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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 01 Dec '14

01 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1034c973ec1d/ Changeset: 1034c973ec1d Branch: next-stable User: guerler Date: 2014-12-01 17:52:01+00:00 Summary: Pages: Sanitize name column in items grid Affected #: 1 file diff -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee -r 1034c973ec1d2ce424f711d750ecc6de582d02aa lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -8,6 +8,7 @@ from galaxy import util from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor from galaxy.util.json import loads +from markupsafe import escape def format_bool( b ): if b: @@ -89,9 +90,9 @@ class NameColumn( grids.TextColumn ): def get_value(self, trans, grid, item): if hasattr( item, "get_display_name" ): - return item.get_display_name() + return escape(item.get_display_name()) else: - return item.name + return escape(item.name) # Grid definition. show_item_checkboxes = True https://bitbucket.org/galaxy/galaxy-central/commits/5393f6389105/ Changeset: 5393f6389105 User: guerler Date: 2014-12-01 17:52:17+00:00 Summary: Merge Affected #: 1 file diff -r d094b6d5953c1379a69050d4cadef03c55413f06 -r 5393f6389105d22bc8791f908075c152f11a4d2e lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -8,6 +8,7 @@ from galaxy import util from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor from galaxy.util.json import loads +from markupsafe import escape def format_bool( b ): if b: @@ -89,9 +90,9 @@ class NameColumn( grids.TextColumn ): def get_value(self, trans, grid, item): if hasattr( item, "get_display_name" ): - return item.get_display_name() + return escape(item.get_display_name()) else: - return item.name + return escape(item.name) # Grid definition. show_item_checkboxes = True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] 8806f0: Update galaxy role from ansible-galaxy.
by GitHub 01 Dec '14

01 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8806f00147b362ccecca457f346abd1e309338fc https://github.com/galaxyproject/usegalaxy-playbook/commit/8806f00147b362cc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2014-12-01 (Mon, 01 Dec 2014) Changed paths: M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/clone.yml Log Message: ----------- Update galaxy role from ansible-galaxy.

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[galaxyproject/ansible-galaxy]
by GitHub 01 Dec '14

01 Dec '14

Branch: refs/tags/0.4 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 6906b2: universe_wsgi.ini.sample is not useful for detecti...
by GitHub 01 Dec '14

01 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 6906b2bed6bd73f2c63b5b3e5046bba6da2bcc82 https://github.com/galaxyproject/ansible-galaxy/commit/6906b2bed6bd73f2c63b… Author: dannon <dannon.baker(a)gmail.com> Date: 2014-12-01 (Mon, 01 Dec 2014) Changed paths: M tasks/clone.yml Log Message: ----------- universe_wsgi.ini.sample is not useful for detecting existence of Galaxy anymore, switch to run.sh Commit: c9559f7d9c4cd7d289a0569a3059c943bfd689ba https://github.com/galaxyproject/ansible-galaxy/commit/c9559f7d9c4cd7d289a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-01 (Mon, 01 Dec 2014) Changed paths: M tasks/clone.yml Log Message: ----------- Merge pull request #1 from dannon/master universe_wsgi.ini.sample is not useful for detecting existence of Galaxy... Compare: https://github.com/galaxyproject/ansible-galaxy/compare/aa1a0e0e0b87...c955…

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 01 Dec '14

01 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4569b8f31c88/ Changeset: 4569b8f31c88 Branch: next-stable User: jmchilton Date: 2014-12-01 16:26:20+00:00 Summary: Merge stable. Affected #: 9 files diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 +acb2548443ae42d39ef200d035ccc0481d6b930c latest_2014.10.06 diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee templates/display_base.mako --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -214,7 +214,7 @@ %else: Private ${get_class_display_name( item.__class__ )} %endif - | ${get_item_name( item )} + | ${get_item_name( item ) | h} <div style="float: right"> ${self.render_item_links( item )} diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee templates/embed_base.mako --- a/templates/embed_base.mako +++ b/templates/embed_base.mako @@ -49,7 +49,7 @@ <div style="float: right;"> ${self.render_item_links( item )} </div> - <h4><a class="toggle-embed" href="${display_href}" title="Show or hide ${item_display_name} content">Galaxy ${get_class_display_name( item.__class__ )} | ${get_item_name( item )}</a></h4> + <h4><a class="toggle-embed" href="${display_href}" title="Show or hide ${item_display_name} content">Galaxy ${get_class_display_name( item.__class__ )} | ${get_item_name( item ) | h}</a></h4> %if hasattr( item, "annotation") and item.annotation: <div class="annotation">${item.annotation}</div> %endif diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee templates/export_base.mako --- a/templates/export_base.mako +++ b/templates/export_base.mako @@ -42,7 +42,7 @@ </%def><%def name="title()"> - Export ${get_class_display_name( item.__class__ )} '${get_item_name( item )}' + Export ${get_class_display_name( item.__class__ )} '${get_item_name( item ) | h}' </%def><%def name="stylesheets()"> @@ -108,7 +108,7 @@ <% item_name = get_item_name(item) %> - <h2>Download or Export ${self.item_class_name} '${item_name}'</h2> + <h2>Download or Export ${self.item_class_name} '${item_name | h}'</h2> ${self.render_download_to_file(item)} diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee templates/ind_share_base.mako --- a/templates/ind_share_base.mako +++ b/templates/ind_share_base.mako @@ -83,7 +83,7 @@ %><div class="toolForm"> - <div class="toolFormTitle">Share ${item_class_name} '${item_name}' with Another User</div> + <div class="toolFormTitle">Share ${item_class_name} '${item_name | h}' with Another User</div><div class="toolFormBody"><form action="${h.url_for(controller=item_controller, action='share', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"> diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee templates/sharing_base.mako --- a/templates/sharing_base.mako +++ b/templates/sharing_base.mako @@ -35,7 +35,7 @@ </%def><%def name="title()"> - Sharing and Publishing ${get_class_display_name( item.__class__ )} '${get_item_name( item )}' + Sharing and Publishing ${get_class_display_name( item.__class__ )} '${get_item_name( item ) | h}' </%def><%def name="javascripts()"> @@ -122,7 +122,7 @@ item_name = get_item_name(item) %> - <h2>Share or Publish ${item_class_name} '${item_name}'</h2> + <h2>Share or Publish ${item_class_name} '${item_name | h}'</h2> ## Require that user have a public username before sharing or publishing an item. %if trans.get_user().username is None or trans.get_user().username is "": diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -19,7 +19,7 @@ </div><h4><a class="toggle-embed" href="${display_href}" title="Show or hide history contents"> - Galaxy History | ${get_item_name( item )} + Galaxy History | ${get_item_name( item ) | h} </a></h4> %if hasattr( item, "annotation") and item.annotation: diff -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee templates/webapps/galaxy/mobile/history/list.mako --- a/templates/webapps/galaxy/mobile/history/list.mako +++ b/templates/webapps/galaxy/mobile/history/list.mako @@ -20,7 +20,7 @@ <li><a href="${h.url_for(controller='mobile', action="history_detail", id=history.id )}"> - ${history.name} + ${history.name | h} <div class="secondary">${h.date.distance_of_time_in_words( history.update_time, h.date.datetime.utcnow() )} ago</div> https://bitbucket.org/galaxy/galaxy-central/commits/d094b6d5953c/ Changeset: d094b6d5953c User: jmchilton Date: 2014-12-01 16:26:58+00:00 Summary: Merge next-stable. Affected #: 9 files diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 +acb2548443ae42d39ef200d035ccc0481d6b930c latest_2014.10.06 diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 templates/display_base.mako --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -214,7 +214,7 @@ %else: Private ${get_class_display_name( item.__class__ )} %endif - | ${get_item_name( item )} + | ${get_item_name( item ) | h} <div style="float: right"> ${self.render_item_links( item )} diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 templates/embed_base.mako --- a/templates/embed_base.mako +++ b/templates/embed_base.mako @@ -49,7 +49,7 @@ <div style="float: right;"> ${self.render_item_links( item )} </div> - <h4><a class="toggle-embed" href="${display_href}" title="Show or hide ${item_display_name} content">Galaxy ${get_class_display_name( item.__class__ )} | ${get_item_name( item )}</a></h4> + <h4><a class="toggle-embed" href="${display_href}" title="Show or hide ${item_display_name} content">Galaxy ${get_class_display_name( item.__class__ )} | ${get_item_name( item ) | h}</a></h4> %if hasattr( item, "annotation") and item.annotation: <div class="annotation">${item.annotation}</div> %endif diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 templates/export_base.mako --- a/templates/export_base.mako +++ b/templates/export_base.mako @@ -42,7 +42,7 @@ </%def><%def name="title()"> - Export ${get_class_display_name( item.__class__ )} '${get_item_name( item )}' + Export ${get_class_display_name( item.__class__ )} '${get_item_name( item ) | h}' </%def><%def name="stylesheets()"> @@ -108,7 +108,7 @@ <% item_name = get_item_name(item) %> - <h2>Download or Export ${self.item_class_name} '${item_name}'</h2> + <h2>Download or Export ${self.item_class_name} '${item_name | h}'</h2> ${self.render_download_to_file(item)} diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 templates/ind_share_base.mako --- a/templates/ind_share_base.mako +++ b/templates/ind_share_base.mako @@ -83,7 +83,7 @@ %><div class="toolForm"> - <div class="toolFormTitle">Share ${item_class_name} '${item_name}' with Another User</div> + <div class="toolFormTitle">Share ${item_class_name} '${item_name | h}' with Another User</div><div class="toolFormBody"><form action="${h.url_for(controller=item_controller, action='share', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"> diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 templates/sharing_base.mako --- a/templates/sharing_base.mako +++ b/templates/sharing_base.mako @@ -35,7 +35,7 @@ </%def><%def name="title()"> - Sharing and Publishing ${get_class_display_name( item.__class__ )} '${get_item_name( item )}' + Sharing and Publishing ${get_class_display_name( item.__class__ )} '${get_item_name( item ) | h}' </%def><%def name="javascripts()"> @@ -122,7 +122,7 @@ item_name = get_item_name(item) %> - <h2>Share or Publish ${item_class_name} '${item_name}'</h2> + <h2>Share or Publish ${item_class_name} '${item_name | h}'</h2> ## Require that user have a public username before sharing or publishing an item. %if trans.get_user().username is None or trans.get_user().username is "": diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -19,7 +19,7 @@ </div><h4><a class="toggle-embed" href="${display_href}" title="Show or hide history contents"> - Galaxy History | ${get_item_name( item )} + Galaxy History | ${get_item_name( item ) | h} </a></h4> %if hasattr( item, "annotation") and item.annotation: diff -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 -r d094b6d5953c1379a69050d4cadef03c55413f06 templates/webapps/galaxy/mobile/history/list.mako --- a/templates/webapps/galaxy/mobile/history/list.mako +++ b/templates/webapps/galaxy/mobile/history/list.mako @@ -20,7 +20,7 @@ <li><a href="${h.url_for(controller='mobile', action="history_detail", id=history.id )}"> - ${history.name} + ${history.name | h} <div class="secondary">${h.date.distance_of_time_in_words( history.update_time, h.date.datetime.utcnow() )} ago</div> 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: ToolForm: Add baseurl, fix dynamic drill down options
by commits-noreply＠bitbucket.org 01 Dec '14

01 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b208a4b38f9/ Changeset: 7b208a4b38f9 User: guerler Date: 2014-12-01 06:18:16+00:00 Summary: ToolForm: Add baseurl, fix dynamic drill down options Affected #: 7 files diff -r a1fff5e41925f99d95def300a162e12db0f4b8c7 -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -342,6 +342,11 @@ case 'drill_down': field = this._fieldDrilldown(input_def); break; + + // base url field + case 'baseurl': + field = this._fieldHidden(input_def); + break; // field not found default: diff -r a1fff5e41925f99d95def300a162e12db0f4b8c7 -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 client/galaxy/scripts/mvc/ui/ui-drilldown.js --- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -16,8 +16,7 @@ */ _templateOption: function(name, value, selected) { return '<div>' + - '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + - Utils.sanitize(name) + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name + '<div/>'; }, diff -r a1fff5e41925f99d95def300a162e12db0f4b8c7 -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -650,6 +650,11 @@ def get_label( self ): # BaseURLToolParameters are ultimately "hidden" parameters return None + + def to_dict( self, trans, view='collection', value_mapper=None ): + d = super( BaseURLToolParameter, self ).to_dict( trans ) + d['value'] = self.get_value( trans ) + return d DEFAULT_VALUE_MAP = lambda x: x @@ -1606,13 +1611,13 @@ """ return self.filtered.keys() - def to_dict( self, trans, view='collection', value_mapper=None, context={} ): + def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ): # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here d = ToolParameter.to_dict( self, trans ) options = [] try: - options = self.get_options( trans, context ) + options = self.get_options( trans=trans, other_values=other_values ) except KeyError: # will sometimes error if self.is_dynamic and self.filtered # bc we dont/cant fill out other_values above ({}) diff -r a1fff5e41925f99d95def300a162e12db0f4b8c7 -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -342,6 +342,11 @@ case 'drill_down': field = this._fieldDrilldown(input_def); break; + + // base url field + case 'baseurl': + field = this._fieldHidden(input_def); + break; // field not found default: diff -r a1fff5e41925f99d95def300a162e12db0f4b8c7 -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 static/scripts/mvc/ui/ui-drilldown.js --- a/static/scripts/mvc/ui/ui-drilldown.js +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -16,8 +16,7 @@ */ _templateOption: function(name, value, selected) { return '<div>' + - '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + - Utils.sanitize(name) + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name + '<div/>'; }, diff -r a1fff5e41925f99d95def300a162e12db0f4b8c7 -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r a1fff5e41925f99d95def300a162e12db0f4b8c7 -r 7b208a4b38f934cdea8f4f331f2721adcc7c1166 static/scripts/packed/mvc/ui/ui-drilldown.js --- a/static/scripts/packed/mvc/ui/ui-drilldown.js +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+d+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ 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: guerler: ToolForm: Fix select2 value selection
by commits-noreply＠bitbucket.org 01 Dec '14

01 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a1fff5e41925/ Changeset: a1fff5e41925 User: guerler Date: 2014-12-01 05:21:40+00:00 Summary: ToolForm: Fix select2 value selection Affected #: 9 files diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 client/galaxy/scripts/mvc/ui/ui-drilldown.js --- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -23,7 +23,7 @@ /** Template to create options tree */ - _templateOptions: function(data, current) { + _templateOptions: function(options) { // link this var self = this; @@ -48,10 +48,10 @@ } // recursive function which iterates through options - function iterate ($tmpl, data) { - for (i in data) { + function iterate ($tmpl, options) { + for (i in options) { // current option level in hierarchy - var level = data[i]; + var level = options[i]; // check for options var has_options = level.options.length > 0; @@ -84,7 +84,7 @@ // iterate through options and create dom var $tmpl = $('<div/>'); - iterate($tmpl, data); + iterate($tmpl, options); return $tmpl; }, diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -7,7 +7,6 @@ initialize: function(options) { // options this.optionsDefault = { - value : [], visible : true, data : [], id : Utils.uuid(), @@ -38,7 +37,7 @@ this.update(this.options.data); // set initial value - if (this.options.value) { + if (this.options.value !== undefined) { this.value(this.options.value); } @@ -88,13 +87,13 @@ /** Return/Set current value */ value: function (new_value) { - // check if its an array - if (typeof new_value === 'string') { - new_value = [new_value]; - } - - // set new value + // set new value if provided if (new_value !== undefined) { + // check if its an array + if (!(new_value instanceof Array)) { + new_value = [new_value]; + } + // reset selection this.$el.find('input').prop('checked', false); @@ -111,12 +110,14 @@ /** Check if selected value exists (or any if multiple) */ exists: function(value) { - if (typeof value === 'string') { - value = [value]; - } - for (var i in value) { - if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { - return true; + if (value !== undefined) { + if (!(value instanceof Array)) { + value = [value]; + } + for (var i in value) { + if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + return true; + } } } return false; diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -75,6 +75,9 @@ value : function (new_value) { if (new_value !== undefined) { this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } return this.$select.val(); }, diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 static/scripts/mvc/ui/ui-drilldown.js --- a/static/scripts/mvc/ui/ui-drilldown.js +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -23,7 +23,7 @@ /** Template to create options tree */ - _templateOptions: function(data, current) { + _templateOptions: function(options) { // link this var self = this; @@ -48,10 +48,10 @@ } // recursive function which iterates through options - function iterate ($tmpl, data) { - for (i in data) { + function iterate ($tmpl, options) { + for (i in options) { // current option level in hierarchy - var level = data[i]; + var level = options[i]; // check for options var has_options = level.options.length > 0; @@ -84,7 +84,7 @@ // iterate through options and create dom var $tmpl = $('<div/>'); - iterate($tmpl, data); + iterate($tmpl, options); return $tmpl; }, diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -7,7 +7,6 @@ initialize: function(options) { // options this.optionsDefault = { - value : [], visible : true, data : [], id : Utils.uuid(), @@ -38,7 +37,7 @@ this.update(this.options.data); // set initial value - if (this.options.value) { + if (this.options.value !== undefined) { this.value(this.options.value); } @@ -88,13 +87,13 @@ /** Return/Set current value */ value: function (new_value) { - // check if its an array - if (typeof new_value === 'string') { - new_value = [new_value]; - } - - // set new value + // set new value if provided if (new_value !== undefined) { + // check if its an array + if (!(new_value instanceof Array)) { + new_value = [new_value]; + } + // reset selection this.$el.find('input').prop('checked', false); @@ -111,12 +110,14 @@ /** Check if selected value exists (or any if multiple) */ exists: function(value) { - if (typeof value === 'string') { - value = [value]; - } - for (var i in value) { - if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { - return true; + if (value !== undefined) { + if (!(value instanceof Array)) { + value = [value]; + } + for (var i in value) { + if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + return true; + } } } return false; diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -75,6 +75,9 @@ value : function (new_value) { if (new_value !== undefined) { this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } return this.$select.val(); }, diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 static/scripts/packed/mvc/ui/ui-drilldown.js --- a/static/scripts/packed/mvc/ui/ui-drilldown.js +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(g,h){var e=this;function f(l,m){function k(n){if(n){m.fadeIn("fast");l.removeClass("toggle-expand");l.addClass("toggle");l.is_expanded=true}else{m.hide();l.removeClass("toggle");l.addClass("toggle-expand");l.is_expanded=false}}l.on("click",function(){k(!l.is_expanded)})}function d(q,o){for(i in o){var r=o[i];var m=r.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var k=$("<div/>");k.append(n);k.append(e._templateOption(r.name,r.value));l.append(k);var p=$('<div style="display: none; margin-left: 25px;"/>');d(p,r.options);l.append(p);f(n,p)}else{l.append(e._templateOption(r.name,r.value))}q.append(l)}}var j=$("<div/>");d(j,g);return j},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(typeof g==="string"){g=[g]}if(g!==undefined){this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd -r a1fff5e41925f99d95def300a162e12db0f4b8c7 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Add drill down element
by commits-noreply＠bitbucket.org 01 Dec '14

01 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3ecc2541d8fc/ Changeset: 3ecc2541d8fc User: guerler Date: 2014-12-01 04:40:38+00:00 Summary: ToolForm: Add drill down element Affected #: 25 files diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -211,7 +211,7 @@ this.tree.matchModel(new_model, function(input_id, node) { var input = self.input_list[input_id]; if (input && input.options) { - if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + if (!_.isEqual(input.options, node.options)) { // backup new options input.options = node.options; @@ -223,6 +223,9 @@ case 'data': new_options = input.options; break; + case 'drill_down': + new_options = input.options; + break; default: for (var i in node.options) { var opt = node.options[i]; diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -337,7 +337,12 @@ input_def.searchable = true; field = this._fieldSelect(input_def); break; - + + // drill down field + case 'drill_down': + field = this._fieldDrilldown(input_def); + break; + // field not found default: // flag @@ -417,6 +422,20 @@ }); }, + /** Drill down options field + */ + _fieldDrilldown : function (input_def) { + var self = this; + return new Ui.Drilldown.View({ + id : 'field-' + input_def.id, + data : input_def.options, + display : input_def.display, + onchange : function() { + self.app.refresh(); + } + }); + }, + /** Text input field */ _fieldText : function(input_def) { diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -90,6 +90,11 @@ // update options this.update(options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // refresh view this.refresh(); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/ui/ui-drilldown.js --- /dev/null +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -0,0 +1,102 @@ +// dependencies +define(['utils/utils', 'mvc/ui/ui-options'], function(Utils, Options) { + +/** + * This class creates/wraps a drill down element. + */ +var View = Options.Base.extend({ + // initialize + initialize: function(options) { + this.display = options.display || 'checkbox'; + options.multiple = (this.display == 'checkbox'); + Options.Base.prototype.initialize.call(this, options); + }, + + /** Template for input field + */ + _templateOption: function(name, value, selected) { + return '<div>' + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + + Utils.sanitize(name) + + '<div/>'; + }, + + /** Template to create options tree + */ + _templateOptions: function(data, current) { + // link this + var self = this; + + // attach show/hide event + function attachEvents($button, $subgroup) { + function setVisibility (visible) { + if (visible) { + $subgroup.fadeIn('fast') + $button.removeClass('toggle-expand'); + $button.addClass('toggle'); + $button.is_expanded = true; + } else { + $subgroup.hide(); + $button.removeClass('toggle'); + $button.addClass('toggle-expand'); + $button.is_expanded = false; + } + }; + $button.on('click', function() { + setVisibility(!$button.is_expanded); + }); + } + + // recursive function which iterates through options + function iterate ($tmpl, data) { + for (i in data) { + // current option level in hierarchy + var level = data[i]; + + // check for options + var has_options = level.options.length > 0; + + // build template + var $group = $('<div/>'); + if (has_options) { + // create button and add flag + var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>'); + + // add expand group + var $buttongroup = $('<div/>'); + $buttongroup.append($button); + $buttongroup.append(self._templateOption(level.name, level.value)); + $group.append($buttongroup); + + // add sub group + var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); + iterate($subgroup, level.options); + $group.append($subgroup); + + // attach click event to collapse/expand hierarchy + attachEvents($button, $subgroup); + } else { + $group.append(self._templateOption(level.name, level.value)); + } + $tmpl.append($group); + } + } + + // iterate through options and create dom + var $tmpl = $('<div/>'); + iterate($tmpl, data); + return $tmpl; + }, + + /** Template for drill down view + */ + _template: function(options) { + return '<div class="ui-options drilldown-container" id="' + options.id + '"/>'; + } +}); + +return { + View: View +} + +}); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/ui/ui-misc.js --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Options, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -339,7 +339,6 @@ var Input = Backbone.View.extend({ // options optionsDefault: { - value : '', type : 'text', placeholder : '', disabled : false, @@ -356,6 +355,11 @@ // create new element this.setElement(this._template(this.options)); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // disable input field if (this.options.disabled) { this.$el.prop('disabled', true); @@ -395,18 +399,18 @@ // plugin var Hidden = Backbone.View.extend({ - // options - optionsDefault: { - value : '' - }, - // initialize initialize : function(options) { // configure options - this.options = Utils.merge(options, this.optionsDefault); + this.options = options; // create new element this.setElement(this._template(this.options)); + + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } }, // value @@ -441,6 +445,7 @@ Searchbox : Searchbox, Select : Select, Hidden : Hidden, - Slider : Slider + Slider : Slider, + Drilldown : Drilldown } }); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -2,7 +2,7 @@ define(['utils/utils'], function(Utils) { /** Base class for options based ui elements **/ -var OptionsBase = Backbone.View.extend({ +var Base = Backbone.View.extend({ // initialize initialize: function(options) { // options @@ -56,16 +56,19 @@ var current = this._getValue(); // remove all options - this.$el.find('.ui-option').remove(); + this.$options.empty(); - // add new options - for (var key in options) { - // load option template - var $option = $(this._templateOption(options[key])); - $option.addClass('ui-option'); - - // append to dom - this.$options.append($option); + // add new options using single option templates or full template + if (this._templateOptions) { + // rebuild options using full template + this.$options.append(this._templateOptions(options)); + } else { + // rebuild options using single option templates + for (var key in options) { + var $option = $(this._templateOption(options[key])); + $option.addClass('ui-option'); + this.$options.append($option); + } } // add change events @@ -82,6 +85,29 @@ this.value(current); }, + /** Return/Set current value + */ + value: function (new_value) { + // check if its an array + if (typeof new_value === 'string') { + new_value = [new_value]; + } + + // set new value + if (new_value !== undefined) { + // reset selection + this.$el.find('input').prop('checked', false); + + // update to new selection + for (var i in new_value) { + this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true); + }; + } + + // get and return value + return this._getValue(); + }, + /** Check if selected value exists (or any if multiple) */ exists: function(value) { @@ -198,46 +224,6 @@ */ _messageHide: function() { this.$message.hide(); - } -}); - -/** Radio button field **/ -var Radio = {}; -Radio.View = OptionsBase.extend({ - // initialize - initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); - }, - - /** Return/Set current value - */ - value: function (new_val) { - // check if its an array - if (typeof new_val === 'string') { - new_val = [new_val]; - } - - // set new value - if (new_val !== undefined) { - // reset selection - this.$el.find('input').prop('checked', false); - - // update to new selection - for (var i in new_val) { - this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); - }; - } - - // get and return value - return this._getValue(); - }, - - /** Template for options - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; }, /** Main template function @@ -247,16 +233,33 @@ } }); +/** Radio button field **/ +var Radio = {}; +Radio.View = Base.extend({ + // initialize + initialize: function(options) { + Base.prototype.initialize.call(this, options); + }, + + /** Template for a single option + */ + _templateOption: function(pair) { + return '<div>' + + '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + + '</div>'; + } +}); + /** Checkbox options field **/ var Checkbox = {}; -Checkbox.View = Radio.View.extend({ +Checkbox.View = Base.extend({ // initialize initialize: function(options) { options.multiple = true; - Radio.View.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { return '<div>' + @@ -267,27 +270,27 @@ /** Radio button options field styled as classic buttons **/ var RadioButton = {}; -RadioButton.View = OptionsBase.extend({ +RadioButton.View = Base.extend({ // initialize initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, /** Return/Set current value */ - value: function (new_val) { + value: function (new_value) { // set new value - if (new_val !== undefined) { + if (new_value !== undefined) { this.$el.find('input').prop('checked', false); this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active'); + this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); } // get and return value return this._getValue(); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { var tmpl = '<label class="btn btn-default">'; @@ -307,6 +310,7 @@ }); return { + Base : Base, Radio : Radio, RadioButton : RadioButton, Checkbox : Checkbox diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -41,6 +41,11 @@ // refresh this.update(this.options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // show/hide if (!this.options.visible) { this.hide(); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd client/galaxy/scripts/mvc/ui/ui-slider.js --- a/client/galaxy/scripts/mvc/ui/ui-slider.js +++ b/client/galaxy/scripts/mvc/ui/ui-slider.js @@ -5,7 +5,6 @@ var View = Backbone.View.extend({ // options optionsDefault: { - value : '', min : null, max : null, step : null, @@ -49,6 +48,11 @@ // link text input field this.$text = this.$el.find('#text'); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // add text field event this.$text.on('change', function () { self.value($(this).val()); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1606,19 +1606,20 @@ """ return self.filtered.keys() - def to_dict( self, trans, view='collection', value_mapper=None ): + def to_dict( self, trans, view='collection', value_mapper=None, context={} ): # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here d = ToolParameter.to_dict( self, trans ) options = [] try: - options = self.get_options( trans, {} ) + options = self.get_options( trans, context ) except KeyError: # will sometimes error if self.is_dynamic and self.filtered # bc we dont/cant fill out other_values above ({}) pass - d[ 'options' ] = options + d[ 'display' ] = self.display + d[ 'is_dynamic' ] = self.is_dynamic return d diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -211,7 +211,7 @@ this.tree.matchModel(new_model, function(input_id, node) { var input = self.input_list[input_id]; if (input && input.options) { - if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + if (!_.isEqual(input.options, node.options)) { // backup new options input.options = node.options; @@ -223,6 +223,9 @@ case 'data': new_options = input.options; break; + case 'drill_down': + new_options = input.options; + break; default: for (var i in node.options) { var opt = node.options[i]; diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -337,7 +337,12 @@ input_def.searchable = true; field = this._fieldSelect(input_def); break; - + + // drill down field + case 'drill_down': + field = this._fieldDrilldown(input_def); + break; + // field not found default: // flag @@ -417,6 +422,20 @@ }); }, + /** Drill down options field + */ + _fieldDrilldown : function (input_def) { + var self = this; + return new Ui.Drilldown.View({ + id : 'field-' + input_def.id, + data : input_def.options, + display : input_def.display, + onchange : function() { + self.app.refresh(); + } + }); + }, + /** Text input field */ _fieldText : function(input_def) { diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -90,6 +90,11 @@ // update options this.update(options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // refresh view this.refresh(); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/ui/ui-drilldown.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -0,0 +1,102 @@ +// dependencies +define(['utils/utils', 'mvc/ui/ui-options'], function(Utils, Options) { + +/** + * This class creates/wraps a drill down element. + */ +var View = Options.Base.extend({ + // initialize + initialize: function(options) { + this.display = options.display || 'checkbox'; + options.multiple = (this.display == 'checkbox'); + Options.Base.prototype.initialize.call(this, options); + }, + + /** Template for input field + */ + _templateOption: function(name, value, selected) { + return '<div>' + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + + Utils.sanitize(name) + + '<div/>'; + }, + + /** Template to create options tree + */ + _templateOptions: function(data, current) { + // link this + var self = this; + + // attach show/hide event + function attachEvents($button, $subgroup) { + function setVisibility (visible) { + if (visible) { + $subgroup.fadeIn('fast') + $button.removeClass('toggle-expand'); + $button.addClass('toggle'); + $button.is_expanded = true; + } else { + $subgroup.hide(); + $button.removeClass('toggle'); + $button.addClass('toggle-expand'); + $button.is_expanded = false; + } + }; + $button.on('click', function() { + setVisibility(!$button.is_expanded); + }); + } + + // recursive function which iterates through options + function iterate ($tmpl, data) { + for (i in data) { + // current option level in hierarchy + var level = data[i]; + + // check for options + var has_options = level.options.length > 0; + + // build template + var $group = $('<div/>'); + if (has_options) { + // create button and add flag + var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>'); + + // add expand group + var $buttongroup = $('<div/>'); + $buttongroup.append($button); + $buttongroup.append(self._templateOption(level.name, level.value)); + $group.append($buttongroup); + + // add sub group + var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); + iterate($subgroup, level.options); + $group.append($subgroup); + + // attach click event to collapse/expand hierarchy + attachEvents($button, $subgroup); + } else { + $group.append(self._templateOption(level.name, level.value)); + } + $tmpl.append($group); + } + } + + // iterate through options and create dom + var $tmpl = $('<div/>'); + iterate($tmpl, data); + return $tmpl; + }, + + /** Template for drill down view + */ + _template: function(options) { + return '<div class="ui-options drilldown-container" id="' + options.id + '"/>'; + } +}); + +return { + View: View +} + +}); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Options, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -339,7 +339,6 @@ var Input = Backbone.View.extend({ // options optionsDefault: { - value : '', type : 'text', placeholder : '', disabled : false, @@ -356,6 +355,11 @@ // create new element this.setElement(this._template(this.options)); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // disable input field if (this.options.disabled) { this.$el.prop('disabled', true); @@ -395,18 +399,18 @@ // plugin var Hidden = Backbone.View.extend({ - // options - optionsDefault: { - value : '' - }, - // initialize initialize : function(options) { // configure options - this.options = Utils.merge(options, this.optionsDefault); + this.options = options; // create new element this.setElement(this._template(this.options)); + + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } }, // value @@ -441,6 +445,7 @@ Searchbox : Searchbox, Select : Select, Hidden : Hidden, - Slider : Slider + Slider : Slider, + Drilldown : Drilldown } }); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -2,7 +2,7 @@ define(['utils/utils'], function(Utils) { /** Base class for options based ui elements **/ -var OptionsBase = Backbone.View.extend({ +var Base = Backbone.View.extend({ // initialize initialize: function(options) { // options @@ -56,16 +56,19 @@ var current = this._getValue(); // remove all options - this.$el.find('.ui-option').remove(); + this.$options.empty(); - // add new options - for (var key in options) { - // load option template - var $option = $(this._templateOption(options[key])); - $option.addClass('ui-option'); - - // append to dom - this.$options.append($option); + // add new options using single option templates or full template + if (this._templateOptions) { + // rebuild options using full template + this.$options.append(this._templateOptions(options)); + } else { + // rebuild options using single option templates + for (var key in options) { + var $option = $(this._templateOption(options[key])); + $option.addClass('ui-option'); + this.$options.append($option); + } } // add change events @@ -82,6 +85,29 @@ this.value(current); }, + /** Return/Set current value + */ + value: function (new_value) { + // check if its an array + if (typeof new_value === 'string') { + new_value = [new_value]; + } + + // set new value + if (new_value !== undefined) { + // reset selection + this.$el.find('input').prop('checked', false); + + // update to new selection + for (var i in new_value) { + this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true); + }; + } + + // get and return value + return this._getValue(); + }, + /** Check if selected value exists (or any if multiple) */ exists: function(value) { @@ -198,46 +224,6 @@ */ _messageHide: function() { this.$message.hide(); - } -}); - -/** Radio button field **/ -var Radio = {}; -Radio.View = OptionsBase.extend({ - // initialize - initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); - }, - - /** Return/Set current value - */ - value: function (new_val) { - // check if its an array - if (typeof new_val === 'string') { - new_val = [new_val]; - } - - // set new value - if (new_val !== undefined) { - // reset selection - this.$el.find('input').prop('checked', false); - - // update to new selection - for (var i in new_val) { - this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); - }; - } - - // get and return value - return this._getValue(); - }, - - /** Template for options - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; }, /** Main template function @@ -247,16 +233,33 @@ } }); +/** Radio button field **/ +var Radio = {}; +Radio.View = Base.extend({ + // initialize + initialize: function(options) { + Base.prototype.initialize.call(this, options); + }, + + /** Template for a single option + */ + _templateOption: function(pair) { + return '<div>' + + '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + + '</div>'; + } +}); + /** Checkbox options field **/ var Checkbox = {}; -Checkbox.View = Radio.View.extend({ +Checkbox.View = Base.extend({ // initialize initialize: function(options) { options.multiple = true; - Radio.View.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { return '<div>' + @@ -267,27 +270,27 @@ /** Radio button options field styled as classic buttons **/ var RadioButton = {}; -RadioButton.View = OptionsBase.extend({ +RadioButton.View = Base.extend({ // initialize initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, /** Return/Set current value */ - value: function (new_val) { + value: function (new_value) { // set new value - if (new_val !== undefined) { + if (new_value !== undefined) { this.$el.find('input').prop('checked', false); this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active'); + this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); } // get and return value return this._getValue(); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { var tmpl = '<label class="btn btn-default">'; @@ -307,6 +310,7 @@ }); return { + Base : Base, Radio : Radio, RadioButton : RadioButton, Checkbox : Checkbox diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -41,6 +41,11 @@ // refresh this.update(this.options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // show/hide if (!this.options.visible) { this.hide(); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/mvc/ui/ui-slider.js --- a/static/scripts/mvc/ui/ui-slider.js +++ b/static/scripts/mvc/ui/ui-slider.js @@ -5,7 +5,6 @@ var View = Backbone.View.extend({ // options optionsDefault: { - value : '', min : null, max : null, step : null, @@ -49,6 +48,11 @@ // link text input field this.$text = this.$el.find('#text'); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // add text field event this.$text.on('change', function () { self.value($(this).val()); diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(!_.isEqual(p.options,u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;case"drill_down":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/ui/ui-drilldown.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -0,0 +1,1 @@ +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(g,h){var e=this;function f(l,m){function k(n){if(n){m.fadeIn("fast");l.removeClass("toggle-expand");l.addClass("toggle");l.is_expanded=true}else{m.hide();l.removeClass("toggle");l.addClass("toggle-expand");l.is_expanded=false}}l.on("click",function(){k(!l.is_expanded)})}function d(q,o){for(i in o){var r=o[i];var m=r.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var k=$("<div/>");k.append(n);k.append(e._templateOption(r.name,r.value));l.append(k);var p=$('<div style="display: none; margin-left: 25px;"/>');d(p,r.options);l.append(p);f(n,p)}else{l.append(e._templateOption(r.name,r.value))}q.append(l)}}var j=$("<div/>");d(j,g);return j},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(q.onclick){q.onclick()}});$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="'+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var q=this;$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick&&!q.disabled){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="'+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Searchbox:a,Select:b,Hidden:o,Slider:e}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,o,l,q,m){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$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.$button.removeClass("disabled");this.disabled=false},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="'+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(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:"",status:"info",persistent:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement("<div></div>")},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.$el.fadeIn();if(!s.persistent){var r=this;window.setTimeout(function(){if(r.$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.$el.val()},_template:function(r){if(r.area){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'"></textarea>'}else{return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}}});var p=Backbone.View.extend({initialize:function(r){this.options=r;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<hidden id="'+r.id+'" value="'+r.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:q,Icon:c,Image:d,Input:i,Label:j,Message:n,Modal:m,RadioButton:o.RadioButton,Checkbox:o.Checkbox,Radio:o.Radio,Searchbox:a,Select:b,Hidden:p,Slider:e,Drilldown:l}}); \ No newline at end of file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find('input[value="'+f[g]+'"]').prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(typeof g==="string"){g=[g]}if(g!==undefined){this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 3ecc2541d8fc5170d9337f06b206ec09557f3afd static/scripts/packed/mvc/ui/ui-slider.js --- a/static/scripts/packed/mvc/ui/ui-slider.js +++ b/static/scripts/packed/mvc/ui/ui-slider.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");if(this.options.value!==undefined){this.value(this.options.value)}this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ 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: natefoo: Update tag latest_2014.10.06 for changeset acb2548443ae
by commits-noreply＠bitbucket.org 27 Nov '14

27 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26aab19109ce/ Changeset: 26aab19109ce Branch: stable User: natefoo Date: 2014-11-27 14:00:14+00:00 Summary: Update tag latest_2014.10.06 for changeset acb2548443ae Affected #: 1 file diff -r acb2548443ae42d39ef200d035ccc0481d6b930c -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -adc4aa8b3d9ad77ef85f8b0d7e4d90bd29775167 latest_2014.10.06 +acb2548443ae42d39ef200d035ccc0481d6b930c latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] 49ee6f: Update Test.
by GitHub 26 Nov '14

26 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 49ee6f1dff6ade330d324428197fdc1674963b6f https://github.com/galaxyproject/usegalaxy-playbook/commit/49ee6f1dff6ade33… Author: dannon <dannon.baker(a)gmail.com> Date: 2014-11-26 (Wed, 26 Nov 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M stage/group_vars/all.yml Log Message: ----------- Update Test.

1 0

commit/galaxy-central: dannon: Merge next-stable.
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3975b317ffdc/ Changeset: 3975b317ffdc User: dannon Date: 2014-11-26 18:25:30+00:00 Summary: Merge next-stable. Affected #: 1 file diff -r c5321f66c314cdfcaeb0aaedcc65c479558abf3a -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -148,7 +148,7 @@ """ raise TypeError( "Abstract method" ) - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): """ Determine the runtime state (potentially different from self.state which describes configuration state). This (again unlike self.state) is currently always a `DefaultToolState` object. @@ -259,7 +259,7 @@ errors[ name ] = error return errors - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): if step_updates and "tool_state" in step_updates: # Fix this for multiple inputs state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) ) @@ -716,7 +716,7 @@ def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans, allow_workflow_parameters=True ) - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): # Warning: This method destructively modifies existing step state. step_errors = None state = self.state @@ -727,7 +727,7 @@ old_errors = state.inputs.pop( "__errors__", {} ) # Update the state step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, - update_only=True, old_errors=old_errors, source="json" ) + update_only=True, old_errors=old_errors, source=source ) return state, step_errors def execute( self, trans, progress, invocation, step ): @@ -956,7 +956,7 @@ def __init__( self, trans ): self.trans = trans - def inject( self, step, step_args=None ): + def inject( self, step, step_args=None, source="html" ): """ Pre-condition: `step` is an ORM object coming from the database, if supplied `step_args` is the representation of the inputs for that step supplied via web form. @@ -998,7 +998,7 @@ # are not persisted so we need to do it every time) module.add_dummy_datasets( connections=step.input_connections ) - state, step_errors = module.compute_runtime_state( trans, step_args ) + state, step_errors = module.compute_runtime_state( trans, step_args, source=source ) step.state = state return step_errors @@ -1011,7 +1011,7 @@ module_injector = WorkflowModuleInjector( trans ) for step in workflow.steps: step_args = param_map.get( step.id, {} ) - step_errors = module_injector.inject( step, step_args=step_args ) + step_errors = module_injector.inject( step, step_args=step_args, source="json" ) if step.type == 'tool' or step.type is None: if step_errors: message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jmchilton: Fix boolean parameter handling at workflow runtime.
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a30a79840d4/ Changeset: 3a30a79840d4 Branch: next-stable User: jmchilton Date: 2014-11-26 17:42:00+00:00 Summary: Fix boolean parameter handling at workflow runtime. Broken with 011c8b2118be778eaf1ba952730ff876d6447ba9. Note to self - update pause module when merging into next-stable. Affected #: 1 file diff -r d94fef1095439d5cf7145ca6eb13b9f12f453874 -r 3a30a79840d4e5e4896910dcf2f161a38d7977b0 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -148,7 +148,7 @@ """ raise TypeError( "Abstract method" ) - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): """ Determine the runtime state (potentially different from self.state which describes configuration state). This (again unlike self.state) is currently always a `DefaultToolState` object. @@ -259,7 +259,7 @@ errors[ name ] = error return errors - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): if step_updates and "tool_state" in step_updates: # Fix this for multiple inputs state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) ) @@ -716,7 +716,7 @@ def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans, allow_workflow_parameters=True ) - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): # Warning: This method destructively modifies existing step state. step_errors = None state = self.state @@ -727,7 +727,7 @@ old_errors = state.inputs.pop( "__errors__", {} ) # Update the state step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, - update_only=True, old_errors=old_errors, source="json" ) + update_only=True, old_errors=old_errors, source=source ) return state, step_errors def execute( self, trans, progress, invocation, step ): @@ -956,7 +956,7 @@ def __init__( self, trans ): self.trans = trans - def inject( self, step, step_args=None ): + def inject( self, step, step_args=None, source="html" ): """ Pre-condition: `step` is an ORM object coming from the database, if supplied `step_args` is the representation of the inputs for that step supplied via web form. @@ -998,7 +998,7 @@ # are not persisted so we need to do it every time) module.add_dummy_datasets( connections=step.input_connections ) - state, step_errors = module.compute_runtime_state( trans, step_args ) + state, step_errors = module.compute_runtime_state( trans, step_args, source=source ) step.state = state return step_errors @@ -1011,7 +1011,7 @@ module_injector = WorkflowModuleInjector( trans ) for step in workflow.steps: step_args = param_map.get( step.id, {} ) - step_errors = module_injector.inject( step, step_args=step_args ) + step_errors = module_injector.inject( step, step_args=step_args, source="json" ) if step.type == 'tool' or step.type is None: if step_errors: message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jmchilton: Fix boolean parameter handling at workflow runtime.
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/acb2548443ae/ Changeset: acb2548443ae Branch: stable User: jmchilton Date: 2014-11-26 17:42:00+00:00 Summary: Fix boolean parameter handling at workflow runtime. Broken with 011c8b2118be778eaf1ba952730ff876d6447ba9. Note to self - update pause module when merging into next-stable. Affected #: 1 file diff -r c50a228167b0a1a4541f46bb19b8d67c9010248d -r acb2548443ae42d39ef200d035ccc0481d6b930c lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -147,7 +147,7 @@ """ raise TypeError( "Abstract method" ) - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): """ Determine the runtime state (potentially different from self.state which describes configuration state). This (again unlike self.state) is currently always a `DefaultToolState` object. @@ -258,7 +258,7 @@ errors[ name ] = error return errors - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): if step_updates: # Fix this for multiple inputs state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) ) @@ -598,7 +598,7 @@ def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans, allow_workflow_parameters=True ) - def compute_runtime_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None, source="html" ): # Warning: This method destructively modifies existing step state. step_errors = None state = self.state @@ -609,7 +609,7 @@ old_errors = state.inputs.pop( "__errors__", {} ) # Update the state step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, - update_only=True, old_errors=old_errors, source="json" ) + update_only=True, old_errors=old_errors, source=source ) return state, step_errors def execute( self, trans, progress, invocation, step ): @@ -784,7 +784,7 @@ def __init__( self, trans ): self.trans = trans - def inject( self, step, step_args=None ): + def inject( self, step, step_args=None, source="html" ): """ Pre-condition: `step` is an ORM object coming from the database, if supplied `step_args` is the representation of the inputs for that step supplied via web form. @@ -827,7 +827,7 @@ # are not persisted so we need to do it every time) module.add_dummy_datasets( connections=step.input_connections ) - state, step_errors = module.compute_runtime_state( trans, step_args ) + state, step_errors = module.compute_runtime_state( trans, step_args, source=source ) step.state = state return step_errors @@ -840,7 +840,7 @@ module_injector = WorkflowModuleInjector( trans ) for step in workflow.steps: step_args = param_map.get( step.id, {} ) - step_errors = module_injector.inject( step, step_args=step_args ) + step_errors = module_injector.inject( step, step_args=step_args, source="json" ) if step.type == 'tool' or step.type is None: if step_errors: message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d94fef109543/ Changeset: d94fef109543 Branch: next-stable User: guerler Date: 2014-11-26 17:42:46+00:00 Summary: ToolForm: Ensure that the correct definition for booleans is used Affected #: 1 file diff -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 -r d94fef1095439d5cf7145ca6eb13b9f12f453874 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -587,7 +587,7 @@ error = 'State validation failed.' try: # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code - if input.type == 'boolean': + if input.type == 'boolean' and isinstance(default_value, basestring): value, error = [util.string_as_bool(default_value), None] else: value, error = check_param(trans, input, default_value, context) https://bitbucket.org/galaxy/galaxy-central/commits/c5321f66c314/ Changeset: c5321f66c314 User: guerler Date: 2014-11-26 17:43:05+00:00 Summary: Merge Affected #: 1 file diff -r 5f178251e9b579f62ceb172ab562d67d1c841b73 -r c5321f66c314cdfcaeb0aaedcc65c479558abf3a lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -594,7 +594,7 @@ error = 'State validation failed.' try: # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code - if input.type == 'boolean': + if input.type == 'boolean' and isinstance(default_value, basestring): value, error = [util.string_as_bool(default_value), None] else: value, error = check_param(trans, input, default_value, context) 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: carlfeberhard: merge
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f178251e9b5/ Changeset: 5f178251e9b5 User: carlfeberhard Date: 2014-11-26 17:29:18+00:00 Summary: merge Affected #: 18 files diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 client/galaxy/scripts/mvc/annotations.js --- a/client/galaxy/scripts/mvc/annotations.js +++ b/client/galaxy/scripts/mvc/annotations.js @@ -56,7 +56,7 @@ '<label class="prompt">', _l( 'Annotation' ), '</label>', // set up initial tags by adding as CSV to input vals (necc. to init select2) '<div class="annotation" title="', _l( 'Edit annotation' ), '">', - annotation, + _.escape( annotation ), '</div>' ].join( '' ); }, diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 client/galaxy/scripts/mvc/tags.js --- a/client/galaxy/scripts/mvc/tags.js +++ b/client/galaxy/scripts/mvc/tags.js @@ -56,7 +56,9 @@ if( !_.isArray( tagsArray ) || _.isEmpty( tagsArray ) ){ return ''; } - return tagsArray.sort().join( ',' ); + return tagsArray.map( function( tag ){ + return _.escape( tag ); + }).sort().join( ',' ); }, /** @returns {jQuery} the input for this view */ diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 static/scripts/mvc/annotations.js --- a/static/scripts/mvc/annotations.js +++ b/static/scripts/mvc/annotations.js @@ -56,7 +56,7 @@ '<label class="prompt">', _l( 'Annotation' ), '</label>', // set up initial tags by adding as CSV to input vals (necc. to init select2) '<div class="annotation" title="', _l( 'Edit annotation' ), '">', - annotation, + _.escape( annotation ), '</div>' ].join( '' ); }, diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 static/scripts/mvc/tags.js --- a/static/scripts/mvc/tags.js +++ b/static/scripts/mvc/tags.js @@ -56,7 +56,9 @@ if( !_.isArray( tagsArray ) || _.isEmpty( tagsArray ) ){ return ''; } - return tagsArray.sort().join( ',' ); + return tagsArray.map( function( tag ){ + return _.escape( tag ); + }).sort().join( ',' ); }, /** @returns {jQuery} the input for this view */ diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 static/scripts/packed/mvc/annotations.js --- a/static/scripts/packed/mvc/annotations.js +++ b/static/scripts/packed/mvc/annotations.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,c){var b=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(d){d=d||{};this.tooltipConfig=d.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(e){d.$annotation().text(e);d.model.save({annotation:e},{silent:true}).fail(function(){d.$annotation().text(d.model.previous("annotation"))})}});return this},_template:function(){var d=this.model.get("annotation");return['<label class="prompt">',c("Annotation"),"</label>",'<div class="annotation" title="',c("Edit annotation"),'">',d,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:b}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,c){var b=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(d){d=d||{};this.tooltipConfig=d.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(e){d.$annotation().text(e);d.model.save({annotation:e},{silent:true}).fail(function(){d.$annotation().text(d.model.previous("annotation"))})}});return this},_template:function(){var d=this.model.get("annotation");return['<label class="prompt">',c("Annotation"),"</label>",'<div class="annotation" title="',c("Edit annotation"),'">',_.escape(d),"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:b}}); \ No newline at end of file diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 static/scripts/packed/mvc/tags.js --- a/static/scripts/packed/mvc/tags.js +++ b/static/scripts/packed/mvc/tags.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,b){var c=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(d){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return d._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',b("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var d=this.model.get("tags");if(!_.isArray(d)||_.isEmpty(d)){return""}return d.sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var d=this;this.$input().on("change",function(e){d.model.save({tags:e.val},{silent:true});if(e.added){d._addNewTagToTagsUsed(e.added.text+"")}})},_addNewTagToTagsUsed:function(d){var e=Galaxy.currUser.get("tags_used");if(!_.contains(e,d)){e.push(d);e.sort();Galaxy.currUser.set("tags_used",e)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,b){var c=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(d){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return d._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',b("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var d=this.model.get("tags");if(!_.isArray(d)||_.isEmpty(d)){return""}return d.map(function(e){return _.escape(e)}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var d=this;this.$input().on("change",function(e){d.model.save({tags:e.val},{silent:true});if(e.added){d._addNewTagToTagsUsed(e.added.text+"")}})},_addNewTagToTagsUsed:function(d){var e=Galaxy.currUser.get("tags_used");if(!_.contains(e,d)){e.push(d);e.sort();Galaxy.currUser.set("tags_used",e)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:c}}); \ No newline at end of file diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/dataset/copy_view.mako --- a/templates/webapps/galaxy/dataset/copy_view.mako +++ b/templates/webapps/galaxy/dataset/copy_view.mako @@ -53,7 +53,7 @@ %><option value="${trans.security.encode_id(hist.id)}" ${selected}> - ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30)}${current_history_text} + ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30) | h}${current_history_text} </option> %endfor </select> @@ -70,7 +70,7 @@ %><div class="form-row"><input type="checkbox" name="source_content_ids" id="${input_id}" value="${input_id}"${checked}/> - <label for="${input_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label> + <label for="${input_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name) | h}</label></div> %endfor %else: @@ -95,7 +95,7 @@ if encoded_id == target_history_id: selected = " selected='selected'" %> - <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30)}${source_history_text}</option> + <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30) | h}${source_history_text}</option> %endfor </select><br /><br /><a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> @@ -110,7 +110,7 @@ %><div class="form-row"><input type="checkbox" name="target_history_ids" id="hist_${encoded_id}" value="${encoded_id}"/> - <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) }${cur_history_text}</label> + <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) | h }${cur_history_text}</label></div> %endfor </div> diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -26,13 +26,11 @@ data.createTabularDatasetChunkedView({ // TODO: encode id. dataset_config: - _.extend( ${h.dumps( item.to_dict() )}, - { - chunk_url: "${h.url_for( controller='/dataset', action='display', - dataset_id=trans.security.encode_id( item.id ))}", - first_data_chunk: ${first_chunk} - } - ), + _.extend( ${h.dumps( item.to_dict() )}, { + chunk_url: "${h.url_for( controller='/dataset', action='display', + dataset_id=trans.security.encode_id( item.id ))}", + first_data_chunk: ${first_chunk} + }), parent_elt: $('.page-body') }); }); diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/dataset/embed.mako --- a/templates/webapps/galaxy/dataset/embed.mako +++ b/templates/webapps/galaxy/dataset/embed.mako @@ -4,10 +4,13 @@ %><%def name="render_item_links( dataset )"> - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk"></a> + <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" + title="Save dataset" class="icon-button disk"></a> ## Links for importing and viewing an item. - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import"></a> - <a class="icon-button go-to-full-screen" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a> + <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" + title="Import dataset" class="icon-button import"></a> + <a href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" + title="Go to dataset" class="icon-button go-to-full-screen"></a></%def> diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -49,7 +49,7 @@ <body><h2>Dataset generation errors</h2> - <p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p> + <p><b>Dataset ${hda.hid}: ${hda.display_name() | h}</b></p><% job = hda.creating_job %> %if job: diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/dataset/security_common.mako --- a/templates/webapps/galaxy/dataset/security_common.mako +++ b/templates/webapps/galaxy/dataset/security_common.mako @@ -77,7 +77,7 @@ else: current_actions = [] permitted_actions = {}.items() - obj_str = 'unknown object %s' %obj_name + obj_str = 'unknown object %s' % obj_name obj_type = '' %><script type="text/javascript"> @@ -104,7 +104,7 @@ }); </script><div class="toolForm"> - <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str}</div> + <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str | h}</div><div class="toolFormBody"><form name="edit_role_associations" id="edit_role_associations" action="${form_url}" method="post"><div class="form-row"></div> diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -15,14 +15,12 @@ } }); - require(['mvc/data'], function(data) { + require([ 'mvc/data' ], function( data ) { data.createTabularDatasetChunkedView({ - dataset_config: _.extend( ${h.dumps( trans.security.encode_dict_ids( dataset.to_dict() ) )}, - { - first_data_chunk: ${chunk} - } - ), - parent_elt: $('body') + dataset_config : _.extend( ${ h.dumps( trans.security.encode_dict_ids( dataset.to_dict() ) )}, { + first_data_chunk: ${ chunk } + }), + parent_elt : $( 'body' ) }); }); </script> diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -23,7 +23,7 @@ </a></h4> %if hasattr( item, "annotation") and item.annotation: - <div class="annotation">${item.annotation}</div> + <div class="annotation">${item.annotation | h}</div> %endif </div><div class='summary-content'> diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/history/history_panel.mako --- a/templates/webapps/galaxy/history/history_panel.mako +++ /dev/null @@ -1,14 +0,0 @@ -## shortcuts for script tags that create history panels -## ---------------------------------------------------------------------------- -<%def name="current_history_panel( selector_to_attach_to=None, options )"> -</%def> - - -## ---------------------------------------------------------------------------- -<%def name="history_panel( history_id, selector_to_attach_to=None, options )"> -</%def> - - -## ---------------------------------------------------------------------------- -<%def name="bootstrapped_history_panel( history, hdas, selector_to_attach_to=None, options )"> -</%def> diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -20,7 +20,7 @@ <tr><td><input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${ util.unicodify( history.name )} + ${ util.unicodify( history.name ) | h } </td><td> %if len( history.datasets ) < 1: diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -1,4 +1,4 @@ -<%namespace file="/galaxy.masthead.mako" import="get_user_json" /> +<%namespace file="/galaxy_client_app.mako" import="get_user_json" /> ## ---------------------------------------------------------------------------- <%! @@ -166,9 +166,9 @@ // use_panels effects where the the center_panel() is rendered: // w/o it renders to the body, w/ it renders to #center - we need to adjust a few things for scrolling to work var hasMasthead = ${ 'true' if use_panels else 'false' }, - userIsOwner = ${'true' if user_is_owner else 'false'}, - historyJSON = ${h.dumps( history )}, - hdaJSON = ${h.dumps( hdas )}, + userIsOwner = ${ 'true' if user_is_owner else 'false' }, + historyJSON = ${ h.dumps( history ) }, + hdaJSON = ${ h.dumps( hdas ) }, panelToUse = ( userIsOwner )? //TODO: change class names ({ location: 'mvc/history/history-panel-edit', className: 'HistoryPanelEdit' }): diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/page/editor.mako --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -47,7 +47,7 @@ <a id="close-button" class="panel-header-button">Close</a></div><div class="unified-panel-header-inner"> - Page Editor <span style="font-weight: normal">| Title : ${page.title}</span> + Page Editor <span style="font-weight: normal">| Title : ${page.title | h}</span></div></div> diff -r d32c333831cc36c13430ca17ab893cab79554873 -r 5f178251e9b579f62ceb172ab562d67d1c841b73 templates/webapps/galaxy/page/index.mako --- a/templates/webapps/galaxy/page/index.mako +++ b/templates/webapps/galaxy/page/index.mako @@ -30,7 +30,7 @@ <% page = association.page %><tr><td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title}</a> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title | h}</a></td><td>${page.user.username}</td><td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Security, UI: minor fixes to history, dataset, and page escaping; escape js tag and annotation displays
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9dc543bfedd7/ Changeset: 9dc543bfedd7 Branch: next-stable User: carlfeberhard Date: 2014-11-26 17:28:28+00:00 Summary: Security, UI: minor fixes to history, dataset, and page escaping; escape js tag and annotation displays Affected #: 18 files diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 client/galaxy/scripts/mvc/annotations.js --- a/client/galaxy/scripts/mvc/annotations.js +++ b/client/galaxy/scripts/mvc/annotations.js @@ -56,7 +56,7 @@ '<label class="prompt">', _l( 'Annotation' ), '</label>', // set up initial tags by adding as CSV to input vals (necc. to init select2) '<div class="annotation" title="', _l( 'Edit annotation' ), '">', - annotation, + _.escape( annotation ), '</div>' ].join( '' ); }, diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 client/galaxy/scripts/mvc/tags.js --- a/client/galaxy/scripts/mvc/tags.js +++ b/client/galaxy/scripts/mvc/tags.js @@ -56,7 +56,9 @@ if( !_.isArray( tagsArray ) || _.isEmpty( tagsArray ) ){ return ''; } - return tagsArray.sort().join( ',' ); + return tagsArray.map( function( tag ){ + return _.escape( tag ); + }).sort().join( ',' ); }, /** @returns {jQuery} the input for this view */ diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 static/scripts/mvc/annotations.js --- a/static/scripts/mvc/annotations.js +++ b/static/scripts/mvc/annotations.js @@ -56,7 +56,7 @@ '<label class="prompt">', _l( 'Annotation' ), '</label>', // set up initial tags by adding as CSV to input vals (necc. to init select2) '<div class="annotation" title="', _l( 'Edit annotation' ), '">', - annotation, + _.escape( annotation ), '</div>' ].join( '' ); }, diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 static/scripts/mvc/tags.js --- a/static/scripts/mvc/tags.js +++ b/static/scripts/mvc/tags.js @@ -56,7 +56,9 @@ if( !_.isArray( tagsArray ) || _.isEmpty( tagsArray ) ){ return ''; } - return tagsArray.sort().join( ',' ); + return tagsArray.map( function( tag ){ + return _.escape( tag ); + }).sort().join( ',' ); }, /** @returns {jQuery} the input for this view */ diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 static/scripts/packed/mvc/annotations.js --- a/static/scripts/packed/mvc/annotations.js +++ b/static/scripts/packed/mvc/annotations.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,c){var b=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(d){d=d||{};this.tooltipConfig=d.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(e){d.$annotation().text(e);d.model.save({annotation:e},{silent:true}).fail(function(){d.$annotation().text(d.model.previous("annotation"))})}});return this},_template:function(){var d=this.model.get("annotation");return['<label class="prompt">',c("Annotation"),"</label>",'<div class="annotation" title="',c("Edit annotation"),'">',d,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:b}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,c){var b=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(d){d=d||{};this.tooltipConfig=d.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(e){d.$annotation().text(e);d.model.save({annotation:e},{silent:true}).fail(function(){d.$annotation().text(d.model.previous("annotation"))})}});return this},_template:function(){var d=this.model.get("annotation");return['<label class="prompt">',c("Annotation"),"</label>",'<div class="annotation" title="',c("Edit annotation"),'">',_.escape(d),"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:b}}); \ No newline at end of file diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 static/scripts/packed/mvc/tags.js --- a/static/scripts/packed/mvc/tags.js +++ b/static/scripts/packed/mvc/tags.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,b){var c=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(d){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return d._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',b("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var d=this.model.get("tags");if(!_.isArray(d)||_.isEmpty(d)){return""}return d.sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var d=this;this.$input().on("change",function(e){d.model.save({tags:e.val},{silent:true});if(e.added){d._addNewTagToTagsUsed(e.added.text+"")}})},_addNewTagToTagsUsed:function(d){var e=Galaxy.currUser.get("tags_used");if(!_.contains(e,d)){e.push(d);e.sort();Galaxy.currUser.set("tags_used",e)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,b){var c=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(d){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(d.$activator,d)},render:function(){var d=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return d._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',b("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var d=this.model.get("tags");if(!_.isArray(d)||_.isEmpty(d)){return""}return d.map(function(e){return _.escape(e)}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var d=this;this.$input().on("change",function(e){d.model.save({tags:e.val},{silent:true});if(e.added){d._addNewTagToTagsUsed(e.added.text+"")}})},_addNewTagToTagsUsed:function(d){var e=Galaxy.currUser.get("tags_used");if(!_.contains(e,d)){e.push(d);e.sort();Galaxy.currUser.set("tags_used",e)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:c}}); \ No newline at end of file diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/dataset/copy_view.mako --- a/templates/webapps/galaxy/dataset/copy_view.mako +++ b/templates/webapps/galaxy/dataset/copy_view.mako @@ -53,7 +53,7 @@ %><option value="${trans.security.encode_id(hist.id)}" ${selected}> - ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30)}${current_history_text} + ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30) | h}${current_history_text} </option> %endfor </select> @@ -70,7 +70,7 @@ %><div class="form-row"><input type="checkbox" name="source_content_ids" id="${input_id}" value="${input_id}"${checked}/> - <label for="${input_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label> + <label for="${input_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name) | h}</label></div> %endfor %else: @@ -95,7 +95,7 @@ if encoded_id == target_history_id: selected = " selected='selected'" %> - <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30)}${source_history_text}</option> + <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30) | h}${source_history_text}</option> %endfor </select><br /><br /><a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> @@ -110,7 +110,7 @@ %><div class="form-row"><input type="checkbox" name="target_history_ids" id="hist_${encoded_id}" value="${encoded_id}"/> - <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) }${cur_history_text}</label> + <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) | h }${cur_history_text}</label></div> %endfor </div> diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -26,13 +26,11 @@ data.createTabularDatasetChunkedView({ // TODO: encode id. dataset_config: - _.extend( ${h.dumps( item.to_dict() )}, - { - chunk_url: "${h.url_for( controller='/dataset', action='display', - dataset_id=trans.security.encode_id( item.id ))}", - first_data_chunk: ${first_chunk} - } - ), + _.extend( ${h.dumps( item.to_dict() )}, { + chunk_url: "${h.url_for( controller='/dataset', action='display', + dataset_id=trans.security.encode_id( item.id ))}", + first_data_chunk: ${first_chunk} + }), parent_elt: $('.page-body') }); }); diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/dataset/embed.mako --- a/templates/webapps/galaxy/dataset/embed.mako +++ b/templates/webapps/galaxy/dataset/embed.mako @@ -4,10 +4,13 @@ %><%def name="render_item_links( dataset )"> - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk"></a> + <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" + title="Save dataset" class="icon-button disk"></a> ## Links for importing and viewing an item. - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import"></a> - <a class="icon-button go-to-full-screen" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a> + <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" + title="Import dataset" class="icon-button import"></a> + <a href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" + title="Go to dataset" class="icon-button go-to-full-screen"></a></%def> diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -49,7 +49,7 @@ <body><h2>Dataset generation errors</h2> - <p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p> + <p><b>Dataset ${hda.hid}: ${hda.display_name() | h}</b></p><% job = hda.creating_job %> %if job: diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/dataset/security_common.mako --- a/templates/webapps/galaxy/dataset/security_common.mako +++ b/templates/webapps/galaxy/dataset/security_common.mako @@ -77,7 +77,7 @@ else: current_actions = [] permitted_actions = {}.items() - obj_str = 'unknown object %s' %obj_name + obj_str = 'unknown object %s' % obj_name obj_type = '' %><script type="text/javascript"> @@ -104,7 +104,7 @@ }); </script><div class="toolForm"> - <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str}</div> + <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str | h}</div><div class="toolFormBody"><form name="edit_role_associations" id="edit_role_associations" action="${form_url}" method="post"><div class="form-row"></div> diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -15,14 +15,12 @@ } }); - require(['mvc/data'], function(data) { + require([ 'mvc/data' ], function( data ) { data.createTabularDatasetChunkedView({ - dataset_config: _.extend( ${h.dumps( trans.security.encode_dict_ids( dataset.to_dict() ) )}, - { - first_data_chunk: ${chunk} - } - ), - parent_elt: $('body') + dataset_config : _.extend( ${ h.dumps( trans.security.encode_dict_ids( dataset.to_dict() ) )}, { + first_data_chunk: ${ chunk } + }), + parent_elt : $( 'body' ) }); }); </script> diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -23,7 +23,7 @@ </a></h4> %if hasattr( item, "annotation") and item.annotation: - <div class="annotation">${item.annotation}</div> + <div class="annotation">${item.annotation | h}</div> %endif </div><div class='summary-content'> diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/history/history_panel.mako --- a/templates/webapps/galaxy/history/history_panel.mako +++ /dev/null @@ -1,14 +0,0 @@ -## shortcuts for script tags that create history panels -## ---------------------------------------------------------------------------- -<%def name="current_history_panel( selector_to_attach_to=None, options )"> -</%def> - - -## ---------------------------------------------------------------------------- -<%def name="history_panel( history_id, selector_to_attach_to=None, options )"> -</%def> - - -## ---------------------------------------------------------------------------- -<%def name="bootstrapped_history_panel( history, hdas, selector_to_attach_to=None, options )"> -</%def> diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -20,7 +20,7 @@ <tr><td><input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${ util.unicodify( history.name )} + ${ util.unicodify( history.name ) | h } </td><td> %if len( history.datasets ) < 1: diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -1,4 +1,4 @@ -<%namespace file="/galaxy.masthead.mako" import="get_user_json" /> +<%namespace file="/galaxy_client_app.mako" import="get_user_json" /> ## ---------------------------------------------------------------------------- <%! @@ -166,9 +166,9 @@ // use_panels effects where the the center_panel() is rendered: // w/o it renders to the body, w/ it renders to #center - we need to adjust a few things for scrolling to work var hasMasthead = ${ 'true' if use_panels else 'false' }, - userIsOwner = ${'true' if user_is_owner else 'false'}, - historyJSON = ${h.dumps( history )}, - hdaJSON = ${h.dumps( hdas )}, + userIsOwner = ${ 'true' if user_is_owner else 'false' }, + historyJSON = ${ h.dumps( history ) }, + hdaJSON = ${ h.dumps( hdas ) }, panelToUse = ( userIsOwner )? //TODO: change class names ({ location: 'mvc/history/history-panel-edit', className: 'HistoryPanelEdit' }): diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/page/editor.mako --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -47,7 +47,7 @@ <a id="close-button" class="panel-header-button">Close</a></div><div class="unified-panel-header-inner"> - Page Editor <span style="font-weight: normal">| Title : ${page.title}</span> + Page Editor <span style="font-weight: normal">| Title : ${page.title | h}</span></div></div> diff -r 06100e9a5626c38f3182e353470e882c29564c63 -r 9dc543bfedd7121cecb0e3f5a980fa387b09ff10 templates/webapps/galaxy/page/index.mako --- a/templates/webapps/galaxy/page/index.mako +++ b/templates/webapps/galaxy/page/index.mako @@ -30,7 +30,7 @@ <% page = association.page %><tr><td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title}</a> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title | h}</a></td><td>${page.user.username}</td><td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/06100e9a5626/ Changeset: 06100e9a5626 Branch: next-stable User: jmchilton Date: 2014-11-26 13:57:49+00:00 Summary: galaxy.ini.sample doc clarifications. Fix typo caught by Martin. Add warning message about why public servers should not disable sanitize_all_html. Affected #: 1 file diff -r 9925a5adf6c4b65d3242d99bc16138839ad7ef21 -r 06100e9a5626c38f3182e353470e882c29564c63 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -523,13 +523,14 @@ # it faster on the fly. #upstream_gzip = False -# The following default adds a header to web request responses that will cause -# modern web browsers to not allow Galaxy to be embedded in the frames of web -# applications hosted at other hosts - this can help prevent a class of attack -# called clickjacking (https://www.owasp.org/index.php/Clickjacking) If you -# configuring a proxy to sit infront of Galaxy - please ensure this header -# remains intact to protect your users. Uncomment and leave empty to not set -# the `X-Frame-Options` header. +# The following default adds a header to web request responses that +# will cause modern web browsers to not allow Galaxy to be embedded in +# the frames of web applications hosted at other hosts - this can help +# prevent a class of attack called clickjacking +# (https://www.owasp.org/index.php/Clickjacking) If you configure a +# proxy in front of Galaxy - please ensure this header remains intact +# to protect your users. Uncomment and leave empty to not set the +# `X-Frame-Options` header. #x_frame_options = SAMEORIGIN # nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. @@ -586,10 +587,11 @@ # log_events and log_actions functionality will eventually be merged. #log_actions = True -# Sanitize All HTML Tool Output -# By default, all tool output served as 'text/html' will be sanitized -# thoroughly. This can be disabled if you have special tools that require -# unaltered output. +# Sanitize All HTML Tool Output By default, all tool output served as +# 'text/html' will be sanitized thoroughly. This can be disabled if +# you have special tools that require unaltered output. WARNING: +# Disabling this does make the Galxy instance susceptible to XSS +# attacks initiated by your users. #sanitize_all_html = True # By default Galaxy will serve non-HTML tool output that may potentially https://bitbucket.org/galaxy/galaxy-central/commits/d32c333831cc/ Changeset: d32c333831cc User: jmchilton Date: 2014-11-26 13:58:14+00:00 Summary: Merge next-stable. Affected #: 1 file diff -r bf6fe8748b4d6f9096e9aa11f5abe7abcd372e27 -r d32c333831cc36c13430ca17ab893cab79554873 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -523,13 +523,14 @@ # it faster on the fly. #upstream_gzip = False -# The following default adds a header to web request responses that will cause -# modern web browsers to not allow Galaxy to be embedded in the frames of web -# applications hosted at other hosts - this can help prevent a class of attack -# called clickjacking (https://www.owasp.org/index.php/Clickjacking) If you -# configuring a proxy to sit infront of Galaxy - please ensure this header -# remains intact to protect your users. Uncomment and leave empty to not set -# the `X-Frame-Options` header. +# The following default adds a header to web request responses that +# will cause modern web browsers to not allow Galaxy to be embedded in +# the frames of web applications hosted at other hosts - this can help +# prevent a class of attack called clickjacking +# (https://www.owasp.org/index.php/Clickjacking) If you configure a +# proxy in front of Galaxy - please ensure this header remains intact +# to protect your users. Uncomment and leave empty to not set the +# `X-Frame-Options` header. #x_frame_options = SAMEORIGIN # nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. @@ -586,10 +587,11 @@ # log_events and log_actions functionality will eventually be merged. #log_actions = True -# Sanitize All HTML Tool Output -# By default, all tool output served as 'text/html' will be sanitized -# thoroughly. This can be disabled if you have special tools that require -# unaltered output. +# Sanitize All HTML Tool Output By default, all tool output served as +# 'text/html' will be sanitized thoroughly. This can be disabled if +# you have special tools that require unaltered output. WARNING: +# Disabling this does make the Galxy instance susceptible to XSS +# attacks initiated by your users. #sanitize_all_html = True # By default Galaxy will serve non-HTML tool output that may potentially 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 26 Nov '14

26 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d43f611d5a9/ Changeset: 1d43f611d5a9 Branch: next-stable User: jmchilton Date: 2014-11-26 04:02:05+00:00 Summary: Skip galaxy.tools.watcher test if watchdog unavailable. Instead of failing. Affected #: 1 file diff -r c16fea918b33fd4e1ec52c3b5c38981d9c88cfa0 -r 1d43f611d5a98003c7d3b488bdb6a3ba9e982d8a test/unit/tools/test_watcher.py --- a/test/unit/tools/test_watcher.py +++ b/test/unit/tools/test_watcher.py @@ -9,6 +9,10 @@ def test_watcher(): + if not watcher.can_watch: + from nose.plugins.skip import SkipTest + raise SkipTest() + with __test_directory() as t: tool_path = path.join(t, "test.xml") toolbox = Toolbox() https://bitbucket.org/galaxy/galaxy-central/commits/9925a5adf6c4/ Changeset: 9925a5adf6c4 Branch: next-stable User: jmchilton Date: 2014-11-26 04:02:05+00:00 Summary: Attempt fix of test/unit/test_lazy_process.py which transiently fails. Affected #: 1 file diff -r 1d43f611d5a98003c7d3b488bdb6a3ba9e982d8a -r 9925a5adf6c4b65d3242d99bc16138839ad7ef21 test/unit/test_lazy_process.py --- a/test/unit/test_lazy_process.py +++ b/test/unit/test_lazy_process.py @@ -11,9 +11,8 @@ lazy_process = LazyProcess(["bash", "-c", "touch %s; sleep 100" % t.name]) assert not os.path.exists(t.name) lazy_process.start_process() - time.sleep(.02) + while not os.path.exists(t.name): + time.sleep(.01) assert lazy_process.process.poll() is None - assert os.path.exists(t.name) lazy_process.shutdown() - time.sleep(.02) assert lazy_process.process.poll() https://bitbucket.org/galaxy/galaxy-central/commits/bf6fe8748b4d/ Changeset: bf6fe8748b4d User: jmchilton Date: 2014-11-26 04:03:03+00:00 Summary: Merge next-stable. Affected #: 2 files diff -r 30132ca365effac14fe5fd419ed39d20b83fcbc6 -r bf6fe8748b4d6f9096e9aa11f5abe7abcd372e27 test/unit/test_lazy_process.py --- a/test/unit/test_lazy_process.py +++ b/test/unit/test_lazy_process.py @@ -11,9 +11,8 @@ lazy_process = LazyProcess(["bash", "-c", "touch %s; sleep 100" % t.name]) assert not os.path.exists(t.name) lazy_process.start_process() - time.sleep(.02) + while not os.path.exists(t.name): + time.sleep(.01) assert lazy_process.process.poll() is None - assert os.path.exists(t.name) lazy_process.shutdown() - time.sleep(.02) assert lazy_process.process.poll() diff -r 30132ca365effac14fe5fd419ed39d20b83fcbc6 -r bf6fe8748b4d6f9096e9aa11f5abe7abcd372e27 test/unit/tools/test_watcher.py --- a/test/unit/tools/test_watcher.py +++ b/test/unit/tools/test_watcher.py @@ -9,6 +9,10 @@ def test_watcher(): + if not watcher.can_watch: + from nose.plugins.skip import SkipTest + raise SkipTest() + with __test_directory() as t: tool_path = path.join(t, "test.xml") toolbox = Toolbox() 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: 4 new changesets
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b040f24f2dff/ Changeset: b040f24f2dff User: gvk Date: 2014-11-21 18:35:02+00:00 Summary: Enhance the collect_primary_datasets() method to allow assignment of the defined output parameter for 3rd-party tools that manage tool outputs internally. Affected #: 1 file diff -r 7cb167299a13cc273a794f19363f32083096efdb -r b040f24f2dff8e748ff4385637916363d43ce1e2 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -5,7 +5,6 @@ import glob import json - from galaxy import jobs from galaxy import util from galaxy.util import odict @@ -30,8 +29,10 @@ # Loop through output file names, looking for generated primary # datasets in form of: # 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)' + primary_output_assigned = False + new_outdata_name = None primary_datasets = {} - for name, outdata in output.items(): + for output_index, ( name, outdata ) in enumerate( output.items() ): dataset_collectors = tool.outputs[ name ].dataset_collectors if name in tool.outputs else [ DEFAULT_DATASET_COLLECTOR ] filenames = odict.odict() if 'new_file_path' in app.config.collect_outputs_from: @@ -56,14 +57,20 @@ continue if extra_file_collector.match( outdata, filename ): filenames[ path ] = extra_file_collector - for filename, extra_file_collector in filenames.iteritems(): - if not name in primary_datasets: - primary_datasets[name] = {} + for filename_index, ( filename, extra_file_collector ) in enumerate( filenames.iteritems() ): fields_match = extra_file_collector.match( outdata, os.path.basename( filename ) ) if not fields_match: # Before I guess pop() would just have thrown an IndexError raise Exception( "Problem parsing metadata fields for file %s" % filename ) designation = fields_match.designation + if filename_index == 0 and extra_file_collector.assign_primary_output and output_index == 0: + new_outdata_name = fields_match.name or "%s (%s)" % ( outdata.name, designation ) + # Move data from temp location to dataset location + app.object_store.update_from_file( outdata.dataset, file_name=filename, create=True ) + primary_output_assigned = True + continue + if not name in primary_datasets: + primary_datasets[ name ] = {} visible = fields_match.visible ext = fields_match.ext if ext == "input": @@ -145,6 +152,13 @@ dataset.history.add_dataset( new_data ) sa_session.add( new_data ) sa_session.flush() + if primary_output_assigned: + outdata.name = new_outdata_name + outdata.init_meta() + outdata.set_meta() + outdata.set_peek() + sa_session.add( outdata ) + sa_session.flush() return primary_datasets @@ -178,6 +192,7 @@ self.default_ext = kwargs.get( "ext", None ) self.default_visible = util.asbool( kwargs.get( "visible", None ) ) self.directory = kwargs.get( "directory", None ) + self.assign_primary_output = util.asbool( kwargs.get( 'assign_primary_output', False ) ) def pattern_for_dataset( self, dataset_instance=None ): token_replacement = r'\d+' https://bitbucket.org/galaxy/galaxy-central/commits/45f92195479a/ Changeset: 45f92195479a User: jmchilton Date: 2014-11-26 03:01:49+00:00 Summary: Make dynamic discovery of output datasets deterministic. Should aid in testing and ... lets say ... reproducibility because that is popular in these parts. Affected #: 1 file diff -r b040f24f2dff8e748ff4385637916363d43ce1e2 -r 45f92195479ad49c8bf5a9564bfc6078dbc59bc1 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -51,7 +51,7 @@ raise Exception( "Problem with tool configuration, attempting to pull in datasets from outside working directory." ) if not os.path.isdir( directory ): continue - for filename in os.listdir( directory ): + for filename in sorted( os.listdir( directory ) ): path = os.path.join( directory, filename ) if not os.path.isfile( path ): continue https://bitbucket.org/galaxy/galaxy-central/commits/ef0e65b55ebb/ Changeset: ef0e65b55ebb User: jmchilton Date: 2014-11-26 03:13:17+00:00 Summary: Implement tool test demonstrating pull request 569. The new assign_primary_output attribute on discover_datasets tag. Affected #: 2 files diff -r 45f92195479ad49c8bf5a9564bfc6078dbc59bc1 -r ef0e65b55ebba822c8420f825e4b306e8018d7cb test/functional/tools/multi_output_assign_primary.xml --- /dev/null +++ b/test/functional/tools/multi_output_assign_primary.xml @@ -0,0 +1,34 @@ +<tool id="multi_output_assign_primary" name="multi_output_assign_primary" description="multi_output_assign_primary" version="0.1.0"> + <command> + echo "1" > sample1.report.tsv; + echo "2" > sample2.report.tsv; + echo "3" > sample3.report.tsv; + </command> + <inputs> + <param name="num_param" type="integer" value="7" /> + <param name="input" type="data" /> + </inputs> + <outputs> + <data format="tabular" name="sample"> + <discover_datasets pattern="(?P<designation>.+)\.report\.tsv" ext="tabular" visible="true" assign_primary_output="true" /> + </data> + </outputs> + <tests> + <test> + <param name="num_param" value="7" /> + <param name="input" ftype="txt" value="simple_line.txt"/> + <output name="sample"> + <assert_contents> + <has_line line="1" /> + </assert_contents> +  + <discovered_dataset designation="sample2" ftype="tabular"> + <assert_contents><has_line line="2" /></assert_contents> + </discovered_dataset> + <discovered_dataset designation="sample3" ftype="tabular"> + <assert_contents><has_line line="3" /></assert_contents> + </discovered_dataset> + </output> + </test> + </tests> +</tool> diff -r 45f92195479ad49c8bf5a9564bfc6078dbc59bc1 -r ef0e65b55ebba822c8420f825e4b306e8018d7cb test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -9,6 +9,7 @@ <tool file="multi_select.xml" /><tool file="multi_output.xml" /><tool file="multi_output_configured.xml" /> + <tool file="multi_output_assign_primary.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" /><tool file="output_order.xml" /> https://bitbucket.org/galaxy/galaxy-central/commits/30132ca365ef/ Changeset: 30132ca365ef User: jmchilton Date: 2014-11-26 03:14:18+00:00 Summary: Merge pull request 569 with test implemented to demonstrate. Affected #: 3 files diff -r e4e1f70bc2d1a84219038b7e58b933a94b424da7 -r 30132ca365effac14fe5fd419ed39d20b83fcbc6 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -5,7 +5,6 @@ import glob import json - from galaxy import jobs from galaxy import util from galaxy.util import odict @@ -30,8 +29,10 @@ # Loop through output file names, looking for generated primary # datasets in form of: # 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)' + primary_output_assigned = False + new_outdata_name = None primary_datasets = {} - for name, outdata in output.items(): + for output_index, ( name, outdata ) in enumerate( output.items() ): dataset_collectors = tool.outputs[ name ].dataset_collectors if name in tool.outputs else [ DEFAULT_DATASET_COLLECTOR ] filenames = odict.odict() if 'new_file_path' in app.config.collect_outputs_from: @@ -50,20 +51,26 @@ raise Exception( "Problem with tool configuration, attempting to pull in datasets from outside working directory." ) if not os.path.isdir( directory ): continue - for filename in os.listdir( directory ): + for filename in sorted( os.listdir( directory ) ): path = os.path.join( directory, filename ) if not os.path.isfile( path ): continue if extra_file_collector.match( outdata, filename ): filenames[ path ] = extra_file_collector - for filename, extra_file_collector in filenames.iteritems(): - if not name in primary_datasets: - primary_datasets[name] = {} + for filename_index, ( filename, extra_file_collector ) in enumerate( filenames.iteritems() ): fields_match = extra_file_collector.match( outdata, os.path.basename( filename ) ) if not fields_match: # Before I guess pop() would just have thrown an IndexError raise Exception( "Problem parsing metadata fields for file %s" % filename ) designation = fields_match.designation + if filename_index == 0 and extra_file_collector.assign_primary_output and output_index == 0: + new_outdata_name = fields_match.name or "%s (%s)" % ( outdata.name, designation ) + # Move data from temp location to dataset location + app.object_store.update_from_file( outdata.dataset, file_name=filename, create=True ) + primary_output_assigned = True + continue + if not name in primary_datasets: + primary_datasets[ name ] = {} visible = fields_match.visible ext = fields_match.ext if ext == "input": @@ -145,6 +152,13 @@ dataset.history.add_dataset( new_data ) sa_session.add( new_data ) sa_session.flush() + if primary_output_assigned: + outdata.name = new_outdata_name + outdata.init_meta() + outdata.set_meta() + outdata.set_peek() + sa_session.add( outdata ) + sa_session.flush() return primary_datasets @@ -178,6 +192,7 @@ self.default_ext = kwargs.get( "ext", None ) self.default_visible = util.asbool( kwargs.get( "visible", None ) ) self.directory = kwargs.get( "directory", None ) + self.assign_primary_output = util.asbool( kwargs.get( 'assign_primary_output', False ) ) def pattern_for_dataset( self, dataset_instance=None ): token_replacement = r'\d+' diff -r e4e1f70bc2d1a84219038b7e58b933a94b424da7 -r 30132ca365effac14fe5fd419ed39d20b83fcbc6 test/functional/tools/multi_output_assign_primary.xml --- /dev/null +++ b/test/functional/tools/multi_output_assign_primary.xml @@ -0,0 +1,34 @@ +<tool id="multi_output_assign_primary" name="multi_output_assign_primary" description="multi_output_assign_primary" version="0.1.0"> + <command> + echo "1" > sample1.report.tsv; + echo "2" > sample2.report.tsv; + echo "3" > sample3.report.tsv; + </command> + <inputs> + <param name="num_param" type="integer" value="7" /> + <param name="input" type="data" /> + </inputs> + <outputs> + <data format="tabular" name="sample"> + <discover_datasets pattern="(?P<designation>.+)\.report\.tsv" ext="tabular" visible="true" assign_primary_output="true" /> + </data> + </outputs> + <tests> + <test> + <param name="num_param" value="7" /> + <param name="input" ftype="txt" value="simple_line.txt"/> + <output name="sample"> + <assert_contents> + <has_line line="1" /> + </assert_contents> +  + <discovered_dataset designation="sample2" ftype="tabular"> + <assert_contents><has_line line="2" /></assert_contents> + </discovered_dataset> + <discovered_dataset designation="sample3" ftype="tabular"> + <assert_contents><has_line line="3" /></assert_contents> + </discovered_dataset> + </output> + </test> + </tests> +</tool> diff -r e4e1f70bc2d1a84219038b7e58b933a94b424da7 -r 30132ca365effac14fe5fd419ed39d20b83fcbc6 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -9,6 +9,7 @@ <tool file="multi_select.xml" /><tool file="multi_output.xml" /><tool file="multi_output_configured.xml" /> + <tool file="multi_output_assign_primary.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" /><tool file="output_order.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: PEP-8 fixes for test.base.asserts.
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4e1f70bc2d1/ Changeset: e4e1f70bc2d1 User: jmchilton Date: 2014-11-26 01:57:56+00:00 Summary: PEP-8 fixes for test.base.asserts. Some of the first Python code I ever wrote - and one can tell :). Affected #: 4 files diff -r bfa13d090966889c74512497bfcaafb732c08a41 -r e4e1f70bc2d1a84219038b7e58b933a94b424da7 test/base/asserts/__init__.py --- a/test/base/asserts/__init__.py +++ b/test/base/asserts/__init__.py @@ -8,7 +8,7 @@ # Code for loading modules containing assertion checking functions, to # create a new module of assertion functions, create the needed python # source file "test/base/asserts/<MODULE_NAME>.py" and add -# <MODULE_NAME> to the list of assertion module names defined above. +# <MODULE_NAME> to the list of assertion module names defined above. assertion_modules = [] for assertion_module_name in assertion_module_names: full_assertion_module_name = 'base.asserts.' + assertion_module_name @@ -19,7 +19,8 @@ assertion_module = sys.modules[full_assertion_module_name] assertion_modules.append(assertion_module) except Exception, e: - log.exception( 'Failed to load assertion module: %s %s' % (assertion_module_name, str(e))) + log.exception('Failed to load assertion module: %s %s' % (assertion_module_name, str(e))) + def verify_assertions(data, assertion_description_list): """ This function takes a list of assertions and a string to check @@ -27,6 +28,7 @@ for assertion_description in assertion_description_list: verify_assertion(data, assertion_description) + def verify_assertion(data, assertion_description): tag = assertion_description["tag"] assert_function_name = "assert_" + tag @@ -73,4 +75,3 @@ # TODO: Verify all needed function arguments are specified. assert_function(**args) - diff -r bfa13d090966889c74512497bfcaafb732c08a41 -r e4e1f70bc2d1a84219038b7e58b933a94b424da7 test/base/asserts/tabular.py --- a/test/base/asserts/tabular.py +++ b/test/base/asserts/tabular.py @@ -1,13 +1,15 @@ import re + def get_first_line(output): - match = re.search("^(.*)$", output, flags = re.MULTILINE) + match = re.search("^(.*)$", output, flags=re.MULTILINE) if match is None: return None else: return match.group(1) -def assert_has_n_columns(output, n, sep = '\t'): + +def assert_has_n_columns(output, n, sep='\t'): """ Asserts the tabular output contains n columns. The optional sep argument specifies the column seperator used to determine the number of columns.""" diff -r bfa13d090966889c74512497bfcaafb732c08a41 -r e4e1f70bc2d1a84219038b7e58b933a94b424da7 test/base/asserts/text.py --- a/test/base/asserts/text.py +++ b/test/base/asserts/text.py @@ -1,30 +1,34 @@ import re + def assert_has_text(output, text): """ Asserts specified output contains the substring specified by the argument text.""" assert output.find(text) >= 0, "Output file did not contain expected text '%s' (ouptut '%s')" % (text, output) - + + def assert_not_has_text(output, text): """ Asserts specified output does not contain the substring specified the argument text.""" assert output.find(text) < 0, "Output file contains unexpected text '%s'" % text + def assert_has_line(output, line): """ Asserts the specified output contains the line specified the argument line.""" - match = re.search("^%s$" % re.escape(line), output, flags = re.MULTILINE) - assert match != None, "No line of output file was '%s' (output was '%s') " % (line, output) + match = re.search("^%s$" % re.escape(line), output, flags=re.MULTILINE) + assert match is not None, "No line of output file was '%s' (output was '%s') " % (line, output) + def assert_has_text_matching(output, expression): """ Asserts the specified output contains text matching the regular expression specified by the argument expression.""" match = re.search(expression, output) - assert match != None, "No text matching expression '%s' was found in output file." % expression + assert match is not None, "No text matching expression '%s' was found in output file." % expression + def assert_has_line_matching(output, expression): """ Asserts the specified output contains a line matching the regular expression specified by the argument expression.""" - match = re.search("^%s$" % expression, output, flags = re.MULTILINE) - assert match != None, "No line matching expression '%s' was found in output file." % expression - + match = re.search("^%s$" % expression, output, flags=re.MULTILINE) + assert match is not None, "No line matching expression '%s' was found in output file." % expression diff -r bfa13d090966889c74512497bfcaafb732c08a41 -r e4e1f70bc2d1a84219038b7e58b933a94b424da7 test/base/asserts/xml.py --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -1,77 +1,88 @@ import elementtree.ElementTree import re + # Helper functions used to work with XML output. def to_xml(output): - return elementtree.ElementTree.fromstring(output) + return elementtree.ElementTree.fromstring(output) + def xml_find_text(output, path): - xml = to_xml(output) - text = xml.findtext(path) - return text + xml = to_xml(output) + text = xml.findtext(path) + return text + def xml_find(output, path): - xml = to_xml(output) - return xml.find(path) + xml = to_xml(output) + return xml.find(path) + def assert_is_valid_xml(output): - """ Simple assertion that just verifies the specified output - is valid XML.""" - try: - to_xml(output) - except Exception, e: - # TODO: Narrow caught exception to just parsing failure - raise AssertionError("Expected valid XML, but could not parse output. %s" % str(e)) + """ Simple assertion that just verifies the specified output + is valid XML.""" + try: + to_xml(output) + except Exception, e: + # TODO: Narrow caught exception to just parsing failure + raise AssertionError("Expected valid XML, but could not parse output. %s" % str(e)) + def assert_has_element_with_path(output, path): - """ Asserts the specified output has at least one XML element with a - path matching the specified path argument. Valid paths are the - simplified subsets of XPath implemented by elementtree (currently - Galaxy makes use of elementtree 1.2). See - http://effbot.org/zone/element-xpath.htm for more information.""" - if xml_find(output, path) is None: - errmsg = "Expected to find XML element matching expression %s, not such match was found." % path - raise AssertionError(errmsg) + """ Asserts the specified output has at least one XML element with a + path matching the specified path argument. Valid paths are the + simplified subsets of XPath implemented by elementtree (currently + Galaxy makes use of elementtree 1.2). See + http://effbot.org/zone/element-xpath.htm for more information.""" + if xml_find(output, path) is None: + errmsg = "Expected to find XML element matching expression %s, not such match was found." % path + raise AssertionError(errmsg) + def assert_has_n_elements_with_path(output, path, n): - """ Asserts the specified output has exactly n elements matching the - path specified.""" - xml = to_xml(output) - n = int(n) - num_elements = len(xml.findall(path)) - if num_elements != n: - errmsg = "Expected to find %d elements with path %s, but %d were found." % (n, path, num_elements) - raise AssertionError(errmsg) + """ Asserts the specified output has exactly n elements matching the + path specified.""" + xml = to_xml(output) + n = int(n) + num_elements = len(xml.findall(path)) + if num_elements != n: + errmsg = "Expected to find %d elements with path %s, but %d were found." % (n, path, num_elements) + raise AssertionError(errmsg) + def assert_element_text_matches(output, path, expression): - """ Asserts the text of the first element matching the specified - path matches the specified regular expression.""" - text = xml_find_text(output, path) - if re.match(expression, text) is None: - errmsg = "Expected element with path '%s' to contain text matching '%s', instead text '%s' was found." % (path, text, actual_text) - raise AssertionError(errmsg) + """ Asserts the text of the first element matching the specified + path matches the specified regular expression.""" + text = xml_find_text(output, path) + if re.match(expression, text) is None: + errmsg = "Expected element with path '%s' to contain text matching '%s', instead text '%s' was found." % (path, expression, text) + raise AssertionError(errmsg) + def assert_element_text_is(output, path, text): - """ Asserts the text of the first element matching the specified - path matches exactly the specified text. """ - assert_element_text_matches(output, path, re.escape(text)) + """ Asserts the text of the first element matching the specified + path matches exactly the specified text. """ + assert_element_text_matches(output, path, re.escape(text)) + def assert_attribute_matches(output, path, attribute, expression): - """ Asserts the specified attribute of the first element matching - the specified path matches the specified regular expression.""" - xml = xml_find(output, path) - attribute_value = xml.attrib[attribute] - if re.match(expression, attribute_value) is None: - errmsg = "Expected attribute '%s' on element with path '%s' to match '%s', instead attribute value was '%s'." % (attribute, path, expression, attribute_value) - raise AssertionError(errmsg) + """ Asserts the specified attribute of the first element matching + the specified path matches the specified regular expression.""" + xml = xml_find(output, path) + attribute_value = xml.attrib[attribute] + if re.match(expression, attribute_value) is None: + errmsg = "Expected attribute '%s' on element with path '%s' to match '%s', instead attribute value was '%s'." % (attribute, path, expression, attribute_value) + raise AssertionError(errmsg) + def assert_attribute_is(output, path, attribute, text): - """ Asserts the specified attribute of the first element matching - the specified path matches exactly the specified text.""" - assert_attribute_matches(output, path, attribute, re.escape(text)) + """ Asserts the specified attribute of the first element matching + the specified path matches exactly the specified text.""" + assert_attribute_matches(output, path, attribute, re.escape(text)) + def assert_element_text(output, path, verify_assertions_function, children): - """ Recursively checks the specified assertions against the text of - the first element matching the specified path.""" - text = xml_find_text(output, path) - verify_assertions_function(text, children) + """ Recursively checks the specified assertions against the text of + the first element matching the specified path.""" + text = xml_find_text(output, path) + verify_assertions_function(text, children) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Nov '14

26 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c16fea918b33/ Changeset: c16fea918b33 Branch: next-stable User: jmchilton Date: 2014-11-26 01:52:30+00:00 Summary: Fixes for /dataset_collections API endpoint. Guess this is not as utilized as the variant under /histories. Affected #: 1 file diff -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a -r c16fea918b33fd4e1ec52c3b5c38981d9c88cfa0 lib/galaxy/webapps/galaxy/api/dataset_collections.py --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -56,7 +56,8 @@ @expose_api def show( self, trans, instance_type, id, **kwds ): - dataset_collection_instance = self.__service( trans ).get( + dataset_collection_instance = self.__service( trans ).get_dataset_collection_instance( + trans, id=id, instance_type=instance_type, ) @@ -67,7 +68,12 @@ else: trans.status = 501 return - return dictify_dataset_collection_instance( trans, dataset_collection_instance, parent ) + return dictify_dataset_collection_instance( + dataset_collection_instance, + security=trans.security, + parent=parent, + view='element' + ) def __service( self, trans ): service = trans.app.dataset_collections_service https://bitbucket.org/galaxy/galaxy-central/commits/bfa13d090966/ Changeset: bfa13d090966 User: jmchilton Date: 2014-11-26 01:53:50+00:00 Summary: Merge next-stable into default. Affected #: 12 files diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 client/galaxy/scripts/galaxy.masthead.js --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 client/galaxy/scripts/galaxy.menu.js --- a/client/galaxy/scripts/galaxy.menu.js +++ b/client/galaxy/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/api/dataset_collections.py --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -56,7 +56,8 @@ @expose_api def show( self, trans, instance_type, id, **kwds ): - dataset_collection_instance = self.__service( trans ).get( + dataset_collection_instance = self.__service( trans ).get_dataset_collection_instance( + trans, id=id, instance_type=instance_type, ) @@ -67,7 +68,12 @@ else: trans.status = 501 return - return dictify_dataset_collection_instance( trans, dataset_collection_instance, parent ) + return dictify_dataset_collection_instance( + dataset_collection_instance, + security=trans.security, + parent=parent, + view='element' + ) def __service( self, trans ): service = trans.app.dataset_collections_service diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -9,8 +9,7 @@ from galaxy.util.sanitize_html import sanitize_html from galaxy.util.json import loads from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesExtendedMetadataMixin -from galaxy.web.framework.helpers import grids, iff, time_ago -from galaxy.web.framework.helpers import to_unicode +from galaxy.web.framework.helpers import grids, iff, time_ago, to_unicode, escape from galaxy.tools.errors import EmailErrorReporter eggs.require( "Paste" ) @@ -506,7 +505,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) # Error checking. diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -19,7 +19,7 @@ from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin from galaxy.web.base.controller import ERROR, INFO, SUCCESS, WARNING -from galaxy.web.framework.helpers import grids, iff, time_ago +from galaxy.web.framework.helpers import grids, iff, time_ago, escape log = logging.getLogger( __name__ ) @@ -1291,7 +1291,7 @@ else: referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -611,8 +611,8 @@ else: refresh_frames = [ 'masthead' ] trans.handle_user_logout( logout_all=logout_all ) - message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ - ( trans.request.referer, url_for( '/' ) ) + message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % \ + ( url_for( '/' ) ) if biostar.biostar_logged_in( trans ): biostar_url = biostar.biostar_logout( trans ) if biostar_url: diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -9,7 +9,7 @@ from galaxy import model, web from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from galaxy import util from galaxy.datatypes.interval import Bed from galaxy.util.json import loads @@ -123,7 +123,7 @@ # or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ # ) # ) - + class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ @@ -360,7 +360,7 @@ @web.expose @web.require_login( "use Galaxy visualizations", use_panels=True ) def list( self, trans, *args, **kwargs ): - + # Handle operation if 'operation' in kwargs and 'id' in kwargs: session = trans.sa_session @@ -388,7 +388,7 @@ kwargs[ 'embedded' ] = True grid = self._user_list_grid( trans, *args, **kwargs ) return trans.fill_template( "visualization/list.mako", embedded_grid=grid, shared_by_others=shared_by_others ) - + # # -- Functions for operating on visualizations. -- # @@ -459,7 +459,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % web.url_for( '/' ) diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -22,8 +22,7 @@ from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.helpers import grids, time_ago -from galaxy.web.framework.helpers import to_unicode +from galaxy.web.framework.helpers import grids, time_ago, to_unicode, escape from galaxy.workflow.modules import WorkflowModuleInjector from galaxy.workflow.modules import MissingToolException from galaxy.workflow.modules import module_factory, is_tool_module_type @@ -389,7 +388,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/packed/galaxy.masthead.js --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content!==undefined&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ 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: 3 new changesets
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba9188b955ef/ Changeset: ba9188b955ef Branch: next-stable User: dannon Date: 2014-11-25 20:14:25+00:00 Summary: Referer-in-okmessage reflective xss fix Affected #: 4 files diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r ba9188b955ef5fadbf261271555297b7ba57c162 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -9,8 +9,7 @@ from galaxy.util.sanitize_html import sanitize_html from galaxy.util.json import loads from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesExtendedMetadataMixin -from galaxy.web.framework.helpers import grids, iff, time_ago -from galaxy.web.framework.helpers import to_unicode +from galaxy.web.framework.helpers import grids, iff, time_ago, to_unicode, escape from galaxy.tools.errors import EmailErrorReporter eggs.require( "Paste" ) @@ -506,7 +505,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) # Error checking. diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r ba9188b955ef5fadbf261271555297b7ba57c162 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -19,7 +19,7 @@ from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin from galaxy.web.base.controller import ERROR, INFO, SUCCESS, WARNING -from galaxy.web.framework.helpers import grids, iff, time_ago +from galaxy.web.framework.helpers import grids, iff, time_ago, escape log = logging.getLogger( __name__ ) @@ -1291,7 +1291,7 @@ else: referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r ba9188b955ef5fadbf261271555297b7ba57c162 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -9,7 +9,7 @@ from galaxy import model, web from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from galaxy import util from galaxy.datatypes.interval import Bed from galaxy.util.json import loads @@ -123,7 +123,7 @@ # or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ # ) # ) - + class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ @@ -360,7 +360,7 @@ @web.expose @web.require_login( "use Galaxy visualizations", use_panels=True ) def list( self, trans, *args, **kwargs ): - + # Handle operation if 'operation' in kwargs and 'id' in kwargs: session = trans.sa_session @@ -388,7 +388,7 @@ kwargs[ 'embedded' ] = True grid = self._user_list_grid( trans, *args, **kwargs ) return trans.fill_template( "visualization/list.mako", embedded_grid=grid, shared_by_others=shared_by_others ) - + # # -- Functions for operating on visualizations. -- # @@ -459,7 +459,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % web.url_for( '/' ) diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r ba9188b955ef5fadbf261271555297b7ba57c162 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -22,8 +22,7 @@ from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.helpers import grids, time_ago -from galaxy.web.framework.helpers import to_unicode +from galaxy.web.framework.helpers import grids, time_ago, to_unicode, escape from galaxy.workflow.modules import WorkflowModuleInjector from galaxy.workflow.modules import MissingToolException from galaxy.workflow.modules import module_factory, is_tool_module_type @@ -389,7 +388,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) https://bitbucket.org/galaxy/galaxy-central/commits/7c635c1a08ad/ Changeset: 7c635c1a08ad Branch: next-stable User: dannon Date: 2014-11-25 20:14:58+00:00 Summary: Referer-in-logout reflective xss fix. Affected #: 1 file diff -r ba9188b955ef5fadbf261271555297b7ba57c162 -r 7c635c1a08adb89bc968bffb1a57bdf4ed1f825d lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -611,8 +611,8 @@ else: refresh_frames = [ 'masthead' ] trans.handle_user_logout( logout_all=logout_all ) - message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ - ( trans.request.referer, url_for( '/' ) ) + message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % \ + ( url_for( '/' ) ) if biostar.biostar_logged_in( trans ): biostar_url = biostar.biostar_logout( trans ) if biostar_url: https://bitbucket.org/galaxy/galaxy-central/commits/2d80e9cfb833/ Changeset: 2d80e9cfb833 Branch: next-stable User: dannon Date: 2014-11-25 20:25:25+00:00 Summary: Merge. Affected #: 6 files diff -r 7c635c1a08adb89bc968bffb1a57bdf4ed1f825d -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a client/galaxy/scripts/galaxy.masthead.js --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r 7c635c1a08adb89bc968bffb1a57bdf4ed1f825d -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a client/galaxy/scripts/galaxy.menu.js --- a/client/galaxy/scripts/galaxy.menu.js +++ b/client/galaxy/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r 7c635c1a08adb89bc968bffb1a57bdf4ed1f825d -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r 7c635c1a08adb89bc968bffb1a57bdf4ed1f825d -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r 7c635c1a08adb89bc968bffb1a57bdf4ed1f825d -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a static/scripts/packed/galaxy.masthead.js --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content!==undefined&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file diff -r 7c635c1a08adb89bc968bffb1a57bdf4ed1f825d -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ 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: martenson: fix the behavior of masthead.js when passed an empty string as a item content (link target)
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/15f7c2ef93c1/ Changeset: 15f7c2ef93c1 Branch: next-stable User: martenson Date: 2014-11-25 20:19:08+00:00 Summary: fix the behavior of masthead.js when passed an empty string as a item content (link target) Affected #: 6 files diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r 15f7c2ef93c1296aa61607fcceb190d94eb2701b client/galaxy/scripts/galaxy.masthead.js --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r 15f7c2ef93c1296aa61607fcceb190d94eb2701b client/galaxy/scripts/galaxy.menu.js --- a/client/galaxy/scripts/galaxy.menu.js +++ b/client/galaxy/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r 15f7c2ef93c1296aa61607fcceb190d94eb2701b static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r 15f7c2ef93c1296aa61607fcceb190d94eb2701b static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r 15f7c2ef93c1296aa61607fcceb190d94eb2701b static/scripts/packed/galaxy.masthead.js --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content!==undefined&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file diff -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 -r 15f7c2ef93c1296aa61607fcceb190d94eb2701b static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ 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: Merge next stable.
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce8a617dcdb1/ Changeset: ce8a617dcdb1 User: dannon Date: 2014-11-25 19:35:25+00:00 Summary: Merge next stable. Affected #: 2 files diff -r 720b9c3936980d5af25df714c5c65e5d4793327c -r ce8a617dcdb199e97e7d4249f548e78a4530d18a lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -3,13 +3,13 @@ """ import time -from cgi import escape from datetime import datetime, timedelta from galaxy import eggs from galaxy.util import hash_util from galaxy.util.json import safe_dumps as dumps eggs.require( "MarkupSafe" ) #required by WebHelpers eggs.require( "WebHelpers" ) +from markupsafe import escape from webhelpers import date from webhelpers.html.tags import stylesheet_link, javascript_link diff -r 720b9c3936980d5af25df714c5c65e5d4793327c -r ce8a617dcdb199e97e7d4249f548e78a4530d18a lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -15,8 +15,8 @@ from galaxy.tools.parameters.basic import UnvalidatedValue from galaxy.util.bunch import Bunch from galaxy.util.hash_util import is_hashable -from galaxy.web import error -from galaxy.web import url_for +from galaxy.web import error, url_for +from galaxy.web.framework.helpers import escape from galaxy.web.base.controller import BaseUIController import tool_shed.util.shed_util_common as suc @@ -57,7 +57,7 @@ return trans.response.send_redirect( url_for( controller="root", action="welcome" ) ) # When the tool form is initially loaded, the received kwd will not include a 'refresh' # entry (which only is included when another option is selected in the tool_version_select_field), - # so the default selected option should be the most recent version of the tool. The following + # so the default selected option should be the most recent version of the tool. The following # check will mae sure this occurs. refreshed_on_change = kwd.get( 'refresh', False ) tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, @@ -69,7 +69,7 @@ log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 - return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) + return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) )) if tool.require_login and not trans.user: message = "You must be logged in to use this tool." status = "info" @@ -291,7 +291,7 @@ log.error( "data_source_redirect called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 - return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) + return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) )) if isinstance( tool, DataSourceTool ): link = url_for( tool.action, **tool.get_static_param_values( trans ) ) 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: 4 new changesets
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ecb1efececd/ Changeset: 4ecb1efececd Branch: next-stable User: dannon Date: 2014-11-25 19:26:52+00:00 Summary: Prevent XSS in unknown tool display, update to actually use show_error_message instead of replying with plain text. Affected #: 2 files diff -r c53f747732a115c7ec6ed3e192bb059d12266865 -r 4ecb1efececdb58d16087a58d1f168851899aa4a lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -3,13 +3,13 @@ """ import time -from cgi import escape from datetime import datetime, timedelta from galaxy import eggs from galaxy.util import hash_util from galaxy.util.json import safe_dumps as dumps eggs.require( "MarkupSafe" ) #required by WebHelpers eggs.require( "WebHelpers" ) +from markupsafe import escape from webhelpers import date from webhelpers.html.tags import stylesheet_link, javascript_link diff -r c53f747732a115c7ec6ed3e192bb059d12266865 -r 4ecb1efececdb58d16087a58d1f168851899aa4a lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -15,8 +15,8 @@ from galaxy.tools.parameters.basic import UnvalidatedValue from galaxy.util.bunch import Bunch from galaxy.util.hash_util import is_hashable -from galaxy.web import error -from galaxy.web import url_for +from galaxy.web import error, url_for +from galaxy.web.framework.helpers import escape from galaxy.web.base.controller import BaseUIController import tool_shed.util.shed_util_common as suc @@ -57,7 +57,7 @@ return trans.response.send_redirect( url_for( controller="root", action="welcome" ) ) # When the tool form is initially loaded, the received kwd will not include a 'refresh' # entry (which only is included when another option is selected in the tool_version_select_field), - # so the default selected option should be the most recent version of the tool. The following + # so the default selected option should be the most recent version of the tool. The following # check will mae sure this occurs. refreshed_on_change = kwd.get( 'refresh', False ) tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, @@ -69,7 +69,7 @@ log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 - return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) + return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) )) if tool.require_login and not trans.user: message = "You must be logged in to use this tool." status = "info" https://bitbucket.org/galaxy/galaxy-central/commits/988dd20de45b/ Changeset: 988dd20de45b Branch: next-stable User: dannon Date: 2014-11-25 19:27:04+00:00 Summary: Merge. Affected #: 8 files diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py +++ b/lib/galaxy/tags/tag_handler.py @@ -1,5 +1,7 @@ -import re, logging -from sqlalchemy.sql.expression import func, and_ +import re +import logging +from sqlalchemy.sql.expression import func +from sqlalchemy.sql.expression import and_ from sqlalchemy.sql import select log = logging.getLogger( __name__ ) @@ -25,12 +27,15 @@ self.key_value_separators = "=:" # Initialize with known classes - add to this in subclasses. self.item_tag_assoc_info = {} + def get_tag_assoc_class( self, item_class ): """Returns tag association class for item class.""" return self.item_tag_assoc_info[item_class.__name__].tag_assoc_class + def get_id_col_in_item_tag_assoc_table( self, item_class ): """Returns item id column in class' item-tag association table.""" return self.item_tag_assoc_info[item_class.__name__].item_id_col + def get_community_tags( self, trans, item=None, limit=None ): """Returns community tags for an item.""" # Get item-tag association class. @@ -58,6 +63,7 @@ tag_id = row[0] community_tags.append( self.get_tag_by_id( trans, tag_id ) ) return community_tags + def get_tool_tags( self, trans ): result_set = trans.sa_session.execute( select( columns=[ trans.app.model.ToolTagAssociation.table.c.tag_id ], from_obj=trans.app.model.ToolTagAssociation.table ).distinct() ) @@ -67,6 +73,7 @@ tag_id = row[0] tags.append( self.get_tag_by_id( trans, tag_id ) ) return tags + def remove_item_tag( self, trans, user, item, tag_name ): """Remove a tag from an item.""" # Get item tag association. @@ -78,6 +85,7 @@ item.tags.remove( item_tag_assoc ) return True return False + def delete_item_tags( self, trans, user, item ): """Delete tags from an item.""" # Delete item-tag associations. @@ -85,6 +93,7 @@ trans.sa_session.delete( tag ) # Delete tags from item. del item.tags[:] + def item_has_tag( self, trans, user, item, tag ): """Returns true if item is has a given tag.""" # Get tag name. @@ -97,6 +106,7 @@ if item_tag_assoc: return True return False + def apply_item_tag( self, trans, user, item, name, value=None ): # Use lowercase name for searching/creating tag. lc_name = name.lower() @@ -124,6 +134,7 @@ item_tag_assoc.user_value = value item_tag_assoc.value = lc_value return item_tag_assoc + def apply_item_tags( self, trans, user, item, tags_str ): """Apply tags to an item.""" # Parse tags. @@ -131,6 +142,7 @@ # Apply each tag. for name, value in parsed_tags.items(): self.apply_item_tag( trans, user, item, name, value ) + def get_tags_str( self, tags ): """Build a string from an item's tags.""" # Return empty string if there are no tags. @@ -144,14 +156,17 @@ tag_str += ":" + tag.user_value tags_str_list.append( tag_str ) return ", ".join( tags_str_list ) + def get_tag_by_id( self, trans, tag_id ): """Get a Tag object from a tag id.""" return trans.sa_session.query( trans.app.model.Tag ).filter_by( id=tag_id ).first() + def get_tag_by_name( self, trans, tag_name ): """Get a Tag object from a tag name (string).""" if tag_name: return trans.sa_session.query( trans.app.model.Tag ).filter_by( name=tag_name.lower() ).first() return None + def _create_tag( self, trans, tag_str ): """Create a Tag object from a tag string.""" tag_hierarchy = tag_str.split( self.hierarchy_separator ) @@ -169,6 +184,7 @@ parent_tag = tag tag_prefix = tag.name + self.hierarchy_separator return tag + def _get_or_create_tag( self, trans, tag_str ): """Get or create a Tag object from a tag string.""" # Scrub tag; if tag is None after being scrubbed, return None. @@ -181,6 +197,7 @@ if tag is None: tag = self._create_tag( trans, scrubbed_tag_str ) return tag + def _get_item_tag_assoc( self, user, item, tag_name ): """ Return ItemTagAssociation object for a user, item, and tag string; returns None if there is @@ -191,6 +208,7 @@ if ( item_tag_assoc.user == user ) and ( item_tag_assoc.user_tname == scrubbed_tag_name ): return item_tag_assoc return None + def parse_tags( self, tag_str ): """ Returns a list of raw (tag-name, value) pairs derived from a string; method scrubs tag names and values as well. @@ -210,6 +228,7 @@ scrubbed_value = self._scrub_tag_value( nv_pair[1] ) name_value_pairs[scrubbed_name] = scrubbed_value return name_value_pairs + def _scrub_tag_value( self, value ): """Scrub a tag value.""" # Gracefully handle None: @@ -219,6 +238,7 @@ reg_exp = re.compile( '\s' ) scrubbed_value = re.sub( reg_exp, "", value ) return scrubbed_value + def _scrub_tag_name( self, name ): """Scrub a tag name.""" # Gracefully handle None: @@ -234,12 +254,14 @@ if len( scrubbed_name ) < self.min_tag_len or len( scrubbed_name ) > self.max_tag_len: return None return scrubbed_name + def _scrub_tag_name_list( self, tag_name_list ): """Scrub a tag name list.""" scrubbed_tag_list = list() for tag in tag_name_list: scrubbed_tag_list.append( self._scrub_tag_name( tag ) ) return scrubbed_tag_list + def _get_name_value_pair( self, tag_str ): """Get name, value pair from a tag string.""" # Use regular expression to parse name, value. @@ -250,6 +272,7 @@ name_value_pair.append( None ) return name_value_pair + class GalaxyTagHandler( TagHandler ): def __init__( self ): from galaxy import model @@ -271,6 +294,7 @@ model.VisualizationTagAssociation, model.VisualizationTagAssociation.table.c.visualization_id ) + class CommunityTagHandler( TagHandler ): def __init__( self ): from galaxy.webapps.tool_shed import model diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -52,7 +52,7 @@ return val -def safe_dumps(*args, **kwargs): +def safe_dumps( *args, **kwargs ): """ This is a wrapper around dumps that encodes Infinity and NaN values. It's a fairly rare case (which will be low in request volume). Basically, we tell @@ -60,10 +60,12 @@ re-encoding. """ try: - dumped = json.dumps(*args, allow_nan=False, **kwargs) + dumped = json.dumps( *args, allow_nan=False, **kwargs ) except ValueError: - obj = swap_inf_nan(copy.deepcopy(args[0])) - dumped = json.dumps(obj, allow_nan=False, **kwargs) + obj = swap_inf_nan( copy.deepcopy( args[0] ) ) + dumped = json.dumps( obj, allow_nan=False, **kwargs ) + if kwargs.get( 'escape_closing_tags', True ): + return dumped.replace( '</', '<\\/' ) return dumped diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 lib/galaxy/util/validation.py --- a/lib/galaxy/util/validation.py +++ b/lib/galaxy/util/validation.py @@ -8,8 +8,8 @@ def validate_and_sanitize_basestring( key, val ): if not isinstance( val, basestring ): - raise exceptions.RequestParameterInvalidException( '%s must be a string or unicode: %s' - % ( key, str( type( val ) ) ) ) + raise exceptions.RequestParameterInvalidException( '%s must be a string or unicode: %s' + % ( key, str( type( val ) ) ) ) return unicode( sanitize_html( val, 'utf-8', 'text/html' ), 'utf-8' ) diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -111,4 +111,3 @@ Returns true if input is a boolean and true or is a string and looks like a true value. """ return val == True or val in [ 'True', 'true', 'T', 't' ] - diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 lib/galaxy/webapps/galaxy/controllers/tag.py --- a/lib/galaxy/webapps/galaxy/controllers/tag.py +++ b/lib/galaxy/webapps/galaxy/controllers/tag.py @@ -64,7 +64,7 @@ trans.log_action( user, unicode( "untag" ), context, params ) # Retag an item. All previous tags are deleted and new tags are applied. - #(a)web.expose + @web.expose @web.require_login( "Apply a new set of tags to an item; previous tags are deleted." ) def retag_async( self, trans, item_id=None, item_class=None, new_tags=None ): """ @@ -73,7 +73,7 @@ # Apply tags. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).delete_item_tags( trans, item ) + self.get_tag_handler( trans ).delete_item_tags( trans, user, item ) self.get_tag_handler( trans ).apply_item_tags( trans, user, item, new_tags.encode( 'utf-8' ) ) trans.sa_session.flush() diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -15,7 +15,7 @@ //TODO: global... %for key in kwargs: ( window.bootstrapped = window.bootstrapped || {} )[ '${key}' ] = ( - ${ h.dumps( kwargs[ key ], indent=( 2 if trans.debug else 0 ) )} ); + ${ h.dumps( kwargs[ key ], indent=( 2 if trans.debug else 0 ) ).replace( '</', '<\\/' ) } ); %endfor define( 'bootstrapped-data', function(){ return window.bootstrapped; @@ -76,11 +76,17 @@ user_dict = trans.user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) + user_dict[ 'is_admin' ] = trans.user_is_admin() # tags used users_api_controller = trans.webapp.api_controllers[ 'users' ] - user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user ) - user_dict[ 'is_admin' ] = trans.user_is_admin() + tags_used = [] + for tag in users_api_controller.get_user_tags_used( trans, user=trans.user ): + tag = tag | h + if tag: + tags_used.append( tag ) + user_dict[ 'tags_used' ] = tags_used + return user_dict usage = 0 diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 templates/tagging_common.mako --- a/templates/tagging_common.mako +++ b/templates/tagging_common.mako @@ -19,7 +19,7 @@ ## Render HTML for a list of tags. <%def name="render_tagging_element_html(elt_id=None, tags=None, editable=True, use_toggle_link=True, input_size='15', in_form=False, tag_type='individual', render_add_tag_button=True)"> ## Useful attributes. - <% + <% num_tags = len( tags ) %><div class="tag-element" @@ -50,6 +50,7 @@ elif isinstance( tag, ItemTagAssociation ): tag_name = tag.user_tname tag_value = tag.user_value + ## Convert tag name, value to unicode. if isinstance( tag_name, str ): tag_name = unicode( escape( tag_name ), 'utf-8' ) @@ -61,7 +62,7 @@ tag_str = tag_name %><span class="tag-button"> - <span class="tag-name">${tag_str}</span> + <span class="tag-name">${tag_str | h}</span> %if editable: <img class="delete-tag-img" src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/> %endif @@ -186,10 +187,11 @@ ## Build dict of tag name, values. tag_names_and_values = dict() for tag in item_tags: - tag_name = tag.user_tname + tag_name = escape( tag.user_tname ) tag_value = "" if tag.value is not None: - tag_value = tag.user_value + tag_value = escape( tag.user_value ) + ## Tag names and values may be string or unicode object. if isinstance( tag_name, str ): tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') diff -r 4ecb1efececdb58d16087a58d1f168851899aa4a -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -1,32 +1,4 @@ -## get user data -<%def name="get_user_json()"> -<% - """Bootstrapping user API JSON""" - #TODO: move into common location (poss. BaseController) - if trans.user: - user_dict = trans.user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, - 'total_disk_usage': float } ) - user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) - users_api_controller = trans.webapp.api_controllers[ 'users' ] - user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user ) - user_dict[ 'is_admin' ] = trans.user_is_admin() - else: - usage = 0 - percent = None - try: - usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) - percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) - except AssertionError, assertion: - # no history for quota_agent.get_usage assertion - pass - user_dict = { - 'total_disk_usage' : int( usage ), - 'nice_total_disk_usage' : util.nice_size( usage ), - 'quota_percent' : percent - } - return user_dict -%> -</%def> +<%namespace file="/galaxy_client_app.mako" import="get_user_json" /> ## masthead head generator <%def name="load(active_view = None)"> @@ -87,7 +59,7 @@ ], function( mod_masthead, mod_menu, mod_modal, mod_frame, GalaxyUpload, user, quotameter ){ if( !Galaxy.currUser ){ // this doesn't need to wait for the page being readied - Galaxy.currUser = new user.User(${ h.dumps( get_user_json(), indent=2 ) }); + Galaxy.currUser = new user.User(${ h.dumps( masthead_config[ 'user' ][ 'json' ], indent=2 ) }); } $(function() { https://bitbucket.org/galaxy/galaxy-central/commits/66ea70fbc161/ Changeset: 66ea70fbc161 Branch: next-stable User: dannon Date: 2014-11-25 19:31:55+00:00 Summary: Another instance of tool_id reflected xss (in data_source_redirect). Affected #: 1 file diff -r 988dd20de45bb4d6a361da1febe7ca0631cb7b95 -r 66ea70fbc161602121d364f4ef7d8c3a9126d01d lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -291,7 +291,7 @@ log.error( "data_source_redirect called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 - return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) + return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) )) if isinstance( tool, DataSourceTool ): link = url_for( tool.action, **tool.get_static_param_values( trans ) ) https://bitbucket.org/galaxy/galaxy-central/commits/b017300f1867/ Changeset: b017300f1867 Branch: next-stable User: dannon Date: 2014-11-25 19:34:20+00:00 Summary: Merge. Affected #: 1 file diff -r 66ea70fbc161602121d364f4ef7d8c3a9126d01d -r b017300f1867b23c4e77fa3810a7cdbf196e7de1 templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -15,7 +15,7 @@ //TODO: global... %for key in kwargs: ( window.bootstrapped = window.bootstrapped || {} )[ '${key}' ] = ( - ${ h.dumps( kwargs[ key ], indent=( 2 if trans.debug else 0 ) ).replace( '</', '<\\/' ) } ); + ${ h.dumps( kwargs[ key ], indent=( 2 if trans.debug else 0 ) ) } ); %endfor define( 'bootstrapped-data', function(){ return window.bootstrapped; 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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