
diffstat:
lib/galaxy/web/controllers/history.py | 2 +-
lib/galaxy/web/controllers/page.py | 2 +-
lib/galaxy/web/controllers/workflow.py | 2 +-
static/june_2007_style/base.css.tmpl | 6 +++---
static/june_2007_style/blue/base.css | 4 ++--
static/scripts/autocomplete_tagging.js | 9 +++++++--
static/scripts/galaxy.base.js | 7 +++++++
static/scripts/packed/autocomplete_tagging.js | 2 +-
static/scripts/packed/galaxy.base.js | 2 +-
static/scripts/packed/trackster.js | 2 +-
templates/root/history.mako | 6 +++---
templates/sharing_base.mako | 2 +-
templates/tagging_common.mako | 26 ++++++++++++--------------
13 files changed, 41 insertions(+), 31 deletions(-)
diffs (246 lines):
diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Fri Feb 05 23:03:03 2010 -0500
+++ b/lib/galaxy/web/controllers/history.py Mon Feb 08 09:03:07 2010 -0500
@@ -405,7 +405,7 @@
if history:
history.slug = new_slug
trans.sa_session.flush()
- return
+ return history.slug
@web.expose
def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ):
diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/page.py
--- a/lib/galaxy/web/controllers/page.py Fri Feb 05 23:03:03 2010 -0500
+++ b/lib/galaxy/web/controllers/page.py Mon Feb 08 09:03:07 2010 -0500
@@ -547,7 +547,7 @@
if page:
page.slug = new_slug
trans.sa_session.flush()
- return
+ return page.slug
@web.expose
@web.json
diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py Fri Feb 05 23:03:03 2010 -0500
+++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:03:07 2010 -0500
@@ -389,7 +389,7 @@
if stored:
stored.slug = new_slug
trans.sa_session.flush()
- return
+ return stored.slug
@web.expose
@web.json
diff -r 60308825b252 -r aa81684b9275 static/june_2007_style/base.css.tmpl
--- a/static/june_2007_style/base.css.tmpl Fri Feb 05 23:03:03 2010 -0500
+++ b/static/june_2007_style/base.css.tmpl Mon Feb 08 09:03:07 2010 -0500
@@ -718,7 +718,7 @@
cursor: pointer;
}
-.tooltip span.tip {
+span.tip {
display: none
}
@@ -726,8 +726,8 @@
font-size: 90%;
display: block;
position: absolute;
- right:2em;top:-1.75em;
- width: inherit;
+ left:2em;
+ bottom:1.75em;
background-color: black;
color: white;
text-align: center;
diff -r 60308825b252 -r aa81684b9275 static/june_2007_style/blue/base.css
--- a/static/june_2007_style/blue/base.css Fri Feb 05 23:03:03 2010 -0500
+++ b/static/june_2007_style/blue/base.css Mon Feb 08 09:03:07 2010 -0500
@@ -120,7 +120,7 @@
.icon-button.tag{background-image:url(/static/images/tag-label.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;}
.icon-button.annotate{background-image:url(/static/images/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;}
.tooltip {position: relative; cursor: pointer}
-.tooltip span.tip{display: none;}
-.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;right:2em;top:-1.75em; width: inherit; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;}
+span.tip{display: none;}
+.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;left:3em;bottom:1.75em; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;}
.editable-text{cursor:pointer}
.editable-text:hover{background-image:url();background-repeat:no-repeat;background-position:right}
\ No newline at end of file
diff -r 60308825b252 -r aa81684b9275 static/scripts/autocomplete_tagging.js
--- a/static/scripts/autocomplete_tagging.js Fri Feb 05 23:03:03 2010 -0500
+++ b/static/scripts/autocomplete_tagging.js Mon Feb 08 09:03:07 2010 -0500
@@ -259,6 +259,7 @@
add_tag_button.show();
tag_input_field.hide();
tag_area.removeClass("active-tag-area");
+ tag_area.addClass("tooltip");
}
else
{
@@ -273,11 +274,14 @@
// If a "delete image" object was pressed and area is inactive, do nothing.
if ($(e.target).hasClass("delete-tag-img") && !is_active)
- return false;
+ return false;
// If a "tag name" object was pressed and area is inactive, do nothing.
if ($(e.target).hasClass("tag-name") && !is_active)
- return false;
+ return false;
+
+ // Remove tooltip.
+ $(this).removeClass("tooltip");
// Hide add tag button, show tag_input field. Change background to show
// area is active.
@@ -299,6 +303,7 @@
{
tag_area.blur();
$(document).unbind("click", handle_document_click);
+ $(this).addClass("tooltip");
}
};
// TODO: we should attach the click handler to all frames in order to capture
diff -r 60308825b252 -r aa81684b9275 static/scripts/galaxy.base.js
--- a/static/scripts/galaxy.base.js Fri Feb 05 23:03:03 2010 -0500
+++ b/static/scripts/galaxy.base.js Mon Feb 08 09:03:07 2010 -0500
@@ -229,9 +229,13 @@
t.blur( function() {
$(this).remove();
$("#" + text_elt_id).show();
+ if (has_tooltip)
+ tooltip_elt.addClass("tooltip");
if (on_finish != null)
on_finish(t);
});
+ var has_tooltip = $(this).hasClass("tooltip");
+ var tooltip_elt = $(this);
t.keyup( function( e ) {
if ( e.keyCode == 27 ) {
// Escape key
@@ -268,6 +272,9 @@
t.insertAfter( $("#" + text_elt_id) );
t.focus();
t.select();
+
+ // Remove tooltip so that it doesn't show during editing.
+ $(this).removeClass("tooltip");
return false;
});
diff -r 60308825b252 -r aa81684b9275 static/scripts/packed/autocomplete_tagging.js
--- a/static/scripts/packed/autocomplete_tagging.js Fri Feb 05 23:03:03 2010 -0500
+++ b/static/scripts/packed/autocomplete_tagging.js Mon Feb 08 09:03:07 2010 -0500
@@ -1,1 +1,1 @@
-function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(q){var g={get_toggle_link_text_fn:function(r){var t="";var s=o(r);if(s!=0){t=s+(s!=0?" Tags":" Tag")}else{t="Add tags"}return t},tag_click_fn:function(r,s){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var e=jQuery.extend(g,q);var o=function(r){if(r.length){return r.length}var s=0;for(element in r){s++}return s};var h=$(this);var c=h.find(".tag-area");var f=h.find(".toggle-link");var b=h.find(".tag-input");var n=h.find(".add-tag-button");f.click(function(){var r=(c.css("display")=="none");var s;if(r){s=function(){var t=$(this).find(".tag-button").length;if(t==0){c.click()}}}else{s=func
tion(){c.blur()}}c.slideToggle("fast",s);return $(this)});if(e.editable){b.hide()}b.keyup(function(w){if(w.keyCode==27){$(this).trigger("blur")}else{if((w.keyCode==13)||(w.keyCode==188)||(w.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((w.keyCode==188)||(w.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var t=k(new_value);var s=c.children(".tag-button");if(s.length!=0){var x=s.slice(s.length-1);x.after(t)}else{c.prepend(t)}var r=new_value.split(":");e.tags[r[0]]=r[1];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);var v=$(this);$.ajax({url:e.ajax_add_tag_url,data:{new_tag:new_value},error:function(){t.remove();delete e.tags[r[0]];var y=e.get_toggle_link_te
xt_fn(e.tags);f.text(y);alert("Add tag failed")},success:function(){v.flushCache()}});return false}}});var j=function(t,s,r,v,u){tag_name_and_value=v.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var i={selectFirst:false,formatItem:j,autoFill:false,highlight:false};b.autocomplete(e.ajax_autocomplete_tag_url,i);h.find(".delete-tag-img").each(function(){d($(this))});init_tag_click_function($(this),e.tag_click_fn);n.click(function(){$(this).hide();c.click();return false});if(e.editable){c.blur(function(r){p=o(e.tags);if(p!=0){n.show();b.hide();c.removeClass("active-tag-area")}else{}});c.click(function(t){var s=$(this).hasClass("active-tag-area");if($(t.target).hasClass("delete-tag-img")&&!s){return false}if($(t.target).hasClass("tag-name")&&!s){return false}$(this).addClass("active-tag-area");n.hide();b.show();b.focus();var r=function(v){var u=c.attr("id");if(($(v.target).attr("id")!=u)&&($(v.target).parents().filter(u).length==0))
{c.blur();$(document).unbind("click",r)}};$(window).click(r);return false})}if(e.use_toggle_link){c.hide()}else{var p=o(e.tags);if(p==0){n.hide();b.show()}}function l(s,r){return s+((r!=""&&r)?":"+r:"")}function d(r){$(r).mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});$(r).mouseleave(function(){$(this).attr("src",e.delete_tag_img)});$(r).click(function(){var x=$(this).parent();var w=x.find(".tag-name").eq(0);var v=w.text();var t=m(v);var z=t[0];var s=t[1];var y=x.prev();x.remove();delete e.tags[z];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);$.ajax({url:e.ajax_delete_tag_url,data:{tag_name:z},error:function(){e.tags[z]=s;if(y.hasClass("tag-button")){y.after(x)}else{c.prepend(x)}var A=e.get_toggle_link_text_fn(e.tags);alert("Remove tag failed");f.text(A);r.mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});r.mouseleave(function(){$(this).attr("src",e.delete_tag_img)})},success:function(){}});return true})}function a(r){var s=new
Array();for(key in r){s[s.length]=key+"-->"+r[key]}return"{"+s.join(",")+"}"}function m(r){return r.split(":")}function k(r){var s=$("<img src='"+e.delete_tag_img+"'/>").addClass("delete-tag-img");d(s);var t=$("<span>").text(r).addClass("tag-name");t.click(function(){tag_name_and_value=r.split(":");e.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var u=$("<span></span>").addClass("tag-button");u.append(t);if(e.editable){u.append(s)}return u}};
\ No newline at end of file
+function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(q){var g={get_toggle_link_text_fn:function(r){var t="";var s=o(r);if(s!=0){t=s+(s!=0?" Tags":" Tag")}else{t="Add tags"}return t},tag_click_fn:function(r,s){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var e=jQuery.extend(g,q);var o=function(r){if(r.length){return r.length}var s=0;for(element in r){s++}return s};var h=$(this);var c=h.find(".tag-area");var f=h.find(".toggle-link");var b=h.find(".tag-input");var n=h.find(".add-tag-button");f.click(function(){var r=(c.css("display")=="none");var s;if(r){s=function(){var t=$(this).find(".tag-button").length;if(t==0){c.click()}}}else{s=func
tion(){c.blur()}}c.slideToggle("fast",s);return $(this)});if(e.editable){b.hide()}b.keyup(function(w){if(w.keyCode==27){$(this).trigger("blur")}else{if((w.keyCode==13)||(w.keyCode==188)||(w.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((w.keyCode==188)||(w.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var t=k(new_value);var s=c.children(".tag-button");if(s.length!=0){var x=s.slice(s.length-1);x.after(t)}else{c.prepend(t)}var r=new_value.split(":");e.tags[r[0]]=r[1];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);var v=$(this);$.ajax({url:e.ajax_add_tag_url,data:{new_tag:new_value},error:function(){t.remove();delete e.tags[r[0]];var y=e.get_toggle_link_te
xt_fn(e.tags);f.text(y);alert("Add tag failed")},success:function(){v.flushCache()}});return false}}});var j=function(t,s,r,v,u){tag_name_and_value=v.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var i={selectFirst:false,formatItem:j,autoFill:false,highlight:false};b.autocomplete(e.ajax_autocomplete_tag_url,i);h.find(".delete-tag-img").each(function(){d($(this))});init_tag_click_function($(this),e.tag_click_fn);n.click(function(){$(this).hide();c.click();return false});if(e.editable){c.blur(function(r){p=o(e.tags);if(p!=0){n.show();b.hide();c.removeClass("active-tag-area");c.addClass("tooltip")}else{}});c.click(function(t){var s=$(this).hasClass("active-tag-area");if($(t.target).hasClass("delete-tag-img")&&!s){return false}if($(t.target).hasClass("tag-name")&&!s){return false}$(this).removeClass("tooltip");$(this).addClass("active-tag-area");n.hide();b.show();b.focus();var r=function(v){var u=c.attr("id");if(($(v.target).attr("i
d")!=u)&&($(v.target).parents().filter(u).length==0)){c.blur();$(document).unbind("click",r);$(this).addClass("tooltip")}};$(window).click(r);return false})}if(e.use_toggle_link){c.hide()}else{var p=o(e.tags);if(p==0){n.hide();b.show()}}function l(s,r){return s+((r!=""&&r)?":"+r:"")}function d(r){$(r).mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});$(r).mouseleave(function(){$(this).attr("src",e.delete_tag_img)});$(r).click(function(){var x=$(this).parent();var w=x.find(".tag-name").eq(0);var v=w.text();var t=m(v);var z=t[0];var s=t[1];var y=x.prev();x.remove();delete e.tags[z];var u=e.get_toggle_link_text_fn(e.tags);f.text(u);$.ajax({url:e.ajax_delete_tag_url,data:{tag_name:z},error:function(){e.tags[z]=s;if(y.hasClass("tag-button")){y.after(x)}else{c.prepend(x)}var A=e.get_toggle_link_text_fn(e.tags);alert("Remove tag failed");f.text(A);r.mouseenter(function(){$(this).attr("src",e.delete_tag_img_rollover)});r.mouseleave(function(){$(this).attr("src",e
.delete_tag_img)})},success:function(){}});return true})}function a(r){var s=new Array();for(key in r){s[s.length]=key+"-->"+r[key]}return"{"+s.join(",")+"}"}function m(r){return r.split(":")}function k(r){var s=$("<img src='"+e.delete_tag_img+"'/>").addClass("delete-tag-img");d(s);var t=$("<span>").text(r).addClass("tag-name");t.click(function(){tag_name_and_value=r.split(":");e.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var u=$("<span></span>").addClass("tag-button");u.append(t);if(e.editable){u.append(s)}return u}};
\ No newline at end of file
diff -r 60308825b252 -r aa81684b9275 static/scripts/packed/galaxy.base.js
--- a/static/scripts/packed/galaxy.base.js Fri Feb 05 23:03:03 2010 -0500
+++ b/static/scripts/packed/galaxy.base.js Mon Feb 08 09:03:07 2010 -0500
@@ -1,1 +1,1 @@
-$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t
op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element
in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.
attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var k=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+k+"</textarea>")}else{var j=$("<input type='text' value='"+k+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(b!=null){b(j)}});j.keyup(function(m){if(m.keyCode==27){$(this).trigger("blur")}else{if(m.keyCode==13){new_text=this.value;$(this).trigger("blur");var l=new Object();l[a]=new_text;$.ajax({url:e,data:l,error:function(){alert("Text editing for elt "+f+" failed")},success:function(n){$("#"+f).text(n);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();return false})};
\ No newline at end of file
+$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t
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diff -r 60308825b252 -r aa81684b9275 static/scripts/packed/trackster.js
--- a/static/scripts/packed/trackster.js Fri Feb 05 23:03:03 2010 -0500
+++ b/static/scripts/packed/trackster.js Mon Feb 08 09:03:07 2010 -0500
@@ -1,1 +1,1 @@
-var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_i
mg_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(c,a,b){this.chrom=c;this.config=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},remove_track:function(a){delete this
.tracks[a]},update_options:function(){for(var b in view.tracks){var a=view.tracks[b];if(a.update_options){a.update_options(b)}}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.lo
w<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this
.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.widt
h(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null
,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d.min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.he
ight_px+55+"px"});e.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(!this.vertical_range){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f
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ue);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dat
aset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end
-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined
){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.vie
w.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);
p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=func
tion(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.lengt
h;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}});
\ No newline at end of file
+var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_i
mg_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},add_label_track:function
(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){delete this.tracks[a]},update_options:function(){for(var b in view.tracks){var a=view.tracks[b];if(a.update_options){a.update_options(b)}}},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){f
or(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.v
iew.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.
addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{i
nit:function(){this.data_queue={};this.data_cache=new Cache(CACHED_DATA);var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d.length===0||d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d.min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;if($("#linetrack_"+b
+"_minval").length===0){var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)}a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(this.vertical_range===undefined){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:
0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#trac
k_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20);this.prefs={block_color:"black",l
abel_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.adClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.get
JSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(thi
s.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slo
ts[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var
Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e
=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0
).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}});
\ No newline at end of file
diff -r 60308825b252 -r aa81684b9275 templates/root/history.mako
--- a/templates/root/history.mako Fri Feb 05 23:03:03 2010 -0500
+++ b/templates/root/history.mako Mon Feb 08 09:03:07 2010 -0500
@@ -43,7 +43,7 @@
}));
// Rename management.
- async_save_text("history-name", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18);
+ async_save_text("history-name-container", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18);
// Tag management.
$('#history-tag').click( function()
@@ -57,7 +57,7 @@
$('#history-annotation-area').toggle("fast");
return false;
});
- async_save_text("history-annotation", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4);
+ async_save_text("history-annotation-container", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4);
// Updater
updater({
@@ -322,7 +322,7 @@
## Annotation elt.
<div id="history-annotation-area" class="form-row" style="display: none">
<label>Annotation / Notes:</label>
- <div class="tooltip">
+ <div id="history-annotation-container" class="tooltip">
%if annotation:
<span id="history-annotation">${annotation | h}</span>
%else:
diff -r 60308825b252 -r aa81684b9275 templates/sharing_base.mako
--- a/templates/sharing_base.mako Fri Feb 05 23:03:03 2010 -0500
+++ b/templates/sharing_base.mako Mon Feb 08 09:03:07 2010 -0500
@@ -49,7 +49,7 @@
};
<% controller_name = get_controller_name( item ) %>
- async_save_text("edit-identifier", "item-identifier", "${h.url_for( controller=controller_name, action='set_slug_async', id=trans.security.encode_id( item.id ) )}", "new_slug", false, 0, on_start, on_finish);
+ async_save_text("edit-identifier", "item-identifier", "${h.url_for( controller=controller_name, action='set_slug_async', id=trans.security.encode_id( item.id ) )}", "new_slug", null, false, 0, on_start, on_finish);
});
</script>
</%def>
diff -r 60308825b252 -r aa81684b9275 templates/tagging_common.mako
--- a/templates/tagging_common.mako Fri Feb 05 23:03:03 2010 -0500
+++ b/templates/tagging_common.mako Mon Feb 08 09:03:07 2010 -0500
@@ -37,7 +37,7 @@
%if use_toggle_link:
<a class="toggle-link" href="#">${num_tags} Tag${iff( num_tags == 1, "", "s")}</a>
%endif
- <div class="tag-area
+ <div class="tag-area tooltip
%if tag_type == 'individual':
individual-tag-area
%endif
@@ -72,20 +72,18 @@
%endfor
## Add tag input field. If element is in form, tag input is a textarea; otherwise element is a input type=text.
- <div class="tooltip">
- %if editable:
- %if in_form:
- <textarea class="tag-input" rows='1' cols='${input_size}'></textarea>
- %else:
- <input class="tag-input" type='text' size='${input_size}'/>
- %endif
- ## Add "add tag" button.
- %if render_add_tag_button:
- <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/>
- %endif
+ %if editable:
+ %if in_form:
+ <textarea class="tag-input" rows='1' cols='${input_size}'></textarea>
+ %else:
+ <input class="tag-input" type='text' size='${input_size}'/>
%endif
- <span class="tip">Click to add tags</span>
- </div>
+ ## Add "add tag" button.
+ %if render_add_tag_button:
+ <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/>
+ %endif
+ <span class="tip">Click to edit tags</span>
+ %endif
</div>
</div>
</%def>
1
0
09 Feb '10
details: http://www.bx.psu.edu/hg/galaxy/rev/60308825b252
changeset: 3351:60308825b252
user: Ross Lazarus <ross.lazarus(a)gmail.com>
date: Fri Feb 05 23:03:03 2010 -0500
description:
python2.4 sha.new() cannot be based to hmac - this patch tested with 2.4 and 2.5
diffstat:
lib/galaxy/util/hash_util.py | 11 ++++++-----
1 files changed, 6 insertions(+), 5 deletions(-)
diffs (30 lines):
diff -r 4af74d038535 -r 60308825b252 lib/galaxy/util/hash_util.py
--- a/lib/galaxy/util/hash_util.py Fri Feb 05 19:35:52 2010 -0500
+++ b/lib/galaxy/util/hash_util.py Fri Feb 05 23:03:03 2010 -0500
@@ -6,15 +6,16 @@
import sys, logging
# Use hashlib module if for Python 2.5+, fall back on old sha and md5 modules
+# sha1 requires explicit calls to new if also being passed to hmac (!)
try:
import hashlib
sha1 = hashlib.sha1
+ sha = sha1
md5 = hashlib.md5
except ImportError, e:
- import sha, md5
- sha1 = sha.new
- md5 = md5.new
-
+ from sha import new as sha1
+ import sha
+ from md5 import new as md5
import hmac
log = logging.getLogger( __name__ )
@@ -30,4 +31,4 @@
return sha1()
def hmac_new( key, value ):
- return hmac.new( key, value, sha1 ).hexdigest()
+ return hmac.new( key, value, sha ).hexdigest()
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/4af74d038535
changeset: 3350:4af74d038535
user: Kanwei Li <kanwei(a)gmail.com>
date: Fri Feb 05 19:35:52 2010 -0500
description:
typo
diffstat:
lib/galaxy/web/controllers/tracks.py | 6 +++++-
1 files changed, 5 insertions(+), 1 deletions(-)
diffs (16 lines):
diff -r 432a32ba55bb -r 4af74d038535 lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:08:37 2010 -0500
+++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:35:52 2010 -0500
@@ -121,7 +121,11 @@
latest_revision = vis.latest_revision
tracks = []
- dbkey = latest_revision.config['dbkey']
+ try:
+ dbkey = latest_revision.config['dbkey']
+ except KeyError:
+ dbkey = None
+
hda_query = session.query( model.HistoryDatasetAssociation )
for t in vis.latest_revision.config['tracks']:
dataset_id = t['dataset_id']
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/432a32ba55bb
changeset: 3349:432a32ba55bb
user: Kanwei Li <kanwei(a)gmail.com>
date: Fri Feb 05 19:08:37 2010 -0500
description:
trackster:
- New interface for new track browsers
- Saving shows progress bar
- Can now add tracks async
- Switching dbkeys is now async
diffstat:
lib/galaxy/web/controllers/tracks.py | 128 ++++------
lib/galaxy/web/controllers/visualization.py | 2 +-
static/scripts/trackster.js | 61 +++-
static/trackster.css | 1 +
templates/grid_base.mako | 4 +
templates/tracks/add_tracks.mako | 3 +-
templates/tracks/browser.mako | 344 ++++++++++++++++-----------
templates/tracks/index.mako | 52 +++-
templates/tracks/new_browser.mako | 81 +-----
9 files changed, 359 insertions(+), 317 deletions(-)
diffs (955 lines):
diff -r 99483ae6c738 -r 432a32ba55bb lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py Fri Feb 05 16:34:30 2010 -0500
+++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:08:37 2010 -0500
@@ -57,10 +57,7 @@
use_paging = False
columns = [
grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ),
- # grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"),
grids.GridColumn( "Filetype", key="extension" ),
- # Columns that are valid for filtering but are not visible.
- # SharingColumn( "Shared", key="shared", visible=False, filterable="advanced" )
]
def apply_default_filter( self, trans, query, **kwargs ):
if self.available_tracks is None:
@@ -80,62 +77,40 @@
@web.expose
def index( self, trans ):
- return trans.fill_template( "tracks/index.mako" )
-
+ config = {}
+
+ return trans.fill_template( "tracks/browser.mako", config=config )
+
@web.expose
@web.require_login()
- def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None, title=None ):
- """
- Build a new browser from datasets in the current history. Redirects
- to 'browser' once datasets to browse have been selected.
- """
- session = trans.sa_session
- # If the user clicked the submit button explicitly, try to build the browser
- if title and browse and dataset_ids:
- if not isinstance( dataset_ids, list ):
- dataset_ids = [ dataset_ids ]
- # Build config
- tracks = []
- for dataset_id in dataset_ids:
- tracks.append( { "dataset_id": str( dataset_id ) } )
- config = { "tracks": tracks }
- # Build visualization object
- vis = model.Visualization()
- vis.user = trans.user
- vis.title = title
- vis.type = "trackster"
- vis_rev = model.VisualizationRevision()
- vis_rev.visualization = vis
- vis_rev.title = title
- vis_rev.config = config
- vis.latest_revision = vis_rev
- session.add( vis )
- session.add( vis_rev )
- session.flush()
- trans.response.send_redirect( web.url_for( controller='tracks', action='browser', id=trans.security.encode_id( vis.id ) ) )
+ def new_browser( self, trans ):
+ dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ]
+ dbkey_set = set( dbkeys )
+ if not dbkey_set:
+ return trans.show_error_message( "Current history has no valid datasets to visualize." )
else:
- # Determine the set of all dbkeys that are used in the current history
- dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ]
- dbkey_set = set( dbkeys )
- if not dbkey_set:
- return trans.show_error_message( "Current history has no valid datasets to visualize." )
-
- # If a dbkey argument was not provided, or is no longer valid, default
- # to the first one
- if dbkey is None or dbkey not in dbkey_set:
- dbkey = dbkeys[0]
- # Find all datasets in the current history that are of that dbkey
- # and can be displayed
- datasets = {}
- if self.available_tracks is None:
- self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
- for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ):
- if dataset.metadata.dbkey == dbkey and dataset.extension in self.available_tracks:
- datasets[dataset.id] = (dataset.extension, dataset.name)
- # Render the template
- return trans.fill_template( "tracks/new_browser.mako", available_tracks=self.available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets )
-
+ return trans.fill_template( "tracks/new_browser.mako", dbkey_set=dbkey_set )
+
+ @web.json
+ @web.require_login()
+ def add_track_async(self, trans, id):
+ dataset_id = trans.security.decode_id( id )
+
+ hda_query = trans.sa_session.query( model.HistoryDatasetAssociation )
+ dataset = hda_query.get( dataset_id )
+ track_type, indexer = dataset.datatype.get_track_type()
+
+ track = {
+ "track_type": track_type,
+ "indexer": indexer,
+ "name": dataset.name,
+ "dataset_id": dataset.id,
+ "prefs": {},
+ }
+ return track
+
@web.expose
+ @web.require_login()
def browser(self, trans, id, chrom=""):
"""
Display browser for the datasets listed in `dataset_ids`.
@@ -143,8 +118,10 @@
decoded_id = trans.security.decode_id( id )
session = trans.sa_session
vis = session.query( model.Visualization ).get( decoded_id )
+ latest_revision = vis.latest_revision
tracks = []
- dbkey = ""
+
+ dbkey = latest_revision.config['dbkey']
hda_query = session.query( model.HistoryDatasetAssociation )
for t in vis.latest_revision.config['tracks']:
dataset_id = t['dataset_id']
@@ -161,18 +138,10 @@
"dataset_id": dataset.id,
"prefs": simplejson.dumps(prefs),
} )
- dbkey = dataset.dbkey
- chrom_lengths = self._chroms( trans, dbkey )
- if chrom_lengths is None:
- error( "No chromosome lengths file found for '%s'" % dataset.name )
- return trans.fill_template( 'tracks/browser.mako',
- #dataset_ids=dataset_ids,
- title = vis.title,
- id=id,
- tracks=tracks,
- chrom=chrom,
- dbkey=dbkey,
- LEN=chrom_lengths.get(chrom, 0) )
+ if dbkey is None: dbkey = dataset.dbkey # Hack for backward compat
+
+ config = { "title": vis.title, "vis_id": id, "tracks": tracks, "chrom": chrom, "dbkey": dbkey }
+ return trans.fill_template( 'tracks/browser.mako', config=config )
@web.json
def chroms(self, trans, dbkey=None ):
@@ -288,9 +257,19 @@
@web.json
def save( self, trans, **kwargs ):
- decoded_id = trans.security.decode_id( kwargs['id'] )
session = trans.sa_session
- vis = session.query( model.Visualization ).get( decoded_id )
+ vis_id = kwargs['vis_id'].strip('"')
+ dbkey = kwargs['dbkey']
+
+ if vis_id == "undefined": # new vis
+ vis = model.Visualization()
+ vis.user = trans.user
+ vis.title = kwargs['vis_title']
+ vis.type = "trackster"
+ session.add( vis )
+ else:
+ decoded_id = trans.security.decode_id( vis_id )
+ vis = session.query( model.Visualization ).get( decoded_id )
decoded_payload = simplejson.loads( kwargs['payload'] )
vis_rev = model.VisualizationRevision()
@@ -304,10 +283,11 @@
"track_type": track['track_type'],
"prefs": track['prefs']
} )
- vis_rev.config = { "tracks": tracks }
+ vis_rev.config = { "dbkey": dbkey, "tracks": tracks }
vis.latest_revision = vis_rev
session.add( vis_rev )
session.flush()
+ return trans.security.encode_id(vis.id)
data_grid = DatasetSelectionGrid()
@@ -316,11 +296,5 @@
def list_datasets( self, trans, **kwargs ):
"""List all datasets that can be added as tracks"""
-
# Render the list view
- # return trans.fill_template( 'tracks/add_tracks.mako', grid=data_grid( trans, status=status, message=message, **kwargs ) )
return self.data_grid( trans, **kwargs )
-
- #
-
-
\ No newline at end of file
diff -r 99483ae6c738 -r 432a32ba55bb lib/galaxy/web/controllers/visualization.py
--- a/lib/galaxy/web/controllers/visualization.py Fri Feb 05 16:34:30 2010 -0500
+++ b/lib/galaxy/web/controllers/visualization.py Fri Feb 05 19:08:37 2010 -0500
@@ -7,7 +7,7 @@
# Grid definition
title = "Visualizations"
model_class = model.Visualization
- default_sort_key = "-create_time"
+ default_sort_key = "-update_time"
columns = [
grids.GridColumn( "Title", key="title", attach_popup=True,
link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ),
diff -r 99483ae6c738 -r 432a32ba55bb static/scripts/trackster.js
--- a/static/scripts/trackster.js Fri Feb 05 16:34:30 2010 -0500
+++ b/static/scripts/trackster.js Fri Feb 05 19:08:37 2010 -0500
@@ -77,14 +77,16 @@
}
});
-var View = function( chrom, max_high, config ) {
+var View = function( chrom, title, vis_id, dbkey ) {
+ this.vis_id = vis_id;
+ this.dbkey = dbkey;
+ this.title = title;
this.chrom = chrom;
- this.config = config;
this.tracks = [];
+ this.label_tracks = [];
this.max_low = 0;
- this.max_high = max_high;
+ this.max_high = 0;
this.center = (this.max_high - this.max_low) / 2;
- this.span = this.max_high - this.max_low;
this.zoom_factor = 3;
this.zoom_level = 0;
};
@@ -94,6 +96,10 @@
this.tracks.push( track );
if (track.init) { track.init(); }
},
+ add_label_track: function ( label_track ) {
+ label_track.view = this;
+ this.label_tracks.push( label_track );
+ },
remove_track: function( track ) {
delete this.tracks[track];
},
@@ -105,7 +111,8 @@
}
}
},
- redraw: function() {
+ redraw: function(nodraw) {
+ this.span = this.max_high - this.max_low;
var span = this.span / Math.pow(this.zoom_factor, this.zoom_level),
low = this.center - (span / 2),
high = low + span;
@@ -134,11 +141,14 @@
}).show();
$("#low").val( commatize(this.low) );
$("#high").val( commatize(this.high) );
- for ( var i = 0, len = this.tracks.length; i < len; i++ ) {
- this.tracks[i].draw();
+ if (!nodraw) {
+ for ( var i = 0, len = this.tracks.length; i < len; i++ ) {
+ this.tracks[i].draw();
+ }
+ for ( var i = 0, len = this.label_tracks.length; i < len; i++ ) {
+ this.label_tracks[i].draw();
+ }
}
- //$("#bottom-spacer").remove();
- //$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>');
},
zoom_in: function ( point ) {
if (this.max_high === 0 || this.high - this.low < 30) {
@@ -238,6 +248,7 @@
var LabelTrack = function ( parent_element ) {
Track.call( this, null, parent_element );
+ this.track_type = "LabelTrack";
this.hidden = true;
this.container_div.addClass( "label-track" );
};
@@ -273,26 +284,27 @@
this.height_px = 100;
this.container_div.addClass( "line-track" );
this.dataset_id = dataset_id;
- this.data_queue = {};
- this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of
- // asynchronous calls
this.prefs = { 'min_value': undefined, 'max_value': undefined };
if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; }
if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; }
};
$.extend( LineTrack.prototype, TiledTrack.prototype, {
init: function() {
+ this.data_queue = {};
+ this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of
+ // asynchronous calls
var track = this,
track_id = track.view.tracks.indexOf(track);
-
+
track.content_div.text(DATA_LOADING);
+ track.container_div.removeClass("nodata error pending");
$.getJSON( data_url, { stats: true, indexer: track.indexer,
chrom: track.view.chrom, low: null, high: null,
dataset_id: track.dataset_id }, function ( data ) {
if (!data || data == "error") {
track.container_div.addClass("error");
track.content_div.text(DATA_ERROR);
- } else if (data == "no data") {
+ } else if (data.length === 0 || data == "no data") {
track.container_div.addClass("nodata");
track.content_div.text(DATA_NONE);
} else if (data == "pending") {
@@ -313,15 +325,17 @@
}
track.vertical_range = track.prefs.max_value - track.prefs.min_value;
- // Draw y-axis labels
- var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value);
- var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value);
+ // Draw y-axis labels if necessary
+ if ( $('#linetrack_' + track_id + '_minval').length === 0) {
+ var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value);
+ var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value);
- max_label.css({ position: "relative", top: "25px" });
- max_label.prependTo(track.container_div);
+ max_label.css({ position: "relative", top: "25px" });
+ max_label.prependTo(track.container_div);
- min_label.css({ position: "relative", top: track.height_px + 55 + "px" });
- min_label.prependTo(track.container_div);
+ min_label.css({ position: "relative", top: track.height_px + 55 + "px" });
+ min_label.prependTo(track.container_div);
+ }
track.draw();
}
@@ -345,7 +359,7 @@
}
},
draw_tile: function( resolution, tile_index, parent_element, w_scale ) {
- if (!this.vertical_range) { // We don't have the necessary information yet
+ if (this.vertical_range === undefined) { // We don't have the necessary information yet
return;
}
@@ -463,6 +477,7 @@
init: function() {
var track = this;
track.content_div.text(DATA_LOADING);
+ track.container_div.removeClass("nodata error pending");
$.getJSON( data_url, { indexer: track.indexer, low: track.view.max_low,
high: track.view.max_high, dataset_id: track.dataset_id,
chrom: track.view.chrom }, function ( data ) {
@@ -473,7 +488,7 @@
track.container_div.addClass("nodata");
track.content_div.text(DATA_NONE);
} else if (data == "pending") {
- track.container_div.addClass("pending");
+ track.container_div.adClass("pending");
track.content_div.text(DATA_PENDING);
setTimeout(function() { track.init(); }, 5000);
} else {
diff -r 99483ae6c738 -r 432a32ba55bb static/trackster.css
--- a/static/trackster.css Fri Feb 05 16:34:30 2010 -0500
+++ b/static/trackster.css Fri Feb 05 19:08:37 2010 -0500
@@ -8,6 +8,7 @@
#nav-container {
position: fixed;
+ left: 0;
bottom: 0;
}
diff -r 99483ae6c738 -r 432a32ba55bb templates/grid_base.mako
--- a/templates/grid_base.mako Fri Feb 05 16:34:30 2010 -0500
+++ b/templates/grid_base.mako Fri Feb 05 19:08:37 2010 -0500
@@ -27,6 +27,10 @@
<%def name="javascripts()">
${parent.javascripts()}
+ ${self.grid_javascripts()}
+</%def>
+
+<%def name="grid_javascripts()">
${h.js("jquery.autocomplete", "autocomplete_tagging" )}
<script type="text/javascript">
## TODO: generalize and move into galaxy.base.js
diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/add_tracks.mako
--- a/templates/tracks/add_tracks.mako Fri Feb 05 16:34:30 2010 -0500
+++ b/templates/tracks/add_tracks.mako Fri Feb 05 19:08:37 2010 -0500
@@ -1,8 +1,9 @@
## Template generates a grid that enables user to add tracks
<%namespace file="../grid_base.mako" import="*" />
-${javascripts()}
${stylesheets()}
+${grid_javascripts()}
+
${render_grid_table( grid, show_item_checkboxes=True )}
## Initialize the grid.
diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/browser.mako
--- a/templates/tracks/browser.mako Fri Feb 05 16:34:30 2010 -0500
+++ b/templates/tracks/browser.mako Fri Feb 05 19:08:37 2010 -0500
@@ -45,7 +45,7 @@
</div>
</div>
-<div id="nav-container">
+<div id="nav-container" style="width:100%;">
<div id="nav-labeltrack"></div>
<div id="nav">
<div id="overview">
@@ -59,8 +59,7 @@
<option value="">Loading</option>
</select>
<input id="low" size="12" />:<input id="high" size="12" />
- ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" />
- <input type="hidden" name="id" value="${id}" />
+ <input type="hidden" name="id" value="${config.get('vis_id', '')}" />
<a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a>
<a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a>
</form>
@@ -75,11 +74,10 @@
<div class="unified-panel-header-inner">Configuration</div>
</div>
<form action="${h.url_for( action='update_config' )}">
-## <input name="title" id="title" value="${title}" />
+## <input name="title" id="title" value="${config.title}" />
<div id="show-hide-move">
<ul id="sortable-ul"></ul>
</div>
-## <input type="submit" id="update-config" value="Save settings" />
<input type="button" id="refresh-button" value="Refresh" />
<input type="button" id="save-button" value="Save" />
<input id="add-track" type="button" value="Add Track" />
@@ -89,154 +87,227 @@
<%def name="javascripts()">
${parent.javascripts()}
-${h.js( "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )}
+${h.js( 'galaxy.base', 'galaxy.panels', "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )}
<script type="text/javascript">
var data_url = "${h.url_for( action='data' )}";
- var view = new View( "${chrom}", ${LEN} );
+ var view;
$(function() {
- view.add_track( new LabelTrack( $("#top-labeltrack" ) ) );
- view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) );
-
- %for track in tracks:
- view.add_track(
- new ${track["track_type"]}( "${track['name']}", ${track['dataset_id']}, "${track['indexer']}", ${track['prefs']} )
- );
- %endfor
-
- $(document).bind( "redraw", function( e ) {
- view.redraw();
- });
-
- $("#content").bind("mousewheel", function( e, delta ) {
- if (delta > 0) {
- view.zoom_in(e.pageX);
- } else {
- view.zoom_out();
- }
- e.preventDefault();
- });
-
- $("#content").bind("dblclick", function( e ) {
- view.zoom_in(e.pageX);
- });
-
- // To let the overview box be draggable
- $("#overview-box").bind("dragstart", function( e ) {
- this.current_x = e.offsetX;
- }).bind("drag", function( e ) {
- var delta = e.offsetX - this.current_x;
- this.current_x = e.offsetX;
-
- var delta_chrom = Math.round(delta / $(document).width() * view.span);
- view.center += delta_chrom;
- view.redraw();
- });
-
- // To adjust the size of the viewport to fit the fixed-height footer
- var refresh = function( e ) {
- $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height());
- $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() );
- $("#nav-container").width( $("#center").width() );
- view.redraw();
- };
- $(window).bind( "resize", function(e) { refresh(e); } );
- $("#right-border").bind( "click", function(e) { refresh(e); } );
- $("#right-border").bind( "dragend", function(e) { refresh(e); } );
- $(window).trigger( "resize" );
-
- $("#viewport").bind( "dragstart", function( e ) {
- this.original_low = view.low;
- this.current_height = e.clientY;
- this.current_x = e.offsetX;
- }).bind( "drag", function( e ) {
- var container = $(this).parent();
- var delta = e.offsetX - this.current_x;
- var new_scroll = container.scrollTop() - (e.clientY - this.current_height);
- if ( new_scroll < container.get(0).scrollHeight - container.height() ) {
- container.scrollTop(new_scroll);
- }
- this.current_height = e.clientY;
- this.current_x = e.offsetX;
-
- var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low));
- view.center -= delta_chrom;
- view.redraw();
- });
-
- $("#refresh-button").bind( "click", function(e) {
- view.update_options();
- });
-
- // Use a popup grid to add more tracks
- $("#add-track").bind( "click", function(e) {
+ %if config:
+ view = new View( "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" );
+ %for track in config.get('tracks'):
+ view.add_track(
+ new ${track["track_type"]}( "${track['name'] | h}", ${track['dataset_id']}, "${track['indexer']}", ${track['prefs']} )
+ );
+ %endfor
+ init();
+ %else:
$.ajax({
- url: "${h.url_for( action='list_datasets' )}",
+ url: "${h.url_for( action='new_browser' )}",
data: {},
- error: function() { alert( "Grid refresh failed" ) },
- success: function(table_html) {
- show_modal("Add Track — Select Dataset(s)", table_html, {
- "Insert": function() {
- hide_modal();
- },
- "Cancel": function() {
+ error: function() { alert( "Couldn't create new browser" ) },
+ success: function(form_html) {
+ show_modal("New Track Browser", form_html, {
+ "Continue": function() {
+ view = new View( undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() );
+ init();
hide_modal();
}
});
}
});
- });
+ %endif
- $("#save-button").bind("click", function(e) {
- view.update_options();
- var sorted = $("ul#sortable-ul").sortable('toArray');
- var payload = [];
- for (var i in sorted) {
- var track_id = parseInt(sorted[i].split("track_")[1]),
- track = view.tracks[track_id];
-
- payload.push( {
- "track_type": track.track_type,
- "indexer": track.indexer,
- "name": track.name,
- "dataset_id": track.dataset_id,
- "prefs": track.prefs
- });
- }
- $.ajax({
- url: "${h.url_for( action='save' )}",
- data: {
- 'id': '${id}',
- 'payload': JSON.stringify(payload)
+ // Execute this when everything is ready
+ function init() {
+ $("ul#sortable-ul").sortable({
+ update: function(event, ui) {
+ for (var track_id in view.tracks) {
+ var track = view.tracks[track_id];
+ }
}
});
- });
-
- // Execute this on page load
- (function () {
- $.getJSON( "${h.url_for( action='chroms' )}", { dbkey: "${dbkey}" }, function ( data ) {
+
+ $(document).bind( "redraw", function( e ) {
+ view.redraw();
+ });
+
+ $("#content").bind("mousewheel", function( e, delta ) {
+ if (delta > 0) {
+ view.zoom_in(e.pageX);
+ } else {
+ view.zoom_out();
+ }
+ e.preventDefault();
+ });
+
+ $("#content").bind("dblclick", function( e ) {
+ view.zoom_in(e.pageX);
+ });
+
+ // To let the overview box be draggable
+ $("#overview-box").bind("dragstart", function( e ) {
+ this.current_x = e.offsetX;
+ }).bind("drag", function( e ) {
+ var delta = e.offsetX - this.current_x;
+ this.current_x = e.offsetX;
+
+ var delta_chrom = Math.round(delta / $(document).width() * view.span);
+ view.center += delta_chrom;
+ view.redraw();
+ });
+
+ // To adjust the size of the viewport to fit the fixed-height footer
+ var refresh = function( e ) {
+ $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height());
+ $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() );
+ $("#nav-container").width( $("#center").width() );
+ view.redraw();
+ };
+ $(window).bind( "resize", function(e) { refresh(e); } );
+ $("#right-border").bind( "click", function(e) { refresh(e); } );
+ $("#right-border").bind( "dragend", function(e) { refresh(e); } );
+ $(window).trigger( "resize" );
+
+ $("#viewport").bind( "dragstart", function( e ) {
+ this.original_low = view.low;
+ this.current_height = e.clientY;
+ this.current_x = e.offsetX;
+ }).bind( "drag", function( e ) {
+ var container = $(this).parent();
+ var delta = e.offsetX - this.current_x;
+ var new_scroll = container.scrollTop() - (e.clientY - this.current_height);
+ if ( new_scroll < container.get(0).scrollHeight - container.height() ) {
+ container.scrollTop(new_scroll);
+ }
+ this.current_height = e.clientY;
+ this.current_x = e.offsetX;
+
+ var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low));
+ view.center -= delta_chrom;
+ view.redraw();
+ });
+
+ $("#refresh-button").bind( "click", function(e) {
+ view.update_options();
+ });
+
+ // Use a popup grid to add more tracks
+ $("#add-track").bind( "click", function(e) {
+ $.ajax({
+ url: "${h.url_for( action='list_datasets' )}",
+ data: {},
+ error: function() { alert( "Grid refresh failed" ) },
+ success: function(table_html) {
+ show_modal("Add Track — Select Dataset(s)", table_html, {
+ "Insert": function() {
+ $('input[name=id]:checked').each(function() {
+ var item_id = $(this).val();
+ $.ajax( {
+ url: "${h.url_for( action='add_track_async' )}",
+ data: { id: item_id },
+ dataType: "json",
+ error: function() {},
+ success: function(track_data) {
+ var new_track;
+ var td = track_data;
+ switch(track_data.track_type) {
+ case "LineTrack":
+ new_track = new LineTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs );
+ break;
+ case "FeatureTrack":
+ new_track = new FeatureTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs );
+ break;
+ case "ReadTrack":
+ new_track = new ReadTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs );
+ break;
+ }
+ view.add_track(new_track);
+ sidebar_box(new_track);
+ }
+ });
+
+ });
+
+ hide_modal();
+ },
+ "Cancel": function() {
+ hide_modal();
+ }
+ });
+ }
+ });
+ });
+
+ $("#save-button").bind("click", function(e) {
+ view.update_options();
+ var sorted = $("ul#sortable-ul").sortable('toArray');
+ var payload = [];
+ for (var i in sorted) {
+ var track_id = parseInt(sorted[i].split("track_")[1]),
+ track = view.tracks[track_id];
+
+ payload.push( {
+ "track_type": track.track_type,
+ "indexer": track.indexer,
+ "name": track.name,
+ "dataset_id": track.dataset_id,
+ "prefs": track.prefs
+ });
+ }
+ // Show saving dialog box
+ show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>");
+
+ $.ajax({
+ url: "${h.url_for( action='save' )}",
+ data: {
+ 'vis_id': view.vis_id,
+ 'vis_title': view.title,
+ 'dbkey': view.dbkey,
+ 'payload': JSON.stringify(payload)
+ },
+ success: function(vis_id) {
+ view.vis_id = vis_id;
+ hide_modal();
+ }
+ });
+ });
+
+ view.add_label_track( new LabelTrack( $("#top-labeltrack" ) ) );
+ view.add_label_track( new LabelTrack( $("#nav-labeltrack" ) ) );
+
+ $.getJSON( "${h.url_for( action='chroms' )}", { dbkey: view.dbkey }, function ( data ) {
+ view.chrom_data = data;
var chrom_options = '<option value="">Select Chrom/Contig</option>';
for (i in data) {
- chrom = data[i]['chrom']
- if( chrom == view.chrom ) {
- chrom_options += '<option value="' + chrom + '" selected="true">' + chrom + '</option>';
- } else {
- chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
- }
+ var chrom = data[i]['chrom']
+ chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
}
$("#chrom").html(chrom_options);
$("#chrom").bind( "change", function () {
- $("#chr").submit();
+ view.chrom = $("#chrom").val();
+ var found = $.grep(view.chrom_data, function(v, i) {
+ return v.chrom === view.chrom;
+ })[0];
+ view.max_high = found.len;
+ view.redraw(true);
+
+ for (var track_id in view.tracks) {
+ var track = view.tracks[track_id];
+ if (track.init) {
+ track.init();
+ }
+ }
+ // view.redraw();
});
});
- // Populate sort/move ul
- for (var track_id in view.tracks) {
- var track = view.tracks[track_id];
+ function sidebar_box(track) {
if (!track.hidden) {
+ var track_id = view.tracks.length -1; // Track was just added to view, so index is current length -1
var label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>');
var title = $('<div class="historyItemTitle"></div>');
var del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />');
@@ -255,18 +326,17 @@
li.append(div);
$("ul#sortable-ul").append(li);
}
+ };
+
+ // Populate sort/move ul
+ for (var track_id in view.tracks) {
+ var track = view.tracks[track_id];
+ sidebar_box(track);
}
- $("ul#sortable-ul").sortable({
- update: function(event, ui) {
- for (var track_id in view.tracks) {
- var track = view.tracks[track_id];
- }
- }
- });
-
- })();
- $(window).trigger("resize");
+ $(window).trigger("resize");
+ };
+
});
</script>
diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/index.mako
--- a/templates/tracks/index.mako Fri Feb 05 16:34:30 2010 -0500
+++ b/templates/tracks/index.mako Fri Feb 05 19:08:37 2010 -0500
@@ -1,16 +1,38 @@
-<%inherit file="/base_panels.mako"/>
+<form id="form" method="POST">
+ <div class="form-row">
+ <label for="dbkey">Browser name:</label>
+ <div class="form-row-input">
+ <input type="text" name="title" id="title" value="Unnamed Browser"></input>
+ </div>
+ <div style="clear: both;"></div>
+ </div>
+ <div class="form-row">
+ <label for="dbkey">Reference genome build (dbkey): </label>
+ <div class="form-row-input">
+ <select name="dbkey" id="dbkey" refresh_on_change="true">
+ %for tmp_dbkey in dbkey_set:
+ <option value="${tmp_dbkey}"
+ %if tmp_dbkey == dbkey:
+ selected="selected"
+ %endif
+ >${tmp_dbkey}</option>
+ %endfor
+ </select>
+ </div>
+ <div style="clear: both;"></div>
+ </div>
+ <div class="form-row">
+ <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label>
+ %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems():
+ <div>
+ <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" />
+ <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label>
+ </div>
+ %endfor
-<%def name="init()">
-<%
- self.has_left_panel=False
- self.has_right_panel=False
- self.active_view="visualization"
- self.message_box_visible=False
-%>
-</%def>
-
-<%def name="center_panel()">
-
- <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="tracks", action="new_browser" )}"> </iframe>
-
-</%def>
\ No newline at end of file
+ <div style="clear: both;"></div>
+ </div>
+ <div class="form-row">
+ <input type="submit" name="browse" value="Browse"/>
+ </div>
+</form>
diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/new_browser.mako
--- a/templates/tracks/new_browser.mako Fri Feb 05 16:34:30 2010 -0500
+++ b/templates/tracks/new_browser.mako Fri Feb 05 19:08:37 2010 -0500
@@ -1,65 +1,20 @@
-<%inherit file="/base.mako"/>
-
-<%def name="javascripts()">
-${parent.javascripts()}
-<script type="text/javascript">
-$( function() {
- $( "select[refresh_on_change='true']").change( function() {
- $("#form").submit();
- });
-});
-</script>
-</%def>
-
-% if not available_tracks:
- <div class="errormessagelarge">
- There are no available converters needed for visualization. Please verify that your tool_conf.xml file contains
- converters for datatypes (see tool_conf.xml.sample) for examples.
+<form id="form" method="POST">
+ <div class="form-row">
+ <label for="title">Browser name:</label>
+ <div class="form-row-input">
+ <input type="text" name="title" id="new-title" value="Unnamed Browser"></input>
+ </div>
+ <div style="clear: both;"></div>
</div>
-
-% else:
- <div class="form">
- <div class="form-title">Create new track browser</div>
-
- <div id="dbkey" class="form-body">
- <form id="form" method="POST">
- <div class="form-row">
- <label for="dbkey">Browser name:</label>
- <div class="form-row-input">
- <input type="text" name="title" id="title" value="Unnamed Browser"></input>
- </div>
- <div style="clear: both;"></div>
- </div>
- <div class="form-row">
- <label for="dbkey">Reference genome build (dbkey): </label>
- <div class="form-row-input">
- <select name="dbkey" id="dbkey" refresh_on_change="true">
- %for tmp_dbkey in dbkey_set:
- <option value="${tmp_dbkey}"
- %if tmp_dbkey == dbkey:
- selected="selected"
- %endif
- >${tmp_dbkey}</option>
- %endfor
- </select>
- </div>
- <div style="clear: both;"></div>
- </div>
- <div class="form-row">
- <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label>
- %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems():
- <div>
- <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" />
- <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label>
- </div>
- %endfor
-
- <div style="clear: both;"></div>
- </div>
- </div>
- <div class="form-row">
- <input type="submit" name="browse" value="Browse"/>
- </div>
- </form>
+ <div class="form-row">
+ <label for="dbkey">Reference genome build (dbkey): </label>
+ <div class="form-row-input">
+ <select name="dbkey" id="new-dbkey">
+ %for dbkey in dbkey_set:
+ <option value="${dbkey}">${dbkey}</option>
+ %endfor
+ </select>
+ </div>
+ <div style="clear: both;"></div>
</div>
-% endif
+</form>
1
0
09 Feb '10
details: http://www.bx.psu.edu/hg/galaxy/rev/99483ae6c738
changeset: 3348:99483ae6c738
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Fri Feb 05 16:34:30 2010 -0500
description:
Prevent history tag and annotation icons from wrapping.
diffstat:
templates/root/history.mako | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
diffs (14 lines):
diff -r 656e1014f2fa -r 99483ae6c738 templates/root/history.mako
--- a/templates/root/history.mako Fri Feb 05 16:27:18 2010 -0500
+++ b/templates/root/history.mako Fri Feb 05 16:34:30 2010 -0500
@@ -286,8 +286,8 @@
<span class="tip">Click to edit</span></a>
</div>
</td>
- <td align="right">
- <div style="float: right">
+ <td align="right" style="width: 40px">
+ <div style="float: right; white-space: nowrap">
<a id="history-tag" title="Tag" class="icon-button tag tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='tag' )}"></a>
<a id="history-annotate" title="Annotate" class="icon-button annotate" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a>
</div>
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/656e1014f2fa
changeset: 3347:656e1014f2fa
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Fri Feb 05 16:27:18 2010 -0500
description:
Add a label for experiment name in MACs
diffstat:
tools/peak_calling/macs_wrapper.xml | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diffs (12 lines):
diff -r e9de35947c06 -r 656e1014f2fa tools/peak_calling/macs_wrapper.xml
--- a/tools/peak_calling/macs_wrapper.xml Fri Feb 05 16:06:27 2010 -0500
+++ b/tools/peak_calling/macs_wrapper.xml Fri Feb 05 16:27:18 2010 -0500
@@ -6,7 +6,7 @@
<requirement type="binary">macs</requirement>
</requirements>
<inputs>
- <param name="experiment_name" type="text" value="MACS in Galaxy" size="50"/>
+ <param name="experiment_name" type="text" value="MACS in Galaxy" size="50" label="Experiment Name"/>
<conditional name="input_type">
<param name="input_type_selector" type="select" label="Paired End Sequencing">
<option value="paired_end">Paired End (requires elandmultipet format)</option>
1
0
09 Feb '10
details: http://www.bx.psu.edu/hg/galaxy/rev/e9de35947c06
changeset: 3346:e9de35947c06
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Fri Feb 05 16:06:27 2010 -0500
description:
Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.
diffstat:
test-data/chipseq_enriched.bed.gz | 0
test-data/chipseq_input.bed.gz | 0
test-data/macs_test_1_out.bed | 1271 ++++++++++++++++++++
test-data/macs_test_2_neg_peaks_out.interval | 59 +
test-data/macs_test_2_peaks_out.interval | 1289 +++++++++++++++++++++
tool_conf.xml.main | 6 +-
tool_conf.xml.sample | 7 +-
tools/genetrack/genetrack_indexer.py | 42 +
tools/genetrack/genetrack_indexer.xml | 54 +
tools/genetrack/genetrack_peak_prediction.py | 40 +
tools/genetrack/genetrack_peak_prediction.xml | 59 +
tools/peak_calling/macs_wrapper.py | 138 ++
tools/peak_calling/macs_wrapper.xml | 213 +++
tools/samtools/sam2interval.xml | 2 +-
tools/visualization/genetrack_indexer.py | 39 -
tools/visualization/genetrack_indexer.xml | 54 -
tools/visualization/genetrack_peak_prediction.py | 40 -
tools/visualization/genetrack_peak_prediction.xml | 59 -
18 files changed, 3176 insertions(+), 196 deletions(-)
diffs (truncated from 3460 to 3000 lines):
diff -r 49961332adb6 -r e9de35947c06 test-data/chipseq_enriched.bed.gz
Binary file test-data/chipseq_enriched.bed.gz has changed
diff -r 49961332adb6 -r e9de35947c06 test-data/chipseq_input.bed.gz
Binary file test-data/chipseq_input.bed.gz has changed
diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_1_out.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/macs_test_1_out.bed Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,1271 @@
+track name="MACS peaks for MACS_in_Galaxy"
+chr1 3138857 3139271 MACS_peak_1 53.08
+chr1 4133899 4134700 MACS_peak_2 51.91
+chr1 4323670 4324367 MACS_peak_3 272.01
+chr1 4336486 4337946 MACS_peak_4 228.35
+chr1 4407086 4409120 MACS_peak_5 300.46
+chr1 4507832 4508710 MACS_peak_6 161.74
+chr1 4657704 4658572 MACS_peak_7 280.37
+chr1 4658705 4659021 MACS_peak_8 131.25
+chr1 4659147 4660581 MACS_peak_9 463.08
+chr1 4661156 4661317 MACS_peak_10 174.88
+chr1 4661505 4661617 MACS_peak_11 100.24
+chr1 4661790 4662463 MACS_peak_12 219.58
+chr1 4662710 4663434 MACS_peak_13 395.94
+chr1 4664135 4664430 MACS_peak_14 169.10
+chr1 4665001 4665113 MACS_peak_15 100.24
+chr1 4665839 4666425 MACS_peak_16 332.40
+chr1 4666581 4666693 MACS_peak_17 100.24
+chr1 4666840 4666981 MACS_peak_18 174.88
+chr1 4667600 4667712 MACS_peak_19 100.24
+chr1 4668711 4669005 MACS_peak_20 169.17
+chr1 4669126 4669238 MACS_peak_21 100.24
+chr1 4669537 4669752 MACS_peak_22 174.88
+chr1 4669936 4670048 MACS_peak_23 100.24
+chr1 4670216 4670449 MACS_peak_24 212.68
+chr1 4673856 4674051 MACS_peak_25 137.07
+chr1 4674349 4674478 MACS_peak_26 137.07
+chr1 4675027 4675152 MACS_peak_27 137.07
+chr1 4676227 4676339 MACS_peak_28 100.24
+chr1 4676511 4676623 MACS_peak_29 100.24
+chr1 4676954 4677151 MACS_peak_30 100.24
+chr1 4677646 4677758 MACS_peak_31 100.24
+chr1 4678360 4678472 MACS_peak_32 100.24
+chr1 4678659 4679136 MACS_peak_33 230.04
+chr1 4679439 4679551 MACS_peak_34 100.24
+chr1 4680106 4680523 MACS_peak_35 126.43
+chr1 4680822 4680934 MACS_peak_36 100.24
+chr1 4681075 4682050 MACS_peak_37 241.81
+chr1 4682229 4682387 MACS_peak_38 100.24
+chr1 4682594 4682706 MACS_peak_39 100.24
+chr1 4683158 4683270 MACS_peak_40 100.24
+chr1 4683473 4683585 MACS_peak_41 100.24
+chr1 4683832 4683944 MACS_peak_42 100.24
+chr1 4684591 4684775 MACS_peak_43 100.24
+chr1 4685292 4685404 MACS_peak_44 100.24
+chr1 4685810 4686198 MACS_peak_45 127.69
+chr1 4686493 4686605 MACS_peak_46 100.24
+chr1 4686818 4686930 MACS_peak_47 100.24
+chr1 4687387 4687499 MACS_peak_48 100.24
+chr1 4687692 4687902 MACS_peak_49 174.88
+chr1 4688181 4688790 MACS_peak_50 258.16
+chr1 4689101 4689557 MACS_peak_51 231.41
+chr1 4690039 4690151 MACS_peak_52 100.24
+chr1 4690290 4690402 MACS_peak_53 100.24
+chr1 4690780 4690907 MACS_peak_54 137.07
+chr1 4691478 4692335 MACS_peak_55 315.89
+chr1 4692464 4692768 MACS_peak_56 131.92
+chr1 4693243 4693751 MACS_peak_57 228.13
+chr1 4694306 4694418 MACS_peak_58 100.24
+chr1 4694738 4695016 MACS_peak_59 170.38
+chr1 4695207 4695378 MACS_peak_60 100.24
+chr1 4695503 4696600 MACS_peak_61 374.29
+chr1 4696903 4697015 MACS_peak_62 100.24
+chr1 4697569 4697912 MACS_peak_63 240.07
+chr1 4698224 4698395 MACS_peak_64 100.24
+chr1 4698790 4698904 MACS_peak_65 137.07
+chr1 4699223 4699430 MACS_peak_66 137.07
+chr1 4699642 4699754 MACS_peak_67 100.24
+chr1 4700457 4700569 MACS_peak_68 100.24
+chr1 4700853 4700965 MACS_peak_69 100.24
+chr1 4708474 4708898 MACS_peak_70 126.15
+chr1 4709426 4709741 MACS_peak_71 167.67
+chr1 4709925 4710127 MACS_peak_72 137.07
+chr1 4710465 4710577 MACS_peak_73 100.24
+chr1 4710812 4711277 MACS_peak_74 194.68
+chr1 4711462 4711762 MACS_peak_75 132.15
+chr1 4712202 4712479 MACS_peak_76 97.58
+chr1 4712673 4713163 MACS_peak_77 340.17
+chr1 4713659 4714656 MACS_peak_78 414.78
+chr1 4714840 4715470 MACS_peak_79 221.59
+chr1 4715671 4715783 MACS_peak_80 100.24
+chr1 4715908 4716811 MACS_peak_81 530.04
+chr1 4717318 4717430 MACS_peak_82 100.24
+chr1 4717789 4718230 MACS_peak_83 232.43
+chr1 4718990 4719236 MACS_peak_84 99.13
+chr1 4719718 4719830 MACS_peak_85 100.24
+chr1 4720276 4720388 MACS_peak_86 100.24
+chr1 4721061 4721173 MACS_peak_87 100.24
+chr1 4721620 4721782 MACS_peak_88 100.24
+chr1 4722229 4722341 MACS_peak_89 100.24
+chr1 4723262 4723374 MACS_peak_90 100.24
+chr1 4724496 4724608 MACS_peak_91 100.24
+chr1 4726179 4726291 MACS_peak_92 100.24
+chr1 4726472 4727091 MACS_peak_93 187.23
+chr1 4727268 4727705 MACS_peak_94 196.30
+chr1 4727871 4727983 MACS_peak_95 100.24
+chr1 4728976 4729088 MACS_peak_96 100.24
+chr1 4729473 4729611 MACS_peak_97 137.07
+chr1 4729954 4730093 MACS_peak_98 137.07
+chr1 4730636 4730805 MACS_peak_99 100.24
+chr1 4730936 4731305 MACS_peak_100 164.24
+chr1 4731799 4732585 MACS_peak_101 355.47
+chr1 4733192 4733304 MACS_peak_102 100.24
+chr1 4733710 4733831 MACS_peak_103 137.07
+chr1 4734062 4734891 MACS_peak_104 352.92
+chr1 4735075 4735290 MACS_peak_105 137.07
+chr1 4735523 4736190 MACS_peak_106 185.28
+chr1 4736399 4737184 MACS_peak_107 355.53
+chr1 4737395 4737601 MACS_peak_108 137.07
+chr1 4737973 4738425 MACS_peak_109 231.68
+chr1 4738796 4739212 MACS_peak_110 197.58
+chr1 4739379 4739491 MACS_peak_111 100.24
+chr1 4739612 4740720 MACS_peak_112 588.51
+chr1 4741405 4741655 MACS_peak_113 135.32
+chr1 4741998 4742300 MACS_peak_114 132.04
+chr1 4742829 4742952 MACS_peak_115 137.07
+chr1 4743079 4743327 MACS_peak_116 135.46
+chr1 4743612 4744566 MACS_peak_117 453.30
+chr1 4744719 4745224 MACS_peak_118 264.66
+chr1 4745398 4745786 MACS_peak_119 236.32
+chr1 4746034 4746316 MACS_peak_120 170.07
+chr1 4747206 4748408 MACS_peak_121 474.57
+chr1 4748814 4748926 MACS_peak_122 100.24
+chr1 4749222 4749334 MACS_peak_123 100.24
+chr1 4749686 4750054 MACS_peak_124 275.66
+chr1 4750335 4750697 MACS_peak_125 164.65
+chr1 4750863 4751682 MACS_peak_126 247.87
+chr1 4751853 4752428 MACS_peak_127 189.15
+chr1 4752581 4753611 MACS_peak_128 412.95
+chr1 4754241 4754864 MACS_peak_129 329.74
+chr1 4755088 4755200 MACS_peak_130 100.24
+chr1 4755722 4756029 MACS_peak_131 205.50
+chr1 4756768 4756880 MACS_peak_132 100.24
+chr1 4757199 4758615 MACS_peak_133 569.34
+chr1 4758753 4762214 MACS_peak_134 3100.00
+chr1 4763207 4763319 MACS_peak_135 100.24
+chr1 4763614 4763726 MACS_peak_136 100.24
+chr1 4763998 4764322 MACS_peak_137 358.13
+chr1 4764568 4764850 MACS_peak_138 133.23
+chr1 4765104 4765765 MACS_peak_139 291.01
+chr1 4765892 4766067 MACS_peak_140 100.24
+chr1 4766232 4766420 MACS_peak_141 100.24
+chr1 4766539 4767148 MACS_peak_142 367.65
+chr1 4767417 4767529 MACS_peak_143 100.24
+chr1 4768245 4768357 MACS_peak_144 100.24
+chr1 4768587 4768870 MACS_peak_145 170.00
+chr1 4768989 4769272 MACS_peak_146 133.17
+chr1 4769463 4769684 MACS_peak_147 174.88
+chr1 4769861 4770236 MACS_peak_148 200.29
+chr1 4770689 4771270 MACS_peak_149 224.05
+chr1 4771393 4772502 MACS_peak_150 1799.39
+chr1 4772633 4772916 MACS_peak_151 133.17
+chr1 4773121 4773284 MACS_peak_152 100.24
+chr1 4773476 4773614 MACS_peak_153 137.07
+chr1 4773827 4774279 MACS_peak_154 159.83
+chr1 4774510 4774622 MACS_peak_155 100.24
+chr1 4775041 4775694 MACS_peak_156 291.49
+chr1 4775832 4775944 MACS_peak_157 100.24
+chr1 4776166 4776310 MACS_peak_158 137.07
+chr1 4776506 4776851 MACS_peak_159 165.70
+chr1 4777100 4777321 MACS_peak_160 137.07
+chr1 4777505 4777617 MACS_peak_161 100.24
+chr1 4777764 4778298 MACS_peak_162 156.21
+chr1 4778680 4778792 MACS_peak_163 100.24
+chr1 4779265 4779377 MACS_peak_164 100.24
+chr1 4780814 4780926 MACS_peak_165 100.24
+chr1 4781238 4781436 MACS_peak_166 137.07
+chr1 4781600 4781712 MACS_peak_167 100.24
+chr1 4784249 4784487 MACS_peak_168 173.76
+chr1 4784800 4784912 MACS_peak_169 100.24
+chr1 4785500 4785612 MACS_peak_170 100.24
+chr1 4786820 4787357 MACS_peak_171 226.44
+chr1 4787570 4787682 MACS_peak_172 100.24
+chr1 4789440 4789978 MACS_peak_173 262.47
+chr1 4790257 4790424 MACS_peak_174 100.24
+chr1 4790723 4791308 MACS_peak_175 223.84
+chr1 4791871 4792641 MACS_peak_176 392.73
+chr1 4792756 4793323 MACS_peak_177 189.52
+chr1 4794493 4794929 MACS_peak_178 232.77
+chr1 4795046 4795357 MACS_peak_179 131.53
+chr1 4795495 4795607 MACS_peak_180 100.24
+chr1 4796218 4796432 MACS_peak_181 174.88
+chr1 4796841 4796953 MACS_peak_182 100.24
+chr1 4797267 4797499 MACS_peak_183 99.89
+chr1 4797910 4798022 MACS_peak_184 100.24
+chr1 4799151 4799263 MACS_peak_185 100.24
+chr1 4799518 4800266 MACS_peak_186 216.37
+chr1 4800415 4800527 MACS_peak_187 100.24
+chr1 4800989 4801101 MACS_peak_188 100.24
+chr1 4801344 4802288 MACS_peak_189 311.70
+chr1 4802600 4802712 MACS_peak_190 100.24
+chr1 4802944 4803056 MACS_peak_191 100.24
+chr1 4803408 4803520 MACS_peak_192 100.24
+chr1 4803899 4804011 MACS_peak_193 100.24
+chr1 4804278 4804390 MACS_peak_194 100.24
+chr1 4804716 4805427 MACS_peak_195 360.26
+chr1 4805843 4806018 MACS_peak_196 100.24
+chr1 4806294 4806406 MACS_peak_197 100.24
+chr1 4806523 4806849 MACS_peak_198 241.61
+chr1 4807024 4807205 MACS_peak_199 174.88
+chr1 4807520 4807740 MACS_peak_200 100.24
+chr1 4808021 4808133 MACS_peak_201 100.24
+chr1 4809641 4810406 MACS_peak_202 320.82
+chr1 4810853 4812088 MACS_peak_203 508.29
+chr1 4812253 4812665 MACS_peak_204 234.49
+chr1 4813090 4813202 MACS_peak_205 100.24
+chr1 4813466 4813836 MACS_peak_206 200.64
+chr1 4814068 4814180 MACS_peak_207 100.24
+chr1 4814343 4814700 MACS_peak_208 129.13
+chr1 4814902 4815014 MACS_peak_209 100.24
+chr1 4815190 4815343 MACS_peak_210 174.88
+chr1 4815570 4816098 MACS_peak_211 191.37
+chr1 4816683 4817303 MACS_peak_212 222.07
+chr1 4817449 4817735 MACS_peak_213 97.17
+chr1 4818299 4818411 MACS_peak_214 100.24
+chr1 4819699 4819870 MACS_peak_215 137.07
+chr1 4820406 4821178 MACS_peak_216 429.22
+chr1 4821318 4821821 MACS_peak_217 192.64
+chr1 4822130 4822242 MACS_peak_218 100.24
+chr1 4822509 4823010 MACS_peak_219 192.74
+chr1 4823526 4823638 MACS_peak_220 100.24
+chr1 4823838 4823996 MACS_peak_221 174.88
+chr1 4824146 4824258 MACS_peak_222 100.24
+chr1 4824694 4824806 MACS_peak_223 100.24
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+chr1 4827008 4827120 MACS_peak_227 100.24
+chr1 4827550 4827866 MACS_peak_228 95.87
+chr1 4828619 4829306 MACS_peak_229 184.51
+chr1 4829921 4830483 MACS_peak_230 409.14
+chr1 4830656 4830878 MACS_peak_231 137.07
+chr1 4831394 4831506 MACS_peak_232 100.24
+chr1 4831844 4831956 MACS_peak_233 100.24
+chr1 4832109 4832299 MACS_peak_234 137.07
+chr1 4832653 4832765 MACS_peak_235 100.24
+chr1 4833194 4833306 MACS_peak_236 100.24
+chr1 4833562 4834290 MACS_peak_237 322.98
+chr1 4834418 4834761 MACS_peak_238 129.83
+chr1 4835007 4835561 MACS_peak_239 225.49
+chr1 4835772 4835884 MACS_peak_240 100.24
+chr1 4836111 4836342 MACS_peak_241 136.69
+chr1 4836700 4836872 MACS_peak_242 100.24
+chr1 4837011 4837326 MACS_peak_243 95.91
+chr1 4837787 4838061 MACS_peak_244 97.73
+chr1 4838509 4838621 MACS_peak_245 100.24
+chr1 4838750 4839072 MACS_peak_246 130.92
+chr1 4839375 4839615 MACS_peak_247 211.91
+chr1 4840334 4840446 MACS_peak_248 100.24
+chr1 4841036 4841160 MACS_peak_249 137.07
+chr1 4841416 4841762 MACS_peak_250 165.63
+chr1 4842486 4842598 MACS_peak_251 100.24
+chr1 4842727 4843432 MACS_peak_252 183.84
+chr1 4843856 4844363 MACS_peak_253 301.38
+chr1 4844645 4845031 MACS_peak_254 163.26
+chr1 4845512 4845972 MACS_peak_255 159.45
+chr1 4846211 4846346 MACS_peak_256 213.48
+chr1 4846821 4847168 MACS_peak_257 129.63
+chr1 4847291 4847699 MACS_peak_258 126.81
+chr1 4847873 4848128 MACS_peak_259 98.66
+chr1 4848823 4848969 MACS_peak_260 137.07
+chr1 4849335 4850291 MACS_peak_261 453.17
+chr1 4850534 4850878 MACS_peak_262 129.78
+chr1 4851485 4851770 MACS_peak_263 97.21
+chr1 4852224 4852336 MACS_peak_264 100.24
+chr1 4852629 4852893 MACS_peak_265 171.51
+chr1 4853247 4853359 MACS_peak_266 100.24
+chr1 4853500 4853612 MACS_peak_267 100.24
+chr1 4854342 4854454 MACS_peak_268 100.24
+chr1 4854696 4854915 MACS_peak_269 137.07
+chr1 4855160 4855749 MACS_peak_270 154.08
+chr1 4856482 4857364 MACS_peak_271 211.36
+chr1 4857573 4857697 MACS_peak_272 213.48
+chr1 4857830 4857942 MACS_peak_273 100.24
+chr1 4858204 4858599 MACS_peak_274 235.78
+chr1 4858812 4859245 MACS_peak_275 125.78
+chr1 4859843 4859955 MACS_peak_276 100.24
+chr1 4860077 4860209 MACS_peak_277 137.07
+chr1 4860573 4861449 MACS_peak_278 458.48
+chr1 4861747 4861976 MACS_peak_279 100.06
+chr1 4862268 4862651 MACS_peak_280 93.36
+chr1 4863414 4863526 MACS_peak_281 100.24
+chr1 4864845 4865021 MACS_peak_282 100.24
+chr1 4865297 4865766 MACS_peak_283 230.56
+chr1 4865923 4866035 MACS_peak_284 100.24
+chr1 4866382 4866494 MACS_peak_285 100.24
+chr1 4867682 4867807 MACS_peak_286 137.07
+chr1 4868654 4868766 MACS_peak_287 100.24
+chr1 4868930 4869268 MACS_peak_288 94.99
+chr1 4869676 4869788 MACS_peak_289 100.24
+chr1 4872133 4872544 MACS_peak_290 271.82
+chr1 4872662 4873337 MACS_peak_291 254.59
+chr1 4874062 4874473 MACS_peak_292 271.82
+chr1 4874975 4875211 MACS_peak_293 173.94
+chr1 4876698 4876810 MACS_peak_294 100.24
+chr1 4877028 4877284 MACS_peak_295 98.61
+chr1 4877427 4877588 MACS_peak_296 100.24
+chr1 4878177 4878289 MACS_peak_297 100.24
+chr1 4878676 4878788 MACS_peak_298 100.24
+chr1 4879245 4880188 MACS_peak_299 209.33
+chr1 4880427 4881235 MACS_peak_300 318.45
+chr1 4881879 4882060 MACS_peak_301 137.07
+chr1 4882471 4883064 MACS_peak_302 295.25
+chr1 4883301 4883864 MACS_peak_303 155.06
+chr1 4884407 4884593 MACS_peak_304 100.24
+chr1 4884796 4884908 MACS_peak_305 100.24
+chr1 4885346 4886192 MACS_peak_306 212.63
+chr1 4886722 4886834 MACS_peak_307 100.24
+chr1 4887003 4887328 MACS_peak_308 130.76
+chr1 4887618 4887730 MACS_peak_309 100.24
+chr1 4889449 4889763 MACS_peak_310 95.95
+chr1 4890020 4890132 MACS_peak_311 100.24
+chr1 4890331 4890463 MACS_peak_312 137.07
+chr1 4890662 4891095 MACS_peak_313 270.01
+chr1 4891457 4893061 MACS_peak_314 701.27
+chr1 4893216 4893887 MACS_peak_315 290.43
+chr1 4894234 4894346 MACS_peak_316 100.24
+chr1 4894464 4894730 MACS_peak_317 171.34
+chr1 4895365 4895858 MACS_peak_318 157.95
+chr1 4896603 4896715 MACS_peak_319 100.24
+chr1 4897044 4897793 MACS_peak_320 216.33
+chr1 4898184 4898296 MACS_peak_321 100.24
+chr1 4898589 4898701 MACS_peak_322 100.24
+chr1 4898838 4899317 MACS_peak_323 124.03
+chr1 4899461 4900031 MACS_peak_324 296.80
+chr1 4900244 4900356 MACS_peak_325 100.24
+chr1 4900490 4900638 MACS_peak_326 137.07
+chr1 4900927 4901039 MACS_peak_327 100.24
+chr1 4901371 4901558 MACS_peak_328 137.07
+chr1 4901767 4902496 MACS_peak_329 359.06
+chr1 4902621 4903202 MACS_peak_330 259.79
+chr1 4903396 4903692 MACS_peak_331 169.02
+chr1 4903871 4903983 MACS_peak_332 100.24
+chr1 4904596 4904708 MACS_peak_333 100.24
+chr1 4905302 4905414 MACS_peak_334 100.24
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+chr1 5615704 5615816 MACS_peak_1137 100.24
+chr1 5616141 5616253 MACS_peak_1138 100.24
+chr1 5616372 5616484 MACS_peak_1139 100.24
+chr1 5616668 5617219 MACS_peak_1140 335.07
+chr1 5617497 5617795 MACS_peak_1141 96.63
+chr1 5619893 5620086 MACS_peak_1142 100.24
+chr1 5620435 5620547 MACS_peak_1143 100.24
+chr1 5621379 5622034 MACS_peak_1144 220.40
+chr1 5624571 5624683 MACS_peak_1145 100.24
+chr1 5625232 5625344 MACS_peak_1146 100.24
+chr1 5627078 5627190 MACS_peak_1147 100.24
+chr1 5632017 5632129 MACS_peak_1148 100.24
+chr1 5632376 5632652 MACS_peak_1149 170.54
+chr1 5633321 5633535 MACS_peak_1150 137.07
+chr1 5633696 5633881 MACS_peak_1151 100.24
+chr1 5634469 5634687 MACS_peak_1152 100.24
+chr1 5635062 5635329 MACS_peak_1153 98.06
+chr1 5635461 5635573 MACS_peak_1154 100.24
+chr1 5635728 5635840 MACS_peak_1155 100.24
+chr1 5636596 5636789 MACS_peak_1156 100.24
+chr1 5637075 5637187 MACS_peak_1157 100.24
+chr1 5637607 5637719 MACS_peak_1158 100.24
+chr1 5640953 5641065 MACS_peak_1159 100.24
+chr1 5643184 5643361 MACS_peak_1160 100.24
+chr1 5644450 5644562 MACS_peak_1161 100.24
+chr1 5646326 5646650 MACS_peak_1162 130.82
+chr1 5646766 5647194 MACS_peak_1163 125.98
+chr1 5647474 5647766 MACS_peak_1164 132.62
+chr1 5648437 5649089 MACS_peak_1165 364.39
+chr1 5649411 5650167 MACS_peak_1166 467.44
+chr1 5650744 5650944 MACS_peak_1167 137.07
+chr1 5651395 5651820 MACS_peak_1168 197.02
+chr1 5652003 5652323 MACS_peak_1169 167.33
+chr1 5652795 5653010 MACS_peak_1170 137.07
+chr1 5653365 5653689 MACS_peak_1171 318.88
+chr1 5653877 5653989 MACS_peak_1172 100.24
+chr1 5654231 5654343 MACS_peak_1173 100.24
+chr1 5654571 5654866 MACS_peak_1174 96.76
+chr1 5655769 5656176 MACS_peak_1175 198.15
+chr1 5656312 5656424 MACS_peak_1176 100.24
+chr1 5657271 5657383 MACS_peak_1177 100.24
+chr1 5657651 5657988 MACS_peak_1178 166.21
+chr1 5658525 5658637 MACS_peak_1179 100.24
+chr1 5659194 5659308 MACS_peak_1180 137.07
+chr1 5660375 5660575 MACS_peak_1181 137.07
+chr1 5660781 5660893 MACS_peak_1182 100.24
+chr1 5661327 5661439 MACS_peak_1183 100.24
+chr1 5662504 5662697 MACS_peak_1184 137.07
+chr1 5663691 5663885 MACS_peak_1185 137.07
+chr1 5664582 5664750 MACS_peak_1186 100.24
+chr1 5665076 5665188 MACS_peak_1187 100.24
+chr1 5665895 5666007 MACS_peak_1188 100.24
+chr1 5666448 5666930 MACS_peak_1189 193.75
+chr1 5667751 5667934 MACS_peak_1190 100.24
+chr1 5674057 5674169 MACS_peak_1191 100.24
+chr1 5675063 5675175 MACS_peak_1192 100.24
+chr1 5676274 5676386 MACS_peak_1193 100.24
+chr1 5676599 5676711 MACS_peak_1194 100.24
+chr1 5677228 5677340 MACS_peak_1195 100.24
+chr1 5677740 5677852 MACS_peak_1196 100.24
+chr1 5679022 5679667 MACS_peak_1197 291.97
+chr1 5680026 5681034 MACS_peak_1198 240.66
+chr1 5682911 5683023 MACS_peak_1199 100.24
+chr1 5688032 5688144 MACS_peak_1200 100.24
+chr1 5688335 5688657 MACS_peak_1201 130.92
+chr1 5688801 5688913 MACS_peak_1202 100.24
+chr1 5689087 5689348 MACS_peak_1203 98.36
+chr1 5689475 5689587 MACS_peak_1204 100.24
+chr1 5689771 5689883 MACS_peak_1205 100.24
+chr1 5690261 5690373 MACS_peak_1206 100.24
+chr1 5690750 5690873 MACS_peak_1207 137.07
+chr1 5694742 5695180 MACS_peak_1208 160.51
+chr1 5695333 5695675 MACS_peak_1209 129.88
+chr1 5696080 5696192 MACS_peak_1210 100.24
+chr1 5696612 5697345 MACS_peak_1211 251.72
+chr1 5697961 5698073 MACS_peak_1212 100.24
+chr1 5698235 5698383 MACS_peak_1213 137.07
+chr1 5698832 5699021 MACS_peak_1214 100.24
+chr1 5699479 5699591 MACS_peak_1215 100.24
+chr1 5700029 5700141 MACS_peak_1216 100.24
+chr1 5700387 5700503 MACS_peak_1217 137.07
+chr1 5703736 5703848 MACS_peak_1218 100.24
+chr1 5704571 5704683 MACS_peak_1219 100.24
+chr1 5704979 5705219 MACS_peak_1220 136.03
+chr1 5705728 5705840 MACS_peak_1221 100.24
+chr1 5706213 5706482 MACS_peak_1222 247.45
+chr1 5706879 5706991 MACS_peak_1223 100.24
+chr1 5707211 5707414 MACS_peak_1224 100.24
+chr1 5707733 5707955 MACS_peak_1225 100.24
+chr1 5708418 5708530 MACS_peak_1226 100.24
+chr1 5708711 5708823 MACS_peak_1227 100.24
+chr1 5709009 5709168 MACS_peak_1228 100.24
+chr1 5709626 5709738 MACS_peak_1229 100.24
+chr1 5710175 5710287 MACS_peak_1230 100.24
+chr1 5711491 5711603 MACS_peak_1231 100.24
+chr1 5712452 5712913 MACS_peak_1232 159.40
+chr1 5713590 5713702 MACS_peak_1233 100.24
+chr1 5714277 5714835 MACS_peak_1234 189.93
+chr1 5715628 5715793 MACS_peak_1235 100.24
+chr1 5715919 5716031 MACS_peak_1236 100.24
+chr1 5716150 5716384 MACS_peak_1237 174.12
+chr1 5717000 5717112 MACS_peak_1238 100.24
+chr1 5717383 5717774 MACS_peak_1239 127.55
+chr1 5718298 5718531 MACS_peak_1240 136.54
+chr1 5718754 5719002 MACS_peak_1241 172.86
+chr1 5719627 5719739 MACS_peak_1242 100.24
+chr1 5720578 5720690 MACS_peak_1243 100.24
+chr1 5721523 5721843 MACS_peak_1244 95.71
+chr1 5722221 5722388 MACS_peak_1245 100.24
+chr1 5722739 5722851 MACS_peak_1246 100.24
+chr1 5723148 5723403 MACS_peak_1247 134.98
+chr1 5724342 5724566 MACS_peak_1248 100.24
+chr1 5725453 5725597 MACS_peak_1249 137.07
+chr1 5725942 5726075 MACS_peak_1250 137.07
+chr1 5726202 5726647 MACS_peak_1251 306.48
+chr1 5726801 5726913 MACS_peak_1252 100.24
+chr1 5727303 5727415 MACS_peak_1253 100.24
+chr1 5727541 5727720 MACS_peak_1254 213.48
+chr1 5728015 5728127 MACS_peak_1255 100.24
+chr1 5728661 5728922 MACS_peak_1256 98.36
+chr1 5729591 5729703 MACS_peak_1257 100.24
+chr1 5729971 5730118 MACS_peak_1258 137.07
+chr1 5735097 5735209 MACS_peak_1259 100.24
+chr1 5738165 5738277 MACS_peak_1260 100.24
+chr1 5741886 5742013 MACS_peak_1261 137.07
+chr1 5742222 5742493 MACS_peak_1262 133.92
+chr1 5742624 5742892 MACS_peak_1263 98.02
+chr1 5743479 5743591 MACS_peak_1264 100.24
+chr1 5743802 5743943 MACS_peak_1265 137.07
+chr1 5744327 5745001 MACS_peak_1266 185.01
+chr1 5745544 5746174 MACS_peak_1267 221.59
+chr1 5746482 5747182 MACS_peak_1268 218.38
+chr1 5747751 5747863 MACS_peak_1269 100.24
+chr1 5749480 5749592 MACS_peak_1270 100.24
diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_2_neg_peaks_out.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/macs_test_2_neg_peaks_out.interval Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,59 @@
+#negative peaks file
+#chr start end length summit tags -10*log10(pvalue) fold_enrichment
+chr1 3012338 3012474 136 69 3 79.72 265.54
+chr1 3012631 3012751 120 61 3 79.72 265.54
+chr1 3055826 3056120 294 96 9 59.49 18.22
+chr1 3066934 3067568 634 101 10 53.35 18.44
+chr1 3076059 3076339 280 112 6 58.24 29.50
+chr1 3092687 3093270 583 344 11 50.81 10.32
+chr1 3114123 3114523 400 107 10 51.47 11.06
+chr1 3125324 3126255 931 573 13 65.69 12.07
+chr1 3126473 3127174 701 249 11 65.43 13.28
+chr1 3127353 3127879 526 265 14 110.59 22.13
+chr1 3195224 3195844 620 395 13 56.61 13.28
+chr1 3228283 3228748 465 388 6 50.25 26.55
+chr1 3275975 3276467 492 404 9 55.17 15.39
+chr1 3285007 3286005 998 891 18 66.19 11.06
+chr1 3312699 3313743 1044 204 21 60.12 11.06
+chr1 3446632 3447508 876 176 14 61.26 14.75
+chr1 3468402 3469436 1034 109 18 50.75 7.08
+chr1 3474772 3476374 1602 960 22 66.92 12.29
+chr1 3514508 3515086 578 110 13 59.90 11.06
+chr1 3517009 3518094 1085 84 14 50.75 11.80
+chr1 3599829 3601141 1312 109 19 65.77 10.41
+chr1 3605828 3605951 123 62 4 52.20 18.63
+chr1 3606596 3607433 837 548 10 66.22 27.23
+chr1 3613851 3614116 265 103 6 57.63 34.04
+chr1 3614432 3615882 1450 85 15 63.55 13.28
+chr1 3617465 3617784 319 211 9 51.03 11.06
+chr1 3640315 3641949 1634 273 32 81.39 10.68
+chr1 3647349 3648562 1213 411 19 67.14 9.83
+chr1 3735801 3736852 1051 878 17 73.61 14.75
+chr1 3796005 3796544 539 65 5 54.89 44.26
+chr1 3797371 3797763 392 70 6 54.44 26.55
+chr1 3835421 3835673 252 171 6 53.74 22.13
+chr1 3856581 3857561 980 110 19 52.84 9.48
+chr1 3968246 3968621 375 85 7 60.72 34.04
+chr1 3970428 3970718 290 69 5 56.15 50.58
+chr1 4034953 4036094 1141 465 15 66.64 18.44
+chr1 4051823 4055268 3445 669 46 119.08 9.32
+chr1 4099917 4100882 965 256 18 84.48 11.39
+chr1 4112353 4113269 916 72 15 53.99 9.32
+chr1 4139620 4140296 676 399 14 71.23 11.06
+chr1 4191034 4191488 454 386 9 51.16 15.81
+chr1 4191774 4192345 571 102 10 51.50 12.64
+chr1 4201259 4202176 917 651 13 64.28 19.24
+chr1 4218597 4219458 861 460 16 53.64 5.77
+chr1 4223608 4224231 623 472 14 78.93 14.75
+chr1 4238528 4239382 854 90 14 54.69 15.12
+chr1 4283406 4284196 790 400 11 60.42 22.13
+chr1 4368609 4369824 1215 504 19 72.89 10.75
+chr1 4382657 4385390 2733 1297 36 97.80 12.10
+chr1 4439048 4440167 1119 927 19 80.31 13.83
+chr1 4447108 4448669 1561 1375 31 62.31 7.54
+chr1 4462162 4466719 4557 4366 75 90.49 8.30
+chr1 4479282 4480091 809 700 19 60.40 10.33
+chr1 4568704 4569556 852 319 25 69.71 8.62
+chr1 4596926 4597745 819 449 17 51.74 9.48
+chr1 4636007 4637827 1820 110 30 51.27 8.57
+chr1 4646136 4647867 1731 101 28 53.47 7.38
diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_2_peaks_out.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/macs_test_2_peaks_out.interval Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,1289 @@
+#peaks file
+# This file is generated by MACS
+# ARGUMENTS LIST:
+# name = MACS_in_Galaxy
+# format = BED
+# ChIP-seq file = /galaxy/home/dan/central/database/files/000/dataset_404.dat
+# control file = /galaxy/home/dan/central/database/files/000/dataset_405.dat
+# effective genome size = 2.70e+09
+# tag size = 36
+# band width = 300
+# model fold = 13
+# pvalue cutoff = 1.00e-05
+# Ranges for calculating regional lambda are : peak_region,1000,5000,10000
+# unique tags in treatment: 9898
+# total tags in treatment: 10000
+# unique tags in control: 9896
+# total tags in control: 10000
+# d = 113
+#chr start end length summit tags -10*log10(pvalue) fold_enrichment FDR(%)
+chr1 3138857 3139271 414 95 6 53.08 35.39 3.55
+chr1 4133899 4134700 801 157 27 51.91 9.92 3.70
+chr1 4323670 4324367 697 306 49 272.01 29.81 0.00
+chr1 4336486 4337946 1460 1216 65 228.35 32.00 0.00
+chr1 4407086 4409120 2034 1133 105 300.46 29.27 0.00
+chr1 4507832 4508710 878 245 44 161.74 18.90 0.00
+chr1 4657704 4658572 868 775 9 280.37 7242.01 0.00
+chr1 4658705 4659021 316 110 4 131.25 4828.01 0.00
+chr1 4659147 4660581 1434 844 15 463.08 7242.01 0.00
+chr1 4661156 4661317 161 81 4 174.88 9656.01 0.00
+chr1 4661505 4661617 112 57 2 100.24 4828.01 0.17
+chr1 4661790 4662463 673 287 7 219.58 4828.01 0.00
+chr1 4662710 4663434 724 623 12 395.94 9656.01 0.00
+chr1 4664135 4664430 295 64 5 169.10 7242.01 0.00
+chr1 4665001 4665113 112 57 2 100.24 4828.01 0.17
+chr1 4665839 4666425 586 475 10 332.40 12070.02 0.00
+chr1 4666581 4666693 112 57 2 100.24 4828.01 0.17
+chr1 4666840 4666981 141 71 4 174.88 9656.01 0.00
+chr1 4667600 4667712 112 57 2 100.24 4828.01 0.17
+chr1 4668711 4669005 294 75 5 169.17 7242.01 0.00
+chr1 4669126 4669238 112 57 2 100.24 4828.01 0.17
+chr1 4669537 4669752 215 108 5 174.88 12070.02 0.00
+chr1 4669936 4670048 112 57 2 100.24 4828.01 0.17
+chr1 4670216 4670449 233 97 6 212.68 12070.02 0.00
+chr1 4673856 4674051 195 98 4 137.07 9656.01 0.00
+chr1 4674349 4674478 129 65 3 137.07 7242.01 0.00
+chr1 4675027 4675152 125 63 3 137.07 7242.01 0.00
+chr1 4676227 4676339 112 57 2 100.24 4828.01 0.17
+chr1 4676511 4676623 112 57 2 100.24 4828.01 0.17
+chr1 4676954 4677151 197 99 3 100.24 7242.01 0.17
+chr1 4677646 4677758 112 57 2 100.24 4828.01 0.17
+chr1 4678360 4678472 112 57 2 100.24 4828.01 0.17
+chr1 4678659 4679136 477 307 7 230.04 7242.01 0.00
+chr1 4679439 4679551 112 57 2 100.24 4828.01 0.17
+chr1 4680106 4680523 417 103 5 126.43 4828.01 0.00
+chr1 4680822 4680934 112 57 2 100.24 4828.01 0.17
+chr1 4681075 4682050 975 104 8 241.81 4828.01 0.00
+chr1 4682229 4682387 158 80 3 100.24 7242.01 0.17
+chr1 4682594 4682706 112 57 2 100.24 4828.01 0.17
+chr1 4683158 4683270 112 57 2 100.24 4828.01 0.17
+chr1 4683473 4683585 112 57 2 100.24 4828.01 0.17
+chr1 4683832 4683944 112 57 2 100.24 4828.01 0.17
+chr1 4684591 4684775 184 93 3 100.24 7242.01 0.17
+chr1 4685292 4685404 112 57 2 100.24 4828.01 0.17
+chr1 4685810 4686198 388 75 4 127.69 4828.01 0.00
+chr1 4686493 4686605 112 57 2 100.24 4828.01 0.17
+chr1 4686818 4686930 112 57 2 100.24 4828.01 0.17
+chr1 4687387 4687499 112 57 2 100.24 4828.01 0.17
+chr1 4687692 4687902 210 106 5 174.88 12070.02 0.00
+chr1 4688181 4688790 609 96 8 258.16 9656.01 0.00
+chr1 4689101 4689557 456 250 7 231.41 9656.01 0.00
+chr1 4690039 4690151 112 57 2 100.24 4828.01 0.17
+chr1 4690290 4690402 112 57 2 100.24 4828.01 0.17
+chr1 4690780 4690907 127 64 3 137.07 7242.01 0.00
+chr1 4691478 4692335 857 509 10 315.89 7242.01 0.00
+chr1 4692464 4692768 304 67 4 131.92 7242.01 0.00
+chr1 4693243 4693751 508 307 7 228.13 9656.01 0.00
+chr1 4694306 4694418 112 57 2 100.24 4828.01 0.17
+chr1 4694738 4695016 278 75 5 170.38 9656.01 0.00
+chr1 4695207 4695378 171 86 3 100.24 7242.01 0.17
+chr1 4695503 4696600 1097 535 12 374.29 7242.01 0.00
+chr1 4696903 4697015 112 57 2 100.24 4828.01 0.17
+chr1 4697569 4697912 343 106 7 240.07 12070.02 0.00
+chr1 4698224 4698395 171 86 3 100.24 7242.01 0.17
+chr1 4698790 4698904 114 58 3 137.07 7242.01 0.00
+chr1 4699223 4699430 207 104 4 137.07 9656.01 0.00
+chr1 4699642 4699754 112 57 2 100.24 4828.01 0.17
+chr1 4700457 4700569 112 57 2 100.24 4828.01 0.17
+chr1 4700853 4700965 112 57 2 100.24 4828.01 0.17
+chr1 4708474 4708898 424 57 4 126.15 4828.01 0.00
+chr1 4709426 4709741 315 102 5 167.67 9656.01 0.00
+chr1 4709925 4710127 202 102 4 137.07 9656.01 0.00
+chr1 4710465 4710577 112 57 2 100.24 4828.01 0.17
+chr1 4710812 4711277 465 111 6 194.68 7242.01 0.00
+chr1 4711462 4711762 300 102 4 132.15 4828.01 0.00
+chr1 4712202 4712479 277 57 3 97.58 4828.01 0.24
+chr1 4712673 4713163 490 111 10 340.17 9656.01 0.00
+chr1 4713659 4714656 997 230 13 414.78 7242.01 0.00
+chr1 4714840 4715470 630 83 7 221.59 7242.01 0.00
+chr1 4715671 4715783 112 57 2 100.24 4828.01 0.17
+chr1 4715908 4716811 903 824 16 530.04 12070.02 0.00
+chr1 4717318 4717430 112 57 2 100.24 4828.01 0.17
+chr1 4717789 4718230 441 103 7 232.43 12070.02 0.00
+chr1 4718990 4719236 246 57 3 99.13 4828.01 0.16
+chr1 4719718 4719830 112 57 2 100.24 4828.01 0.17
+chr1 4720276 4720388 112 57 2 100.24 4828.01 0.17
+chr1 4721061 4721173 112 57 2 100.24 4828.01 0.17
+chr1 4721620 4721782 162 82 3 100.24 7242.01 0.17
+chr1 4722229 4722341 112 57 2 100.24 4828.01 0.17
+chr1 4723262 4723374 112 57 2 100.24 4828.01 0.17
+chr1 4724496 4724608 112 57 2 100.24 4828.01 0.17
+chr1 4726179 4726291 112 57 2 100.24 4828.01 0.17
+chr1 4726472 4727091 619 82 6 187.23 7242.01 0.00
+chr1 4727268 4727705 437 66 6 196.30 7242.01 0.00
+chr1 4727871 4727983 112 57 2 100.24 4828.01 0.17
+chr1 4728976 4729088 112 57 2 100.24 4828.01 0.17
+chr1 4729473 4729611 138 70 3 137.07 7242.01 0.00
+chr1 4729954 4730093 139 70 3 137.07 7242.01 0.00
+chr1 4730636 4730805 169 85 3 100.24 7242.01 0.17
+chr1 4730936 4731305 369 111 5 164.24 9656.01 0.00
+chr1 4731799 4732585 786 443 11 355.47 7242.01 0.00
+chr1 4733192 4733304 112 57 2 100.24 4828.01 0.17
+chr1 4733710 4733831 121 61 3 137.07 7242.01 0.00
+chr1 4734062 4734891 829 75 11 352.92 9656.01 0.00
+chr1 4735075 4735290 215 108 4 137.07 9656.01 0.00
+chr1 4735523 4736190 667 236 7 185.28 4828.01 0.00
+chr1 4736399 4737184 785 80 11 355.53 9656.01 0.00
+chr1 4737395 4737601 206 104 4 137.07 9656.01 0.00
+chr1 4737973 4738425 452 188 7 231.68 7242.01 0.00
+chr1 4738796 4739212 416 311 6 197.58 7242.01 0.00
+chr1 4739379 4739491 112 57 2 100.24 4828.01 0.17
+chr1 4739612 4740720 1108 105 18 588.51 9656.01 0.00
+chr1 4741405 4741655 250 80 4 135.32 7242.01 0.00
+chr1 4741998 4742300 302 79 4 132.04 4828.01 0.00
+chr1 4742829 4742952 123 62 3 137.07 7242.01 0.00
+chr1 4743079 4743327 248 101 4 135.46 4828.01 0.00
+chr1 4743612 4744566 954 97 14 453.30 12070.02 0.00
+chr1 4744719 4745224 505 260 8 264.66 7242.01 0.00
+chr1 4745398 4745786 388 301 8 236.32 9656.01 0.00
+chr1 4746034 4746316 282 112 5 170.07 9656.01 0.00
+chr1 4747206 4748408 1202 316 15 474.57 9656.01 0.00
+chr1 4748814 4748926 112 57 2 100.24 4828.01 0.17
+chr1 4749222 4749334 112 57 2 100.24 4828.01 0.17
+chr1 4749686 4750054 368 97 8 275.66 12070.02 0.00
+chr1 4750335 4750697 362 79 5 164.65 7242.01 0.00
+chr1 4750863 4751682 819 109 8 247.87 4828.01 0.00
+chr1 4751853 4752428 575 78 6 189.15 7242.01 0.00
+chr1 4752581 4753611 1030 565 13 412.95 9656.01 0.00
+chr1 4754241 4754864 623 233 10 329.74 9656.01 0.00
+chr1 4755088 4755200 112 57 2 100.24 4828.01 0.17
+chr1 4755722 4756029 307 100 6 205.50 12070.02 0.00
+chr1 4756768 4756880 112 57 2 100.24 4828.01 0.17
+chr1 4757199 4758615 1416 753 18 569.34 7242.01 0.00
+chr1 4758753 4762214 3461 1125 247 3100.00 217260.30 0.00
+chr1 4763207 4763319 112 57 2 100.24 4828.01 0.17
+chr1 4763614 4763726 112 57 2 100.24 4828.01 0.17
+chr1 4763998 4764322 324 233 10 358.13 14484.02 0.00
+chr1 4764568 4764850 282 62 4 133.23 7242.01 0.00
+chr1 4765104 4765765 661 112 9 291.01 12070.02 0.00
+chr1 4765892 4766067 175 88 3 100.24 7242.01 0.17
+chr1 4766232 4766420 188 95 3 100.24 7242.01 0.17
+chr1 4766539 4767148 609 171 11 367.65 14484.02 0.00
+chr1 4767417 4767529 112 57 2 100.24 4828.01 0.17
+chr1 4768245 4768357 112 57 2 100.24 4828.01 0.17
+chr1 4768587 4768870 283 99 5 170.00 9656.01 0.00
+chr1 4768989 4769272 283 104 4 133.17 4828.01 0.00
+chr1 4769463 4769684 221 111 5 174.88 12070.02 0.00
+chr1 4769861 4770236 375 287 6 200.29 7242.01 0.00
+chr1 4770689 4771270 581 256 7 224.05 7242.01 0.00
+chr1 4771393 4772502 1109 197 49 1799.39 57936.08 0.00
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diff -r 49961332adb6 -r e9de35947c06 tool_conf.xml.main
--- a/tool_conf.xml.main Fri Feb 05 15:51:01 2010 -0500
+++ b/tool_conf.xml.main Fri Feb 05 16:06:27 2010 -0500
@@ -298,5 +298,9 @@
<tool file="samtools/pileup_parser.xml" />
<tool file="samtools/pileup_interval.xml" />
</section>
-
+ <section name="NGS: Peak Calling" id="peak_calling">
+ <tool file="peak_calling/macs_wrapper.xml" />
+ <tool file="genetrack/genetrack_indexer.xml" />
+ <tool file="genetrack/genetrack_peak_prediction.xml" />
+ </section>
</toolbox>
diff -r 49961332adb6 -r e9de35947c06 tool_conf.xml.sample
--- a/tool_conf.xml.sample Fri Feb 05 15:51:01 2010 -0500
+++ b/tool_conf.xml.sample Fri Feb 05 16:06:27 2010 -0500
@@ -129,8 +129,6 @@
<tool file="visualization/GMAJ.xml" />
<tool file="visualization/LAJ.xml" />
<tool file="visualization/build_ucsc_custom_track.xml" />
- <tool file="visualization/genetrack_indexer.xml" />
- <tool file="visualization/genetrack_peak_prediction.xml" />
</section>
<section name="Regional Variation" id="regVar">
<tool file="regVariation/windowSplitter.xml" />
@@ -207,6 +205,11 @@
<tool file="samtools/pileup_parser.xml" />
<tool file="samtools/pileup_interval.xml" />
</section>
+ <section name="NGS: Peak Calling" id="peak_calling">
+ <tool file="peak_calling/macs_wrapper.xml" />
+ <tool file="genetrack/genetrack_indexer.xml" />
+ <tool file="genetrack/genetrack_peak_prediction.xml" />
+ </section>
<section name="Rg Data" id="rgData1">
<tool file="rgenetics/rgenetics_import.xml"/>
<tool file="rgenetics/rgLpedPbed.xml"/>
diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_indexer.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/genetrack/genetrack_indexer.py Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+"""
+Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy.
+
+usage: %prog input output shift
+"""
+
+import sys, shutil, os
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "GeneTrack" )
+
+from genetrack.scripts import tabs2genetrack
+from genetrack import logger
+
+if __name__ == "__main__":
+ import os
+ os.environ[ 'LC_ALL' ] = 'C'
+ #os.system( 'export' )
+
+ parser = tabs2genetrack.option_parser()
+
+ options, args = parser.parse_args()
+
+ # uppercase the format
+ options.format = options.format.upper()
+
+ if options.format not in ('BED', 'GFF'):
+ sys.stdout = sys.stderr
+ parser.print_help()
+ sys.exit(-1)
+
+ logger.disable(options.verbosity)
+
+ # missing file names
+ if not (options.inpname and options.outname and options.format):
+ parser.print_help()
+ sys.exit(-1)
+ else:
+ tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\
+ format=options.format, shift=options.shift, index=options.index, options=options)
diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_indexer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/genetrack/genetrack_indexer.xml Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,54 @@
+<tool id="bed2genetrack" name="GeneTrack indexer">
+
+ <description>on a BED file</description>
+
+ <command interpreter="python">
+ genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
+ </command>
+
+ <inputs>
+
+ <param format="bed" name="input" type="data" help="Input data">
+ <label>Select input bed file</label>
+ </param>
+
+ <param name="shift" size="4" type="integer" value="0" help="distance in basepairs">
+ <label>Shift at 5' end</label>
+ </param>
+
+ <!-- this parameter is currently not used, may not be feasible to use it
+ <param name="coverage" type="select" label="Full coverage">
+ <option value="no">NO</option>
+ <option value="yes">YES</option>
+ </param>
+ -->
+
+ </inputs>
+
+ <outputs>
+ <data format="genetrack" name="output" />
+ </outputs>
+
+<help>
+**Help**
+
+This tool will create a visualization of the bed file that is selected.
+
+**Parameters**
+
+- **Shift at 5' end** should be used when the location of interest is at a fixed distance from
+ the 5' end for **all sequenced fragments**!
+
+ For example if the sequenced sample consists
+ mono-nucleosomal DNA (146bp) we should expect that
+ each nucleosome midpoint is located at 73 bp from the 5' end of the fragment.
+ Therefore we would enter 73 as the shift parameter. Once corrected the reads
+ on each strand will coincide and indicate the actual midpoints
+ of the nucleosomes.
+
+ When shifting the averaging process in GeneTrack is able correct for longer or shorter
+ than expected fragment sizes as long as the errors are reasonably random.
+
+</help>
+
+</tool>
diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_peak_prediction.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/genetrack/genetrack_peak_prediction.py Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+"""
+Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy.
+
+usage: %prog input output level sigma mode exclusion strand
+"""
+
+import sys
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "GeneTrack" )
+
+from genetrack.scripts import peakpred
+from genetrack import logger
+
+if __name__ == "__main__":
+
+ parser = peakpred.option_parser()
+
+ options, args = parser.parse_args()
+
+ logger.disable(options.verbosity)
+
+ from genetrack import conf
+
+ # trigger test mode
+ if options.test:
+ options.inpname = conf.testdata('test-hdflib-input.gtrack')
+ options.outname = conf.testdata('predictions.bed')
+
+ # missing input file name
+ if not options.inpname and not options.outname:
+ parser.print_help()
+ else:
+ print 'Sigma = %s' % options.sigma
+ print 'Minimum peak = %s' % options.level
+ print 'Peak-to-peak = %s' % options.exclude
+
+ peakpred.predict(options.inpname, options.outname, options)
diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_peak_prediction.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/genetrack/genetrack_peak_prediction.xml Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,59 @@
+<tool id="predict2genetrack" name="Peak predictor">
+
+ <description>on GeneTrack index</description>
+
+ <command interpreter="python">
+ genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x
+ </command>
+
+ <inputs>
+
+ <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/>
+
+ <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values">
+ <option value="gauss">Gaussian kernel</option>
+ <!-- <option value="yes">Moving averages</option> -->
+ </param>
+
+ <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" />
+
+
+ <param name="mode" type="select" label="Peak prediction" help="Peak prediction method">
+ <option value="nolap">Maximal non-overlapping</option>
+ <!-- <option value="above">Above a threshold</option> -->
+ <option value="all">All peaks</option>
+ </param>
+
+ <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance">
+ </param>
+
+ <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" />
+
+ <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately">
+ <option value="all">Merge strands</option>
+ <!-- <option value="yes1">Above a threshold</option> -->
+ <option value="two">Separate strands</option>
+ </param>
+
+ </inputs>
+
+ <outputs>
+ <data format="bed" name="output" />
+ </outputs>
+
+<help>
+**Help**
+
+This tool will generate genome wide peak prediction from an index file.
+
+**Parameters**
+
+- **Smoothing method** the function used to average nearby values
+
+- **Smoothing value** the factor used in the method
+
+- **Prediction method** the function used to average nearby values
+
+</help>
+
+</tool>
diff -r 49961332adb6 -r e9de35947c06 tools/peak_calling/macs_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/peak_calling/macs_wrapper.py Fri Feb 05 16:06:27 2010 -0500
@@ -0,0 +1,138 @@
+import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "simplejson" )
+import simplejson
+
+CHUNK_SIZE = 1024
+ERROR_LINES = [ 'ERROR', 'command not found' ] #'Fatal' errors that should be passed back to stderr
+WARNING_LINE_START = 'WARNING @'
+
+def gunzip_cat_glob_path( glob_path, target_filename, delete = False ):
+ out = open( target_filename, 'wb' )
+ for filename in glob.glob( glob_path ):
+ fh = gzip.open( filename, 'rb' )
+ while True:
+ data = fh.read( CHUNK_SIZE )
+ if data:
+ out.write( data )
+ else:
+ break
+ fh.close()
+ if delete:
+ os.unlink( filename )
+ out.close()
+
+def xls_to_interval( xls_file, interval_file, header = None ):
+ out = open( interval_file, 'wb' )
+ if header:
+ out.write( '#%s\n' % header )
+ wrote_header = False
+ #From macs readme: Coordinates in XLS is 1-based which is different with BED format.
+ for line in open( xls_file ):
+ #keep all existing comment lines
+ if line.startswith( '#' ):
+ out.write( line )
+ elif not wrote_header:
+ out.write( '#%s' % line )
+ wrote_header = True
+ else:
+ fields = line.split( '\t' )
+ if len( fields ) > 1:
+ fields[1] = str( int( fields[1] ) - 1 )
+ out.write( '\t'.join( fields ) )
+ out.close()
+
+def main():
+ options = simplejson.load( open( sys.argv[1] ) )
+ output_bed = sys.argv[2]
+ output_extra_html = sys.argv[3]
+ output_extra_path = sys.argv[4]
+
+ experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for filenames (gzip of wig files will fail with spaces - macs doesn't properly escape them)..need to replace all whitespace, split makes this easier
+ cmdline = "macs -t %s" % ",".join( options['input_chipseq'] )
+ if options['input_control']:
+ cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) )
+ cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] )
+ if 'wig' in options:
+ wigextend = int( options['wig']['wigextend'] )
+ if wigextend >= 0:
+ wigextend = "--wigextend='%s'" % wigextend
+ else:
+ wigextend = ''
+ cmdline = "%s --wig %s --space='%s'" % ( cmdline, wigextend, options['wig']['space'] )
+ if 'nomodel' in options:
+ cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] )
+ if 'diag' in options:
+ cmdline = "%s --diag --fe-min='%s' --fe-max='%s' --fe-step='%s'" % ( cmdline, options['diag']['fe-min'], options['diag']['fe-max'], options['diag']['fe-step'] )
+
+ tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user
+ stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report
+ proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
+ proc.wait()
+
+ #Need to lightly parse stderr file to see if there is a fatal error (e.g. macs is not installed on system)
+ #We don't want to set tool run to error state if only warnings or info, e.g. mfold needs to be decreased, rather create empty outputs, but let user view macs log
+ for line in open( stderr_name ):
+ for err_text in ERROR_LINES:
+ if err_text in line:
+ #print error, but don't quit, allow cleanup to occur at end
+ print >> sys.stderr, line.rstrip( '\n\r' )
+ if line.startswith( WARNING_LINE_START ):
+ #print warnings so they are viewable from info
+ print line.split( ':' )[-1].strip()
+
+ #run R to create pdf from model script
+ if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ):
+ cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name )
+ proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir )
+ proc.wait()
+
+
+ #move bed out to proper output file
+ created_bed_name = os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name )
+ if os.path.exists( created_bed_name ):
+ shutil.move( created_bed_name, output_bed )
+
+ #parse xls files to interval files as needed
+ if options['xls_to_interval']:
+ create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name )
+ if os.path.exists( create_peak_xls_file ):
+ xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' )
+ create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name )
+ if os.path.exists( create_peak_xls_file ):
+ xls_to_interval( create_peak_xls_file, options['xls_to_interval']['negative_peaks_file'], header = 'negative peaks file' )
+
+ #merge and move wig files as needed, delete gz'd files and remove emptied dirs
+ if 'wig' in options:
+ wig_base_dir = os.path.join( tmp_dir, "%s_MACS_wiggle" % experiment_name )
+ if os.path.exists( wig_base_dir ):
+ #treatment
+ treatment_dir = os.path.join( wig_base_dir, "treat" )
+ if os.path.exists( treatment_dir ):
1
0
09 Feb '10
details: http://www.bx.psu.edu/hg/galaxy/rev/49961332adb6
changeset: 3345:49961332adb6
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Fri Feb 05 15:51:01 2010 -0500
description:
Data library UI cleanup and improvements. Widgets are now displayed for the currently selected tempalte when adding one to a library item.
diffstat:
lib/galaxy/web/controllers/library_common.py | 41 +++++++++++-
templates/library/common/browse_library.mako | 10 +-
templates/library/common/common.mako | 36 +++++++---
templates/library/common/ldda_info.mako | 28 ++++----
templates/library/common/library_info.mako | 57 +++++++++++++++--
templates/library/common/select_info_template.mako | 70 +++++++++++++++++----
test/base/twilltestcase.py | 5 +-
test/functional/test_security_and_libraries.py | 2 +-
8 files changed, 190 insertions(+), 59 deletions(-)
diffs (435 lines):
diff -r e3af9317e829 -r 49961332adb6 lib/galaxy/web/controllers/library_common.py
--- a/lib/galaxy/web/controllers/library_common.py Fri Feb 05 15:29:22 2010 -0500
+++ b/lib/galaxy/web/controllers/library_common.py Fri Feb 05 15:51:01 2010 -0500
@@ -1,4 +1,4 @@
-import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile
+import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy
from galaxy.web.base.controller import *
from galaxy import util, jobs
from galaxy.datatypes import sniff
@@ -6,6 +6,7 @@
from galaxy.util.json import to_json_string
from galaxy.tools.actions import upload_common
from galaxy.web.controllers.forms import get_all_forms
+from galaxy.web.form_builder import SelectField
from galaxy.model.orm import *
from galaxy.util.streamball import StreamBall
import logging, tempfile, zipfile, tarfile, os, sys
@@ -1314,7 +1315,7 @@
action = 'ldda_edit_info'
id = ldda_id
if params.get( 'add_info_template_button', False ):
- form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.form_id ) )
+ form = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id( params.form_id ) )
form_values = trans.app.model.FormValues( form, [] )
trans.sa_session.add( form_values )
trans.sa_session.flush()
@@ -1326,7 +1327,7 @@
assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, form, form_values )
trans.sa_session.add( assoc )
trans.sa_session.flush()
- msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc )
+ msg = 'A template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc )
trans.response.send_redirect( web.url_for( controller='library_common',
action=action,
cntrller=cntrller,
@@ -1336,6 +1337,36 @@
show_deleted=show_deleted,
msg=msg,
messagetype='done' ) )
+ def generate_template_stuff( trans, forms, form_id ):
+ # Returns the following:
+ # - a list of template ids
+ # - a list of dictionaries whose keys are template ids and whose values are templates widgets.
+ # The dictionary built using the received forms param
+ # - a select list whose options are templates
+ template_ids = [ 'none' ]
+ widgets = []
+ for form in forms:
+ template_ids.append( trans.security.encode_id( form.id ) )
+ template_select_list = SelectField( 'form_id',
+ refresh_on_change=True,
+ refresh_on_change_values=template_ids[1:] )
+ if form_id == 'none':
+ template_select_list.add_option( 'Select one', 'none', selected=True )
+ decoded_form_id = None
+ else:
+ template_select_list.add_option( 'Select one', 'none' )
+ decoded_form_id = trans.security.decode_id( form_id )
+ for form in forms:
+ if decoded_form_id and decoded_form_id == form.id:
+ template_select_list.add_option( form.name, trans.security.encode_id( form.id ), selected=True )
+ widgets = form.get_widgets( trans.user )
+ else:
+ template_select_list.add_option( form.name, trans.security.encode_id( form.id ) )
+ return template_ids, widgets, template_select_list
+ if params.get( 'refresh', False ):
+ template_ids, widgets, template_select_list = generate_template_stuff( trans, forms, kwd.get( 'form_id' ) )
+ else:
+ template_ids, widgets, template_select_list = generate_template_stuff( trans, forms, 'none' )
return trans.fill_template( '/library/common/select_info_template.mako',
cntrller=cntrller,
library_item_name=item.name,
@@ -1344,7 +1375,9 @@
library_id=library_id,
folder_id=folder_id,
ldda_id=ldda_id,
- forms=forms,
+ template_ids=template_ids,
+ widgets=widgets,
+ template_select_list=template_select_list,
show_deleted=show_deleted,
msg=msg,
messagetype=messagetype )
diff -r e3af9317e829 -r 49961332adb6 templates/library/common/browse_library.mako
--- a/templates/library/common/browse_library.mako Fri Feb 05 15:29:22 2010 -0500
+++ b/templates/library/common/browse_library.mako Fri Feb 05 15:51:01 2010 -0500
@@ -17,8 +17,6 @@
<%
if cntrller in [ 'library', 'requests' ]:
can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library )
- if can_add:
- info_association, inherited = library.get_info_association()
can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library )
can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library )
info_association, inherited = library.get_info_association()
@@ -277,7 +275,7 @@
%if folder.deleted:
<span class="libraryItem-error">
%endif
- ${folder.name}
+ <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">${folder.name}</a>
%if folder.description:
<i>- ${folder.description}</i>
%endif
@@ -372,7 +370,7 @@
<tr class="libraryTitle">
%if cntrller == 'library_admin' or can_add or can_modify or can_manage:
<th style="padding-left: 42px;">
- ${library.name}
+ <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a>
<a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a>
<div popupmenu="library-${library.id}-popup">
%if not library.deleted:
@@ -406,7 +404,9 @@
</div>
</th>
%else:
- <th style="padding-left: 42px;">${library.name}</th>
+ <th style="padding-left: 42px;">
+ <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a>
+ </th>
%endif
<th>Information</th>
<th>Uploaded By</th>
diff -r e3af9317e829 -r 49961332adb6 templates/library/common/common.mako
--- a/templates/library/common/common.mako Fri Feb 05 15:29:22 2010 -0500
+++ b/templates/library/common/common.mako Fri Feb 05 15:51:01 2010 -0500
@@ -1,23 +1,20 @@
<%def name="render_template_info( cntrller, item_type, library_id, widgets, folder_id=None, ldda_id=None, editable=True )">
<%
if item_type == 'library':
- item_desc = 'library'
item = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
elif item_type == 'folder':
- item_desc = 'folder'
item = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
elif item_type == 'ldda':
- item_desc = 'dataset'
item = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
if cntrller == 'library':
current_user_roles = trans.get_current_user_roles()
%>
%if widgets:
- <p/>
- <div class="toolForm">
- <div class="toolFormTitle">Other information about ${item_desc} ${item.name}</div>
- <div class="toolFormBody">
- %if editable and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
+ %if editable and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ):
+ <p/>
+ <div class="toolForm">
+ <div class="toolFormTitle">Other information about ${item.name}</div>
+ <div class="toolFormBody">
<form name="edit_info" action="${h.url_for( controller='library_common', action='edit_template_info', cntrller=cntrller, item_type=item_type, library_id=library_id, num_widgets=len( widgets ), folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post">
%for i, field in enumerate( widgets ):
<div class="form-row">
@@ -33,7 +30,22 @@
<input type="submit" name="edit_info_button" value="Save"/>
</div>
</form>
- %else:
+ </div>
+ </div>
+ %else:
+ <% contents = False %>
+ %for i, field in enumerate( widgets ):
+ %if field[ 'widget' ].value:
+ <%
+ contents = True
+ break
+ %>
+ %endif
+ %endfor
+ %if contents:
+ <div class="toolForm">
+ <div class="toolFormTitle">Other information about ${item.name}</div>
+ <div class="toolFormBody">
%for i, field in enumerate( widgets ):
%if field[ 'widget' ].value:
<div class="form-row">
@@ -46,9 +58,9 @@
</div>
%endif
%endfor
- %endif
- </div>
- </div>
+ </div>
+ %endif
+ %endif
%endif
</%def>
diff -r e3af9317e829 -r 49961332adb6 templates/library/common/ldda_info.mako
--- a/templates/library/common/ldda_info.mako Fri Feb 05 15:29:22 2010 -0500
+++ b/templates/library/common/ldda_info.mako Fri Feb 05 15:51:01 2010 -0500
@@ -98,18 +98,18 @@
</div>
%endif
</div>
- %if widgets:
- ${render_template_info( cntrller=cntrller, item_type='ldda', library_id=library_id, widgets=widgets, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), editable=False )}
+</div>
+%if widgets:
+ ${render_template_info( cntrller=cntrller, item_type='ldda', library_id=library_id, widgets=widgets, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), editable=False )}
+%endif
+%if current_version:
+ <% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %>
+ %if expired_lddas:
+ <div class="toolFormTitle">Expired versions of ${ldda.name}</div>
+ %for expired_ldda in expired_lddas:
+ <div class="form-row">
+ <a href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( expired_ldda.library_dataset.folder.id ), id=trans.security.encode_id( expired_ldda.id ), show_deleted=show_deleted )}">${expired_ldda.name}</a>
+ </div>
+ %endfor
%endif
- %if current_version:
- <% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %>
- %if expired_lddas:
- <div class="toolFormTitle">Expired versions of ${ldda.name}</div>
- %for expired_ldda in expired_lddas:
- <div class="form-row">
- <a href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( expired_ldda.library_dataset.folder.id ), id=trans.security.encode_id( expired_ldda.id ), show_deleted=show_deleted )}">${expired_ldda.name}</a>
- </div>
- %endfor
- %endif
- %endif
-</div>
+%endif
diff -r e3af9317e829 -r 49961332adb6 templates/library/common/library_info.mako
--- a/templates/library/common/library_info.mako Fri Feb 05 15:29:22 2010 -0500
+++ b/templates/library/common/library_info.mako Fri Feb 05 15:51:01 2010 -0500
@@ -2,6 +2,14 @@
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/library/common/common.mako" import="render_template_info" />
+<%
+ if cntrller in [ 'library', 'requests' ]:
+ can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library )
+ can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library )
+ can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library )
+ info_association, inherited = library.get_info_association()
+%>
+
<br/><br/>
<ul class="manage-table-actions">
<li>
@@ -13,7 +21,7 @@
${render_msg( msg, messagetype )}
%endif
-%if cntrller == 'library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, library ):
+%if cntrller == 'library_admin' or can_modify:
<div class="toolForm">
<div class="toolFormTitle">Change library name and description</div>
<div class="toolFormBody">
@@ -32,21 +40,56 @@
</div>
<div style="clear: both"></div>
</div>
- <input type="submit" name="rename_library_button" value="Save"/>
+ <div class="form-row">
+ <input type="submit" name="rename_library_button" value="Save"/>
+ </div>
</form>
</div>
</div>
<p/>
%else:
<div class="toolForm">
- <div class="toolFormTitle">View information about ${library.name}</div>
+ <div class="toolFormTitle">
+ %if cntrller == 'library_admin' or can_add or can_manage:
+ <th style="padding-left: 42px;">
+ <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a>
+ <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a>
+ <div popupmenu="library-${library.id}-popup">
+ %if not library.deleted:
+ %if ( cntrller == 'library_admin' or can_add ) and not library.info_association:
+ <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Add template</a>
+ %endif
+ %if cntrller == 'library_admin' and info_association:
+ <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Delete template</a>
+ %endif
+ %if cntrller == 'library_admin' or can_manage:
+ <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Edit permissions</a>
+ %endif
+ %if cntrller == 'library_admin':
+ <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), library_item_id=trans.security.encode_id( library.id ), library_item_type='library' )}">Delete this data library and its contents</a>
+ %endif
+ %elif cntrller == 'library_admin' and not library.purged:
+ <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), library_item_id=trans.security.encode_id( library.id ), library_item_type='library' )}">Undelete this data library</a>
+ %endif
+ </div>
+ </th>
+ %else:
+ <th style="padding-left: 42px;">
+ <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a>
+ </th>
+ %endif
+ </div>
<div class="toolFormBody">
<div class="form-row">
- <b>Name:</b> ${library.name}
- <div style="clear: both"></div>
- <b>Description:</b> ${library.description}
- <div style="clear: both"></div>
+ <label>Name:</label>
+ ${library.name}
</div>
+ <div style="clear: both"></div>
+ <div class="form-row">
+ <label>Description:</label>
+ ${library.description}
+ </div>
+ <div style="clear: both"></div>
</div>
</div>
%endif
diff -r e3af9317e829 -r 49961332adb6 templates/library/common/select_info_template.mako
--- a/templates/library/common/select_info_template.mako Fri Feb 05 15:29:22 2010 -0500
+++ b/templates/library/common/select_info_template.mako Fri Feb 05 15:51:01 2010 -0500
@@ -1,6 +1,31 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
+<script type="text/javascript">
+$( function() {
+ $( "select[refresh_on_change='true']").change( function() {
+ var refresh = false;
+ var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+ if ( refresh_on_change_values ) {
+ refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+ var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+ for( i= 0; i < refresh_on_change_values.length; i++ ) {
+ if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+ refresh = true;
+ break;
+ }
+ }
+ }
+ else {
+ refresh = true;
+ }
+ if ( refresh ){
+ $( "#select_info_template" ).submit();
+ }
+ });
+});
+</script>
+
<br/><br/>
<ul class="manage-table-actions">
<li>
@@ -13,21 +38,38 @@
%endif
<div class="toolForm">
- <div class="toolFormTitle">Select a form on which to base the template for the ${library_item_desc} '${library_item_name}'</div>
- <form name="new_info_template" action="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post" >
+ <div class="toolFormTitle">Select a template for the ${library_item_desc} '${library_item_name}'</div>
+ <form id="select_info_template" name="select_info_template" action="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post" >
<div class="toolFormBody">
- <div class="form-row">
- <label>Template:</label>
- <select name="form_id">
- %for form in forms:
- <option value="${form.id}">${form.name}</option>
- %endfor
- </select>
- </div>
- <div style="clear: both"></div>
- <div class="form-row">
- <input type="submit" name="add_info_template_button" value="Add template to ${library_item_desc}"/>
- </div>
+ <table class="grid">
+ <tr>
+ <div class="form-row">
+ <td>
+ <input type="hidden" name="refresh" value="true" size="40"/>
+ <label>Template:</label>
+ ${template_select_list.get_html()}
+ </td>
+ <td>
+ <input type="submit" name="add_info_template_button" value="Add template to ${library_item_desc}"/>
+ </td>
+ </div>
+ </tr>
+ </table>
+ %if template_select_list.get_selected() != ('Select one', 'none'):
+ <div style="clear: both"></div>
+ <div class="form-row">
+ %for i, field in enumerate( widgets ):
+ <div class="form-row">
+ <label>${field[ 'label' ]}</label>
+ ${field[ 'widget' ].get_html()}
+ <div class="toolParamHelp" style="clear: both;">
+ ${field[ 'helptext' ]}
+ </div>
+ <div style="clear: both"></div>
+ </div>
+ %endfor
+ </div>
+ %endif
</div>
</form>
</div>
diff -r e3af9317e829 -r 49961332adb6 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py Fri Feb 05 15:29:22 2010 -0500
+++ b/test/base/twilltestcase.py Fri Feb 05 15:51:01 2010 -0500
@@ -1403,9 +1403,10 @@
elif item_type == 'ldda':
url = "%s/library_common/add_info_template?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s&ldda_id=%s" % ( self.url, cntrller, item_type, library_id, folder_id, ldda_id )
self.visit_url( url )
- self.check_page_for_string ( "Select a form on which to base the template" )
+ self.check_page_for_string ( "Select a template for the" )
+ tc.fv( '1', 'form_id', form_id )
tc.submit( 'add_info_template_button' )
- self.check_page_for_string = 'An information template based on the form "%s" has been added to this' % form_name
+ self.check_page_for_string = 'A template based on the form "%s" has been added to this' % form_name
self.home()
def library_info( self, library_id, library_name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents, controller='library_admin' ):
"""Add information to a library using an existing template with 2 elements"""
diff -r e3af9317e829 -r 49961332adb6 test/functional/test_security_and_libraries.py
--- a/test/functional/test_security_and_libraries.py Fri Feb 05 15:29:22 2010 -0500
+++ b/test/functional/test_security_and_libraries.py Fri Feb 05 15:51:01 2010 -0500
@@ -582,7 +582,7 @@
self.add_info_template( 'library_admin',
'library',
self.security.encode_id( library_one.id ),
- str( form_one.id ),
+ self.security.encode_id( form_one.id ),
form_one.name )
# Make sure the template fields are displayed on the library information page
field_dict = form_one.fields[ 0 ]
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/e3af9317e829
changeset: 3344:e3af9317e829
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Fri Feb 05 15:29:22 2010 -0500
description:
Merge.
diffstat:
buildbot_setup.sh | 9 +++++++++
1 files changed, 9 insertions(+), 0 deletions(-)
diffs (19 lines):
diff -r 952795dbbe74 -r e3af9317e829 buildbot_setup.sh
--- a/buildbot_setup.sh Fri Feb 05 15:29:01 2010 -0500
+++ b/buildbot_setup.sh Fri Feb 05 15:29:22 2010 -0500
@@ -10,6 +10,15 @@
kernel=`uname -r | cut -f1,2 -d.`
HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy"
;;
+ darwin*)
+ this_minor=`uname -r | awk -F. '{print ($1-4)}'`
+ machine=`machine`
+ for minor in `jot - 3 $this_minor 1`; do
+ HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy"
+ [ -d "$HYPHY" ] && break
+ done
+ [ ! -d "$HYPHY" ] && unset HYPHY
+ ;;
esac
LINKS="
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/952795dbbe74
changeset: 3343:952795dbbe74
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Fri Feb 05 15:29:01 2010 -0500
description:
Pack script.
diffstat:
static/scripts/packed/galaxy.base.js | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diffs (8 lines):
diff -r 207298b5ea39 -r 952795dbbe74 static/scripts/packed/galaxy.base.js
--- a/static/scripts/packed/galaxy.base.js Fri Feb 05 15:28:03 2010 -0500
+++ b/static/scripts/packed/galaxy.base.js Fri Feb 05 15:29:01 2010 -0500
@@ -1,1 +1,1 @@
-$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t
op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element
in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.
attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var k=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+k+"</textarea>")}else{var j=$("<input type='text' value='"+k+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(b!=null){b(j)}});j.keyup(function(m){if(m.keyCode==27){$(this).trigger("blur")}else{if(m.keyCode==13){new_text=this.value;$(this).trigger("blur");var l=new Object();l[a]=new_text;$.ajax({url:e,data:l,error:function(){alert("Text editing for elt "+f+" failed")},success:function(){$("#"+f).text(new_text);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();return false})};
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+$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t
op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element
in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.
attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var k=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+k+"</textarea>")}else{var j=$("<input type='text' value='"+k+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(b!=null){b(j)}});j.keyup(function(m){if(m.keyCode==27){$(this).trigger("blur")}else{if(m.keyCode==13){new_text=this.value;$(this).trigger("blur");var l=new Object();l[a]=new_text;$.ajax({url:e,data:l,error:function(){alert("Text editing for elt "+f+" failed")},success:function(n){$("#"+f).text(n);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();return false})};
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