diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js index 67d8dd07c35..6da2b057a0b 100644 --- a/client/galaxy/scripts/viz/trackster.js +++ b/client/galaxy/scripts/viz/trackster.js @@ -12,7 +12,6 @@ require( [ // load js libraries 'utils/utils', - 'mvc/ui/icon-button', 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.mousewheel', @@ -32,9 +31,8 @@ require( }); // trackster viewer -define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization"], - function(_, base, tracks, visualization) { - +define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ], + function(_, base, tracks, visualization, mod_icon_btn) { /** * User interface controls for trackster */ diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index 50b55b28cca..6d3f80a57c2 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -140,6 +140,7 @@ + @@ -304,6 +305,7 @@ + diff --git a/eggs.ini b/eggs.ini index 409cf5a4951..9cea83e2a5b 100644 --- a/eggs.ini +++ b/eggs.ini @@ -15,7 +15,7 @@ no_auto = pbs_python bx_python = 0.7.2 Cheetah = 2.2.2 MarkupSafe = 0.12 -mercurial = 2.2.3 +mercurial = 3.2.4 MySQL_python = 1.2.3c1 PyRods = 3.2.4 numpy = 1.6.0 diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index 58bb9a7bee5..98530928512 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -17,7 +17,7 @@ from galaxy.datatypes import metadata from galaxy.datatypes.checkers import is_gzip from galaxy.datatypes.sniff import get_test_fname, get_headers from galaxy.datatypes.metadata import MetadataElement - +from galaxy.datatypes.util.image_util import check_image_type try: eggs.require( "bx-python" ) @@ -814,3 +814,34 @@ class Lav( data.Text ): except: return False + +class RNADotPlotMatrix( data.Data ): + file_ext = "rna_eps" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = 'RNA Dot Plot format (Postscript derivative)' + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def sniff(self, filename): + """Determine if the file is in RNA dot plot format.""" + if check_image_type( filename, ['EPS'] ): + seq = False + coor = False + pairs = False + with open( filename ) as handle: + for line in handle: + line = line.strip() + if line: + if line.startswith('/sequence'): + seq = True + elif line.startswith('/coor'): + coor = True + elif line.startswith('/pairs'): + pairs = True + if seq and coor and pairs: + return True + return False \ No newline at end of file diff --git a/lib/galaxy/datatypes/util/image_util.py b/lib/galaxy/datatypes/util/image_util.py index 81855f02b65..01a0b66ef1e 100644 --- a/lib/galaxy/datatypes/util/image_util.py +++ b/lib/galaxy/datatypes/util/image_util.py @@ -71,6 +71,4 @@ def get_image_ext ( file_path, image ): return 'pbm' if format == 'PGM': return 'pgm' - if format == 'EPS': - return 'eps' return None diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py index 06f89c2baff..1b20c02b1af 100644 --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -394,7 +394,7 @@ class AbstractToolBox( object, Dictifiable ): section.elems.stub_label( section_id ) self._integrated_tool_panel.append_section( key, section ) elif elem.tag == 'label': - section.stub_label( key ) + self._integrated_tool_panel.stub_label( key ) def _write_integrated_tool_panel_config_file( self ): """ diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py index 66dfab9071c..1f46ab953d1 100644 --- a/lib/tool_shed/util/hg_util.py +++ b/lib/tool_shed/util/hg_util.py @@ -16,7 +16,7 @@ from mercurial import cmdutil from mercurial import commands from mercurial import hg from mercurial import ui -from mercurial.changegroup import readbundle +from mercurial.exchange import readbundle from mercurial.changegroup import readexactly from tool_shed.util import basic_util @@ -26,7 +26,7 @@ log = logging.getLogger( __name__ ) INITIAL_CHANGELOG_HASH = '000000000000' def add_changeset( repo_ui, repo, path_to_filename_in_archive ): - commands.add( repo_ui, repo, path_to_filename_in_archive ) + commands.add( repo_ui, repo, str( path_to_filename_in_archive ) ) def archive_repository_revision( app, repository, archive_dir, changeset_revision ): '''Create an un-versioned archive of a repository.''' @@ -49,7 +49,7 @@ def bundle_to_json( fh ): command line) to a json object. """ # See http://www.wstein.org/home/wstein/www/home/was/patches/hg_json - hg_unbundle10_obj = readbundle( fh, None ) + hg_unbundle10_obj = readbundle( None, fh, None ) groups = [ group for group in unpack_groups( hg_unbundle10_obj ) ] return json.dumps( groups, indent=4 ) diff --git a/static/scripts/packed/viz/trackster.js b/static/scripts/packed/viz/trackster.js index e55bdf6a94c..b7051135501 100644 --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1 +1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/utils","mvc/ui/icon-button","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating"],function(b,a){b.cssLoadFile("static/style/jquery.rating.css");b.cssLoadFile("static/style/autocomplete_tagging.css");b.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");b.cssLoadFile("static/style/library.css");b.cssLoadFile("static/style/trackster.css")});define(["libs/underscore","base","viz/trackster/tracks","viz/visualization"],function(b,e,a,c){var d=e.Base.extend({initialize:function(g){this.baseURL=g},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var g=[];$(".bookmark").each(function(){g.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var h=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),j={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:h},bookmarks:g};return $.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(j)}}).success(function(k){Galaxy.modal.hide();view.vis_id=k.vis_id;view.has_changes=false;window.history.pushState({},"",k.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var g=this,h=mod_icon_btn.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(j){b.each(j,function(k){view.add_drawable(a.object_from_template(k,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new a.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=g.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){g.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){g.handle_unsaved_changes(view)}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=h;return h},add_bookmarks:function(){var g=this,h=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:j,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json"}).then(function(m){for(i=0;i").addClass("bookmark").appendTo(n);var q=$("
").addClass("position").appendTo(p),m=$("").text(l).appendTo(q).click(function(){view.go_to(l);return false}),k=$("
").text(j).appendTo(p);if(g){var o=$("
").addClass("delete-icon-container").prependTo(p).click(function(){p.slideUp("fast");p.remove();view.has_changes=true;return false}),h=$("").addClass("icon-button delete").appendTo(o);k.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return p},create_visualization:function(m,g,l,n,k){var j=this,h=new a.TracksterView(b.extend(m,{header:false}));h.editor=true;$.when(h.load_chroms_deferred).then(function(y){if(g){var w=g.chrom,o=g.start,t=g.end,q=g.overview;if(w&&(o!==undefined)&&t){h.change_chrom(w,o,t)}else{h.change_chrom(y[0].chrom)}}else{h.change_chrom(y[0].chrom)}if(l){var r,p,s;for(var u=0;u");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},view_existing:function(){var g=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:g.title,vis_id:g.vis_id,dbkey:g.dbkey},g.viewport,g.tracks,g.bookmarks,true);this.init_editor()},view_new:function(){var g=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(h){Galaxy.modal.show({title:"New Visualization",body:g.template_view_new(h),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){g.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(g){var j='
Is the build not listed here? Add a Custom Build
';return j},create_browser:function(h,g){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:h,dbkey:g},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.config.get_value("name")+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(g){view.add_drawable(a.object_from_template(g,view,view))}})}$("#add-bookmark-button").click(function(){var h=view.chrom+":"+view.low+"-"+view.high,g="Bookmark description";return ui.add_bookmark(h,g,true)});ui.init_keyboard_nav(view);$(window).on("beforeunload",function(){if(view.has_changes){return"There are unsaved changes to your visualization that will be lost if you leave this page."}})}});return{TracksterUI:d,GalaxyApp:f}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/utils","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating"],function(b,a){b.cssLoadFile("static/style/jquery.rating.css");b.cssLoadFile("static/style/autocomplete_tagging.css");b.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");b.cssLoadFile("static/style/library.css");b.cssLoadFile("static/style/trackster.css")});define(["libs/underscore","base","viz/trackster/tracks","viz/visualization","mvc/ui/icon-button"],function(b,f,a,d,c){var e=f.Base.extend({initialize:function(h){this.baseURL=h},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var h=[];$(".bookmark").each(function(){h.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var j=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),k={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:j},bookmarks:h};return $.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(k)}}).success(function(l){Galaxy.modal.hide();view.vis_id=l.vis_id;view.has_changes=false;window.history.pushState({},"",l.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var h=this,j=c.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){d.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(k){b.each(k,function(l){view.add_drawable(a.object_from_template(l,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new a.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=h.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){h.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){h.handle_unsaved_changes(view)}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=j;return j},add_bookmarks:function(){var h=this,j=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(k){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:k,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var l,m=$(this).val();if($(this).attr("name")==="id"){l={hda_id:m}}else{l={ldda_id:m}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:l,dataType:"json"}).then(function(n){for(i=0;i").addClass("bookmark").appendTo(o);var r=$("
").addClass("position").appendTo(q),n=$("").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("
").text(k).appendTo(q);if(h){var p=$("
").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q},create_visualization:function(n,h,m,o,l){var k=this,j=new a.TracksterView(b.extend(n,{header:false}));j.editor=true;$.when(j.load_chroms_deferred).then(function(z){if(h){var x=h.chrom,p=h.start,u=h.end,r=h.overview;if(x&&(p!==undefined)&&u){j.change_chrom(x,p,u)}else{j.change_chrom(z[0].chrom)}}else{j.change_chrom(z[0].chrom)}if(m){var s,q,t;for(var v=0;v");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},view_existing:function(){var h=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:h.title,vis_id:h.vis_id,dbkey:h.dbkey},h.viewport,h.tracks,h.bookmarks,true);this.init_editor()},view_new:function(){var h=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(j){Galaxy.modal.show({title:"New Visualization",body:h.template_view_new(j),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){h.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(h){var k='
Is the build not listed here? Add a Custom Build
';return k},create_browser:function(j,h){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:j,dbkey:h},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.config.get_value("name")+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(h){view.add_drawable(a.object_from_template(h,view,view))}})}$("#add-bookmark-button").click(function(){var j=view.chrom+":"+view.low+"-"+view.high,h="Bookmark description";return ui.add_bookmark(j,h,true)});ui.init_keyboard_nav(view);$(window).on("beforeunload",function(){if(view.has_changes){return"There are unsaved changes to your visualization that will be lost if you leave this page."}})}});return{TracksterUI:e,GalaxyApp:g}}); \ No newline at end of file diff --git a/static/scripts/viz/trackster.js b/static/scripts/viz/trackster.js index 67d8dd07c35..6da2b057a0b 100644 --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -12,7 +12,6 @@ require( [ // load js libraries 'utils/utils', - 'mvc/ui/icon-button', 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.mousewheel', @@ -32,9 +31,8 @@ require( }); // trackster viewer -define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization"], - function(_, base, tracks, visualization) { - +define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ], + function(_, base, tracks, visualization, mod_icon_btn) { /** * User interface controls for trackster */ diff --git a/templates/tagging_common.mako b/templates/tagging_common.mako index 35ccfb4550a..b85388b793f 100644 --- a/templates/tagging_common.mako +++ b/templates/tagging_common.mako @@ -89,7 +89,7 @@ <%def name="render_tool_tagging_elements()"> <% elt_id = int ( floor ( random()*maxint ) ) - tags = trans.app.tag_handler.get_tool_tags( trans ) + tags = trans.app.tag_handler.get_tool_tags() %> ${self.render_tagging_element_html(elt_id=elt_id, \ tags=tags, \ @@ -105,7 +105,7 @@ ## Build HTML. <% elt_id = int ( floor ( random()*maxint ) ) - community_tags = trans.app.tag_handler.get_community_tags( trans, item=tagged_item, limit=5 ) + community_tags = trans.app.tag_handler.get_community_tags( item=tagged_item, limit=5 ) %> ${self.render_tagging_element_html(elt_id=elt_id, \ tags=community_tags, \