2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0b9aa69e2785/
Changeset: 0b9aa69e2785
User: saketkc
Date: 2014-06-09 08:26:06
Summary: PEP8 fixes, close find handles for 'convert delimiters to tab' tool
Affected #: 1 file
diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 0b9aa69e2785650b0496546053710bde08121b60 tools/filters/convert_characters.py
--- a/tools/filters/convert_characters.py
+++ b/tools/filters/convert_characters.py
@@ -1,52 +1,57 @@
#!/usr/bin/env python
#By, Guruprasad Ananda.
-from galaxy import eggs
-import sys, re
+import sys
+import re
+
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
-
+
+
def main():
if len(sys.argv) != 4:
stop_err("usage: convert_characters infile from_char outfile")
try:
- fin = open(sys.argv[1],'r')
+ fin = open(sys.argv[1], 'r')
except:
stop_err("Input file cannot be opened for reading.")
-
+
from_char = sys.argv[2]
-
+
try:
- fout = open(sys.argv[3],'w')
+ fout = open(sys.argv[3], 'w')
except:
stop_err("Output file cannot be opened for writing.")
-
- char_dict = {
+
+ char_dict = {
'T': '\t',
- 's': '\s',
+ 's': '\s',
'Dt': '\.',
'C': ',',
'D': '-',
- 'U': '_',
+ 'U': '_',
'P': '\|',
'Co': ':',
'Sc': ';'
}
- from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences.
+ # regexp to match 1 or more occurences.
+ from_ch = char_dict[from_char] + '+'
skipped = 0
-
+
for line in fin:
line = line.strip()
try:
- fout.write("%s\n" %(re.sub(from_ch,'\t',line)))
+ fout.write("%s\n" % (re.sub(from_ch, '\t', line)))
except:
skipped += 1
-
+
+ fin.close()
+ fout.close()
if skipped:
- print "Skipped %d lines as invalid." %skipped
-
-if __name__ == "__main__":
- main()
\ No newline at end of file
+ print "Skipped %d lines as invalid." % skipped
+
+if __name__ == "__main__":
+ main()
https://bitbucket.org/galaxy/galaxy-central/commits/633c27341859/
Changeset: 633c27341859
User: dannon
Date: 2014-06-09 16:52:03
Summary: Merged in saketkc/galaxy-fork (pull request #403)
PEP8 fixes, close find handles for 'convert delimiters to tab' tool
Affected #: 1 file
diff -r 42d46284ef22b9520b637661d3f15e31b5f5379a -r 633c27341859df116d2dd039bb16e9c29bedd65a tools/filters/convert_characters.py
--- a/tools/filters/convert_characters.py
+++ b/tools/filters/convert_characters.py
@@ -1,52 +1,57 @@
#!/usr/bin/env python
#By, Guruprasad Ananda.
-from galaxy import eggs
-import sys, re
+import sys
+import re
+
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
-
+
+
def main():
if len(sys.argv) != 4:
stop_err("usage: convert_characters infile from_char outfile")
try:
- fin = open(sys.argv[1],'r')
+ fin = open(sys.argv[1], 'r')
except:
stop_err("Input file cannot be opened for reading.")
-
+
from_char = sys.argv[2]
-
+
try:
- fout = open(sys.argv[3],'w')
+ fout = open(sys.argv[3], 'w')
except:
stop_err("Output file cannot be opened for writing.")
-
- char_dict = {
+
+ char_dict = {
'T': '\t',
- 's': '\s',
+ 's': '\s',
'Dt': '\.',
'C': ',',
'D': '-',
- 'U': '_',
+ 'U': '_',
'P': '\|',
'Co': ':',
'Sc': ';'
}
- from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences.
+ # regexp to match 1 or more occurences.
+ from_ch = char_dict[from_char] + '+'
skipped = 0
-
+
for line in fin:
line = line.strip()
try:
- fout.write("%s\n" %(re.sub(from_ch,'\t',line)))
+ fout.write("%s\n" % (re.sub(from_ch, '\t', line)))
except:
skipped += 1
-
+
+ fin.close()
+ fout.close()
if skipped:
- print "Skipped %d lines as invalid." %skipped
-
-if __name__ == "__main__":
- main()
\ No newline at end of file
+ print "Skipped %d lines as invalid." % skipped
+
+if __name__ == "__main__":
+ main()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Swap require_admin decorator and trans.user_is_amdin to use the newer correctly filtered admin_users_list in app.config
by commits-noreply＠bitbucket.org 09 Jun '14
by commits-noreply＠bitbucket.org 09 Jun '14
09 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/42d46284ef22/
Changeset: 42d46284ef22
User: dannon
Date: 2014-06-09 16:42:33
Summary: Swap require_admin decorator and trans.user_is_amdin to use the newer correctly filtered admin_users_list in app.config
Affected #: 1 file
diff -r 749062450f1b531489524c12333a6d3e449d50c2 -r 42d46284ef22b9520b637661d3f15e31b5f5379a lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -370,9 +370,8 @@
def decorator( self, trans, *args, **kwargs ):
if not trans.user_is_admin():
msg = "You must be an administrator to access this feature."
- admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
user = trans.get_user()
- if not admin_users:
+ if not trans.app.config.admin_users_list:
msg = "You must be logged in as an administrator to access this feature, but no administrators are set in the Galaxy configuration."
elif not user:
msg = "You must be logged in as an administrator to access this feature."
@@ -1104,8 +1103,7 @@
def user_is_admin( self ):
if self.api_inherit_admin:
return True
- admin_users = [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ]
- return self.user and admin_users and self.user.email in admin_users
+ return self.user and self.user.email in self.app.config.admin_users_list
def user_can_do_run_as( self ):
run_as_users = [ user for user in self.app.config.get( "api_allow_run_as", "" ).split( "," ) if user ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Add correctly prefiltered admin_users_list to app.config and use it for remote auth.
by commits-noreply＠bitbucket.org 09 Jun '14
by commits-noreply＠bitbucket.org 09 Jun '14
09 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/749062450f1b/
Changeset: 749062450f1b
User: dannon
Date: 2014-06-09 16:37:10
Summary: Add correctly prefiltered admin_users_list to app.config and use it for remote auth.
Affected #: 2 files
diff -r df20b99bc7db3d3daab5b843b73b6890c85fd390 -r 749062450f1b531489524c12333a6d3e449d50c2 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -168,6 +168,7 @@
h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ]
self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h )
self.admin_users = kwargs.get( "admin_users", "" )
+ self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u]
self.reset_password_length = int( kwargs.get('reset_password_length', '15') )
self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu")
self.error_email_to = kwargs.get( 'error_email_to', None )
diff -r df20b99bc7db3d3daab5b843b73b6890c85fd390 -r 749062450f1b531489524c12333a6d3e449d50c2 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -753,7 +753,7 @@
galaxy_session_requires_flush = True
elif (galaxy_session.user.email != remote_user_email and
self.app.config.allow_user_impersonation and
- remote_user_email not in [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ]):
+ remote_user_email not in self.app.config.admin_users_list):
# Session exists but is not associated with the correct
# remote user, and the currently set remote_user is not a
# potentially impersonating admin.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/879c4859eee1/
Changeset: 879c4859eee1
User: jmchilton
Date: 2014-06-09 15:30:40
Summary: Tools: MATCH (pair) multi-run datasets by default instead of doing ALL-V-ALL.
Worried this might be responsible for problems on main. TODO is to make this an optional and explicit like with workflows.
Affected #: 1 file
diff -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d -r 879c4859eee151c7445b95eb0bdb04b4a7d0716e lib/galaxy/tools/parameters/meta.py
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -19,7 +19,7 @@
if multirun_key in incoming:
multi_value = util.listify( incoming[ multirun_key ] )
if len( multi_value ) > 1:
- return permutations.input_classification.MULTIPLIED, multi_value
+ return permutations.input_classification.MATCHED, multi_value
else:
if len( multi_value ) == 0:
multi_value = None
https://bitbucket.org/galaxy/galaxy-central/commits/df20b99bc7db/
Changeset: df20b99bc7db
User: jmchilton
Date: 2014-06-09 15:32:24
Summary: Merge.
Affected #: 1 file
diff -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 -r df20b99bc7db3d3daab5b843b73b6890c85fd390 lib/galaxy/tools/parameters/meta.py
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -19,7 +19,7 @@
if multirun_key in incoming:
multi_value = util.listify( incoming[ multirun_key ] )
if len( multi_value ) > 1:
- return permutations.input_classification.MULTIPLIED, multi_value
+ return permutations.input_classification.MATCHED, multi_value
else:
if len( multi_value ) == 0:
multi_value = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b9c73972a1a8/
Changeset: b9c73972a1a8
User: dannon
Date: 2014-06-09 15:09:45
Summary: Wrap remote user conditional on multiple lines.
Affected #: 1 file
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r b9c73972a1a839244b48dbf4d435aab5083588e4 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -751,7 +751,9 @@
# No user, associate
galaxy_session.user = self.get_or_create_remote_user( remote_user_email )
galaxy_session_requires_flush = True
- elif galaxy_session.user.email != remote_user_email and self.app.config.allow_user_impersonation and remote_user_email not in [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ]:
+ elif (galaxy_session.user.email != remote_user_email and
+ self.app.config.allow_user_impersonation and
+ remote_user_email not in [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ]):
# Session exists but is not associated with the correct
# remote user, and the currently set remote_user is not a
# potentially impersonating admin.
https://bitbucket.org/galaxy/galaxy-central/commits/7f5f8ac18c60/
Changeset: 7f5f8ac18c60
User: dannon
Date: 2014-06-09 15:10:10
Summary: Merge.
Affected #: 18 files
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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'),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),a=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="ui-button-menu '+e.cls+'">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:i,Button:s,Icon:o,ButtonIcon:u,Input:h,Anchor:a,Message:f,Searchbox:l,Select:t,ButtonMenu:c,Modal:n,Textarea:p,Image:r,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),e.find(".highcharts-button").hide(),o+=s.serializeToString(this),e.find(".highcharts-button").show()}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find(".charts-viewport-container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info"));var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning"),t.hide();break;default:r.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=this.chart_definition.use_panels||e.settings.get("use_panels")==="true",s=1;i&&(s=e.groups.length),this._createContainer(this.chart_definition.tag,s),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=r.merge({index:e.get(o)},u)}t.groups.push({key:++n+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=[],f=n[e];o&&a.push({label:"Column: Row Number",value:"auto"});var l=t.metadata_column_types;for(var c in l){var h=!1;l[c]=="int"||l[c]=="float"?h=u:h=s,h&&a.push({label:"Column: "+(parseInt(c)+1)+" ["+l[c]+"]",value:c})}f.update(a);if(!f.exists(this.group.get(e))){var p=f.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+p+'".'),this.group.set(e,p)}f.value(this.group.get(e)),f.setOnChange(function(t){i.group.set(e,t),i.chart.set("modified",!0)}),f.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){var r=this;this.app=t,this.options=e.merge(n,this.optionsDefault);var i=$('<div class="charts-grid"/>');this.setElement(i),this._render(),this._filter("default")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=r.keywords||"";s.indexOf(e)==-1&&e!="all"?i.hide():i.show()}},_render:function(){var t={},n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;t[s]||(t[s]={}),t[s][r]=i}for(var s in t){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({title:s})));for(var r in t[s]){var i=t[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" ("+i.library+")",url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","highcharts_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in 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'+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:i,Button:s,Icon:o,ButtonIcon:u,Input:h,Anchor:a,Message:f,Searchbox:l,Select:t,ButtonMenu:c,Modal:n,Textarea:p,Image:r,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),e.find(".highcharts-button").hide(),o+=s.serializeToString(this),e.find(".highcharts-button").show()}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find(".charts-viewport-container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info"));var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning"),t.hide();break;default:r.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=this.chart_definition.use_panels||e.settings.get("use_panels")==="true",s=1;i&&(s=e.groups.length),this._createContainer(this.chart_definition.tag,s),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=r.merge({index:e.get(o)},u)}t.groups.push({key:++n+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=[],f=n[e];o&&a.push({label:"Column: Row Number",value:"auto"});var l=t.metadata_column_types;for(var c in l){var h=!1;l[c]=="int"||l[c]=="float"?h=u:h=s,h&&a.push({label:"Column: "+(parseInt(c)+1)+" ["+l[c]+"]",value:c})}f.update(a);if(!f.exists(this.group.get(e))){var p=f.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+p+'".'),this.group.set(e,p)}f.value(this.group.get(e)),f.setOnChange(function(t){i.group.set(e,t),i.chart.set("modified",!0)}),f.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div 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i=$('<div class="charts-grid"/>');this.setElement(i),this._render(),this._filter("default")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=r.keywords||"";s.indexOf(e)==-1&&e!="all"?i.hide():i.show()}},_render:function(){var t={},n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;t[s]||(t[s]={}),t[s][r]=i}for(var s in t){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({title:s})));for(var r in t[s]){var i=t[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" 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o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","highcharts_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100,screenshot_url:"http://export.highcharts.com/"}})}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return 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arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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--",value:"hide",hide:["x_axis_tick"]},{label:"Auto",value:"auto",hide:["x_axis_tick"]},{label:"Float",value:"f",show:["x_axis_tick"]},{label:"Exponent",value:"e",show:["x_axis_tick"]},{label:"Integer",value:"d",hide:["x_axis_tick"]},{label:"Percentage",value:"p",show:["x_axis_tick"]},{label:"Rounded",value:"r",show:["x_axis_tick"]},{label:"SI-prefix",value:"s",show:["x_axis_tick"]}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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$.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/dygraph/common/config",[],function(){return{title:"",category:"",library:"Dygraph",tag:"div",keywords:"default dygraph",settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["x_axis_tick"]},{label:"Auto",value:"auto",hide:["x_axis_tick"]},{label:"Float",value:"f",show:["x_axis_tick"]},{label:"Exponent",value:"e",show:["x_axis_tick"]},{label:"Integer",value:"d",hide:["x_axis_tick"]},{label:"Percentage",value:"p",show:["x_axis_tick"]},{label:"Rounded",value:"r",show:["x_axis_tick"]},{label:"SI-prefix",value:"s",show:["x_axis_tick"]}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["y_axis_tick"]},{label:"Auto",value:"auto",hide:["y_axis_tick"]},{label:"Float",value:"f",show:["y_axis_tick"]},{label:"Exponent",value:"e",show:["y_axis_tick"]},{label:"Integer",value:"d",hide:["y_axis_tick"]},{label:"Percentage",value:"p",show:["y_axis_tick"]},{label:"Rounded",value:"r",show:["y_axis_tick"]},{label:"SI-prefix",value:"s",show:["y_axis_tick"]}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},legend_enabled:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/dygraph/bar/config",["plugin/charts/dygraph/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/others/boxplot/config",[],function(){return $.extend(!0,{},{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"Highcharts",tag:"div",execute:"boxplot",keywords:"default others",columns:{y:{title:"Observations",is_numeric:!0}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["y_axis_tick"]},{label:"Auto",value:"auto",hide:["y_axis_tick"]},{label:"Float",value:"f",show:["y_axis_tick"]},{label:"Exponent",value:"e",show:["y_axis_tick"]},{label:"Integer",value:"d",hide:["y_axis_tick"]},{label:"Percentage",value:"p",show:["y_axis_tick"]},{label:"Rounded",value:"r",show:["y_axis_tick"]},{label:"SI-prefix",value:"s",show:["y_axis_tick"]}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for this axis?",type:"radiobutton",init:"1",data:[{label:"On",value:"1"},{label:"Off",value:"0"}]}}})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/flot/bar/config","plugin/charts/dygraph/bar/config","plugin/charts/others/boxplot/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f,flot_bar:p}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
@@ -4,11 +4,6 @@
title : 'Stacked',
category : 'Bar diagrams',
columns : {
- x : {
- title : 'Values for x-axis',
- is_label : true,
- is_auto : true
- },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
@@ -1,4 +1,4 @@
-define([], function() {
+define(['plugin/plugins/nvd3/nv.d3'], function() {
return {
title : '',
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
@@ -1,5 +1,5 @@
// dependencies
-define(['plugin/charts/tools', 'plugin/plugins/nvd3/nv.d3'], function(Tools) {
+define(['plugin/charts/tools'], function(Tools) {
// widget
return Backbone.View.extend(
@@ -29,7 +29,7 @@
render : function(type, chart, groups, canvas, callback)
{
// create nvd3 model
- var d3chart = nv.models[type]();
+ var d3chart = nv.models[type]()
// request data
var self = this;
@@ -46,7 +46,7 @@
// y axis label
d3chart.yAxis.axisLabel(chart.settings.get('y_axis_label'))
- .axisLabelDistance(30);
+ .axisLabelDistance(30);
// controls
d3chart.options({showControls: false});
@@ -65,11 +65,23 @@
callback(d3chart);
}
- // parse data to canvas
+ // make categories
+ self._makeCategories(chart, groups, d3chart);
+
+ // hide min/max values
+ d3chart.xAxis.showMaxMin(false);
+ d3chart.yAxis.showMaxMin(chart.definition.showmaxmin);
+
+ // draw chart
canvas.datum(groups)
.call(d3chart);
-
-
+
+ // add zoom/pan handler
+ var zoom_mode = chart.definition.zoomable;
+ if (zoom_mode == 'axis' || zoom_mode == 'svg') {
+ self._addZoom(d3chart, canvas, zoom_mode);
+ }
+
// refresh on window resize
nv.utils.windowResize(d3chart.update);
} catch (err) {
@@ -80,6 +92,64 @@
return true;
},
+ // add zoom handler
+ _addZoom: function(nvd3_model, svg, zoom_mode) {
+ // get canvas dimensions
+ var width = parseInt(svg.style('width'));
+ var height = parseInt(svg.style('height'));
+
+ // create x scales
+ var x_domain = nvd3_model.xAxis.scale().domain();
+ var x = d3.scale.linear()
+ .domain(x_domain)
+ .range([0, width]);
+
+ // create y scale
+ var y_domain = nvd3_model.yAxis.scale().domain();
+ var y = d3.scale.linear()
+ .domain(y_domain)
+ .range([height, 0]);
+
+ // zoom event handler
+ function zoomed() {
+ if (zoom_mode == 'axis') {
+ nvd3_model.xDomain(x.domain());
+ nvd3_model.yDomain(y.domain());
+ nvd3_model.update();
+ } else {
+ var translate = d3.event.translate;
+ svg.select('.nvd3').attr("transform", "translate(" + translate + ") scale(" + d3.event.scale + ")");
+ }
+ }
+
+ // d3 zoom wrapper
+ var d3zoom = d3.behavior.zoom()
+ .x(x)
+ .y(y)
+ .scaleExtent([1, 10])
+ .on("zoom", zoomed);
+
+ // add handler
+ svg.call(d3zoom);
+ },
+
+ // create categories
+ _makeCategories: function(chart, groups, d3chart) {
+ // result
+ var result = Tools.makeCategories(chart, groups);
+
+ // add categories to flot configuration
+ for (var key in result.array) {
+ var axis = key + 'Axis';
+ if (d3chart[axis]) {
+ var a = result.array[key];
+ d3chart[axis].tickFormat(function(value) {
+ return a[value];
+ });
+ }
+ }
+ },
+
// make axis
_axis: function(axis, type, tick) {
switch (type) {
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
@@ -3,7 +3,13 @@
return $.extend(true, {}, nvd3_config, {
title : 'Line chart',
category : 'Others',
+ zoomable : 'axis',
columns : {
+ x : {
+ title : 'Values for x-axis',
+ is_label : true,
+ is_auto : true
+ },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
@@ -11,8 +11,7 @@
},
// render
- draw : function(process_id, chart, request_dictionary)
- {
+ draw : function(process_id, chart, request_dictionary) {
var nvd3 = new NVD3(this.app, this.options);
nvd3.draw('lineChart', process_id, chart, request_dictionary);
}
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
@@ -5,6 +5,11 @@
category : 'Others',
keywords : 'default nvd3',
columns : {
+ x : {
+ title : 'Values for x-axis',
+ is_label : true,
+ is_auto : true
+ },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
@@ -1,4 +1,4 @@
-define([], function() {
+define(['plugin/plugins/nvd3/nv.d3'], function() {
return $.extend(true, {}, {
title : 'Pie chart',
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
@@ -36,66 +36,69 @@
// draw group
_draw_group: function(chart, group, canvas) {
-
- // add title
- var title = canvas.append('text');
-
- // configure title attributes
- this._fix_title(chart, canvas, title, group.key);
-
- // format chart data
- var pie_data = [];
- for (var key in group.values) {
- var value = group.values[key];
- pie_data.push ({
- y : value.y,
- x : value.label
+ try {
+ // add title
+ var title = canvas.append('text');
+
+ // configure title attributes
+ this._fix_title(chart, canvas, title, group.key);
+
+ // format chart data
+ var pie_data = [];
+ for (var key in group.values) {
+ var value = group.values[key];
+ pie_data.push ({
+ y : value.y,
+ x : value.label
+ });
+ }
+
+ // add graph to screen
+ var self = this;
+ nv.addGraph(function() {
+ // legend
+ var legend_visible = true;
+ if (chart.settings.get('show_legend') == 'false') {
+ legend_visible = false;
+ }
+
+ // legend
+ var label_outside = true;
+ if (chart.settings.get('label_outside') == 'false') {
+ label_outside = false;
+ }
+
+ // label type
+ var label_type = chart.settings.get('label_type');
+
+ // ratio
+ var donut_ratio = parseFloat(chart.settings.get('donut_ratio'))
+
+ // create chart model
+ var chart_3d = nv.models.pieChart()
+ .donut(true)
+ .labelThreshold(.05)
+ .showLegend(legend_visible)
+ .labelType(label_type)
+ .donutRatio(donut_ratio)
+ .donutLabelsOutside(label_outside);
+
+ // add data to canvas
+ canvas.datum(pie_data)
+ .call(chart_3d);
+
+ // add resize trigger
+ nv.utils.windowResize(function() {
+ // update chart
+ chart_3d.update();
+
+ // fix title
+ self._fix_title(chart, canvas, title, group.key);
+ });
});
+ } catch (err) {
+ console.log(err);
}
-
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- // legend
- var legend_visible = true;
- if (chart.settings.get('show_legend') == 'false') {
- legend_visible = false;
- }
-
- // legend
- var label_outside = true;
- if (chart.settings.get('label_outside') == 'false') {
- label_outside = false;
- }
-
- // label type
- var label_type = chart.settings.get('label_type');
-
- // ratio
- var donut_ratio = parseFloat(chart.settings.get('donut_ratio'))
-
- // create chart model
- var chart_3d = nv.models.pieChart()
- .donut(true)
- .labelThreshold(.05)
- .showLegend(legend_visible)
- .labelType(label_type)
- .donutRatio(donut_ratio)
- .donutLabelsOutside(label_outside);
-
- // add data to canvas
- canvas.datum(pie_data)
- .call(chart_3d);
-
- // add resize trigger
- nv.utils.windowResize(function() {
- // update chart
- chart_3d.update();
-
- // fix title
- self._fix_title(chart, canvas, title, group.key);
- });
- });
},
// fix title
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
@@ -3,6 +3,7 @@
return $.extend(true, {}, nvd3_config, {
title : 'Scatter plot',
category : 'Others',
+ zoomable : 'axis',
columns : {
x : {
title : 'Values for x-axis',
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
@@ -2,8 +2,14 @@
return $.extend(true, {}, nvd3_config, {
title : 'Regular',
+ zoomable : 'axis',
category : 'Area charts',
columns : {
+ x : {
+ title : 'Values for x-axis',
+ is_label : true,
+ is_auto : true
+ },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
@@ -2,6 +2,7 @@
return $.extend(true, {}, nvd3_config, {
title : 'Expanded',
+ zoomable : 'axis',
category : 'Area charts',
columns : {
y : {
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
@@ -3,7 +3,9 @@
return $.extend(true, {}, nvd3_config, {
title : 'Stream',
category : 'Area charts',
+ zoomable : 'axis',
keywords : 'default nvd3',
+ showmaxmin : true,
columns : {
y : {
title : 'Values for y-axis',
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/tools.js
--- a/config/plugins/visualizations/charts/static/charts/tools.js
+++ b/config/plugins/visualizations/charts/static/charts/tools.js
@@ -41,7 +41,7 @@
chart.deferred.done(process_id);
} catch (err) {
// log
- console.debug('FAILED: Tools::draw() - ' + err);
+ console.debug('FAILED: Tools::panelHelper() - ' + err);
// set chart state
chart.state('failed', err);
@@ -52,6 +52,35 @@
});
};
+// get domain boundaries value
+function getDomains(groups, keys) {
+
+ // get value
+ function _apply(operator, key) {
+ var value = undefined;
+ for (var group_index in groups) {
+ var value_sub = d3[operator](groups[group_index].values, function(d) { return d[key]; });
+ if (value === undefined) {
+ value = value_sub;
+ } else {
+ value = Math[operator](value, value_sub);
+ }
+ }
+ return value;
+ };
+
+ var result = {};
+ for (var index in keys) {
+ var key = keys[index];
+ result[key] = {
+ min : _apply('min', key),
+ max : _apply('max', key),
+ };
+
+ }
+ return result;
+};
+
// series maker
function makeSeries(group) {
// reset data
@@ -74,7 +103,7 @@
};
// category maker
-function makeCategories(chart, groups) {
+function makeCategories(chart, groups, with_index) {
// hashkeys, arrays and counter for labeled columns
var categories = {};
var array = {};
@@ -99,8 +128,17 @@
for (var key in categories) {
var value = String(value_dict[key]);
if (categories[key][value] === undefined) {
+ // add index
categories[key][value] = counter[key];
- array[key].push([counter[key], value]);
+
+ // array formatter
+ if (with_index) {
+ array[key].push([counter[key], value]);
+ } else {
+ array[key].push(value);
+ }
+
+ // increase counter
counter[key]++;
}
}
@@ -131,7 +169,8 @@
return {
panelHelper : panelHelper,
makeCategories : makeCategories,
- makeSeries : makeSeries
+ makeSeries : makeSeries,
+ getDomains : getDomains
}
});
\ No newline at end of file
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/charts/types.js
--- a/config/plugins/visualizations/charts/static/charts/types.js
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -11,9 +11,10 @@
'plugin/charts/nvd3/histogram_discrete/config',
'plugin/charts/nvd3/line/config',
'plugin/charts/nvd3/scatter/config',
- 'plugin/charts/nvd3/stackedarea/config'
- //'plugin/charts/flot/bar/config',
- //'plugin/charts/others/boxplot/config',
+ 'plugin/charts/nvd3/stackedarea/config',
+ 'plugin/charts/flot/bar/config',
+ 'plugin/charts/dygraph/bar/config',
+ 'plugin/charts/others/boxplot/config',
], function(nvd3_bar,
nvd3_bar_stacked,
nvd3_bar_horizontal,
@@ -26,9 +27,10 @@
nvd3_histogram_discrete,
nvd3_line,
nvd3_scatter,
- nvd3_stackedarea
- //flot_bar,
- //others_boxplot
+ nvd3_stackedarea,
+ flot_bar,
+ dygraph_bar,
+ others_boxplot
) {
// widget
@@ -48,8 +50,9 @@
'nvd3_line' : nvd3_line,
'nvd3_scatter' : nvd3_scatter,
'nvd3_histogram' : nvd3_histogram,
- 'nvd3_histogram_discrete' : nvd3_histogram_discrete
- //'flot_bar' : flot_bar,
+ 'nvd3_histogram_discrete' : nvd3_histogram_discrete,
+ 'flot_bar' : flot_bar,
+ //'dygraph_bar' : dygraph_bar,
//'others_boxplot' : others_boxplot
}
});
diff -r b9c73972a1a839244b48dbf4d435aab5083588e4 -r 7f5f8ac18c60c89775f7f992e6bfedacf0d917b4 config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -6,7 +6,7 @@
{
// options
defaults : {
- query_limit : 1000,
+ query_limit : 500,
query_timeout : 100,
screenshot_url : 'http://export.highcharts.com/'
}
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Charts: Add custom d3-zooming and panning for nvd3, patch nvd3 transitions
by commits-noreply＠bitbucket.org 09 Jun '14
by commits-noreply＠bitbucket.org 09 Jun '14
09 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d61ee3309864/
Changeset: d61ee3309864
User: guerler
Date: 2014-06-09 14:49:49
Summary: Charts: Add custom d3-zooming and panning for nvd3, patch nvd3 transitions
Affected #: 18 files
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
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t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),e.find(".highcharts-button").hide(),o+=s.serializeToString(this),e.find(".highcharts-button").show()}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find(".charts-viewport-container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info"));var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning"),t.hide();break;default:r.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=this.chart_definition.use_panels||e.settings.get("use_panels")==="true",s=1;i&&(s=e.groups.length),this._createContainer(this.chart_definition.tag,s),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=r.merge({index:e.get(o)},u)}t.groups.push({key:++n+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=[],f=n[e];o&&a.push({label:"Column: Row Number",value:"auto"});var l=t.metadata_column_types;for(var c in l){var h=!1;l[c]=="int"||l[c]=="float"?h=u:h=s,h&&a.push({label:"Column: "+(parseInt(c)+1)+" ["+l[c]+"]",value:c})}f.update(a);if(!f.exists(this.group.get(e))){var p=f.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to 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this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){var r=this;this.app=t,this.options=e.merge(n,this.optionsDefault);var i=$('<div class="charts-grid"/>');this.setElement(i),this._render(),this._filter("default")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=r.keywords||"";s.indexOf(e)==-1&&e!="all"?i.hide():i.show()}},_render:function(){var t={},n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;t[s]||(t[s]={}),t[s][r]=i}for(var s in t){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({title:s})));for(var r in t[s]){var i=t[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" ("+i.library+")",url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","highcharts_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:100,screenshot_url:"http://export.highcharts.com/"}})}),define("plugin/charts/nvd3/common/config",[],function(){return{title:"",category:"",library:"NVD3",tag:"svg",keywords:"default nvd3",settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["x_axis_tick"]},{label:"Auto",value:"auto",hide:["x_axis_tick"]},{label:"Float",value:"f",show:["x_axis_tick"]},{label:"Exponent",value:"e",show:["x_axis_tick"]},{label:"Integer",value:"d",hide:["x_axis_tick"]},{label:"Percentage",value:"p",show:["x_axis_tick"]},{label:"Rounded",value:"r",show:["x_axis_tick"]},{label:"SI-prefix",value:"s",show:["x_axis_tick"]}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["y_axis_tick"]},{label:"Auto",value:"auto",hide:["y_axis_tick"]},{label:"Float",value:"f",show:["y_axis_tick"]},{label:"Exponent",value:"e",show:["y_axis_tick"]},{label:"Integer",value:"d",hide:["y_axis_tick"]},{label:"Percentage",value:"p",show:["y_axis_tick"]},{label:"Rounded",value:"r",show:["y_axis_tick"]},{label:"SI-prefix",value:"s",show:["y_axis_tick"]}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3/bar/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_stacked/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_horizontal/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3/bar_horizontal_stacked/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/line_focus/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others",keywords:"default nvd3",columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/pie/config",[],function(){return $.extend(!0,{},{title:"Pie chart",category:"Area charts",library:"NVD3",tag:"svg",keywords:"default nvd3",use_panels:!0,columns:{label:{title:"Labels",is_label:!0,is_auto:!0},y:{title:"Values",is_numeric:!0}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}})}),define("plugin/charts/nvd3/stackedarea_full/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts",columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea_stream/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts",keywords:"default nvd3",columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3/histogram_discrete/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts",columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new 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e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data 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n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div 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n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:i,Button:s,Icon:o,ButtonIcon:u,Input:h,Anchor:a,Message:f,Searchbox:l,Select:t,ButtonMenu:c,Modal:n,Textarea:p,Image:r,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return 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The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),e.find(".highcharts-button").hide(),o+=s.serializeToString(this),e.find(".highcharts-button").show()}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find(".charts-viewport-container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info"));var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning"),t.hide();break;default:r.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=this.chart_definition.use_panels||e.settings.get("use_panels")==="true",s=1;i&&(s=e.groups.length),this._createContainer(this.chart_definition.tag,s),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=r.merge({index:e.get(o)},u)}t.groups.push({key:++n+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=[],f=n[e];o&&a.push({label:"Column: Row Number",value:"auto"});var l=t.metadata_column_types;for(var c in l){var h=!1;l[c]=="int"||l[c]=="float"?h=u:h=s,h&&a.push({label:"Column: "+(parseInt(c)+1)+" ["+l[c]+"]",value:c})}f.update(a);if(!f.exists(this.group.get(e))){var p=f.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+p+'".'),this.group.set(e,p)}f.value(this.group.get(e)),f.setOnChange(function(t){i.group.set(e,t),i.chart.set("modified",!0)}),f.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div 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i=$('<div class="charts-grid"/>');this.setElement(i),this._render(),this._filter("default")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=r.keywords||"";s.indexOf(e)==-1&&e!="all"?i.hide():i.show()}},_render:function(){var t={},n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;t[s]||(t[s]={}),t[s][r]=i}for(var s in t){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({title:s})));for(var r in t[s]){var i=t[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" 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o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","highcharts_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100,screenshot_url:"http://export.highcharts.com/"}})}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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--",value:"hide",hide:["y_axis_tick"]},{label:"Auto",value:"auto",hide:["y_axis_tick"]},{label:"Float",value:"f",show:["y_axis_tick"]},{label:"Exponent",value:"e",show:["y_axis_tick"]},{label:"Integer",value:"d",hide:["y_axis_tick"]},{label:"Percentage",value:"p",show:["y_axis_tick"]},{label:"Rounded",value:"r",show:["y_axis_tick"]},{label:"SI-prefix",value:"s",show:["y_axis_tick"]}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},legend_enabled:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/dygraph/bar/config",["plugin/charts/dygraph/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/others/boxplot/config",[],function(){return $.extend(!0,{},{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"Highcharts",tag:"div",execute:"boxplot",keywords:"default others",columns:{y:{title:"Observations",is_numeric:!0}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["y_axis_tick"]},{label:"Auto",value:"auto",hide:["y_axis_tick"]},{label:"Float",value:"f",show:["y_axis_tick"]},{label:"Exponent",value:"e",show:["y_axis_tick"]},{label:"Integer",value:"d",hide:["y_axis_tick"]},{label:"Percentage",value:"p",show:["y_axis_tick"]},{label:"Rounded",value:"r",show:["y_axis_tick"]},{label:"SI-prefix",value:"s",show:["y_axis_tick"]}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for this axis?",type:"radiobutton",init:"1",data:[{label:"On",value:"1"},{label:"Off",value:"0"}]}}})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/flot/bar/config","plugin/charts/dygraph/bar/config","plugin/charts/others/boxplot/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f,flot_bar:p}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
@@ -4,11 +4,6 @@
title : 'Stacked',
category : 'Bar diagrams',
columns : {
- x : {
- title : 'Values for x-axis',
- is_label : true,
- is_auto : true
- },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
@@ -1,4 +1,4 @@
-define([], function() {
+define(['plugin/plugins/nvd3/nv.d3'], function() {
return {
title : '',
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
@@ -1,5 +1,5 @@
// dependencies
-define(['plugin/charts/tools', 'plugin/plugins/nvd3/nv.d3'], function(Tools) {
+define(['plugin/charts/tools'], function(Tools) {
// widget
return Backbone.View.extend(
@@ -29,7 +29,7 @@
render : function(type, chart, groups, canvas, callback)
{
// create nvd3 model
- var d3chart = nv.models[type]();
+ var d3chart = nv.models[type]()
// request data
var self = this;
@@ -46,7 +46,7 @@
// y axis label
d3chart.yAxis.axisLabel(chart.settings.get('y_axis_label'))
- .axisLabelDistance(30);
+ .axisLabelDistance(30);
// controls
d3chart.options({showControls: false});
@@ -65,11 +65,23 @@
callback(d3chart);
}
- // parse data to canvas
+ // make categories
+ self._makeCategories(chart, groups, d3chart);
+
+ // hide min/max values
+ d3chart.xAxis.showMaxMin(false);
+ d3chart.yAxis.showMaxMin(chart.definition.showmaxmin);
+
+ // draw chart
canvas.datum(groups)
.call(d3chart);
-
-
+
+ // add zoom/pan handler
+ var zoom_mode = chart.definition.zoomable;
+ if (zoom_mode == 'axis' || zoom_mode == 'svg') {
+ self._addZoom(d3chart, canvas, zoom_mode);
+ }
+
// refresh on window resize
nv.utils.windowResize(d3chart.update);
} catch (err) {
@@ -80,6 +92,64 @@
return true;
},
+ // add zoom handler
+ _addZoom: function(nvd3_model, svg, zoom_mode) {
+ // get canvas dimensions
+ var width = parseInt(svg.style('width'));
+ var height = parseInt(svg.style('height'));
+
+ // create x scales
+ var x_domain = nvd3_model.xAxis.scale().domain();
+ var x = d3.scale.linear()
+ .domain(x_domain)
+ .range([0, width]);
+
+ // create y scale
+ var y_domain = nvd3_model.yAxis.scale().domain();
+ var y = d3.scale.linear()
+ .domain(y_domain)
+ .range([height, 0]);
+
+ // zoom event handler
+ function zoomed() {
+ if (zoom_mode == 'axis') {
+ nvd3_model.xDomain(x.domain());
+ nvd3_model.yDomain(y.domain());
+ nvd3_model.update();
+ } else {
+ var translate = d3.event.translate;
+ svg.select('.nvd3').attr("transform", "translate(" + translate + ") scale(" + d3.event.scale + ")");
+ }
+ }
+
+ // d3 zoom wrapper
+ var d3zoom = d3.behavior.zoom()
+ .x(x)
+ .y(y)
+ .scaleExtent([1, 10])
+ .on("zoom", zoomed);
+
+ // add handler
+ svg.call(d3zoom);
+ },
+
+ // create categories
+ _makeCategories: function(chart, groups, d3chart) {
+ // result
+ var result = Tools.makeCategories(chart, groups);
+
+ // add categories to flot configuration
+ for (var key in result.array) {
+ var axis = key + 'Axis';
+ if (d3chart[axis]) {
+ var a = result.array[key];
+ d3chart[axis].tickFormat(function(value) {
+ return a[value];
+ });
+ }
+ }
+ },
+
// make axis
_axis: function(axis, type, tick) {
switch (type) {
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
@@ -3,7 +3,13 @@
return $.extend(true, {}, nvd3_config, {
title : 'Line chart',
category : 'Others',
+ zoomable : 'axis',
columns : {
+ x : {
+ title : 'Values for x-axis',
+ is_label : true,
+ is_auto : true
+ },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
@@ -11,8 +11,7 @@
},
// render
- draw : function(process_id, chart, request_dictionary)
- {
+ draw : function(process_id, chart, request_dictionary) {
var nvd3 = new NVD3(this.app, this.options);
nvd3.draw('lineChart', process_id, chart, request_dictionary);
}
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
@@ -5,6 +5,11 @@
category : 'Others',
keywords : 'default nvd3',
columns : {
+ x : {
+ title : 'Values for x-axis',
+ is_label : true,
+ is_auto : true
+ },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
@@ -1,4 +1,4 @@
-define([], function() {
+define(['plugin/plugins/nvd3/nv.d3'], function() {
return $.extend(true, {}, {
title : 'Pie chart',
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
@@ -36,66 +36,69 @@
// draw group
_draw_group: function(chart, group, canvas) {
-
- // add title
- var title = canvas.append('text');
-
- // configure title attributes
- this._fix_title(chart, canvas, title, group.key);
-
- // format chart data
- var pie_data = [];
- for (var key in group.values) {
- var value = group.values[key];
- pie_data.push ({
- y : value.y,
- x : value.label
+ try {
+ // add title
+ var title = canvas.append('text');
+
+ // configure title attributes
+ this._fix_title(chart, canvas, title, group.key);
+
+ // format chart data
+ var pie_data = [];
+ for (var key in group.values) {
+ var value = group.values[key];
+ pie_data.push ({
+ y : value.y,
+ x : value.label
+ });
+ }
+
+ // add graph to screen
+ var self = this;
+ nv.addGraph(function() {
+ // legend
+ var legend_visible = true;
+ if (chart.settings.get('show_legend') == 'false') {
+ legend_visible = false;
+ }
+
+ // legend
+ var label_outside = true;
+ if (chart.settings.get('label_outside') == 'false') {
+ label_outside = false;
+ }
+
+ // label type
+ var label_type = chart.settings.get('label_type');
+
+ // ratio
+ var donut_ratio = parseFloat(chart.settings.get('donut_ratio'))
+
+ // create chart model
+ var chart_3d = nv.models.pieChart()
+ .donut(true)
+ .labelThreshold(.05)
+ .showLegend(legend_visible)
+ .labelType(label_type)
+ .donutRatio(donut_ratio)
+ .donutLabelsOutside(label_outside);
+
+ // add data to canvas
+ canvas.datum(pie_data)
+ .call(chart_3d);
+
+ // add resize trigger
+ nv.utils.windowResize(function() {
+ // update chart
+ chart_3d.update();
+
+ // fix title
+ self._fix_title(chart, canvas, title, group.key);
+ });
});
+ } catch (err) {
+ console.log(err);
}
-
- // add graph to screen
- var self = this;
- nv.addGraph(function() {
- // legend
- var legend_visible = true;
- if (chart.settings.get('show_legend') == 'false') {
- legend_visible = false;
- }
-
- // legend
- var label_outside = true;
- if (chart.settings.get('label_outside') == 'false') {
- label_outside = false;
- }
-
- // label type
- var label_type = chart.settings.get('label_type');
-
- // ratio
- var donut_ratio = parseFloat(chart.settings.get('donut_ratio'))
-
- // create chart model
- var chart_3d = nv.models.pieChart()
- .donut(true)
- .labelThreshold(.05)
- .showLegend(legend_visible)
- .labelType(label_type)
- .donutRatio(donut_ratio)
- .donutLabelsOutside(label_outside);
-
- // add data to canvas
- canvas.datum(pie_data)
- .call(chart_3d);
-
- // add resize trigger
- nv.utils.windowResize(function() {
- // update chart
- chart_3d.update();
-
- // fix title
- self._fix_title(chart, canvas, title, group.key);
- });
- });
},
// fix title
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
@@ -3,6 +3,7 @@
return $.extend(true, {}, nvd3_config, {
title : 'Scatter plot',
category : 'Others',
+ zoomable : 'axis',
columns : {
x : {
title : 'Values for x-axis',
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
@@ -2,8 +2,14 @@
return $.extend(true, {}, nvd3_config, {
title : 'Regular',
+ zoomable : 'axis',
category : 'Area charts',
columns : {
+ x : {
+ title : 'Values for x-axis',
+ is_label : true,
+ is_auto : true
+ },
y : {
title : 'Values for y-axis',
is_numeric : true
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
@@ -2,6 +2,7 @@
return $.extend(true, {}, nvd3_config, {
title : 'Expanded',
+ zoomable : 'axis',
category : 'Area charts',
columns : {
y : {
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
@@ -3,7 +3,9 @@
return $.extend(true, {}, nvd3_config, {
title : 'Stream',
category : 'Area charts',
+ zoomable : 'axis',
keywords : 'default nvd3',
+ showmaxmin : true,
columns : {
y : {
title : 'Values for y-axis',
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/tools.js
--- a/config/plugins/visualizations/charts/static/charts/tools.js
+++ b/config/plugins/visualizations/charts/static/charts/tools.js
@@ -41,7 +41,7 @@
chart.deferred.done(process_id);
} catch (err) {
// log
- console.debug('FAILED: Tools::draw() - ' + err);
+ console.debug('FAILED: Tools::panelHelper() - ' + err);
// set chart state
chart.state('failed', err);
@@ -52,6 +52,35 @@
});
};
+// get domain boundaries value
+function getDomains(groups, keys) {
+
+ // get value
+ function _apply(operator, key) {
+ var value = undefined;
+ for (var group_index in groups) {
+ var value_sub = d3[operator](groups[group_index].values, function(d) { return d[key]; });
+ if (value === undefined) {
+ value = value_sub;
+ } else {
+ value = Math[operator](value, value_sub);
+ }
+ }
+ return value;
+ };
+
+ var result = {};
+ for (var index in keys) {
+ var key = keys[index];
+ result[key] = {
+ min : _apply('min', key),
+ max : _apply('max', key),
+ };
+
+ }
+ return result;
+};
+
// series maker
function makeSeries(group) {
// reset data
@@ -74,7 +103,7 @@
};
// category maker
-function makeCategories(chart, groups) {
+function makeCategories(chart, groups, with_index) {
// hashkeys, arrays and counter for labeled columns
var categories = {};
var array = {};
@@ -99,8 +128,17 @@
for (var key in categories) {
var value = String(value_dict[key]);
if (categories[key][value] === undefined) {
+ // add index
categories[key][value] = counter[key];
- array[key].push([counter[key], value]);
+
+ // array formatter
+ if (with_index) {
+ array[key].push([counter[key], value]);
+ } else {
+ array[key].push(value);
+ }
+
+ // increase counter
counter[key]++;
}
}
@@ -131,7 +169,8 @@
return {
panelHelper : panelHelper,
makeCategories : makeCategories,
- makeSeries : makeSeries
+ makeSeries : makeSeries,
+ getDomains : getDomains
}
});
\ No newline at end of file
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/charts/types.js
--- a/config/plugins/visualizations/charts/static/charts/types.js
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -11,9 +11,10 @@
'plugin/charts/nvd3/histogram_discrete/config',
'plugin/charts/nvd3/line/config',
'plugin/charts/nvd3/scatter/config',
- 'plugin/charts/nvd3/stackedarea/config'
- //'plugin/charts/flot/bar/config',
- //'plugin/charts/others/boxplot/config',
+ 'plugin/charts/nvd3/stackedarea/config',
+ 'plugin/charts/flot/bar/config',
+ 'plugin/charts/dygraph/bar/config',
+ 'plugin/charts/others/boxplot/config',
], function(nvd3_bar,
nvd3_bar_stacked,
nvd3_bar_horizontal,
@@ -26,9 +27,10 @@
nvd3_histogram_discrete,
nvd3_line,
nvd3_scatter,
- nvd3_stackedarea
- //flot_bar,
- //others_boxplot
+ nvd3_stackedarea,
+ flot_bar,
+ dygraph_bar,
+ others_boxplot
) {
// widget
@@ -48,8 +50,9 @@
'nvd3_line' : nvd3_line,
'nvd3_scatter' : nvd3_scatter,
'nvd3_histogram' : nvd3_histogram,
- 'nvd3_histogram_discrete' : nvd3_histogram_discrete
- //'flot_bar' : flot_bar,
+ 'nvd3_histogram_discrete' : nvd3_histogram_discrete,
+ 'flot_bar' : flot_bar,
+ //'dygraph_bar' : dygraph_bar,
//'others_boxplot' : others_boxplot
}
});
diff -r 095b6ea1888ee97313a9aff40258a96bb471b219 -r d61ee3309864a69027dacbf5fb3389a33e3f0a4d config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -6,7 +6,7 @@
{
// options
defaults : {
- query_limit : 1000,
+ query_limit : 500,
query_timeout : 100,
screenshot_url : 'http://export.highcharts.com/'
}
This diff is so big that we needed to truncate the remainder.
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0
6 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cfd108a99a24/
Changeset: cfd108a99a24
User: dannon
Date: 2014-06-09 13:58:18
Summary: Update user honeypot error message.
Affected #: 1 file
diff -r 2f1a585a7eaf76c687675c84c054bcc326812af1 -r cfd108a99a24d97eafbd81fd5c9ab565fd3486a2 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -628,7 +628,7 @@
# If the honeypot field is not empty we are dealing with a bot.
honeypot_field = params.get( 'bear_field', '' )
if honeypot_field != '':
- return trans.show_error_message( "You are considered a bot. If you are not one please try registering again and follow the form's legend. <a target=\"_top\" href=\"%s\">Go to the home page</a>." ) % url_for( '/' )
+ return trans.show_error_message( "You've been flagged as a possible bot. If you are not, please try registering again and fill the form out carefully. <a target=\"_top\" href=\"%s\">Go to the home page</a>." ) % url_for( '/' )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
https://bitbucket.org/galaxy/galaxy-central/commits/9b908e6dd95b/
Changeset: 9b908e6dd95b
User: dannon
Date: 2014-06-09 14:14:18
Summary: Fix impersonation when using external authentication. Admins can now impersonate (and then log out of) users when using external auth.
Affected #: 2 files
diff -r cfd108a99a24d97eafbd81fd5c9ab565fd3486a2 -r 9b908e6dd95b9949dd47065528093c1ae36950b7 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -743,8 +743,10 @@
# No user, associate
galaxy_session.user = self.get_or_create_remote_user( remote_user_email )
galaxy_session_requires_flush = True
- elif galaxy_session.user.email != remote_user_email:
- # Session exists but is not associated with the correct remote user
+ elif galaxy_session.user.email != remote_user_email and self.app.config.allow_user_impersonation and remote_user_email not in [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ]:
+ # Session exists but is not associated with the correct
+ # remote user, and the currently set remote_user is not a
+ # potentially impersonating admin.
invalidate_existing_session = True
user_for_new_session = self.get_or_create_remote_user( remote_user_email )
log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
diff -r cfd108a99a24d97eafbd81fd5c9ab565fd3486a2 -r 9b908e6dd95b9949dd47065528093c1ae36950b7 lib/galaxy/web/framework/middleware/remoteuser.py
--- a/lib/galaxy/web/framework/middleware/remoteuser.py
+++ b/lib/galaxy/web/framework/middleware/remoteuser.py
@@ -76,6 +76,8 @@
return self.error( start_response, title, message )
if path_info.startswith( '/user/create' ) and environ[ self.remote_user_header ] in self.admin_users:
pass # admins can create users
+ elif path_info.startswith( '/user/logout' ) and environ[ self.remote_user_header ] in self.admin_users:
+ pass # Admin users may be impersonating, allow logout.
elif path_info.startswith( '/user/api_keys' ):
pass # api keys can be managed when remote_user is in use
elif path_info.startswith( '/user/edit_username' ):
https://bitbucket.org/galaxy/galaxy-central/commits/fe917a59d474/
Changeset: fe917a59d474
User: dannon
Date: 2014-06-09 14:33:25
Summary: pep8/cleanup. set NERD_tree_1noqa for impossible sqlalchemy lines.
Affected #: 1 file
diff -r 9b908e6dd95b9949dd47065528093c1ae36950b7 -r fe917a59d4749503db66fe7c01ffe3e41fb1a3cf lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -35,10 +35,10 @@
import mako.lookup
import mako.runtime
-eggs.require( "pytz" ) # Used by Babel.
+eggs.require( "pytz" ) # Used by Babel.
eggs.require( "Babel" )
from babel.support import Translations
-from babel import Locale, UnknownLocaleError
+from babel import Locale
eggs.require( "SQLAlchemy >= 0.4" )
from sqlalchemy import and_
@@ -63,6 +63,7 @@
'hgw8.cse.ucsc.edu',
)
+
def expose( func ):
"""
Decorator: mark a function as 'exposed' and thus web accessible
@@ -70,6 +71,7 @@
func.exposed = True
return func
+
def json( func ):
@wraps(func)
def decorator( self, trans, *args, **kwargs ):
@@ -80,6 +82,7 @@
decorator.exposed = True
return decorator
+
def json_pretty( func ):
@wraps(func)
def decorator( self, trans, *args, **kwargs ):
@@ -90,6 +93,7 @@
decorator.exposed = True
return decorator
+
def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ):
def argcatcher( func ):
@wraps(func)
@@ -132,6 +136,7 @@
payload = util.recursively_stringify_dictionary_keys( from_json_string( trans.request.body ) )
return payload
+
def expose_api_raw( func ):
"""
Expose this function via the API but don't dump the results
@@ -139,7 +144,7 @@
"""
return expose_api( func, to_json=False )
-#DBTODO refactor these post-dist.
+
def expose_api_raw_anonymous( func ):
"""
Expose this function via the API but don't dump the results
@@ -147,12 +152,14 @@
"""
return expose_api( func, to_json=False, user_required=False )
+
def expose_api_anonymous( func, to_json=True ):
"""
Expose this function via the API but don't require a set user.
"""
return expose_api( func, to_json=to_json, user_required=False )
+
def expose_api( func, to_json=True, user_required=True ):
"""
Expose this function via the API.
@@ -203,7 +210,7 @@
rval = to_json_string( rval )
return rval
except paste.httpexceptions.HTTPException:
- raise # handled
+ raise # handled
except:
log.exception( 'Uncaught exception in exposed API method:' )
raise paste.httpexceptions.HTTPServerError()
@@ -379,9 +386,11 @@
NOT_SET = object()
+
def error( message ):
raise MessageException( message, type='error' )
+
def form( *args, **kwargs ):
return FormBuilder( *args, **kwargs )
@@ -405,15 +414,15 @@
# Then look in root directory
paths.append( galaxy_app.config.template_path )
# Create TemplateLookup with a small cache
- return mako.lookup.TemplateLookup(
- directories = paths,
- module_directory = galaxy_app.config.template_cache,
- collection_size = 500,
- output_encoding = 'utf-8' )
+ return mako.lookup.TemplateLookup(directories=paths,
+ module_directory=galaxy_app.config.template_cache,
+ collection_size=500,
+ output_encoding='utf-8' )
def handle_controller_exception( self, e, trans, **kwargs ):
if isinstance( e, MessageException ):
- #In the case of a controller exception, sanitize to make sure unsafe html input isn't reflected back to the user
+ # In the case of a controller exception, sanitize to make sure
+ # unsafe html input isn't reflected back to the user
return trans.show_message( sanitize_html(e.err_msg), e.type )
def make_body_iterable( self, trans, body ):
@@ -509,7 +518,7 @@
elif self.app.name == "reports":
self.galaxy_session = None
else:
- #This is a web request, get or create session.
+ # This is a web request, get or create session.
self._ensure_valid_session( session_cookie )
if self.galaxy_session:
# When we've authenticated by session, we have to check the
@@ -534,7 +543,7 @@
# Default to English
locales = 'en'
t = Translations.load( dirname='locale', locales=locales, domain='ginga' )
- self.template_context.update ( dict( _=t.ugettext, n_=t.ugettext, N_=t.ungettext ) )
+ self.template_context.update( dict( _=t.ugettext, n_=t.ugettext, N_=t.ungettext ) )
@property
def anonymous( self ):
@@ -644,8 +653,8 @@
# using a server secret key. Any other value is invalid and could pose security issues.
self.response.cookies[name] = value
self.response.cookies[name]['path'] = path
- self.response.cookies[name]['max-age'] = 3600 * 24 * age # 90 days
- tstamp = time.localtime ( time.time() + 3600 * 24 * age )
+ self.response.cookies[name]['max-age'] = 3600 * 24 * age # 90 days
+ tstamp = time.localtime( time.time() + 3600 * 24 * age )
self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp )
self.response.cookies[name]['version'] = version
try:
@@ -724,14 +733,13 @@
if session_key:
# Retrieve the galaxy_session id via the unique session_key
galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \
- .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key,
- self.app.model.GalaxySession.table.c.is_valid==True ) ) \
- .first()
+ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, #noqa
+ self.app.model.GalaxySession.table.c.is_valid==True ) ).first() #noqa
# If remote user is in use it can invalidate the session and in some
# cases won't have a cookie set above, so we need to to check some
# things now.
if self.app.config.use_remote_user:
- #If this is an api request, and they've passed a key, we let this go.
+ # If this is an api request, and they've passed a key, we let this go.
assert self.app.config.remote_user_header in self.environ, \
"use_remote_user is set but %s header was not provided" % self.app.config.remote_user_header
remote_user_email = self.environ[ self.app.config.remote_user_header ]
@@ -828,9 +836,9 @@
if self.request.path.startswith( external_display_path ):
request_path_split = self.request.path.split( '/' )
try:
- if self.app.datatypes_registry.display_applications.get( request_path_split[-5] ) and \
- request_path_split[-4] in self.app.datatypes_registry.display_applications.get( request_path_split[-5] ).links and \
- request_path_split[-3] != 'None':
+ if (self.app.datatypes_registry.display_applications.get( request_path_split[-5] )
+ and request_path_split[-4] in self.app.datatypes_registry.display_applications.get( request_path_split[-5] ).links
+ and request_path_split[-3] != 'None'):
return
except IndexError:
pass
@@ -849,9 +857,9 @@
galaxy_session = self.app.model.GalaxySession(
session_key=session_key,
is_valid=True,
- remote_host = self.request.remote_host,
- remote_addr = self.request.remote_addr,
- referer = self.request.headers.get( 'Referer', None ) )
+ remote_host=self.request.remote_host,
+ remote_addr=self.request.remote_addr,
+ referer=self.request.headers.get( 'Referer', None ) )
if prev_galaxy_session:
# Invalidated an existing session for some reason, keep track
galaxy_session.prev_session_id = prev_galaxy_session.id
@@ -868,9 +876,8 @@
return None
if getattr( self.app.config, "normalize_remote_user_email", False ):
remote_user_email = remote_user_email.lower()
- user = self.sa_session.query( self.app.model.User ) \
- .filter( self.app.model.User.table.c.email==remote_user_email ) \
- .first()
+ user = self.sa_session.query( self.app.model.User
+ ).filter( self.app.model.User.table.c.email==remote_user_email ).first() #noqa
if user:
# GVK: June 29, 2009 - This is to correct the behavior of a previous bug where a private
# role and default user / history permissions were not set for remote users. When a
@@ -903,7 +910,7 @@
# We set default user permissions, before we log in and set the default history permissions
if 'webapp' not in self.environ or self.environ['webapp'] != 'tool_shed':
self.app.security_agent.user_set_default_permissions( user )
- #self.log_event( "Automatically created account '%s'", user.email )
+ # self.log_event( "Automatically created account '%s'", user.email )
return user
def __update_session_cookie( self, name='galaxysession' ):
@@ -973,7 +980,6 @@
# This method is not called from the Galaxy reports, so the cookie will always be galaxysession
self.__update_session_cookie( name=cookie_name )
-
def handle_user_logout( self, logout_all=False ):
"""
Logout the current user:
@@ -986,10 +992,10 @@
self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) )
galaxy_user_id = prev_galaxy_session.user_id
if logout_all and galaxy_user_id is not None:
- for other_galaxy_session in self.sa_session.query( self.app.model.GalaxySession ) \
- .filter( and_( self.app.model.GalaxySession.table.c.user_id==galaxy_user_id,
- self.app.model.GalaxySession.table.c.is_valid==True,
- self.app.model.GalaxySession.table.c.id!=prev_galaxy_session.id ) ):
+ for other_galaxy_session in self.sa_session.query( self.app.model.GalaxySession
+ ).filter( and_( self.app.model.GalaxySession.table.c.user_id==galaxy_user_id, #noqa
+ self.app.model.GalaxySession.table.c.is_valid==True, #noqa
+ self.app.model.GalaxySession.table.c.id!=prev_galaxy_session.id ) ): #noqa
other_galaxy_session.is_valid = False
self.sa_session.add( other_galaxy_session )
self.sa_session.flush()
@@ -1041,9 +1047,9 @@
# (b) has no datasets. If suitable history found, use it; otherwise, create
# new history.
unnamed_histories = self.sa_session.query( self.app.model.History ).filter_by(
- user=self.galaxy_session.user,
- name=self.app.model.History.default_name,
- deleted=False )
+ user=self.galaxy_session.user,
+ name=self.app.model.History.default_name,
+ deleted=False )
default_history = None
for history in unnamed_histories:
if len( history.datasets ) == 0:
@@ -1180,8 +1186,9 @@
Convenience method for displaying a simple page with a single HTML
form.
"""
- return self.fill_template( template, form=form, header=header, use_panels=( form.use_panels or use_panels ),
- active_view=active_view )
+ return self.fill_template( template, form=form, header=header,
+ use_panels=( form.use_panels or use_panels ),
+ active_view=active_view )
def fill_template(self, filename, **kwargs):
"""
@@ -1214,9 +1221,10 @@
data = dict( caller=self, t=self, trans=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app )
data.update( self.template_context )
data.update( kwargs )
- ## return template.render( **data )
+
def render( environ, start_response ):
response_write = start_response( self.response.wsgi_status(), self.response.wsgi_headeritems() )
+
class StreamBuffer( object ):
def write( self, d ):
response_write( d.encode( 'utf-8' ) )
@@ -1240,7 +1248,7 @@
Returns the builds defined by galaxy and the builds defined by
the user (chromInfo in history).
"""
- #FIXME: This method should be removed
+ # FIXME: This method should be removed
return self.app.genome_builds.get_genome_build_names( trans=self )
@property
@@ -1365,6 +1373,6 @@
def __getattr__( self, key ):
if key not in self: raise AttributeError, key
return self[key]
+
def __setattr__( self, key, value ):
self[key] = value
-
https://bitbucket.org/galaxy/galaxy-central/commits/305d4bd1db40/
Changeset: 305d4bd1db40
User: dannon
Date: 2014-06-09 14:35:32
Summary: One more touchup in webframework -- correct raise form and use multiple lines.
Affected #: 1 file
diff -r fe917a59d4749503db66fe7c01ffe3e41fb1a3cf -r 305d4bd1db404b13f49b6cc49e36115b4d2e33d4 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -1371,7 +1371,8 @@
Bunch based on a dict
"""
def __getattr__( self, key ):
- if key not in self: raise AttributeError, key
+ if key not in self:
+ raise AttributeError(key)
return self[key]
def __setattr__( self, key, value ):
https://bitbucket.org/galaxy/galaxy-central/commits/8e4483daa6e8/
Changeset: 8e4483daa6e8
User: dannon
Date: 2014-06-09 14:38:47
Summary: Cleanup/pep8 of remoteuser middleware.
Affected #: 1 file
diff -r 305d4bd1db404b13f49b6cc49e36115b4d2e33d4 -r 8e4483daa6e8a76044b7ec0bc06877b4244a0125 lib/galaxy/web/framework/middleware/remoteuser.py
--- a/lib/galaxy/web/framework/middleware/remoteuser.py
+++ b/lib/galaxy/web/framework/middleware/remoteuser.py
@@ -35,6 +35,7 @@
</html>
"""
+
class RemoteUser( object ):
def __init__( self, app, maildomain=None, display_servers=None, admin_users=None, remote_user_header=None ):
self.app = app
@@ -42,9 +43,10 @@
self.display_servers = display_servers or []
self.admin_users = admin_users or []
self.remote_user_header = remote_user_header or 'HTTP_REMOTE_USER'
+
def __call__( self, environ, start_response ):
# Allow display servers
- if self.display_servers and environ.has_key( 'REMOTE_ADDR' ):
+ if self.display_servers and 'REMOTE_ADDR' in environ:
try:
host = socket.gethostbyaddr( environ[ 'REMOTE_ADDR' ] )[0]
except( socket.error, socket.herror, socket.gaierror, socket.timeout ):
@@ -57,7 +59,7 @@
# Rewrite* method for passing REMOTE_USER and a user is
# un-authenticated. Any other possible values need to go here as well.
path_info = environ.get('PATH_INFO', '')
- if environ.has_key( self.remote_user_header ) and environ[ self.remote_user_header ] != '(null)':
+ if self.remote_user_header in environ and environ[ self.remote_user_header ] != '(null)':
if not environ[ self.remote_user_header ].count( '@' ):
if self.maildomain is not None:
environ[ self.remote_user_header ] += '@' + self.maildomain
@@ -75,15 +77,15 @@
"""
return self.error( start_response, title, message )
if path_info.startswith( '/user/create' ) and environ[ self.remote_user_header ] in self.admin_users:
- pass # admins can create users
+ pass # admins can create users
elif path_info.startswith( '/user/logout' ) and environ[ self.remote_user_header ] in self.admin_users:
pass # Admin users may be impersonating, allow logout.
elif path_info.startswith( '/user/api_keys' ):
- pass # api keys can be managed when remote_user is in use
+ pass # api keys can be managed when remote_user is in use
elif path_info.startswith( '/user/edit_username' ):
- pass # username can be managed when remote_user is in use
+ pass # username can be managed when remote_user is in use
elif path_info.startswith( '/user/dbkeys' ):
- pass # dbkeys can be managed when remote_user is in use
+ pass # dbkeys can be managed when remote_user is in use
elif path_info.startswith( '/user' ):
title = "Access to Galaxy user controls is disabled"
message = """
@@ -105,6 +107,7 @@
<p>Please contact your local Galaxy administrator.
"""
return self.error( start_response, title, message )
+
def error( self, start_response, title="Access denied", message="Please contact your local Galaxy administrator." ):
start_response( '403 Forbidden', [('Content-type', 'text/html')] )
return [errorpage % (title, message)]
https://bitbucket.org/galaxy/galaxy-central/commits/095b6ea1888e/
Changeset: 095b6ea1888e
User: dannon
Date: 2014-06-09 14:40:40
Summary: Slightly simplify remote_user_header access logic.
Affected #: 1 file
diff -r 8e4483daa6e8a76044b7ec0bc06877b4244a0125 -r 095b6ea1888ee97313a9aff40258a96bb471b219 lib/galaxy/web/framework/middleware/remoteuser.py
--- a/lib/galaxy/web/framework/middleware/remoteuser.py
+++ b/lib/galaxy/web/framework/middleware/remoteuser.py
@@ -59,7 +59,7 @@
# Rewrite* method for passing REMOTE_USER and a user is
# un-authenticated. Any other possible values need to go here as well.
path_info = environ.get('PATH_INFO', '')
- if self.remote_user_header in environ and environ[ self.remote_user_header ] != '(null)':
+ if environ.get(self.remote_user_header, '(null)') != '(null)':
if not environ[ self.remote_user_header ].count( '@' ):
if self.maildomain is not None:
environ[ self.remote_user_header ] += '@' + self.maildomain
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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09 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2f1a585a7eaf/
Changeset: 2f1a585a7eaf
User: jmchilton
Date: 2014-06-09 02:41:51
Summary: Merge latest stable.
Affected #: 2 files
diff -r fdff233d2fc6b10c31a613bd60cd1f42ff1a1113 -r 2f1a585a7eaf76c687675c84c054bcc326812af1 static/scripts/galaxy.tools.js
--- a/static/scripts/galaxy.tools.js
+++ b/static/scripts/galaxy.tools.js
@@ -110,9 +110,9 @@
enableSelectBy: function( enableIndex, onValue ) {
var selectionType = SELECTION_TYPE[onValue];
if(selectionType["allow_remap"]) {
+ $("div#remap-row").css("display", "inherit");
+ } else {
$("div#remap-row").css("display", "none");
- } else {
- $("div#remap-row").css("display", "inherit");
}
this.formRow().find( "i" ).each(function(index, iElement) {
if(index == enableIndex) {
diff -r fdff233d2fc6b10c31a613bd60cd1f42ff1a1113 -r 2f1a585a7eaf76c687675c84c054bcc326812af1 static/scripts/packed/galaxy.tools.js
--- a/static/scripts/packed/galaxy.tools.js
+++ b/static/scripts/packed/galaxy.tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/tools"],function(c,b){var a=function(g,f){$("input[name='"+g+"'][type='checkbox']").attr("checked",!!f)};$("div.checkUncheckAllPlaceholder").each(function(){var f=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){a(f,true)});unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){a(f,false)});$(this).append(select_link).append(" ").append(unselect_link)});var e={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:true},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:false,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:false},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:true},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:false,},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:true},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:false,}};var d=Backbone.View.extend({initialize:function(l){var g=l.default_option;var m=null;var k=l.switch_options;this.switchOptions=k;this.prefix=l.prefix;var j=this.$el;var f=this;var h=0;var i=0;c.each(this.switchOptions,function(r,t){var n=c.size(r.options);var q=e[t];var p=h++;var s=false;if(g==t){m=p}else{if(n<(q.min_option_count||1)){s=true}}if(!s){i++;var o=$('<i class="fa '+q.icon_class+' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){f.enableSelectBy(p,t)}).attr("title",q.select_by);f.formRow().find("label").append(o)}});if(i<2){f.formRow().find("i.runOptionIcon").hide()}if(m!=null){f.enableSelectBy(m,g)}},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(k,j){var h=e[j];if(h.allow_remap){$("div#remap-row").css("display","none")}else{$("div#remap-row").css("display","inherit")}this.formRow().find("i").each(function(l,m){if(l==k){$(m).css("color","black")}else{$(m).css("color","Gray")}});var g=this.$("select");var f=this.switchOptions[j];g.attr("name",this.prefix+f.name);g.attr("multiple",f.multiple);var i=this.$(".select2-container").length>0;g.html("");c.each(f.options,function(m){var o=m[0];var n=m[1];var l=m[2];g.append($("<option />",{text:o,val:n,selected:l}))});if(i){g.select2()}}});return{SwitchSelectView:d}});
\ No newline at end of file
+define(["libs/underscore","mvc/tools"],function(c,b){var a=function(g,f){$("input[name='"+g+"'][type='checkbox']").attr("checked",!!f)};$("div.checkUncheckAllPlaceholder").each(function(){var f=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){a(f,true)});unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){a(f,false)});$(this).append(select_link).append(" ").append(unselect_link)});var e={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:true},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:false,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:false},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:true},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:false,},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:true},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:false,}};var d=Backbone.View.extend({initialize:function(l){var g=l.default_option;var m=null;var k=l.switch_options;this.switchOptions=k;this.prefix=l.prefix;var j=this.$el;var f=this;var h=0;var i=0;c.each(this.switchOptions,function(r,t){var n=c.size(r.options);var q=e[t];var p=h++;var s=false;if(g==t){m=p}else{if(n<(q.min_option_count||1)){s=true}}if(!s){i++;var o=$('<i class="fa '+q.icon_class+' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){f.enableSelectBy(p,t)}).attr("title",q.select_by);f.formRow().find("label").append(o)}});if(i<2){f.formRow().find("i.runOptionIcon").hide()}if(m!=null){f.enableSelectBy(m,g)}},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(k,j){var h=e[j];if(h.allow_remap){$("div#remap-row").css("display","inherit")}else{$("div#remap-row").css("display","none")}this.formRow().find("i").each(function(l,m){if(l==k){$(m).css("color","black")}else{$(m).css("color","Gray")}});var g=this.$("select");var f=this.switchOptions[j];g.attr("name",this.prefix+f.name);g.attr("multiple",f.multiple);var i=this.$(".select2-container").length>0;g.html("");c.each(f.options,function(m){var o=m[0];var n=m[1];var l=m[2];g.append($("<option />",{text:o,val:n,selected:l}))});if(i){g.select2()}}});return{SwitchSelectView:d}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9721c563cdfa/
Changeset: 9721c563cdfa
Branch: stable
User: jmchilton
Date: 2014-06-07 19:30:02
Summary: Bugfix: Tool form logic for displaying allow_remap option was inverted.
Affected #: 1 file
diff -r b62f649f1955f64deb94c7e20093e31f5f411867 -r 9721c563cdfacdb3de47331ed81ea07edbfd23e0 static/scripts/galaxy.tools.js
--- a/static/scripts/galaxy.tools.js
+++ b/static/scripts/galaxy.tools.js
@@ -110,9 +110,9 @@
enableSelectBy: function( enableIndex, onValue ) {
var selectionType = SELECTION_TYPE[onValue];
if(selectionType["allow_remap"]) {
+ $("div#remap-row").css("display", "inherit");
+ } else {
$("div#remap-row").css("display", "none");
- } else {
- $("div#remap-row").css("display", "inherit");
}
this.formRow().find( "i" ).each(function(index, iElement) {
if(index == enableIndex) {
https://bitbucket.org/galaxy/galaxy-central/commits/2ade3d7303fa/
Changeset: 2ade3d7303fa
Branch: stable
User: jmchilton
Date: 2014-06-07 19:31:44
Summary: Pack scripts.
Affected #: 1 file
diff -r 9721c563cdfacdb3de47331ed81ea07edbfd23e0 -r 2ade3d7303fadb457d766ec928157e824264dbf6 static/scripts/packed/galaxy.tools.js
--- a/static/scripts/packed/galaxy.tools.js
+++ b/static/scripts/packed/galaxy.tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/tools"],function(c,b){var a=function(g,f){$("input[name='"+g+"'][type='checkbox']").attr("checked",!!f)};$("div.checkUncheckAllPlaceholder").each(function(){var f=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){a(f,true)});unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){a(f,false)});$(this).append(select_link).append(" ").append(unselect_link)});var e={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:true},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:false,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:false},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:true},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:false,},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:true},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:false,}};var d=Backbone.View.extend({initialize:function(l){var g=l.default_option;var m=null;var k=l.switch_options;this.switchOptions=k;this.prefix=l.prefix;var j=this.$el;var f=this;var h=0;var i=0;c.each(this.switchOptions,function(r,t){var n=c.size(r.options);var q=e[t];var p=h++;var s=false;if(g==t){m=p}else{if(n<(q.min_option_count||1)){s=true}}if(!s){i++;var o=$('<i class="fa '+q.icon_class+' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){f.enableSelectBy(p,t)}).attr("title",q.select_by);f.formRow().find("label").append(o)}});if(i<2){f.formRow().find("i.runOptionIcon").hide()}if(m!=null){f.enableSelectBy(m,g)}},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(k,j){var h=e[j];if(h.allow_remap){$("div#remap-row").css("display","none")}else{$("div#remap-row").css("display","inherit")}this.formRow().find("i").each(function(l,m){if(l==k){$(m).css("color","black")}else{$(m).css("color","Gray")}});var g=this.$("select");var f=this.switchOptions[j];g.attr("name",this.prefix+f.name);g.attr("multiple",f.multiple);var i=this.$(".select2-container").length>0;g.html("");c.each(f.options,function(m){var o=m[0];var n=m[1];var l=m[2];g.append($("<option />",{text:o,val:n,selected:l}))});if(i){g.select2()}}});return{SwitchSelectView:d}});
\ No newline at end of file
+define(["libs/underscore","mvc/tools"],function(c,b){var a=function(g,f){$("input[name='"+g+"'][type='checkbox']").attr("checked",!!f)};$("div.checkUncheckAllPlaceholder").each(function(){var f=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){a(f,true)});unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){a(f,false)});$(this).append(select_link).append(" ").append(unselect_link)});var e={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:true},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:false,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:false},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:true},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:false,},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:true},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:false,}};var d=Backbone.View.extend({initialize:function(l){var g=l.default_option;var m=null;var k=l.switch_options;this.switchOptions=k;this.prefix=l.prefix;var j=this.$el;var f=this;var h=0;var i=0;c.each(this.switchOptions,function(r,t){var n=c.size(r.options);var q=e[t];var p=h++;var s=false;if(g==t){m=p}else{if(n<(q.min_option_count||1)){s=true}}if(!s){i++;var o=$('<i class="fa '+q.icon_class+' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){f.enableSelectBy(p,t)}).attr("title",q.select_by);f.formRow().find("label").append(o)}});if(i<2){f.formRow().find("i.runOptionIcon").hide()}if(m!=null){f.enableSelectBy(m,g)}},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(k,j){var h=e[j];if(h.allow_remap){$("div#remap-row").css("display","inherit")}else{$("div#remap-row").css("display","none")}this.formRow().find("i").each(function(l,m){if(l==k){$(m).css("color","black")}else{$(m).css("color","Gray")}});var g=this.$("select");var f=this.switchOptions[j];g.attr("name",this.prefix+f.name);g.attr("multiple",f.multiple);var i=this.$(".select2-container").length>0;g.html("");c.each(f.options,function(m){var o=m[0];var n=m[1];var l=m[2];g.append($("<option />",{text:o,val:n,selected:l}))});if(i){g.select2()}}});return{SwitchSelectView:d}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: More fixes for handling 307 redirects not being handled nicely by urllib2.urlopen() when the urllib2.Request has data provided.
by commits-noreply＠bitbucket.org 08 Jun '14
by commits-noreply＠bitbucket.org 08 Jun '14
08 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fdff233d2fc6/
Changeset: fdff233d2fc6
User: greg
Date: 2014-06-08 14:45:16
Summary: More fixes for handling 307 redirects not being handled nicely by urllib2.urlopen() when the urllib2.Request has data provided.
Affected #: 1 file
diff -r a932242dc2da4fd532c640006aa2ae4d35a7d72b -r fdff233d2fc6b10c31a613bd60cd1f42ff1a1113 lib/tool_shed/scripts/api/common.py
--- a/lib/tool_shed/scripts/api/common.py
+++ b/lib/tool_shed/scripts/api/common.py
@@ -18,6 +18,9 @@
"""
try:
url = make_url( url, api_key=api_key, args=None )
+ # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the
+ # urllib2.Request has data provided.
+ url = urllib2.urlopen( urllib2.Request( url ) ).geturl()
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
req.get_method = lambda: 'DELETE'
r = json.loads( urllib2.urlopen( req ).read() )
@@ -174,12 +177,18 @@
def post( url, data, api_key=None ):
"""Do the POST."""
url = make_url( url, api_key=api_key, args=None )
+ # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the
+ # urllib2.Request has data provided.
+ url = urllib2.urlopen( urllib2.Request( url ) ).geturl()
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) )
return json.loads( urllib2.urlopen( req ).read() )
def put( url, data, api_key=None ):
"""Do the PUT."""
url = make_url( url, api_key=api_key, args=None )
+ # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the
+ # urllib2.Request has data provided.
+ url = urllib2.urlopen( urllib2.Request( url ) ).geturl()
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
req.get_method = lambda: 'PUT'
return json.loads( urllib2.urlopen( req ).read() )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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