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February 2015

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/becbbe264e9d/ Changeset: becbbe264e9d User: roalva1 Date: 2015-02-25 22:25:32+00:00 Summary: Restore function necessary for splitting. Affected #: 1 file diff -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f -r becbbe264e9d2780949dd5b2df27809db02c7fb7 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -203,7 +203,26 @@ return None raise NotImplementedError("Can't split generic sequence files") + def get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count): + """ + Does a brain-dead sequential scan & extract of certain sequences + >>> Sequence.get_split_commands_sequential(True, './input.gz', './output.gz', start_sequence=0, sequence_count=10) + ['zcat "./input.gz" | ( tail -n +1 2> /dev/null) | head -40 | gzip -c > "./output.gz"'] + >>> Sequence.get_split_commands_sequential(False, './input.fastq', './output.fastq', start_sequence=10, sequence_count=10) + ['tail -n +41 "./input.fastq" 2> /dev/null | head -40 > "./output.fastq"'] + """ + start_line = start_sequence * 4 + line_count = sequence_count * 4 + # TODO: verify that tail can handle 64-bit numbers + if is_compressed: + cmd = 'zcat "%s" | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c' % (input_name, start_line+1, line_count) + else: + cmd = 'tail -n +%s "%s" 2> /dev/null | head -%s' % (start_line+1, input_name, line_count) + cmd += ' > "%s"' % output_name + return [cmd] + get_split_commands_sequential = staticmethod(get_split_commands_sequential) + class Alignment( data.Text ): """Class describing an alignment""" https://bitbucket.org/galaxy/galaxy-central/commits/8b70692766ec/ Changeset: 8b70692766ec User: roalva1 Date: 2015-02-26 15:00:12+00:00 Summary: added get_split_commands_with_toc method Affected #: 1 file diff -r becbbe264e9d2780949dd5b2df27809db02c7fb7 -r 8b70692766ec172eb4ac141a5d7266b88526f852 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -203,6 +203,75 @@ return None raise NotImplementedError("Can't split generic sequence files") + def get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count): + """ + Uses a Table of Contents dict, parsed from an FQTOC file, to come up with a set of + shell commands that will extract the parts necessary + >>> three_sections=[dict(start=0, end=74, sequences=10), dict(start=74, end=148, sequences=10), dict(start=148, end=148+76, sequences=10)] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=10) + ['dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=1, sequence_count=5) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +5 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=20) + ['dd bs=1 skip=0 count=148 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=10) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', '(dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=10, sequence_count=10) + ['dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=20) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', 'dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz', '(dd bs=1 skip=148 count=76 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + """ + sections = toc_file['sections'] + result = [] + + current_sequence = long(0) + i=0 + # skip to the section that contains my starting sequence + while i < len(sections) and start_sequence >= current_sequence + long(sections[i]['sequences']): + current_sequence += long(sections[i]['sequences']) + i += 1 + if i == len(sections): # bad input data! + raise Exception('No FQTOC section contains starting sequence %s' % start_sequence) + + # These two variables act as an accumulator for consecutive entire blocks that + # can be copied verbatim (without decompressing) + start_chunk = long(-1) + end_chunk = long(-1) + copy_chunk_cmd = 'dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s' + + while sequence_count > 0 and i < len(sections): + # we need to extract partial data. So, find the byte offsets of the chunks that contain the data we need + # use a combination of dd (to pull just the right sections out) tail (to skip lines) and head (to get the + # right number of lines + sequences = long(sections[i]['sequences']) + skip_sequences = start_sequence-current_sequence + sequences_to_extract = min(sequence_count, sequences-skip_sequences) + start_copy = long(sections[i]['start']) + end_copy = long(sections[i]['end']) + if sequences_to_extract < sequences: + if start_chunk > -1: + result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name)) + start_chunk = -1 + # extract, unzip, trim, recompress + result.append('(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s' % + (start_copy, end_copy-start_copy, input_name, skip_sequences*4+1, sequences_to_extract*4, output_name)) + else: # whole section - add it to the start_chunk/end_chunk accumulator + if start_chunk == -1: + start_chunk = start_copy + end_chunk = end_copy + sequence_count -= sequences_to_extract + start_sequence += sequences_to_extract + current_sequence += sequences + i += 1 + if start_chunk > -1: + result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name)) + + if sequence_count > 0: + raise Exception('%s sequences not found in file' % sequence_count) + + return result + get_split_commands_with_toc = staticmethod(get_split_commands_with_toc) + def get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count): """ Does a brain-dead sequential scan & extract of certain sequences @@ -222,7 +291,7 @@ return [cmd] get_split_commands_sequential = staticmethod(get_split_commands_sequential) - + class Alignment( data.Text ): """Class describing an alignment""" 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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[galaxyproject/usegalaxy-playbook] a634b7: Update Test again
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a634b792e9e5b8fcfb99da5fc5a3fec697a7556c https://github.com/galaxyproject/usegalaxy-playbook/commit/a634b792e9e5b8fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test again

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commit/galaxy-central: guerler: ToolForm: Fix dataset order for multi select run
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df564c852b3c/ Changeset: df564c852b3c User: guerler Date: 2015-02-27 15:12:13+00:00 Summary: ToolForm: Fix dataset order for multi select run Affected #: 3 files diff -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file 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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[galaxyproject/usegalaxy-playbook] a8df06: Update Main
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a8df0635efc627a83ba685dfaabfc99e835ae6fa https://github.com/galaxyproject/usegalaxy-playbook/commit/a8df0635efc627a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main

1 0

commit/galaxy-central: 10 new changesets
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

10 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/563defcf9c83/ Changeset: 563defcf9c83 Branch: release_15.03 User: dan Date: 2015-02-26 22:16:55+00:00 Summary: Allow TabularToolDataTable to be loaded from a url instead of a path. Affected #: 1 file diff -r b046e38c21d140d9fdbba80fc1861cd6cf4e8352 -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -14,6 +14,8 @@ import hashlib from glob import glob +from tempfile import NamedTemporaryFile +from urllib2 import urlopen from galaxy import util from galaxy.util.odict import odict @@ -279,7 +281,22 @@ repo_info = None # Read every file for file_element in config_element.findall( 'file' ): - filename = file_path = expand_here_template( file_element.get( 'path', None ), here=self.here ) + tmp_file = None + filename = file_element.get( 'path', None ) + if filename is None: + # Handle URLs as files + filename = file_element.get( 'url', None ) + if filename: + tmp_file = NamedTemporaryFile( prefix='TTDT_URL_%s-' % self.name ) + try: + tmp_file.write( urlopen( filename ).read() ) + except Exception, e: + log.error( 'Error loading Data Table URL "%s": %s', filename, e ) + continue + log.debug( 'Loading Data Table URL "%s" as filename "%s".', filename, tmp_file.name ) + filename = tmp_file.name + tmp_file.flush() + filename = file_path = expand_here_template( filename, here=self.here ) found = False if file_path is None: log.debug( "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string( file_element ), self.name ) @@ -325,6 +342,9 @@ config_element=config_element, tool_shed_repository=repo_info, errors=errors ) else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) + # Remove URL tmp file + if tmp_file is not None: + tmp_file.close() def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): assert self.columns == other_table.columns, "Merging tabular data tables with non matching columns is not allowed: %s:%s != %s:%s" % ( self.name, self.columns, other_table.name, other_table.columns ) https://bitbucket.org/galaxy/galaxy-central/commits/c35498a73b41/ Changeset: c35498a73b41 Branch: release_15.03 User: guerler Date: 2015-02-27 06:30:48+00:00 Summary: ToolForm: Show initial validation errors on re-run Affected #: 3 files diff -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f -r c35498a73b41c76446223123721f8a9c08bec03c client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f -r c35498a73b41c76446223123721f8a9c08bec03c static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f -r c35498a73b41c76446223123721f8a9c08bec03c static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/441d5188382c/ Changeset: 441d5188382c Branch: release_15.03 User: guerler Date: 2015-02-27 06:35:38+00:00 Summary: ToolForm/Collections: Re-introduce parameter expansion Affected #: 4 files diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2366,7 +2366,7 @@ else: value, error = check_param(trans, input, default_value, context) except Exception, err: - log.error('Checking parameter failed. %s', str(err)) + log.error('Checking parameter %s failed. %s', input.name, str(err)) pass return [value, error] @@ -2482,6 +2482,11 @@ else: state[k] = jsonify(state[k]) + # expand incoming parameters (parameters might trigger multiple tool executions, + # here we select the first execution only in order to resolve dynamic parameters) + expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) + params.__dict__ = expanded_incomings[ 0 ] + # do param translation here, used by datasource tools if self.input_translator: self.input_translator.translate( params ) diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var h=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(k);f.deferred.done(i)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/9e16f3d9fafe/ Changeset: 9e16f3d9fafe Branch: release_15.03 User: guerler Date: 2015-02-27 06:49:53+00:00 Summary: Parameters: Prevent uncaught exception on unavailable datasets in column validation Affected #: 1 file diff -r 441d5188382c775009e6612c57e9317d8cb9a944 -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1335,6 +1335,10 @@ datasets = util.listify( context[ self.data_ref ] ) for dataset in datasets: if dataset: + # Check if metadata is available + if not hasattr(dataset, 'metadata'): + return True + # Check if the dataset does not have the expected metadata for columns if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready https://bitbucket.org/galaxy/galaxy-central/commits/84e665326798/ Changeset: 84e665326798 Branch: release_15.03 User: guerler Date: 2015-02-27 06:57:39+00:00 Summary: ToolForm/Ui: Limit selection to available options Affected #: 3 files diff -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 -r 84e665326798aba03ff4e9acca501a7a96d16741 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 -r 84e665326798aba03ff4e9acca501a7a96d16741 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 -r 84e665326798aba03ff4e9acca501a7a96d16741 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/ba82b4086c84/ Changeset: ba82b4086c84 Branch: release_15.03 User: guerler Date: 2015-02-27 06:59:43+00:00 Summary: Parameters: Fix deleted datasets validation message Affected #: 1 file diff -r 84e665326798aba03ff4e9acca501a7a96d16741 -r ba82b4086c84446e0f2e5f75873fc94f52306be7 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2016,7 +2016,7 @@ for v in values: if v: if v.deleted: - raise ValueError( "The previously selected dataset has been previously deleted" ) + raise ValueError( "The previously selected dataset has been deleted." ) if hasattr( v, "dataset" ) and v.dataset.state in [ galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: raise ValueError( "The previously selected dataset has entered an unusable state" ) if not self.multiple: https://bitbucket.org/galaxy/galaxy-central/commits/a3bc4324eb02/ Changeset: a3bc4324eb02 Branch: release_15.03 User: guerler Date: 2015-02-27 09:26:15+00:00 Summary: Parameters: Set hidden attribute for hidden dataset parameter Affected #: 1 file diff -r ba82b4086c84446e0f2e5f75873fc94f52306be7 -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2420,6 +2420,7 @@ DataToolParameter.__init__( self, tool, elem ) self.value = "None" self.type = "hidden_data" + self.hidden = True def get_initial_value( self, trans, context, history=None ): return None https://bitbucket.org/galaxy/galaxy-central/commits/1a1cc1be950f/ Changeset: 1a1cc1be950f Branch: release_15.03 User: guerler Date: 2015-02-27 09:36:20+00:00 Summary: ToolForm/Ui: Restrict available option requirement to single select fields Affected #: 3 files diff -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)||this.options.multiple){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/04d4f727c2ff/ Changeset: 04d4f727c2ff Branch: release_15.03 User: carlfeberhard Date: 2015-02-27 15:03:47+00:00 Summary: Fix display_structure by using serializer; fix structure by removing extra decode_id Affected #: 2 files diff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -543,8 +543,10 @@ def structure( self, trans, id=None, **kwargs ): """ """ - id = self.decode_id( id ) if id else trans.history.id - history_to_view = self.history_manager.get_accessible( trans, id, trans.user ) + unencoded_history_id = trans.history.id + if id: + unencoded_history_id = self.decode_id( id ) + history_to_view = self.history_manager.get_accessible( trans, unencoded_history_id, trans.user ) history_data = self.history_manager._get_history_data( trans, history_to_view ) history_dictionary = history_data[ 'history' ] @@ -552,7 +554,7 @@ jobs = ( trans.sa_session.query( trans.app.model.Job ) .filter( trans.app.model.Job.user == trans.user ) - .filter( trans.app.model.Job.history_id == self.decode_id( id ) ) ).all() + .filter( trans.app.model.Job.history_id == unencoded_history_id ) ).all() jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs ) tools = {} diff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -128,13 +128,15 @@ ## ---------------------------------------------------------------------------- <%def name="javascripts()"><% + from galaxy.managers import hdas + hda_serializer = hdas.HDASerializer( trans.app ) self.js_app = 'display-structured' controller = trans.webapp.controllers[ 'history' ] hda_dicts = [] id_hda_dict_map = {} for hda in history.active_datasets: - hda_dict = controller.get_hda_dict( trans, hda ) + hda_dict = hda_serializer.serialize_to_view( trans, hda, 'detailed' ) id_hda_dict_map[ hda_dict[ 'id' ] ] = hda_dict hda_dicts.append( hda_dict ) %> https://bitbucket.org/galaxy/galaxy-central/commits/2a238115b21c/ Changeset: 2a238115b21c Branch: release_15.03 User: guerler Date: 2015-02-27 15:12:13+00:00 Summary: ToolForm: Fix dataset order for multi select run Affected #: 3 files diff -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa -r 2a238115b21ccce4391355329e322132716daecc client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa -r 2a238115b21ccce4391355329e322132716daecc static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa -r 2a238115b21ccce4391355329e322132716daecc static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file 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

[galaxyproject/usegalaxy-playbook] 827e17: Update Test. And integrated_tool_panel.xml has cha...
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 827e17cca73c7e6fa9f5e95d79d2b84746fde0c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/827e17cca73c7e6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M stage/group_vars/all.yml Log Message: ----------- Update Test. And integrated_tool_panel.xml has changed again...

1 0

commit/galaxy-central: 13 new changesets
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

13 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a6e7085ce60/ Changeset: 0a6e7085ce60 User: dan Date: 2015-02-26 22:16:55+00:00 Summary: Allow TabularToolDataTable to be loaded from a url instead of a path. Affected #: 1 file diff -r 71596d6f10285ebb23d2a257eda3b70cb04ff655 -r 0a6e7085ce60c53e4a97aedd2e0561177b6f913a lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -14,6 +14,8 @@ import hashlib from glob import glob +from tempfile import NamedTemporaryFile +from urllib2 import urlopen from galaxy import util from galaxy.util.odict import odict @@ -279,7 +281,22 @@ repo_info = None # Read every file for file_element in config_element.findall( 'file' ): - filename = file_path = expand_here_template( file_element.get( 'path', None ), here=self.here ) + tmp_file = None + filename = file_element.get( 'path', None ) + if filename is None: + # Handle URLs as files + filename = file_element.get( 'url', None ) + if filename: + tmp_file = NamedTemporaryFile( prefix='TTDT_URL_%s-' % self.name ) + try: + tmp_file.write( urlopen( filename ).read() ) + except Exception, e: + log.error( 'Error loading Data Table URL "%s": %s', filename, e ) + continue + log.debug( 'Loading Data Table URL "%s" as filename "%s".', filename, tmp_file.name ) + filename = tmp_file.name + tmp_file.flush() + filename = file_path = expand_here_template( filename, here=self.here ) found = False if file_path is None: log.debug( "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string( file_element ), self.name ) @@ -325,6 +342,9 @@ config_element=config_element, tool_shed_repository=repo_info, errors=errors ) else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) + # Remove URL tmp file + if tmp_file is not None: + tmp_file.close() def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): assert self.columns == other_table.columns, "Merging tabular data tables with non matching columns is not allowed: %s:%s != %s:%s" % ( self.name, self.columns, other_table.name, other_table.columns ) https://bitbucket.org/galaxy/galaxy-central/commits/b6fe31e55f48/ Changeset: b6fe31e55f48 User: dannon Date: 2015-02-27 00:59:26+00:00 Summary: Fix server_starttime being in app for reports, toolshed. I will be refactoring this shortly to have a base UniverseApplication from which things inherit. Affected #: 2 files diff -r 0a6e7085ce60c53e4a97aedd2e0561177b6f913a -r b6fe31e55f48916a4b83a5e9982dda3eab9a5a1b lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -1,5 +1,7 @@ +import config import sys -import config +import time + import galaxy.model from galaxy.web import security @@ -26,6 +28,8 @@ self.targets_mysql = 'mysql' in self.config.database_connection # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. + self.server_starttime = int(time.time()) def shutdown( self ): pass diff -r 0a6e7085ce60c53e4a97aedd2e0561177b6f913a -r b6fe31e55f48916a4b83a5e9982dda3eab9a5a1b lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -1,17 +1,18 @@ import config import sys +import time +import galaxy.datatypes.registry +import galaxy.quota +import galaxy.tools.data +import galaxy.webapps.tool_shed.model from galaxy import tools -import galaxy.tools.data -import galaxy.quota -import galaxy.datatypes.registry -import galaxy.webapps.tool_shed.model +from galaxy.managers.tags import CommunityTagManager from galaxy.openid.providers import OpenIDProviders from galaxy.util.dbkeys import GenomeBuilds from galaxy.web import security -from galaxy.managers.tags import CommunityTagManager -from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager import tool_shed.repository_registry import tool_shed.repository_types.registry +from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager class UniverseApplication( object ): @@ -70,6 +71,8 @@ self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir # Initialize the repository registry. self.repository_registry = tool_shed.repository_registry.Registry( self ) + # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. + self.server_starttime = int(time.time()) print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config def shutdown( self ): https://bitbucket.org/galaxy/galaxy-central/commits/eed154f337fc/ Changeset: eed154f337fc User: dannon Date: 2015-02-27 01:13:48+00:00 Summary: Fix reports webapp under default database broken in ba825fc5 Affected #: 1 file diff -r b6fe31e55f48916a4b83a5e9982dda3eab9a5a1b -r eed154f337fc090168956bcbec92491d0a5d75c9 lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -25,7 +25,10 @@ db_url, self.config.database_engine_options, create_tables=True ) - self.targets_mysql = 'mysql' in self.config.database_connection + if not self.config.database_connection: + self.targets_mysql = False + else: + self.targets_mysql = 'mysql' in self.config.database_connection # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. https://bitbucket.org/galaxy/galaxy-central/commits/4e30957ab121/ Changeset: 4e30957ab121 User: jmchilton Date: 2015-02-27 03:36:14+00:00 Summary: Fix incorrect usage of __all__ not containing strings... ...for plugin_config.py plugins. Affected #: 12 files diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/core.py --- a/lib/galaxy/jobs/metrics/instrumenters/core.py +++ b/lib/galaxy/jobs/metrics/instrumenters/core.py @@ -82,4 +82,4 @@ pass return value -__all__ = [ CorePlugin ] +__all__ = [ 'CorePlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py --- a/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py +++ b/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py @@ -59,4 +59,4 @@ def __instrument_cpuinfo_path( self, job_directory ): return self._instrument_file_path( job_directory, "cpuinfo" ) -__all__ = [ CpuInfoPlugin ] +__all__ = [ 'CpuInfoPlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/env.py --- a/lib/galaxy/jobs/metrics/instrumenters/env.py +++ b/lib/galaxy/jobs/metrics/instrumenters/env.py @@ -68,4 +68,4 @@ def __env_file( self, job_directory ): return self._instrument_file_path( job_directory, "vars" ) -__all__ = [ EnvPlugin ] +__all__ = [ 'EnvPlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/meminfo.py --- a/lib/galaxy/jobs/metrics/instrumenters/meminfo.py +++ b/lib/galaxy/jobs/metrics/instrumenters/meminfo.py @@ -56,4 +56,4 @@ def __instrument_meminfo_path( self, job_directory ): return self._instrument_file_path( job_directory, "meminfo" ) -__all__ = [ MemInfoPlugin ] +__all__ = [ 'MemInfoPlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/jobs/metrics/instrumenters/uname.py --- a/lib/galaxy/jobs/metrics/instrumenters/uname.py +++ b/lib/galaxy/jobs/metrics/instrumenters/uname.py @@ -31,4 +31,4 @@ return self._instrument_file_path( job_directory, "uname" ) -__all__ = [ UnamePlugin ] +__all__ = [ 'UnamePlugin' ] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py --- a/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py @@ -147,4 +147,4 @@ return base -__all__ = [HomebrewToolShedDependencyResolver] +__all__ = ['HomebrewToolShedDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/galaxy_packages.py --- a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py +++ b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py @@ -71,4 +71,4 @@ commands = 'PACKAGE_BASE=%s; export PACKAGE_BASE; . %s' % ( base_path, self.script ) return commands -__all__ = [GalaxyPackageDependencyResolver, GalaxyPackageDependency] +__all__ = ['GalaxyPackageDependencyResolver', 'GalaxyPackageDependency'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/homebrew.py --- a/lib/galaxy/tools/deps/resolvers/homebrew.py +++ b/lib/galaxy/tools/deps/resolvers/homebrew.py @@ -53,4 +53,4 @@ return str( value ).lower() == "true" -__all__ = [HomebrewDependencyResolver] +__all__ = ['HomebrewDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/modules.py --- a/lib/galaxy/tools/deps/resolvers/modules.py +++ b/lib/galaxy/tools/deps/resolvers/modules.py @@ -153,4 +153,4 @@ def _string_as_bool( value ): return str( value ).lower() == "true" -__all__ = [ModuleDependencyResolver] +__all__ = ['ModuleDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/tools/deps/resolvers/tool_shed_packages.py --- a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py @@ -56,4 +56,4 @@ return INDETERMINATE_DEPENDENCY -__all__ = [ToolShedPackageDependencyResolver] +__all__ = ['ToolShedPackageDependencyResolver'] diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/util/plugin_config.py --- a/lib/galaxy/util/plugin_config.py +++ b/lib/galaxy/util/plugin_config.py @@ -25,6 +25,10 @@ # FIXME: this is not how one is suppose to use __all__ why did you do # this past John? for clazz in getattr( plugin_module, "__all__", [] ): + try: + clazz = getattr( plugin_module, clazz ) + except TypeError: + clazz = clazz plugin_type = getattr( clazz, plugin_type_identifier, None ) if plugin_type: plugin_dict[ plugin_type ] = clazz diff -r eed154f337fc090168956bcbec92491d0a5d75c9 -r 4e30957ab1217c50dbaed105d00b0a5afbea858e lib/galaxy/workflow/schedulers/core.py --- a/lib/galaxy/workflow/schedulers/core.py +++ b/lib/galaxy/workflow/schedulers/core.py @@ -43,4 +43,4 @@ workflow_invocation=workflow_invocation, ) -__all__ = [ CoreWorkflowSchedulingPlugin ] +__all__ = [ 'CoreWorkflowSchedulingPlugin' ] https://bitbucket.org/galaxy/galaxy-central/commits/e8c37fd94209/ Changeset: e8c37fd94209 User: jmchilton Date: 2015-02-27 05:29:07+00:00 Summary: Update pulsar client and related modules. Affected #: 24 files diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/collectl/cli.py --- a/lib/galaxy/jobs/metrics/collectl/cli.py +++ b/lib/galaxy/jobs/metrics/collectl/cli.py @@ -12,7 +12,8 @@ class CollectlCli( object ): - """ Abstraction over (some of) the command-line arguments of collectl. + """ + Abstraction over (some of) the command-line arguments of collectl. Ideally this will be useful for building up command line arguments for remote execution as well as runnning directly on local host. @@ -20,33 +21,43 @@ collectl CLI - logic more directly related to the Galaxy job metric plugin plugin should be placed in other modules. - Keyword Arguments: - collectl_path: Path to collectl executable (defaults to collectl - i.e. - search the PATH). + **Keyword Arguments:** - playback_path (defaults to None): If this is None collectl will run in - record mode, else it will playback specified file. + ``collectl_path`` + Path to collectl executable (defaults to collectl - i.e. + search the PATH). - Playback Mode Options: - - sep : Separator used in playback mode (set to 9 to produce tsv) - (defaults to None). + ``playback_path`` (defaults to ``None``) + If this is ``None``, collectl will run in + record mode, else it will playback specified file. - Record Mode Options (some of these may work in playback mode also): + **Playback Mode Options:** - destination_path: Location of path files to write to (defaults to None - and collectl will just use cwd). Really this is just to prefix - - collectl will append hostname and datetime to file. - interval: Setup polling interval (secs) for most subsystems (defaults - to None and when unspecified collectl will use default of 1 second). - interval2: Setup polling interval (secs) for process information - (defaults to None and when unspecified collectl will use default to - 60 seconds). - interval3: Setup polling interval (secs) for environment information - (defaults to None and when unspecified collectl will use default to - 300 seconds). - procfilt: Optional argument to procfilt. (defaults to None). - flush : Optional flush interval (defaults to None). + ``sep`` + Separator used in playback mode (set to 9 to produce tsv) + (defaults to None). + + **Record Mode Options** (some of these may work in playback mode also) + + ``destination_path`` + Location of path files to write to (defaults to None + and collectl will just use cwd). Really this is just to prefix - + collectl will append hostname and datetime to file. + ``interval`` + Setup polling interval (secs) for most subsystems (defaults + to None and when unspecified collectl will use default of 1 second). + ``interval2`` + Setup polling interval (secs) for process information + (defaults to None and when unspecified collectl will use default to + 60 seconds). + ``interval3`` + Setup polling interval (secs) for environment information + (defaults to None and when unspecified collectl will use default to + 300 seconds). + ``procfilt`` + Optional argument to procfilt. (defaults to None). + ``flush`` + Optional flush interval (defaults to None). """ def __init__( self, **kwargs ): @@ -125,4 +136,4 @@ if return_code: raise Exception( "Problem running collectl command." ) -__all__ = [ CollectlCli ] +__all__ = [ 'CollectlCli' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/collectl/processes.py --- a/lib/galaxy/jobs/metrics/collectl/processes.py +++ b/lib/galaxy/jobs/metrics/collectl/processes.py @@ -26,7 +26,7 @@ # # Process data dumped one row per process per interval. -#http://collectl.sourceforge.net/Data-detail.html +# http://collectl.sourceforge.net/Data-detail.html PROCESS_COLUMNS = [ "#Date", # Date of interval - e.g. 20140322 "Time", # Time of interval - 12:18:58 @@ -36,7 +36,7 @@ "PPID", # Parent PID of process. "THRD", # Thread??? "S", # Process state - S - Sleeping, D - Uninterruptable Sleep, R - Running, Z - Zombie or T - Stopped/Traced - ## Memory options - http://ewx.livejournal.com/579283.html + # Memory options - http://ewx.livejournal.com/579283.html "VmSize", "VmLck", "VmRSS", @@ -93,7 +93,7 @@ statistics = DEFAULT_STATISTICS statistics = util.listify( statistics ) - statistics = map( __tuplize_statistic, statistics ) + statistics = map( _tuplize_statistic, statistics ) # Check for validity... for statistic in statistics: if statistic[ 0 ] not in STATISTIC_TYPES: @@ -109,10 +109,10 @@ with tempfile.NamedTemporaryFile( ) as tmp_tsv: collectl_playback_cli.run( stdout=tmp_tsv ) with open( tmp_tsv.name, "r" ) as tsv_file: - return __read_process_statistics( tsv_file, pid, statistics ) + return _read_process_statistics( tsv_file, pid, statistics ) -def __read_process_statistics( tsv_file, pid, statistics ): +def _read_process_statistics( tsv_file, pid, statistics ): process_summarizer = CollectlProcessSummarizer( pid, statistics ) current_interval = None @@ -167,7 +167,7 @@ to_num = float else: to_num = long - + interval_stat = sum( to_num( r[ column_index ] ) for r in rows ) self.tree_statistics[ column_name ].track( interval_stat ) @@ -228,7 +228,7 @@ ability to filter out just rows corresponding to the process tree corresponding to a given pid. """ - + def __init__( self ): self.rows = [] @@ -242,11 +242,11 @@ self.rows.append( row ) -def __tuplize_statistic( statistic ): +def _tuplize_statistic( statistic ): if not isinstance( statistic, tuple ): statistic_split = statistic.split( "_", 1 ) statistic = ( statistic_split[ 0 ].lower(), statistic_split[ 1 ] ) return statistic -__all__ = [ generate_process_statistics ] +__all__ = [ 'generate_process_statistics' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/collectl/subsystems.py --- a/lib/galaxy/jobs/metrics/collectl/subsystems.py +++ b/lib/galaxy/jobs/metrics/collectl/subsystems.py @@ -69,4 +69,4 @@ """ return SUBSYSTEM_DICT[ name ] -__all__ = [ get_subsystem ] +__all__ = [ 'get_subsystem' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/metrics/instrumenters/collectl.py --- a/lib/galaxy/jobs/metrics/instrumenters/collectl.py +++ b/lib/galaxy/jobs/metrics/instrumenters/collectl.py @@ -211,4 +211,4 @@ return "" -__all__ = [ CollectlPlugin ] +__all__ = [ 'CollectlPlugin' ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/__init__.py --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -7,4 +7,4 @@ from .kill import kill_pid -__all__ = [kill_pid, Bunch] +__all__ = ['kill_pid', 'Bunch'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/__init__.py --- a/lib/galaxy/jobs/runners/util/cli/__init__.py +++ b/lib/galaxy/jobs/runners/util/cli/__init__.py @@ -6,6 +6,9 @@ DEFAULT_SHELL_PLUGIN = 'LocalShell' +ERROR_MESSAGE_NO_JOB_PLUGIN = "No job plugin parameter found, cannot create CLI job interface" +ERROR_MESSAGE_NO_SUCH_JOB_PLUGIN = "Failed to find job_plugin of type %s, available types include %s" + class CliInterface(object): """ @@ -53,8 +56,14 @@ return shell def get_job_interface(self, job_params): - job_plugin = job_params['plugin'] - job_interface = self.cli_job_interfaces[job_plugin](**job_params) + job_plugin = job_params.get('plugin', None) + if not job_plugin: + raise ValueError(ERROR_MESSAGE_NO_JOB_PLUGIN) + job_plugin_class = self.cli_job_interfaces.get(job_plugin, None) + if not job_plugin_class: + raise ValueError(ERROR_MESSAGE_NO_SUCH_JOB_PLUGIN % (job_plugin, self.cli_job_interfaces.keys())) + job_interface = job_plugin_class(**job_params) + return job_interface diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/factory.py --- a/lib/galaxy/jobs/runners/util/cli/factory.py +++ b/lib/galaxy/jobs/runners/util/cli/factory.py @@ -12,7 +12,11 @@ code_dir = '.' +def build_cli_interface(): + return CliInterface(code_dir=code_dir) + + def get_shell(params): - cli_interface = CliInterface(code_dir=code_dir) + cli_interface = build_cli_interface() shell_params, _ = split_params(params) return cli_interface.get_shell_plugin(shell_params) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/job/slurm.py --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -1,6 +1,10 @@ # A simple CLI runner for slurm that can be used when running Galaxy from a # non-submit host and using a Slurm cluster. +from ..job import BaseJobExec + +from logging import getLogger + try: from galaxy.model import Job job_states = Job.states @@ -9,11 +13,6 @@ from galaxy.util import enum job_states = enum(RUNNING='running', OK='complete', QUEUED='queued', ERROR="failed") -from ..job import BaseJobExec - -__all__ = ('Slurm',) - -from logging import getLogger log = getLogger(__name__) argmap = { @@ -94,3 +93,6 @@ }.get(state) except KeyError: raise KeyError("Failed to map slurm status code [%s] to job state." % state) + + +__all__ = ('Slurm',) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/job/torque.py --- a/lib/galaxy/jobs/runners/util/cli/job/torque.py +++ b/lib/galaxy/jobs/runners/util/cli/job/torque.py @@ -1,3 +1,4 @@ +from logging import getLogger try: import xml.etree.cElementTree as et except: @@ -13,10 +14,10 @@ from ..job import BaseJobExec -__all__ = ('Torque',) +log = getLogger(__name__) -from logging import getLogger -log = getLogger(__name__) +ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s' + argmap = {'destination': '-q', 'Execution_Time': '-a', @@ -58,8 +59,8 @@ if not k.startswith('-'): k = argmap[k] pbsargs[k] = v - except: - log.warning('Unrecognized long argument passed to Torque CLI plugin: %s' % k) + except KeyError: + log.warning(ERROR_MESSAGE_UNRECOGNIZED_ARG % k) template_pbsargs = '' for k, v in pbsargs.items(): template_pbsargs += '#PBS %s %s\n' % (k, v) @@ -118,3 +119,6 @@ }.get(state) except KeyError: raise KeyError("Failed to map torque status code [%s] to job state." % state) + + +__all__ = ('Torque',) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/galaxy/jobs/runners/util/cli/shell/local.py --- a/lib/galaxy/jobs/runners/util/cli/shell/local.py +++ b/lib/galaxy/jobs/runners/util/cli/shell/local.py @@ -24,7 +24,7 @@ True >>> exec_result.stdout.strip() == u'Hello World' True - >>> exec_result = exec_python("import time; time.sleep(90)", timeout=3, timeout_check_interval=1) + >>> exec_result = exec_python("import time; time.sleep(90)", timeout=1, timeout_check_interval=.1) >>> exec_result.stdout == u'' True >>> exec_result.stderr == 'Execution timed out' diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/__init__.py --- a/lib/pulsar/client/__init__.py +++ b/lib/pulsar/client/__init__.py @@ -1,6 +1,6 @@ """ pulsar client -====== +================= This module contains logic for interfacing with an external Pulsar server. @@ -50,13 +50,13 @@ from .path_mapper import PathMapper __all__ = [ - build_client_manager, - OutputNotFoundException, - url_to_destination_params, - finish_job, - submit_job, - ClientJobDescription, - PulsarOutputs, - ClientOutputs, - PathMapper, + 'build_client_manager', + 'OutputNotFoundException', + 'url_to_destination_params', + 'finish_job', + 'submit_job', + 'ClientJobDescription', + 'PulsarOutputs', + 'ClientOutputs', + 'PathMapper', ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/action_mapper.py --- a/lib/pulsar/client/action_mapper.py +++ b/lib/pulsar/client/action_mapper.py @@ -1,5 +1,6 @@ from json import load from os import makedirs +from os import unlink from os.path import exists from os.path import abspath from os.path import dirname @@ -16,6 +17,9 @@ from .util import unique_path_prefix from .transport import get_file from .transport import post_file +from .transport import rsync_get_file, scp_get_file +from .transport import rsync_post_file, scp_post_file +import tempfile DEFAULT_MAPPED_ACTION = 'transfer' # Not really clear to me what this should be, exception? @@ -130,6 +134,7 @@ if config is None: config = self.__client_to_config(client) self.default_action = config.get("default_action", "transfer") + self.ssh_key = config.get("ssh_key", None) self.mappers = mappers_from_dicts(config.get("paths", [])) self.files_endpoint = config.get("files_endpoint", None) @@ -155,6 +160,7 @@ return dict( default_action=self.default_action, files_endpoint=self.files_endpoint, + ssh_key=self.ssh_key, paths=map(lambda m: m.to_dict(), self.mappers) ) @@ -166,6 +172,8 @@ config = dict() config["default_action"] = client.default_file_action config["files_endpoint"] = client.files_endpoint + if hasattr(client, 'ssh_key'): + config["ssh_key"] = client.ssh_key return config def __load_action_config(self, path): @@ -209,6 +217,9 @@ # TODO: URL encode path. url = "%s&path=%s&file_type=%s" % (url_base, action.path, file_type) action.url = url + elif action.action_type in ["remote_rsync_transfer", "remote_scp_transfer"]: + # Required, so no check for presence + action.ssh_key = self.ssh_key REQUIRED_ACTION_KWD = object() @@ -375,6 +386,95 @@ post_file(self.url, pulsar_path) +class PubkeyAuthenticatedTransferAction(BaseAction): + """Base class for file transfers requiring an SSH public/private key + """ + action_spec = dict( + ssh_user=REQUIRED_ACTION_KWD, + ssh_host=REQUIRED_ACTION_KWD, + ssh_port=REQUIRED_ACTION_KWD, + ) + action_type = "remote_pubkey_transfer" + staging = STAGING_ACTION_REMOTE + ssh_key = None + + def __init__(self, path, file_lister=None, url=None, ssh_user=None, + ssh_host=None, ssh_port=None, ssh_key=None): + super(PubkeyAuthenticatedTransferAction, self).__init__(path, file_lister=file_lister) + self.url = url + self.ssh_user = ssh_user + self.ssh_host = ssh_host + self.ssh_port = ssh_port + self.ssh_key = ssh_key + + def to_dict(self): + return dict(path=self.path, action_type=self.action_type, url=self.url, + ssh_user=self.ssh_user, ssh_host=self.ssh_host, + ssh_port=self.ssh_port) + + def serialize_ssh_key(self): + f = tempfile.NamedTemporaryFile(delete=False) + if self.ssh_key is not None: + f.write(self.ssh_key) + else: + raise Exception("SSH_KEY not available") + return f.name + + def cleanup_ssh_key(self, keyfile): + if exists(keyfile): + unlink(keyfile) + + +class RsyncTransferAction(PubkeyAuthenticatedTransferAction): + action_type = "remote_rsync_transfer" + + @classmethod + def from_dict(cls, action_dict): + return RsyncTransferAction(path=action_dict["path"], + url=action_dict["url"], + ssh_user=action_dict["ssh_user"], + ssh_host=action_dict["ssh_host"], + ssh_port=action_dict["ssh_port"], + ssh_key=action_dict["ssh_key"]) + + def write_to_path(self, path): + key_file = self.serialize_ssh_key() + rsync_get_file(self.path, path, self.ssh_user, self.ssh_host, + self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + def write_from_path(self, pulsar_path): + key_file = self.serialize_ssh_key() + rsync_post_file(pulsar_path, self.path, self.ssh_user, + self.ssh_host, self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + +class ScpTransferAction(PubkeyAuthenticatedTransferAction): + action_type = "remote_scp_transfer" + + @classmethod + def from_dict(cls, action_dict): + return ScpTransferAction(path=action_dict["path"], + url=action_dict["url"], + ssh_user=action_dict["ssh_user"], + ssh_host=action_dict["ssh_host"], + ssh_port=action_dict["ssh_port"], + ssh_key=action_dict["ssh_key"]) + + def write_to_path(self, path): + key_file = self.serialize_ssh_key() + scp_get_file(self.path, path, self.ssh_user, self.ssh_host, + self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + def write_from_path(self, pulsar_path): + key_file = self.serialize_ssh_key() + scp_post_file(pulsar_path, self.path, self.ssh_user, self.ssh_host, + self.ssh_port, key_file) + self.cleanup_ssh_key(key_file) + + class MessageAction(object): """ Sort of pseudo action describing "files" store in memory and transferred via message (HTTP, Python-call, MQ, etc...) @@ -408,7 +508,7 @@ open(path, "w").write(self.contents) -DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, RemoteTransferAction, MessageAction] +DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, RemoteTransferAction, MessageAction, RsyncTransferAction, ScpTransferAction] def from_dict(action_dict): @@ -517,10 +617,10 @@ def mappers_from_dicts(mapper_def_list): - return map(lambda m: __mappper_from_dict(m), mapper_def_list) + return map(lambda m: _mappper_from_dict(m), mapper_def_list) -def __mappper_from_dict(mapper_dict): +def _mappper_from_dict(mapper_dict): map_type = mapper_dict.get('match_type', DEFAULT_PATH_MAPPER_TYPE) return MAPPER_CLASS_DICT[map_type](mapper_dict) @@ -554,14 +654,16 @@ CopyAction, RemoteCopyAction, RemoteTransferAction, + RsyncTransferAction, + ScpTransferAction, ] actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES]) __all__ = [ - FileActionMapper, - path_type, - from_dict, - MessageAction, - RemoteTransferAction, # For testing + 'FileActionMapper', + 'path_type', + 'from_dict', + 'MessageAction', + 'RemoteTransferAction', # For testing ] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/amqp_exchange.py --- a/lib/pulsar/client/amqp_exchange.py +++ b/lib/pulsar/client/amqp_exchange.py @@ -1,13 +1,16 @@ +import copy +import uuid +import socket +import logging +import threading +from time import sleep + try: import kombu from kombu import pools except ImportError: kombu = None -import socket -import logging -import threading -from time import sleep log = logging.getLogger(__name__) @@ -101,24 +104,45 @@ log.debug('AMQP heartbeat thread exiting') def publish(self, name, payload): + # Consider optionally disabling if throughput becomes main concern. + transaction_uuid = uuid.uuid1() key = self.__queue_name(name) - log.debug("Begin publishing to key %s" % key) + publish_log_prefix = self.__publish_log_prefex(transaction_uuid) + log.debug("%sBegin publishing to key %s", publish_log_prefix, key) with self.connection(self.__url) as connection: with pools.producers[connection].acquire() as producer: - log.debug("Have producer for publishing to key %s" % key) + log.debug("%sHave producer for publishing to key %s", publish_log_prefix, key) + publish_kwds = self.__prepare_publish_kwds(publish_log_prefix) producer.publish( payload, serializer='json', exchange=self.__exchange, declare=[self.__exchange], routing_key=key, - **self.__publish_kwds + **publish_kwds ) - log.debug("Published to key %s" % key) + log.debug("%sPublished to key %s", publish_log_prefix, key) - def __publish_errback(self, exc, interval): - log.error("Connection error while publishing: %r", exc, exc_info=1) - log.info("Retrying in %s seconds", interval) + def __prepare_publish_kwds(self, publish_log_prefix): + if "retry_policy" in self.__publish_kwds: + publish_kwds = copy.deepcopy(self.__publish_kwds) + + def errback(exc, interval): + return self.__publish_errback(exc, interval, publish_log_prefix) + publish_kwds["retry_policy"]["errback"] = errback + else: + publish_kwds = self.__publish_kwds + return publish_kwds + + def __publish_errback(self, exc, interval, publish_log_prefix=""): + log.error("%sConnection error while publishing: %r", publish_log_prefix, exc, exc_info=1) + log.info("%sRetrying in %s seconds", publish_log_prefix, interval) + + def __publish_log_prefex(self, transaction_uuid=None): + prefix = "" + if transaction_uuid: + prefix = "[publish:%s] " % str(transaction_uuid) + return prefix def connection(self, connection_string, **kwargs): if "ssl" not in kwargs: diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/client.py --- a/lib/pulsar/client/client.py +++ b/lib/pulsar/client/client.py @@ -41,6 +41,12 @@ ) else: job_directory = None + + if "ssh_key" in (destination_params or {}): + self.ssh_key = destination_params["ssh_key"] + else: + self.ssh_key = None + self.env = destination_params.get("env", []) self.files_endpoint = destination_params.get("files_endpoint", None) self.job_directory = job_directory @@ -271,6 +277,7 @@ launch_params['env'] = env if remote_staging: launch_params['remote_staging'] = remote_staging + launch_params['remote_staging']['ssh_key'] = self.ssh_key if job_config and self.setup_handler.local: # Setup not yet called, job properties were inferred from # destination arguments. Hence, must have Pulsar setup job diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/manager.py --- a/lib/pulsar/client/manager.py +++ b/lib/pulsar/client/manager.py @@ -220,4 +220,8 @@ int_val = int(val) return int_val -__all__ = [ClientManager, ObjectStoreClientManager, HttpPulsarInterface] +__all__ = [ + 'ClientManager', + 'ObjectStoreClientManager', + 'HttpPulsarInterface' +] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/path_mapper.py --- a/lib/pulsar/client/path_mapper.py +++ b/lib/pulsar/client/path_mapper.py @@ -95,4 +95,4 @@ message = "PathMapper cannot handle path type %s" % dataset_path_type raise Exception(message) -__all__ = [PathMapper] +__all__ = ['PathMapper'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/setup_handler.py --- a/lib/pulsar/client/setup_handler.py +++ b/lib/pulsar/client/setup_handler.py @@ -82,6 +82,7 @@ unstructured_files_directory = job_directory.unstructured_files_directory() sep = system_properties.get("sep", os.sep) job_config = { + "job_directory": job_directory.path, "working_directory": working_directory, "outputs_directory": outputs_directory, "configs_directory": configs_directory, @@ -100,4 +101,4 @@ return job_config -__all__ = [build_job_config, build] +__all__ = ['build_job_config', 'build'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/staging/down.py --- a/lib/pulsar/client/staging/down.py +++ b/lib/pulsar/client/staging/down.py @@ -152,4 +152,4 @@ except Exception: log.warn("Failed to cleanup remote Pulsar job") -__all__ = [finish_job] +__all__ = ['finish_job'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/staging/up.py --- a/lib/pulsar/client/staging/up.py +++ b/lib/pulsar/client/staging/up.py @@ -349,14 +349,18 @@ local_action = action.staging_action_local if local_action: response = self.client.put_file(path, type, name=name, contents=contents) - get_path = lambda: response['path'] + + def get_path(): + return response['path'] else: job_directory = self.client.job_directory assert job_directory, "job directory required for action %s" % action if not name: name = basename(path) self.__add_remote_staging_input(action, name, type) - get_path = lambda: job_directory.calculate_path(name, type) + + def get_path(): + return job_directory.calculate_path(name, type) register = self.rewrite_paths or type == 'tool' # Even if inputs not rewritten, tool must be. if register: self.register_rewrite(path, get_path(), type, force=True) @@ -417,4 +421,4 @@ input.close() -__all__ = [submit_job] +__all__ = ['submit_job'] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/__init__.py --- a/lib/pulsar/client/transport/__init__.py +++ b/lib/pulsar/client/transport/__init__.py @@ -2,26 +2,8 @@ from .curl import PycurlTransport import os - -def get_transport(transport_type=None, os_module=os): - transport_type = __get_transport_type(transport_type, os_module) - if transport_type == 'urllib': - transport = Urllib2Transport() - else: - transport = PycurlTransport() - return transport - - -def __get_transport_type(transport_type, os_module): - if not transport_type: - use_curl = os_module.getenv('PULSAR_CURL_TRANSPORT', "0") - # If PULSAR_CURL_TRANSPORT is unset or set to 0, use default, - # else use curl. - if use_curl.isdigit() and not int(use_curl): - transport_type = 'urllib' - else: - transport_type = 'curl' - return transport_type +from .ssh import rsync_get_file, scp_get_file +from .ssh import rsync_post_file, scp_post_file from .curl import curl_available from .requests import requests_multipart_post_available @@ -35,4 +17,33 @@ from .poster import get_file from .poster import post_file -__all__ = [get_transport, get_file, post_file] + +def get_transport(transport_type=None, os_module=os): + transport_type = _get_transport_type(transport_type, os_module) + if transport_type == 'urllib': + transport = Urllib2Transport() + else: + transport = PycurlTransport() + return transport + + +def _get_transport_type(transport_type, os_module): + if not transport_type: + use_curl = os_module.getenv('PULSAR_CURL_TRANSPORT', "0") + # If PULSAR_CURL_TRANSPORT is unset or set to 0, use default, + # else use curl. + if use_curl.isdigit() and not int(use_curl): + transport_type = 'urllib' + else: + transport_type = 'curl' + return transport_type + +__all__ = [ + 'get_transport', + 'get_file', + 'post_file', + 'rsync_get_file', + 'rsync_post_file', + 'scp_get_file', + 'scp_post_file' +] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/curl.py --- a/lib/pulsar/client/transport/curl.py +++ b/lib/pulsar/client/transport/curl.py @@ -2,32 +2,37 @@ from cStringIO import StringIO except ImportError: from io import StringIO -curl_available = True + try: - from pycurl import Curl + from pycurl import Curl, HTTP_CODE + curl_available = True except ImportError: curl_available = False -from os.path import getsize + +import os.path PYCURL_UNAVAILABLE_MESSAGE = \ "You are attempting to use the Pycurl version of the Pulsar client but pycurl is unavailable." +NO_SUCH_FILE_MESSAGE = "Attempt to post file %s to URL %s, but file does not exist." +POST_FAILED_MESSAGE = "Failed to post_file properly for url %s, remote server returned status code of %s." +GET_FAILED_MESSAGE = "Failed to get_file properly for url %s, remote server returned status code of %s." + class PycurlTransport(object): def execute(self, url, method=None, data=None, input_path=None, output_path=None): buf = _open_output(output_path) try: - c = _new_curl_object() - c.setopt(c.URL, url.encode('ascii')) + c = _new_curl_object_for_url(url) c.setopt(c.WRITEFUNCTION, buf.write) if method: c.setopt(c.CUSTOMREQUEST, method) if input_path: c.setopt(c.UPLOAD, 1) c.setopt(c.READFUNCTION, open(input_path, 'rb').read) - filesize = getsize(input_path) + filesize = os.path.getsize(input_path) c.setopt(c.INFILESIZE, filesize) if data: c.setopt(c.POST, 1) @@ -42,19 +47,30 @@ def post_file(url, path): - c = _new_curl_object() - c.setopt(c.URL, url.encode('ascii')) + if not os.path.exists(path): + # pycurl doesn't always produce a great exception for this, + # wrap it in a better one. + message = NO_SUCH_FILE_MESSAGE % (path, url) + raise Exception(message) + c = _new_curl_object_for_url(url) c.setopt(c.HTTPPOST, [("file", (c.FORM_FILE, path.encode('ascii')))]) c.perform() + status_code = c.getinfo(HTTP_CODE) + if int(status_code) != 200: + message = POST_FAILED_MESSAGE % (url, status_code) + raise Exception(message) def get_file(url, path): buf = _open_output(path) try: - c = _new_curl_object() - c.setopt(c.URL, url.encode('ascii')) + c = _new_curl_object_for_url(url) c.setopt(c.WRITEFUNCTION, buf.write) c.perform() + status_code = c.getinfo(HTTP_CODE) + if int(status_code) != 200: + message = GET_FAILED_MESSAGE % (url, status_code) + raise Exception(message) finally: buf.close() @@ -63,10 +79,20 @@ return open(output_path, 'wb') if output_path else StringIO() +def _new_curl_object_for_url(url): + c = _new_curl_object() + c.setopt(c.URL, url.encode('ascii')) + return c + + def _new_curl_object(): try: return Curl() except NameError: raise ImportError(PYCURL_UNAVAILABLE_MESSAGE) -___all__ = [PycurlTransport, post_file, get_file] +__all__ = [ + 'PycurlTransport', + 'post_file', + 'get_file' +] diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/poster.py --- a/lib/pulsar/client/transport/poster.py +++ b/lib/pulsar/client/transport/poster.py @@ -1,4 +1,7 @@ from __future__ import absolute_import + +import logging + try: from urllib2 import urlopen except ImportError: @@ -20,7 +23,6 @@ POSTER_UNAVAILABLE_MESSAGE = "Pulsar configured to use poster module - but it is unavailable. Please install poster." -import logging log = logging.getLogger(__name__) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/requests.py --- a/lib/pulsar/client/transport/requests.py +++ b/lib/pulsar/client/transport/requests.py @@ -1,4 +1,7 @@ from __future__ import absolute_import + +import logging + try: from galaxy import eggs eggs.require("requests") @@ -9,18 +12,18 @@ import requests except ImportError: requests = None -requests_multipart_post_available = False + try: import requests_toolbelt requests_multipart_post_available = True except ImportError: + requests_multipart_post_available = False requests_toolbelt = None REQUESTS_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests module - but it is unavailable. Please install requests." REQUESTS_TOOLBELT_UNAVAILABLE_MESSAGE = "Pulsar configured to use requests_toolbelt module - but it is unavailable. Please install requests_toolbelt." -import logging log = logging.getLogger(__name__) diff -r 4e30957ab1217c50dbaed105d00b0a5afbea858e -r e8c37fd942090370354baee82a6baf9fdc0ac0ce lib/pulsar/client/transport/ssh.py --- /dev/null +++ b/lib/pulsar/client/transport/ssh.py @@ -0,0 +1,64 @@ +import subprocess +SSH_OPTIONS = ('-o', 'StrictHostKeyChecking=no', '-o', 'PreferredAuthentications=publickey', '-o', 'PubkeyAuthentication=yes') + + +def rsync_get_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'rsync', + '-e', + 'ssh -i %s -p %s %s' % (key, port, ' '.join(SSH_OPTIONS)), + '%s@%s:%s' % (user, host, uri_from), + uri_to, + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("Rsync exited with code %s" % exit_code) + + +def rsync_post_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'rsync', + '-e', + 'ssh -i %s -p %s %s' % (key, port, ' '.join(SSH_OPTIONS)), + uri_from, + '%s@%s:%s' % (user, host, uri_to), + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("Rsync exited with code %s" % exit_code) + + +def scp_get_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'scp', + '-P', str(port), + '-i', key, + SSH_OPTIONS, + '%s@%s:%s' % (user, host, uri_from), + uri_to, + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("scp exited with code %s" % exit_code) + + +def scp_post_file(uri_from, uri_to, user, host, port, key): + cmd = [ + 'scp', + '-P', str(port), + '-i', key, + SSH_OPTIONS, + uri_from, + '%s@%s:%s' % (user, host, uri_to), + ] + exit_code = subprocess.check_call(cmd) + if exit_code != 0: + raise Exception("scp exited with code %s" % exit_code) + + +___all__ = [ + 'rsync_post_file', + 'rsync_get_file', + 'scp_post_file', + 'scp_get_file' +] https://bitbucket.org/galaxy/galaxy-central/commits/e630e74d5571/ Changeset: e630e74d5571 User: guerler Date: 2015-02-27 06:30:48+00:00 Summary: ToolForm: Show initial validation errors on re-run Affected #: 3 files diff -r e8c37fd942090370354baee82a6baf9fdc0ac0ce -r e630e74d5571462111045b7db9b021427c7ab6ef client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r e8c37fd942090370354baee82a6baf9fdc0ac0ce -r e630e74d5571462111045b7db9b021427c7ab6ef static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r e8c37fd942090370354baee82a6baf9fdc0ac0ce -r e630e74d5571462111045b7db9b021427c7ab6ef static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/eb6b7fb7a91c/ Changeset: eb6b7fb7a91c User: guerler Date: 2015-02-27 06:35:38+00:00 Summary: ToolForm/Collections: Re-introduce parameter expansion Affected #: 4 files diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2366,7 +2366,7 @@ else: value, error = check_param(trans, input, default_value, context) except Exception, err: - log.error('Checking parameter failed. %s', str(err)) + log.error('Checking parameter %s failed. %s', input.name, str(err)) pass return [value, error] @@ -2482,6 +2482,11 @@ else: state[k] = jsonify(state[k]) + # expand incoming parameters (parameters might trigger multiple tool executions, + # here we select the first execution only in order to resolve dynamic parameters) + expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) + params.__dict__ = expanded_incomings[ 0 ] + # do param translation here, used by datasource tools if self.input_translator: self.input_translator.translate( params ) diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r e630e74d5571462111045b7db9b021427c7ab6ef -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}}u.update(s);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var h=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(k);f.deferred.done(i)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/46feb8f33ba9/ Changeset: 46feb8f33ba9 User: guerler Date: 2015-02-27 06:49:53+00:00 Summary: Parameters: Prevent uncaught exception on unavailable datasets in column validation Affected #: 1 file diff -r eb6b7fb7a91cc4e344bcf23ba23ff14807e11ce5 -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1340,6 +1340,10 @@ datasets = util.listify( referent ) for dataset in datasets: if dataset: + # Check if metadata is available + if not hasattr(dataset, 'metadata'): + return True + # Check if the dataset does not have the expected metadata for columns if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready https://bitbucket.org/galaxy/galaxy-central/commits/448272e06e42/ Changeset: 448272e06e42 User: guerler Date: 2015-02-27 06:57:39+00:00 Summary: ToolForm/Ui: Limit selection to available options Affected #: 3 files diff -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 -r 448272e06e42db47dec46a3a0dae58f9ca265160 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 -r 448272e06e42db47dec46a3a0dae58f9ca265160 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 46feb8f33ba97dc193fb9cecd9025c18803e2307 -r 448272e06e42db47dec46a3a0dae58f9ca265160 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/94298235c5c4/ Changeset: 94298235c5c4 User: guerler Date: 2015-02-27 06:59:43+00:00 Summary: Parameters: Fix deleted datasets validation message Affected #: 1 file diff -r 448272e06e42db47dec46a3a0dae58f9ca265160 -r 94298235c5c4df5f53bbfc5f7bb742837781001c lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2021,7 +2021,7 @@ for v in values: if v: if v.deleted: - raise ValueError( "The previously selected dataset has been previously deleted" ) + raise ValueError( "The previously selected dataset has been deleted." ) if hasattr( v, "dataset" ) and v.dataset.state in [ galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: raise ValueError( "The previously selected dataset has entered an unusable state" ) if not self.multiple: https://bitbucket.org/galaxy/galaxy-central/commits/81c09bf641da/ Changeset: 81c09bf641da User: guerler Date: 2015-02-27 09:26:15+00:00 Summary: Parameters: Set hidden attribute for hidden dataset parameter Affected #: 1 file diff -r 94298235c5c4df5f53bbfc5f7bb742837781001c -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2425,6 +2425,7 @@ DataToolParameter.__init__( self, tool, elem ) self.value = "None" self.type = "hidden_data" + self.hidden = True def get_initial_value( self, trans, context, history=None ): return None https://bitbucket.org/galaxy/galaxy-central/commits/b11c4470b151/ Changeset: b11c4470b151 User: guerler Date: 2015-02-27 09:36:20+00:00 Summary: ToolForm/Ui: Restrict available option requirement to single select fields Affected #: 3 files diff -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 -r b11c4470b151100c14f1a2abfb8047ac16b26f30 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 -r b11c4470b151100c14f1a2abfb8047ac16b26f30 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r 81c09bf641da8461655ded2b8638fe2c203aa0b1 -r b11c4470b151100c14f1a2abfb8047ac16b26f30 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)||this.options.multiple){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/6bd6c350296c/ Changeset: 6bd6c350296c User: carlfeberhard Date: 2015-02-27 15:03:47+00:00 Summary: Fix display_structure by using serializer; fix structure by removing extra decode_id Affected #: 2 files diff -r b11c4470b151100c14f1a2abfb8047ac16b26f30 -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -543,8 +543,10 @@ def structure( self, trans, id=None, **kwargs ): """ """ - id = self.decode_id( id ) if id else trans.history.id - history_to_view = self.history_manager.get_accessible( trans, id, trans.user ) + unencoded_history_id = trans.history.id + if id: + unencoded_history_id = self.decode_id( id ) + history_to_view = self.history_manager.get_accessible( trans, unencoded_history_id, trans.user ) history_data = self.history_manager._get_history_data( trans, history_to_view ) history_dictionary = history_data[ 'history' ] @@ -552,7 +554,7 @@ jobs = ( trans.sa_session.query( trans.app.model.Job ) .filter( trans.app.model.Job.user == trans.user ) - .filter( trans.app.model.Job.history_id == self.decode_id( id ) ) ).all() + .filter( trans.app.model.Job.history_id == unencoded_history_id ) ).all() jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs ) tools = {} diff -r b11c4470b151100c14f1a2abfb8047ac16b26f30 -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -128,13 +128,15 @@ ## ---------------------------------------------------------------------------- <%def name="javascripts()"><% + from galaxy.managers import hdas + hda_serializer = hdas.HDASerializer( trans.app ) self.js_app = 'display-structured' controller = trans.webapp.controllers[ 'history' ] hda_dicts = [] id_hda_dict_map = {} for hda in history.active_datasets: - hda_dict = controller.get_hda_dict( trans, hda ) + hda_dict = hda_serializer.serialize_to_view( trans, hda, 'detailed' ) id_hda_dict_map[ hda_dict[ 'id' ] ] = hda_dict hda_dicts.append( hda_dict ) %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] 7c39ef: Update Test and Main, update datatypes_conf.xml fo...
by GitHub 26 Feb '15

26 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7c39efb81374ba5ff8c37d2e6069cb04b69518fd https://github.com/galaxyproject/usegalaxy-playbook/commit/7c39efb81374ba5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-26 (Thu, 26 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/group_vars/all.yml M stage/group_vars/all.yml M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update Test and Main, update datatypes_conf.xml for both, fetch mutable configs.

1 0

commit/galaxy-central: 14 new changesets
by commits-noreply＠bitbucket.org 26 Feb '15

26 Feb '15

14 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3fb019e8e64/ Changeset: a3fb019e8e64 Branch: release_15.03 User: guerler Date: 2015-02-23 22:56:38+00:00 Summary: Allow text selection in tool form Affected #: 2 files diff -r 9dcc6d00e76eae06705d79ec7d276202494ad545 -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1410,7 +1410,7 @@ .upload-header .header-selection{width:200px;min-width:200px;font-size:11px;padding-right:10px} .upload-header .select2-choice{max-height:20px;line-height:18px;background:transparent;text-align:center;font-weight:normal}.upload-header .select2-choice .select2-arrow b{background-position:0 -3px} .upload-top{height:5%;text-align:center}.upload-top .upload-info{margin-top:0px;font-weight:normal;text-align:center} -.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} +.no-highlight,.ui-button-icon{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} .no-padding{padding:0px !important} .ui-margin-top{padding-top:5px !important} .ui-margin-bottom{margin-bottom:5px !important} @@ -1434,7 +1434,7 @@ .ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-table-form-info{clear:both !important} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} -.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{border:solid #d6b161 1px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-limited .portlet-header,.ui-portlet-narrow .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-limited .portlet-header .portlet-title,.ui-portlet-narrow .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-limited .portlet-header .portlet-title .portlet-title-text,.ui-portlet-narrow .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:22px} +.ui-portlet,.ui-portlet-repeat,.ui-portlet-limited,.ui-portlet-section,.ui-portlet-narrow{border:solid #d6b161 1px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-limited .portlet-header,.ui-portlet-narrow .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-limited .portlet-header .portlet-title,.ui-portlet-narrow .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-limited .portlet-header .portlet-title .portlet-title-text,.ui-portlet-narrow .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:22px} .ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-limited .portlet-header .portlet-title .icon,.ui-portlet-narrow .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} .ui-portlet .portlet-header .portlet-operations .ui-button-icon,.ui-portlet-limited .portlet-header .portlet-operations .ui-button-icon,.ui-portlet-narrow .portlet-header .portlet-operations .ui-button-icon{margin-left:5px} .ui-portlet .portlet-content,.ui-portlet-limited .portlet-content,.ui-portlet-narrow .portlet-content{height:inherit;padding-left:10px;padding-right:10px;clear:both}.ui-portlet .portlet-content .content,.ui-portlet-limited .portlet-content .content,.ui-portlet-narrow .portlet-content .content{padding:0px;height:100%;width:100%} diff -r 9dcc6d00e76eae06705d79ec7d276202494ad545 -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -182,7 +182,6 @@ // portlets .ui-portlet { - &:extend(.no-highlight); border: solid @form-border 1px; border-radius: @border-radius-base; https://bitbucket.org/galaxy/galaxy-central/commits/aaa07e311e79/ Changeset: aaa07e311e79 Branch: release_15.03 User: guerler Date: 2015-02-23 23:04:02+00:00 Summary: Fix job ids in success message Affected #: 3 files diff -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 -r aaa07e311e7963270fd138688b3773333c0472a1 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -10,17 +10,17 @@ '</div>' + '</div>'; }, - + success: function(response) { // check if (!response.jobs || !response.jobs.length) { console.debug('tools-template::success() - Failed jobs.'); return; } - + // number of jobs var njobs = response.jobs.length; - + // job count info text var njobs_text = ''; if (njobs == 1) { @@ -28,20 +28,20 @@ } else { njobs_text = njobs + ' jobs have'; } - + // create template string var tmpl = '<div class="donemessagelarge">' + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; for (var i in response.outputs) { - tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + tmpl += '<p style="padding: 10px 20px;"><b>' + response.outputs[i].hid + ': ' + response.outputs[i].name + '</b></p>'; } tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + '</div>'; - + // return success message element return tmpl; }, - + error: function(job_def) { return '<div>' + '<p>' + @@ -52,14 +52,14 @@ '</textarea>' + '</div>'; }, - + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; }, - + requirements: function(options) { var requirements_message = 'This tool requires '; for (var i in options.requirements) { diff -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 -r aaa07e311e7963270fd138688b3773333c0472a1 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -10,17 +10,17 @@ '</div>' + '</div>'; }, - + success: function(response) { // check if (!response.jobs || !response.jobs.length) { console.debug('tools-template::success() - Failed jobs.'); return; } - + // number of jobs var njobs = response.jobs.length; - + // job count info text var njobs_text = ''; if (njobs == 1) { @@ -28,20 +28,20 @@ } else { njobs_text = njobs + ' jobs have'; } - + // create template string var tmpl = '<div class="donemessagelarge">' + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; for (var i in response.outputs) { - tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + tmpl += '<p style="padding: 10px 20px;"><b>' + response.outputs[i].hid + ': ' + response.outputs[i].name + '</b></p>'; } tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + '</div>'; - + // return success message element return tmpl; }, - + error: function(job_def) { return '<div>' + '<p>' + @@ -52,14 +52,14 @@ '</textarea>' + '</div>'; }, - + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; }, - + requirements: function(options) { var requirements_message = 'This tool requires '; for (var i in options.requirements) { diff -r a3fb019e8e641a01f2af2d7cb23a715b24d4c511 -r aaa07e311e7963270fd138688b3773333c0472a1 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/a67681113778/ Changeset: a67681113778 Branch: release_15.03 User: guerler Date: 2015-02-24 23:37:52+00:00 Summary: Show error message on server error Affected #: 3 files diff -r aaa07e311e7963270fd138688b3773333c0472a1 -r a67681113778d17a81b941c956b1df1e4355060a client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r aaa07e311e7963270fd138688b3773333c0472a1 -r a67681113778d17a81b941c956b1df1e4355060a static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r aaa07e311e7963270fd138688b3773333c0472a1 -r a67681113778d17a81b941c956b1df1e4355060a static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){return this.error(c)}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/27c9c0c6b072/ Changeset: 27c9c0c6b072 Branch: release_15.03 User: guerler Date: 2015-02-25 00:08:36+00:00 Summary: Charts: Rebuild and update charts Affected #: 4 files diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 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) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // 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;$.each(this.options.buttons,function(e,r){var 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i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert 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no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e)},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function i(t,r,s){s=s||[];for(o in r){var u=r[o],a=u.options.length>0,f=s.slice(0),l=$("<div/>");if(a){var c=e.uuid(),h=$('<span id="button-'+c+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),p=$('<div id="subgroup-'+c+'" style="display: none; margin-left: 25px;"/>');f.push(c);var d=$("<div/>");d.append(h),d.append(n._templateOption({label:u.name,value:u.value})),l.append(d),i(p,u.options,f),l.append(p)}else l.append(n._templateOption({label:u.name,value:u.value})),n.header_index[u.value]=f;t.append(l)}}var n=this;this.header_index={},this.header_list=[];var s=$("<div/>");i(s,t);for(var o in this.header_index)this.header_list=_.uniq(this.header_list.concat(this.header_index[o]));for(var o in this.header_list)r(s,this.header_list[o]);return s},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<label>"+e.info+"</label>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. 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Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return 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i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata 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"'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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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 n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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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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arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var A=d3.select(this),_=this,D=(a||parseInt(A.style("width"))||960)-u.left-u.right,P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom;M.update=function(){A.call(M)},M.container=this,S.disabled=y.map(function(e){return!!e.disabled});if(!x){var H;x={};for(H in S)S[H]instanceof Array?x[H]=S[H].slice(0):x[H]=S[H]}if(!y||!y.length||!y.filter(function(e){return e.values.length}).length){var B=A.selectAll(".nv-noData").data([T]);return B.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),B.attr("x",u.left+D/2).attr("y",u.top+P/2).text(function(e){return e}),M}A.selectAll(".nv-noData").remove(),b=t.xScale(),w=t.yScale();var j=A.selectAll("g.nv-wrap.nv-stackedAreaChart").data([y]),F=j.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedAreaChart").append("g"),I=j.select("g");F.append("rect").style("opacity",0),F.append("g").attr("class","nv-x nv-axis"),F.append("g").attr("class","nv-y 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U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right"},$title:null,$content:null,$buttons:null,$operations:null,$header:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find(".content"),this.$title=this.$el.find(".portlet-title-text"),this.$header=this.$el.find(".portlet-header");var n=this.$el.find(".portlet-content");this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find(".buttons");if(this.options.buttons){var 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=$(this.el).find(".portlet-operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(e){this.$content.append(e)},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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div class="portlet-header"><div class="portlet-operations" style="float: '+e.operations_flt+';"></div>'+'<div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div class="portlet-content">',e.placement=="top"&&(t+='<div class="buttons"></div>'),t+='<div class="content"></div>',e.placement=="bottom"&&(t+='<div class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&(e===null&&(e="__null__"),this.$select.val(e),this.$select.select2&&this.$select.select2("val",e)),this._getValue()},first:function(){var e=this.$select.find("option").first();return e.length>0?e.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2()),this.value(t),this._getValue()===null&&this.value(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_getValue:function(){var t=this.$select.val();return e.validate(t)?t:null},_refresh:function(){var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.empty(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'" class="'+e.cls+'">'+'<select id="'+e.id+'_select" class="select"/>'+'<div class="button">'+'<i class="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.options.value!==undefined&&this.value(this.options.value),this.$text.on("change",function(){n.value($(this).val())});var r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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","nvd3_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]==="__undefined__"){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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var 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 n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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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 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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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:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -189,7 +189,7 @@ if (valid) { // add to selection columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'label' : 'Column: ' + (parseInt(key) + 1), 'value' : key }); } diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -115,7 +115,7 @@ }); // append portlet - this.portlet.append(this.message.$el); + this.portlet.append(this.message.$el.addClass('ui-margin-top')); this.portlet.append(this.viewport_view.$el); // set element diff -r a67681113778d17a81b941c956b1df1e4355060a -r 27c9c0c6b072e138c59323a163757f123fa87445 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -12,6 +12,7 @@ ## install shared libraries ${h.js( 'libs/jquery/jquery', + 'libs/jquery/select2', 'libs/bootstrap', 'libs/require', 'libs/underscore', https://bitbucket.org/galaxy/galaxy-central/commits/03993b5418ab/ Changeset: 03993b5418ab Branch: release_15.03 User: guerler Date: 2015-02-25 00:41:30+00:00 Summary: Charts: Fix missing data message Affected #: 2 files diff -r 27c9c0c6b072e138c59323a163757f123fa87445 -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right"},$title:null,$content:null,$buttons:null,$operations:null,$header:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find(".content"),this.$title=this.$el.find(".portlet-title-text"),this.$header=this.$el.find(".portlet-header");var n=this.$el.find(".portlet-content");this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find(".buttons");if(this.options.buttons){var 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=$(this.el).find(".portlet-operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(e){this.$content.append(e)},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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div class="portlet-header"><div class="portlet-operations" style="float: '+e.operations_flt+';"></div>'+'<div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div class="portlet-content">',e.placement=="top"&&(t+='<div class="buttons"></div>'),t+='<div class="content"></div>',e.placement=="bottom"&&(t+='<div class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&(e===null&&(e="__null__"),this.$select.val(e),this.$select.select2&&this.$select.select2("val",e)),this._getValue()},first:function(){var e=this.$select.find("option").first();return e.length>0?e.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2()),this.value(t),this._getValue()===null&&this.value(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_getValue:function(){var t=this.$select.val();return e.validate(t)?t:null},_refresh:function(){var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.empty(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'" class="'+e.cls+'">'+'<select id="'+e.id+'_select" class="select"/>'+'<div class="button">'+'<i class="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.options.value!==undefined&&this.value(this.options.value),this.$text.on("change",function(){n.value($(this).val())});var r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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","nvd3_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]==="__undefined__"){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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var 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 n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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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 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(e){this.$content.append(e)},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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div class="portlet-header"><div class="portlet-operations" style="float: '+e.operations_flt+';"></div>'+'<div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div class="portlet-content">',e.placement=="top"&&(t+='<div class="buttons"></div>'),t+='<div class="content"></div>',e.placement=="bottom"&&(t+='<div class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&(e===null&&(e="__null__"),this.$select.val(e),this.$select.select2&&this.$select.select2("val",e)),this._getValue()},first:function(){var e=this.$select.find("option").first();return e.length>0?e.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2()),this.value(t),this._getValue()===null&&this.value(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_getValue:function(){var t=this.$select.val();return e.validate(t)?t:null},_refresh:function(){var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.empty(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'" class="'+e.cls+'">'+'<select id="'+e.id+'_select" class="select"/>'+'<div class="button">'+'<i class="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.options.value!==undefined&&this.value(this.options.value),this.$text.on("change",function(){n.value($(this).val())});var r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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","nvd3_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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{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:"0"}]},separator_y:{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 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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arguments.length?(o=e,t.x(e),m):o},m.y=function(e){return arguments.length?(u=e,t.y(e),m):u},m.clipEdge=function(e){return arguments.length?(l=e,m):l},m.color=function(n){return arguments.length?(s=e.utils.getColor(n),t.color(s),m):s},m.interpolate=function(e){return arguments.length?(p=e,m):p},m.defined=function(e){return arguments.length?(a=e,m):a},m.isArea=function(e){return arguments.length?(f=d3.functor(e),m):f},m},e.models.lineChart=function(){function N(m){return m.each(function(m){var x=d3.select(this),C=this,k=(a||parseInt(x.style("width"))||960)-o.left-o.right,L=(f||parseInt(x.style("height"))||400)-o.top-o.bottom;N.update=function(){x.call(N)},N.container=this,b.disabled=m.map(function(e){return!!e.disabled});if(!w){var A;w={};for(A in b)b[A]instanceof Array?w[A]=b[A].slice(0):w[A]=b[A]}if(!m||!m.length||!m.filter(function(e){return e.values.length}).length){var O=x.selectAll(".nv-noData").data([E]);return O.enter().append("text").attr("class","nvd3 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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 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return arguments.length?(l=e,C):l},C.showLegend=function(e){return arguments.length?(c=e,C):c},C.showXAxis=function(e){return arguments.length?(h=e,C):h},C.showYAxis=function(e){return arguments.length?(p=e,C):p},C.tooltip=function(e){return arguments.length?(m=e,C):m},C.tooltips=function(e){return arguments.length?(v=e,C):v},C.tooltipContent=function(e){return arguments.length?(m=e,C):m},C.state=function(e){return arguments.length?(b=e,C):b},C.defaultState=function(e){return arguments.length?(w=e,C):w},C.noData=function(e){return arguments.length?(E=e,C):E},C.transitionDuration=function(e){return arguments.length?(T=e,C):T},C},e.models.multiChart=function(){function C(e){return e.each(function(e){var u=d3.select(this),f=this;C.update=function(){u.call(C)},C.container=this;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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small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},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",keywords:"small medium large",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_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},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",zoomable:!0,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",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/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,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/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}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),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/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){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:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r 27c9c0c6b072e138c59323a163757f123fa87445 -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -295,7 +295,7 @@ return; } for (var key in chart_def.columns) { - if (group.attributes[key] === '__undefined__') { + if (group.attributes[key] === '__null__') { self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); self.tabs.show(group.id); valid = false; https://bitbucket.org/galaxy/galaxy-central/commits/462142655af2/ Changeset: 462142655af2 Branch: release_15.03 User: guerler Date: 2015-02-25 01:31:43+00:00 Summary: ToolForm: Enable collection for multiple data parameter Affected #: 3 files diff -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 -r 462142655af2a768ca01afac78b67ee8eb4f3b79 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 -r 462142655af2a768ca01afac78b67ee8eb4f3b79 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 03993b5418ab8da2284125cd50884c4d6c1efaf3 -r 462142655af2a768ca01afac78b67ee8eb4f3b79 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/81a68eaf2ebd/ Changeset: 81a68eaf2ebd Branch: release_15.03 User: dannon Date: 2015-02-25 14:14:59+00:00 Summary: Fix returning encoded None library folder parent ids in library_contents API; thanks to nsoranzo Affected #: 1 file diff -r 462142655af2a768ca01afac78b67ee8eb4f3b79 -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -128,7 +128,8 @@ content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True ) rval = content.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) rval[ 'id' ] = 'F' + str( rval[ 'id' ] ) - rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) ) + if rval[ 'parent_id' ] is not None: # This can happen for root folders. + rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) ) rval[ 'parent_library_id' ] = trans.security.encode_id( rval[ 'parent_library_id' ] ) else: content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True ) https://bitbucket.org/galaxy/galaxy-central/commits/79bf433cb5fe/ Changeset: 79bf433cb5fe Branch: release_15.03 User: guerler Date: 2015-02-26 06:05:27+00:00 Summary: Collections: Enable the batch mode execution for nested collections (without adding a new button) Affected #: 4 files diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2364,24 +2364,6 @@ return True # TODO def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): - d = super( DataCollectionToolParameter, self ).to_dict( trans ) - if other_values is None: - # No need to produce lists of datasets for history. - return d - - dataset_matcher = DatasetMatcher( trans, self, None, other_values ) - history = trans.history - - for hdca in self.match_collections( trans, history, dataset_matcher ): - pass - - for hdca in self.match_multirun_collections( trans, history, dataset_matcher ): - subcollection_type = self._history_query( trans ).collection_type_description.collection_type - pass - - return d - - def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): # create dictionary and fill default parameters d = super( DataCollectionToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions @@ -2414,7 +2396,8 @@ 'id_uncoded' : hdca.id, 'hid' : hdca.hid, 'name' : hdca.name, - 'src' : 'hdca' + 'src' : 'hdca', + 'map_over_type' : subcollection_type }) # sort both lists diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 81a68eaf2ebd70feb52c961367ee907e32cd8a6f -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/7cb17705d749/ Changeset: 7cb17705d749 Branch: release_15.03 User: guerler Date: 2015-02-26 16:12:45+00:00 Summary: Remove collection expansion Affected #: 1 file diff -r 79bf433cb5fec8149ad27c6d7bc47d789352def3 -r 7cb17705d74906d937ef71e070b1a759fb04653e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2299,8 +2299,6 @@ # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) - expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) - params.__dict__ = expanded_incomings[ 0 ] # convert value to jsonifiable value def jsonify(v): https://bitbucket.org/galaxy/galaxy-central/commits/ee8e400d704f/ Changeset: ee8e400d704f Branch: release_15.03 User: dannon Date: 2015-02-26 17:40:26+00:00 Summary: Fix cache-busting under require.js. Affected #: 13 files diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -2,10 +2,11 @@ Provides factory methods to assemble the Galaxy web application """ -import sys +import atexit +import time import os import os.path -import atexit +import sys from paste import httpexceptions import pkg_resources @@ -114,6 +115,8 @@ except: pass + app.server_starttime = int(time.time()) # used for cachebusting + if not app.config.is_uwsgi: postfork_setup() diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -79,7 +79,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -89,7 +89,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -13,7 +13,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(['mvc/data'], function(data) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -12,7 +12,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/data' ], function( data ) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -97,7 +97,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); var galaxy_config = ${ h.dumps( self.galaxy_config ) }; diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -49,7 +49,8 @@ hdaJSON = ${h.dumps( hda_dicts )}; require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ // history module is already in the dpn chain from the panel. We can re-scope it here. var historyModel = require( 'mvc/history/history-model' ), diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -48,7 +48,8 @@ $embeddedHistory = $( thisScript ).prev(); require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -177,7 +177,8 @@ baseUrl : "${h.url_for( '/static/scripts' )}", paths : { 'jquery' : 'libs/jquery/jquery' - } + }, + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/user/user-model', panelToUse.location, diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -9,7 +9,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/underscore": { exports: "_" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["mvc/tools"], function(tools_mod) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -58,7 +58,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require( ["viz/trackster"], function(trackster) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/visualization/phyloviz.mako --- a/templates/webapps/galaxy/visualization/phyloviz.mako +++ b/templates/webapps/galaxy/visualization/phyloviz.mako @@ -147,7 +147,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["viz/phyloviz"], function(phyloviz_mod) { diff -r 7cb17705d74906d937ef71e070b1a759fb04653e -r ee8e400d704f066ef61dc01c3df406931a13efac templates/webapps/galaxy/visualization/sweepster.mako --- a/templates/webapps/galaxy/visualization/sweepster.mako +++ b/templates/webapps/galaxy/visualization/sweepster.mako @@ -116,7 +116,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["libs/d3", "viz/sweepster"], function(d3, sweepster) { https://bitbucket.org/galaxy/galaxy-central/commits/6a1e3bd62bab/ Changeset: 6a1e3bd62bab Branch: release_15.03 User: dannon Date: 2015-02-26 17:47:50+00:00 Summary: Move server_starttime to base universe application so shared templates between galaxy/shed/etc don't break. Affected #: 2 files diff -r ee8e400d704f066ef61dc01c3df406931a13efac -r 6a1e3bd62baba48ea26e011b287aa9cd8daf69ed lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -2,6 +2,7 @@ import sys import os +import time from galaxy import config, jobs import galaxy.model import galaxy.security @@ -147,6 +148,7 @@ self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self ) self.model.engine.dispose() + self.server_starttime = int(time.time()) # used for cachebusting def setup_control_queue(self): self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), diff -r ee8e400d704f066ef61dc01c3df406931a13efac -r 6a1e3bd62baba48ea26e011b287aa9cd8daf69ed lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -3,7 +3,6 @@ """ import atexit -import time import os import os.path import sys @@ -115,8 +114,6 @@ except: pass - app.server_starttime = int(time.time()) # used for cachebusting - if not app.config.is_uwsgi: postfork_setup() https://bitbucket.org/galaxy/galaxy-central/commits/12b292368631/ Changeset: 12b292368631 Branch: release_15.03 User: jmchilton Date: 2015-02-26 17:48:28+00:00 Summary: Bugfix: serializing "None" for UUIDs for older workflows. Prevents workflows from being saved :(. Affected #: 1 file diff -r 6a1e3bd62baba48ea26e011b287aa9cd8daf69ed -r 12b2923686314fb1482ef1fa7b67b39161bf0c98 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -346,7 +346,7 @@ 'form_html': module.get_config_form(), 'annotation': annotation_str, 'post_job_actions': {}, - 'uuid': str(step.uuid), + 'uuid': str(step.uuid) if step.uuid else None, 'label': step.label or None, 'workflow_outputs': [] } https://bitbucket.org/galaxy/galaxy-central/commits/322022d07ed5/ Changeset: 322022d07ed5 Branch: release_15.03 User: dannon Date: 2015-02-26 19:07:35+00:00 Summary: Attempt at a fix for get('') in tools/params/basic.py Affected #: 1 file diff -r 12b2923686314fb1482ef1fa7b67b39161bf0c98 -r 322022d07ed5216ab7b6d0de5d727f39fef59212 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1977,7 +1977,7 @@ return None if not value and not self.optional: raise ValueError( "History does not include a dataset of the required format / build" ) - if value in [None, "None"]: + if value in [None, "None", '']: return None if isinstance( value, str ) and value.find( "," ) > 0: value = [ int( value_part ) for value_part in value.split( "," ) ] https://bitbucket.org/galaxy/galaxy-central/commits/b046e38c21d1/ Changeset: b046e38c21d1 Branch: release_15.03 User: carlfeberhard Date: 2015-02-26 19:15:47+00:00 Summary: Fix visualization controller to use security.decode_id in grids Affected #: 1 file diff -r 322022d07ed5216ab7b6d0de5d727f39fef59212 -r b046e38c21d140d9fdbba80fc1861cd6cf4e8352 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -128,7 +128,7 @@ class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ def filter( self, trans, user, query, history_id ): - return query.filter( model.History.id==self.decode_id(history_id) ) + return query.filter( model.History.id==trans.security.decode_id(history_id) ) class HistoryDatasetsSelectionGrid( grids.Grid ): # Grid definition. @@ -157,7 +157,7 @@ Current item for grid is the history being queried. This is a bit of hack since current_item typically means the current item in the grid. """ - return trans.sa_session.query( model.History ).get( self.decode_id( kwargs[ 'f-history' ] ) ) + return trans.sa_session.query( model.History ).get( trans.security.decode_id( kwargs[ 'f-history' ] ) ) def build_initial_query( self, trans, **kwargs ): return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table ) def apply_query_filter( self, trans, query, **kwargs ): 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: 17 new changesets
by commits-noreply＠bitbucket.org 26 Feb '15

26 Feb '15

17 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/79a7008a2140/ Changeset: 79a7008a2140 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Show error message on server error Affected #: 3 files diff -r 51264e606805464d65d032b06d80021d1bf2800e -r 79a7008a214098fa7b2b6804e206dc892881cce0 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r 51264e606805464d65d032b06d80021d1bf2800e -r 79a7008a214098fa7b2b6804e206dc892881cce0 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -14,8 +14,7 @@ success: function(response) { // check if (!response.jobs || !response.jobs.length) { - console.debug('tools-template::success() - Failed jobs.'); - return; + return this.error(response); } // number of jobs @@ -42,13 +41,13 @@ return tmpl; }, - error: function(job_def) { + error: function(response) { return '<div>' + '<p>' + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + - '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + - JSON.stringify(job_def, undefined, 4) + + '<textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">' + + JSON.stringify(response, undefined, 4) + '</textarea>' + '</div>'; }, diff -r 51264e606805464d65d032b06d80021d1bf2800e -r 79a7008a214098fa7b2b6804e206dc892881cce0 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){return this.error(c)}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+c.outputs[e].hid+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/924245fea397/ Changeset: 924245fea397 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Charts: Rebuild and update charts Affected #: 4 files diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 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) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // 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;$.each(this.options.buttons,function(e,r){var 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i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert 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no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e)},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function i(t,r,s){s=s||[];for(o in r){var u=r[o],a=u.options.length>0,f=s.slice(0),l=$("<div/>");if(a){var c=e.uuid(),h=$('<span id="button-'+c+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),p=$('<div id="subgroup-'+c+'" style="display: none; margin-left: 25px;"/>');f.push(c);var d=$("<div/>");d.append(h),d.append(n._templateOption({label:u.name,value:u.value})),l.append(d),i(p,u.options,f),l.append(p)}else l.append(n._templateOption({label:u.name,value:u.value})),n.header_index[u.value]=f;t.append(l)}}var n=this;this.header_index={},this.header_list=[];var s=$("<div/>");i(s,t);for(var o in this.header_index)this.header_list=_.uniq(this.header_list.concat(this.header_index[o]));for(var o in this.header_list)r(s,this.header_list[o]);return s},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<label>"+e.info+"</label>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. 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Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return 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i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata 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"'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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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 n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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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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arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var A=d3.select(this),_=this,D=(a||parseInt(A.style("width"))||960)-u.left-u.right,P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom;M.update=function(){A.call(M)},M.container=this,S.disabled=y.map(function(e){return!!e.disabled});if(!x){var H;x={};for(H in S)S[H]instanceof Array?x[H]=S[H].slice(0):x[H]=S[H]}if(!y||!y.length||!y.filter(function(e){return e.values.length}).length){var B=A.selectAll(".nv-noData").data([T]);return B.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),B.attr("x",u.left+D/2).attr("y",u.top+P/2).text(function(e){return e}),M}A.selectAll(".nv-noData").remove(),b=t.xScale(),w=t.yScale();var j=A.selectAll("g.nv-wrap.nv-stackedAreaChart").data([y]),F=j.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedAreaChart").append("g"),I=j.select("g");F.append("rect").style("opacity",0),F.append("g").attr("class","nv-x nv-axis"),F.append("g").attr("class","nv-y 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U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right"},$title:null,$content:null,$buttons:null,$operations:null,$header:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find(".content"),this.$title=this.$el.find(".portlet-title-text"),this.$header=this.$el.find(".portlet-header");var n=this.$el.find(".portlet-content");this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find(".buttons");if(this.options.buttons){var 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=$(this.el).find(".portlet-operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(e){this.$content.append(e)},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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div class="portlet-header"><div class="portlet-operations" style="float: '+e.operations_flt+';"></div>'+'<div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div class="portlet-content">',e.placement=="top"&&(t+='<div class="buttons"></div>'),t+='<div class="content"></div>',e.placement=="bottom"&&(t+='<div class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&(e===null&&(e="__null__"),this.$select.val(e),this.$select.select2&&this.$select.select2("val",e)),this._getValue()},first:function(){var e=this.$select.find("option").first();return e.length>0?e.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2()),this.value(t),this._getValue()===null&&this.value(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_getValue:function(){var t=this.$select.val();return e.validate(t)?t:null},_refresh:function(){var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.empty(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'" class="'+e.cls+'">'+'<select id="'+e.id+'_select" class="select"/>'+'<div class="button">'+'<i class="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.options.value!==undefined&&this.value(this.options.value),this.$text.on("change",function(){n.value($(this).val())});var r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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","nvd3_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]==="__undefined__"){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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var 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 n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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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 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -189,7 +189,7 @@ if (valid) { // add to selection columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'label' : 'Column: ' + (parseInt(key) + 1), 'value' : key }); } diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -115,7 +115,7 @@ }); // append portlet - this.portlet.append(this.message.$el); + this.portlet.append(this.message.$el.addClass('ui-margin-top')); this.portlet.append(this.viewport_view.$el); // set element diff -r 79a7008a214098fa7b2b6804e206dc892881cce0 -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -12,6 +12,7 @@ ## install shared libraries ${h.js( 'libs/jquery/jquery', + 'libs/jquery/select2', 'libs/bootstrap', 'libs/require', 'libs/underscore', https://bitbucket.org/galaxy/galaxy-central/commits/1ec20f0f8da0/ Changeset: 1ec20f0f8da0 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Charts: Fix missing data message Affected #: 2 files diff -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 -r 1ec20f0f8da089f06ea73fc45970b76c914216fd config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right"},$title:null,$content:null,$buttons:null,$operations:null,$header:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find(".content"),this.$title=this.$el.find(".portlet-title-text"),this.$header=this.$el.find(".portlet-header");var n=this.$el.find(".portlet-content");this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find(".buttons");if(this.options.buttons){var 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=$(this.el).find(".portlet-operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(e){this.$content.append(e)},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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div class="portlet-header"><div class="portlet-operations" style="float: '+e.operations_flt+';"></div>'+'<div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div class="portlet-content">',e.placement=="top"&&(t+='<div class="buttons"></div>'),t+='<div class="content"></div>',e.placement=="bottom"&&(t+='<div class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&(e===null&&(e="__null__"),this.$select.val(e),this.$select.select2&&this.$select.select2("val",e)),this._getValue()},first:function(){var e=this.$select.find("option").first();return e.length>0?e.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2()),this.value(t),this._getValue()===null&&this.value(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_getValue:function(){var t=this.$select.val();return e.validate(t)?t:null},_refresh:function(){var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.empty(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'" class="'+e.cls+'">'+'<select id="'+e.id+'_select" class="select"/>'+'<div class="button">'+'<i class="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.options.value!==undefined&&this.value(this.options.value),this.$text.on("change",function(){n.value($(this).val())});var r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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","nvd3_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]==="__undefined__"){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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var 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 n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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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 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(e){this.$content.append(e)},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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div class="portlet-header"><div class="portlet-operations" style="float: '+e.operations_flt+';"></div>'+'<div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div class="portlet-content">',e.placement=="top"&&(t+='<div class="buttons"></div>'),t+='<div class="content"></div>',e.placement=="bottom"&&(t+='<div class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon=this.$el.find(".icon"),this.$button=this.$el.find(".button"),this.options.multiple&&(this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$button.remove()),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&(e===null&&(e="__null__"),this.$select.val(e),this.$select.select2&&this.$select.select2("val",e)),this._getValue()},first:function(){var e=this.$select.find("option").first();return e.length>0?e.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2()),this.value(t),this._getValue()===null&&this.value(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_getValue:function(){var t=this.$select.val();return e.validate(t)?t:null},_refresh:function(){var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.empty(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'" class="'+e.cls+'">'+'<select id="'+e.id+'_select" class="select"/>'+'<div class="button">'+'<i class="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.options.value!==undefined&&this.value(this.options.value),this.$text.on("change",function(){n.value($(this).val())});var r=[];this.$text.on("keyup",function(e){r[e.which]=!1}),this.$text.on("keydown",function(e){var t=e.which;r[t]=!0,t==8||t==9||t==13||t==37||t==39||t>=48&&t<=57||t==190&&$(this).val().indexOf(".")==-1&&n.options.precise||t==189&&$(this).val().indexOf("-")==-1||r[91]||r[17]||event.preventDefault()})},value:function(e){return e!==undefined&&(isNaN(e)&&(e=0),this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.$slider&&this.$slider.slider("value",e),this.$text.val(e),this.options.onchange&&this.options.onchange(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-button-check",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($("<div/>")),this.value(this.options.value);var n=this;this.$el.on("click",function(){n.current=!n.current&&2||0,n.value(n.current),n.options.onclick&&n.options.onclick()})},value:function(e){return e!==undefined&&(this.current=e,this.$el.removeClass().addClass("ui-button-check").addClass(this.options.icons[e]),this.options.onchange&&this.options.onchange(e)),this.current}})}),define("mvc/ui/ui-options",["utils/utils","mvc/ui/ui-button-check"],function(e,t){var n=Backbone.View.extend({initialize:function(n){this.optionsDefault={visible:!0,data:[],id:e.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:!1},this.options=e.merge(n,this.optionsDefault),this.setElement('<div class="ui-options"/>'),this.$message=$("<div/>"),this.$options=$(this._template(n)),this.$menu=$('<div class="ui-options-menu"/>'),this.$el.append(this.$message),this.$el.append(this.$menu),this.$el.append(this.$options),this.options.multiple&&(this.select_button=new t({onclick:function(){r.$("input").prop("checked",r.select_button.value()!==0),r._change()}}),this.$menu.addClass("ui-margin-bottom"),this.$menu.append(this.select_button.$el),this.$menu.append("Select/Unselect all")),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value!==undefined&&this.value(this.options.value);var r=this;this.on("change",function(){r._change()})},update:function(e){var t=this._getValue();this.$options.empty();if(this._templateOptions)this.$options.append(this._templateOptions(e));else for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),r.tooltip({title:e[n].tooltip,placement:"bottom"}),this.$options.append(r)}var i=this;this.$("input").on("change",function(){i.value(i._getValue()),i._change()}),this.value(t)},value:function(e){if(e!==undefined){this.$("input").prop("checked",!1);if(e!==null){e instanceof Array||(e=[e]);for(var t in e)this.$('input[value="'+e[t]+'"]').first().prop("checked",!0)}}return this._refresh(),this._getValue()},exists:function(e){if(e!==undefined){e instanceof Array||(e=[e]);for(var t in e)if(this.$('input[value="'+e[t]+'"]').length>0)return!0}return!1},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}}),r=n.extend({_templateOption:function(t){var n=e.uuid();return'<div class="ui-option"><input id="'+n+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+t.value+'"/>'+'<label class="ui-options-label" for="'+n+'">'+t.label+"</label>"+"</div>"}}),i={};i.View=r.extend({initialize:function(e){e.type="radio",r.prototype.initialize.call(this,e)}});var s={};s.View=r.extend({initialize:function(e){e.multiple=!0,e.type="checkbox",r.prototype.initialize.call(this,e)}});var o={};return o.View=n.extend({initialize:function(e){n.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t="fa "+e.icon;e.label||(t+=" no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=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+'"/>'}}),v=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>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;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"||a==="zero")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,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){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var 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("Datasets::_fill_from_cache() - Reached data range limit.");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];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default: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=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$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,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),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){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_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 r=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]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+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="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","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=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","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(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append((new t.Label({title:"How many data points would you like to analyze?"})).$el),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(this.library.$el.addClass("ui-margin-bottom")),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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","mvc/ui/ui-misc","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({initialize:function(r,i){var s=this;this.app=r,this.chart=this.app.chart,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(){s._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){s.app.go("viewer"),s.app.storage.load()}})}}),this.types=new a(r,{onchange:function(e){var t=s.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),s.chart.definition=t,s.chart.settings.clear(),s.chart.set({type:e}),s.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){s._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=s._addGroupModel();s.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){s.chart.set("title",s.title.value())}});var o=$("<div/>");o.append((new t.Label({title:"Provide a chart title:"})).$el),o.append(this.title.$el),o.append($("<div/>").addClass("ui-table-form-info").html("This title will appear in the list of 'Saved Visualizations'. Charts are saved upon creation.")),o.append(this.types.$el.addClass("ui-margin-top")),this.tabs.add({id:"main",title:"Start",$el:o}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.tabs.$el.addClass("ui-margin-top")),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var s=this;this.chart.on("change:title",function(e){s._refreshTitle()}),this.chart.on("change:type",function(e){s.types.value(e.get("type"))}),this.chart.on("reset",function(e){s._resetChart()}),this.app.chart.on("redraw",function(e){s.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){s._addGroup(e)}),this.app.chart.groups.on("remove",function(e){s._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){s._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){s._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value()!=e&&this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$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","nvd3_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.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{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",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{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:"0"}]},separator_y:{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 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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arguments.length?(o=e,t.x(e),m):o},m.y=function(e){return arguments.length?(u=e,t.y(e),m):u},m.clipEdge=function(e){return arguments.length?(l=e,m):l},m.color=function(n){return arguments.length?(s=e.utils.getColor(n),t.color(s),m):s},m.interpolate=function(e){return arguments.length?(p=e,m):p},m.defined=function(e){return arguments.length?(a=e,m):a},m.isArea=function(e){return arguments.length?(f=d3.functor(e),m):f},m},e.models.lineChart=function(){function N(m){return m.each(function(m){var x=d3.select(this),C=this,k=(a||parseInt(x.style("width"))||960)-o.left-o.right,L=(f||parseInt(x.style("height"))||400)-o.top-o.bottom;N.update=function(){x.call(N)},N.container=this,b.disabled=m.map(function(e){return!!e.disabled});if(!w){var A;w={};for(A in b)b[A]instanceof Array?w[A]=b[A].slice(0):w[A]=b[A]}if(!m||!m.length||!m.filter(function(e){return e.values.length}).length){var O=x.selectAll(".nv-noData").data([E]);return O.enter().append("text").attr("class","nvd3 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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 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return arguments.length?(l=e,C):l},C.showLegend=function(e){return arguments.length?(c=e,C):c},C.showXAxis=function(e){return arguments.length?(h=e,C):h},C.showYAxis=function(e){return arguments.length?(p=e,C):p},C.tooltip=function(e){return arguments.length?(m=e,C):m},C.tooltips=function(e){return arguments.length?(v=e,C):v},C.tooltipContent=function(e){return arguments.length?(m=e,C):m},C.state=function(e){return arguments.length?(b=e,C):b},C.defaultState=function(e){return arguments.length?(w=e,C):w},C.noData=function(e){return arguments.length?(E=e,C):E},C.transitionDuration=function(e){return arguments.length?(T=e,C):T},C},e.models.multiChart=function(){function C(e){return e.each(function(e){var u=d3.select(this),f=this;C.update=function(){u.call(C)},C.container=this;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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y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/pie/config",["plugin/plugins/nvd3/nv.d3"],function(){return $.extend(!0,{},{title:"Pie chart",category:"Area charts",library:"NVD3",tag:"svg",keywords:"small",columns:{label:{title:"Labels",is_label:!0,is_auto:!0},y:{title:"Values",is_numeric:!0}},settings:{main_separator:{type:"separator",title:"Pie chart settings"},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"}]},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},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 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small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},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",keywords:"small medium large",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_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},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",zoomable:!0,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",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/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,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/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}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),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/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){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:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","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,h){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 l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".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)}})}); \ No newline at end of file diff -r 924245fea3979969ce13f222d2ad7d5ce8a57a97 -r 1ec20f0f8da089f06ea73fc45970b76c914216fd config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -295,7 +295,7 @@ return; } for (var key in chart_def.columns) { - if (group.attributes[key] === '__undefined__') { + if (group.attributes[key] === '__null__') { self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); self.tabs.show(group.id); valid = false; https://bitbucket.org/galaxy/galaxy-central/commits/a9779a00f055/ Changeset: a9779a00f055 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: ToolForm: Enable collection for multiple data parameter Affected #: 3 files diff -r 1ec20f0f8da089f06ea73fc45970b76c914216fd -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 1ec20f0f8da089f06ea73fc45970b76c914216fd -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -88,7 +88,7 @@ } // add collection selector - if (this.mode == 'single' || this.mode == 'collection') { + if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { radio_buttons.push({ icon : 'fa-folder-o', value : 'collection', diff -r 1ec20f0f8da089f06ea73fc45970b76c914216fd -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/ebaf186a2db8/ Changeset: ebaf186a2db8 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Fix two incorrect (undefined) references and misc cleanup in installed_repository_manager.py Affected #: 1 file diff -r a9779a00f055a1db5b072de2b269a6a1433e4ac7 -r ebaf186a2db8eeb73885a9154294d9ab29a71e9e lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -103,12 +103,12 @@ # Hack to add repository.name here, which is actually the root of the installed repository data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) - new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - repository.metadata, - repository.get_shed_config_dict( self.app ), - data_manager_relative_install_dir, - repository, - repository_tools_tups ) + dmh.install_data_managers( self.app.config.shed_data_manager_config_file, + repository.metadata, + repository.get_shed_config_dict( self.app ), + data_manager_relative_install_dir, + repository, + repository_tools_tups ) self.install_model.context.add( repository ) self.install_model.context.flush() if repository.includes_datatypes: @@ -400,14 +400,8 @@ installed_repository_dependencies = {} missing_rd_tups = [] installed_rd_tups = [] - description, \ - repository_clone_url, \ - changeset_revision, \ - ctx_rev, \ - repository_owner, \ - repository_dependencies, \ - tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) + ( description, repository_clone_url, changeset_revision, ctx_rev, + repository_owner, repository_dependencies, tool_dependencies ) = suc.get_repo_info_tuple_contents( repo_info_tuple ) if repository_dependencies: description = repository_dependencies[ 'description' ] root_key = repository_dependencies[ 'root_key' ] @@ -460,7 +454,7 @@ prior_installation_required, only_if_compiling_contained_td, None, - 'Never installed' ] + 'Never installed' ] if not util.asbool( only_if_compiling_contained_td ): # A repository dependency that is not installed will not be considered missing if its value for # only_if_compiling_contained_td is True - see above... @@ -564,10 +558,10 @@ continue if required_repository_tup not in dependency_tups: dependency_tups.append( required_repository_tup ) - return get_repository_dependency_tups_for_installed_repository( required_repository, - dependency_tups=dependency_tups ) + return self.get_repository_dependency_tups_for_installed_repository( required_repository, + dependency_tups=dependency_tups ) return dependency_tups - + def get_repository_tuple_for_installed_repository_manager( self, repository ): return ( str( repository.tool_shed ), str( repository.name ), @@ -611,10 +605,10 @@ contents = open( env_shell_file_path, 'r' ).read() except Exception, e: contents = None - log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % \ - ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) + log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % + ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) if contents is not None and contents.find( required_env_shell_file_path ) >= 0: - td_tuple = get_tool_dependency_tuple_for_installed_repository_manager( td ) + td_tuple = self.get_tool_dependency_tuple_for_installed_repository_manager( td ) runtime_dependent_tool_dependency_tups.append( td_tuple ) return runtime_dependent_tool_dependency_tups @@ -672,8 +666,7 @@ # Remove this tool_dependency from all values in # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - for td_tup, installed_runtime_dependent_tool_dependency_tups in \ - self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items(): + for ( td_tup, installed_runtime_dependent_tool_dependency_tups ) in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items(): if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups: # Remove the tool_dependency from the list. installed_runtime_dependent_tool_dependency_tups.remove( tool_dependency_tup ) @@ -684,7 +677,7 @@ altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies. self.remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) - # Remove the entry for this tool_dependency from + # Remove the entry for this tool_dependency from # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. self.remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) # Remove this repository's entry from self.installed_tool_dependencies_of_installed_repositories. @@ -864,7 +857,7 @@ else: status = 'error' message = 'A repository must have the status <b>New</b> in order to be purged. This repository has ' - message += ' the status %s.' % str( repository.status ) + message += ' the status %s.' % str( repository.status ) return status, message def remove_entry_from_installed_repository_dependencies_of_installed_repositories( self, repository ): @@ -884,7 +877,7 @@ debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % \ ( r_installed_changeset_revision, r_name, r_owner ) debug_msg += "in installed_repository_dependencies_of_installed_repositories." - log.debug( debug_msg ) + log.debug( debug_msg ) v_tups.remove( repository_tup ) altered_installed_dependent_repositories_of_installed_repositories[ r_tup ] = v_tups self.installed_dependent_repositories_of_installed_repositories = \ @@ -957,7 +950,7 @@ if cleaned_repository_dependency_tool_shed == cleaned_tool_shed and \ repository_dependency.name == name and \ repository_dependency.owner == owner and \ - ( repository_dependency.installed_changeset_revision == changeset_revision or \ + ( repository_dependency.installed_changeset_revision == changeset_revision or repository_dependency.changeset_revision == changeset_revision ): return True return False @@ -970,9 +963,9 @@ # This method is called only from Galaxy when rendering repository dependencies # for an installed tool shed repository. # TODO: Do we need to check more than changeset_revision here? - required_repository_tup = [ required_repository.tool_shed, \ - required_repository.name, \ - required_repository.owner, \ + required_repository_tup = [ required_repository.tool_shed, + required_repository.name, + required_repository.owner, required_repository.changeset_revision ] for tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: partial_tup = tup[ 0:4 ] @@ -1009,12 +1002,12 @@ pulled by a Galaxy administrator when getting updates to an installed tool shed repository. The original_dependency_dict is a single tool dependency definition, an example of which is:: - + {"name": "bwa", "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", "type": "package", "version": "0.6.2"} - + The new_dependencies_dict is the dictionary generated by the metadata_util.generate_tool_dependency_metadata method. """ new_tool_dependency = None @@ -1046,12 +1039,12 @@ break if new_dependency_name and new_dependency_type and new_dependency_version: # Update all attributes of the tool_dependency record in the database. - log.debug( "Updating version %s of tool dependency %s %s to have new version %s and type %s." % \ - ( str( tool_dependency.version ), - str( tool_dependency.type ), - str( tool_dependency.name ), - str( new_dependency_version ), - str( new_dependency_type ) ) ) + log.debug( "Updating version %s of tool dependency %s %s to have new version %s and type %s." + % ( str( tool_dependency.version ), + str( tool_dependency.type ), + str( tool_dependency.name ), + str( new_dependency_version ), + str( new_dependency_type ) ) ) tool_dependency.type = new_dependency_type tool_dependency.version = new_dependency_version tool_dependency.status = self.app.install_model.ToolDependency.installation_status.UNINSTALLED @@ -1062,8 +1055,8 @@ else: # We have no new tool dependency definition based on a matching dependency name, so remove # the existing tool dependency record from the database. - log.debug( "Deleting version %s of tool dependency %s %s from the database since it is no longer defined." % \ - ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) ) + log.debug( "Deleting version %s of tool dependency %s %s from the database since it is no longer defined." + % ( str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) ) context.delete( tool_dependency ) context.flush() return new_tool_dependency https://bitbucket.org/galaxy/galaxy-central/commits/067a4072a9a0/ Changeset: 067a4072a9a0 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Cleanup in galaxy.web.framework.base, correct bug where encoding didn't exist and would blow up if (not that this ever happened afaik) we attempted to stream back a nested iterable. Affected #: 1 file diff -r ebaf186a2db8eeb73885a9154294d9ab29a71e9e -r 067a4072a9a08ef7bb67b5e12a41da5076f6d3ba lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -2,7 +2,7 @@ A simple WSGI application/framework. """ -import cgi # For FieldStorage +import cgi # For FieldStorage import logging import os.path import socket @@ -67,7 +67,7 @@ # FIXME: The following two options are deprecated and should be # removed. Consult the Routes documentation. self.mapper.minimization = True - #self.mapper.explicit = False + # self.mapper.explicit = False self.transaction_factory = DefaultWebTransaction # Set if trace logging is enabled self.trace_logger = None @@ -79,12 +79,12 @@ method use `add_route`. """ log.debug( "Enabling '%s' controller, class: %s", - controller_name, controller.__class__.__name__ ) + controller_name, controller.__class__.__name__ ) self.controllers[ controller_name ] = controller def add_api_controller( self, controller_name, controller ): log.debug( "Enabling '%s' API controller, class: %s", - controller_name, controller.__class__.__name__ ) + controller_name, controller.__class__.__name__ ) self.api_controllers[ controller_name ] = controller def add_route( self, route, **kwargs ): @@ -148,7 +148,7 @@ else: environ[ 'is_api_request' ] = False controllers = self.controllers - if map == None: + if map is None: raise httpexceptions.HTTPNotFound( "No route for " + path_info ) self.trace( path_info=path_info, map=map ) # Setup routes @@ -239,11 +239,13 @@ associated object (provides property style access to keys in the WSGI environment) """ - def __init__( self, key, default = '' ): + def __init__( self, key, default='' ): self.key = key self.default = default - def __get__( self, obj, type = None ): - if obj is None: return self + + def __get__( self, obj, type=None ): + if obj is None: + return self return obj.environ.get( self.key, self.default ) @@ -254,8 +256,10 @@ """ def __init__( self, func ): self.func = func - def __get__(self, obj, type = None ): - if obj is None: return self + + def __get__(self, obj, type=None ): + if obj is None: + return self value = self.func( obj ) setattr( obj, self.func.func_name, value ) return value @@ -273,6 +277,7 @@ self.environ = environ self.request = Request( environ ) self.response = Response() + @lazy_property def session( self ): """ @@ -291,11 +296,14 @@ # but for performance reasons it's way better to use Paste's tempfile than to # create a new one and copy. import tempfile + + class FieldStorage( cgi.FieldStorage ): def make_file(self, binary=None): return tempfile.NamedTemporaryFile() + def read_lines(self): - # Always make a new file + # Always make a new file self.file = self.make_file() self.__file = None if self.outerboundary: @@ -313,45 +321,58 @@ """ Create a new request wrapping the WSGI environment `environ` """ - ## self.environ = environ + # self.environ = environ webob.Request.__init__( self, environ, charset='utf-8', decode_param_names=False ) # Properties that are computed and cached on first use + @lazy_property def remote_host( self ): try: return socket.gethostbyname( self.remote_addr ) except socket.error: return self.remote_addr + @lazy_property def remote_hostname( self ): try: return socket.gethostbyaddr( self.remote_addr )[0] except socket.error: return self.remote_addr + @lazy_property def cookies( self ): return get_cookies( self.environ ) + @lazy_property def base( self ): return ( self.scheme + "://" + self.host ) - ## @lazy_property - ## def params( self ): - ## return parse_formvars( self.environ ) + + # @lazy_property + # def params( self ): + # return parse_formvars( self.environ ) + @lazy_property def path( self ): return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] + @lazy_property def browser_url( self ): return self.base + self.path + # Descriptors that map properties to the associated environment - ## scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' ) - ## remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' ) + + # scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' ) + # remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' ) + remote_port = WSGIEnvironmentProperty( 'REMOTE_PORT' ) - ## method = WSGIEnvironmentProperty( 'REQUEST_METHOD' ) - ## script_name = WSGIEnvironmentProperty( 'SCRIPT_NAME' ) + + # method = WSGIEnvironmentProperty( 'REQUEST_METHOD' ) + # script_name = WSGIEnvironmentProperty( 'SCRIPT_NAME' ) + protocol = WSGIEnvironmentProperty( 'SERVER_PROTOCOL' ) - ## query_string = WSGIEnvironmentProperty( 'QUERY_STRING' ) - ## path_info = WSGIEnvironmentProperty( 'PATH_INFO' ) + + # query_string = WSGIEnvironmentProperty( 'QUERY_STRING' ) + # path_info = WSGIEnvironmentProperty( 'PATH_INFO' ) class Response( object ): @@ -406,7 +427,8 @@ # ---- Utilities ------------------------------------------------------------ -CHUNK_SIZE = 2**16 +CHUNK_SIZE = 2 ** 16 + def send_file( start_response, trans, body ): # If configured use X-Accel-Redirect header for nginx @@ -426,6 +448,7 @@ trans.response.wsgi_headeritems() ) return body + def iterate_file( file ): """ Progressively return chunks from `file`. @@ -436,13 +459,14 @@ break yield chunk + def flatten( seq ): """ Flatten a possible nested set of iterables """ for x in seq: if isinstance( x, ( types.GeneratorType, list, tuple ) ): - for y in flatten( x, encoding ): + for y in flatten( x ): yield y else: yield x https://bitbucket.org/galaxy/galaxy-central/commits/7dd485f6027a/ Changeset: 7dd485f6027a User: martenson Date: 2015-02-26 19:32:48+00:00 Summary: Revert "create library root folder with '/' as default name" This reverts commit 9dfa83bf0f2abd1c2182da9edef1bb0996d7d757. Affected #: 2 files diff -r 067a4072a9a08ef7bb67b5e12a41da5076f6d3ba -r 7dd485f6027abc56edd8b427218a4ec15bd79c42 lib/galaxy/managers/libraries.py --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -54,7 +54,7 @@ raise exceptions.ItemAccessibilityException( 'Only administrators can create libraries.' ) else: library = trans.app.model.Library( name=name, description=description, synopsis=synopsis ) - root_folder = trans.app.model.LibraryFolder( name='/', description='' ) + root_folder = trans.app.model.LibraryFolder( name=name, description='' ) library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() diff -r 067a4072a9a08ef7bb67b5e12a41da5076f6d3ba -r 7dd485f6027abc56edd8b427218a4ec15bd79c42 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -85,13 +85,12 @@ raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' ) - root_encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) - root_name = library.root_folder.name + encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) # appending root folder - rval.append( dict( id=root_encoded_id, + rval.append( dict( id=encoded_id, type='folder', - name=root_name, - url=url_for( 'library_content', library_id=library_id, id=root_encoded_id ) ) ) + name='/', + url=url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) library.root_folder.api_path = '' # appending all other items in the library recursively for content in traverse( library.root_folder ): https://bitbucket.org/galaxy/galaxy-central/commits/6af59c8cc870/ Changeset: 6af59c8cc870 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Fix bug in scramble exception, incorrect reference to source_path Affected #: 1 file diff -r 7dd485f6027abc56edd8b427218a4ec15bd79c42 -r 6af59c8cc8702d937ced0829db7df5206c615b63 lib/galaxy/eggs/scramble.py --- a/lib/galaxy/eggs/scramble.py +++ b/lib/galaxy/eggs/scramble.py @@ -134,7 +134,7 @@ elif zipfile.is_zipfile( self.source_path ): self.unpack_zip() else: - raise Exception( "%s(): Unknown archive file type for %s" % ( sys._getframe().f_code.co_name, source_path ) ) + raise Exception( "%s(): Unknown archive file type for %s" % ( sys._getframe().f_code.co_name, self.source_path ) ) log.warning( "%s(): Unpacked to:" % sys._getframe().f_code.co_name ) log.warning( " %s" % self.buildpath ) def unpack_zip( self ): https://bitbucket.org/galaxy/galaxy-central/commits/8252c18ebf34/ Changeset: 8252c18ebf34 User: jmchilton Date: 2015-02-26 19:32:48+00:00 Summary: Add test case demonstrating data params don't need namespace... ... unlike other parameters. Is this a bug? Has been this way for at least three releases it seems. https://github.com/galaxyproject/tools-devteam/commit/c01b354711d982f61f1fd… Affected #: 2 files diff -r 6af59c8cc8702d937ced0829db7df5206c615b63 -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -27,6 +27,7 @@ <tool file="column_param.xml" /><tool file="column_multi_param.xml" /><tool file="special_params.xml" /> + <tool file="top_level_data.xml" /><tool file="validation_default.xml" /><tool file="validation_sanitizer.xml" /><tool file="validation_repeat.xml" /> diff -r 6af59c8cc8702d937ced0829db7df5206c615b63 -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 test/functional/tools/tol_level_data.xml --- /dev/null +++ b/test/functional/tools/tol_level_data.xml @@ -0,0 +1,34 @@ +<tool id="top_level_data" name="top_level_data" version="0.1.0"> + <command> + cat '${f1}' >> $out1; + echo '${library.f2}' >> $out2;  + </command> + <inputs> + <conditional name="library"> + <param name="type" type="select" label="Parameter Settings"> + <option value="no">Use defaults</option> + <option value="yes">Full parameter list</option> + </param> + <when value="yes"> + <param name="f1" type="data" format="txt" label="Data 1" /> + <param name="f2" type="text" label="Text 1" /> + </when> + <when value="no"> + <param name="f1" type="data" format="txt" label="Data 1" /> + <param name="f2" type="text" label="TExt 1" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="out1" /> + <data format="txt" name="out2" /> + </outputs> + <tests> + <test> + <param name="f1" value="simple_line.txt" /> + <param name="f2" value="This is a line of text." /> + <output name="out1" file="simple_line.txt" /> + <output name="out2" file="simple_line.txt" /> + </test> + </tests> +</tool> https://bitbucket.org/galaxy/galaxy-central/commits/1e6f3918b2d6/ Changeset: 1e6f3918b2d6 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Collections: Enable the batch mode execution for nested collections (without adding a new button) Affected #: 4 files diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2369,24 +2369,6 @@ return True # TODO def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): - d = super( DataCollectionToolParameter, self ).to_dict( trans ) - if other_values is None: - # No need to produce lists of datasets for history. - return d - - dataset_matcher = DatasetMatcher( trans, self, None, other_values ) - history = trans.history - - for hdca in self.match_collections( trans, history, dataset_matcher ): - pass - - for hdca in self.match_multirun_collections( trans, history, dataset_matcher ): - subcollection_type = self._history_query( trans ).collection_type_description.collection_type - pass - - return d - - def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): # create dictionary and fill default parameters d = super( DataCollectionToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions @@ -2419,7 +2401,8 @@ 'id_uncoded' : hdca.id, 'hid' : hdca.hid, 'name' : hdca.name, - 'src' : 'hdca' + 'src' : 'hdca', + 'map_over_type' : subcollection_type }) # sort both lists diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -123,20 +123,22 @@ // number of radio buttons var n_buttons = _.size(this.list); - + // add button to dom var button_width = 0; if (n_buttons > 1) { this.$el.append(this.button_type.$el); button_width = Math.max(0, _.size(this.list) * 35) + 'px'; } - + // append field elements for (var i in this.list) { this.$el.append(this.list[i].field.$el.css({ 'margin-left': button_width })); } + + // append batch message this.$el.append(this.$batch.css({ 'margin-left': button_width })); @@ -176,30 +178,27 @@ /** Update content selector */ update: function(options) { - // identify dataset options - var dataset_options = []; - for (var i in options.hda) { - var hda = options.hda[i]; - dataset_options.push({ - label: hda.hid + ': ' + hda.name, - value: hda.id - }); + // update a particular select field + function _update(field, options) { + if (field) { + // identify available options + var select_options = []; + for (var i in options) { + var item = options[i]; + select_options.push({ + label: item.hid + ': ' + item.name, + value: item.id + }); + } + // update field + field.update(select_options); + } } - // identify collection options - var collection_options = []; - for (var i in options.hdca) { - var hdca = options.hdca[i]; - collection_options.push({ - label: hdca.hid + ': ' + hdca.name, - value: hdca.id - }); - } - - // update selection fields - this.select_single && this.select_single.update(dataset_options); - this.select_multiple && this.select_multiple.update(dataset_options); - this.select_collection && this.select_collection.update(collection_options); + // update available options + _update(this.select_single, options.hda); + _update(this.select_multiple, options.hda); + _update(this.select_collection, options.hdca); // add to content list this.app.content.add(options); @@ -234,13 +233,15 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value(null); - this.select_multiple && this.select_multiple.value(null); - this.select_collection && this.select_collection.value(null); + for (var i in this.list) { + this.list[i].field.value(null); + } } - this.refresh(); } + // refresh view + this.refresh(); + // validate value var id_list = this._select().value(); if (id_list === null) { @@ -259,16 +260,21 @@ // prepare result dict var result = { - batch : this.mode == 'single' && this.current != 'single', + batch : this._batch(), values : [] } // append to dataset ids for (var i in id_list) { - result.values.push({ + var details = this.app.content.get({ id : id_list[i], src : this.list[this.current].type }); + if (details) { + result.values.push(details); + } else { + return null; + } } // return @@ -286,7 +292,7 @@ $el.hide(); } } - if (this.mode == 'single' && this.current != 'single') { + if (this._batch()) { this.$batch.show(); } else { this.$batch.hide(); @@ -296,6 +302,25 @@ /** Assists in selecting the current field */ _select: function() { return this.list[this.current].field; + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + if (this.current == 'collection') { + var hdca = this.app.content.get({ + id : this._select().value(), + src : 'hdca' + }); + if (hdca && hdca.map_over_type) { + return true; + } + } + if (this.current != 'single') { + if (this.mode == 'single') { + return true; + } + } + return false; } }); diff -r 8252c18ebf343b8d5b30b61a2627d67bb1330c99 -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/9111c6aed248/ Changeset: 9111c6aed248 User: guerler Date: 2015-02-26 19:32:48+00:00 Summary: Remove collection expansion Affected #: 1 file diff -r 1e6f3918b2d6868983f77c348bc1c2bff0dd5e59 -r 9111c6aed248e894112d0ace01446c89b72a208e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2299,8 +2299,6 @@ # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) - expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) - params.__dict__ = expanded_incomings[ 0 ] # convert value to jsonifiable value def jsonify(v): https://bitbucket.org/galaxy/galaxy-central/commits/743840286044/ Changeset: 743840286044 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Fix cache-busting under require.js. Affected #: 13 files diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -2,10 +2,11 @@ Provides factory methods to assemble the Galaxy web application """ -import sys +import atexit +import time import os import os.path -import atexit +import sys from paste import httpexceptions import pkg_resources @@ -114,6 +115,8 @@ except: pass + app.server_starttime = int(time.time()) # used for cachebusting + if not app.config.is_uwsgi: postfork_setup() diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -79,7 +79,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -89,7 +89,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); </script> diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -13,7 +13,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(['mvc/data'], function(data) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -12,7 +12,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/data' ], function( data ) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -97,7 +97,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); var galaxy_config = ${ h.dumps( self.galaxy_config ) }; diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -49,7 +49,8 @@ hdaJSON = ${h.dumps( hda_dicts )}; require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ // history module is already in the dpn chain from the panel. We can re-scope it here. var historyModel = require( 'mvc/history/history-model' ), diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -48,7 +48,8 @@ $embeddedHistory = $( thisScript ).prev(); require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" + baseUrl : "${h.url_for( '/static/scripts' )}", + urlArgs: 'v=${int(app.server_starttime)}' }); require([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -177,7 +177,8 @@ baseUrl : "${h.url_for( '/static/scripts' )}", paths : { 'jquery' : 'libs/jquery/jquery' - } + }, + urlArgs: 'v=${int(app.server_starttime)}' })([ 'mvc/user/user-model', panelToUse.location, diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -9,7 +9,8 @@ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/underscore": { exports: "_" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["mvc/tools"], function(tools_mod) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -58,7 +58,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require( ["viz/trackster"], function(trackster) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/visualization/phyloviz.mako --- a/templates/webapps/galaxy/visualization/phyloviz.mako +++ b/templates/webapps/galaxy/visualization/phyloviz.mako @@ -147,7 +147,8 @@ shim: { "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" } - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["viz/phyloviz"], function(phyloviz_mod) { diff -r 9111c6aed248e894112d0ace01446c89b72a208e -r 743840286044c18aaef85ac6400b78a196e5c0bb templates/webapps/galaxy/visualization/sweepster.mako --- a/templates/webapps/galaxy/visualization/sweepster.mako +++ b/templates/webapps/galaxy/visualization/sweepster.mako @@ -116,7 +116,8 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, - } + }, + urlArgs: 'v=${int(app.server_starttime)}' }); require(["libs/d3", "viz/sweepster"], function(d3, sweepster) { https://bitbucket.org/galaxy/galaxy-central/commits/714deef6027b/ Changeset: 714deef6027b User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Move server_starttime to base universe application so shared templates between galaxy/shed/etc don't break. Affected #: 2 files diff -r 743840286044c18aaef85ac6400b78a196e5c0bb -r 714deef6027bb404b8156bc0401c7c2ceb7f1d64 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -2,6 +2,7 @@ import sys import os +import time from galaxy import config, jobs import galaxy.model import galaxy.security @@ -147,6 +148,7 @@ self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self ) self.model.engine.dispose() + self.server_starttime = int(time.time()) # used for cachebusting def setup_control_queue(self): self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), diff -r 743840286044c18aaef85ac6400b78a196e5c0bb -r 714deef6027bb404b8156bc0401c7c2ceb7f1d64 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -3,7 +3,6 @@ """ import atexit -import time import os import os.path import sys @@ -115,8 +114,6 @@ except: pass - app.server_starttime = int(time.time()) # used for cachebusting - if not app.config.is_uwsgi: postfork_setup() https://bitbucket.org/galaxy/galaxy-central/commits/3765ae2904ff/ Changeset: 3765ae2904ff User: jmchilton Date: 2015-02-26 19:32:48+00:00 Summary: Bugfix: serializing "None" for UUIDs for older workflows. Prevents workflows from being saved :(. Affected #: 1 file diff -r 714deef6027bb404b8156bc0401c7c2ceb7f1d64 -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -346,7 +346,7 @@ 'form_html': module.get_config_form(), 'annotation': annotation_str, 'post_job_actions': {}, - 'uuid': str(step.uuid), + 'uuid': str(step.uuid) if step.uuid else None, 'label': step.label or None, 'workflow_outputs': [] } https://bitbucket.org/galaxy/galaxy-central/commits/5f8bb3b239c0/ Changeset: 5f8bb3b239c0 User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Remove unnecessary casting to int of what's already an int that got left in w/ modifications to cache busting. Affected #: 12 files diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -80,7 +80,7 @@ "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); </script> diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -90,7 +90,7 @@ "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); </script> diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -14,7 +14,7 @@ shim: { "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(['mvc/data'], function(data) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -13,7 +13,7 @@ shim: { "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require([ 'mvc/data' ], function( data ) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -98,7 +98,7 @@ "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); var galaxy_config = ${ h.dumps( self.galaxy_config ) }; diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -50,7 +50,7 @@ require.config({ baseUrl : "${h.url_for( '/static/scripts' )}", - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' })([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ // history module is already in the dpn chain from the panel. We can re-scope it here. var historyModel = require( 'mvc/history/history-model' ), diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -49,7 +49,7 @@ require.config({ baseUrl : "${h.url_for( '/static/scripts' )}", - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require([ 'mvc/history/history-panel-annotated' ], function( panelMod ){ diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -178,7 +178,7 @@ paths : { 'jquery' : 'libs/jquery/jquery' }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' })([ 'mvc/user/user-model', panelToUse.location, diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -10,7 +10,7 @@ shim: { "libs/underscore": { exports: "_" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(["mvc/tools"], function(tools_mod) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -59,7 +59,7 @@ "libs/underscore": { exports: "_" }, "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require( ["viz/trackster"], function(trackster) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/visualization/phyloviz.mako --- a/templates/webapps/galaxy/visualization/phyloviz.mako +++ b/templates/webapps/galaxy/visualization/phyloviz.mako @@ -148,7 +148,7 @@ "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" } }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(["viz/phyloviz"], function(phyloviz_mod) { diff -r 3765ae2904ff4e2782afe3c5abec8454c97a07e3 -r 5f8bb3b239c06e00f5e661d638316baf5546974f templates/webapps/galaxy/visualization/sweepster.mako --- a/templates/webapps/galaxy/visualization/sweepster.mako +++ b/templates/webapps/galaxy/visualization/sweepster.mako @@ -117,7 +117,7 @@ "libs/d3": { exports: "d3" }, "libs/backbone/backbone": { exports: "Backbone" }, }, - urlArgs: 'v=${int(app.server_starttime)}' + urlArgs: 'v=${app.server_starttime}' }); require(["libs/d3", "viz/sweepster"], function(d3, sweepster) { https://bitbucket.org/galaxy/galaxy-central/commits/cecbf657cd9f/ Changeset: cecbf657cd9f User: dannon Date: 2015-02-26 19:32:48+00:00 Summary: Attempt at a fix for get('') in tools/params/basic.py Affected #: 1 file diff -r 5f8bb3b239c06e00f5e661d638316baf5546974f -r cecbf657cd9f9a9ba3684c1d847a1c51a3a7e06a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1982,7 +1982,7 @@ return None if not value and not self.optional: raise ValueError( "History does not include a dataset of the required format / build" ) - if value in [None, "None"]: + if value in [None, "None", '']: return None if isinstance( value, str ) and value.find( "," ) > 0: value = [ int( value_part ) for value_part in value.split( "," ) ] https://bitbucket.org/galaxy/galaxy-central/commits/71596d6f1028/ Changeset: 71596d6f1028 User: carlfeberhard Date: 2015-02-26 19:32:48+00:00 Summary: Fix visualization controller to use security.decode_id in grids Affected #: 1 file diff -r cecbf657cd9f9a9ba3684c1d847a1c51a3a7e06a -r 71596d6f10285ebb23d2a257eda3b70cb04ff655 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -128,7 +128,7 @@ class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ def filter( self, trans, user, query, history_id ): - return query.filter( model.History.id==self.decode_id(history_id) ) + return query.filter( model.History.id==trans.security.decode_id(history_id) ) class HistoryDatasetsSelectionGrid( grids.Grid ): # Grid definition. @@ -157,7 +157,7 @@ Current item for grid is the history being queried. This is a bit of hack since current_item typically means the current item in the grid. """ - return trans.sa_session.query( model.History ).get( self.decode_id( kwargs[ 'f-history' ] ) ) + return trans.sa_session.query( model.History ).get( trans.security.decode_id( kwargs[ 'f-history' ] ) ) def build_initial_query( self, trans, **kwargs ): return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table ) def apply_query_filter( self, trans, query, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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