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commit/galaxy-central: dannon: Reorder imports post-PR 403.
by commits-noreply＠bitbucket.org 09 Jun '14

09 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b18fb85eed5/ Changeset: 9b18fb85eed5 User: dannon Date: 2014-06-09 16:53:00 Summary: Reorder imports post-PR 403. Affected #: 1 file diff -r 633c27341859df116d2dd039bb16e9c29bedd65a -r 9b18fb85eed5129f5fd50a44c97ec6fd3a71dd9d tools/filters/convert_characters.py --- a/tools/filters/convert_characters.py +++ b/tools/filters/convert_characters.py @@ -1,8 +1,8 @@ #!/usr/bin/env python #By, Guruprasad Ananda. +import re import sys -import re def stop_err(msg): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in saketkc/galaxy-fork (pull request #403)
by commits-noreply＠bitbucket.org 09 Jun '14

09 Jun '14

1 new commit in galaxy-central: 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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Jun '14

09 Jun '14

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Jun '14

09 Jun '14

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Jun '14

09 Jun '14

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. 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src="'+e.url+'"/>'}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new 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i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:100,screenshot_url:"http://export.highcharts.com/"}})}),define("plugin/charts/nvd3/common/config",[],function(){return{title:"",category:"",library:"NVD3",tag:"svg",keywords:"default nvd3",settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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n=$(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 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 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 e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new Date),e.logs.totalTime=e.logs.endTime-e.logs.startTime,e.log("total",e.logs.totalTime)})),e.log=function(){if(e.dev&&console.log&&console.log.apply)console.log.apply(console,arguments);else if(e.dev&&typeof console.log=="function"&&Function.prototype.bind){var t=Function.prototype.bind.call(console.log,console);t.apply(console,arguments)}return arguments[arguments.length-1]},e.render=function(n){n=n||1,e.render.active=!0,e.dispatch.render_start(),setTimeout(function(){var t,r;for(var i=0;i<n&&(r=e.render.queue[i]);i++)t=r.generate(),typeof r.callback==typeof Function&&r.callback(t),e.graphs.push(t);e.render.queue.splice(0,i),e.render.queue.length?setTimeout(arguments.callee,0):(e.dispatch.render_end(),e.render.active=!1)},0)},e.render.active=!1,e.render.queue=[],e.addGraph=function(t){typeof arguments[0]==typeof Function&&(t={generate:arguments[0],callback:arguments[1]}),e.render.queue.push(t),e.render.active||e.render()},e.identity=function(e){return e},e.strip=function(e){return e.replace(/(\s|&)/g,"")},d3.time.monthEnd=function(e){return new Date(e.getFullYear(),e.getMonth(),0)},d3.time.monthEnds=n(d3.time.monthEnd,function(e){e.setUTCDate(e.getUTCDate()+1),e.setDate(t(e.getMonth()+1,e.getFullYear()))},function(e){return e.getMonth()}),e.interactiveGuideline=function(){function c(o){o.each(function(o){function g(){var 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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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?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return 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 e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.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,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return 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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--",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/flot/bar/config",["plugin/charts/flot/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/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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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

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. -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.$buttons.find("#"+t).show()},hideButton:function(e){var 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n=this;this.$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 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+" 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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: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 $.extend(!0,{},e,{title:"Regular",category:"Area charts",columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$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 +define("mvc/ui/ui-modal",[],function(){var 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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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$.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. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 09 Jun '14

09 Jun '14

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jmchilton: Merge latest stable.
by commits-noreply＠bitbucket.org 09 Jun '14

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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 08 Jun '14

08 Jun '14

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/ -- This is a commit notification from bitbucket.org. 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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

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Refactor nvd3 wrappers, remove excluded wrappers
by commits-noreply＠bitbucket.org 07 Jun '14

07 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a932242dc2da/ Changeset: a932242dc2da User: guerler Date: 2014-06-07 23:51:41 Summary: Charts: Refactor nvd3 wrappers, remove excluded wrappers Affected #: 59 files diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b 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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available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","mvc/ui/ui-modal"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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,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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new 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r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return 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 available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa 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e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","mvc/ui/ui-modal"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" 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'+e.icon+'"></i> '),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 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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: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 $.extend(!0,{},e,{title:"Regular",category:"Area charts",columns:{y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/histogram_discrete/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:h,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:l,nvd3_scatter:c,nvd3_histogram:a,nvd3_histogram_discrete:f}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$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 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar/config.js +++ /dev/null @@ -1,20 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Regular', - category : 'Bar diagrams', - keywords : 'highcharts', - columns : { - x : { - title : 'Values for x-axis', - is_label : true, - is_auto : true - }, - y : { - title : 'Values for y-axis', - is_numeric : true - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/bar/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar/wrapper.js +++ /dev/null @@ -1,20 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'column', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal/config.js +++ /dev/null @@ -1,25 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Horizontal', - category : 'Bar diagrams', - keywords : 'highcharts', - columns : { - x : { - title : 'Values for x-axis', - is_label : true, - is_auto : true - }, - y : { - title : 'Values for y-axis', - is_numeric : true - } - }, - settings : { - x_axis_type : { - init : 'hide' - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal/wrapper.js +++ /dev/null @@ -1,20 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'bar', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/config.js +++ /dev/null @@ -1,25 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Stacked horizontal', - category : 'Bar diagrams', - keywords : 'highcharts', - settings : { - x_axis_type : { - init : 'hide' - } - }, - columns : { - x : { - title : 'Values for x-axis', - is_label : true, - is_auto : true - }, - y : { - title : 'Values for y-axis', - is_numeric : true - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js +++ /dev/null @@ -1,24 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - // finalize configuration - chart.settings.set('plotoptions_series_stacking', 'normal'); - - // draw chart - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'bar', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/config.js +++ /dev/null @@ -1,20 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Stacked', - category : 'Bar diagrams', - keywords : 'highcharts', - columns : { - x : { - title : 'Values for x-axis', - is_label : true, - is_auto : true - }, - y : { - title : 'Values for y-axis', - is_numeric : true - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js +++ /dev/null @@ -1,25 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // finalize configuration - chart.settings.set('plotoptions_series_stacking', 'normal'); - - // draw chart - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'column', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/config.js +++ /dev/null @@ -1,138 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, { - title : 'Box plot', - category : 'Data processing (requires \'charts\' tool from Toolshed)', - library : 'Highcharts', - tag : 'div', - execute : 'boxplot', - keywords : 'highcharts', - columns : { - y : { - title : 'Observations', - is_numeric : true - } - }, - 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' - } - ] - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/boxplot/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js +++ /dev/null @@ -1,79 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/highcharts-config', 'plugin/charts/highcharts/common/wrapper'], function(configmaker, Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary, callback) { - // configure request - var index = 0; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = null; - group.columns = { - x: { - index: index++ - } - } - } - - // hide legend - chart.settings.set('legend_enabled', 'false') - - // create configuration - this.hc_config = configmaker(chart, callback); - - // request data - var self = this; - this.app.datasets.request(request_dictionary, function() { - // reset data/categories - var data = []; - var categories = []; - - // loop through data groups - for (var key in request_dictionary.groups) { - // get group - var group = request_dictionary.groups[key]; - - // add category - categories.push(group.key); - - // format chart data - var point = []; - for (var key in group.values) { - point.push(group.values[key].x); - } - - // add to data - data.push (point); - } - - // categories - self.hc_config.xAxis.categories = categories; - - // update data - self.hc_config.series.push({ - type : 'boxplot', - data : data - }); - - // draw plot - self.options.canvas[0].highcharts(self.hc_config); - - // set chart state - chart.state('ok', 'Box plot drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/common/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/config.js +++ /dev/null @@ -1,249 +0,0 @@ -define([], function() { - -return { - title : '', - category : '', - library : 'Highcharts', - tag : 'div', - keywords : 'highcharts', - 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' - } - ] - - }, - x_axis_grid : { - title : 'Axis grid', - info : 'Would you like to show grid lines for this axis?', - type : 'radiobutton', - init : '0', - data : [ - { - label : 'On', - value : '1' - }, - { - label : 'Off', - value : '0' - } - ] - }, - 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' - } - ] - }, - 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' - } - ] - } - } -}; - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js +++ /dev/null @@ -1,103 +0,0 @@ -// dependencies -define([], function() { - -// highcharts configuration -return function(chart) { - - // get chart settings - var settings = chart.settings; - - // initialize config object - var hc_config = { - chart: { - type : '', - zoomType : 'xy' - }, - - title: { - text : '' - }, - - legend: { - enabled : settings.get('legend_enabled') == undefined || settings.get('legend_enabled') == 'true' - }, - - credits: { - enabled : false - }, - - xAxis: { - title: { - text : settings.get('x_axis_label') - }, - stackLabels: { - enabled: false, - style: { - fontWeight : 'bold', - color : (Highcharts.theme && Highcharts.theme.textColor) || 'gray' - } - }, - labels: { - formatter : function() { - var axis_type = settings.get('x_axis_type'); - if (axis_type == 'auto' || axis_type === undefined) - return this.value; - var format = d3.format(settings.get('x_axis_tick') + axis_type); - return format(this.value); - }, - enabled : !(settings.get('x_axis_type') == 'hide') - }, - gridLineWidth : settings.get('x_axis_grid') - }, - - yAxis: { - title: { - text : settings.get('y_axis_label') - }, - labels: { - formatter : function() { - var axis_type = settings.get('y_axis_type'); - if (axis_type == 'auto' || axis_type === undefined) - return this.value; - var format = d3.format(settings.get('y_axis_tick') + axis_type); - return format(this.value); - }, - enabled : !(settings.get('y_axis_type') == 'hide') - }, - gridLineWidth : settings.get('y_axis_grid') - }, - plotOptions: { - series: { - animation : false, - stacking : settings.get('plotoptions_series_stacking') - }, - column: { - stacking : settings.get('plotoptions_column_stacking') - }, - area: { - stacking : settings.get('plotoptions_area_stacking'), - lineColor : '#ffffff', - lineWidth : 1, - marker: { - lineWidth : 1, - lineColor : '#ffffff' - } - }, - pie: { - allowPointSelect : true, - cursor : 'pointer', - dataLabels: { - enabled : false, - distance : -1 - } - } - }, - - series: [] - } - - // callback - return hc_config; -}; - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js +++ /dev/null @@ -1,179 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/highcharts/common/highcharts-config'], function(Utils, configmaker) { - -// widget -return Backbone.View.extend( -{ - // highcharts series - hc_series: { - name : '', - data : [], - tooltip: { - headerFormat : '<em>{point.key}</em><br/>' - } - }, - - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, hc_type, chart, request_dictionary, callback) - { - // request data - var self = this; - this.app.datasets.request(request_dictionary, function() { - // check if this chart has multiple panels - if (!chart.definition.use_panels) { - // draw all groups into a single panel - if (self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0], callback)) { - chart.state('ok', 'Chart drawn.'); - } - } else { - // draw groups in separate panels - var valid = true; - for (var group_index in request_dictionary.groups) { - var group = request_dictionary.groups[group_index]; - if (!self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index], callback)) { - valid = false; - break; - } - } - if (valid) { - chart.state('ok', 'Multi-panel chart drawn.'); - } - } - - // unregister process - chart.deferred.done(process_id); - }); - }, - - // draw all data into a single canvas - _drawGroups: function(hc_type, chart, groups, canvas, callback) { - // create configuration - var hc_config = configmaker(chart); - - // fix title - if (!chart.definition.use_panels) { - hc_config.title.text = chart.get('title'); - } - - // identify categories - this._makeCategories(chart, groups, hc_config); - - // loop through data groups - for (var key in groups) { - // get group - var group = groups[key]; - - // reset data - var data = []; - - // format chart data - for (var value_index in group.values) { - // parse data - var point = []; - for (var column_index in group.values[value_index]) { - point.push(group.values[value_index][column_index]); - } - - // add to data - data.push (point); - } - - // highcharts series - var hc_series = { - name : group.key, - type : hc_type, - data : data - }; - - // append series - hc_config.series.push(hc_series); - } - - // make custom wrapper callback - if (callback) { - callback(hc_config); - } - - // draw plot - try { - canvas.highcharts(hc_config); - return true; - } catch (err) { - this._handleError(chart, err); - return false; - } - }, - - // create categories - _makeCategories: function(chart, groups, hc_config) { - // hashkeys, arrays and counter for labeled columns - var categories = {}; - var array = {}; - var counter = {}; - - // identify label columns - var chart_definition = groups[0]; - for (var key in chart_definition.columns) { - var column_def = chart_definition.columns[key]; - if (column_def.is_label) { - categories[key] = {}; - array[key] = []; - counter[key] = 0; - } - } - - // index all values contained in label columns (for all groups) - for (var i in groups) { - var group = groups[i]; - for (var j in group.values) { - var value_dict = group.values[j]; - for (var key in categories) { - var value = String(value_dict[key]); - if (categories[key][value] === undefined) { - categories[key][value] = counter[key]++; - array[key].push(value); - } - } - } - } - - // convert group values into category indeces - for (var i in groups) { - var group = groups[i]; - for (var j in group.values) { - var value_dict = group.values[j]; - for (var key in categories) { - var value = String(value_dict[key]); - value_dict[key] = categories[key][value] - } - } - } - console.log(array); - // add categories to highcharts configuration - for (var key in array) { - var axis = key + 'Axis'; - if (hc_config[axis]) { - hc_config[axis].categories = array[key]; - } - } - }, - - // handle error - _handleError: function(chart, err) { - var regex = /\www\.highcharts\.com([^&]+)/; - var match = err.match(regex); - if (match.length > 0) { - chart.state('failed', 'Highcharts error: <a target="_blank" href="http://' + match[0] + '">' + match[0] + '</a>'); - } else { - chart.state('failed', err); - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js +++ /dev/null @@ -1,31 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Heatmap', - category : 'Others', - use_panels : true, - keywords : 'highcharts', - columns: { - x: { - title : 'Column labels', - is_label : true, - is_numeric : true - }, - y: { - title : 'Row labels', - is_label : true, - is_numeric : true - }, - z: { - title : 'Observations', - is_numeric : true - } - }, - settings: { - y_axis_grid : { - init : '0' - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/heatmap/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/heatmap/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js +++ /dev/null @@ -1,25 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(HighchartsWrapper) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var hc = new HighchartsWrapper(this.app, this.options); - hc.draw(process_id, 'heatmap', chart, request_dictionary, function(model) { - model.colorAxis = { - minColor : '#00FF99', - maxColor : '#000066' - } - }); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/histogram/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/histogram/config.js +++ /dev/null @@ -1,30 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Histogram', - category : 'Data processing (requires \'charts\' tool from Toolshed)', - execute : 'histogram', - keywords : 'highcharts', - columns : { - y : { - title : 'Observations', - is_numeric : true - } - }, - settings : { - x_axis_label : { - init : 'Values' - }, - y_axis_label : { - init : 'Density' - }, - y_axis_type : { - init : 'f' - }, - y_axis_tick : { - init : '.2' - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/histogram/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/histogram/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/histogram/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/histogram/wrapper.js +++ /dev/null @@ -1,34 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - // configure request - var index = 1; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = { - x: { - index: 0 - }, - y: { - index: index++ - } - } - } - - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'column', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/histogram_discrete/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/histogram_discrete/config.js +++ /dev/null @@ -1,24 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Discrete Histogram', - category : 'Data processing (requires \'charts\' tool from Toolshed)', - execute : 'histogramdiscrete', - keywords : 'highcharts', - columns : { - y : { - title : 'Observations', - is_label : true - } - }, - settings : { - x_axis_label : { - init : 'Labels' - }, - y_axis_label : { - init : 'Density' - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/histogram_discrete/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/histogram_discrete/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/histogram_discrete/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/histogram_discrete/wrapper.js +++ /dev/null @@ -1,46 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - // configure request - var tmp_dict = { - id : request_dictionary.id, - groups : [] - }; - - // configure groups - var index = 0; - for (var group_index in request_dictionary.groups) { - var group = request_dictionary.groups[group_index]; - tmp_dict.groups.push({ - key : group.key, - columns : { - x: { - index : 0, - is_label : true - }, - y: { - index : ++index, - is_numeric : true - } - } - }); - } - - // draw chart - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'column', chart, tmp_dict); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/line/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/line/config.js +++ /dev/null @@ -1,21 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Line', - category : 'Others', - keywords : 'highcharts', - columns : { - x : { - title : 'Values for x-axis', - is_label : true, - is_auto : true, - is_numeric : false - }, - y : { - title : 'Values for y-axis', - is_numeric : true - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/line/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/line/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/line/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/line/wrapper.js +++ /dev/null @@ -1,20 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'line', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/pie/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/pie/config.js +++ /dev/null @@ -1,116 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Pie chart', - category : 'Area charts', - keywords : 'highcharts', - use_panels : true, - columns : { - label : { - title : 'Labels', - is_label : true, - is_auto : true - }, - y : { - title : 'Values', - is_numeric : true - } - }, - - 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' - } - ] - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/pie/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/pie/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/pie/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/pie/wrapper.js +++ /dev/null @@ -1,20 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'pie', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/scatter/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/scatter/config.js +++ /dev/null @@ -1,19 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Scatter plot', - category : 'Others', - keywords : 'highcharts', - columns : { - x : { - title : 'Values for x-axis', - is_numeric : true - }, - y : { - title : 'Values for y-axis', - is_numeric : true - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/scatter/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/scatter/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/scatter/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/scatter/wrapper.js +++ /dev/null @@ -1,20 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'scatter', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/stackedarea/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/stackedarea/config.js +++ /dev/null @@ -1,21 +0,0 @@ -define(['plugin/charts/highcharts/common/config'], function(config) { - -return $.extend(true, {}, config, { - title : 'Regular', - category : 'Area charts', - keywords : 'highcharts', - columns : { - x : { - title : 'Values for x-axis', - is_label : true, - is_auto : true, - is_numeric : false - }, - y : { - title : 'Values for y-axis', - is_numeric : true - } - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/stackedarea/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts/stackedarea/logo.png has changed diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/highcharts/stackedarea/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/stackedarea/wrapper.js +++ /dev/null @@ -1,20 +0,0 @@ -// dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'area', chart, request_dictionary); - } -}); - -}); \ No newline at end of file diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); + nvd3.draw('multiBarChart', process_id, chart, request_dictionary); } }); diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary); + nvd3.draw('multiBarHorizontalChart', process_id, chart, request_dictionary); } }); diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarHorizontalChart(), chart, request_dictionary, function(nvd3_model) { + nvd3.draw('multiBarHorizontalChart', process_id, chart, request_dictionary, function(nvd3_model) { nvd3_model.stacked(true); }); } diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b 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 @@ -4,6 +4,11 @@ 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 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary, function(nvd3_model) { + nvd3.draw('multiBarChart', process_id, chart, request_dictionary, function(nvd3_model) { nvd3_model.stacked(true); }); } diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b 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 @@ -210,6 +210,22 @@ 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' + } + ] } } }; diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b 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([], function() { +define(['plugin/charts/tools', 'plugin/plugins/nvd3/nv.d3'], function(Tools) { // widget return Backbone.View.extend( @@ -9,58 +9,75 @@ this.app = app; this.options = options; }, - + // render - draw : function(process_id, nvd3_model, chart, request_dictionary, callback) + draw : function(type, process_id, chart, request_dictionary, callback) { + var self = this; + var plot = Tools.panelHelper({ + app : this.app, + process_id : process_id, + canvas : this.options.canvas, + chart : chart, + request_dictionary : request_dictionary, + render : function(chart, groups, canvas) { + return self.render(type, chart, groups, canvas, callback) + } + }); + }, + + // render + render : function(type, chart, groups, canvas, callback) { + // create nvd3 model + var d3chart = nv.models[type](); + // request data var self = this; - this.app.datasets.request(request_dictionary, function() { - nv.addGraph(function() { + nv.addGraph(function() { + try { // x axis - self._axis(nvd3_model.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick')); + self._axis(d3chart.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick')); // x axis label - nvd3_model.xAxis.axisLabel(chart.settings.get('x_axis_label')); + d3chart.xAxis.axisLabel(chart.settings.get('x_axis_label')); // y axis - self._axis(nvd3_model.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick')); + self._axis(d3chart.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick')); // y axis label - nvd3_model.yAxis.axisLabel(chart.settings.get('y_axis_label')) + d3chart.yAxis.axisLabel(chart.settings.get('y_axis_label')) .axisLabelDistance(30); // controls - nvd3_model.options({showControls: false}); + d3chart.options({showControls: false}); // legend - if (nvd3_model.showLegend) { + if (d3chart.showLegend) { var legend_visible = true; if (chart.settings.get('show_legend') == 'false') { legend_visible = false; } - nvd3_model.showLegend(legend_visible); + d3chart.showLegend(legend_visible); } // custom callback if (callback) { - callback(nvd3_model); + callback(d3chart); } // parse data to canvas - self.options.canvas[0].datum(request_dictionary.groups) - .call(nvd3_model); + canvas.datum(groups) + .call(d3chart); + // refresh on window resize - nv.utils.windowResize(nvd3_model.update); - - // set chart state - chart.state('ok', 'Chart has been drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); + nv.utils.windowResize(d3chart.update); + } catch (err) { + self._handleError(chart, err); + } }); + + return true; }, // make axis @@ -74,6 +91,11 @@ default: axis.tickFormat(d3.format(tick + type)); } + }, + + // handle error + _handleError: function(chart, err) { + chart.state('failed', err); } }); diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js @@ -32,7 +32,7 @@ // load nvd3 var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary, function(nvd3_model) { + nvd3.draw('multiBarChart', process_id, chart, request_dictionary, function(nvd3_model) { nvd3_model.options({showControls: true}); }); } diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js @@ -39,7 +39,7 @@ // draw var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarChart(), chart, tmp_dict, function(nvd3_model) { + nvd3.draw('multiBarChart', process_id, chart, tmp_dict, function(nvd3_model) { nvd3_model.options({showControls: false}); }); } diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b 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 @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.lineChart(), chart, request_dictionary); + nvd3.draw('lineChart', process_id, chart, request_dictionary); } }); diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.lineWithFocusChart(), chart, request_dictionary); + nvd3.draw('lineWithFocusChart', process_id, chart, request_dictionary); } }); diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.scatterChart(), chart, request_dictionary, function(nvd3_model) { + nvd3.draw('scatterChart', process_id, chart, request_dictionary, function(nvd3_model) { nvd3_model.showDistX(true) .showDistY(true) .color(d3.scale.category10().range()); diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) { + nvd3.draw('stackedAreaChart', process_id, chart, request_dictionary, function(nvd3_model) { // make plot nvd3_model.x(function(d) { return d.x }) .y(function(d) { return d.y }) diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) { + nvd3.draw('stackedAreaChart', process_id, chart, request_dictionary, function(nvd3_model) { // make plot nvd3_model.x(function(d) { return d.x }) .y(function(d) { return d.y }) diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js @@ -14,7 +14,7 @@ draw : function(process_id, chart, request_dictionary) { var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.stackedAreaChart(), chart, request_dictionary, function(nvd3_model) { + nvd3.draw('stackedAreaChart', process_id, chart, request_dictionary, function(nvd3_model) { // make plot nvd3_model.x(function(d) { return d.x }) .y(function(d) { return d.y }) diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r a932242dc2da4fd532c640006aa2ae4d35a7d72b config/plugins/visualizations/charts/static/charts/tools.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/tools.js @@ -0,0 +1,137 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// render +function panelHelper (options) +{ + // require parameters + var process_id = options.process_id; + var chart = options.chart; + var request_dictionary = options.request_dictionary; + var render = options.render; + var canvas = options.canvas; + var app = options.app; + + // request data + var self = this; + app.datasets.request(request_dictionary, function() { + try { + // check if this chart has multiple panels + if (!chart.definition.use_panels && chart.settings.get('use_panels') !== 'true') { + // draw all groups into a single panel + if (render(chart, request_dictionary.groups, canvas[0])) { + chart.state('ok', 'Chart drawn.'); + } + } else { + // draw groups in separate panels + var valid = true; + for (var group_index in request_dictionary.groups) { + var group = request_dictionary.groups[group_index]; + if (!render(chart, [group], canvas[group_index])) { + valid = false; + break; + } + } + if (valid) { + chart.state('ok', 'Multi-panel chart drawn.'); + } + } + + // unregister process + chart.deferred.done(process_id); + } catch (err) { + // log + console.debug('FAILED: Tools::draw() - ' + err); + + // set chart state + chart.state('failed', err); + + // unregister process + chart.deferred.done(process_id); + } + }); +}; + +// series maker +function makeSeries(group) { + // reset data + var data = []; + + // format chart data + for (var value_index in group.values) { + // parse data + var point = []; + for (var column_index in group.values[value_index]) { + point.push(group.values[value_index][column_index]); + } + + // add to data + data.push (point); + } + + // return + return data; +}; + +// category maker +function makeCategories(chart, groups) { + // hashkeys, arrays and counter for labeled columns + var categories = {}; + var array = {}; + var counter = {}; + + // identify label columns + var chart_definition = groups[0]; + for (var key in chart_definition.columns) { + var column_def = chart_definition.columns[key]; + if (column_def.is_label) { + categories[key] = {}; + array[key] = []; + counter[key] = 0; + } + } + + // index all values contained in label columns (for all groups) + for (var i in groups) { + var group = groups[i]; + for (var j in group.values) { + var value_dict = group.values[j]; + for (var key in categories) { + var value = String(value_dict[key]); + if (categories[key][value] === undefined) { + categories[key][value] = counter[key]; + array[key].push([counter[key], value]); + counter[key]++; + } + } + } + } + + // convert group values into category indeces + for (var i in groups) { + var group = groups[i]; + for (var j in group.values) { + var value_dict = group.values[j]; + for (var key in categories) { + var value = String(value_dict[key]); + value_dict[key] = categories[key][value] + } + } + } + + // return dictionary + return { + categories : categories, + array : array, + counter : counter + } +}; + +// return +return { + panelHelper : panelHelper, + makeCategories : makeCategories, + makeSeries : makeSeries +} + +}); \ No newline at end of file This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Clarify language in DeleteIntermediateDataset PJA.
by commits-noreply＠bitbucket.org 06 Jun '14

06 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/84a00e4f7d06/ Changeset: 84a00e4f7d06 User: dannon Date: 2014-06-06 23:12:30 Summary: Clarify language in DeleteIntermediateDataset PJA. Affected #: 1 file diff -r 6a90c63fe697c60350129d6c245d7516fc649bc4 -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -404,7 +404,7 @@ p_str += "<label for='pja__"+pja.output_name+"__DeleteIntermediatesAction'>There are no additional options for this action.</label>\ <input type='hidden' name='pja__"+pja.output_name+"__DeleteIntermediatesAction'/>"; """ - return get_form_template(cls.name, cls.verbose_name, form, "All steps in this workflow will have non-output datasets deleted if they are no longer being used as job inputs at the time of this job finishing.", on_output=False) + return get_form_template(cls.name, cls.verbose_name, form, "All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this PostJobAction is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect.", on_output=False) @classmethod def get_short_str(cls, pja): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Cleanup, pep8 for postjobactions.
by commits-noreply＠bitbucket.org 06 Jun '14

06 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6a90c63fe697/ Changeset: 6a90c63fe697 User: dannon Date: 2014-06-06 22:44:47 Summary: Cleanup, pep8 for postjobactions. Affected #: 1 file diff -r f23dd6b6b6a54c09b0a6f6b890170869ded5723b -r 6a90c63fe697c60350129d6c245d7516fc649bc4 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -9,7 +9,8 @@ log = logging.getLogger( __name__ ) -def get_form_template(action_type, title, content, help, on_output = True ): + +def get_form_template(action_type, title, content, help, on_output=True ): if on_output: form = """ if (pja.action_type == "%s"){ @@ -19,7 +20,7 @@ p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) else: - form = """ + form = """ if (pja.action_type == "%s"){ p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; @@ -37,7 +38,7 @@ verbose_name = "Default Job" @classmethod - def execute(cls, app, sa_session, action, job, replacement_dict = None): + def execute(cls, app, sa_session, action, job, replacement_dict=None): pass @classmethod @@ -61,12 +62,12 @@ @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): - if action.action_arguments and action.action_arguments.has_key('host'): + if action.action_arguments and 'host' in action.action_arguments: host = action.action_arguments['host'] else: host = 'usegalaxy.org' frm = 'galaxy-noreply@%s' % host - to = job.user.email + to = job.user.email subject = "Galaxy workflow step notification '%s'" % (job.history.name) outdata = ', '.join(ds.dataset.display_name() for ds in job.output_datasets) body = "Your Galaxy job generating dataset '%s' is complete as of %s." % (outdata, datetime.datetime.now().strftime( "%I:%M" )) @@ -81,11 +82,11 @@ p_str += "<label for='pja__"+pja.output_name+"__EmailAction'>There are no additional options for this action. You will be emailed upon job completion.</label>\ <input type='hidden' value='%s' name='pja__"+pja.output_name+"__EmailAction__host'/><input type='hidden' name='pja__"+pja.output_name+"__EmailAction'/>"; """ % trans.request.host - return get_form_template(cls.name, cls.verbose_name, form, "This action will send an email notifying you when the job is done.", on_output = False) + return get_form_template(cls.name, cls.verbose_name, form, "This action will send an email notifying you when the job is done.", on_output=False) @classmethod def get_short_str(cls, pja): - if pja.action_arguments and pja.action_arguments.has_key('host'): + if pja.action_arguments and 'host' in pja.action_arguments: return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] else: return "Email the current user when this job is complete." @@ -94,6 +95,7 @@ class ChangeDatatypeAction(DefaultJobAction): name = "ChangeDatatypeAction" verbose_name = "Change Datatype" + @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: @@ -116,7 +118,7 @@ p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>"; } """ % dt_list - # Note the scrip + t hack above. Is there a better way? + # Note the scrip + t hack above. Is there a better way? return get_form_template(cls.name, cls.verbose_name, ps, 'This action will change the datatype of the output to the indicated value.') @classmethod @@ -131,7 +133,7 @@ @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): # Prevent renaming a dataset to the empty string. - if action.action_arguments and action.action_arguments.has_key('newname') and action.action_arguments['newname'] != '': + if action.action_arguments and action.action_arguments.get('newname', ''): new_name = action.action_arguments['newname'] # TODO: Unify and simplify replacement options. @@ -165,10 +167,9 @@ tokens = to_be_replaced.split("|") operations = [] if len(tokens) > 1: - input_file_var = tokens[0].strip() - for i in range(1, len(tokens)): - operations.append(tokens[i].strip()) - + input_file_var = tokens[0].strip() + for i in range(1, len(tokens)): + operations.append(tokens[i].strip()) replacement = "" # Lookp through inputs find one with "to_be_replaced" input # variable name, and get the replacement name @@ -220,7 +221,7 @@ @classmethod def get_short_str(cls, pja): # Prevent renaming a dataset to the empty string. - if pja.action_arguments and pja.action_arguments.has_key('newname') and pja.action_arguments['newname'] != '': + if pja.action_arguments and pja.action_arguments.get('newname', ''): return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) else: return "Rename action used without a new name specified. Output name will be unchanged." @@ -234,19 +235,21 @@ def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: if dataset_assoc.dataset.state != dataset_assoc.dataset.states.ERROR and ( action.output_name == '' or dataset_assoc.name == action.output_name ): - dataset_assoc.dataset.visible=False + dataset_assoc.dataset.visible = False @classmethod def get_config_form(cls, trans): - return """ - if (pja.action_type == "HideDatasetAction"){ - p_str += "<input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>"; - } - """ + return """ + if (pja.action_type == "HideDatasetAction"){ + p_str += "<input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>"; + } + """ + @classmethod def get_short_str(cls, pja): return "Hide output '%s'." % pja.output_name + class DeleteDatasetAction(DefaultJobAction): # This is disabled for right now. Deleting a dataset in the middle of a workflow causes errors (obviously) for the subsequent steps using the data. name = "DeleteDatasetAction" @@ -256,7 +259,7 @@ def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: if action.output_name == '' or dataset_assoc.name == action.output_name: - dataset_assoc.dataset.deleted=True + dataset_assoc.dataset.deleted = True @classmethod def get_config_form(cls, trans): @@ -271,10 +274,10 @@ return "Delete this dataset after creation." - class ColumnSetAction(DefaultJobAction): name = "ColumnSetAction" verbose_name = "Assign Columns" + @classmethod def execute(cls, app, sa_session, action, job, replacement_dict): for dataset_assoc in job.output_datasets: @@ -401,22 +404,21 @@ p_str += "<label for='pja__"+pja.output_name+"__DeleteIntermediatesAction'>There are no additional options for this action.</label>\ <input type='hidden' name='pja__"+pja.output_name+"__DeleteIntermediatesAction'/>"; """ - return get_form_template(cls.name, cls.verbose_name, form, "All steps in this workflow will have non-output datasets deleted if they are no longer being used as job inputs at the time of this job finishing.This action will delete non-output datasets of parent steps in this workflow.", on_output = False) + return get_form_template(cls.name, cls.verbose_name, form, "All steps in this workflow will have non-output datasets deleted if they are no longer being used as job inputs at the time of this job finishing.", on_output=False) @classmethod def get_short_str(cls, pja): return "Delete parent datasets of this step created in this workflow that aren't flagged as outputs." - class ActionBox(object): - actions = { "RenameDatasetAction" : RenameDatasetAction, - "HideDatasetAction" : HideDatasetAction, + actions = { "RenameDatasetAction": RenameDatasetAction, + "HideDatasetAction": HideDatasetAction, "ChangeDatatypeAction": ChangeDatatypeAction, - "ColumnSetAction" : ColumnSetAction, - "EmailAction" : EmailAction, - "DeleteIntermediatesAction" : DeleteIntermediatesAction, + "ColumnSetAction": ColumnSetAction, + "EmailAction": EmailAction, + "DeleteIntermediatesAction": DeleteIntermediatesAction, } public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction', 'ColumnSetAction', 'EmailAction', @@ -438,10 +440,10 @@ sp = key.split('__') ao_key = sp[2] + sp[1] # flag / output_name / pjatype / desc - if not ao_key in npd: - npd[ao_key] = {'action_type' : sp[2], - 'output_name' : sp[1], - 'action_arguments' : {}} + if ao_key not in npd: + npd[ao_key] = {'action_type': sp[2], + 'output_name': sp[1], + 'action_arguments': {}} if len(sp) > 3: if sp[3] == 'output_name': npd[ao_key]['output_name'] = val @@ -468,6 +470,6 @@ return forms @classmethod - def execute(cls, app, sa_session, pja, job, replacement_dict = None): - if ActionBox.actions.has_key(pja.action_type): + def execute(cls, app, sa_session, pja, job, replacement_dict=None): + if pja.action_type in ActionBox.actions: ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Initial version of delete intermediate output steps action for workflows.
by commits-noreply＠bitbucket.org 06 Jun '14

06 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f23dd6b6b6a5/ Changeset: f23dd6b6b6a5 User: dannon Date: 2014-06-06 22:32:44 Summary: Initial version of delete intermediate output steps action for workflows. Affected #: 1 file diff -r 20d6c7849901c2669562ee6c0ccbb5089372ec03 -r f23dd6b6b6a54c09b0a6f6b890170869ded5723b lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -1,3 +1,7 @@ +""" +Actions to be run at job completion. Currently only used in workflows. +""" + import datetime import logging from galaxy.util import send_mail @@ -5,8 +9,6 @@ log = logging.getLogger( __name__ ) -# DBTODO This still needs refactoring and general cleanup. - def get_form_template(action_type, title, content, help, on_output = True ): if on_output: form = """ @@ -26,14 +28,11 @@ }""" % (action_type, title, content, help) return form -# def get_field(action, argument, i_type, label = None): -# fstr = '' -# fname = """pja__"+pja.output_name+"__%s__%s""" % (action, argument) -# if label: -# fstr += """<label for='pja__"+pja.output_name+"__ColumnSetAction__chromCol'>Chrom Column</label>""" -# fstr += """<input type='text' value=" + chromCol + " name='pja__"+pja.output_name+"__ColumnSetAction__chromCol'/>""" class DefaultJobAction(object): + """ + Base job action. + """ name = "DefaultJobAction" verbose_name = "Default Job" @@ -54,6 +53,9 @@ class EmailAction(DefaultJobAction): + """ + This action sends an email to the galaxy user responsible for a job. + """ name = "EmailAction" verbose_name = "Email Notification" @@ -358,6 +360,54 @@ return get_form_template(cls.name, cls.verbose_name, form, "This action will set metadata in the output dataset.") +class DeleteIntermediatesAction(DefaultJobAction): + name = "DeleteIntermediatesAction" + verbose_name = "Delete Non-Output Completed Intermediate Steps" + + @classmethod + def execute(cls, app, sa_session, action, job, replacement_dict): + # TODO Optimize this later. Just making it work for now. + # TODO Support purging as well as deletion if user_purge is enabled. + # Dataset candidates for deletion must be + # 1) Created by the workflow. + # 2) Not have any job_to_input_dataset associations with states other + # than OK or DELETED. If a step errors, we don't want to delete/purge it + # automatically. + # 3) Not marked as a workflow output. + # POTENTIAL ISSUES: When many outputs are being finish()ed + # concurrently, sometimes non-terminal steps won't be cleaned up + # because of the lag in job state updates. + wfi = job.workflow_invocation_step.workflow_invocation + if wfi.workflow.has_outputs_defined(): + jobs_to_check = [wfistep.job for wfistep in wfi.steps if not wfistep.workflow_step.workflow_outputs] + for j2c in jobs_to_check: + for input_dataset in [x.dataset for x in j2c.input_datasets if x.dataset.creating_job.workflow_invocation_step and x.dataset.creating_job.workflow_invocation_step.workflow_invocation == wfi]: + safe_to_delete = True + for job_to_check in [d_j.job for d_j in input_dataset.dependent_jobs]: + if job_to_check != job and job_to_check.state not in [job.states.OK, job.states.DELETED]: + log.debug("Workflow Intermediates cleanup attempted, but non-terminal state '%s' detected for job %s" % (job_to_check.state, job_to_check.id)) + safe_to_delete = False + if safe_to_delete: + # Support purging here too. + input_dataset.mark_deleted() + else: + # No workflow outputs defined, so we can't know what to delete. + # We could make this work differently in the future + pass + + @classmethod + def get_config_form(cls, trans): + form = """ + p_str += "<label for='pja__"+pja.output_name+"__DeleteIntermediatesAction'>There are no additional options for this action.</label>\ + <input type='hidden' name='pja__"+pja.output_name+"__DeleteIntermediatesAction'/>"; + """ + return get_form_template(cls.name, cls.verbose_name, form, "All steps in this workflow will have non-output datasets deleted if they are no longer being used as job inputs at the time of this job finishing.This action will delete non-output datasets of parent steps in this workflow.", on_output = False) + + @classmethod + def get_short_str(cls, pja): + return "Delete parent datasets of this step created in this workflow that aren't flagged as outputs." + + class ActionBox(object): @@ -366,10 +416,11 @@ "ChangeDatatypeAction": ChangeDatatypeAction, "ColumnSetAction" : ColumnSetAction, "EmailAction" : EmailAction, - # "SetMetadataAction" : SetMetadataAction, - # "DeleteDatasetAction" : DeleteDatasetAction, + "DeleteIntermediatesAction" : DeleteIntermediatesAction, } - public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction', 'ColumnSetAction', 'EmailAction'] + public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction', + 'ColumnSetAction', 'EmailAction', + 'DeleteIntermediatesAction'] immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction'] @classmethod Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Add Workflow.has_outputs_defined to the Workflow model.
by commits-noreply＠bitbucket.org 06 Jun '14

06 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20d6c7849901/ Changeset: 20d6c7849901 User: dannon Date: 2014-06-06 21:36:07 Summary: Add Workflow.has_outputs_defined to the Workflow model. Affected #: 2 files diff -r c113771db6b2f50800f045e7b74a8d650c0474e8 -r 20d6c7849901c2669562ee6c0ccbb5089372ec03 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2978,6 +2978,16 @@ self.has_errors = None self.steps = [] + def has_outputs_defined(self): + """ + Returns true or false indicating whether or not a workflow has outputs defined. + """ + for step in self.steps: + if step.workflow_outputs: + return True + return False + + class WorkflowStep( object ): diff -r c113771db6b2f50800f045e7b74a8d650c0474e8 -r 20d6c7849901c2669562ee6c0ccbb5089372ec03 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1915,10 +1915,7 @@ order_by=asc(model.WorkflowStep.table.c.order_index), cascade="all, delete-orphan", lazy=False ), - # outputs = relation( WorkflowOutput, backref='workflow', - # primaryjoin=(Workflow.table.c.id == WorkflowStep.table.c.workflow_id), - # secondaryjoin=(WorkflowStep.table.c.id == WorkflowOutput.table.c.workflow_step_id)) - ) ) + ) ) mapper( model.WorkflowStep, model.WorkflowStep.table, properties=dict( @@ -2140,9 +2137,9 @@ def db_next_hid( self ): """ db_next_hid( self ) - + Override __next_hid to generate from the database in a concurrency safe way. - Loads the next history ID from the DB and returns it. + Loads the next history ID from the DB and returns it. It also saves the future next_id into the DB. :rtype: int Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Reduce number of available chart types
by commits-noreply＠bitbucket.org 06 Jun '14

06 Jun '14

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1 0

commit/galaxy-central: dannon: Update amqp_internal_connection sqlite default in universe_sample to be correct.
by commits-noreply＠bitbucket.org 06 Jun '14

06 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bfc11a137427/ Changeset: bfc11a137427 User: dannon Date: 2014-06-06 18:08:16 Summary: Update amqp_internal_connection sqlite default in universe_sample to be correct. Affected #: 1 file diff -r b45044f8372a282065af34175c465f3f9c1c671e -r bfc11a137427bb1b0471f97c53d8c4d2ea0540a3 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -845,7 +845,7 @@ # will automatically create and use a separate sqlite database located in your # <galaxy>/database folder (indicated in the commented out line below). -#amqp_internal_connection = sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE +#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for getting updates to an installed repository that has a dependency on a Tool dependency definition repository that also has available updates.
by commits-noreply＠bitbucket.org 06 Jun '14

06 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b45044f8372a/ Changeset: b45044f8372a User: greg Date: 2014-06-06 15:45:37 Summary: Fix for getting updates to an installed repository that has a dependency on a Tool dependency definition repository that also has available updates. Affected #: 6 files diff -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 -r b45044f8372a282065af34175c465f3f9c1c671e lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -517,7 +517,7 @@ tmp_clone_url = common_util.url_join( tool_shed_url, 'repos', owner, name ) tmp_repo_info_tuple = ( None, tmp_clone_url, latest_downloadable_revision, None, owner, None, None ) installed_repository, installed_changeset_revision = \ - suc.repository_was_previously_installed( trans, tool_shed_url, name, tmp_repo_info_tuple ) + suc.repository_was_previously_installed( trans, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False ) if installed_repository: current_changeset_revision = str( installed_repository.changeset_revision ) message = 'Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b> has already been installed.' % \ @@ -1854,6 +1854,10 @@ name, owner, changeset_revision ) + original_metadata_dict = repository.metadata + original_repository_dependencies_dict = original_metadata_dict.get( 'repository_dependencies', {} ) + original_repository_dependencies = original_repository_dependencies_dict.get( 'repository_dependencies', [] ) + original_tool_dependencies_dict = original_metadata_dict.get( 'tool_dependencies', {} ) if changeset_revision and latest_changeset_revision and latest_ctx_rev: if changeset_revision == latest_changeset_revision: message = "The installed repository named '%s' is current, there are no updates available. " % name @@ -1910,32 +1914,80 @@ repository, repository_tools_tups ) if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: - if 'repository_dependencies' in metadata_dict: - # Updates received include newly defined repository dependencies, so allow the user - # the option of installting them. We cannot update the repository with the changes - # until that happens, so we have to send them along. - new_kwd = dict( tool_shed_url=tool_shed_url, - updating_repository_id=trans.security.encode_id( repository.id ), + new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) + new_tool_dependencies_dict = metadata_dict.get( 'tool_dependencies', {} ) + if new_repository_dependencies: + # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] + proceed_to_install = False + if new_repository_dependencies == original_repository_dependencies: + for new_repository_tup in new_repository_dependencies: + # Make sure all dependencies are installed. + # TODO: Repository dependencies that are not installed should be displayed to to the user, + # giving them the option to install them or now. This is the same behavior as when initially + # installing and when re-installing. + new_tool_shed, new_name, new_owner, new_changeset_revision, new_pir, new_oicct = \ + common_util.parse_repository_dependency_tuple( new_repository_tup ) + # Mock up a repo_info_tupe that has the information needed to see if the repository dependency + # was previously installed. + repo_info_tuple = ( '', new_tool_shed, new_changeset_revision, '', new_owner, [], [] ) + # Since the value of new_changeset_revision came from a repository dependency + # definition, it may occur earlier in the Tool Shed's repository changelog than + # the Galaxy tool_shed_repository.installed_changeset_revision record value, so + # we set from_tip to True to make sure we get the entire set of changeset revisions + # from the Tool Shed. + new_repository_db_record, installed_changeset_revision = \ + suc.repository_was_previously_installed( trans, + tool_shed_url, + new_name, + repo_info_tuple, + from_tip=True ) + if new_repository_db_record: + if new_repository_db_record.status in [ trans.install_model.ToolShedRepository.installation_status.ERROR, + trans.install_model.ToolShedRepository.installation_status.NEW, + trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: + proceed_to_install = True + break + else: + proceed_to_install = True + break + if proceed_to_install: + # Updates received include newly defined repository dependencies, so allow the user + # the option of installting them. We cannot update the repository with the changes + # until that happens, so we have to send them along. + new_kwd = dict( tool_shed_url=tool_shed_url, + updating_repository_id=trans.security.encode_id( repository.id ), + updating_to_ctx_rev=latest_ctx_rev, + updating_to_changeset_revision=latest_changeset_revision, + encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + updating=True ) + return self.prepare_for_install( trans, **new_kwd ) + # Updates received did not include any newly defined repository dependencies but did include + # newly defined tool dependencies. If the newly defined tool dependencies are not the same + # as the originally defined tool dependencies, we need to install them. + proceed_to_install = False + for new_key, new_val in new_tool_dependencies_dict.items(): + if new_key not in original_tool_dependencies_dict: + proceed_to_install = True + break + original_val = original_tool_dependencies_dict[ new_key ] + if new_val != original_val: + proceed_to_install = True + break + if proceed_to_install: + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) + new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), - updating=True ) - return self.prepare_for_install( trans, **new_kwd ) - # Updates received did not include any newly defined repository dependencies but did include - # newly defined tool dependencies. - encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) - encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) - new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), - updating_to_ctx_rev=latest_ctx_rev, - updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), - encoded_relative_install_dir=encoded_relative_install_dir, - encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, - message=message, - status = status ) - return self.install_tool_dependencies_with_update( trans, **new_kwd ) + encoded_relative_install_dir=encoded_relative_install_dir, + encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, + message=message, + status = status ) + return self.install_tool_dependencies_with_update( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies or newly defined - # tool dependencies. + # tool dependencies that need to be installed. repository = repository_util.update_repository_record( trans, repository=repository, updated_metadata_dict=metadata_dict, diff -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 -r b45044f8372a282065af34175c465f3f9c1c671e lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2594,31 +2594,44 @@ status=status ) @web.expose - def previous_changeset_revisions( self, trans, **kwd ): + def previous_changeset_revisions( self, trans, from_tip=False, **kwd ): """ - Handle a request from a local Galaxy instance. This method will handle the case where the repository was previously installed using an - older changeset_revsion, but later the repository was updated in the tool shed and the Galaxy admin is trying to install the latest - changeset revision of the same repository instead of updating the one that was previously installed. + Handle a request from a local Galaxy instance. This method will handle two scenarios: (1) the + repository was previously installed using an older changeset_revsion, but later the repository + was updated in the tool shed and the Galaxy admin is trying to install the latest changeset + revision of the same repository instead of updating the one that was previously installed. (2) + the admin is attempting to get updates for an installed repository that has a repository dependency + and both the repository and its dependency have available updates. In this case, the from_tip + parameter will be True because the repository dependency definition may define a changeset hash + for the dependency that is newer than the installed changeset revision of the dependency (this is + due to the behavior of "Tool dependency definition" repositories, whose metadata is always the tip), + so the complete list of changset hashes in the changelog must be returned. """ name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) - changeset_revision = kwd.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) - # Get the lower bound changeset revision. - lower_bound_changeset_revision = metadata_util.get_previous_metadata_changeset_revision( repository, - repo, - changeset_revision, - downloadable=True ) - # Build the list of changeset revision hashes. - changeset_hashes = [] - for changeset in hg_util.reversed_lower_upper_bounded_changelog( repo, - lower_bound_changeset_revision, - changeset_revision ): - changeset_hashes.append( str( repo.changectx( changeset ) ) ) - if changeset_hashes: - changeset_hashes_str = ','.join( changeset_hashes ) - return changeset_hashes_str + if name is not None and owner is not None: + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + from_tip = util.string_as_bool( from_tip ) + if from_tip: + changeset_revision = repository.tip( trans.app ) + else: + changeset_revision = kwd.get( 'changeset_revision', None ) + if changeset_revision is not None: + repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False ) + # Get the lower bound changeset revision. + lower_bound_changeset_revision = metadata_util.get_previous_metadata_changeset_revision( repository, + repo, + changeset_revision, + downloadable=True ) + # Build the list of changeset revision hashes. + changeset_hashes = [] + for changeset in hg_util.reversed_lower_upper_bounded_changelog( repo, + lower_bound_changeset_revision, + changeset_revision ): + changeset_hashes.append( str( repo.changectx( changeset ) ) ) + if changeset_hashes: + changeset_hashes_str = ','.join( changeset_hashes ) + return changeset_hashes_str return '' @web.expose diff -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 -r b45044f8372a282065af34175c465f3f9c1c671e lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -264,7 +264,8 @@ repository, installed_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed, name, - tmp_repo_info_tuple ) + tmp_repo_info_tuple, + from_tip=False ) if repository: new_rd_tup = [ tool_shed, name, diff -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 -r b45044f8372a282065af34175c465f3f9c1c671e lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -75,6 +75,10 @@ # Make sure required_repository is in the repository_dependency table. repository_dependency = get_repository_dependency_by_repository_id( trans, required_repository.id ) if not repository_dependency: + log.debug( 'Creating new repository_dependency record for installed revision %s of repository: %s owned by %s.' % \ + ( str( required_repository.installed_changeset_revision ), + str( required_repository.name ), + str( required_repository.owner ) ) ) repository_dependency = trans.install_model.RepositoryDependency( tool_shed_repository_id=required_repository.id ) trans.install_model.context.add( repository_dependency ) trans.install_model.context.flush() @@ -129,7 +133,7 @@ for repo_info_dict in all_repo_info_dicts: # If the user elected to install repository dependencies, all items in the all_repo_info_dicts list will # be processed. However, if repository dependencies are not to be installed, only those items contained - # in the received repo_info_dicts list will be processed but the the all_repo_info_dicts list will be used + # in the received repo_info_dicts list will be processed but the all_repo_info_dicts list will be used # to create all defined repository dependency relationships. if is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies: for name, repo_info_tuple in repo_info_dict.items(): @@ -138,7 +142,7 @@ suc.get_repo_info_tuple_contents( repo_info_tuple ) # See if the repository has an existing record in the database. repository_db_record, installed_changeset_revision = \ - suc.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) + suc.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, from_tip=False ) if repository_db_record: if repository_db_record.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLED, trans.install_model.ToolShedRepository.installation_status.CLONING, diff -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 -r b45044f8372a282065af34175c465f3f9c1c671e lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1352,7 +1352,7 @@ folder_contents.append( node ) return folder_contents -def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): +def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple, from_tip=False ): """ Find out if a repository is already installed into Galaxy - there are several scenarios where this is necessary. For example, this method will handle the case where the repository was previously @@ -1375,10 +1375,11 @@ return tool_shed_repository, changeset_revision # Get all previous changeset revisions from the tool shed for the repository back to, but excluding, # the previous valid changeset revision to see if it was previously installed using one of them. - params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % ( url_for( '/', qualified=True ), - str( repository_name ), - str( repository_owner ), - changeset_revision ) + params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&from_tip=%s' % ( url_for( '/', qualified=True ), + str( repository_name ), + str( repository_owner ), + changeset_revision, + str( from_tip ) ) url = common_util.url_join( tool_shed_url, 'repository/previous_changeset_revisions%s' % params ) text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) diff -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 -r b45044f8372a282065af34175c465f3f9c1c671e lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -617,7 +617,7 @@ tool_dependencies=tool_dependencies ) # The required_repository may have been installed with a different changeset revision. required_repository, installed_changeset_revision = \ - suc.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) + suc.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, from_tip=False ) if required_repository: required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \ get_installed_and_missing_tool_dependencies_for_installed_repository( trans, required_repository, tool_dependencies ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Another fix for remotely populated metadata FileParameters.
by commits-noreply＠bitbucket.org 05 Jun '14

05 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e56736a7d9ba/ Changeset: e56736a7d9ba User: jmchilton Date: 2014-06-06 00:08:24 Summary: Another fix for remotely populated metadata FileParameters. Requires update to remote LWR as well. Affected #: 3 files diff -r 5449a8b1c9d531ee2347b2b219ffb7a2e0946590 -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -126,13 +126,18 @@ rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy ) return rval - def from_JSON_dict( self, filename ): + def from_JSON_dict( self, filename, path_rewriter=None ): dataset = self.parent log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) ) JSONified_dict = json.load( open( filename ) ) for name, spec in self.spec.items(): if name in JSONified_dict: - dataset._metadata[ name ] = spec.param.from_external_value( JSONified_dict[ name ], dataset ) + from_ext_kwds = {} + external_value = JSONified_dict[ name ] + param = spec.param + if isinstance( param, FileParameter ): + from_ext_kwds[ 'path_rewriter' ] = path_rewriter + dataset._metadata[ name ] = param.from_external_value( external_value, dataset, **from_ext_kwds ) elif name in dataset._metadata: #if the metadata value is not found in our externally set metadata but it has a value in the 'old' #metadata associated with our dataset, we'll delete it from our dataset's metadata dict @@ -521,7 +526,7 @@ value = value.id return value - def from_external_value( self, value, parent ): + def from_external_value( self, value, parent, path_rewriter=None ): """ Turns a value read from a external dict into its value to be pushed directly into the metadata dict. """ @@ -532,8 +537,13 @@ if mf is None: mf = self.new_file( dataset = parent, **value.kwds ) # Ensure the metadata file gets updated with content - parent.dataset.object_store.update_from_file( mf, file_name=value.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) ) - os.unlink( value.file_name ) + file_name = value.file_name + if path_rewriter: + # Job may have run with a different (non-local) tmp/working + # directory. Correct. + file_name = path_rewriter( file_name ) + parent.dataset.object_store.update_from_file( mf, file_name=file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) ) + os.unlink( file_name ) value = mf.id return value diff -r 5449a8b1c9d531ee2347b2b219ffb7a2e0946590 -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -952,7 +952,7 @@ self.sa_session.add(job) self.sa_session.flush() - def finish( self, stdout, stderr, tool_exit_code=None ): + def finish( self, stdout, stderr, tool_exit_code=None, remote_working_directory=None ): """ Called to indicate that the associated command has been run. Updates the output datasets based on stderr and stdout from the command, and @@ -1070,7 +1070,14 @@ #since if it is edited, the metadata changed on the running output will no longer match #the metadata that was stored to disk for use via the external process, #and the changes made by the user will be lost, without warning or notice - dataset.metadata.from_JSON_dict( self.external_output_metadata.get_output_filenames_by_dataset( dataset, self.sa_session ).filename_out ) + output_filename = self.external_output_metadata.get_output_filenames_by_dataset( dataset, self.sa_session ).filename_out + + def path_rewriter( path ): + if remote_working_directory and path and path.startswith( remote_working_directory ): + return path.replace( remote_working_directory, self.working_directory, 1 ) + return path + + dataset.metadata.from_JSON_dict( output_filename, path_rewriter=path_rewriter ) try: assert context.get( 'line_count', None ) is not None if ( not dataset.datatype.composite_type and dataset.dataset.is_multi_byte() ) or self.tool.is_multi_byte: diff -r 5449a8b1c9d531ee2347b2b219ffb7a2e0946590 -r e56736a7d9bafb3fe40379e192634f9ce8eb6d09 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -301,7 +301,7 @@ try: client = self.get_client_from_state(job_state) run_results = client.full_status() - + remote_working_directory = run_results.get("working_directory", None) stdout = run_results.get('stdout', '') stderr = run_results.get('stderr', '') exit_code = run_results.get('returncode', None) @@ -330,7 +330,12 @@ self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job try: - job_wrapper.finish( stdout, stderr, exit_code ) + job_wrapper.finish( + stdout, + stderr, + exit_code, + remote_working_directory=remote_working_directory + ) except Exception: log.exception("Job wrapper finish method failed") job_wrapper.fail("Unable to finish job", exception=True) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Allow hiding tools from the toolbox config.
by commits-noreply＠bitbucket.org 05 Jun '14

05 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5449a8b1c9d5/ Changeset: 5449a8b1c9d5 User: natefoo Date: 2014-06-05 20:46:56 Summary: Allow hiding tools from the toolbox config. Affected #: 1 file diff -r 3ecffd889d5c97478630cd127c8ac4681ec49872 -r 5449a8b1c9d531ee2347b2b219ffb7a2e0946590 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -563,6 +563,8 @@ # a new repository, so any included tools can be loaded into the tool panel. can_load_into_panel_dict = True tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) + if string_as_bool(elem.get( 'hidden', False )): + tool.hidden = True key = 'tool_%s' % str( tool.id ) if can_load_into_panel_dict: if guid is not None: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix working directory used for remote metadata command generation.
by commits-noreply＠bitbucket.org 05 Jun '14

05 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3ecffd889d5c/ Changeset: 3ecffd889d5c User: jmchilton Date: 2014-06-05 18:54:58 Summary: Fix working directory used for remote metadata command generation. In short - should fix bam outputs for LWR jobs when setting metadata on remote resource. Thanks to @natefoo for tracking down problem. Affected #: 1 file diff -r dd6fa0b34036d227900c4b92b514ee86aaca60a5 -r 3ecffd889d5c97478630cd127c8ac4681ec49872 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -722,7 +722,7 @@ sa_session.flush() metadata_files_list.append( metadata_files ) #return command required to build - return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) + return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, compute_tmp_dir or tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) def external_metadata_set_successfully( self, dataset, sa_session ): metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 05 Jun '14

05 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b62f649f1955/ Changeset: b62f649f1955 Branch: stable User: natefoo Date: 2014-06-05 16:13:29 Summary: Updated tag latest_2014.06.02 for changeset fb68af9a775a Affected #: 1 file diff -r fb68af9a775a956fcc397b22d16f2119401d926d -r b62f649f1955f64deb94c7e20093e31f5f411867 .hgtags --- a/.hgtags +++ b/.hgtags @@ -10,3 +10,4 @@ 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.06.02 +fb68af9a775a956fcc397b22d16f2119401d926d latest_2014.06.02 https://bitbucket.org/galaxy/galaxy-central/commits/dd6fa0b34036/ Changeset: dd6fa0b34036 User: natefoo Date: 2014-06-05 16:14:36 Summary: Merge stable Affected #: 1 file diff -r 5cd596d49a53974c48c64199d841e8cded05f43e -r dd6fa0b34036d227900c4b92b514ee86aaca60a5 .hgtags --- a/.hgtags +++ b/.hgtags @@ -10,3 +10,4 @@ 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.06.02 +fb68af9a775a956fcc397b22d16f2119401d926d latest_2014.06.02 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Upgrade kombu/amqp to fix ssl disconnect on consumer timeout bug: https://github.com/celery/py-amqp/pull/38
by commits-noreply＠bitbucket.org 05 Jun '14

05 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5cd596d49a53/ Changeset: 5cd596d49a53 User: natefoo Date: 2014-06-05 16:07:39 Summary: Upgrade kombu/amqp to fix ssl disconnect on consumer timeout bug: https://github.com/celery/py-amqp/pull/38 Affected #: 1 file diff -r cab2ae91c6a96e133748900e1c203ce864f52052 -r 5cd596d49a53974c48c64199d841e8cded05f43e eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -32,7 +32,7 @@ ; msgpack_python = 0.2.4 [eggs:noplatform] -amqp = 1.4.3 +amqp = 1.4.5 anyjson = 0.3.3 Beaker = 1.4 bioblend = 0.4.2 @@ -44,7 +44,7 @@ Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 importlib = 1.0.3 -kombu = 3.0.12 +kombu = 3.0.13 lrucache = 0.2 Mako = 0.4.1 mock = 1.0.1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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