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May 2014

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commit/galaxy-central: carlfeberhard: Style fix: use scrolling overflow for long HDA annotation lines
by commits-noreply＠bitbucket.org 27 May '14

27 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/14c8fee2aedb/ Changeset: 14c8fee2aedb User: carlfeberhard Date: 2014-05-27 17:49:47 Summary: Style fix: use scrolling overflow for long HDA annotation lines Affected #: 2 files diff -r 33b1ff4b998541ae1ca1c302919077f4f29cc57a -r 14c8fee2aedba44f1a21f233bc87412edcbc00aa static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1662,7 +1662,7 @@ .hda.dataset .dataset-body .dataset-actions .right .icon-btn:only-child{margin:0px;border-radius:3px} .hda.dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} .hda.dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.hda.dataset .dataset-body .tags-display .select2-container{min-width:0px}.hda.dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.hda.dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.hda.dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.hda.dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.hda.dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line;overflow:auto} .hda.dataset .dataset-body .annotation-display .annotation:empty{height:22px} .hda.dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} .hda.dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} diff -r 33b1ff4b998541ae1ca1c302919077f4f29cc57a -r 14c8fee2aedba44f1a21f233bc87412edcbc00aa static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -309,6 +309,7 @@ .annotation { .info-section; white-space: pre-line; + overflow: auto; } .annotation:empty { height: @icon-btn-size; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Clarify problematic members of tar archives being uploaded to Tool Shed repositories.
by commits-noreply＠bitbucket.org 27 May '14

27 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/33b1ff4b9985/ Changeset: 33b1ff4b9985 User: greg Date: 2014-05-27 17:13:05 Summary: Clarify problematic members of tar archives being uploaded to Tool Shed repositories. Affected #: 1 file diff -r 3f5ed3658cbecfcdcfa6f130a0d3a361f98d5508 -r 33b1ff4b998541ae1ca1c302919077f4f29cc57a lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -39,20 +39,25 @@ for member in archive.getmembers(): # Allow regular files and directories only if not ( member.isdir() or member.isfile() or member.islnk() ): - message = "Uploaded archives can only include regular directories and files (no symbolic links, devices, etc). Offender: %s" % str( member ) + message = "Uploaded archives can only include regular directories and files (no symbolic links, devices, etc). " + message += "The problematic member in this archive is %s," % str( member.name ) return False, message for item in [ '.hg', '..', '/' ]: if member.name.startswith( item ): - message = "Uploaded archives cannot contain .hg directories, absolute filenames starting with '/', or filenames with two dots '..'." + message = "Uploaded archives cannot contain .hg directories, absolute filenames starting with '/', or filenames with two dots '..'. " + message += "The problematic member in this archive is %s." % str( member.name ) return False, message if member.name in [ 'hgrc' ]: - message = "Uploaded archives cannot contain hgrc files." + message = "Uploaded archives cannot contain hgrc files. " + message += "The problematic member in this archive is %s." % str( member.name ) return False, message if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION and member.name != rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - message = 'Repositories of type <b>Repsoitory suite definition</b> can contain only a single file named <b>repository_dependencies.xml</b>.' + message = 'Repositories of type <b>Repository suite definition</b> can contain only a single file named <b>repository_dependencies.xml</b>.' + message += 'This archive contains a member named %s.' % str( member.name ) return False, message if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and member.name != rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: message = 'Repositories of type <b>Tool dependency definition</b> can contain only a single file named <b>tool_dependencies.xml</b>.' + message += 'This archive contains a member named %s.' % str( member.name ) return False, message return True, '' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 27 May '14

27 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/636f0270fc30/ Changeset: 636f0270fc30 Branch: next-stable User: jmchilton Date: 2014-05-27 16:06:44 Summary: Bugfix: Don't show deleted HDCAs when displaying tool selection options. Affected #: 2 files diff -r a5f097248869df64d6f16a2e7dc14c3ceffbcce1 -r 636f0270fc3009a4da3737ffd1751d40821d3cdd lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -170,7 +170,7 @@ return validated_payload def history_dataset_collections(self, history, query): - collections = history.dataset_collections + collections = history.active_dataset_collections collections = filter( query.direct_match, collections ) return collections diff -r a5f097248869df64d6f16a2e7dc14c3ceffbcce1 -r 636f0270fc3009a4da3737ffd1751d40821d3cdd lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1738,7 +1738,7 @@ dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) - for history_dataset_collection in history.dataset_collections: + for history_dataset_collection in history.active_dataset_collections: if dataset_collection_matcher.hdca_match( history_dataset_collection, reduction=reduction ): name = history_dataset_collection.name hid = str( history_dataset_collection.hid ) @@ -2042,7 +2042,7 @@ dataset_matcher = DatasetMatcher( trans, self, value, other_values ) dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) - for history_dataset_collection in history.dataset_collections: + for history_dataset_collection in history.active_dataset_collections: if not self._history_query( trans ).can_map_over( history_dataset_collection ): continue https://bitbucket.org/galaxy/galaxy-central/commits/2cab30fd7436/ Changeset: 2cab30fd7436 Branch: next-stable User: jmchilton Date: 2014-05-27 16:06:44 Summary: English fix: Spelling error in a5f0972. Affected #: 1 file diff -r 636f0270fc3009a4da3737ffd1751d40821d3cdd -r 2cab30fd7436a0e38bb3d60eea5b5fa929f62244 lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ b/lib/galaxy/dataset_collections/util.py @@ -10,7 +10,7 @@ ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." -ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element idenfier name %s." +ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element identifier name %s." def api_payload_to_create_params( payload ): https://bitbucket.org/galaxy/galaxy-central/commits/3f5ed3658cbe/ Changeset: 3f5ed3658cbe User: jmchilton Date: 2014-05-27 16:07:03 Summary: Merge latest next-stable. Affected #: 3 files diff -r 8f1f131bdeb49f876a06d748d97cfb48ec329550 -r 3f5ed3658cbecfcdcfa6f130a0d3a361f98d5508 lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -170,7 +170,7 @@ return validated_payload def history_dataset_collections(self, history, query): - collections = history.dataset_collections + collections = history.active_dataset_collections collections = filter( query.direct_match, collections ) return collections diff -r 8f1f131bdeb49f876a06d748d97cfb48ec329550 -r 3f5ed3658cbecfcdcfa6f130a0d3a361f98d5508 lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ b/lib/galaxy/dataset_collections/util.py @@ -10,7 +10,7 @@ ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." -ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element idenfier name %s." +ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element identifier name %s." def api_payload_to_create_params( payload ): diff -r 8f1f131bdeb49f876a06d748d97cfb48ec329550 -r 3f5ed3658cbecfcdcfa6f130a0d3a361f98d5508 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1738,7 +1738,7 @@ dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) - for history_dataset_collection in history.dataset_collections: + for history_dataset_collection in history.active_dataset_collections: if dataset_collection_matcher.hdca_match( history_dataset_collection, reduction=reduction ): name = history_dataset_collection.name hid = str( history_dataset_collection.hid ) @@ -2042,7 +2042,7 @@ dataset_matcher = DatasetMatcher( trans, self, value, other_values ) dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) - for history_dataset_collection in history.dataset_collections: + for history_dataset_collection in history.active_dataset_collections: if not self._history_query( trans ).can_map_over( history_dataset_collection ): continue Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 27 May '14

27 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d5125e51cefa/ Changeset: d5125e51cefa Branch: next-stable User: jmchilton Date: 2014-05-24 00:20:55 Summary: Add some more colllection creation logging. Bug report from takadonet of collection request with 280 items only creating 60 - want to know if request got chopped off by proxy or paste, there was some logic error in my code, or if it hit some sort of db/transaction limit. This logging should help dianose that (hopefully). If I find the bug, I will remove this extra logging. Affected #: 2 files diff -r 13e3b3e1c194b70dc8d17fc669d314264a000151 -r d5125e51cefab1b43bf004eaa1b57623149c7202 lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -76,6 +76,7 @@ trans.sa_session.add( output_dataset ) dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ] + log.debug("Created collection with %d elements" % ( len( dataset_collection_instance.collection.elements ) ) ) # Handle setting hid parent.add_dataset_collection( dataset_collection_instance ) elif isinstance( parent, model.LibraryFolder ): diff -r 13e3b3e1c194b70dc8d17fc669d314264a000151 -r d5125e51cefab1b43bf004eaa1b57623149c7202 lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ b/lib/galaxy/dataset_collections/util.py @@ -2,6 +2,9 @@ from galaxy import web from galaxy import model +import logging +log = logging.getLogger( __name__ ) + ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s." ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = "Dataset source new_collection requires nested element_identifiers for new collection." ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" @@ -32,6 +35,7 @@ """ Scan through the list of element identifiers supplied by the API consumer and verify the structure is valid. """ + log.debug( "Validating %d element identifiers for collection creation." % len( element_identifiers ) ) for element_identifier in element_identifiers: if "__object__" in element_identifier: message = ERROR_MESSAGE_INVALID_PARAMETER_FOUND % ( "__model_object__", element_identifier ) https://bitbucket.org/galaxy/galaxy-central/commits/a5f097248869/ Changeset: a5f097248869 Branch: next-stable User: jmchilton Date: 2014-05-27 15:20:39 Summary: Bugfix: Explicitly enforce implicit collection unique element identifier constraint. Think this is responsible for bug when collections API does not create as many collections as requested. Affected #: 2 files diff -r d5125e51cefab1b43bf004eaa1b57623149c7202 -r a5f097248869df64d6f16a2e7dc14c3ceffbcce1 lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ b/lib/galaxy/dataset_collections/util.py @@ -10,6 +10,7 @@ ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." +ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element idenfier name %s." def api_payload_to_create_params( payload ): @@ -36,6 +37,7 @@ and verify the structure is valid. """ log.debug( "Validating %d element identifiers for collection creation." % len( element_identifiers ) ) + identifier_names = set() for element_identifier in element_identifiers: if "__object__" in element_identifier: message = ERROR_MESSAGE_INVALID_PARAMETER_FOUND % ( "__model_object__", element_identifier ) @@ -43,6 +45,12 @@ if "name" not in element_identifier: message = ERROR_MESSAGE_NO_NAME % element_identifier raise exceptions.RequestParameterInvalidException( message ) + name = element_identifier[ "name" ] + if name in identifier_names: + message = ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND % name + raise exceptions.RequestParameterInvalidException( message ) + else: + identifier_names.add( name ) src = element_identifier.get( "src", "hda" ) if src not in [ "hda", "hdca", "ldda", "new_collection" ]: message = ERROR_MESSAGE_UNKNOWN_SRC % src diff -r d5125e51cefab1b43bf004eaa1b57623149c7202 -r a5f097248869df64d6f16a2e7dc14c3ceffbcce1 test/api/test_dataset_collections.py --- a/test/api/test_dataset_collections.py +++ b/test/api/test_dataset_collections.py @@ -106,6 +106,19 @@ create_response = self._post( "dataset_collections", payload ) self._assert_status_code_is( create_response, 403 ) + def test_enforces_unique_names( self ): + element_identifiers = self.dataset_collection_populator.list_identifiers( self.history_id ) + element_identifiers[ 2 ][ "name" ] = element_identifiers[ 0 ][ "name" ] + payload = dict( + instance_type="history", + history_id=self.history_id, + element_identifiers=json.dumps(element_identifiers), + collection_type="list", + ) + + create_response = self._post( "dataset_collections", payload ) + self._assert_status_code_is( create_response, 400 ) + def _check_create_response( self, create_response ): self._assert_status_code_is( create_response, 200 ) dataset_collection = create_response.json() https://bitbucket.org/galaxy/galaxy-central/commits/8f1f131bdeb4/ Changeset: 8f1f131bdeb4 User: jmchilton Date: 2014-05-27 15:21:18 Summary: Merge latest next-stable. Affected #: 2 files diff -r f94244370cfa4b6e685a5ea46a2b2d4ede42b749 -r 8f1f131bdeb49f876a06d748d97cfb48ec329550 lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ b/lib/galaxy/dataset_collections/util.py @@ -10,6 +10,7 @@ ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." +ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element idenfier name %s." def api_payload_to_create_params( payload ): @@ -36,6 +37,7 @@ and verify the structure is valid. """ log.debug( "Validating %d element identifiers for collection creation." % len( element_identifiers ) ) + identifier_names = set() for element_identifier in element_identifiers: if "__object__" in element_identifier: message = ERROR_MESSAGE_INVALID_PARAMETER_FOUND % ( "__model_object__", element_identifier ) @@ -43,6 +45,12 @@ if "name" not in element_identifier: message = ERROR_MESSAGE_NO_NAME % element_identifier raise exceptions.RequestParameterInvalidException( message ) + name = element_identifier[ "name" ] + if name in identifier_names: + message = ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND % name + raise exceptions.RequestParameterInvalidException( message ) + else: + identifier_names.add( name ) src = element_identifier.get( "src", "hda" ) if src not in [ "hda", "hdca", "ldda", "new_collection" ]: message = ERROR_MESSAGE_UNKNOWN_SRC % src diff -r f94244370cfa4b6e685a5ea46a2b2d4ede42b749 -r 8f1f131bdeb49f876a06d748d97cfb48ec329550 test/api/test_dataset_collections.py --- a/test/api/test_dataset_collections.py +++ b/test/api/test_dataset_collections.py @@ -106,6 +106,19 @@ create_response = self._post( "dataset_collections", payload ) self._assert_status_code_is( create_response, 403 ) + def test_enforces_unique_names( self ): + element_identifiers = self.dataset_collection_populator.list_identifiers( self.history_id ) + element_identifiers[ 2 ][ "name" ] = element_identifiers[ 0 ][ "name" ] + payload = dict( + instance_type="history", + history_id=self.history_id, + element_identifiers=json.dumps(element_identifiers), + collection_type="list", + ) + + create_response = self._post( "dataset_collections", payload ) + self._assert_status_code_is( create_response, 400 ) + def _check_create_response( self, create_response ): self._assert_status_code_is( create_response, 200 ) dataset_collection = create_response.json() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Ui: Update ui-tabs style
by commits-noreply＠bitbucket.org 26 May '14

26 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f94244370cfa/ Changeset: f94244370cfa User: guerler Date: 2014-05-27 06:05:24 Summary: Ui: Update ui-tabs style Affected #: 3 files diff -r c42da63a174f7695eb48ee71107b18589e034418 -r f94244370cfa4b6e685a5ea46a2b2d4ede42b749 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var 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id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+="</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"grid"},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s[t],i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=r.is_label,s=r.is_auto,o=[];s&&o.push({label:"Column: Row Number",value:"auto"});var u=t.metadata_column_types;for(var a in u)(!i&&(u[a]=="int"||u[a]=="float")||i)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});n.update(o),n.show();if(!n.exists(this.group.get(e))){var f=n.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+f+'".'),this.group.set(e,f)}n.value(this.group.get(e));var l=this;n.setOnChange(function(t){l.group.set(e,t),l.chart.set("modified",!0)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(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"select":s=new t.Select.View({id:"field_"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},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)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return 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n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+="</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.viewport_view.$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){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".active").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"grid"},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var 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scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{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:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),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_histogram/config","plugin/charts/nvd3_histogram_discrete/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,nvd3_histogram_discrete:s,highcharts_boxplot:p,heatmap:d}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r c42da63a174f7695eb48ee71107b18589e034418 -r f94244370cfa4b6e685a5ea46a2b2d4ede42b749 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1278,6 +1278,8 @@ .upload-ftp .upload-ftp-help{margin-bottom:10px} .upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px} .upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop} +.ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} +.ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} .no-highlight{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} .portlet-view{min-width:300px}.portlet-view .portlet-title-icon{float:left;font-size:1.2em;padding-top:4px} .portlet-view .portlet-title{overflow:hidden;padding:2px 5px 2px 10px} diff -r c42da63a174f7695eb48ee71107b18589e034418 -r f94244370cfa4b6e685a5ea46a2b2d4ede42b749 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -1,3 +1,16 @@ +.ui-tabs { + .ui-tabs-add { + font-size : 0.8em; + margin-right : 5px; + } + + .ui-tabs-delete { + font-size : 0.8em; + margin-left : 5px; + cursor : pointer; + } +} + .no-highlight { -webkit-user-select: none; /* webkit (safari, chrome) browsers */ -moz-user-select: none; /* mozilla browsers */ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Ui: Refactoring of ui-tabs
by commits-noreply＠bitbucket.org 26 May '14

26 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c42da63a174f/ Changeset: c42da63a174f User: guerler Date: 2014-05-27 05:57:16 Summary: Ui: Refactoring of ui-tabs Affected #: 2 files diff -r b0f8204ebc18d7b48cfc7f4940a56be22d501679 -r c42da63a174f7695eb48ee71107b18589e034418 static/scripts/mvc/ui/ui-tabs.js --- a/static/scripts/mvc/ui/ui-tabs.js +++ b/static/scripts/mvc/ui/ui-tabs.js @@ -4,17 +4,6 @@ // return var View = Backbone.View.extend( { - // visibility - visible: false, - - // elements - list: {}, - $nav: null, - $content: null, - - // first - first_tab: null, - // defaults options optionsDefault: { title_new : '', @@ -24,6 +13,12 @@ // initialize initialize : function(options) { + // configure + this.visible = false; + this.$nav = null; + this.$content = null; + this.first_tab = null; + // configure options this.options = Utils.merge(options, this.optionsDefault); @@ -72,41 +67,40 @@ // append add: function(options) { + // self + var self = this; + // get tab id var id = options.id; // create tab object - var tab = { - $title : $(this._template_tab(options)), - $content : $(this._template_tab_content(options)), - removable : options.ondel ? true : false - } + var $tab_title = $(this._template_tab(options)); + var $tab_content = $(this._template_tab_content(options)); // add to list - this.list[id] = tab; + this.list[id] = options.ondel ? true : false; // add a new tab either before the add-new-tab tab or behind the last tab if (this.options.onnew) { - this.$nav.find('#new-tab').before(tab.$title); + this.$nav.find('#new-tab').before($tab_title); } else { - this.$nav.append(tab.$title); + this.$nav.append($tab_title); } // add content - tab.$content.append(options.$el); - this.$content.append(tab.$content); + $tab_content.append(options.$el); + this.$content.append($tab_content); // activate this tab if this is the first tab if (_.size(this.list) == 1) { - tab.$title.addClass('active'); - tab.$content.addClass('active'); + $tab_title.addClass('active'); + $tab_content.addClass('active'); this.first_tab = id; } // add click event to remove tab if (options.ondel) { - var self = this; - var $del_icon = tab.$title.find('#delete'); + var $del_icon = $tab_title.find('#delete'); $del_icon.tooltip({title: 'Delete this tab', placement: 'bottom', container: self.$el}); $del_icon.on('click', function() { $del_icon.tooltip('destroy'); @@ -117,20 +111,24 @@ } // add custom click event handler - if (options.onclick) { - tab.$title.on('click', function() { + $tab_title.on('click', function(e) { + // prevent default + e.preventDefault(); + + // click + if (options.onclick) { options.onclick(); - }); - } + } else { + self.show(id); + } + }); }, // delete tab del: function(id) { - // delete tab from list/dom - var tab = this.list[id]; - tab.$title.remove(); - tab.$content.remove(); - delete tab; + // delete tab from dom + this.$el.find('#tab-' + id).remove(); + this.$el.find('#tab-content-' + id).remove(); // check if first tab has been deleted if (this.first_tab == id) { @@ -145,10 +143,8 @@ // delete tab delRemovable: function() { - // delete tab from list/dom for (var id in this.list) { - var tab = this.list[id]; - if (tab.removable) { + if (this.list[id]) { this.del(id); } } @@ -162,7 +158,9 @@ // show selected tab if (id) { - this.list[id].$title.find('a').tab('show'); + this.$el.find('.active').removeClass('active'); + this.$el.find('#tab-' + id).addClass('active'); + this.$el.find('#tab-content-' + id).addClass('active'); } }, @@ -191,7 +189,7 @@ // title title: function(id, new_title) { - var $el = this.list[id].$title.find('#text'); + var $el = this.$el.find('#tab-title-text-' + id); if (new_title) { $el.html(new_title); } @@ -200,11 +198,11 @@ // fill template _template: function(options) { - return '<div class="tabbable tabs-left">' + - '<ul class="tab-navigation nav nav-tabs">' + + 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 class="tab-content"/>' + + '<div id="tab-content" class="tab-content"/>' + '</div>'; }, @@ -212,7 +210,7 @@ _template_tab_new: function(options) { return '<li id="new-tab">' + '<a href="javascript:void(0);">' + - '<i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>' + + '<i class="ui-tabs-add fa fa-plus-circle"/>' + options.title_new + '</a>' + '</li>'; @@ -220,12 +218,12 @@ // fill template tab _template_tab: function(options) { - var tmpl = '<li id="title-' + options.id + '">' + - '<a title="" href="#tab-' + options.id + '" data-toggle="tab" data-original-title="">' + - '<span id="text">' + options.title + '</span>'; + var tmpl = '<li id="tab-' + options.id + '">' + + '<a id="tab-title-link-' + options.id + '" title="" href="#tab-content-' + options.id + '" data-original-title="">' + + '<span id="tab-title-text-' + options.id + '">' + options.title + '</span>'; if (options.ondel) { - tmpl += '<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'; + tmpl += '<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'; } tmpl += '</a>' + @@ -236,7 +234,7 @@ // fill template tab content _template_tab_content: function(options) { - return '<div id="tab-' + options.id + '" class="tab-pane"/>'; + return '<div id="tab-content-' + options.id + '" class="tab-pane"/>'; } }); diff -r b0f8204ebc18d7b48cfc7f4940a56be22d501679 -r c42da63a174f7695eb48ee71107b18589e034418 static/scripts/packed/mvc/ui/ui-tabs.js --- a/static/scripts/packed/mvc/ui/ui-tabs.js +++ b/static/scripts/packed/mvc/ui/ui-tabs.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},add:function(e){var g=e.id;var f={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?true:false};this.list[g]=f;if(this.options.onnew){this.$nav.find("#new-tab").before(f.$title)}else{this.$nav.append(f.$title)}f.$content.append(e.$el);this.$content.append(f.$content);if(_.size(this.list)==1){f.$title.addClass("active");f.$content.addClass("active");this.first_tab=g}if(e.ondel){var d=this;var c=f.$title.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:d.$el});c.on("click",function(){c.tooltip("destroy");d.$el.find(".tooltip").remove();e.ondel();return false})}if(e.onclick){f.$title.on("click",function(){e.onclick()})}},del:function(d){var c=this.list[d];c.$title.remove();c.$content.remove();delete c;if(this.first_tab==d){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var d in this.list){var c=this.list[d];if(c.removable){this.del(d)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.list[c].$title.find("a").tab("show")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.list[e].$title.find("#text");if(d){c.html(d)}return c.html()},_template:function(c){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="title-'+d.id+'"><a title="" href="#tab-'+d.id+'" data-toggle="tab" data-original-title=""><span id="text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.visible=false;this.$nav=null;this.$content=null;this.first_tab=null;this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},add:function(f){var e=this;var h=f.id;var g=$(this._template_tab(f));var d=$(this._template_tab_content(f));this.list[h]=f.ondel?true:false;if(this.options.onnew){this.$nav.find("#new-tab").before(g)}else{this.$nav.append(g)}d.append(f.$el);this.$content.append(d);if(_.size(this.list)==1){g.addClass("active");d.addClass("active");this.first_tab=h}if(f.ondel){var c=g.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el});c.on("click",function(){c.tooltip("destroy");e.$el.find(".tooltip").remove();f.ondel();return false})}g.on("click",function(i){i.preventDefault();if(f.onclick){f.onclick()}else{e.show(h)}})},del:function(c){this.$el.find("#tab-"+c).remove();this.$el.find("#tab-content-"+c).remove();if(this.first_tab==c){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var c in this.list){if(this.list[c]){this.del(c)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.$el.find(".active").removeClass("active");this.$el.find("#tab-"+c).addClass("active");this.$el.find("#tab-content-"+c).addClass("active")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.$el.find("#tab-title-text-"+e);if(d){c.html(d)}return c.html()},_template:function(c){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(c){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="tab-'+d.id+'"><a id="tab-title-link-'+d.id+'" title="" href="#tab-content-'+d.id+'" data-original-title=""><span id="tab-title-text-'+d.id+'">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-content-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 May '14

25 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/13e3b3e1c194/ Changeset: 13e3b3e1c194 Branch: next-stable User: guerler Date: 2014-05-25 22:46:02 Summary: Charts: Pack scripts Affected #: 1 file diff -r 6d7b80314cd1b74db1cc1c714c42f4b5d66dfeb9 -r 13e3b3e1c194b70dc8d17fc669d314264a000151 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var 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id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=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.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","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.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;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(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" 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r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},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)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw 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u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_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()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar 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btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","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,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;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(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},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.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},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)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_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()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_histogram_discrete/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram (discrete)",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",columns:{y:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others"})}),define("plugin/charts/nvd3_line_focus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others"})}),define("plugin/charts/nvd3_pie/config",[],function(){return{title:"Pie chart",library:"nvd3.js",category:"Area charts",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{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:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),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_histogram/config","plugin/charts/nvd3_histogram_discrete/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,highcharts_boxplot:p,heatmap:d}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/b0f8204ebc18/ Changeset: b0f8204ebc18 User: guerler Date: 2014-05-25 22:56:34 Summary: Merge Affected #: 1 file diff -r 8160200aa4a2d75ccf88953098d7ad1e2227606f -r b0f8204ebc18d7b48cfc7f4940a56be22d501679 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" 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n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+="</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"grid"},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s[t],i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=r.is_label,s=r.is_auto,o=[];s&&o.push({label:"Column: Row Number",value:"auto"});var u=t.metadata_column_types;for(var a in u)(!i&&(u[a]=="int"||u[a]=="float")||i)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});n.update(o),n.show();if(!n.exists(this.group.get(e))){var f=n.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+f+'".'),this.group.set(e,f)}n.value(this.group.get(e));var l=this;n.setOnChange(function(t){l.group.set(e,t),l.chart.set("modified",!0)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(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"select":s=new t.Select.View({id:"field_"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},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)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new 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href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+="</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var 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$.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis"}},settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_histogram_discrete/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram (discrete)",category:"Data processing 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a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ 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

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 May '14

25 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d7b80314cd1/ Changeset: 6d7b80314cd1 Branch: next-stable User: guerler Date: 2014-05-25 22:40:05 Summary: Charts: Fix queue Affected #: 1 file diff -r c7fdc917044bf6b72d4ea3d476113c324e583bb4 -r 6d7b80314cd1b74db1cc1c714c42f4b5d66dfeb9 config/plugins/visualizations/charts/static/library/deferred.js --- a/config/plugins/visualizations/charts/static/library/deferred.js +++ b/config/plugins/visualizations/charts/static/library/deferred.js @@ -20,11 +20,14 @@ this.on('refresh', function() { if (this.counter == 0) { for (var index in this.queue) { - // execute callback - this.queue[index](); + // get callback + var callback = this.queue[index]; // remove callback this.queue.splice(index, 1); + + // execute callback + callback(); } } }); https://bitbucket.org/galaxy/galaxy-central/commits/8160200aa4a2/ Changeset: 8160200aa4a2 User: guerler Date: 2014-05-25 22:40:49 Summary: Merge Affected #: 1 file diff -r 7ef5ea0fc02cdb4af301832f27672210b1942d5b -r 8160200aa4a2d75ccf88953098d7ad1e2227606f config/plugins/visualizations/charts/static/library/deferred.js --- a/config/plugins/visualizations/charts/static/library/deferred.js +++ b/config/plugins/visualizations/charts/static/library/deferred.js @@ -20,11 +20,14 @@ this.on('refresh', function() { if (this.counter == 0) { for (var index in this.queue) { - // execute callback - this.queue[index](); + // get callback + var callback = this.queue[index]; // remove callback this.queue.splice(index, 1); + + // execute callback + callback(); } } }); 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: guerler: Charts: Update table form
by commits-noreply＠bitbucket.org 25 May '14

25 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ef5ea0fc02c/ Changeset: 7ef5ea0fc02c User: guerler Date: 2014-05-25 22:36:40 Summary: Charts: Update table form Affected #: 3 files diff -r 57302d6608addb1fd6154483e93a0f0abf3f5cb3 -r 7ef5ea0fc02cdb4af301832f27672210b1942d5b config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu 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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500,screenshot_url:"http://export.highcharts.com/"}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["x_axis_tick"]},{label:"Auto",value:"auto",hide:["x_axis_tick"]},{label:"Float",value:"f",show:["x_axis_tick"]},{label:"Exponent",value:"e",show:["x_axis_tick"]},{label:"Integer",value:"d",hide:["x_axis_tick"]},{label:"Percentage",value:"p",show:["x_axis_tick"]},{label:"Rounded",value:"r",show:["x_axis_tick"]},{label:"SI-prefix",value:"s",show:["x_axis_tick"]}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick 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axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis"}},settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_histogram_discrete/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram (discrete)",category:"Data processing 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legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"},y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{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:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),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_histogram/config","plugin/charts/nvd3_histogram_discrete/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,nvd3_histogram_discrete:s,highcharts_boxplot:p,heatmap:d}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new 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n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu 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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. 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The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var 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window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.viewport_view.$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){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},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.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"grid"},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s[t],i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=r.is_label,s=r.is_auto,o=[];s&&o.push({label:"Column: Row Number",value:"auto"});var u=t.metadata_column_types;for(var a in u)(!i&&(u[a]=="int"||u[a]=="float")||i)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});n.update(o),n.show();if(!n.exists(this.group.get(e))){var f=n.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+f+'".'),this.group.set(e,f)}n.value(this.group.get(e));var l=this;n.setOnChange(function(t){l.group.set(e,t),l.chart.set("modified",!0)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field_"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"select":s=new t.Select.View({id:"field_"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}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),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var 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Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500,screenshot_url:"http://export.highcharts.com/"}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:["x_axis_tick"]},{label:"Auto",value:"auto",hide:["x_axis_tick"]},{label:"Float",value:"f",show:["x_axis_tick"]},{label:"Exponent",value:"e",show:["x_axis_tick"]},{label:"Integer",value:"d",hide:["x_axis_tick"]},{label:"Percentage",value:"p",show:["x_axis_tick"]},{label:"Rounded",value:"r",show:["x_axis_tick"]},{label:"SI-prefix",value:"s",show:["x_axis_tick"]}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick 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y-axis"}}})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{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:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by 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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_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,nvd3_histogram_discrete:s,highcharts_boxplot:p,heatmap:d}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 57302d6608addb1fd6154483e93a0f0abf3f5cb3 -r 7ef5ea0fc02cdb4af301832f27672210b1942d5b config/plugins/visualizations/charts/static/library/ui-table-form.js --- a/config/plugins/visualizations/charts/static/library/ui-table-form.js +++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js @@ -5,6 +5,13 @@ // widget var View = Backbone.View.extend( { + // options + optionsDefault: { + title : '', + content : '', + mode : '' + }, + // elements list: [], diff -r 57302d6608addb1fd6154483e93a0f0abf3f5cb3 -r 7ef5ea0fc02cdb4af301832f27672210b1942d5b config/plugins/visualizations/charts/static/library/ui-table.js --- a/config/plugins/visualizations/charts/static/library/ui-table.js +++ b/config/plugins/visualizations/charts/static/library/ui-table.js @@ -13,7 +13,8 @@ content : 'No content available.', onchange : null, ondblclick : null, - onconfirm : null + onconfirm : null, + cls : 'grid' }, // events @@ -197,7 +198,7 @@ _template: function(options) { return '<div>' + - '<table class="grid">' + + '<table class="' + options.cls + '">' + '<thead></thead>' + '<tbody style="cursor: pointer;"></tbody>' + '</table>' + 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: guerler: Charts: Pack scripts
by commits-noreply＠bitbucket.org 24 May '14

24 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/57302d6608ad/ Changeset: 57302d6608ad User: guerler Date: 2014-05-24 07:16:54 Summary: Charts: Pack scripts Affected #: 1 file diff -r 8398063345841d5c9530d9326661405df30c2125 -r 57302d6608addb1fd6154483e93a0f0abf3f5cb3 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="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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this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+="</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" 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r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s[t],i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=r.is_label,s=r.is_auto,o=[];s&&o.push({label:"Column: Row Number",value:"auto"});var u=t.metadata_column_types;for(var a in u)(!i&&(u[a]=="int"||u[a]=="float")||i)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});n.update(o),n.show();if(!n.exists(this.group.get(e))){var f=n.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+f+'".'),this.group.set(e,f)}n.value(this.group.get(e));var l=this;n.setOnChange(function(t){l.group.set(e,t),l.chart.set("modified",!0)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"select":s=new t.Select.View({id:e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});s&&(s.show&&i.$el.find("#"+s.show).fadeIn("fast"),s.hide&&i.$el.find("#"+s.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},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)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_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()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500,screenshot_url:"http://export.highcharts.com/"}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the 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btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+="</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){var s=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);n(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),o+=s.serializeToString(this)}),r(e,t,{filename:i||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function n(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function r(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find("container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info")),t.hide();var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning");break;default:r.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.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_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.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:new t.ButtonIcon({icon:"fa-camera",tooltip:"Download PDF-file ("+o.app.config.get("screenshot_url")+")",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$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.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var 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o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new 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axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0},y:{title:"Values for y-axis"}},settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_histogram_discrete/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram (discrete)",category:"Data processing 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donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"},y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts",columns:{y:{title:"Values for y-axis"}}})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{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:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),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_histogram/config","plugin/charts/nvd3_histogram_discrete/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:l,nvd3_stackedarea_full:c,nvd3_stackedarea_stream:h,nvd3_line:o,nvd3_line_focus:u,nvd3_scatter:f,nvd3_pie:a,nvd3_histogram:i,nvd3_histogram_discrete:s,highcharts_boxplot:p,heatmap:d}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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