January 2015 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Jan '15

26 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2ea487b70602/ Changeset: 2ea487b70602 User: dannon Date: 2015-01-26 13:54:29+00:00 Summary: Log when using virtualenv at Galaxy startup. Affected #: 1 file diff -r 36a5b25e0d33efdaaa0a6abb96468f648ee206f5 -r 2ea487b70602bd94f442243e27f00fca92693c33 run.sh --- a/run.sh +++ b/run.sh @@ -6,6 +6,7 @@ # should run this instance in. if [ -d .venv ]; then + printf "Activating virtualenv at %s/.venv\n" $(pwd) . .venv/bin/activate fi https://bitbucket.org/galaxy/galaxy-central/commits/39f3f0586c48/ Changeset: 39f3f0586c48 User: dannon Date: 2015-01-26 13:58:29+00:00 Summary: Allow admin users to change user information (like email addresses) when using remote_auth; otherwise should a user email address change you had to manually edit the database. Affected #: 1 file diff -r 2ea487b70602bd94f442243e27f00fca92693c33 -r 39f3f0586c48f81452e3a7a6af1f5e97c4ef8ed0 lib/galaxy/web/framework/middleware/remoteuser.py --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -64,7 +64,7 @@ # If the secret header is enabled, we expect upstream to send along some key # in HTTP_GX_SECRET, so we'll need to compare that here to the correct value - # + # # This is not an ideal location for this function. The reason being # that because this check is done BEFORE the REMOTE_USER check, it is # possible to attack the GX_SECRET key without having correct @@ -79,8 +79,8 @@ title = "Access to Galaxy is denied" message = """ Galaxy is configured to authenticate users via an external - method (such as HTTP authentication in Apache), but an - incorrect shared secret key was provided by the + method (such as HTTP authentication in Apache), but an + incorrect shared secret key was provided by the upstream (proxy) server.</p><p>Please contact your local Galaxy administrator. The variable <code>remote_user_secret</code> and @@ -88,7 +88,7 @@ access Galaxy. """ return self.error( start_response, title, message ) - + if not environ.get(self.remote_user_header, '(null)').startswith('(null)'): if not environ[ self.remote_user_header ].count( '@' ): if self.maildomain is not None: @@ -114,6 +114,8 @@ pass # admins can create users elif path_info.startswith( '/user/logout' ) and environ[ self.remote_user_header ] in self.admin_users: pass # Admin users may be impersonating, allow logout. + elif path_info.startswith( '/user/manage_user_info' ) and environ[ self.remote_user_header ] in self.admin_users: + pass # Admin users need to be able to change user information elif path_info.startswith( '/user/api_keys' ): pass # api keys can be managed when remote_user is in use elif path_info.startswith( '/user/edit_username' ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Toolbox: Watch even empty directories if they are explicitly tool_dir specified.
by commits-noreply＠bitbucket.org 25 Jan '15

25 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/36a5b25e0d33/ Changeset: 36a5b25e0d33 User: jmchilton Date: 2015-01-26 00:18:53+00:00 Summary: Toolbox: Watch even empty directories if they are explicitly tool_dir specified. Affected #: 1 file diff -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 -r 36a5b25e0d33efdaaa0a6abb96468f648ee206f5 lib/galaxy/tools/toolbox/base.py --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -759,9 +759,9 @@ def _load_tooldir_tag_set(self, sub_elem, elems, tool_path, integrated_elems, load_panel_dict): directory = os.path.join( tool_path, sub_elem.attrib.get("dir") ) recursive = string_as_bool( sub_elem.attrib.get("recursive", True) ) - self.__watch_directory( directory, elems, integrated_elems, load_panel_dict, recursive ) + self.__watch_directory( directory, elems, integrated_elems, load_panel_dict, recursive, force_watch=True ) - def __watch_directory( self, directory, elems, integrated_elems, load_panel_dict, recursive): + def __watch_directory( self, directory, elems, integrated_elems, load_panel_dict, recursive, force_watch=False ): def quick_load( tool_file, async=True ): try: @@ -793,7 +793,7 @@ elif name.endswith( ".xml" ): quick_load( child_path, async=False ) tool_loaded = True - if tool_loaded: + if tool_loaded or force_watch: self._tool_watcher.watch_directory( directory, quick_load ) def load_tool( self, config_file, guid=None, repository_id=None, **kwds ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Upload: Remove spaces
by commits-noreply＠bitbucket.org 24 Jan '15

24 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31cb0fdae229/ Changeset: 31cb0fdae229 User: guerler Date: 2015-01-24 08:53:07+00:00 Summary: Upload: Remove spaces Affected #: 7 files diff -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 client/galaxy/scripts/mvc/ui/ui-misc.js --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -458,25 +458,25 @@ class_partial : 'fa fa-minus-square-o', value : false }, - + // initialize initialize : function(options) { // configure options this.options = Utils.merge(options, this.optionsDefault); - + // create new element this.setElement($('<div/>')); - + // set initial value this.value(Boolean(this.options.value)); - + // add event handler var self = this; this.$el.on('click', function() { self.value(!self.current); }); }, - + // value value : function (new_val) { if (new_val !== undefined) { diff -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 client/galaxy/scripts/mvc/upload/upload-row.js --- a/client/galaxy/scripts/mvc/upload/upload-row.js +++ b/client/galaxy/scripts/mvc/upload/upload-row.js @@ -3,7 +3,7 @@ 'mvc/upload/upload-model', 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', - 'mvc/ui/ui-select',], + 'mvc/ui/ui-select'], function( Utils, UploadModel, @@ -125,7 +125,7 @@ it.find('#space_to_tabs').on('change', function(e) { self.model.set('space_to_tabs', $(e.target).prop('checked')); }); - + // // model events // diff -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 client/galaxy/scripts/mvc/upload/upload-view.js --- a/client/galaxy/scripts/mvc/upload/upload-view.js +++ b/client/galaxy/scripts/mvc/upload/upload-view.js @@ -40,7 +40,7 @@ // extension selector select_extension : null, - + // genome selector select_genome: null, @@ -226,7 +226,7 @@ container : self.$el.parent().find('#header-extension'), value : self.list_extensions[0] }); - + // handle extension info popover self.$el.parent().find('#header-extension-info').on('click' , function(e) { self.showExtensionInfo({ diff -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -458,25 +458,25 @@ class_partial : 'fa fa-minus-square-o', value : false }, - + // initialize initialize : function(options) { // configure options this.options = Utils.merge(options, this.optionsDefault); - + // create new element this.setElement($('<div/>')); - + // set initial value this.value(Boolean(this.options.value)); - + // add event handler var self = this; this.$el.on('click', function() { self.value(!self.current); }); }, - + // value value : function (new_val) { if (new_val !== undefined) { diff -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -3,7 +3,7 @@ 'mvc/upload/upload-model', 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', - 'mvc/ui/ui-select',], + 'mvc/ui/ui-select'], function( Utils, UploadModel, @@ -125,7 +125,7 @@ it.find('#space_to_tabs').on('change', function(e) { self.model.set('space_to_tabs', $(e.target).prop('checked')); }); - + // // model events // diff -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -40,7 +40,7 @@ // extension selector select_extension : null, - + // genome selector select_genome: null, @@ -226,7 +226,7 @@ container : self.$el.parent().find('#header-extension'), value : self.list_extensions[0] }); - + // handle extension info popover self.$el.parent().find('#header-extension-info').on('click' , function(e) { self.showExtensionInfo({ diff -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 -r 31cb0fdae2298b2a7ad882c465fa88ec98082f26 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select",],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(k,h){this.app=k;var f=this;this.model=new b.Model(h);this.setElement(this._template(h));var j=this.$el;this.settings=new c.View({title:"Upload configuration",container:j.find("#settings"),placement:"bottom"});var i=this.app.select_genome.value();this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:j.find("#genome"),value:i});this.model.set("genome",i);var g=this.app.select_extension.value();this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:j.find("#extension"),value:g});this.model.set("extension",g);j.find("#symbol").on("click",function(){f._removeRow()});j.find("#extension-info").on("click",function(l){f.app.showExtensionInfo({$el:$(l.target),title:f.select_extension.text(),extension:f.select_extension.value()})}).on("mousedown",function(l){l.preventDefault()});j.find("#settings").on("click",function(l){f._showSettings()}).on("mousedown",function(l){l.preventDefault()});j.find("#text-content").on("keyup",function(l){f.model.set("url_paste",$(l.target).val());f.model.set("file_size",$(l.target).val().length)});j.find("#space_to_tabs").on("change",function(l){f.model.set("space_to_tabs",$(l.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:extension",function(){f._refreshExtension()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div class="name-column"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(k,h){this.app=k;var f=this;this.model=new b.Model(h);this.setElement(this._template(h));var j=this.$el;this.settings=new c.View({title:"Upload configuration",container:j.find("#settings"),placement:"bottom"});var i=this.app.select_genome.value();this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:j.find("#genome"),value:i});this.model.set("genome",i);var g=this.app.select_extension.value();this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:j.find("#extension"),value:g});this.model.set("extension",g);j.find("#symbol").on("click",function(){f._removeRow()});j.find("#extension-info").on("click",function(l){f.app.showExtensionInfo({$el:$(l.target),title:f.select_extension.text(),extension:f.select_extension.value()})}).on("mousedown",function(l){l.preventDefault()});j.find("#settings").on("click",function(l){f._showSettings()}).on("mousedown",function(l){l.preventDefault()});j.find("#text-content").on("keyup",function(l){f.model.set("url_paste",$(l.target).val());f.model.set("file_size",$(l.target).val().length)});j.find("#space_to_tabs").on("change",function(l){f.model.set("space_to_tabs",$(l.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:extension",function(){f._refreshExtension()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div class="name-column"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Upload: Add additional options, revise merged pull request
by commits-noreply＠bitbucket.org 24 Jan '15

24 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc3357ffb6d9/ Changeset: dc3357ffb6d9 User: guerler Date: 2015-01-24 08:49:12+00:00 Summary: Upload: Add additional options, revise merged pull request Affected #: 15 files diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 client/galaxy/scripts/mvc/ui/ui-misc.js --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -448,6 +448,54 @@ } }); +// plugin +var CheckButton = Backbone.View.extend({ + + // default options + optionsDefault: { + class_add : 'fa fa-square-o', + class_remove : 'fa fa-check-square-o', + class_partial : 'fa fa-minus-square-o', + value : false + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement($('<div/>')); + + // set initial value + this.value(Boolean(this.options.value)); + + // add event handler + var self = this; + this.$el.on('click', function() { + self.value(!self.current); + }); + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.current = new_val; + if (new_val) { + this.$el.removeClass() + .addClass('ui-checkbutton') + .addClass(this.options.class_remove); + } else { + this.$el.removeClass() + .addClass('ui-checkbutton') + .addClass(this.options.class_add); + } + this.options.onchange && this.options.onchange(new_val); + } + return this.current; + } +}); + // return return { Anchor : Anchor, @@ -463,6 +511,7 @@ RadioButton : Options.RadioButton, Checkbox : Options.Checkbox, Radio : Options.Radio, + CheckButton : CheckButton, Searchbox : Searchbox, Select : Select, Hidden : Hidden, diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 client/galaxy/scripts/mvc/upload/upload-model.js --- a/client/galaxy/scripts/mvc/upload/upload-model.js +++ b/client/galaxy/scripts/mvc/upload/upload-model.js @@ -14,8 +14,6 @@ file_type : null, file_path : '', percentage : 0, - row : null, - // settings space_to_tabs : false, to_posix_lines : true } diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 client/galaxy/scripts/mvc/upload/upload-row.js --- a/client/galaxy/scripts/mvc/upload/upload-row.js +++ b/client/galaxy/scripts/mvc/upload/upload-row.js @@ -3,7 +3,7 @@ 'mvc/upload/upload-model', 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', - 'mvc/ui/ui-select'], + 'mvc/ui/ui-select',], function( Utils, UploadModel, @@ -42,9 +42,6 @@ // link app this.app = app; - // default value for extension of files - var default_ext = 'Auto-detect'; - // link this var self = this; @@ -64,6 +61,9 @@ placement : 'bottom' }); + // initialize default genome through default select field + var default_genome = this.app.select_genome.value(); + // select genomes this.select_genome = new Select.View({ css: 'genome', @@ -72,39 +72,29 @@ }, data: self.app.list_genomes, container: it.find('#genome'), - value: self.model.get('genome') + value: default_genome }); // initialize genome - this.model.set('genome', self.select_genome.value()); + this.model.set('genome', default_genome); - // ensure files added after an individual row has changed - // default to Auto-detect instead of --- - if(!(this.app.select_extension.value() === '---')){ - this.default_ext = this.app.select_extension.value(); - } - + // initialize default extension through default select field + var default_extension = this.app.select_extension.value(); + // select extension this.select_extension = new Select.View({ css: 'extension', onchange : function() { self.model.set('extension', self.select_extension.value()); - // if user has changed individual row type, then change "set all" - // type to '---' - if(!(self.select_extension.value() === app.select_extension.value())) - { - var newExte = '---'; - app.select_extension.value(newExte); - } }, data: self.app.list_extensions, container: it.find('#extension'), - value: self.default_ext + value: default_extension }); // initialize extension - this.model.set('extension', self.select_extension.value()); - + this.model.set('extension', default_extension); + // // ui events // @@ -113,8 +103,13 @@ it.find('#symbol').on('click', function() { self._removeRow(); }); // handle extension info popover - it.find('#extension-info').on('click' , function(e) { self._showExtensionInfo(); }) - .on('mousedown', function(e) { e.preventDefault(); }); + it.find('#extension-info').on('click' , function(e) { + self.app.showExtensionInfo({ + $el : $(e.target), + title : self.select_extension.text(), + extension : self.select_extension.value() + }); + }).on('mousedown', function(e) { e.preventDefault(); }); // handle settings popover it.find('#settings').on('click' , function(e) { self._showSettings(); }) @@ -130,7 +125,7 @@ it.find('#space_to_tabs').on('change', function(e) { self.model.set('space_to_tabs', $(e.target).prop('checked')); }); - + // // model events // @@ -146,6 +141,9 @@ this.model.on('change:genome', function() { self._refreshGenome(); }); + this.model.on('change:extension', function() { + self._refreshExtension(); + }); this.model.on('change:file_size', function() { self._refreshFileSize(); }); @@ -155,7 +153,6 @@ this.app.collection.on('reset', function() { self.remove(); }); - self.model.set('row', self); }, // render @@ -175,8 +172,9 @@ it.find('#size').html(Utils.bytesToString (file_size)); // remove mode class - it.find('#mode').removeClass() - .addClass('mode'); + it.find('#mode') + .removeClass() + .addClass('mode'); // activate text field if file is new if (file_mode == 'new') { @@ -229,11 +227,14 @@ // handle model events // - // genome + // update extension + _refreshExtension: function() { + this.select_extension.value(this.model.get('extension')); + }, + + // update genome _refreshGenome: function() { - // update genome info on screen - var genome = this.model.get('genome'); - this.select_genome.value(genome); + this.select_genome.value(this.model.get('genome')); }, // progress @@ -327,33 +328,6 @@ }, // attach file info popup - _showExtensionInfo : function() { - // initialize - var $el = $(this.el).find('#extension-info'); - var extension = this.model.get('extension'); - var title = this.select_extension.text(); - var description = _.findWhere(this.app.list_extensions, {'id': extension}); - - // create popup - if (!this.extension_popup) { - this.extension_popup = new Popover.View({ - placement: 'bottom', - container: $el - }); - } - - // show / hide popup - if (!this.extension_popup.visible) { - this.extension_popup.title(title); - this.extension_popup.empty(); - this.extension_popup.append(this._templateDescription(description)); - this.extension_popup.show(); - } else { - this.extension_popup.hide(); - } - }, - - // attach file info popup _showSettings : function() { // check if popover is visible if (!this.settings.visible) { @@ -368,23 +342,10 @@ }, // template - _templateDescription: function(options) { - if (options.description) { - var tmpl = options.description; - if (options.description_url) { - tmpl += ' (<a href="' + options.description_url + '" target="_blank">read more</a>)'; - } - return tmpl; - } else { - return 'There is no description available for this file extension.'; - } - }, - - // template _template: function(options) { return '<tr id="upload-item-' + options.id + '" class="upload-item">' + '<td>' + - '<div style="position: relative;">' + + '<div class="name-column">' + '<div id="mode"></div>' + '<div id="title" class="title"></div>' + '<div id="text" class="text">' + diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 client/galaxy/scripts/mvc/upload/upload-view.js --- a/client/galaxy/scripts/mvc/upload/upload-view.js +++ b/client/galaxy/scripts/mvc/upload/upload-view.js @@ -23,7 +23,7 @@ return Backbone.View.extend({ // options options : { - nginx_upload_path : '' + nginx_upload_path : '' }, // own modal @@ -40,6 +40,9 @@ // extension selector select_extension : null, + + // genome selector + select_genome: null, // current upload size upload_size: 0, @@ -130,14 +133,6 @@ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; }); - // add the '---' extension for use when the row types are changed individually - self.list_extensions.push({ - id : "---", - text : "---", - description : "", - description_url : "" - }); - // add auto field if (!self.options.datatypes_disable_auto) { self.list_extensions.unshift(self.auto); @@ -167,14 +162,6 @@ this.collection.on('remove', function(item) { self._eventRemove(item); }); - this.collection.on('change:genome', function(item) { - var genome = item.get('genome'); - self.collection.each(function(item) { - if (item.get('status') == 'init' && item.get('genome') == '?') { - item.set('genome', genome); - } - }); - }); }, // @@ -232,28 +219,30 @@ container : button }); - // select extension + // select extension this.select_extension = new Select.View({ - css: 'extension', - onchange : function() { - var newExten = self.select_extension.value() - var len = self.collection.models.length; - // Only trigger changing the rows if the "set all" isn't set to '---' - // Prevents recursively changing the rows after an individual row has been changed - if(!(newExten === '---')){ - for(i = 0; i < len; i++){ - self.collection.models[i].attributes['row'].select_extension.value(newExten); - } - } - }, - data: self.list_extensions, - container: self.$el.parents().find('#extension'), - value: self.list_extensions[0] + css : 'header-selection', + data : self.list_extensions, + container : self.$el.parent().find('#header-extension'), + value : self.list_extensions[0] }); - + // handle extension info popover - self.$el.parents().find('#extension-info_out').on('click' , function(e) { self._showExtensionInfo(); }) - .on('mousedown', function(e) { e.preventDefault(); }); + self.$el.parent().find('#header-extension-info').on('click' , function(e) { + self.showExtensionInfo({ + $el : $(e.target), + title : self.select_extension.text(), + extension : self.select_extension.value() + }); + }).on('mousedown', function(e) { e.preventDefault(); }); + + // genome extension + this.select_genome = new Select.View({ + css : 'header-selection', + data : self.list_genomes, + container : self.$el.parent().find('#header-genome'), + value : self.list_genomes[0] + }); } // show modal @@ -266,45 +255,27 @@ this._updateScreen(); }, - _showExtensionInfo : function() { + showExtensionInfo : function(options) { // initialize var self = this; - var $el = $(this.el).parents().find('#extension-info_out'); - var extension = self.select_extension.value(); - - var title = this.select_extension.text(); - + var $el = options.$el; + var extension = options.extension; + var title = options.title; var description = _.findWhere(self.list_extensions, {'id': extension}); // create popup - if (!this.extension_popup) { - this.extension_popup = new Popover.View({ - placement: 'bottom', - container: $el - }); - } - - // show / hide popup - if (!this.extension_popup.visible) { - this.extension_popup.title(title); - this.extension_popup.empty(); - this.extension_popup.append(this._templateDescription(description)); - this.extension_popup.show(); - } else { - this.extension_popup.hide(); - } - }, - - _templateDescription: function(options) { - if (options.description) { - var tmpl = options.description; - if (options.description_url) { - tmpl += ' (<a href="' + options.description_url + '" target="_blank">read more</a>)'; - } - return tmpl; - } else { - return 'There is no description available for this file extension.'; - } + this.extension_popup && this.extension_popup.remove(); + this.extension_popup = new Popover.View({ + placement: 'bottom', + container: $el, + destroy: true + }); + + // add content and show popup + this.extension_popup.title(title); + this.extension_popup.empty(); + this.extension_popup.append(this._templateDescription(description)); + this.extension_popup.show(); }, // @@ -593,6 +564,7 @@ // reset value for universal type drop-down this.select_extension.value(this.list_extensions[0]); + this.select_genome.value(this.list_genomes[0]); // reset button this.ui_button.set('percentage', 0); @@ -684,12 +656,28 @@ return (this.upload_completed + (percentage * size)) / this.upload_size; }, + + // template for extensions description + _templateDescription: function(options) { + if (options.description) { + var tmpl = options.description; + if (options.description_url) { + tmpl += ' (<a href="' + options.description_url + '" target="_blank">read more</a>)'; + } + return tmpl; + } else { + return 'There is no description available for this file extension.'; + } + }, + // load html template _template: function(id, idInfo) { - return '<div id="uploadhead" class="uploadhead">' + - '<span class="fftext">"Set All" Types: &nbsp</span>' + - '<span id="extension" class="extension"/> &nbsp' + - '<span id="extension-info_out" class="upload-icon-button fa fa-search"/> ' + + return '<div id="upload-header" class="upload-header">' + + '<span class="header-title">Type (default):</span>' + + '<span id="header-extension"/>' + + '<span id="header-extension-info" class="upload-icon-button fa fa-search"/> ' + + '<span class="header-title">Genome (default):</span>' + + '<span id="header-genome"/>' + '</div>' + '<div id="' + id + '" class="upload-box">' + '<table id="upload-table" class="table table-striped" style="display: none;">' + @@ -707,7 +695,7 @@ '<tbody></tbody>' + '</table>' + '</div>' + - '<div class="uploadfoot">' + + '<div class="upload-footer">' + '<h6 id="' + idInfo + '" class="upload-info"></h6>' + '</div>' ; } diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -448,6 +448,54 @@ } }); +// plugin +var CheckButton = Backbone.View.extend({ + + // default options + optionsDefault: { + class_add : 'fa fa-square-o', + class_remove : 'fa fa-check-square-o', + class_partial : 'fa fa-minus-square-o', + value : false + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement($('<div/>')); + + // set initial value + this.value(Boolean(this.options.value)); + + // add event handler + var self = this; + this.$el.on('click', function() { + self.value(!self.current); + }); + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.current = new_val; + if (new_val) { + this.$el.removeClass() + .addClass('ui-checkbutton') + .addClass(this.options.class_remove); + } else { + this.$el.removeClass() + .addClass('ui-checkbutton') + .addClass(this.options.class_add); + } + this.options.onchange && this.options.onchange(new_val); + } + return this.current; + } +}); + // return return { Anchor : Anchor, @@ -463,6 +511,7 @@ RadioButton : Options.RadioButton, Checkbox : Options.Checkbox, Radio : Options.Radio, + CheckButton : CheckButton, Searchbox : Searchbox, Select : Select, Hidden : Hidden, diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/mvc/upload/upload-model.js --- a/static/scripts/mvc/upload/upload-model.js +++ b/static/scripts/mvc/upload/upload-model.js @@ -14,8 +14,6 @@ file_type : null, file_path : '', percentage : 0, - row : null, - // settings space_to_tabs : false, to_posix_lines : true } diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -3,7 +3,7 @@ 'mvc/upload/upload-model', 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', - 'mvc/ui/ui-select'], + 'mvc/ui/ui-select',], function( Utils, UploadModel, @@ -42,9 +42,6 @@ // link app this.app = app; - // default value for extension of files - var default_ext = 'Auto-detect'; - // link this var self = this; @@ -64,6 +61,9 @@ placement : 'bottom' }); + // initialize default genome through default select field + var default_genome = this.app.select_genome.value(); + // select genomes this.select_genome = new Select.View({ css: 'genome', @@ -72,39 +72,29 @@ }, data: self.app.list_genomes, container: it.find('#genome'), - value: self.model.get('genome') + value: default_genome }); // initialize genome - this.model.set('genome', self.select_genome.value()); + this.model.set('genome', default_genome); - // ensure files added after an individual row has changed - // default to Auto-detect instead of --- - if(!(this.app.select_extension.value() === '---')){ - this.default_ext = this.app.select_extension.value(); - } - + // initialize default extension through default select field + var default_extension = this.app.select_extension.value(); + // select extension this.select_extension = new Select.View({ css: 'extension', onchange : function() { self.model.set('extension', self.select_extension.value()); - // if user has changed individual row type, then change "set all" - // type to '---' - if(!(self.select_extension.value() === app.select_extension.value())) - { - var newExte = '---'; - app.select_extension.value(newExte); - } }, data: self.app.list_extensions, container: it.find('#extension'), - value: self.default_ext + value: default_extension }); // initialize extension - this.model.set('extension', self.select_extension.value()); - + this.model.set('extension', default_extension); + // // ui events // @@ -113,8 +103,13 @@ it.find('#symbol').on('click', function() { self._removeRow(); }); // handle extension info popover - it.find('#extension-info').on('click' , function(e) { self._showExtensionInfo(); }) - .on('mousedown', function(e) { e.preventDefault(); }); + it.find('#extension-info').on('click' , function(e) { + self.app.showExtensionInfo({ + $el : $(e.target), + title : self.select_extension.text(), + extension : self.select_extension.value() + }); + }).on('mousedown', function(e) { e.preventDefault(); }); // handle settings popover it.find('#settings').on('click' , function(e) { self._showSettings(); }) @@ -130,7 +125,7 @@ it.find('#space_to_tabs').on('change', function(e) { self.model.set('space_to_tabs', $(e.target).prop('checked')); }); - + // // model events // @@ -146,6 +141,9 @@ this.model.on('change:genome', function() { self._refreshGenome(); }); + this.model.on('change:extension', function() { + self._refreshExtension(); + }); this.model.on('change:file_size', function() { self._refreshFileSize(); }); @@ -155,7 +153,6 @@ this.app.collection.on('reset', function() { self.remove(); }); - self.model.set('row', self); }, // render @@ -175,8 +172,9 @@ it.find('#size').html(Utils.bytesToString (file_size)); // remove mode class - it.find('#mode').removeClass() - .addClass('mode'); + it.find('#mode') + .removeClass() + .addClass('mode'); // activate text field if file is new if (file_mode == 'new') { @@ -229,11 +227,14 @@ // handle model events // - // genome + // update extension + _refreshExtension: function() { + this.select_extension.value(this.model.get('extension')); + }, + + // update genome _refreshGenome: function() { - // update genome info on screen - var genome = this.model.get('genome'); - this.select_genome.value(genome); + this.select_genome.value(this.model.get('genome')); }, // progress @@ -327,33 +328,6 @@ }, // attach file info popup - _showExtensionInfo : function() { - // initialize - var $el = $(this.el).find('#extension-info'); - var extension = this.model.get('extension'); - var title = this.select_extension.text(); - var description = _.findWhere(this.app.list_extensions, {'id': extension}); - - // create popup - if (!this.extension_popup) { - this.extension_popup = new Popover.View({ - placement: 'bottom', - container: $el - }); - } - - // show / hide popup - if (!this.extension_popup.visible) { - this.extension_popup.title(title); - this.extension_popup.empty(); - this.extension_popup.append(this._templateDescription(description)); - this.extension_popup.show(); - } else { - this.extension_popup.hide(); - } - }, - - // attach file info popup _showSettings : function() { // check if popover is visible if (!this.settings.visible) { @@ -368,23 +342,10 @@ }, // template - _templateDescription: function(options) { - if (options.description) { - var tmpl = options.description; - if (options.description_url) { - tmpl += ' (<a href="' + options.description_url + '" target="_blank">read more</a>)'; - } - return tmpl; - } else { - return 'There is no description available for this file extension.'; - } - }, - - // template _template: function(options) { return '<tr id="upload-item-' + options.id + '" class="upload-item">' + '<td>' + - '<div style="position: relative;">' + + '<div class="name-column">' + '<div id="mode"></div>' + '<div id="title" class="title"></div>' + '<div id="text" class="text">' + diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -23,7 +23,7 @@ return Backbone.View.extend({ // options options : { - nginx_upload_path : '' + nginx_upload_path : '' }, // own modal @@ -40,6 +40,9 @@ // extension selector select_extension : null, + + // genome selector + select_genome: null, // current upload size upload_size: 0, @@ -130,14 +133,6 @@ return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; }); - // add the '---' extension for use when the row types are changed individually - self.list_extensions.push({ - id : "---", - text : "---", - description : "", - description_url : "" - }); - // add auto field if (!self.options.datatypes_disable_auto) { self.list_extensions.unshift(self.auto); @@ -167,14 +162,6 @@ this.collection.on('remove', function(item) { self._eventRemove(item); }); - this.collection.on('change:genome', function(item) { - var genome = item.get('genome'); - self.collection.each(function(item) { - if (item.get('status') == 'init' && item.get('genome') == '?') { - item.set('genome', genome); - } - }); - }); }, // @@ -232,28 +219,30 @@ container : button }); - // select extension + // select extension this.select_extension = new Select.View({ - css: 'extension', - onchange : function() { - var newExten = self.select_extension.value() - var len = self.collection.models.length; - // Only trigger changing the rows if the "set all" isn't set to '---' - // Prevents recursively changing the rows after an individual row has been changed - if(!(newExten === '---')){ - for(i = 0; i < len; i++){ - self.collection.models[i].attributes['row'].select_extension.value(newExten); - } - } - }, - data: self.list_extensions, - container: self.$el.parents().find('#extension'), - value: self.list_extensions[0] + css : 'header-selection', + data : self.list_extensions, + container : self.$el.parent().find('#header-extension'), + value : self.list_extensions[0] }); - + // handle extension info popover - self.$el.parents().find('#extension-info_out').on('click' , function(e) { self._showExtensionInfo(); }) - .on('mousedown', function(e) { e.preventDefault(); }); + self.$el.parent().find('#header-extension-info').on('click' , function(e) { + self.showExtensionInfo({ + $el : $(e.target), + title : self.select_extension.text(), + extension : self.select_extension.value() + }); + }).on('mousedown', function(e) { e.preventDefault(); }); + + // genome extension + this.select_genome = new Select.View({ + css : 'header-selection', + data : self.list_genomes, + container : self.$el.parent().find('#header-genome'), + value : self.list_genomes[0] + }); } // show modal @@ -266,45 +255,27 @@ this._updateScreen(); }, - _showExtensionInfo : function() { + showExtensionInfo : function(options) { // initialize var self = this; - var $el = $(this.el).parents().find('#extension-info_out'); - var extension = self.select_extension.value(); - - var title = this.select_extension.text(); - + var $el = options.$el; + var extension = options.extension; + var title = options.title; var description = _.findWhere(self.list_extensions, {'id': extension}); // create popup - if (!this.extension_popup) { - this.extension_popup = new Popover.View({ - placement: 'bottom', - container: $el - }); - } - - // show / hide popup - if (!this.extension_popup.visible) { - this.extension_popup.title(title); - this.extension_popup.empty(); - this.extension_popup.append(this._templateDescription(description)); - this.extension_popup.show(); - } else { - this.extension_popup.hide(); - } - }, - - _templateDescription: function(options) { - if (options.description) { - var tmpl = options.description; - if (options.description_url) { - tmpl += ' (<a href="' + options.description_url + '" target="_blank">read more</a>)'; - } - return tmpl; - } else { - return 'There is no description available for this file extension.'; - } + this.extension_popup && this.extension_popup.remove(); + this.extension_popup = new Popover.View({ + placement: 'bottom', + container: $el, + destroy: true + }); + + // add content and show popup + this.extension_popup.title(title); + this.extension_popup.empty(); + this.extension_popup.append(this._templateDescription(description)); + this.extension_popup.show(); }, // @@ -593,6 +564,7 @@ // reset value for universal type drop-down this.select_extension.value(this.list_extensions[0]); + this.select_genome.value(this.list_genomes[0]); // reset button this.ui_button.set('percentage', 0); @@ -684,12 +656,28 @@ return (this.upload_completed + (percentage * size)) / this.upload_size; }, + + // template for extensions description + _templateDescription: function(options) { + if (options.description) { + var tmpl = options.description; + if (options.description_url) { + tmpl += ' (<a href="' + options.description_url + '" target="_blank">read more</a>)'; + } + return tmpl; + } else { + return 'There is no description available for this file extension.'; + } + }, + // load html template _template: function(id, idInfo) { - return '<div id="uploadhead" class="uploadhead">' + - '<span class="fftext">"Set All" Types: &nbsp</span>' + - '<span id="extension" class="extension"/> &nbsp' + - '<span id="extension-info_out" class="upload-icon-button fa fa-search"/> ' + + return '<div id="upload-header" class="upload-header">' + + '<span class="header-title">Type (default):</span>' + + '<span id="header-extension"/>' + + '<span id="header-extension-info" class="upload-icon-button fa fa-search"/> ' + + '<span class="header-title">Genome (default):</span>' + + '<span id="header-genome"/>' + '</div>' + '<div id="' + id + '" class="upload-box">' + '<table id="upload-table" class="table table-striped" style="display: none;">' + @@ -707,7 +695,7 @@ '<tbody></tbody>' + '</table>' + '</div>' + - '<div class="uploadfoot">' + + '<div class="upload-footer">' + '<h6 id="' + idInfo + '" class="upload-info"></h6>' + '</div>' ; } diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,o,l,q,m){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$el.html(r)},_template:function(r){return'<label class="ui-label '+r.cls+'">'+r.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){return'<div><span class="fa '+r.icon+'" class="ui-icon"/> '+r.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s='<button id="'+r.id+'" type="submit" style="float: '+r.floating+';" type="button" class="'+r.cls+'">';if(r.icon){s+='<i class="icon fa '+r.icon+'"></i> '}s+=r.title+"</button>";return s}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var r=this;$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick&&!r.disabled){s.onclick()}});$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},setIcon:function(r){this.$("i").removeClass(this.options.icon).addClass(r);this.options.icon=r},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="'+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick)},_template:function(r){return'<div><a href="javascript:void(0)" class="ui-anchor '+r.cls+'">'+r.title+"</a></div>"}});var n=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement("<div></div>");if(this.options.message){this.update(this.options)}},update:function(s){this.options=k.merge(s,this.optionsDefault);if(s.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(s.message);this.$el.fadeIn();if(this.timeout){window.clearTimeout(this.timeout)}if(!s.persistent){var r=this;this.timeout=window.setTimeout(function(){if(r.$el.is(":visible")){r.$el.fadeOut()}else{r.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(r){return'<div class="ui-message alert alert-'+r.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));var r=this;if(this.options.onclick){this.$el.on("submit",function(u){var t=r.$el.find("#search");r.options.onclick(t.val())})}},_template:function(r){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+r.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$el.on("input",function(){if(r.options.onchange){r.options.onchange(r.$el.val())}})},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){if(r.area){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'"></textarea>'}else{return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}}});var p=Backbone.View.extend({initialize:function(r){this.options=r;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(r){if(r!==undefined){this.$("hidden").val(r)}return this.$("hidden").val()},_template:function(s){var r='<div id="'+s.id+'" >';if(s.info){r+="<label>"+s.info+"</label>"}r+='<hidden value="'+s.value+'"/></div>';return r}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:q,Icon:c,Image:d,Input:i,Label:j,Message:n,Modal:m,RadioButton:o.RadioButton,Checkbox:o.Checkbox,Radio:o.Radio,Searchbox:a,Select:b,Hidden:p,Slider:e,Drilldown:l}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(d,g,h,l,k,r,b){var p=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(s){return'<img class="ui-image '+s.cls+'" src="'+s.url+'"/>'}});var i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},title:function(s){this.$el.html(s)},_template:function(s){return'<label class="ui-label '+s.cls+'">'+s.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){return'<div><span class="fa '+s.icon+'" class="ui-icon"/> '+s.title+"</div>"}});var f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick){s.onclick()}});$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t='<button id="'+s.id+'" type="submit" style="float: '+s.floating+';" type="button" class="'+s.cls+'">';if(s.icon){t+='<i class="icon fa '+s.icon+'"></i> '}t+=s.title+"</button>";return t}});var n=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var s=this;$(this.el).on("click",function(){$(".tooltip").hide();if(t.onclick&&!s.disabled){t.onclick()}});$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},setIcon:function(s){this.$("i").removeClass(this.options.icon).addClass(s);this.options.icon=s},_template:function(s){var t="";if(s.title){t="width: auto;"}var u='<div id="'+s.id+'" style="float: '+s.floating+"; "+t+'" class="'+s.cls+'">';if(s.title){u+='<div class="button"><i class="icon fa '+s.icon+'"/> <span class="title">'+s.title+"</span></div>"}else{u+='<i class="icon fa '+s.icon+'"/>'}u+="</div>";return u}});var o=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick)},_template:function(s){return'<div><a href="javascript:void(0)" class="ui-anchor '+s.cls+'">'+s.title+"</a></div>"}});var a=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:false},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement("<div></div>");if(this.options.message){this.update(this.options)}},update:function(t){this.options=d.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(t.message);this.$el.fadeIn();if(this.timeout){window.clearTimeout(this.timeout)}if(!t.persistent){var s=this;this.timeout=window.setTimeout(function(){if(s.$el.is(":visible")){s.$el.fadeOut()}else{s.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(s){return'<div class="ui-message alert alert-'+s.status+'"/>'}});var e=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement(this._template(this.options));var s=this;if(this.options.onclick){this.$el.on("submit",function(v){var u=s.$el.find("#search");s.options.onclick(u.val())})}},_template:function(s){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+s.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var s=this;this.$el.on("input",function(){if(s.options.onchange){s.options.onchange(s.$el.val())}})},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){if(s.area){return'<textarea id="'+s.id+'" class="ui-textarea '+s.cls+'"></textarea>'}else{return'<input id="'+s.id+'" type="'+s.type+'" value="'+s.value+'" placeholder="'+s.placeholder+'" class="ui-input '+s.cls+'">'}}});var j=Backbone.View.extend({initialize:function(s){this.options=s;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(s){if(s!==undefined){this.$("hidden").val(s)}return this.$("hidden").val()},_template:function(t){var s='<div id="'+t.id+'" >';if(t.info){s+="<label>"+t.info+"</label>"}s+='<hidden value="'+t.value+'"/></div>';return s}});var q=Backbone.View.extend({optionsDefault:{class_add:"fa fa-square-o",class_remove:"fa fa-check-square-o",class_partial:"fa fa-minus-square-o",value:false},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement($("<div/>"));this.value(Boolean(this.options.value));var s=this;this.$el.on("click",function(){s.value(!s.current)})},value:function(s){if(s!==undefined){this.current=s;if(s){this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.class_remove)}else{this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.class_add)}this.options.onchange&&this.options.onchange(s)}return this.current}});return{Anchor:o,Button:f,ButtonIcon:n,ButtonMenu:r,Icon:c,Image:p,Input:m,Label:i,Message:a,Modal:b,RadioButton:l.RadioButton,Checkbox:l.Checkbox,Radio:l.Radio,CheckButton:q,Searchbox:e,Select:g,Hidden:j,Slider:h,Drilldown:k}}); \ No newline at end of file diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/packed/mvc/upload/upload-model.js --- a/static/scripts/packed/mvc/upload/upload-model.js +++ b/static/scripts/packed/mvc/upload/upload-model.js @@ -1,1 +1,1 @@ -define([],function(){var b=Backbone.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_mode:"local",file_size:0,file_type:null,file_path:"",percentage:0,row:null,space_to_tabs:false,to_posix_lines:true}});var a=Backbone.Collection.extend({model:b});return{Model:b,Collection:a}}); \ No newline at end of file +define([],function(){var b=Backbone.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_mode:"local",file_size:0,file_type:null,file_path:"",percentage:0,space_to_tabs:false,to_posix_lines:true}});var a=Backbone.Collection.extend({model:b});return{Model:b,Collection:a}}); \ No newline at end of file diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g="Auto-detect";var f=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:i.find("#genome"),value:f.model.get("genome")});this.model.set("genome",f.select_genome.value());if(!(this.app.select_extension.value()==="---")){this.default_ext=this.app.select_extension.value()}this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value());if(!(f.select_extension.value()===j.select_extension.value())){var k="---";j.select_extension.value(k)}},data:f.app.list_extensions,container:i.find("#extension"),value:f.default_ext});this.model.set("extension",f.select_extension.value());i.find("#symbol").on("click",function(){f._removeRow()});i.find("#extension-info").on("click",function(k){f._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){f._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){f.model.set("url_paste",$(k.target).val());f.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){f.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()});f.model.set("row",f)},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var f=this.model.get("genome");this.select_genome.value(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();var g=_.findWhere(this.app.list_extensions,{id:i});if(!this.extension_popup){this.extension_popup=new c.View({placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(g));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_templateDescription:function(g){if(g.description){var f=g.description;if(g.description_url){f+=' (<a href="'+g.description_url+'" target="_blank">read more</a>)'}return f}else{return"There is no description available for this file extension."}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select",],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(k,h){this.app=k;var f=this;this.model=new b.Model(h);this.setElement(this._template(h));var j=this.$el;this.settings=new c.View({title:"Upload configuration",container:j.find("#settings"),placement:"bottom"});var i=this.app.select_genome.value();this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:j.find("#genome"),value:i});this.model.set("genome",i);var g=this.app.select_extension.value();this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:j.find("#extension"),value:g});this.model.set("extension",g);j.find("#symbol").on("click",function(){f._removeRow()});j.find("#extension-info").on("click",function(l){f.app.showExtensionInfo({$el:$(l.target),title:f.select_extension.text(),extension:f.select_extension.value()})}).on("mousedown",function(l){l.preventDefault()});j.find("#settings").on("click",function(l){f._showSettings()}).on("mousedown",function(l){l.preventDefault()});j.find("#text-content").on("keyup",function(l){f.model.set("url_paste",$(l.target).val());f.model.set("file_size",$(l.target).val().length)});j.find("#space_to_tabs").on("change",function(l){f.model.set("space_to_tabs",$(l.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:extension",function(){f._refreshExtension()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div class="name-column"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui/ui-select","utils/uploadbox"],function(f,e,c,b,g,d,a,h){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,select_extension:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(k){var j=this;if(k){this.options=_.defaults(k,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(l){if(l){l.preventDefault();j.show()}},onunload:function(){if(j.counter.running>0){return"Several uploads are still processing."}}});$(".with-upload-button").append((new e.View(this.ui_button)).$el);var j=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(l){for(key in l){j.list_extensions.push({id:l[key].extension,text:l[key].extension,description:l[key].description,description_url:l[key].description_url})}j.list_extensions.sort(function(n,m){return n.id>m.id?1:n.id<m.id?-1:0});j.list_extensions.push({id:"---",text:"---",description:"",description_url:""});if(!j.options.datatypes_disable_auto){j.list_extensions.unshift(j.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(l){for(key in l){j.list_genomes.push({id:l[key][1],text:l[key][0]})}j.list_genomes.sort(function(n,m){return n.id>m.id?1:n.id<m.id?-1:0})}});this.collection.on("remove",function(l){j._eventRemove(l)});this.collection.on("change:genome",function(m){var l=m.get("genome");j.collection.each(function(n){if(n.get("status")=="init"&&n.get("genome")=="?"){n.set("genome",l)}})})},show:function(){var j=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){j.show()},500);return}if(!this.modal){var j=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){j.uploadbox.select()},"Choose FTP file":function(){j._eventFtp()},"Paste/Fetch data":function(){j._eventCreate()},Start:function(){j._eventStart()},Pause:function(){j._eventStop()},Reset:function(){j._eventReset()},Close:function(){j.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var j=this;this.uploadbox=this.$el.uploadbox({announce:function(l,m,n){j._eventAnnounce(l,m,n)},initialize:function(l,m,n){return j._eventInitialize(l,m,n)},progress:function(l,m,n){j._eventProgress(l,m,n)},success:function(l,m,n){j._eventSuccess(l,m,n)},error:function(l,m,n){j._eventError(l,m,n)},complete:function(){j._eventComplete()}});var k=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:k});this.select_extension=new h.View({css:"extension",onchange:function(){var m=j.select_extension.value();var l=j.collection.models.length;if(!(m==="---")){for(i=0;i<l;i++){j.collection.models[i].attributes.row.select_extension.value(m)}}},data:j.list_extensions,container:j.$el.parents().find("#extension"),value:j.list_extensions[0]});j.$el.parents().find("#extension-info_out").on("click",function(l){j._showExtensionInfo()}).on("mousedown",function(l){l.preventDefault()})}this.modal.show();this._updateUser();this._updateScreen()},_showExtensionInfo:function(){var j=this;var k=$(this.el).parents().find("#extension-info_out");var n=j.select_extension.value();var m=this.select_extension.text();var l=_.findWhere(j.list_extensions,{id:n});if(!this.extension_popup){this.extension_popup=new d.View({placement:"bottom",container:k})}if(!this.extension_popup.visible){this.extension_popup.title(m);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(l));this.extension_popup.show()}else{this.extension_popup.hide()}},_templateDescription:function(k){if(k.description){var j=k.description;if(k.description_url){j+=' (<a href="'+k.description_url+'" target="_blank">read more</a>)'}return j}else{return"There is no description available for this file extension."}},_eventRemove:function(k){var j=k.get("status");if(j=="success"){this.counter.success--}else{if(j=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(k.id)},_eventAnnounce:function(j,k,m){this.counter.announce++;this._updateScreen();var l=new b(this,{id:j,file_name:k.name,file_size:k.size,file_mode:k.mode,file_path:k.path});this.collection.add(l.model);$(this.el).find("tbody:first").append(l.$el);l.render()},_eventInitialize:function(o,l,u){var m=this.collection.get(o);m.set("status","running");var q=m.get("file_name");var p=m.get("file_path");var j=m.get("file_mode");var r=m.get("extension");var t=m.get("genome");var s=m.get("url_paste");var n=m.get("space_to_tabs");var k=m.get("to_posix_lines");if(!s&&!(l.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(j=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(j=="new"){tool_input["files_0|url_paste"]=s}if(j=="ftp"){tool_input["files_0|ftp_files"]=p}tool_input.dbkey=t;tool_input.file_type=r;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|space_to_tab"]=n&&"Yes"||null;tool_input["files_0|to_posix_lines"]=k&&"Yes"||null;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(k,l,j){var m=this.collection.get(k);m.set("percentage",j);this.ui_button.set("percentage",this._upload_percentage(j,l.size))},_eventSuccess:function(k,l,n){var m=this.collection.get(k);m.set("percentage",100);m.set("status","success");var j=m.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,j));this.upload_completed+=j*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(j,k,m){var l=this.collection.get(j);l.set("percentage",100);l.set("status","error");l.set("info",m);this.ui_button.set("percentage",this._upload_percentage(100,k.size));this.ui_button.set("status","danger");this.upload_completed+=k.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(j){if(j.get("status")=="queued"){j.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var j=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(k){if(k.get("status")=="init"){k.set("status","queued");j.upload_size+=k.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.select_extension.value(this.list_extensions[0]);this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(j,k){return(this.upload_completed+(j*k))/this.upload_size},_template:function(k,j){return'<div id="uploadhead" class="uploadhead"><span class="fftext">"Set All" Types: &nbsp</span><span id="extension" class="extension"/> &nbsp<span id="extension-info_out" class="upload-icon-button fa fa-search"/></div><div id="'+k+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><div class="uploadfoot"><h6 id="'+j+'" class="upload-info"></h6></div>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui/ui-select","utils/uploadbox"],function(f,e,c,b,g,d,a,h){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,select_extension:null,select_genome:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(j){var i=this;if(j){this.options=_.defaults(j,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(k){if(k){k.preventDefault();i.show()}},onunload:function(){if(i.counter.running>0){return"Several uploads are still processing."}}});$(".with-upload-button").append((new e.View(this.ui_button)).$el);var i=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(k){for(key in k){i.list_extensions.push({id:k[key].extension,text:k[key].extension,description:k[key].description,description_url:k[key].description_url})}i.list_extensions.sort(function(m,l){return m.id>l.id?1:m.id<l.id?-1:0});if(!i.options.datatypes_disable_auto){i.list_extensions.unshift(i.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(k){for(key in k){i.list_genomes.push({id:k[key][1],text:k[key][0]})}i.list_genomes.sort(function(m,l){return m.id>l.id?1:m.id<l.id?-1:0})}});this.collection.on("remove",function(k){i._eventRemove(k)})},show:function(){var i=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){i.show()},500);return}if(!this.modal){var i=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){i.uploadbox.select()},"Choose FTP file":function(){i._eventFtp()},"Paste/Fetch data":function(){i._eventCreate()},Start:function(){i._eventStart()},Pause:function(){i._eventStop()},Reset:function(){i._eventReset()},Close:function(){i.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var i=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){i._eventAnnounce(k,l,m)},initialize:function(k,l,m){return i._eventInitialize(k,l,m)},progress:function(k,l,m){i._eventProgress(k,l,m)},success:function(k,l,m){i._eventSuccess(k,l,m)},error:function(k,l,m){i._eventError(k,l,m)},complete:function(){i._eventComplete()}});var j=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:j});this.select_extension=new h.View({css:"header-selection",data:i.list_extensions,container:i.$el.parent().find("#header-extension"),value:i.list_extensions[0]});i.$el.parent().find("#header-extension-info").on("click",function(k){i.showExtensionInfo({$el:$(k.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(k){k.preventDefault()});this.select_genome=new h.View({css:"header-selection",data:i.list_genomes,container:i.$el.parent().find("#header-genome"),value:i.list_genomes[0]})}this.modal.show();this._updateUser();this._updateScreen()},showExtensionInfo:function(j){var i=this;var k=j.$el;var n=j.extension;var m=j.title;var l=_.findWhere(i.list_extensions,{id:n});this.extension_popup&&this.extension_popup.remove();this.extension_popup=new d.View({placement:"bottom",container:k,destroy:true});this.extension_popup.title(m);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(l));this.extension_popup.show()},_eventRemove:function(j){var i=j.get("status");if(i=="success"){this.counter.success--}else{if(i=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(j.id)},_eventAnnounce:function(i,j,l){this.counter.announce++;this._updateScreen();var k=new b(this,{id:i,file_name:j.name,file_size:j.size,file_mode:j.mode,file_path:j.path});this.collection.add(k.model);$(this.el).find("tbody:first").append(k.$el);k.render()},_eventInitialize:function(n,k,t){var l=this.collection.get(n);l.set("status","running");var p=l.get("file_name");var o=l.get("file_path");var i=l.get("file_mode");var q=l.get("extension");var s=l.get("genome");var r=l.get("url_paste");var m=l.get("space_to_tabs");var j=l.get("to_posix_lines");if(!r&&!(k.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(i=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(i=="new"){tool_input["files_0|url_paste"]=r}if(i=="ftp"){tool_input["files_0|ftp_files"]=o}tool_input.dbkey=s;tool_input.file_type=q;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|space_to_tab"]=m&&"Yes"||null;tool_input["files_0|to_posix_lines"]=j&&"Yes"||null;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(j,k,i){var l=this.collection.get(j);l.set("percentage",i);this.ui_button.set("percentage",this._upload_percentage(i,k.size))},_eventSuccess:function(j,k,m){var l=this.collection.get(j);l.set("percentage",100);l.set("status","success");var i=l.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,i));this.upload_completed+=i*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","error");k.set("info",l);this.ui_button.set("percentage",this._upload_percentage(100,j.size));this.ui_button.set("status","danger");this.upload_completed+=j.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(i){if(i.get("status")=="queued"){i.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var i=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(j){if(j.get("status")=="init"){j.set("status","queued");i.upload_size+=j.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.select_extension.value(this.list_extensions[0]);this.select_genome.value(this.list_genomes[0]);this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(i,j){return(this.upload_completed+(i*j))/this.upload_size},_templateDescription:function(j){if(j.description){var i=j.description;if(j.description_url){i+=' (<a href="'+j.description_url+'" target="_blank">read more</a>)'}return i}else{return"There is no description available for this file extension."}},_template:function(j,i){return'<div id="upload-header" class="upload-header"><span class="header-title">Type (default):</span><span id="header-extension"/><span id="header-extension-info" class="upload-icon-button fa fa-search"/><span class="header-title">Genome (default):</span><span id="header-genome"/></div><div id="'+j+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><div class="upload-footer"><h6 id="'+i+'" class="upload-info"></h6></div>'}})}); \ No newline at end of file diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -119,12 +119,6 @@ .table caption+thead tr:first-child th,.table colgroup+thead tr:first-child th,.table thead:first-child tr:first-child th,.table caption+thead tr:first-child td,.table colgroup+thead tr:first-child td,.table thead:first-child tr:first-child td{border-top:0} .table tbody+tbody{border-top:2px solid #d6b161} .table .table{background-color:#fff} -.uploadhead{height:10%; text-align:left; max-height:20px; line-height:18px; margin-bottom: 5px;} -.uploadfoot{height:5%; text-align:center;} -.uploadhead .fftext{font-weight: bold;} -.uploadhead .select2-container .select2-choice .select2-arrow b{background-position:0 -3px} -.uploadhead .extension{width:100px;min-width:100px;font-size:11px} -.uploadhead .select2-container .select2-choice{max-height:20px;line-height:18px;text-align:center; font-weight: normal;} .table-condensed thead>tr>th,.table-condensed tbody>tr>th,.table-condensed tfoot>tr>th,.table-condensed thead>tr>td,.table-condensed tbody>tr>td,.table-condensed tfoot>tr>td{padding:5px} .table-bordered{border:1px solid #d6b161}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #d6b161} .table-bordered>thead>tr>th,.table-bordered>thead>tr>td{border-bottom-width:2px} @@ -1375,13 +1369,13 @@ .upload-button .label{position:absolute;top:2px;width:inherit;text-align:center;line-height:19px;font-size:1.2em} .upload-icon{font-size:1.2em;width:1.2em} .upload-icon-button{font-size:1.2em;width:1.2em;cursor:pointer} -.upload-info{font-weight:normal;text-align:center} -.upload-box{width:100%;height:85%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%} +.upload-box{width:100%;height:90%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%} .upload-box .table th{text-align:center;white-space:nowrap} .upload-box .table td{margin:0px} .upload-box .upload-item .select2-arrow b{background-position:0 -3px} .upload-box .upload-item .select2-choice{max-height:20px;line-height:18px;background:transparent} .upload-box .upload-item .select2-container-disabled .select2-arrow{background:transparent} +.upload-box .name-column{position:relative} .upload-box .mode{float:left;font-size:1.2em;width:1.2em;color:#555} .upload-box .title{width:130px;word-wrap:break-word;font-size:11px;float:left} .upload-box .text{position:absolute;display:none}.upload-box .text .text-content{font-size:11px;width:100%;height:50px;resize:none;background:inherit;color:#000} @@ -1395,6 +1389,10 @@ .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} +.upload-header{height:5%;text-align:left;max-height:20px;line-height:18px;margin-bottom:15px}.upload-header .header-title{font-weight:bold;padding-left:60px;padding-right:20px} +.upload-header .header-selection{width:200px;min-width:200px;font-size:11px;padding-right:10px} +.upload-header .select2-choice{max-height:20px;line-height:18px;background:transparent;text-align:center;font-weight:normal}.upload-header .select2-choice .select2-arrow b{background-position:0 -3px} +.upload-footer{height:5%;text-align:center}.upload-footer .upload-info{font-weight:normal;text-align:center} .no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-slim,.ui-portlet-repeat,.ui-portlet-section{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} .ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} @@ -1435,6 +1433,7 @@ .ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px} .ui-radiobutton{width:100%}.ui-radiobutton label{height:23px;line-height:1em} .ui-radiobutton i{padding-right:5px} +.ui-checkbutton{font-size:1.2em;width:1.2em;cursor:pointer} .ui-select{position:relative}.ui-select .button{position:absolute;top:5px;right:5px} .ui-select .select2-container{width:100%} .ui-select select{position:relative;top:0px;height:27px;width:100%;padding-left:5px;padding-right:20px;cursor:pointer;background:transparent;-webkit-appearance:none;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px} diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -298,6 +298,12 @@ } } +.ui-checkbutton { + font-size: 1.2em; + width: 1.2em; + cursor: pointer; +} + .ui-select { position: relative; .button { diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r dc3357ffb6d9100b5a6eac4b774b70e180ab0e22 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -52,14 +52,9 @@ cursor: pointer; } -.upload-info { - font-weight: normal; - text-align: center; -} - .upload-box { width : 100%; - height : 95%; + height : 90%; text-align : center; overflow : scroll; font-size : @font-size-base; @@ -102,6 +97,10 @@ } } + .name-column { + position: relative; + } + .mode { float: left; font-size: 1.2em; @@ -214,3 +213,41 @@ cursor: no-drop; } } + +.upload-header { + height:5%; + text-align:left; + max-height:20px; + line-height:18px; + margin-bottom: 15px; + .header-title { + font-weight: bold; + padding-left: 60px; + padding-right: 20px; + } + .header-selection{ + width:200px; + min-width:200px; + font-size:11px; + padding-right: 10px; + } + .select2-choice { + .select2-arrow b { + background-position: 0 -3px; + } + max-height: 20px; + line-height: 18px; + background: transparent; + text-align:center; + font-weight: normal; + } +} + +.upload-footer { + height:5%; + text-align:center; + .upload-info { + font-weight: normal; + text-align: center; + } +} \ 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: dannon: Remove more trailing space from upload.js's.
by commits-noreply＠bitbucket.org 23 Jan '15

23 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/49d651198b3a/ Changeset: 49d651198b3a User: dannon Date: 2015-01-23 20:30:28+00:00 Summary: Remove more trailing space from upload.js's. Affected #: 4 files diff -r 443f25d4608260ee699cf125166d76df003d2ef9 -r 49d651198b3a7756936c4b578ccdd824b2c55e4e client/galaxy/scripts/mvc/upload/upload-row.js --- a/client/galaxy/scripts/mvc/upload/upload-row.js +++ b/client/galaxy/scripts/mvc/upload/upload-row.js @@ -4,7 +4,7 @@ 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', 'mvc/ui/ui-select'], - + function( Utils, UploadModel, UploadSettings, @@ -18,7 +18,7 @@ options: { padding : 8 }, - + // states status_classes : { init : 'upload-icon-button fa fa-trash-o', @@ -27,36 +27,36 @@ success : 'upload-icon-button fa fa-check', error : 'upload-icon-button fa fa-exclamation-triangle' }, - + // handle for settings popover settings: null, - + // genome selector select_genome : null, - + // extension selector select_extension : null, - + // render initialize: function(app, options) { // link app this.app = app; - + // default value for extension of files var default_ext = 'Auto-detect'; // link this var self = this; - + // create model this.model = new UploadModel.Model(options); - + // add upload item this.setElement(this._template(options)); // link item var it = this.$el; - + // append popup to settings icon this.settings = new Popover.View({ title : 'Upload configuration', @@ -74,11 +74,11 @@ container: it.find('#genome'), value: self.model.get('genome') }); - + // initialize genome this.model.set('genome', self.select_genome.value()); - // ensure files added after an individual row has changed + // ensure files added after an individual row has changed // default to Auto-detect instead of --- if(!(this.app.select_extension.value() === '---')){ this.default_ext = this.app.select_extension.value(); @@ -89,7 +89,7 @@ css: 'extension', onchange : function() { self.model.set('extension', self.select_extension.value()); - // if user has changed individual row type, then change "set all" + // if user has changed individual row type, then change "set all" // type to '---' if(!(self.select_extension.value() === app.select_extension.value())) { @@ -101,17 +101,17 @@ container: it.find('#extension'), value: self.default_ext }); - + // initialize extension this.model.set('extension', self.select_extension.value()); - + // // ui events // - + // handle click event it.find('#symbol').on('click', function() { self._removeRow(); }); - + // handle extension info popover it.find('#extension-info').on('click' , function(e) { self._showExtensionInfo(); }) .on('mousedown', function(e) { e.preventDefault(); }); @@ -125,12 +125,12 @@ self.model.set('url_paste', $(e.target).val()); self.model.set('file_size', $(e.target).val().length); }); - + // handle space to tabs button it.find('#space_to_tabs').on('change', function(e) { self.model.set('space_to_tabs', $(e.target).prop('checked')); }); - + // // model events // @@ -157,57 +157,57 @@ }); self.model.set('row', self); }, - + // render render: function() { // read model var file_name = this.model.get('file_name'); var file_size = this.model.get('file_size'); var file_mode = this.model.get('file_mode'); - + // link item var it = this.$el; - + // update title it.find('#title').html(file_name); - + // update info it.find('#size').html(Utils.bytesToString (file_size)); - + // remove mode class it.find('#mode').removeClass() .addClass('mode'); - + // activate text field if file is new if (file_mode == 'new') { // get text component var text = it.find('#text'); - + // get padding var padding = this.options.padding; - + // get dimensions var width = it.width() - 2 * padding; var height = it.height() - padding; - + // set dimensions text.css('width', width + 'px'); text.css('top', height + 'px'); it.height(height + text.height() + 2 * padding); - + // show text field text.show(); - + // update icon it.find('#mode').addClass('fa fa-pencil'); } - + // file from local disk if (file_mode == 'local') { // update icon it.find('#mode').addClass('fa fa-laptop'); } - + // file from ftp if (file_mode == 'ftp') { // update icon @@ -220,7 +220,7 @@ // trigger remove event this.select_genome.remove(); this.select_extension.remove(); - + // call the base class remove method Backbone.View.prototype.remove.apply(this); }, @@ -228,14 +228,14 @@ // // handle model events // - + // genome _refreshGenome: function() { // update genome info on screen var genome = this.model.get('genome'); this.select_genome.value(genome); }, - + // progress _refreshInfo: function() { // write error message @@ -246,7 +246,7 @@ this.$el.find('#info').hide(); } }, - + // progress _refreshPercentage : function() { var percentage = parseInt(this.model.get('percentage')); @@ -256,29 +256,29 @@ else this.$el.find('#percentage').html('Adding to history...'); }, - + // status _refreshStatus : function() { // get element var it = this.$el; - + // identify new status var status = this.model.get('status'); var status_class = this.status_classes[status]; - + // identify symbol and reset classes var sy = this.$el.find('#symbol'); sy.removeClass(); - + // set new status class sy.addClass(status_class); - + // enable form fields if (status == 'init') { // select fields this.select_genome.enable(); this.select_extension.enable(); - + // default fields it.find('#text-content').attr('disabled', false); it.find('#space_to_tabs').attr('disabled', false); @@ -286,18 +286,18 @@ // select fields this.select_genome.disable(); this.select_extension.disable(); - + // default fields it.find('#text-content').attr('disabled', true); it.find('#space_to_tabs').attr('disabled', true); } - + // success if (status == 'success') { it.addClass('success'); it.find('#percentage').html('100%'); } - + // error if (status == 'error') { it.addClass('danger'); @@ -314,18 +314,18 @@ // // handle ui events // - + // remove row _removeRow: function() { // get current status var status = this.model.get('status'); - + // only remove from queue if not in processing line if (status == 'init' || status == 'success' || status == 'error') { this.app.collection.remove(this.model); } }, - + // attach file info popup _showExtensionInfo : function() { // initialize @@ -333,7 +333,7 @@ var extension = this.model.get('extension'); var title = this.select_extension.text(); var description = _.findWhere(this.app.list_extensions, {'id': extension}); - + // create popup if (!this.extension_popup) { this.extension_popup = new Popover.View({ @@ -341,7 +341,7 @@ container: $el }); } - + // show / hide popup if (!this.extension_popup.visible) { this.extension_popup.title(title); @@ -366,7 +366,7 @@ this.settings.hide(); } }, - + // template _templateDescription: function(options) { if (options.description) { @@ -379,7 +379,7 @@ return 'There is no description available for this file extension.'; } }, - + // template _template: function(options) { return '<tr id="upload-item-' + options.id + '" class="upload-item">' + @@ -417,7 +417,7 @@ '</td>' + '</tr>'; } - + }); }); diff -r 443f25d4608260ee699cf125166d76df003d2ef9 -r 49d651198b3a7756936c4b578ccdd824b2c55e4e client/galaxy/scripts/mvc/upload/upload-settings.js --- a/client/galaxy/scripts/mvc/upload/upload-settings.js +++ b/client/galaxy/scripts/mvc/upload/upload-settings.js @@ -8,35 +8,35 @@ class_check : 'upload-icon-button fa fa-check-square-o', class_uncheck : 'upload-icon-button fa fa-square-o' }, - + // render initialize: function(app) { // link app this.app = app; - + // link this var self = this; - + // set template this.setElement(this._template()); - + // link model this.model = this.app.model; - + // ui event: space to tabs this.$el.find('#upload-space-to-tabs').on('click', function() { self._switchState('#upload-space-to-tabs', 'space_to_tabs'); }); - + // ui event: to posix this.$el.find('#upload-to-posix-lines').on('click', function() { self._switchState('#upload-to-posix-lines', 'to_posix_lines'); }); - + // render this.render(); }, - + // events events: { 'mousedown' : function(e) { e.preventDefault(); } @@ -47,7 +47,7 @@ // render states this._renderState('#upload-space-to-tabs', this.model.get('space_to_tabs')); this._renderState('#upload-to-posix-lines', this.model.get('to_posix_lines')); - + // disable options var $cover = this.$el.find('#upload-settings-cover'); if (this.model.get('status') != 'init') { @@ -56,7 +56,7 @@ $cover.hide(); } }, - + // switch state _switchState: function (element_id, parameter_id) { if (this.model.get('status') == 'init') { @@ -65,7 +65,7 @@ this._renderState(element_id, checked); } }, - + // render state _renderState: function (element_id, checked) { // swith icon class @@ -77,7 +77,7 @@ $it.addClass(this.options.class_uncheck); } }, - + // load template _template: function() { return '<div class="upload-settings" style="position: relative;">' + diff -r 443f25d4608260ee699cf125166d76df003d2ef9 -r 49d651198b3a7756936c4b578ccdd824b2c55e4e static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -4,7 +4,7 @@ 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', 'mvc/ui/ui-select'], - + function( Utils, UploadModel, UploadSettings, @@ -18,7 +18,7 @@ options: { padding : 8 }, - + // states status_classes : { init : 'upload-icon-button fa fa-trash-o', @@ -27,36 +27,36 @@ success : 'upload-icon-button fa fa-check', error : 'upload-icon-button fa fa-exclamation-triangle' }, - + // handle for settings popover settings: null, - + // genome selector select_genome : null, - + // extension selector select_extension : null, - + // render initialize: function(app, options) { // link app this.app = app; - + // default value for extension of files var default_ext = 'Auto-detect'; // link this var self = this; - + // create model this.model = new UploadModel.Model(options); - + // add upload item this.setElement(this._template(options)); // link item var it = this.$el; - + // append popup to settings icon this.settings = new Popover.View({ title : 'Upload configuration', @@ -74,11 +74,11 @@ container: it.find('#genome'), value: self.model.get('genome') }); - + // initialize genome this.model.set('genome', self.select_genome.value()); - // ensure files added after an individual row has changed + // ensure files added after an individual row has changed // default to Auto-detect instead of --- if(!(this.app.select_extension.value() === '---')){ this.default_ext = this.app.select_extension.value(); @@ -89,7 +89,7 @@ css: 'extension', onchange : function() { self.model.set('extension', self.select_extension.value()); - // if user has changed individual row type, then change "set all" + // if user has changed individual row type, then change "set all" // type to '---' if(!(self.select_extension.value() === app.select_extension.value())) { @@ -101,17 +101,17 @@ container: it.find('#extension'), value: self.default_ext }); - + // initialize extension this.model.set('extension', self.select_extension.value()); - + // // ui events // - + // handle click event it.find('#symbol').on('click', function() { self._removeRow(); }); - + // handle extension info popover it.find('#extension-info').on('click' , function(e) { self._showExtensionInfo(); }) .on('mousedown', function(e) { e.preventDefault(); }); @@ -125,12 +125,12 @@ self.model.set('url_paste', $(e.target).val()); self.model.set('file_size', $(e.target).val().length); }); - + // handle space to tabs button it.find('#space_to_tabs').on('change', function(e) { self.model.set('space_to_tabs', $(e.target).prop('checked')); }); - + // // model events // @@ -157,57 +157,57 @@ }); self.model.set('row', self); }, - + // render render: function() { // read model var file_name = this.model.get('file_name'); var file_size = this.model.get('file_size'); var file_mode = this.model.get('file_mode'); - + // link item var it = this.$el; - + // update title it.find('#title').html(file_name); - + // update info it.find('#size').html(Utils.bytesToString (file_size)); - + // remove mode class it.find('#mode').removeClass() .addClass('mode'); - + // activate text field if file is new if (file_mode == 'new') { // get text component var text = it.find('#text'); - + // get padding var padding = this.options.padding; - + // get dimensions var width = it.width() - 2 * padding; var height = it.height() - padding; - + // set dimensions text.css('width', width + 'px'); text.css('top', height + 'px'); it.height(height + text.height() + 2 * padding); - + // show text field text.show(); - + // update icon it.find('#mode').addClass('fa fa-pencil'); } - + // file from local disk if (file_mode == 'local') { // update icon it.find('#mode').addClass('fa fa-laptop'); } - + // file from ftp if (file_mode == 'ftp') { // update icon @@ -220,7 +220,7 @@ // trigger remove event this.select_genome.remove(); this.select_extension.remove(); - + // call the base class remove method Backbone.View.prototype.remove.apply(this); }, @@ -228,14 +228,14 @@ // // handle model events // - + // genome _refreshGenome: function() { // update genome info on screen var genome = this.model.get('genome'); this.select_genome.value(genome); }, - + // progress _refreshInfo: function() { // write error message @@ -246,7 +246,7 @@ this.$el.find('#info').hide(); } }, - + // progress _refreshPercentage : function() { var percentage = parseInt(this.model.get('percentage')); @@ -256,29 +256,29 @@ else this.$el.find('#percentage').html('Adding to history...'); }, - + // status _refreshStatus : function() { // get element var it = this.$el; - + // identify new status var status = this.model.get('status'); var status_class = this.status_classes[status]; - + // identify symbol and reset classes var sy = this.$el.find('#symbol'); sy.removeClass(); - + // set new status class sy.addClass(status_class); - + // enable form fields if (status == 'init') { // select fields this.select_genome.enable(); this.select_extension.enable(); - + // default fields it.find('#text-content').attr('disabled', false); it.find('#space_to_tabs').attr('disabled', false); @@ -286,18 +286,18 @@ // select fields this.select_genome.disable(); this.select_extension.disable(); - + // default fields it.find('#text-content').attr('disabled', true); it.find('#space_to_tabs').attr('disabled', true); } - + // success if (status == 'success') { it.addClass('success'); it.find('#percentage').html('100%'); } - + // error if (status == 'error') { it.addClass('danger'); @@ -314,18 +314,18 @@ // // handle ui events // - + // remove row _removeRow: function() { // get current status var status = this.model.get('status'); - + // only remove from queue if not in processing line if (status == 'init' || status == 'success' || status == 'error') { this.app.collection.remove(this.model); } }, - + // attach file info popup _showExtensionInfo : function() { // initialize @@ -333,7 +333,7 @@ var extension = this.model.get('extension'); var title = this.select_extension.text(); var description = _.findWhere(this.app.list_extensions, {'id': extension}); - + // create popup if (!this.extension_popup) { this.extension_popup = new Popover.View({ @@ -341,7 +341,7 @@ container: $el }); } - + // show / hide popup if (!this.extension_popup.visible) { this.extension_popup.title(title); @@ -366,7 +366,7 @@ this.settings.hide(); } }, - + // template _templateDescription: function(options) { if (options.description) { @@ -379,7 +379,7 @@ return 'There is no description available for this file extension.'; } }, - + // template _template: function(options) { return '<tr id="upload-item-' + options.id + '" class="upload-item">' + @@ -417,7 +417,7 @@ '</td>' + '</tr>'; } - + }); }); diff -r 443f25d4608260ee699cf125166d76df003d2ef9 -r 49d651198b3a7756936c4b578ccdd824b2c55e4e static/scripts/mvc/upload/upload-settings.js --- a/static/scripts/mvc/upload/upload-settings.js +++ b/static/scripts/mvc/upload/upload-settings.js @@ -8,35 +8,35 @@ class_check : 'upload-icon-button fa fa-check-square-o', class_uncheck : 'upload-icon-button fa fa-square-o' }, - + // render initialize: function(app) { // link app this.app = app; - + // link this var self = this; - + // set template this.setElement(this._template()); - + // link model this.model = this.app.model; - + // ui event: space to tabs this.$el.find('#upload-space-to-tabs').on('click', function() { self._switchState('#upload-space-to-tabs', 'space_to_tabs'); }); - + // ui event: to posix this.$el.find('#upload-to-posix-lines').on('click', function() { self._switchState('#upload-to-posix-lines', 'to_posix_lines'); }); - + // render this.render(); }, - + // events events: { 'mousedown' : function(e) { e.preventDefault(); } @@ -47,7 +47,7 @@ // render states this._renderState('#upload-space-to-tabs', this.model.get('space_to_tabs')); this._renderState('#upload-to-posix-lines', this.model.get('to_posix_lines')); - + // disable options var $cover = this.$el.find('#upload-settings-cover'); if (this.model.get('status') != 'init') { @@ -56,7 +56,7 @@ $cover.hide(); } }, - + // switch state _switchState: function (element_id, parameter_id) { if (this.model.get('status') == 'init') { @@ -65,7 +65,7 @@ this._renderState(element_id, checked); } }, - + // render state _renderState: function (element_id, checked) { // swith icon class @@ -77,7 +77,7 @@ $it.addClass(this.options.class_uncheck); } }, - + // load template _template: function() { return '<div class="upload-settings" style="position: relative;">' + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Upload: Remove spaces
by commits-noreply＠bitbucket.org 23 Jan '15

23 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/443f25d46082/ Changeset: 443f25d46082 User: guerler Date: 2015-01-23 20:15:31+00:00 Summary: Upload: Remove spaces Affected #: 2 files diff -r 669da7067315a6ce236a2ee753e9af6264279c01 -r 443f25d4608260ee699cf125166d76df003d2ef9 client/galaxy/scripts/mvc/upload/upload-ftp.js --- a/client/galaxy/scripts/mvc/upload/upload-ftp.js +++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js @@ -122,13 +122,13 @@ size : ftp_file.size, path : ftp_file.path }]); - + // add new icon class $icon.addClass(self.options.class_remove); } else { // remove self.app.collection.remove(model_index); - + // add new icon class $icon.addClass(self.options.class_add); } diff -r 669da7067315a6ce236a2ee753e9af6264279c01 -r 443f25d4608260ee699cf125166d76df003d2ef9 static/scripts/mvc/upload/upload-ftp.js --- a/static/scripts/mvc/upload/upload-ftp.js +++ b/static/scripts/mvc/upload/upload-ftp.js @@ -122,13 +122,13 @@ size : ftp_file.size, path : ftp_file.path }]); - + // add new icon class $icon.addClass(self.options.class_remove); } else { // remove self.app.collection.remove(model_index); - + // add new icon class $icon.addClass(self.options.class_add); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in nsoranzo/galaxy-central (pull request #646)
by commits-noreply＠bitbucket.org 23 Jan '15

23 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/669da7067315/ Changeset: 669da7067315 User: jmchilton Date: 2015-01-23 20:12:24+00:00 Summary: Merged in nsoranzo/galaxy-central (pull request #646) Update rolling_restart.sh to treat .venv dir and GALAXY_CONFIG_FILE env variable as run.sh Affected #: 2 files diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/bin/sh cd `dirname $0` check_if_not_started(){ @@ -8,7 +8,7 @@ current_pid_in_file=$(cat $2); # If they're equivalent, then the current pid file agrees with our logs # and we've succesfully started - if [[ $latest_pid -eq $current_pid_in_file ]]; + if [ $latest_pid -eq $current_pid_in_file ]; then echo 0; else @@ -16,17 +16,29 @@ fi } +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi -GALAXY_CONFIG_FILE=config/galaxy.ini -if [ ! -f $GALAXY_CONFIG_FILE ]; then - GALAXY_CONFIG_FILE=universe_wsgi.ini +if [ -z "$GALAXY_CONFIG_FILE" ]; then + if [ -f universe_wsgi.ini ]; then + GALAXY_CONFIG_FILE=universe_wsgi.ini + elif [ -f config/galaxy.ini ]; then + GALAXY_CONFIG_FILE=config/galaxy.ini + else + GALAXY_CONFIG_FILE=config/galaxy.ini.sample + fi + export GALAXY_CONFIG_FILE fi servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` for server in $servers; do # If there's a pid - if [[ -e $server.pid ]] + if [ -e $server.pid ] then # Then kill it echo "Killing $server" @@ -44,12 +56,11 @@ pid=`cat $server.pid` result=1 # Wait for the latest pid in the file to be the pid we've grabbed - while [[ $result -eq 1 ]] + while [ $result -eq 1 ] do result=$(check_if_not_started $server.log $server.pid) - echo -n "." + printf "." sleep 1 done - echo "" + echo done - diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 scripts/build_universe_config.py --- a/scripts/build_universe_config.py +++ b/scripts/build_universe_config.py @@ -6,7 +6,10 @@ def merge(): - "Merges all .ini files in a specified directory into ./universe.ini" + """ + Merges all .ini files in a specified directory into a file (defaults to + ./config/galaxy.ini ). + """ if len(argv) < 2: message = "%s: Must specify directory to merge configuration files from." % argv[0] raise Exception(message) 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 23 Jan '15

23 Jan '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0de04e073983/ Changeset: 0de04e073983 User: nsoranzo Date: 2015-01-23 19:19:15+00:00 Summary: Fix merge() documentation. Affected #: 1 file diff -r 9ef517d8e767037e1633f6063c6edb3023f86499 -r 0de04e073983373e30775252efab83714eaa7184 scripts/build_universe_config.py --- a/scripts/build_universe_config.py +++ b/scripts/build_universe_config.py @@ -6,7 +6,10 @@ def merge(): - "Merges all .ini files in a specified directory into ./universe.ini" + """ + Merges all .ini files in a specified directory into a file (defaults to + ./config/galaxy.ini ). + """ if len(argv) < 2: message = "%s: Must specify directory to merge configuration files from." % argv[0] raise Exception(message) https://bitbucket.org/galaxy/galaxy-central/commits/4f3f92ca8e74/ Changeset: 4f3f92ca8e74 User: nsoranzo Date: 2015-01-23 19:23:41+00:00 Summary: Update rolling_restart.sh to treat .venv dir and GALAXY_CONFIG_FILE env variable as run.sh . Use POSIX shell syntax. Affected #: 1 file diff -r 0de04e073983373e30775252efab83714eaa7184 -r 4f3f92ca8e7488f4f5a90b8d57eddaeb3e1645d6 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/bin/sh cd `dirname $0` check_if_not_started(){ @@ -8,7 +8,7 @@ current_pid_in_file=$(cat $2); # If they're equivalent, then the current pid file agrees with our logs # and we've succesfully started - if [[ $latest_pid -eq $current_pid_in_file ]]; + if [ $latest_pid -eq $current_pid_in_file ]; then echo 0; else @@ -16,17 +16,29 @@ fi } +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi -GALAXY_CONFIG_FILE=config/galaxy.ini -if [ ! -f $GALAXY_CONFIG_FILE ]; then - GALAXY_CONFIG_FILE=universe_wsgi.ini +if [ -z "$GALAXY_CONFIG_FILE" ]; then + if [ -f universe_wsgi.ini ]; then + GALAXY_CONFIG_FILE=universe_wsgi.ini + elif [ -f config/galaxy.ini ]; then + GALAXY_CONFIG_FILE=config/galaxy.ini + else + GALAXY_CONFIG_FILE=config/galaxy.ini.sample + fi + export GALAXY_CONFIG_FILE fi servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` for server in $servers; do # If there's a pid - if [[ -e $server.pid ]] + if [ -e $server.pid ] then # Then kill it echo "Killing $server" @@ -44,12 +56,11 @@ pid=`cat $server.pid` result=1 # Wait for the latest pid in the file to be the pid we've grabbed - while [[ $result -eq 1 ]] + while [ $result -eq 1 ] do result=$(check_if_not_started $server.log $server.pid) - echo -n "." + printf "." sleep 1 done - echo "" + echo done - https://bitbucket.org/galaxy/galaxy-central/commits/669da7067315/ Changeset: 669da7067315 User: jmchilton Date: 2015-01-23 20:12:24+00:00 Summary: Merged in nsoranzo/galaxy-central (pull request #646) Update rolling_restart.sh to treat .venv dir and GALAXY_CONFIG_FILE env variable as run.sh Affected #: 2 files diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/bin/sh cd `dirname $0` check_if_not_started(){ @@ -8,7 +8,7 @@ current_pid_in_file=$(cat $2); # If they're equivalent, then the current pid file agrees with our logs # and we've succesfully started - if [[ $latest_pid -eq $current_pid_in_file ]]; + if [ $latest_pid -eq $current_pid_in_file ]; then echo 0; else @@ -16,17 +16,29 @@ fi } +# If there is a .venv/ directory, assume it contains a virtualenv that we +# should run this instance in. +if [ -d .venv ]; +then + . .venv/bin/activate +fi -GALAXY_CONFIG_FILE=config/galaxy.ini -if [ ! -f $GALAXY_CONFIG_FILE ]; then - GALAXY_CONFIG_FILE=universe_wsgi.ini +if [ -z "$GALAXY_CONFIG_FILE" ]; then + if [ -f universe_wsgi.ini ]; then + GALAXY_CONFIG_FILE=universe_wsgi.ini + elif [ -f config/galaxy.ini ]; then + GALAXY_CONFIG_FILE=config/galaxy.ini + else + GALAXY_CONFIG_FILE=config/galaxy.ini.sample + fi + export GALAXY_CONFIG_FILE fi servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` for server in $servers; do # If there's a pid - if [[ -e $server.pid ]] + if [ -e $server.pid ] then # Then kill it echo "Killing $server" @@ -44,12 +56,11 @@ pid=`cat $server.pid` result=1 # Wait for the latest pid in the file to be the pid we've grabbed - while [[ $result -eq 1 ]] + while [ $result -eq 1 ] do result=$(check_if_not_started $server.log $server.pid) - echo -n "." + printf "." sleep 1 done - echo "" + echo done - diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 scripts/build_universe_config.py --- a/scripts/build_universe_config.py +++ b/scripts/build_universe_config.py @@ -6,7 +6,10 @@ def merge(): - "Merges all .ini files in a specified directory into ./universe.ini" + """ + Merges all .ini files in a specified directory into a file (defaults to + ./config/galaxy.ini ). + """ if len(argv) < 2: message = "%s: Must specify directory to merge configuration files from." % argv[0] raise Exception(message) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Upload: Cleanup ftp popup
by commits-noreply＠bitbucket.org 23 Jan '15

23 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/de9bd9d7d47b/ Changeset: de9bd9d7d47b User: guerler Date: 2015-01-23 20:11:24+00:00 Summary: Upload: Cleanup ftp popup Affected #: 3 files diff -r 892da4d5dcc979919c82d4a57ce897d3e93278ce -r de9bd9d7d47bfcdf45f3f170be391874b79e738f client/galaxy/scripts/mvc/upload/upload-ftp.js --- a/client/galaxy/scripts/mvc/upload/upload-ftp.js +++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js @@ -6,7 +6,8 @@ // options options: { class_add : 'upload-icon-button fa fa-square-o', - class_remove : 'upload-icon-button fa fa-check-square-o' + class_remove : 'upload-icon-button fa fa-check-square-o', + class_partial : 'upload-icon-button fa fa-minus-square-o' }, // render @@ -20,6 +21,9 @@ // set template this.setElement(this._template()); + // list of rows + this.rows = []; + // load extension Utils.get({ url : galaxy_config.root + 'api/ftp_files', @@ -35,7 +39,6 @@ // fill table _fill: function(ftp_files) { - var self = this; if (ftp_files && ftp_files.length > 0) { // add table this.$el.find('#upload-ftp-content').html($(this._templateTable())); @@ -43,7 +46,7 @@ // add files to table var size = 0; for (key in ftp_files) { - this.add(ftp_files[key]); + this.rows.push(this._add(ftp_files[key])); size += ftp_files[key].size; } @@ -51,37 +54,23 @@ this.$el.find('#upload-ftp-number').html(ftp_files.length + ' files'); this.$el.find('#upload-ftp-disk').html(Utils.bytesToString (size, true)); - var selectAll = this.$el.find('#selectAll'); - - // call method to determine and set selectAll status on loading - this._updateSelectAll(selectAll); - - // selectAll checkbox has been clicked - selectAll.on('click', function() { - var checkboxes=$(this).parents().find('tr.upload-ftp-row>td>div'); - var len = checkboxes.length; - $this = $(this); - var allChecked = !($this.hasClass('fa-check-square-o')); - - // change state of the sub-checkboxes - for(i = 0; i < len; i++) { - if(allChecked) { - // all checkboxes should be checked - if(checkboxes.eq(i).hasClass('fa-square-o')) { - // if they are not checked, check them - checkboxes.eq(i).trigger('updateUpBox'); - } - } else { - // no checkboxes should be checked - if(checkboxes.eq(i).hasClass('fa-check-square-o')) { - // if they are checked, uncheck them - checkboxes.eq(i).trigger('updateUpBox'); - } + // add event handler to select/unselect all + this.$select_all = $('#upload-selectall'); + this.$select_all.addClass(this.options.class_add); + var self = this; + this.$select_all.on('click', function() { + var add = self.$select_all.hasClass(self.options.class_add); + for (key in ftp_files) { + var ftp_file = ftp_files[key]; + var model_index = self._find(ftp_file); + if(!model_index && add || model_index && !add) { + self.rows[key].trigger('click'); } } + }); - self._updateSelectAll(selectAll); - }); + // refresh + self._refresh(); } else { // add info this.$el.find('#upload-ftp-content').html($(this._templateInfo())); @@ -92,7 +81,7 @@ }, // add - add: function(ftp_file) { + _add: function(ftp_file) { // link this var self = this; @@ -116,8 +105,8 @@ // add icon class $icon.addClass(icon_class); - // add files to the uploadbox - $it.on('updateUpBox', function() { + // click to add ftp files + $it.on('click', function() { // find model var model_index = self._find(ftp_file); @@ -133,67 +122,51 @@ size : ftp_file.size, path : ftp_file.path }]); - + // add new icon class $icon.addClass(self.options.class_remove); } else { // remove self.app.collection.remove(model_index); - + // add new icon class $icon.addClass(self.options.class_add); } + + // update select all checkbox + self._refresh(); }); - // click to add ftp files - $it.on('click', function() { - //trigger my new event - $icon.trigger('updateUpBox'); - - // click to add ftp files - // modify selectAll box based on number of checkboxes checked - var selectBox=$icon.parents().find('#selectAll'); - // determine and set state of selectAll after sub-checkbox clicked - self._updateSelectAll(selectBox); - }); + // return dom handler + return $it; }, - _updateSelectAll: function(selectBox) { - // array of all checkboxes - var checkboxes=selectBox.parents().find('tr.upload-ftp-row>td>div'); - // array of only checked checkboxes - var checkedCheckboxes=selectBox.parents().find('tr.upload-ftp-row>td>div.fa-check-square-o'); - var lenAll = checkboxes.length; - var lenChecked = checkedCheckboxes.length; - - // determine which state the selectAll checkbox needs to be and setting it - if(lenChecked > 0 && lenChecked !== lenAll) { - // indeterminate state - selectBox.removeClass('fa-square-o fa-check-square-o'); - selectBox.addClass('fa-minus-square-o'); - } else if(lenChecked === lenAll) { - // checked state - selectBox.removeClass('fa-square-o fa-minus-square-o'); - selectBox.addClass('fa-check-square-o'); - } else if(lenChecked === 0) { - // unchecked state - selectBox.removeClass('fa-check-square-o fa-minus-square-o'); - selectBox.addClass('fa-square-o'); + // refresh + _refresh: function() { + var filtered = this.app.collection.where({file_mode : 'ftp'}); + this.$select_all.removeClass(); + if (filtered.length == 0) { + this.$select_all.addClass(this.options.class_add); + } else { + if (filtered.length == this.rows.length) { + this.$select_all.addClass(this.options.class_remove); + } else { + this.$select_all.addClass(this.options.class_partial); + } } }, // get model index _find: function(ftp_file) { - // check if exists already - var filtered = this.app.collection.where({file_path : ftp_file.path}); - var model_index = null; - for (var key in filtered) { - var item = filtered[key]; - if (item.get('status') == 'init' && item.get('file_mode') == 'ftp') { - model_index = item.get('id'); - } + var item = this.app.collection.findWhere({ + file_path : ftp_file.path, + status : 'init', + file_mode : 'ftp' + }); + if (item) { + return item.get('id'); } - return model_index; + return null; }, // template row @@ -218,7 +191,7 @@ '<table class="grid" style="float: left;">' + '<thead>' + '<tr>' + - '<th><div id="selectAll" class="upload-icon-button fa fa-square-o" ></th>' + + '<th><div id="upload-selectall"></th>' + '<th>Name</th>' + '<th>Size</th>' + '<th>Created</th>' + @@ -243,7 +216,6 @@ '<div id="upload-ftp-content"></div>' + '<div>'; } - }); }); diff -r 892da4d5dcc979919c82d4a57ce897d3e93278ce -r de9bd9d7d47bfcdf45f3f170be391874b79e738f static/scripts/mvc/upload/upload-ftp.js --- a/static/scripts/mvc/upload/upload-ftp.js +++ b/static/scripts/mvc/upload/upload-ftp.js @@ -6,7 +6,8 @@ // options options: { class_add : 'upload-icon-button fa fa-square-o', - class_remove : 'upload-icon-button fa fa-check-square-o' + class_remove : 'upload-icon-button fa fa-check-square-o', + class_partial : 'upload-icon-button fa fa-minus-square-o' }, // render @@ -20,6 +21,9 @@ // set template this.setElement(this._template()); + // list of rows + this.rows = []; + // load extension Utils.get({ url : galaxy_config.root + 'api/ftp_files', @@ -35,7 +39,6 @@ // fill table _fill: function(ftp_files) { - var self = this; if (ftp_files && ftp_files.length > 0) { // add table this.$el.find('#upload-ftp-content').html($(this._templateTable())); @@ -43,7 +46,7 @@ // add files to table var size = 0; for (key in ftp_files) { - this.add(ftp_files[key]); + this.rows.push(this._add(ftp_files[key])); size += ftp_files[key].size; } @@ -51,37 +54,23 @@ this.$el.find('#upload-ftp-number').html(ftp_files.length + ' files'); this.$el.find('#upload-ftp-disk').html(Utils.bytesToString (size, true)); - var selectAll = this.$el.find('#selectAll'); - - // call method to determine and set selectAll status on loading - this._updateSelectAll(selectAll); - - // selectAll checkbox has been clicked - selectAll.on('click', function() { - var checkboxes=$(this).parents().find('tr.upload-ftp-row>td>div'); - var len = checkboxes.length; - $this = $(this); - var allChecked = !($this.hasClass('fa-check-square-o')); - - // change state of the sub-checkboxes - for(i = 0; i < len; i++) { - if(allChecked) { - // all checkboxes should be checked - if(checkboxes.eq(i).hasClass('fa-square-o')) { - // if they are not checked, check them - checkboxes.eq(i).trigger('updateUpBox'); - } - } else { - // no checkboxes should be checked - if(checkboxes.eq(i).hasClass('fa-check-square-o')) { - // if they are checked, uncheck them - checkboxes.eq(i).trigger('updateUpBox'); - } + // add event handler to select/unselect all + this.$select_all = $('#upload-selectall'); + this.$select_all.addClass(this.options.class_add); + var self = this; + this.$select_all.on('click', function() { + var add = self.$select_all.hasClass(self.options.class_add); + for (key in ftp_files) { + var ftp_file = ftp_files[key]; + var model_index = self._find(ftp_file); + if(!model_index && add || model_index && !add) { + self.rows[key].trigger('click'); } } + }); - self._updateSelectAll(selectAll); - }); + // refresh + self._refresh(); } else { // add info this.$el.find('#upload-ftp-content').html($(this._templateInfo())); @@ -92,7 +81,7 @@ }, // add - add: function(ftp_file) { + _add: function(ftp_file) { // link this var self = this; @@ -116,8 +105,8 @@ // add icon class $icon.addClass(icon_class); - // add files to the uploadbox - $it.on('updateUpBox', function() { + // click to add ftp files + $it.on('click', function() { // find model var model_index = self._find(ftp_file); @@ -133,67 +122,51 @@ size : ftp_file.size, path : ftp_file.path }]); - + // add new icon class $icon.addClass(self.options.class_remove); } else { // remove self.app.collection.remove(model_index); - + // add new icon class $icon.addClass(self.options.class_add); } + + // update select all checkbox + self._refresh(); }); - // click to add ftp files - $it.on('click', function() { - //trigger my new event - $icon.trigger('updateUpBox'); - - // click to add ftp files - // modify selectAll box based on number of checkboxes checked - var selectBox=$icon.parents().find('#selectAll'); - // determine and set state of selectAll after sub-checkbox clicked - self._updateSelectAll(selectBox); - }); + // return dom handler + return $it; }, - _updateSelectAll: function(selectBox) { - // array of all checkboxes - var checkboxes=selectBox.parents().find('tr.upload-ftp-row>td>div'); - // array of only checked checkboxes - var checkedCheckboxes=selectBox.parents().find('tr.upload-ftp-row>td>div.fa-check-square-o'); - var lenAll = checkboxes.length; - var lenChecked = checkedCheckboxes.length; - - // determine which state the selectAll checkbox needs to be and setting it - if(lenChecked > 0 && lenChecked !== lenAll) { - // indeterminate state - selectBox.removeClass('fa-square-o fa-check-square-o'); - selectBox.addClass('fa-minus-square-o'); - } else if(lenChecked === lenAll) { - // checked state - selectBox.removeClass('fa-square-o fa-minus-square-o'); - selectBox.addClass('fa-check-square-o'); - } else if(lenChecked === 0) { - // unchecked state - selectBox.removeClass('fa-check-square-o fa-minus-square-o'); - selectBox.addClass('fa-square-o'); + // refresh + _refresh: function() { + var filtered = this.app.collection.where({file_mode : 'ftp'}); + this.$select_all.removeClass(); + if (filtered.length == 0) { + this.$select_all.addClass(this.options.class_add); + } else { + if (filtered.length == this.rows.length) { + this.$select_all.addClass(this.options.class_remove); + } else { + this.$select_all.addClass(this.options.class_partial); + } } }, // get model index _find: function(ftp_file) { - // check if exists already - var filtered = this.app.collection.where({file_path : ftp_file.path}); - var model_index = null; - for (var key in filtered) { - var item = filtered[key]; - if (item.get('status') == 'init' && item.get('file_mode') == 'ftp') { - model_index = item.get('id'); - } + var item = this.app.collection.findWhere({ + file_path : ftp_file.path, + status : 'init', + file_mode : 'ftp' + }); + if (item) { + return item.get('id'); } - return model_index; + return null; }, // template row @@ -218,7 +191,7 @@ '<table class="grid" style="float: left;">' + '<thead>' + '<tr>' + - '<th><div id="selectAll" class="upload-icon-button fa fa-square-o" ></th>' + + '<th><div id="upload-selectall"></th>' + '<th>Name</th>' + '<th>Size</th>' + '<th>Created</th>' + @@ -243,7 +216,6 @@ '<div id="upload-ftp-content"></div>' + '<div>'; } - }); }); diff -r 892da4d5dcc979919c82d4a57ce897d3e93278ce -r de9bd9d7d47bfcdf45f3f170be391874b79e738f static/scripts/packed/mvc/upload/upload-ftp.js --- a/static/scripts/packed/mvc/upload/upload-ftp.js +++ b/static/scripts/packed/mvc/upload/upload-ftp.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)},error:function(){b._fill()}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(d){var b=this;if(d&&d.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var c=0;for(key in d){this.add(d[key]);c+=d[key].size}this.$el.find("#upload-ftp-number").html(d.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(c,true));var e=this.$el.find("#selectAll");this._updateSelectAll(e);e.on("click",function(){var h=$(this).parents().find("tr.upload-ftp-row>td>div");var g=h.length;$this=$(this);var f=!($this.hasClass("fa-check-square-o"));for(i=0;i<g;i++){if(f){if(h.eq(i).hasClass("fa-square-o")){h.eq(i).trigger("updateUpBox")}}else{if(h.eq(i).hasClass("fa-check-square-o")){h.eq(i).trigger("updateUpBox")}}}b._updateSelectAll(e)})}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("updateUpBox",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}});e.on("click",function(){b.trigger("updateUpBox");var g=b.parents().find("#selectAll");d._updateSelectAll(g)})},_updateSelectAll:function(e){var d=e.parents().find("tr.upload-ftp-row>td>div");var f=e.parents().find("tr.upload-ftp-row>td>div.fa-check-square-o");var c=d.length;var b=f.length;if(b>0&&b!==c){e.removeClass("fa-square-o fa-check-square-o");e.addClass("fa-minus-square-o")}else{if(b===c){e.removeClass("fa-square-o fa-minus-square-o");e.addClass("fa-check-square-o")}else{if(b===0){e.removeClass("fa-check-square-o fa-minus-square-o");e.addClass("fa-square-o")}}}},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_templateRow:function(b){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th><div id="selectAll" class="upload-icon-button fa fa-square-o" ></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());this.rows=[];a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)},error:function(){b._fill()}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(d){if(d&&d.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var c=0;for(key in d){this.rows.push(this._add(d[key]));c+=d[key].size}this.$el.find("#upload-ftp-number").html(d.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(c,true));this.$select_all=$("#upload-selectall");this.$select_all.addClass(this.options.class_add);var b=this;this.$select_all.on("click",function(){var g=b.$select_all.hasClass(b.options.class_add);for(key in d){var f=d[key];var e=b._find(f);if(!e&&g||e&&!g){b.rows[key].trigger("click")}}});b._refresh()}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},_add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}d._refresh()});return e},_refresh:function(){var b=this.app.collection.where({file_mode:"ftp"});this.$select_all.removeClass();if(b.length==0){this.$select_all.addClass(this.options.class_add)}else{if(b.length==this.rows.length){this.$select_all.addClass(this.options.class_remove)}else{this.$select_all.addClass(this.options.class_partial)}}},_find:function(c){var b=this.app.collection.findWhere({file_path:c.path,status:"init",file_mode:"ftp"});if(b){return b.get("id")}return null},_templateRow:function(b){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th><div id="upload-selectall"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Clarify default reports template cache location.
by commits-noreply＠bitbucket.org 23 Jan '15

23 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/892da4d5dcc9/ Changeset: 892da4d5dcc9 User: jmchilton Date: 2015-01-23 20:08:37+00:00 Summary: Clarify default reports template cache location. Affected #: 1 file diff -r e361766bbcfd8976ee05cb8826ed239d0f2028f6 -r 892da4d5dcc979919c82d4a57ce897d3e93278ce config/reports_wsgi.ini.sample --- a/config/reports_wsgi.ini.sample +++ b/config/reports_wsgi.ini.sample @@ -28,7 +28,7 @@ # Mako templates are compiled as needed and cached for reuse, this directory is # used for the cache -# template_cache_path = database/compiled_templates +#template_cache_path = database/compiled_templates/reports # Session support (beaker) use_beaker_session = 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.

1 0