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commit/galaxy-central: smcmanus: Moved galaxy.web.controllers references to galaxy.webapps.galaxy.controllers
by Bitbucket 05 Oct '12

05 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/210c39f4bf7f/ changeset: 210c39f4bf7f user: smcmanus date: 2012-10-05 03:43:15 summary: Moved galaxy.web.controllers references to galaxy.webapps.galaxy.controllers affected #: 5 files diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -1,7 +1,7 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<% from galaxy.web.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> +<% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %><h3>Rename datasets for Sample "${sample.name}"</h3> diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/library/common/browse_library_opt.mako --- a/templates/library/common/browse_library_opt.mako +++ b/templates/library/common/browse_library_opt.mako @@ -214,7 +214,7 @@ ## children, which are always lddas ). We also need to make sure we're displaying the latest version of this ## library_dataset, so we display the attributes from the ldda. - from galaxy.web.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted is_admin = trans.user_is_admin() and cntrller == 'library_admin' current_version = ( ldda == library_dataset.library_dataset_dataset_association ) @@ -312,7 +312,7 @@ <%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )"><% - from galaxy.web.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas + from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, map_library_datasets_to_lddas, branch_deleted, datasets_for_lddas # SM: DELETEME from datetime import datetime, timedelta @@ -472,7 +472,7 @@ <%def name="render_content(simple=False)"><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime import logging log = logging.getLogger( __name__ ) diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -3,7 +3,7 @@ <%namespace file="/common/template_common.mako" import="render_template_fields" /><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted, get_containing_library_from_library_dataset + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted, get_containing_library_from_library_dataset from galaxy.web.framework.helpers import time_ago if ldda == ldda.library_dataset.library_dataset_dataset_association: diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/library/common/library_dataset_search_results.mako --- a/templates/library/common/library_dataset_search_results.mako +++ b/templates/library/common/library_dataset_search_results.mako @@ -66,8 +66,7 @@ <%def name="render_content()"><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted - #from galaxy.webapps.galaxy.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime class RowCounter( object ): diff -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa templates/webapps/reports/dataset_info.mako --- a/templates/webapps/reports/dataset_info.mako +++ b/templates/webapps/reports/dataset_info.mako @@ -4,6 +4,7 @@ <% from galaxy.web.framework.helpers import time_ago from galaxy.web.controllers.library_common import get_containing_library_from_library_dataset + from galaxy.webapps.galaxy.controllers.library_common import get_containing_library_from_library_dataset %> %if message: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: smcmanus: Cleanup: take out traceback and debug
by Bitbucket 05 Oct '12

05 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2565580bb7cf/ changeset: 2565580bb7cf user: smcmanus date: 2012-10-05 02:48:46 summary: Cleanup: take out traceback and debug affected #: 3 files diff -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -143,8 +143,6 @@ message=message, status=status ) except Exception, e: - import traceback - log.debug( "traceback: %s" % traceback.format_exc() ) message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) ) status = 'error' default_action = params.get( 'default_action', None ) diff -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 lib/galaxy/webapps/galaxy/controllers/requests_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py @@ -284,7 +284,6 @@ request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Manage "%s" datasets' % sample.name - log.debug( "!!!!!!!!!!!!!!!!!!!!!!@@@@@@@@@@@@@@@@@@@@@@@##################" ) self.datatx_grid.global_actions = [ grids.GridAction( "Browse target data library", dict( controller='library_common', action='browse_library', diff -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb -r 2565580bb7cffd28c237ecafab1fbb46fe6185e9 templates/library/common/library_dataset_search_results.mako --- a/templates/library/common/library_dataset_search_results.mako +++ b/templates/library/common/library_dataset_search_results.mako @@ -67,6 +67,7 @@ <% from galaxy import util from galaxy.web.controllers.library_common import branch_deleted + #from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime class RowCounter( object ): 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: smcmanus: The browse_library.mako template referred to galaxy.web.controllers.library_common, which has been updated to galaxy.webapps.galaxy.controllers.library_common. The Data Library browsing should be fixed.
by Bitbucket 05 Oct '12

05 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/029818b7e546/ changeset: 029818b7e546 user: smcmanus date: 2012-10-05 02:43:55 summary: The browse_library.mako template referred to galaxy.web.controllers.library_common, which has been updated to galaxy.webapps.galaxy.controllers.library_common. The Data Library browsing should be fixed. affected #: 3 files diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -131,7 +131,7 @@ comptypes = get_comptypes( trans ) try: # SM: TODO: Add configuration variable asap. - return trans.fill_template( '/library/common/browse_library.mako', + return trans.fill_template( 'library/common/browse_library.mako', cntrller=cntrller, use_panels=use_panels, library=library, @@ -143,6 +143,8 @@ message=message, status=status ) except Exception, e: + import traceback + log.debug( "traceback: %s" % traceback.format_exc() ) message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) ) status = 'error' default_action = params.get( 'default_action', None ) diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb lib/galaxy/webapps/galaxy/controllers/requests_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py @@ -284,6 +284,7 @@ request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Manage "%s" datasets' % sample.name + log.debug( "!!!!!!!!!!!!!!!!!!!!!!@@@@@@@@@@@@@@@@@@@@@@@##################" ) self.datatx_grid.global_actions = [ grids.GridAction( "Browse target data library", dict( controller='library_common', action='browse_library', diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 029818b7e546a3b6835c49ef4f8694c5ac695dfb templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -213,7 +213,7 @@ ## children, which are always lddas ). We also need to make sure we're displaying the latest version of this ## library_dataset, so we display the attributes from the ldda. - from galaxy.web.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted is_admin = trans.user_is_admin() and cntrller == 'library_admin' @@ -312,7 +312,7 @@ <%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False, simple=False )"><% - from galaxy.web.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted is_admin = trans.user_is_admin() and cntrller == 'library_admin' has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) @@ -472,7 +472,7 @@ <%def name="render_content(simple=False)"><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted + from galaxy.webapps.galaxy.controllers.library_common import branch_deleted from time import strftime is_admin = trans.user_is_admin() and cntrller == 'library_admin' 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: jgoecks: Pack scripts and add compiled template.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f3b183e756f9/ changeset: f3b183e756f9 user: jgoecks date: 2012-10-04 18:35:16 summary: Pack scripts and add compiled template. affected #: 3 files diff -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 -r f3b183e756f9b209ef0904718ed547e04c74ab7a static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-scatterplotControlForm"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,o=this;function e(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=k(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=k(r)+"</option>\n ";return q}function c(t,s){var q="",r,p;q+='\n <option value="';p=f.index;if(p){r=p.call(t,{hash:{}})}else{r=t.index;r=typeof r===h?r():r}q+=k(r)+'">';p=f.name;if(p){r=p.call(t,{hash:{}})}else{r=t.name;r=typeof r===h?r():r}q+=k(r)+"</option>\n ";return q}j+='\n<div id="loading-indicator" style="display: none;">\n <img class="loading-img" src="';i=f.loadingIndicatorImagePath;if(i){d=i.call(n,{hash:{}})}else{d=n.loadingIndicatorImagePath;d=typeof d===h?d():d}j+=k(d)+'" />\n <span class="loading-message"></span>\n</div>\n\n';j+='\n<div id="chart-settings">\n\n ';j+='\n <div id="x-column-input">\n <label for="">Data column for X: </label>\n <select name="x-column">\n ';d=n.availableColumns;d=f.each.call(n,d,{hash:{},inverse:o.noop,fn:o.program(1,e,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n <div id="y-column-input">\n <label for="">Data column for Y: </label>\n <select name="y-column">\n ';d=n.availableColumns;d=f.each.call(n,d,{hash:{},inverse:o.noop,fn:o.program(3,c,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n \n <input id="render-button" type="button" value="Draw" />\n <div class="clear"></div>\n</div>';return j})})(); \ No newline at end of file diff -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 -r f3b183e756f9b209ef0904718ed547e04c74ab7a static/scripts/packed/viz/phyloviz.js --- a/static/scripts/packed/viz/phyloviz.js +++ b/static/scripts/packed/viz/phyloviz.js @@ -1,1 +1,1 @@ -var UserMenuBase=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(e,c,a){var b=this,f=e.val(),g=e.attr("displayLabel")||e.attr("id").replace("phyloViz","");function d(h){return !isNaN(parseFloat(h))&&isFinite(h)}if(!d(f)){alert(g+" is not a number!");return false}if(f>a){alert(g+" is too large.");return false}else{if(f<c){alert(g+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(a){if(a.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). 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g==="number"){e=g}else{if(d3.event!==null){e=d3.event.scale}}}if(e<j.MIN_SCALE||e>j.MAX_SCALE){return}j.zoomFunc.scale(e);f="translate("+j.margins[3]+","+j.margins[0]+") scale("+e+")";if(d3.event!==null){h="translate("+d3.event.translate+")"}else{if(typeof c!=="undefined"){var d=c.split(",")[0];var b=c.split(",")[1];if(!isNaN(d)&&!isNaN(b)){i=[i[0]+parseFloat(d),i[1]+parseFloat(b)]}}j.zoomFunc.translate(i);h="translate("+i+")"}j.phyloTree.set("scaleFactor",e);j.phyloTree.set("translate",i);j.vis.attr("transform",h+f)},reloadViz:function(){var b=this,d=$("#phylovizNexSelector :selected").val(),a=b.phyloTree.get("dataset_id"),c="phyloviz/getJsonData?dataset_id="+a+"&treeIndex="+String(d);$.getJSON(c,function(e){window.initPhyloViz(e.data,e.config)})}});var HeaderButtons=Backbone.View.extend({initialize:function(b){var a=this;a.phylovizView=b;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();a.initNavBtns();a.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){a.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var a=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();a.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var b=$("#phylovizNexSelector option:selected").text();if(b){a.phylovizView.phyloTree.set("title",b)}a.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz 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a=this;a.phyloTree=b.phyloTree;a.el=$("#SettingsMenu");a.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){a.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){a.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){a.apply()})},apply:function(){var a=this;if(!a.isAcceptableValue(a.inputs.separation,50,2500)||!a.isAcceptableValue(a.inputs.leafHeight,5,30)||!a.isAcceptableValue(a.inputs.fontSize,5,20)){return}$.each(a.inputs,function(b,c){a.phyloTree.set(b,c.val())})},updateUI:function(){var a=this;$.each(a.inputs,function(b,c){c.val(a.phyloTree.get(b))})},resetToDefaults:function(){$(".bs-tooltip").remove();var a=this;$.each(a.phyloTree.defaults,function(b,c){a.phyloTree.set(b,c)});a.updateUI()},render:function(){}});var NodeSelectionView=UserMenuBase.extend({className:"Settings",initialize:function(b){var a=this;a.el=$("#nodeSelectionView");a.phyloTree=b.phyloTree;a.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};a.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){a.el.hide()});a.UI.saveChanges.off().on("click",function(){a.updateNodes()});a.UI.cancelChanges.off().on("click",function(){a.cancelChanges()});(function(c){c.fn.enable=function(d){return c(this).each(function(){if(d){c(this).removeAttr("disabled")}else{c(this).attr("disabled","disabled")}})}})(jQuery);a.UI.enableEdit.off().on("click",function(){a.toggleUI()})},toggleUI:function(){var a=this,b=a.UI.enableEdit.is(":checked");!b?a.cancelChanges():"";$.each(a.valuesOfConcern,function(c,d){a.UI[c].enable(b)});if(b){a.UI.saveChanges.show();a.UI.cancelChanges.show()}else{a.UI.saveChanges.hide();a.UI.cancelChanges.hide()}},cancelChanges:function(){var a=this,b=a.phyloTree.get("selectedNode");if(b){$.each(a.valuesOfConcern,function(c,d){a.UI[c].val(b[c])})}},updateNodes:function(){var a=this,b=a.phyloTree.get("selectedNode");if(b){if(!a.isAcceptableValue(a.UI.dist,0,1)||a.hasIllegalJsonCharacters(a.UI.name)||a.hasIllegalJsonCharacters(a.UI.annotation)){return}$.each(a.valuesOfConcern,function(c,d){(b[c])=a.UI[c].val()});a.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var PhyloVizSearch=UserMenuBase.extend({initialize:function(){var a=this;$("#phyloVizSearchBtn").on("click",function(){var c=$("#phyloVizSearchTerm"),d=$("#phyloVizSearchCondition").val().split("-"),b=d[0],e=d[1];a.hasIllegalJsonCharacters(c);if(b==="dist"){a.isAcceptableValue(c,0,1)}a.searchTree(b,e,c.val())})},searchTree:function(a,c,b){d3.selectAll("g.node").classed("searchHighlight",function(f){var e=f[a];if(typeof e!=="undefined"&&e!==null){if(a==="dist"){switch(c){case"greaterEqual":return e>=+b;case"lesserEqual":return e<=+b;default:return}}else{if(a==="name"||a==="annotation"){return e.toLowerCase().indexOf(b.toLowerCase())!==-1}}}})}}); \ No newline at end of file +define(["libs/d3","viz/visualization"],function(l,f){var k=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(q,o,m){var n=this,r=q.val(),s=q.attr("displayLabel")||q.attr("id").replace("phyloViz","");function p(t){return !isNaN(parseFloat(t))&&isFinite(t)}if(!p(r)){alert(s+" is not a number!");return false}if(r>m){alert(s+" is too large.");return false}else{if(r<o){alert(s+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(m){if(m.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function g(){var v=this,q=l.layout.hierarchy().sort(null).value(null),u=360,p="Linear",t=18,r=200,s=0,o=0.5,m=50;v.leafHeight=function(w){if(typeof w==="undefined"){return t}else{t=w;return v}};v.layoutMode=function(w){if(typeof w==="undefined"){return p}else{p=w;return v}};v.layoutAngle=function(w){if(typeof w==="undefined"){return u}if(isNaN(w)||w<0||w>360){return v}else{u=w;return v}};v.separation=function(w){if(typeof w==="undefined"){return r}else{r=w;return v}};v.links=function(w){return l.layout.tree().links(w)};v.nodes=function(z,x){var y=q.call(v,z,x),w=[],B=0,A=0;y.forEach(function(C){var D=C.data;D.depth=C.depth;B=D.depth>B?D.depth:B;w.push(D)});w.forEach(function(C){if(!C.children){A+=1;C.depth=B}});t=p==="Circular"?u/A:t;s=0;n(w[0],B,t,null);return w};function n(A,C,z,y){var x=A.children,w=0;var B=A.dist||o;B=B>1?1:B;A.dist=B;if(y!==null){A.y0=y.y0+B*r}else{A.y0=m}if(!x){A.x0=s++*z}else{x.forEach(function(D){D.parent=A;w+=n(D,C,z,A)});A.x0=w/x.length}A.x=A.x0;A.y=A.y0;return A.x0}return v}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},root:{},toggle:function(m){if(typeof m==="undefined"){return}if(m.children){m._children=m.children;m.children=null}else{m.children=m._children;m._children=null}},toggleAll:function(m){if(m.children&&m.children.length!==0){m.children.forEach(this.toggleAll);toggle(m)}},getData:function(){return this.root},save:function(){var m=this.root;n(m);this.set("root",m);function n(p){delete p.parent;if(p._selected){delete p._selected}if(p.children){p.children.forEach(n)}if(p._children){p._children.forEach(n)}}var o=jQuery.extend(true,{},this.attributes);o.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(o)},success:function(p){var q=p.url.split("id=")[1].split("&")[0],r="/phyloviz/visualization?id="+q;window.history.pushState({},"",r+window.location.hash);hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(n){var m=this;m.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",m.updateAndRender,m);m.vis=n.vis;m.i=0;m.maxDepth=-1;m.width=n.width;m.height=n.height},updateAndRender:function(o){var n=l.select(".vis"),m=this;o=o||m.model.root;m.renderNodes(o);m.renderLinks(o);m.addTooltips()},renderLinks:function(m){var v=this;var n=v.diagonal;var o=v.duration;var q=v.layoutMode;var s=v.vis.selectAll("g.completeLink").data(v.tree.links(v.nodes),function(w){return w.target.id});var u=function(w){w.pos0=w.source.y0+" "+w.source.x0;w.pos1=w.source.y0+" "+w.target.x0;w.pos2=w.target.y0+" "+w.target.x0};var t=s.enter().insert("svg:g","g.node").attr("class","completeLink");t.append("svg:path").attr("class","link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1});var r=s.transition().duration(500);r.select("path.link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1+" L "+w.pos2});var p=s.exit().remove()},selectNode:function(n){var m=this;l.selectAll("g.node").classed("selectedHighlight",function(o){if(n.id===o.id){if(n._selected){delete n._selected;return false}else{n._selected=true;return true}}return false});m.model.set("selectedNode",n);$("#phyloVizSelectedNodeName").val(n.name);$("#phyloVizSelectedNodeDist").val(n.dist);$("#phyloVizSelectedNodeAnnotation").val(n.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var n=this.__data__,m=n.annotation||"None";return n?(n.name?n.name+"<br/>":"")+"Dist: "+n.dist+" <br/>Annotation: "+m:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(n){var m=this;m.margins=n.margins;m.layoutMode="Linear";m.stdInit(n);m.layout();m.updateAndRender(m.model.root)},layout:function(){var m=this;m.tree=new g().layoutMode("Linear");m.diagonal=l.svg.diagonal().projection(function(n){return[n.y,n.x]})},renderNodes:function(m){var t=this,u=t.model.get("fontSize")+"px";t.tree.separation(t.model.get("separation")).leafHeight(t.model.get("leafHeight"));var p=500,n=t.tree.separation(t.model.get("separation")).nodes(t.model.root);var o=t.vis.selectAll("g.node").data(n,function(v){return v.name+v.id||(v.id=++t.i)});t.nodes=n;t.duration=p;var q=o.enter().append("svg:g").attr("class","node").on("dblclick",function(){l.event.stopPropagation()}).on("click",function(v){if(l.event.altKey){t.selectNode(v)}else{if(v.children&&v.children.length===0){return}t.model.toggle(v);t.updateAndRender(v)}});q.attr("transform",function(v){return"translate("+m.y0+","+m.x0+")"});q.append("svg:circle").attr("r",0.000001).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});q.append("svg:text").attr("class","nodeLabel").attr("x",function(v){return v.children||v._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(v){return v.children||v._children?"end":"start"}).style("fill-opacity",0.000001);var r=o.transition().duration(p);r.attr("transform",function(v){return"translate("+v.y+","+v.x+")"});r.select("circle").attr("r",t.defaults.nodeRadius).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});r.select("text").style("fill-opacity",1).style("font-size",u).text(function(v){return v.name});var s=o.exit().transition().duration(p).remove();s.select("circle").attr("r",0.000001);s.select("text").style("fill-opacity",0.000001);n.forEach(function(v){v.x0=v.x;v.y0=v.y})}});var i=Backbone.View.extend({className:"phyloviz",initialize:function(n){var m=this;m.MIN_SCALE=0.05;m.MAX_SCALE=5;m.MAX_DISPLACEMENT=500;m.margins=[10,60,10,80];m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.radius=m.width;m.data=n.data;$(window).resize(function(){m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.render()});m.phyloTree=new b(n.config);m.phyloTree.root=m.data;m.zoomFunc=l.behavior.zoom().scaleExtent([m.MIN_SCALE,m.MAX_SCALE]);m.zoomFunc.translate(m.phyloTree.get("translate"));m.zoomFunc.scale(m.phyloTree.get("scaleFactor"));m.navMenu=new c(m);m.settingsMenu=new h({phyloTree:m.phyloTree});m.nodeSelectionView=new e({phyloTree:m.phyloTree});m.search=new j();setTimeout(function(){m.zoomAndPan()},1000)},render:function(){var n=this;$("#PhyloViz").empty();n.mainSVG=l.select("#PhyloViz").append("svg:svg").attr("width",n.width).attr("height",n.height).attr("pointer-events","all").call(n.zoomFunc.on("zoom",function(){n.zoomAndPan()}));n.boundingRect=n.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",n.width).attr("height",n.height).attr("stroke","black").attr("fill","white");n.vis=n.mainSVG.append("svg:g").attr("class","vis");n.layoutOptions={model:n.phyloTree,width:n.width,height:n.height,vis:n.vis,margins:n.margins};$("#title").text("Phylogenetic Tree from "+n.phyloTree.get("title")+":");var m=new a(n.layoutOptions)},zoomAndPan:function(m){var s,o;if(typeof m!=="undefined"){s=m.zoom;o=m.translate}var v=this,q=v.zoomFunc.scale(),u=v.zoomFunc.translate(),r="",t="";switch(s){case"reset":q=1;u=[0,0];break;case"+":q*=1.1;break;case"-":q*=0.9;break;default:if(typeof s==="number"){q=s}else{if(l.event!==null){q=l.event.scale}}}if(q<v.MIN_SCALE||q>v.MAX_SCALE){return}v.zoomFunc.scale(q);r="translate("+v.margins[3]+","+v.margins[0]+") scale("+q+")";if(l.event!==null){t="translate("+l.event.translate+")"}else{if(typeof o!=="undefined"){var p=o.split(",")[0];var n=o.split(",")[1];if(!isNaN(p)&&!isNaN(n)){u=[u[0]+parseFloat(p),u[1]+parseFloat(n)]}}v.zoomFunc.translate(u);t="translate("+u+")"}v.phyloTree.set("scaleFactor",q);v.phyloTree.set("translate",u);v.vis.attr("transform",t+r)},reloadViz:function(){var n=this,p=$("#phylovizNexSelector :selected").val(),m=n.phyloTree.get("dataset_id"),o="phyloviz/getJsonData?dataset_id="+m+"&treeIndex="+String(p);$.getJSON(o,function(q){window.initPhyloViz(q.data,q.config)})}});var c=Backbone.View.extend({initialize:function(n){var m=this;m.phylovizView=n;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();m.initNavBtns();m.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){m.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var m=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();m.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var n=$("#phylovizNexSelector option:selected").text();if(n){m.phylovizView.phyloTree.set("title",n)}m.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("http://wiki.g2.bx.psu.edu/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var m=this,n=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){m.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){m.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){m.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(n.$el)}});var h=k.extend({className:"Settings",initialize:function(n){var m=this;m.phyloTree=n.phyloTree;m.el=$("#SettingsMenu");m.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){m.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){m.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){m.apply()})},apply:function(){var m=this;if(!m.isAcceptableValue(m.inputs.separation,50,2500)||!m.isAcceptableValue(m.inputs.leafHeight,5,30)||!m.isAcceptableValue(m.inputs.fontSize,5,20)){return}$.each(m.inputs,function(n,o){m.phyloTree.set(n,o.val())})},updateUI:function(){var m=this;$.each(m.inputs,function(n,o){o.val(m.phyloTree.get(n))})},resetToDefaults:function(){$(".bs-tooltip").remove();var m=this;$.each(m.phyloTree.defaults,function(n,o){m.phyloTree.set(n,o)});m.updateUI()},render:function(){}});var e=k.extend({className:"Settings",initialize:function(n){var m=this;m.el=$("#nodeSelectionView");m.phyloTree=n.phyloTree;m.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};m.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){m.el.hide()});m.UI.saveChanges.off().on("click",function(){m.updateNodes()});m.UI.cancelChanges.off().on("click",function(){m.cancelChanges()});(function(o){o.fn.enable=function(p){return o(this).each(function(){if(p){o(this).removeAttr("disabled")}else{o(this).attr("disabled","disabled")}})}})(jQuery);m.UI.enableEdit.off().on("click",function(){m.toggleUI()})},toggleUI:function(){var m=this,n=m.UI.enableEdit.is(":checked");if(!n){m.cancelChanges()}$.each(m.valuesOfConcern,function(o,p){m.UI[o].enable(n)});if(n){m.UI.saveChanges.show();m.UI.cancelChanges.show()}else{m.UI.saveChanges.hide();m.UI.cancelChanges.hide()}},cancelChanges:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){$.each(m.valuesOfConcern,function(o,p){m.UI[o].val(n[o])})}},updateNodes:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){if(!m.isAcceptableValue(m.UI.dist,0,1)||m.hasIllegalJsonCharacters(m.UI.name)||m.hasIllegalJsonCharacters(m.UI.annotation)){return}$.each(m.valuesOfConcern,function(o,p){(n[o])=m.UI[o].val()});m.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var j=k.extend({initialize:function(){var m=this;$("#phyloVizSearchBtn").on("click",function(){var o=$("#phyloVizSearchTerm"),p=$("#phyloVizSearchCondition").val().split("-"),n=p[0],q=p[1];m.hasIllegalJsonCharacters(o);if(n==="dist"){m.isAcceptableValue(o,0,1)}m.searchTree(n,q,o.val())})},searchTree:function(m,o,n){l.selectAll("g.node").classed("searchHighlight",function(q){var p=q[m];if(typeof p!=="undefined"&&p!==null){if(m==="dist"){switch(o){case"greaterEqual":return p>=+n;case"lesserEqual":return p<=+n;default:return}}else{if(m==="name"||m==="annotation"){return p.toLowerCase().indexOf(n.toLowerCase())!==-1}}}})}});return{PhylovizView:i}}); \ No newline at end of file diff -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 -r f3b183e756f9b209ef0904718ed547e04c74ab7a static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return(j.length>this.config.maxDataPoints)?(j.slice(0,this.config.maxDataPoints)):(j)};this.setUpDomains=function(j,l,k){this.log("setUpDomains");this.xMin=this.config.xMin||(k)?(k[0].min):(d3.min(j));this.xMax=this.config.xMax||(k)?(k[0].max):(d3.max(j));this.yMin=this.config.yMin||(k)?(k[1].min):(d3.min(l));this.yMax=this.config.yMax||(k)?(k[1].max):(d3.max(l))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(k,l){var j=k[0],m=k[1];this.log("renderScatterplot",j.length,m.length,this.config);j=this.preprocessData(j);m=this.preprocessData(m);this.setUpDomains(j,m,l);this.log("xMin, xMax, yMin, yMax:",this.xMin,this.xMax,this.yMin,this.yMax);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,m)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</option>"}});e+='<div id="loading-indicator" style="display: none;">';e+='<img class="loading-img" src='+this.loadingIndicatorImagePath+" />";e+='<span class="loading-message"></span>';e+="</div>";e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.showLoadingIndicator("Rendering...");d.endpoint=k.endpoint;d.plot.render(k.data,k.meta);d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file +define(["../libs/underscore","../libs/d3","../mvc/base-mvc","../templates/compiled/template-visualization-scatterplotControlForm"],function(){function a(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return(j.length>this.config.maxDataPoints)?(j.slice(0,this.config.maxDataPoints)):(j)};this.setUpDomains=function(j,l,k){this.log("setUpDomains");this.xMin=this.config.xMin||(k)?(k[0].min):(d3.min(j));this.xMax=this.config.xMax||(k)?(k[0].max):(d3.max(j));this.yMin=this.config.yMin||(k)?(k[1].min):(d3.min(l));this.yMax=this.config.yMax||(k)?(k[1].max):(d3.max(l))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(k,l){var j=k[0],m=k[1];this.log("renderScatterplot",j.length,m.length,this.config);j=this.preprocessData(j);m=this.preprocessData(m);this.setUpDomains(j,m,l);this.log("xMin, xMax, yMin, yMax:",this.xMin,this.xMax,this.yMin,this.yMax);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,m)}}var b=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new a(this.chartConfig)},render:function(){var c=this,d="";var e={loadingIndicatorImagePath:this.loadingIndicatorImagePath,config:this.chartConfig,availableColumns:[]};_.each(this.dataset.metadata_column_types.split(", "),function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}e.availableColumns.push({index:g,name:f})}});d=b.templates.form(e);this.$el.append(d);return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.endpoint=k.endpoint;d.showLoadingIndicator("Rendering...");d.plot.render(k.data,k.meta);d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});b.templates=CompiledTemplateLoader.getTemplates({"visualization-templates.html":{form:"template-visualization-scatterplotControlForm"}});return{TwoVarScatterplot:a,ScatterplotControlForm: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: jgoecks: (a) JSLint cleanup for phyloviz.js and (b) make phyloviz, scatterplot available.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/89c27f6b20f8/ changeset: 89c27f6b20f8 user: jgoecks date: 2012-10-04 17:07:29 summary: (a) JSLint cleanup for phyloviz.js and (b) make phyloviz, scatterplot available. affected #: 2 files diff -r d7eba083859770e676f173b75f2053f575305113 -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 static/scripts/viz/phyloviz.js --- a/static/scripts/viz/phyloviz.js +++ b/static/scripts/viz/phyloviz.js @@ -233,12 +233,16 @@ // removing unnecessary attributes if (node._selected){ delete node._selected;} - node.children ? node.children.forEach(cleanTree) : 0; - node._children ? node._children.forEach(cleanTree) : 0; + if (node.children) { + node.children.forEach(cleanTree); + } + if (node._children) { + node._children.forEach(cleanTree); + } } var config = jQuery.extend(true, {}, this.attributes); - config["selectedNode"] = null; + config.selectedNode = null; show_message("Saving to Galaxy", "progress"); @@ -598,9 +602,11 @@ * Function to zoom and pan the svg element which the entire tree is contained within * Uses d3.zoom events, and extend them to allow manual updates and keeping states in model */ + var zoomParams, + translateParams; if (typeof event !== "undefined") { - var zoomParams = event.zoom, - translateParams = event.translate; + zoomParams = event.zoom; + translateParams = event.translate; } var self = this, @@ -761,9 +767,9 @@ * Applying user values to phylotree model. */ var self = this; - if (!self.isAcceptableValue(self.inputs["separation"], 50, 2500) || - !self.isAcceptableValue(self.inputs["leafHeight"], 5, 30) || - !self.isAcceptableValue(self.inputs["fontSize"], 5, 20)){ + if (!self.isAcceptableValue(self.inputs.separation, 50, 2500) || + !self.isAcceptableValue(self.inputs.leafHeight, 5, 30) || + !self.isAcceptableValue(self.inputs.fontSize, 5, 20)){ return; } $.each(self.inputs, function(key, $input){ @@ -854,7 +860,7 @@ var self = this, checked = self.UI.enableEdit.is(':checked'); - !checked ? self.cancelChanges() : ""; + if (!checked) { self.cancelChanges(); } $.each(self.valuesOfConcern, function(key, value) { self.UI[key].enable(checked); diff -r d7eba083859770e676f173b75f2053f575305113 -r 89c27f6b20f8f261a8e45e33abcc2ed9c1509a71 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -227,10 +227,10 @@ ## information--URL base, dataset id, dbkey, visualizations--in anchor. <% visualizations = data.get_visualizations() - ## HACK: if there are visualizations, only provide trackster for now + ## HACK: if there are visualizations, only provide a subset for now ## since others are not ready. - comment out to see all WIP visualizations - #if visualizations: - # visualizations = [ vis for vis in visualizations if vis in [ 'trackster' ] ] + if visualizations: + visualizations = [ vis for vis in visualizations if vis in [ 'trackster', 'phyloviz', 'scatterplot' ] ] %> %if visualizations: <a href="${h.url_for( controller='visualization' )}" 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: jgoecks: Make Phyloviz into an AMD module and use requireJS for Phyloviz.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d7eba0838597/ changeset: d7eba0838597 user: jgoecks date: 2012-10-04 16:51:10 summary: Make Phyloviz into an AMD module and use requireJS for Phyloviz. affected #: 2 files diff -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 -r d7eba083859770e676f173b75f2053f575305113 static/scripts/viz/phyloviz.js --- a/static/scripts/viz/phyloviz.js +++ b/static/scripts/viz/phyloviz.js @@ -1,3 +1,5 @@ +define(['libs/d3', 'viz/visualization'], function(d3, visualization_mod) { + var UserMenuBase = Backbone.View.extend({ /** * Base class of any menus that takes in user interaction. Contains checking methods. @@ -165,7 +167,7 @@ /** * -- PhyloTree Model -- */ -var PhyloTree = Visualization.extend({ +var PhyloTree = visualization_mod.Visualization.extend({ defaults : { layout: "Linear", separation : 250, // px dist between nodes of different depth to represent 1 evolutionary until @@ -588,7 +590,7 @@ $("#title").text("Phylogenetic Tree from " + self.phyloTree.get("title") + ":"); // -- Create Linear view instance -- - var linearView = new PhylovizLinearView(self.layoutOptions) + var linearView = new PhylovizLinearView(self.layoutOptions); }, zoomAndPan : function(event){ @@ -952,4 +954,10 @@ } }); } +}); + +return { + PhylovizView: PhylovizView +}; + }); \ No newline at end of file diff -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 -r d7eba083859770e676f173b75f2053f575305113 templates/visualization/phyloviz.mako --- a/templates/visualization/phyloviz.mako +++ b/templates/visualization/phyloviz.mako @@ -138,7 +138,43 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "galaxy.panels", "libs/d3", "mvc/data", "viz/visualization", "viz/phyloviz")} + ${h.js( "libs/require" )} + + <script type="text/javascript"> + + require.config({ + baseUrl: "${h.url_for('/static/scripts')}", + shim: { + "libs/underscore": { exports: "_" }, + "libs/d3": { exports: "d3" } + } + }); + + require(["viz/phyloviz"], function(phyloviz_mod) { + + function initPhyloViz(data, config) { + var phyloviz; + + // -- Initialization code |--> + phyloviz = new phyloviz_mod.PhylovizView({ + data: data, + layout : "Linear", + config : config + }); + + // -- Render viz. -- + phyloviz.render(); + + } + + $(function firstVizLoad(){ // calls when viz is loaded for the first time + var config = JSON.parse( '${ h.to_json_string( config )}'); + var data = JSON.parse('${h.to_json_string(data)}'); + initPhyloViz(data, config); + }); + }); + + </script></%def> @@ -290,31 +326,6 @@ <div id="PhyloViz" ></div> - <script type="text/javascript"> - - function initPhyloViz(data, config) { - var phyloviz; - - // -- Initialization code |--> - phyloviz = new PhylovizView({ - data: data, - layout : "Linear", - config : config - }); - - // -- Render viz. -- - phyloviz.render(); - - } - - $(function firstVizLoad(){ // calls when viz is loaded for the first time - var config = JSON.parse( '${ h.to_json_string( config )}'); - var data = JSON.parse('${h.to_json_string(data)}'); - initPhyloViz(data, config); - }); - - </script> - </%def> 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: jgoecks: Server-side refactoring for PhyloViz: move parsers + data providers into data_providers directory and remove phyloviz controller.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6f9ce8692bb6/ changeset: 6f9ce8692bb6 user: jgoecks date: 2012-10-04 16:34:57 summary: Server-side refactoring for PhyloViz: move parsers + data providers into data_providers directory and remove phyloviz controller. affected #: 14 files diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/data_providers/phyloviz/__init__.py --- /dev/null +++ b/lib/galaxy/visualization/data_providers/phyloviz/__init__.py @@ -0,0 +1,42 @@ +""" Data providers code for PhyloViz """ + +from galaxy.visualization.data_providers.basic import BaseDataProvider +from galaxy.visualization.data_providers.phyloviz.nexusparser import Nexus_Parser +from galaxy.visualization.data_providers.phyloviz.newickparser import Newick_Parser +from galaxy.visualization.data_providers.phyloviz.phyloxmlparser import Phyloxml_Parser + +class PhylovizDataProvider( BaseDataProvider ): + + def __init__( self, original_dataset=None ): + super( PhylovizDataProvider, self ).__init__( original_dataset=original_dataset ) + + def get_data( self ): + """returns [trees], meta + Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus + """ + + jsonDicts, meta = [], {} + file_ext = self.original_dataset.datatype.file_ext + file_name = self.original_dataset.file_name + try: + if file_ext == "nhx": # parses newick files + newickParser = Newick_Parser() + jsonDicts, parseMsg = newickParser.parseFile( file_name ) + elif file_ext == "phyloxml": # parses phyloXML files + phyloxmlParser = Phyloxml_Parser() + jsonDicts, parseMsg = phyloxmlParser.parseFile( file_name ) + elif file_ext == "nex": # parses nexus files + nexusParser = Nexus_Parser() + jsonDicts, parseMsg = nexusParser.parseFile( file_name ) + meta["trees"] = parseMsg + else: + raise Exception("File type is not supported") + + meta["msg"] = parseMsg + + except Exception, e: + raise e + jsonDicts, meta["msg"] = [], "Parse failed" + + return jsonDicts, meta + diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/data_providers/phyloviz/baseparser.py --- /dev/null +++ b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py @@ -0,0 +1,125 @@ +import json + +class Node(object): + """Node class of PhyloTree, which represents a CLAUDE in a phylogenetic tree""" + def __init__(self, nodeName, **kwargs): + """Creates a node and adds in the typical annotations""" + self.name, self.id = nodeName, kwargs.get("id", 0) + self.depth = kwargs.get("depth", 0) + self.children = [] + + self.isInternal = kwargs.get("isInternal", 0) + self.length, self.bootstrap = kwargs.get("length", 0), kwargs.get("bootstrap", None) + self.events = kwargs.get("events", "") + + # clean up boot strap values + if self.bootstrap == -1: + self.bootstrap = None + + def addChildNode(self, child): + """Adds a child node to the current node""" + if isinstance(child, Node): + self.children.append(child) + else: + self.children += child + + + def __str__(self): + return self.name + " id:" + str(self.id) + ", depth: " + str(self.depth) + + + def toJson(self): + """Converts the data in the node to a dict representation of json""" + thisJson = { + "name" : self.name, + "id" : self.id, + "depth" : self.depth, + "dist" : self.length + } + thisJson = self.addChildrenToJson(thisJson) + thisJson = self.addMiscToJson(thisJson) + return thisJson + + def addChildrenToJson(self, jsonDict): + """Needs a special method to addChildren, such that the key does not appear in the Jsondict when the children is empty + this requirement is due to the layout algorithm used by d3 layout for hiding subtree """ + if len(self.children) > 0: + children = [ node.toJson() for node in self.children] + jsonDict["children"] = children + return jsonDict + + + def addMiscToJson(self, jsonDict): + """Adds other misc attributes to json if they are present""" + if not self.events == "": + jsonDict["events"] = self.events + if not self.bootstrap == None: + jsonDict["bootstrap"] = self.bootstrap + return jsonDict + + + +class PhyloTree(object): + """Standardized python based class to represent the phylogenetic tree parsed from different + phylogenetic file formats.""" + + def __init__(self): + self.root, self.rootAttr = None, {} + self.nodes = {} + self.title = None + self.id = 1 + + def addAttributesToRoot(self, attrDict): + """Adds attributes to root, but first we put it in a temp store and bind it with root when .toJson is called""" + for key, value in attrDict.items(): + self.rootAttr[key] = value + + def makeNode(self, nodeName, **kwargs): + """Called to make a node within PhyloTree, arbitrary kwargs can be passed to annotate nodes + Tracks the number of nodes via internally incremented id""" + kwargs["id"] = self.id + self.id += 1 + return Node(nodeName, **kwargs) + + def addRoot(self, root): + """Creates a root for phyloTree""" + assert isinstance(root, Node) + root.parent = None + self.root = root + + def generateJsonableDict(self): + """Changes itself into a dictonary by recurssively calling the tojson on all its nodes. Think of it + as a dict in an array of dict in an array of dict and so on...""" + jsonTree = "" + if self.root: + assert isinstance(self.root, Node) + jsonTree = self.root.toJson() + for key, value in self.rootAttr.items(): + # transfer temporary stored attr to root + jsonTree[key] = value + else: + raise Exception("Root is not assigned!") + return jsonTree + + + +class Base_Parser(object): + """Base parsers contain all the methods to handle phylogeny tree creation and + converting the data to json that all parsers should have""" + + def __init__(self): + self.phyloTrees = [] + + def parseFile(self, filePath): + """Base method that all phylogeny file parser should have""" + raise Exception("Base method for phylogeny file parsers is not implemented") + + def toJson(self, jsonDict): + """Convenience method to get a json string from a python json dict""" + return json.dumps(jsonDict) + + def _writeJsonToFile(self, filepath, json): + """Writes the file out to the system""" + f = open(filepath, "w") + f.writelines(json) + f.close() diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/data_providers/phyloviz/newickparser.py --- /dev/null +++ b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py @@ -0,0 +1,185 @@ +from baseparser import Base_Parser, PhyloTree +import re + +class Newick_Parser(Base_Parser): + """For parsing trees stored in the newick format (.nhx) + It is necessarily more complex because this parser is later extended by Nexus for parsing newick as well..""" + + + def __init__(self): + super(Newick_Parser, self).__init__() + + + def parseFile(self, filePath): + """Parses a newick file to obtain the string inside. Returns: jsonableDict""" + with open(filePath, "r") as newickFile: + newickString = newickFile.read() + newickString = newickString.replace("\n", "").replace("\r", "") + return [self.parseData(newickString)], "Success" + + + def parseData(self, newickString): + """To be called on a newickString directly to parse it. Returns: jsonableDict""" + return self._parseNewickToJson(newickString) + + + def _parseNewickToJson(self, newickString, treeName=None, nameMap=None): + """parses a newick representation of a tree into a PhyloTree data structure, + which can be easily converted to json""" + self.phyloTree = PhyloTree() + newickString = self.cleanNewickString(newickString) + if nameMap: + newickString = self._mapName(newickString, nameMap) + + self.phyloTree.root = self.parseNode(newickString, 0) + if nameMap: + self.phyloTree.addAttributesToRoot({"treeName": treeName}) + + return self.phyloTree.generateJsonableDict() + + + def cleanNewickString(self, rawNewick): + """removing semi colon, and illegal json characters (\,',") and white spaces""" + return re.sub(r'\s|;|\"|\'|\\', '', rawNewick) + + + def _makeNodesFromString(self, string, depth): + """elements separated by comma could be empty""" + + if string.find("(") != -1: + raise Exception("Tree is not well form, location: " + string) + + childrenString = string.split(",") + childrenNodes = [] + + for childString in childrenString: + if len(childString) == 0: + continue + nodeInfo = childString.split(":") + name, length, bootstrap = "", None, -1 + if len(nodeInfo) == 2: # has length info + length = nodeInfo[1] + # checking for bootstap values + name = nodeInfo[0] + try: # Nexus may bootstrap in names position + name = float(name) + if 0<= name <= 1: + bootstrap = name + elif 1 <= name <= 100: + bootstrap = name / 100 + name = "" + except ValueError: + name = nodeInfo[0] + else: + name = nodeInfo[0] # string only contains name + node = self.phyloTree.makeNode(name, length=length, depth=depth, bootstrap= bootstrap) + childrenNodes += [node] + return childrenNodes + + + + def _mapName(self, newickString, nameMap): + """ + Necessary to replace names of terms inside nexus representation + Also, its here because Mailaud's doesnt deal with id_strings outside of quotes(" ") + """ + newString = "" + start = 0 + end = 0 + + for i in xrange(len(newickString)): + if newickString[i] == "(" or newickString[i] == ",": + if re.match(r"[,(]", newickString[i+1:]): + continue + else: + end = i + 1 + # i now refers to the starting position of the term to be replaced, + # we will next find j which is the ending pos of the term + for j in xrange(i+1, len(newickString)): + enclosingSymbol = newickString[j] # the immediate symbol after a common or left bracket which denotes the end of a term + if enclosingSymbol == ")" or enclosingSymbol == ":" or enclosingSymbol == ",": + termToReplace = newickString[end:j] + + newString += newickString[start : end] + nameMap[termToReplace] #+ "'" "'" + + start = j + break + + newString += newickString[start:] + return newString + + + def parseNode(self, string, depth): + """ Recursive method for parsing newick string, works by stripping down the string into substring + of newick contained with brackers, which is used to call itself. + Eg ... ( A, B, (D, E)C, F, G ) ... + We will make the preceeding nodes first A, B, then the internal node C, its children D, E, + and finally the succeeding nodes F, G""" + + # Base case where there is only an empty string + if string == "": + return + # Base case there its only an internal claude + if string.find("(") == -1: + return self._makeNodesFromString(string, depth) + + nodes, children = [], [] # nodes refer to the nodes on this level, children refers to the child of the + start = 0 + lenOfPreceedingInternalNodeString = 0 + bracketStack = [] + + for j in xrange(len(string)): + if string[j] == "(": #finding the positions of all the open brackets + bracketStack.append(j) + continue + if string[j] == ")": #finding the positions of all the closed brackets to extract claude + i = bracketStack.pop() + + if len(bracketStack) == 0: # is child of current node + + InternalNode = None + + #First flat call to make nodes of the same depth but from the preceeding string. + startSubstring = string[start + lenOfPreceedingInternalNodeString: i] + preceedingNodes = self._makeNodesFromString(startSubstring, depth) + nodes += preceedingNodes + + # Then We will try to see if the substring has any internal nodes first, make it then make nodes preceeding it and succeeding it. + if j + 1 < len(string): + stringRightOfBracket = string[j+1:] # Eg. '(b:0.4,a:0.3)c:0.3, stringRightOfBracket = c:0.3 + match = re.search(r"[\)\,\(]", stringRightOfBracket) + if match: + indexOfNextSymbol = match.start() + stringRepOfInternalNode = stringRightOfBracket[:indexOfNextSymbol] + internalNodes = self._makeNodesFromString( stringRepOfInternalNode, depth) + if len(internalNodes) > 0: + InternalNode = internalNodes[0] + lenOfPreceedingInternalNodeString = len(stringRepOfInternalNode) + else: # sometimes the node can be the last element of a string + InternalNode = self._makeNodesFromString(string[j+1:], depth)[0] + lenOfPreceedingInternalNodeString = len(string) - j + if InternalNode == None: #creating a generic node if it is unnamed + InternalNode = self.phyloTree.makeNode( "", depth=depth, isInternal=True ) #"internal-" + str(depth) + lenOfPreceedingInternalNodeString = 0 + + # recussive call to make the internal claude + childSubString = string[ i + 1 : j ] + InternalNode.addChildNode(self.parseNode(childSubString, depth + 1)) + + nodes.append(InternalNode) # we append the internal node later to preserve order + + start = j + 1 + continue + + if depth == 0: # if its the root node, we do nothing about it and return + return nodes[0] + + # Adding last most set of children + endString = string[start:] + if string[start-1] == ")": # if the symbol belongs to an internal node which is created previously, then we remove it from the string left to parse + match = re.search(r"[\)\,\(]", endString) + if match: + endOfNodeName = start + match.start() + 1 + endString = string[endOfNodeName:] + nodes += self._makeNodesFromString(endString, depth) + + return nodes diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py --- /dev/null +++ b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py @@ -0,0 +1,107 @@ +from newickparser import Newick_Parser +import re + +MAX_READLINES = 200000 + + +class Nexus_Parser(Newick_Parser): + + def __init__(self): + super(Nexus_Parser, self).__init__() + + def parseFile(self, filePath): + """passes a file and extracts its Nexus content.""" + return self.parseNexus(filePath) + + + def parseNexus(self, filename): + """ Nexus data is stored in blocks between a line starting with begin and another line starting with end; + Commends inside square brackets are to be ignored, + For more information: http://wiki.christophchamp.com/index.php/NEXUS_file_format + Nexus can store multiple trees + """ + + with open( filename, "rt") as nex_file: + nexlines = nex_file.readlines() + + rowCount = 0 + inTreeBlock = False # sentinel to check if we are in a tree block + intranslateBlock = False # sentinel to check if we are in the translate region of the tree. Stores synonyms of the labellings + self.inCommentBlock = False + self.nameMapping = None # stores mapping representation used in nexus format + treeNames = [] + + for line in nexlines: + line = line.replace(";\n", "") + lline = line.lower() + + if rowCount > MAX_READLINES or (not nex_file) : + break + rowCount +=1 + # We are only interested in the tree block. + if "begin" in lline and "tree" in lline and not inTreeBlock: + inTreeBlock = True + continue + if inTreeBlock and "end" in lline[:3]: + inTreeBlock, currPhyloTree = False, None + continue + + if inTreeBlock: + + if "title" in lline: # Adding title to the tree + titleLoc = lline.find("title") + title = line[titleLoc + 5:].replace(" ", "") + + continue + + if "translate" in lline: + intranslateBlock = True + self.nameMapping = {} + continue + + if intranslateBlock: + mappingLine = self.splitLinebyWhitespaces(line) + key, value = mappingLine[1], mappingLine[2].replace(",", "").replace("'","") #replacing illegal json characters + self.nameMapping[key] = value + + # Extracting newick Trees + if "tree" in lline: + intranslateBlock = False + + treeLineCols = self.splitLinebyWhitespaces(line) + treeName, newick = treeLineCols[2], treeLineCols[-1] + + if newick == "": # Empty lines can be found in tree blocks + continue + + currPhyloTree = self._parseNewickToJson(newick, treeName, nameMap=self.nameMapping) + + self.phyloTrees.append(currPhyloTree) + treeIndex = len(self.phyloTrees) - 1 + treeNames.append( (treeName, treeIndex) ) # appending name of tree, and its index + continue + + return self.phyloTrees, treeNames + + + def splitLinebyWhitespaces(self, line): + """replace tabs and write spaces to a single write space, so we can properly split it.""" + return re.split(r"\s+", line) + + + def checkComments(self, line): + """Check to see if the line/lines is a comment.""" + if not self.inCommentBlock: + if "[" in line: + if "]" not in line: + self.inCommentBlock = True + else: + return "Nextline" # need to move on to the nextline after getting out of comment + else : + if "]" in line: + if line.rfind("[") > line.rfind("]"): + pass # a comment block is closed but another is open. + else: + self.inCommentBlock = False + return "Nextline" # need to move on to the nextline after getting out of comment + return "" \ No newline at end of file diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py --- /dev/null +++ b/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py @@ -0,0 +1,133 @@ +from baseparser import Base_Parser, PhyloTree, Node +from xml.etree import ElementTree + +class Phyloxml_Parser(Base_Parser): + """Parses a phyloxml file into a json file that will be passed to PhyloViz for display""" + + def __init__(self): + super(Phyloxml_Parser, self).__init__() + self.phyloTree = PhyloTree() + self.tagsOfInterest = { + "clade": "", + "name" : "name", + "branch_length" : "length", + "confidence" : "bootstrap", + "events" : "events" + } + + def parseFile(self, filePath): + """passes a file and extracts its Phylogeny Tree content.""" + phyloXmlFile = open(filePath, "r") + + xmlTree = ElementTree.parse(phyloXmlFile) + xmlRoot = xmlTree.getroot()[0] + self.nameSpaceIndex = xmlRoot.tag.rfind("}") + 1 # used later by the clean tag method to remove the name space in every element.tag + + phyloRoot = None + for child in xmlRoot: + childTag = self.cleanTag(child.tag) + if childTag == "clade": + phyloRoot = child + elif childTag == "name": + self.phyloTree.title = child.text + + self.phyloTree.root = self.parseNode(phyloRoot, 0) + jsonDict = self.phyloTree.generateJsonableDict() + return [jsonDict], "Success" + + + def parseNode(self, node, depth): + """Parses any node within a phyloxml tree and looks out for claude, which signals the creation of + nodes - internal OR leaf""" + + tag = self.cleanTag(node.tag) + if not tag == "clade": + return None + hasInnerClade = False + + # peeking once for parent and once for child to check if the node is internal + for child in node: + childTag = self.cleanTag(child.tag) + if childTag == "clade": + hasInnerClade = True + break + + if hasInnerClade: # this node is an internal node + currentNode = self._makeInternalNode(node, depth= depth) + for child in node: + child = self.parseNode(child, depth + 1) + if isinstance(child, Node): + currentNode.addChildNode(child) + + else: # this node is a leaf node + currentNode = self._makeLeafNode(node, depth=depth+1) + + return currentNode + + + def _makeLeafNode(self, leafNode, depth = 0 ): + """Makes leaf nodes by calling Phylotree methods""" + node = {} + for child in leafNode: + childTag = self.cleanTag(child.tag) + if childTag in self.tagsOfInterest: + key = self.tagsOfInterest[childTag] # need to map phyloxml terms to ours + node[key] = child.text + + node["depth"] = depth + return self.phyloTree.makeNode(self._getNodeName(leafNode), **node) + + def _getNodeName(self, node, depth=-1): + """Gets the name of a claude. It handles the case where a taxonomy node is involved""" + + def getTagFromTaxonomyNode(node): + """Returns the name of a taxonomy node. A taxonomy node have to be treated differently as the name + is embedded one level deeper""" + phyloxmlTaxoNames = { + "common_name" : "", + "scientific_name" : "", + "code" : "" + } + for child in node: + childTag = self.cleanTag(child.tag) + if childTag in phyloxmlTaxoNames: + return child.text + return "" + + nodeName = "" + for child in node: + childTag = self.cleanTag(child.tag) + if childTag == "name" : + nodeName = child.text + break + elif childTag == "taxonomy": + nodeName = getTagFromTaxonomyNode(child) + break + + return nodeName + + + def _makeInternalNode(self, internalNode, depth=0): + """ Makes an internal node from an element object that is guranteed to be a parent node. + Gets the value of interests like events and appends it to a custom node object that will be passed to PhyloTree to make nodes + """ + node = {} + for child in internalNode: + childTag = self.cleanTag(child.tag) + if childTag == "clade": + continue + elif childTag in self.tagsOfInterest: + if childTag == "events": # events is nested 1 more level deeper than others + key, text = "events", self.cleanTag(child[0].tag) + else: + key = self.tagsOfInterest[childTag] + text = child.text + node[key] = text + + + return self.phyloTree.makeNode(self._getNodeName(internalNode, depth), **node) + + + def cleanTag(self, tagString): + return tagString[self.nameSpaceIndex:] + \ No newline at end of file diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/phyloviz/__init__.py --- a/lib/galaxy/visualization/phyloviz/__init__.py +++ /dev/null @@ -1,1 +0,0 @@ -__author__ = 'Tomithy' diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/phyloviz/baseparser.py --- a/lib/galaxy/visualization/phyloviz/baseparser.py +++ /dev/null @@ -1,125 +0,0 @@ -import json - -class Node(object): - """Node class of PhyloTree, which represents a CLAUDE in a phylogenetic tree""" - def __init__(self, nodeName, **kwargs): - """Creates a node and adds in the typical annotations""" - self.name, self.id = nodeName, kwargs.get("id", 0) - self.depth = kwargs.get("depth", 0) - self.children = [] - - self.isInternal = kwargs.get("isInternal", 0) - self.length, self.bootstrap = kwargs.get("length", 0), kwargs.get("bootstrap", None) - self.events = kwargs.get("events", "") - - # clean up boot strap values - if self.bootstrap == -1: - self.bootstrap = None - - def addChildNode(self, child): - """Adds a child node to the current node""" - if isinstance(child, Node): - self.children.append(child) - else: - self.children += child - - - def __str__(self): - return self.name + " id:" + str(self.id) + ", depth: " + str(self.depth) - - - def toJson(self): - """Converts the data in the node to a dict representation of json""" - thisJson = { - "name" : self.name, - "id" : self.id, - "depth" : self.depth, - "dist" : self.length - } - thisJson = self.addChildrenToJson(thisJson) - thisJson = self.addMiscToJson(thisJson) - return thisJson - - def addChildrenToJson(self, jsonDict): - """Needs a special method to addChildren, such that the key does not appear in the Jsondict when the children is empty - this requirement is due to the layout algorithm used by d3 layout for hiding subtree """ - if len(self.children) > 0: - children = [ node.toJson() for node in self.children] - jsonDict["children"] = children - return jsonDict - - - def addMiscToJson(self, jsonDict): - """Adds other misc attributes to json if they are present""" - if not self.events == "": - jsonDict["events"] = self.events - if not self.bootstrap == None: - jsonDict["bootstrap"] = self.bootstrap - return jsonDict - - - -class PhyloTree(object): - """Standardized python based class to represent the phylogenetic tree parsed from different - phylogenetic file formats.""" - - def __init__(self): - self.root, self.rootAttr = None, {} - self.nodes = {} - self.title = None - self.id = 1 - - def addAttributesToRoot(self, attrDict): - """Adds attributes to root, but first we put it in a temp store and bind it with root when .toJson is called""" - for key, value in attrDict.items(): - self.rootAttr[key] = value - - def makeNode(self, nodeName, **kwargs): - """Called to make a node within PhyloTree, arbitrary kwargs can be passed to annotate nodes - Tracks the number of nodes via internally incremented id""" - kwargs["id"] = self.id - self.id += 1 - return Node(nodeName, **kwargs) - - def addRoot(self, root): - """Creates a root for phyloTree""" - assert isinstance(root, Node) - root.parent = None - self.root = root - - def generateJsonableDict(self): - """Changes itself into a dictonary by recurssively calling the tojson on all its nodes. Think of it - as a dict in an array of dict in an array of dict and so on...""" - jsonTree = "" - if self.root: - assert isinstance(self.root, Node) - jsonTree = self.root.toJson() - for key, value in self.rootAttr.items(): - # transfer temporary stored attr to root - jsonTree[key] = value - else: - raise Exception("Root is not assigned!") - return jsonTree - - - -class Base_Parser(object): - """Base parsers contain all the methods to handle phylogeny tree creation and - converting the data to json that all parsers should have""" - - def __init__(self): - self.phyloTrees = [] - - def parseFile(self, filePath): - """Base method that all phylogeny file parser should have""" - raise Exception("Base method for phylogeny file parsers is not implemented") - - def toJson(self, jsonDict): - """Convenience method to get a json string from a python json dict""" - return json.dumps(jsonDict) - - def _writeJsonToFile(self, filepath, json): - """Writes the file out to the system""" - f = open(filepath, "w") - f.writelines(json) - f.close() diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/phyloviz/newickparser.py --- a/lib/galaxy/visualization/phyloviz/newickparser.py +++ /dev/null @@ -1,185 +0,0 @@ -from baseparser import Base_Parser, PhyloTree -import re - -class Newick_Parser(Base_Parser): - """For parsing trees stored in the newick format (.nhx) - It is necessarily more complex because this parser is later extended by Nexus for parsing newick as well..""" - - - def __init__(self): - super(Newick_Parser, self).__init__() - - - def parseFile(self, filePath): - """Parses a newick file to obtain the string inside. Returns: jsonableDict""" - with open(filePath, "r") as newickFile: - newickString = newickFile.read() - newickString = newickString.replace("\n", "").replace("\r", "") - return [self.parseData(newickString)], "Success" - - - def parseData(self, newickString): - """To be called on a newickString directly to parse it. Returns: jsonableDict""" - return self._parseNewickToJson(newickString) - - - def _parseNewickToJson(self, newickString, treeName=None, nameMap=None): - """parses a newick representation of a tree into a PhyloTree data structure, - which can be easily converted to json""" - self.phyloTree = PhyloTree() - newickString = self.cleanNewickString(newickString) - if nameMap: - newickString = self._mapName(newickString, nameMap) - - self.phyloTree.root = self.parseNode(newickString, 0) - if nameMap: - self.phyloTree.addAttributesToRoot({"treeName": treeName}) - - return self.phyloTree.generateJsonableDict() - - - def cleanNewickString(self, rawNewick): - """removing semi colon, and illegal json characters (\,',") and white spaces""" - return re.sub(r'\s|;|\"|\'|\\', '', rawNewick) - - - def _makeNodesFromString(self, string, depth): - """elements separated by comma could be empty""" - - if string.find("(") != -1: - raise Exception("Tree is not well form, location: " + string) - - childrenString = string.split(",") - childrenNodes = [] - - for childString in childrenString: - if len(childString) == 0: - continue - nodeInfo = childString.split(":") - name, length, bootstrap = "", None, -1 - if len(nodeInfo) == 2: # has length info - length = nodeInfo[1] - # checking for bootstap values - name = nodeInfo[0] - try: # Nexus may bootstrap in names position - name = float(name) - if 0<= name <= 1: - bootstrap = name - elif 1 <= name <= 100: - bootstrap = name / 100 - name = "" - except ValueError: - name = nodeInfo[0] - else: - name = nodeInfo[0] # string only contains name - node = self.phyloTree.makeNode(name, length=length, depth=depth, bootstrap= bootstrap) - childrenNodes += [node] - return childrenNodes - - - - def _mapName(self, newickString, nameMap): - """ - Necessary to replace names of terms inside nexus representation - Also, its here because Mailaud's doesnt deal with id_strings outside of quotes(" ") - """ - newString = "" - start = 0 - end = 0 - - for i in xrange(len(newickString)): - if newickString[i] == "(" or newickString[i] == ",": - if re.match(r"[,(]", newickString[i+1:]): - continue - else: - end = i + 1 - # i now refers to the starting position of the term to be replaced, - # we will next find j which is the ending pos of the term - for j in xrange(i+1, len(newickString)): - enclosingSymbol = newickString[j] # the immediate symbol after a common or left bracket which denotes the end of a term - if enclosingSymbol == ")" or enclosingSymbol == ":" or enclosingSymbol == ",": - termToReplace = newickString[end:j] - - newString += newickString[start : end] + nameMap[termToReplace] #+ "'" "'" + - start = j - break - - newString += newickString[start:] - return newString - - - def parseNode(self, string, depth): - """ Recursive method for parsing newick string, works by stripping down the string into substring - of newick contained with brackers, which is used to call itself. - Eg ... ( A, B, (D, E)C, F, G ) ... - We will make the preceeding nodes first A, B, then the internal node C, its children D, E, - and finally the succeeding nodes F, G""" - - # Base case where there is only an empty string - if string == "": - return - # Base case there its only an internal claude - if string.find("(") == -1: - return self._makeNodesFromString(string, depth) - - nodes, children = [], [] # nodes refer to the nodes on this level, children refers to the child of the - start = 0 - lenOfPreceedingInternalNodeString = 0 - bracketStack = [] - - for j in xrange(len(string)): - if string[j] == "(": #finding the positions of all the open brackets - bracketStack.append(j) - continue - if string[j] == ")": #finding the positions of all the closed brackets to extract claude - i = bracketStack.pop() - - if len(bracketStack) == 0: # is child of current node - - InternalNode = None - - #First flat call to make nodes of the same depth but from the preceeding string. - startSubstring = string[start + lenOfPreceedingInternalNodeString: i] - preceedingNodes = self._makeNodesFromString(startSubstring, depth) - nodes += preceedingNodes - - # Then We will try to see if the substring has any internal nodes first, make it then make nodes preceeding it and succeeding it. - if j + 1 < len(string): - stringRightOfBracket = string[j+1:] # Eg. '(b:0.4,a:0.3)c:0.3, stringRightOfBracket = c:0.3 - match = re.search(r"[\)\,\(]", stringRightOfBracket) - if match: - indexOfNextSymbol = match.start() - stringRepOfInternalNode = stringRightOfBracket[:indexOfNextSymbol] - internalNodes = self._makeNodesFromString( stringRepOfInternalNode, depth) - if len(internalNodes) > 0: - InternalNode = internalNodes[0] - lenOfPreceedingInternalNodeString = len(stringRepOfInternalNode) - else: # sometimes the node can be the last element of a string - InternalNode = self._makeNodesFromString(string[j+1:], depth)[0] - lenOfPreceedingInternalNodeString = len(string) - j - if InternalNode == None: #creating a generic node if it is unnamed - InternalNode = self.phyloTree.makeNode( "", depth=depth, isInternal=True ) #"internal-" + str(depth) - lenOfPreceedingInternalNodeString = 0 - - # recussive call to make the internal claude - childSubString = string[ i + 1 : j ] - InternalNode.addChildNode(self.parseNode(childSubString, depth + 1)) - - nodes.append(InternalNode) # we append the internal node later to preserve order - - start = j + 1 - continue - - if depth == 0: # if its the root node, we do nothing about it and return - return nodes[0] - - # Adding last most set of children - endString = string[start:] - if string[start-1] == ")": # if the symbol belongs to an internal node which is created previously, then we remove it from the string left to parse - match = re.search(r"[\)\,\(]", endString) - if match: - endOfNodeName = start + match.start() + 1 - endString = string[endOfNodeName:] - nodes += self._makeNodesFromString(endString, depth) - - return nodes diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/phyloviz/nexusparser.py --- a/lib/galaxy/visualization/phyloviz/nexusparser.py +++ /dev/null @@ -1,107 +0,0 @@ -from newickparser import Newick_Parser -import re - -MAX_READLINES = 200000 - - -class Nexus_Parser(Newick_Parser): - - def __init__(self): - super(Nexus_Parser, self).__init__() - - def parseFile(self, filePath): - """passes a file and extracts its Nexus content.""" - return self.parseNexus(filePath) - - - def parseNexus(self, filename): - """ Nexus data is stored in blocks between a line starting with begin and another line starting with end; - Commends inside square brackets are to be ignored, - For more information: http://wiki.christophchamp.com/index.php/NEXUS_file_format - Nexus can store multiple trees - """ - - with open( filename, "rt") as nex_file: - nexlines = nex_file.readlines() - - rowCount = 0 - inTreeBlock = False # sentinel to check if we are in a tree block - intranslateBlock = False # sentinel to check if we are in the translate region of the tree. Stores synonyms of the labellings - self.inCommentBlock = False - self.nameMapping = None # stores mapping representation used in nexus format - treeNames = [] - - for line in nexlines: - line = line.replace(";\n", "") - lline = line.lower() - - if rowCount > MAX_READLINES or (not nex_file) : - break - rowCount +=1 - # We are only interested in the tree block. - if "begin" in lline and "tree" in lline and not inTreeBlock: - inTreeBlock = True - continue - if inTreeBlock and "end" in lline[:3]: - inTreeBlock, currPhyloTree = False, None - continue - - if inTreeBlock: - - if "title" in lline: # Adding title to the tree - titleLoc = lline.find("title") - title = line[titleLoc + 5:].replace(" ", "") - - continue - - if "translate" in lline: - intranslateBlock = True - self.nameMapping = {} - continue - - if intranslateBlock: - mappingLine = self.splitLinebyWhitespaces(line) - key, value = mappingLine[1], mappingLine[2].replace(",", "").replace("'","") #replacing illegal json characters - self.nameMapping[key] = value - - # Extracting newick Trees - if "tree" in lline: - intranslateBlock = False - - treeLineCols = self.splitLinebyWhitespaces(line) - treeName, newick = treeLineCols[2], treeLineCols[-1] - - if newick == "": # Empty lines can be found in tree blocks - continue - - currPhyloTree = self._parseNewickToJson(newick, treeName, nameMap=self.nameMapping) - - self.phyloTrees.append(currPhyloTree) - treeIndex = len(self.phyloTrees) - 1 - treeNames.append( (treeName, treeIndex) ) # appending name of tree, and its index - continue - - return self.phyloTrees, treeNames - - - def splitLinebyWhitespaces(self, line): - """replace tabs and write spaces to a single write space, so we can properly split it.""" - return re.split(r"\s+", line) - - - def checkComments(self, line): - """Check to see if the line/lines is a comment.""" - if not self.inCommentBlock: - if "[" in line: - if "]" not in line: - self.inCommentBlock = True - else: - return "Nextline" # need to move on to the nextline after getting out of comment - else : - if "]" in line: - if line.rfind("[") > line.rfind("]"): - pass # a comment block is closed but another is open. - else: - self.inCommentBlock = False - return "Nextline" # need to move on to the nextline after getting out of comment - return "" \ No newline at end of file diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- a/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py +++ /dev/null @@ -1,36 +0,0 @@ -from newickparser import Newick_Parser -from nexusparser import Nexus_Parser -from phyloxmlparser import Phyloxml_Parser -from galaxy.visualization.data_providers.basic import BaseDataProvider - -class Phyloviz_DataProvider( BaseDataProvider ): - - def __init__( self, original_dataset=None ): - super( BaseDataProvider, self ).__init__( original_dataset=original_dataset ) - - def get_data( self, **kwargs ): - """returns [trees], meta - Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus - """ - jsonDicts, meta = [], {} - try: - if fileExt == "nhx": # parses newick files - newickParser = Newick_Parser() - jsonDicts, parseMsg = newickParser.parseFile(filepath) - elif fileExt == "phyloxml": # parses phyloXML files - phyloxmlParser = Phyloxml_Parser() - jsonDicts, parseMsg = phyloxmlParser.parseFile(filepath) - elif fileExt == "nex": # parses nexus files - nexusParser = Nexus_Parser() - jsonDicts, parseMsg = nexusParser.parseFile(filepath) - meta["trees"] = parseMsg - else: - raise Exception("File type is not supported") - - meta["msg"] = parseMsg - - except Exception: - jsonDicts, meta["msg"] = [], "Parse failed" - - return jsonDicts, meta - diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/visualization/phyloviz/phyloxmlparser.py --- a/lib/galaxy/visualization/phyloviz/phyloxmlparser.py +++ /dev/null @@ -1,134 +0,0 @@ -from baseparser import Base_Parser, PhyloTree, Node -from xml.etree import ElementTree - -class Phyloxml_Parser(Base_Parser): - """Parses a phyloxml file into a json file that will be passed to PhyloViz for display""" - - def __init__(self): - super(Phyloxml_Parser, self).__init__() - self.phyloTree = PhyloTree() - self.tagsOfInterest = { - "clade": "", - "name" : "name", - "branch_length" : "length", - "confidence" : "bootstrap", - "events" : "events" - } - - def parseFile(self, filePath): - """passes a file and extracts its Phylogeny Tree content.""" - phyloXmlFile = open(filePath, "r") - - xmlTree = ElementTree.parse(phyloXmlFile) - xmlRoot = xmlTree.getroot()[0] - self.nameSpaceIndex = xmlRoot.tag.rfind("}") + 1 # used later by the clean tag method to remove the name space in every element.tag - - phyloRoot = None - for child in xmlRoot: - childTag = self.cleanTag(child.tag) - if childTag == "clade": - phyloRoot = child - elif childTag == "name": - self.phyloTree.title = child.text - - self.phyloTree.root = self.parseNode(phyloRoot, 0) - jsonDict = self.phyloTree.generateJsonableDict() - return [jsonDict], "Success" - - - def parseNode(self, node, depth): - """Parses any node within a phyloxml tree and looks out for claude, which signals the creation of - nodes - internal OR leaf""" - assert isinstance(node, etree._Element) - - tag = self.cleanTag(node.tag) - if not tag == "clade": - return None - hasInnerClade = False - - # peeking once for parent and once for child to check if the node is internal - for child in node: - childTag = self.cleanTag(child.tag) - if childTag == "clade": - hasInnerClade = True - break - - if hasInnerClade: # this node is an internal node - currentNode = self._makeInternalNode(node, depth= depth) - for child in node: - child = self.parseNode(child, depth + 1) - if isinstance(child, Node): - currentNode.addChildNode(child) - - else: # this node is a leaf node - currentNode = self._makeLeafNode(node, depth=depth+1) - - return currentNode - - - def _makeLeafNode(self, leafNode, depth = 0 ): - """Makes leaf nodes by calling Phylotree methods""" - node = {} - for child in leafNode: - childTag = self.cleanTag(child.tag) - if childTag in self.tagsOfInterest: - key = self.tagsOfInterest[childTag] # need to map phyloxml terms to ours - node[key] = child.text - - node["depth"] = depth - return self.phyloTree.makeNode(self._getNodeName(leafNode), **node) - - def _getNodeName(self, node, depth=-1): - """Gets the name of a claude. It handles the case where a taxonomy node is involved""" - - def getTagFromTaxonomyNode(node): - """Returns the name of a taxonomy node. A taxonomy node have to be treated differently as the name - is embedded one level deeper""" - phyloxmlTaxoNames = { - "common_name" : "", - "scientific_name" : "", - "code" : "" - } - for child in node: - childTag = self.cleanTag(child.tag) - if childTag in phyloxmlTaxoNames: - return child.text - return "" - - nodeName = "" - for child in node: - childTag = self.cleanTag(child.tag) - if childTag == "name" : - nodeName = child.text - break - elif childTag == "taxonomy": - nodeName = getTagFromTaxonomyNode(child) - break - - return nodeName - - - def _makeInternalNode(self, internalNode, depth=0): - """ Makes an internal node from an element object that is guranteed to be a parent node. - Gets the value of interests like events and appends it to a custom node object that will be passed to PhyloTree to make nodes - """ - node = {} - for child in internalNode: - childTag = self.cleanTag(child.tag) - if childTag == "clade": - continue - elif childTag in self.tagsOfInterest: - if childTag == "events": # events is nested 1 more level deeper than others - key, text = "events", self.cleanTag(child[0].tag) - else: - key = self.tagsOfInterest[childTag] - text = child.text - node[key] = text - - - return self.phyloTree.makeNode(self._getNodeName(internalNode, depth), **node) - - - def cleanTag(self, tagString): - return tagString[self.nameSpaceIndex:] - \ No newline at end of file diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/webapps/galaxy/controllers/phyloviz.py --- a/lib/galaxy/webapps/galaxy/controllers/phyloviz.py +++ /dev/null @@ -1,97 +0,0 @@ -import pkg_resources -pkg_resources.require( "bx-python" ) - -from galaxy.util.json import to_json_string, from_json_string -from galaxy.web.base.controller import * -from galaxy.visualization.phyloviz.phyloviz_dataprovider import Phyloviz_DataProvider - - -class PhyloVizController( BaseUIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin, SharableMixin ): - """ - Controller for phyloViz browser interface. - """ - def __init__(self, app ): - BaseUIController.__init__( self, app ) - - @web.expose - @web.require_login() - def index( self, trans, dataset_id = None, **kwargs ): - """ - The index method is called using phyloviz/ with a dataset id passed in. - The relevant data set is then retrieved via get_json_from_datasetId which interfaces with the parser - The json representation of the phylogenetic tree along with the config is then written in the .mako template and passed back to the user - """ - json, config = self.get_json_from_datasetId(trans, dataset_id) - config["saved_visualization"] = False - return trans.fill_template( "visualization/phyloviz.mako", data = json, config=config) - - - @web.expose - def visualization(self, trans, id): - """ - Called using a viz_id (id) to retrieved stored visualization data (in json format) and all the viz_config - """ - viz = self.get_visualization(trans, id) - config = self.get_visualization_config(trans, viz) - config["saved_visualization"] = True - data = config["root"] - - return trans.fill_template( "visualization/phyloviz.mako", data = data, config=config) - - - @web.expose - @web.json - def load_visualization_json(self, trans, viz_id): - """ - Though not used in current implementation, this provides user with a convenient method to retrieve the viz_data & viz_config via json. - """ - viz = self.get_visualization(trans, viz_id) - viz_config = self.get_visualization_config(trans, viz) - viz_config["saved_visualization"] = True - return { - "data" : viz_config["root"], - "config" : viz_config - } - - - @web.expose - @web.json - def getJsonData(self, trans, dataset_id, treeIndex=0): - """ - Method to retrieve data asynchronously via json format. Retriving from here rather than - making a direct datasets/ call allows for some processing and event capturing - """ - treeIndex = int(treeIndex) - json, config = self.get_json_from_datasetId(trans, dataset_id, treeIndex) - packedJson = { - "data" : json, - "config" : config - } - - return packedJson - - - def get_json_from_datasetId(self, trans, dataset_id, treeIndex=0): - """ - For interfacing phyloviz controllers with phyloviz visualization data provider (parsers) - """ - dataset = self.get_dataset(trans, dataset_id) - fileExt, filepath = dataset.ext, dataset.file_name # .name stores the name of the dataset from the orginal upload - json, config = "", {} # config contains properties of the tree and file - - if fileExt == "json": - something, json = self.get_data(dataset) - else: - try: - pd = Phyloviz_DataProvider() - json, config = pd.get_data(filepath, fileExt) - json = json[treeIndex] - except Exception: - pass - - config["title"] = dataset.display_name() - config["ext"] = fileExt - config["dataset_id"] = dataset_id - config["treeIndex"] = treeIndex - - return json, config diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -7,7 +7,7 @@ from galaxy.util.sanitize_html import sanitize_html from galaxy.visualization.genomes import decode_dbkey from galaxy.visualization.genome.visual_analytics import get_dataset_job -from galaxy.visualization.data_providers.basic import ColumnDataProvider +from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider from .library import LibraryListGrid @@ -824,6 +824,25 @@ historyID=history_id, kwargs=kwargs ) + @web.expose + def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ): + # Get HDA. + hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) + + # Get data. + pd = PhylovizDataProvider( original_dataset=hda ) + json, config = pd.get_data() + json = json[tree_index] + + config["title"] = hda.display_name() + config["ext"] = hda.datatype.file_ext + config["dataset_id"] = dataset_id + config["treeIndex"] = tree_index + config["saved_visualization"] = False + + # Return viz. + return trans.fill_template_mako( "visualization/phyloviz.mako", data = json, config=config ) + @web.json def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): if hda_id: diff -r 569f7d07801074a4e5207493afe72354ccb8d3ad -r 6f9ce8692bb6aae38d720abd489f8e0edfd5f8c3 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -229,8 +229,8 @@ visualizations = data.get_visualizations() ## HACK: if there are visualizations, only provide trackster for now ## since others are not ready. - comment out to see all WIP visualizations - if visualizations: - visualizations = [ vis for vis in visualizations if vis in [ 'trackster' ] ] + #if visualizations: + # visualizations = [ vis for vis in visualizations if vis in [ 'trackster' ] ] %> %if visualizations: <a href="${h.url_for( controller='visualization' )}" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Refactor PhyloViz components to work in new visualization framework and add sniffers for datatypes.
by Bitbucket 04 Oct '12

04 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/569f7d078010/ changeset: 569f7d078010 user: jgoecks date: 2012-10-04 15:11:04 summary: Refactor PhyloViz components to work in new visualization framework and add sniffers for datatypes. affected #: 6 files diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r 569f7d07801074a4e5207493afe72354ccb8d3ad datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -252,6 +252,7 @@ <sniffer type="galaxy.datatypes.binary:TwoBit"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/> + <sniffer type="galaxy.datatypes.xml:Phyloxml"/><sniffer type="galaxy.datatypes.xml:GenericXml"/><sniffer type="galaxy.datatypes.sequence:Maf"/><sniffer type="galaxy.datatypes.sequence:Lav"/> @@ -272,6 +273,8 @@ <sniffer type="galaxy.datatypes.tabular:Pileup"/><sniffer type="galaxy.datatypes.interval:Interval"/><sniffer type="galaxy.datatypes.tabular:Sam"/> + <sniffer type="galaxy.datatypes.data:Newick"/> + <sniffer type="galaxy.datatypes.data:Nexus"/><sniffer type="galaxy.datatypes.images:Jpg"/><sniffer type="galaxy.datatypes.images:Png"/><sniffer type="galaxy.datatypes.images:Tiff"/> diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r 569f7d07801074a4e5207493afe72354ccb8d3ad lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -734,38 +734,39 @@ """New Hampshire/Newick Format""" file_ext = "nhx" - MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True ) - def __init__(self, **kwd): """Initialize foobar datatype""" - Text.__init__(self, **kwd) + Text.__init__( self, **kwd ) def init_meta( self, dataset, copy_from=None ): Text.init_meta( self, dataset, copy_from=copy_from ) - def sniff( self, filename ): """ Returning false as the newick format is too general and cannot be sniffed.""" return False + def get_visualizations( self, dataset ): + """ + Returns a list of visualizations for datatype. + """ + + return [ 'phyloviz' ] + class Nexus( Text ): """Nexus format as used By Paup, Mr Bayes, etc""" file_ext = "nex" - MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True ) - def __init__(self, **kwd): """Initialize foobar datatype""" - Text.__init__(self, **kwd) + Text.__init__( self, **kwd ) def init_meta( self, dataset, copy_from=None ): Text.init_meta( self, dataset, copy_from=copy_from ) - def sniff( self, filename ): """All Nexus Files Simply puts a '#NEXUS' in its first line""" - f = open(filename, "r") + f = open( filename, "r" ) firstline = f.readline().upper() f.close() @@ -774,6 +775,13 @@ else: return False + def get_visualizations( self, dataset ): + """ + Returns a list of visualizations for datatype. + """ + + return [ 'phyloviz' ] + # ------------- Utility methods -------------- diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r 569f7d07801074a4e5207493afe72354ccb8d3ad lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -91,9 +91,18 @@ def sniff( self, filename ): """"Checking for keyword - 'phyloxml' always in lowercase in the first few lines""" - f = open(filename, "r") - firstlines = "".join(f.readlines(5)) + + f = open( filename, "r" ) + firstlines = "".join( f.readlines(5) ) f.close() + if "phyloxml" in firstlines: return True - return False \ No newline at end of file + return False + + def get_visualizations( self, dataset ): + """ + Returns a list of visualizations for datatype. + """ + + return [ 'phyloviz' ] \ No newline at end of file diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r 569f7d07801074a4e5207493afe72354ccb8d3ad lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- a/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -3,15 +3,12 @@ from phyloxmlparser import Phyloxml_Parser from galaxy.visualization.data_providers.basic import BaseDataProvider -# TODO: bring this class into line with BaseDataProvider by -# using BaseDataProvider.init() and providing original dataset -# and then reading from dataset rather than filepath. class Phyloviz_DataProvider( BaseDataProvider ): - def __init__( self ): - pass + def __init__( self, original_dataset=None ): + super( BaseDataProvider, self ).__init__( original_dataset=original_dataset ) - def get_data( self, filepath, fileExt ): + def get_data( self, **kwargs ): """returns [trees], meta Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus """ diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r 569f7d07801074a4e5207493afe72354ccb8d3ad templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -388,17 +388,6 @@ _.each( $(".visualize-icon"), function(icon) { init_viz_icon(icon); }); - - function init_phyloviz_links() { - // PhyloViz links - // Add to trackster browser functionality - $(".phyloviz-add").live("click", function() { - var dataset = this, - dataset_jquery = $(this); - window.parent.location = dataset_jquery.attr("new-url"); - }); - } - init_phyloviz_links(); // History rename functionality. async_save_text("history-name-container", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r 569f7d07801074a4e5207493afe72354ccb8d3ad templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -29,9 +29,6 @@ ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True, display_structured = False )"><% - - from galaxy.datatypes.xml import Phyloxml - from galaxy.datatypes.data import Newick, Nexus dataset_id = trans.security.encode_id( data.id ) if data.state in ['no state','',None]: @@ -245,14 +242,6 @@ %endif visualizations="${','.join(visualizations)}"></a> %endif - <% - isPhylogenyData = isinstance(data.datatype, (Phyloxml, Nexus, Newick)) - %> - %if isPhylogenyData: - <a href="javascript:void(0)" class="icon-button chart_curve phyloviz-add" - action-url="${h.url_for( controller='phyloviz', action='-', dataset_id=dataset_id)}" - new-url="${h.url_for( controller='phyloviz', action='index', dataset_id=dataset_id)}" title="View in Phyloviz"></a> - %endif %if trans.user: %if not display_structured: <div style="float: right"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix issues with genomes API: handle periods in keys, fix typo, and list genomes when querying.
by Bitbucket 03 Oct '12

03 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e8fc8e57dadc/ changeset: e8fc8e57dadc user: jgoecks date: 2012-10-03 23:49:30 summary: Fix issues with genomes API: handle periods in keys, fix typo, and list genomes when querying. affected #: 2 files diff -r f78de6cddd0f240aede5f02911379db7102981e2 -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -236,7 +236,7 @@ if not len_ds: genome = self.genomes[ dbkey ] else: - gneome = Genome( dbkey, len_file=len_ds.file_name ) + genome = Genome( dbkey, len_file=len_ds.file_name ) return genome.to_dict( num=num, chrom=chrom, low=low ) diff -r f78de6cddd0f240aede5f02911379db7102981e2 -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -5,6 +5,12 @@ def is_true ( a_str ): return is_true == True or a_str in [ 'True', 'true', 'T', 't' ] +def get_id( base, format ): + if format: + return "%s.%s" % ( base, format ) + else: + return base + class GenomesController( BaseAPIController ): """ RESTful controller for interactions with genome data. @@ -16,7 +22,7 @@ GET /api/genomes: returns a list of installed genomes """ - return [] + return self.app.genomes.get_dbkeys_with_chrom_info( trans ) @web.json def show( self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ): @@ -27,6 +33,7 @@ """ # Process kwds. + id = get_id( id, kwd.get( 'format', None ) ) reference = is_true( kwd.get( 'reference', False ) ) # Return info. 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: smcmanus: Added tool exit code to the UI. Modified stdout, stderr, and exit_code retrieval to reference same method.
by Bitbucket 03 Oct '12

03 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f78de6cddd0f/ changeset: f78de6cddd0f user: smcmanus date: 2012-10-03 23:07:40 summary: Added tool exit code to the UI. Modified stdout, stderr, and exit_code retrieval to reference same method. affected #: 2 files diff -r e4e1c621b025b4f0b09846e9d4410d2630394470 -r f78de6cddd0f240aede5f02911379db7102981e2 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -154,12 +154,24 @@ stored_list_grid = HistoryDatasetAssociationListGrid() + def _get_job_for_dataset( self, trans, dataset_id ): + ''' + Return the job for the given dataset. This will throw an error if the + dataset is either nonexistent or inaccessible to the user. This looks + up the job by mapping the dataset to an HDA and then mapping the HDA + to its job. This will throw exceptions so that the caller can determine + the appropriate response. + ''' + hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + return hda.creating_job_associations[0].job + @web.expose def errors( self, trans, id ): hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) return trans.fill_template( "dataset/errors.mako", hda=hda ) @web.expose - def stdout( self, trans, dataset_id=None, **kwargs ): + def stdoutX( self, trans, dataset_id=None, **kwargs ): trans.response.set_content_type( 'text/plain' ) try: hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) @@ -168,16 +180,40 @@ except: return "Invalid dataset ID or you are not allowed to access this dataset" return job.stdout + @web.expose + def stdout( self, trans, dataset_id=None, **kwargs ): + trans.response.set_content_type( 'text/plain' ) + stdout = "" + try: + job = self._get_job_for_dataset( trans, dataset_id ) + stdout = job.stdout + except: + stdout = "Invalid dataset ID or you are not allowed to access this dataset" + return stdout + + @web.expose + # TODO: Migrate stderr and stdout to use _get_job_for_dataset; it wasn't tested. def stderr( self, trans, dataset_id=None, **kwargs ): trans.response.set_content_type( 'text/plain' ) + stderr = "" try: - hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) - job = hda.creating_job_associations[0].job + job = self._get_job_for_dataset( trans, dataset_id ) + stderr = job.stderr except: - return "Invalid dataset ID or you are not allowed to access this dataset" - return job.stderr + stderr = "Invalid dataset ID or you are not allowed to access this dataset" + return stderr + + @web.expose + def exit_code( self, trans, dataset_id=None, **kwargs ): + trans.response.set_content_type( 'text/plain' ) + exit_code = "" + try: + job = _get_job_for_dataset( dataset_id ) + exit_code = job.exit_code + except: + exit_code = "Invalid dataset ID or you are not allowed to access this dataset" + return exit_code @web.expose def report_error( self, trans, id, email='', message="" ): smtp_server = trans.app.config.smtp_server @@ -986,7 +1022,7 @@ pass inherit_chain = source_dataset_chain(hda, []) - return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, tool=tool, params_objects=params_objects ) + return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects ) @web.expose def copy_datasets( self, trans, source_history=None, source_dataset_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): diff -r e4e1c621b025b4f0b09846e9d4410d2630394470 -r f78de6cddd0f240aede5f02911379db7102981e2 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -60,6 +60,7 @@ <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr><tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr><tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr> + <tr><td>Tool Exit Code:</td><td>${job.exit_code}</td></tr> %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name}</td></tr> %endif 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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