- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2683: (1) Unicode support for tagging and (2) added ...
by Greg Von Kuster 15 Sep '09

15 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/032478337b82 changeset: 2683:032478337b82 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Sep 11 14:57:02 2009 -0400 description: (1) Unicode support for tagging and (2) added tagging_common mako file to support creation and standardization of tagging elements across all pages. 9 file(s) affected in this change: lib/galaxy/web/controllers/history.py lib/galaxy/web/controllers/tag.py static/scripts/autocomplete_tagging.js static/scripts/packed/autocomplete_tagging.js templates/dataset/edit_attributes.mako templates/history/grid.mako templates/root/history.mako templates/tagging_common.mako tool_conf.xml.main diffs (781 lines): diff -r ed4cbaf23c88 -r 032478337b82 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Sep 11 09:00:36 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Sep 11 14:57:02 2009 -0400 @@ -38,6 +38,17 @@ if item.users_shared_with or item.importable: return dict( operation="sharing" ) return None + class TagsColumn( grids.GridColumn ): + def __init__(self, col_name): + grids.GridColumn.__init__(self, col_name) + self.tag_elt_id_gen = 0 + + def get_value( self, trans, grid, history ): + self.tag_elt_id_gen += 1 + return trans.fill_template( "/tagging_common.mako", trans=trans, + tagged_item=history, + elt_id="tagging-elt" + str(self.tag_elt_id_gen) ) + # Grid definition title = "Stored histories" model_class = model.History @@ -48,6 +59,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="switch", id=item.id ) ) ), attach_popup=True ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), + #TagsColumn( "Tags" ), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), diff -r ed4cbaf23c88 -r 032478337b82 lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Fri Sep 11 09:00:36 2009 -0400 +++ b/lib/galaxy/web/controllers/tag.py Fri Sep 11 14:57:02 2009 -0400 @@ -4,7 +4,6 @@ from galaxy.model import History, HistoryTagAssociation, Dataset, DatasetTagAssociation, \ HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation, Page, PageTagAssociation - from galaxy.web.base.controller import * from galaxy.tags.tag_handler import * from sqlalchemy.sql.expression import func, and_ @@ -15,65 +14,68 @@ def __init__(self, app): BaseController.__init__(self, app) - # Set up dict for mapping from short-hand to full item class. - self.shorthand_to_item_class_dict = dict() - self.shorthand_to_item_class_dict["history"] = History - self.shorthand_to_item_class_dict["hda"] = HistoryDatasetAssociation + # Keep a list of taggable classes. + self.taggable_classes = dict() + self.taggable_classes[History.__name__] = History + self.taggable_classes[HistoryDatasetAssociation.__name__] = HistoryDatasetAssociation + self.taggable_classes[Page.__name__] = Page - # Set up tag handler to recognize the following items: History, HistoryDatasetAssociation, ... + # Set up tag handler to recognize the following items: History, HistoryDatasetAssociation, Page, ... self.tag_handler = TagHandler() self.tag_handler.add_tag_assoc_class(History, HistoryTagAssociation) self.tag_handler.add_tag_assoc_class(HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation) - + self.tag_handler.add_tag_assoc_class(Page, PageTagAssociation) + @web.expose - def add_tag_async( self, trans, id=None, item_type=None, new_tag=None ): + @web.require_login( "Add tag to an item." ) + def add_tag_async( self, trans, id=None, item_class=None, new_tag=None ): """ Add tag to an item. """ - item = self._get_item(trans, item_type, trans.security.decode_id(id)) + item = self._get_item(trans, item_class, trans.security.decode_id(id)) self._do_security_check(trans, item) - self.tag_handler.apply_item_tags(trans.sa_session, item, new_tag) + self.tag_handler.apply_item_tags( trans.sa_session, item, unicode(new_tag).encode('utf-8') ) trans.sa_session.flush() @web.expose - def remove_tag_async( self, trans, id=None, item_type=None, tag_name=None ): + @web.require_login( "Remove tag from an item." ) + def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None ): """ Remove tag from an item. """ - item = self._get_item(trans, item_type, trans.security.decode_id(id)) + item = self._get_item(trans, item_class, trans.security.decode_id(id)) self._do_security_check(trans, item) - self.tag_handler.remove_item_tag(item, tag_name) + self.tag_handler.remove_item_tag( item, unicode(tag_name).encode('utf-8') ) + #print tag_name + #print unicode(tag_name) trans.sa_session.flush() # Retag an item. All previous tags are deleted and new tags are applied. @web.expose - def retag_async( self, trans, id=None, item_type=None, new_tags=None ): + @web.require_login( "Apply a new set of tags to an item; previous tags are deleted." ) + def retag_async( self, trans, id=None, item_class=None, new_tags=None ): """ Apply a new set of tags to an item; previous tags are deleted. """ - item = self._get_item(trans, item_type, trans.security.decode_id(id)) + item = self._get_item(trans, item_class, trans.security.decode_id(id)) self._do_security_check(trans, item) tag_handler.delete_item_tags(item) - self.tag_handler.apply_item_tags(trans.sa_session, item, new_tag) + self.tag_handler.apply_item_tags( trans.sa_session, item, unicode(new_tags).encode('utf-8') ) trans.sa_session.flush() - - tag_handler.delete_item_tags(history) - tag_handler.apply_item_tags(trans.sa_session, history, new_tags) - # Flush to complete changes. - trans.sa_session.flush() - + @web.expose @web.require_login( "get autocomplete data for an item's tags" ) - def tag_autocomplete_data(self, trans, id=None, item_type=None, q=None, limit=None, timestamp=None): + def tag_autocomplete_data(self, trans, id=None, item_class=None, q=None, limit=None, timestamp=None): """ Get autocomplete data for an item's tags. """ # # Get item, do security check, and get autocomplete data. # - item = self._get_item(trans, item_type, trans.security.decode_id(id)) + item = self._get_item(trans, item_class, trans.security.decode_id(id)) self._do_security_check(trans, item) + q = unicode(q).encode('utf-8') if q.find(":") == -1: return self._get_tag_autocomplete_names(trans, item, q, limit, timestamp) else: @@ -184,9 +186,9 @@ # Use the user_id associated with the HDA's history. return History.table.c.user_id - def _get_item(self, trans, item_type, id): + def _get_item(self, trans, item_class_name, id): """ Get an item based on type and id. """ - item_class = self.shorthand_to_item_class_dict[item_type] + item_class = self.taggable_classes[item_class_name] item = trans.sa_session.query(item_class).filter("id=" + str(id))[0] return item; diff -r ed4cbaf23c88 -r 032478337b82 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Fri Sep 11 09:00:36 2009 -0400 +++ b/static/scripts/autocomplete_tagging.js Fri Sep 11 14:57:02 2009 -0400 @@ -187,13 +187,14 @@ // Tag button is image's parent. var tag_button = $(this).parent(); - // Get tag name. + // Get tag name, value. var tag_name_elt = tag_button.find(".tag-name").eq(0); var tag_str = tag_name_elt.text(); - var tag_name = get_tag_name_and_value(tag_str)[0]; + var tag_name_and_value = get_tag_name_and_value(tag_str); + var tag_name = tag_name_and_value[0]; + var tag_value = tag_name_and_value[1]; - // TODO: should remove succeed if tag is not already applied to - // history? + var prev_button = tag_button.prev(); tag_button.remove(); // Remove tag from local list for consistency. @@ -209,12 +210,28 @@ data: { tag_name: tag_name }, error: function() { - // Failed. - alert( "Remove tag failed" ); + // Failed. Roll back changes and show alert. + settings.tags[tag_name] = tag_value; + if (prev_button.hasClass("tag-button")) + prev_button.after(tag_button); + else + tag_area.prepend(tag_button); + var new_text = settings.get_toggle_link_text_fn(settings.tags); + alert( "Remove tag failed" ); + + toggle_link.text(new_text); + + // TODO: no idea why it's necessary to set this up again. + delete_img.mouseenter( function () + { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + delete_img.mouseleave( function () + { + $(this).attr("src", settings.delete_tag_img); + }); }, - success: function() - { - } + success: function() {} }); return true; @@ -323,8 +340,9 @@ data: { new_tag: new_value }, error: function() { - // Remove tag and show alert. + // Failed. Roll back changes and show alert. new_tag_button.remove(); + delete settings.tags[tag_name_and_value[0]]; var new_text = settings.get_toggle_link_text_fn(settings.tags); toggle_link.text(new_text); alert( "Add tag failed" ); diff -r ed4cbaf23c88 -r 032478337b82 static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Fri Sep 11 09:00:36 2009 -0400 +++ b/static/scripts/packed/autocomplete_tagging.js Fri Sep 11 14:57:02 2009 -0400 @@ -1,1 +1,1 @@ -var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u){},input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div></div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>"+u+"</a>").addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};var s=b(); if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var B=$(this).parent();var A=B.find(".tag-name").eq(0);var z=A.text();var C=h(z)[0];B.remove();delete p.tags[C];var y=p.get_toggle_link_text_fn(p.tags);s.text(y);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:C},error:function(){alert("Remove tag failed")},success:function(){}});return true});var w=$("<span>"+u+" </span>").addClass("tag-name");w.click(function(){p.tag_click_fn(u);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);x.append(v);return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+v+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+v+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag -button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,formatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClas s("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false});if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file +var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u){},input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div></div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>"+u+"</a>").addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};var s=b(); if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E.after(D) }else{m.prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>"+u+"</span>").addClass("tag-name");w.click(function(){p.tag_click_fn(u);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);x.append(v);return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+v+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+v+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){thi s.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,formatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input ");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false});if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file diff -r ed4cbaf23c88 -r 032478337b82 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Fri Sep 11 09:00:36 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Fri Sep 11 14:57:02 2009 -0400 @@ -9,43 +9,8 @@ <% user, user_roles = trans.get_user_and_roles() %> <%def name="javascripts()"> - ##  - ${h.js( "jquery", "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> - $( document ).ready( function() { - // Set up autocomplete tagger. -<% - ## Build string of tag name, values. - tag_names_and_values = list() - for tag in data.tags: - tag_name = tag.user_tname - tag_value = "" - if tag.value is not None: - tag_value = tag.user_value - tag_names_and_values.append("\"" + tag_name + "\" : \"" + tag_value + "\"") -%> - var options = { - tags : {${", ".join(tag_names_and_values)}}, - tag_click_fn: function(tag) { /* Do nothing. */ }, - use_toggle_link: false, - input_size: 30, - in_form: true, - <% encoded_data_id = trans.security.encode_id(data.id) %> - ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=encoded_data_id, item_type="hda" )}", - ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=encoded_data_id, item_type="hda" )}", - ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=encoded_data_id, item_type="hda" )}", - delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", - delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", - add_tag_img: "${h.url_for('/static/images/add_icon.png')}", - add_tag_img_rollover: "${h.url_for('/static/images/add_icon_dark.png')}", - }; -% if trans.get_user() is not None: - $("#dataset-tag-area").autocomplete_tagging(options); -% endif -}); - </script> + ${parent.javascripts()} + ${h.js( "jquery.autocomplete", "autocomplete_tagging" )} </%def> <%def name="datatype( dataset, datatypes )"> @@ -84,16 +49,18 @@ <div style="clear: both"></div> </div> %if trans.get_user() is not None: - <div class="form-row"> - <label> - Tags: - </label> - <div id="dataset-tag-area" + <%namespace file="../tagging_common.mako" import="render_tagging_element" /> + <div class="form-row"> + <label> + Tags: + </label> + <div id="dataset-tag-area" style="float: left; margin-left: 1px; width: 295px; margin-right: 10px; border-style: inset; border-color: #ddd; border-width: 1px"> - </div> - <div style="clear: both"></div> - </div> - %endif + </div> + <div style="clear: both"></div> + </div> + ${render_tagging_element(data, "dataset-tag-area", use_toggle_link="false", in_form="true", input_size="30")} + %endif %for name, spec in data.metadata.spec.items(): %if spec.visible: <div class="form-row"> diff -r ed4cbaf23c88 -r 032478337b82 templates/history/grid.mako --- a/templates/history/grid.mako Fri Sep 11 09:00:36 2009 -0400 +++ b/templates/history/grid.mako Fri Sep 11 14:57:02 2009 -0400 @@ -10,6 +10,7 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${h.js("jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> ## TODO: generalize and move into galaxy.base.js $(document).ready(function() { @@ -58,7 +59,7 @@ </%def> <%def name="stylesheets()"> - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + ${h.css( "base", "autocomplete_tagging" )} <style> ## Not generic to all grids -- move to base? .count-box { diff -r ed4cbaf23c88 -r 032478337b82 templates/root/history.mako --- a/templates/root/history.mako Fri Sep 11 09:00:36 2009 -0400 +++ b/templates/root/history.mako Fri Sep 11 14:57:02 2009 -0400 @@ -77,83 +77,6 @@ <% updateable = [data for data in reversed( datasets ) if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]] %> ${ ",".join( map(lambda data: "\"%s\" : \"%s\"" % (data.id, data.state), updateable) ) } }); - - // Set up autocomplete tagger. -<% - ## Build string of tag name, values. - tag_names_and_values = list() - for tag in history.tags: - tag_name = tag.user_tname - tag_value = "" - if tag.value is not None: - tag_value = tag.user_value - tag_names_and_values.append("\"" + tag_name + "\" : \"" + tag_value + "\"") -%> - // Returns the number of keys (elements) in an array/dictionary. - var array_length = function(an_array) - { - if (an_array.length) - return an_array.length; - - var count = 0; - for (element in an_array) - count++; - return count; - }; - - // Function get text to display on the toggle link. - var get_toggle_link_text = function(tags) - { - var text = ""; - var num_tags = array_length(tags); - if (num_tags != 0) { - text = num_tags + (num_tags != 1 ? " Tags" : " Tag"); - /* - // Show first N tags; hide the rest. - var max_to_show = 1; - - // Build tag string. - var tag_strs = new Array(); - var count = 0; - for (tag_name in tags) - { - tag_value = tags[tag_name]; - tag_strs[tag_strs.length] = build_tag_str(tag_name, tag_value); - if (++count == max_to_show) - break; - } - tag_str = tag_strs.join(", "); - - // Finalize text. - var num_tags_hiding = num_tags - max_to_show; - text = "Tags: " + tag_str + - (num_tags_hiding != 0 ? " and " + num_tags_hiding + " more" : ""); - */ - } else { - // No tags. - text = "Add tags to this history"; - } - return text; - }; - - var options = { - tags : {${", ".join(tag_names_and_values)}}, - get_toggle_link_text_fn: get_toggle_link_text, - input_size: 15, - tag_click_fn: function(tag) { /* Do nothing. */ }, - <% encoded_history_id = trans.security.encode_id(history.id) %> - ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=encoded_history_id, item_type="history" )}", - ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=encoded_history_id, item_type="history" )}", - ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=encoded_history_id, item_type="history" )}", - delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", - delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", - add_tag_img: "${h.url_for('/static/images/add_icon.png')}", - add_tag_img_rollover: "${h.url_for('/static/images/add_icon_dark.png')}", - }; -% if trans.get_user() is not None: - $("#history-tag-area").autocomplete_tagging(options); -% endif - }); // Functionized so AJAX'd datasets can call them function initShowHide() { @@ -361,7 +284,13 @@ <div id="history-tag-area" style="margin-bottom: 1em"> </div> +<%namespace file="../tagging_common.mako" import="render_tagging_element" /> <%namespace file="history_common.mako" import="render_dataset" /> + +%if trans.get_user() is not None: + <div id='history-tag-area' class="tag-element"></div> + ${render_tagging_element(history, "history-tag-area")} +%endif %if not datasets: diff -r ed4cbaf23c88 -r 032478337b82 templates/tagging_common.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/tagging_common.mako Fri Sep 11 14:57:02 2009 -0400 @@ -0,0 +1,92 @@ +## Render the tags 'tags' as an autocomplete element. +<%def name="render_tagging_element(tagged_item, elt_id, use_toggle_link='true', in_form='false', input_size='15')"> + <script type="text/javascript"> + + // + // Set up autocomplete tagger. + // + <% + ## Build string of tag name, values. + tag_names_and_values = list() + for tag in tagged_item.tags: + tag_name = tag.user_tname + tag_value = "" + if tag.value is not None: + tag_value = tag.user_value + tag_names_and_values.append( ("\"" + tag_name + "\" : \"" + tag_value + "\"") ) + %> + // + // Returns the number of keys (elements) in an array/dictionary. + // + var array_length = function(an_array) + { + if (an_array.length) + return an_array.length; + + var count = 0; + for (element in an_array) + count++; + return count; + }; + + // + // Function get text to display on the toggle link. + // + var get_toggle_link_text = function(tags) + { + var text = ""; + var num_tags = array_length(tags); + if (num_tags != 0) + { + text = num_tags + (num_tags != 1 ? " Tags" : " Tag"); + /* + // Show first N tags; hide the rest. + var max_to_show = 1; + + // Build tag string. + var tag_strs = new Array(); + var count = 0; + for (tag_name in tags) + { + tag_value = tags[tag_name]; + tag_strs[tag_strs.length] = build_tag_str(tag_name, tag_value); + if (++count == max_to_show) + break; + } + tag_str = tag_strs.join(", "); + + // Finalize text. + var num_tags_hiding = num_tags - max_to_show; + text = "Tags: " + tag_str + + (num_tags_hiding != 0 ? " and " + num_tags_hiding + " more" : ""); + */ + } + else + { + // No tags. + text = "Add tags to history"; + } + return text; + }; + + var options = + { + tags : {${unicode(", ".join(tag_names_and_values), 'utf-8')}}, + get_toggle_link_text_fn: get_toggle_link_text, + tag_click_fn: function(tag) { /* Do nothing. */ }, + <% tagged_item_id = trans.security.encode_id(tagged_item.id) %> + ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", + delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", + add_tag_img: "${h.url_for('/static/images/add_icon.png')}", + add_tag_img_rollover: "${h.url_for('/static/images/add_icon_dark.png')}", + input_size: ${input_size}, + in_form: ${in_form}, + use_toggle_link: ${use_toggle_link} + }; + + $("#${elt_id}").autocomplete_tagging(options) + </script> +</%def> \ No newline at end of file diff -r ed4cbaf23c88 -r 032478337b82 tool_conf.xml.main --- a/tool_conf.xml.main Fri Sep 11 09:00:36 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,263 +0,0 @@ -<?xml version="1.0"?> -<toolbox> - <section name="Get Data" id="getext"> - <tool file="data_source/upload.xml"/> - <tool file="data_source/ucsc_tablebrowser.xml" /> - <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> - <tool file="data_source/microbial_import.xml" /> - <tool file="data_source/biomart.xml" /> - <tool file="data_source/gramene_mart.xml" /> - <tool file="data_source/flymine.xml" /> - <tool file="data_source/encode_db.xml" /> - <tool file="data_source/epigraph_import.xml" /> - </section> - <section name="Send Data" id="send"> - <tool file="data_destination/epigraph.xml" /> - </section> - <section name="ENCODE Tools" id="EncodeTools"> - <tool file="encode/gencode_partition.xml" /> - <tool file="encode/random_intervals.xml" /> - </section> - <section name="Lift-Over" id="liftOver"> - <tool file="extract/liftOver_wrapper.xml" /> - </section> - <section name="Text Manipulation" id="textutil"> - <tool file="filters/fixedValueColumn.xml" /> - <tool file="stats/column_maker.xml" /> - <tool file="filters/catWrapper.xml" /> - <tool file="filters/condense_characters.xml" /> - <tool file="filters/convert_characters.xml" /> - <tool file="filters/CreateInterval.xml" /> - <tool file="filters/cutWrapper.xml" /> - <tool file="filters/changeCase.xml" /> - <tool file="filters/pasteWrapper.xml" /> - <tool file="filters/remove_beginning.xml" /> - <tool file="filters/headWrapper.xml" /> - <tool file="filters/tailWrapper.xml" /> - </section> - <section name="Convert Formats" id="convert"> - <tool file="filters/bed2gff.xml" /> - <tool file="fasta_tools/fasta_to_tabular.xml" /> - <tool file="filters/gff2bed.xml" /> - <tool file="maf/maf_to_bed.xml" /> - <tool file="maf/maf_to_fasta.xml" /> - <tool file="fasta_tools/tabular_to_fasta.xml" /> - </section> - <section name="FASTA manipulation" id="fasta_manipulation"> - <tool file="fasta_tools/fasta_compute_length.xml" /> - <tool file="fasta_tools/fasta_filter_by_length.xml" /> - <tool file="fasta_tools/fasta_concatenate_by_species.xml" /> - <tool file="fasta_tools/fasta_to_tabular.xml" /> - <tool file="fasta_tools/tabular_to_fasta.xml" /> - </section> - <section name="Filter and Sort" id="filter"> - <tool file="stats/filtering.xml" /> - <tool file="filters/sorter.xml" /> - <tool file="filters/grep.xml" /> - </section> - <section name="Join, Subtract and Group" id="group"> - <tool file="filters/joiner.xml" /> - <tool file="filters/compare.xml"/> - <tool file="new_operations/subtract_query.xml"/> - <tool file="stats/grouping.xml" /> - </section> - <section name="Extract Features" id="features"> - <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> - <tool file="extract/extract_GFF_Features.xml" /> - </section> - <section name="Fetch Sequences" id="fetchSeq"> - <tool file="extract/extract_genomic_dna.xml" /> - </section> - <section name="Fetch Alignments" id="fetchAlign"> - <tool file="maf/interval2maf_pairwise.xml" /> - <tool file="maf/interval2maf.xml" /> - <tool file="maf/interval_maf_to_merged_fasta.xml" /> - <tool file="maf/genebed_maf_to_fasta.xml"/> - <tool file="maf/maf_stats.xml"/> - <tool file="maf/maf_thread_for_species.xml"/> - <tool file="maf/maf_limit_to_species.xml"/> - <tool file="maf/maf_limit_size.xml"/> - <tool file="maf/maf_by_block_number.xml"/> - <tool file="maf/maf_filter.xml"/> -  - </section> - <section name="Get Genomic Scores" id="scores"> - <tool file="stats/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - <tool file="extract/phastOdds/phastOdds_tool.xml" /> - </section> - <section name="Operate on Genomic Intervals" id="bxops"> - <tool file="new_operations/intersect.xml" /> - <tool file="new_operations/subtract.xml" /> - <tool file="new_operations/merge.xml" /> - <tool file="new_operations/concat.xml" /> - <tool file="new_operations/basecoverage.xml" /> - <tool file="new_operations/coverage.xml" /> - <tool file="new_operations/complement.xml" /> - <tool file="new_operations/cluster.xml" id="cluster" /> - <tool file="new_operations/join.xml" /> - <tool file="new_operations/get_flanks.xml" /> - <tool file="new_operations/flanking_features.xml" /> - <tool file="annotation_profiler/annotation_profiler.xml" /> - </section> - <section name="Statistics" id="stats"> - <tool file="stats/gsummary.xml" /> - <tool file="filters/uniq.xml" /> - <tool file="stats/cor.xml" /> - </section> - <section name="Graph/Display Data" id="plots"> - <tool file="plotting/histogram2.xml" /> - <tool file="plotting/scatterplot.xml" /> - <tool file="plotting/xy_plot.xml" /> - <tool file="visualization/GMAJ.xml" /> - <tool file="visualization/build_ucsc_custom_track.xml" /> - </section> - <section name="Regional Variation" id="regVar"> - <tool file="regVariation/windowSplitter.xml" /> - <tool file="regVariation/featureCounter.xml" /> - <tool file="regVariation/quality_filter.xml" /> - <tool file="regVariation/maf_cpg_filter.xml" /> - <tool file="regVariation/getIndels_2way.xml" /> - <tool file="regVariation/getIndels_3way.xml" /> - <tool file="regVariation/getIndelRates_3way.xml" /> - <tool file="regVariation/substitutions.xml" /> - <tool file="regVariation/substitution_rates.xml" /> - <tool file="regVariation/microsats_alignment_level.xml" /> - <tool file="regVariation/microsats_mutability.xml" /> - </section> - <section name="Multiple regression" id="multReg"> - <tool file="regVariation/linear_regression.xml" /> - <tool file="regVariation/best_regression_subsets.xml" /> - <tool file="regVariation/rcve.xml" /> - </section> - <section name="Evolution: HyPhy" id="hyphy"> - <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> - <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> - <tool file="hyphy/hyphy_dnds_wrapper.xml" /> - </section> - <section name="Metagenomic analyses" id="tax_manipulation"> - <tool file="taxonomy/gi2taxonomy.xml" /> - <tool file="taxonomy/t2t_report.xml" /> - <tool file="taxonomy/t2ps_wrapper.xml" /> - <tool file="taxonomy/find_diag_hits.xml" /> - <tool file="taxonomy/lca.xml" /> - <tool file="taxonomy/poisson2test.xml" /> - </section> - <section name="Short Read Analysis" id="short_read_analysis"> - <tool file="metag_tools/short_reads_figure_score.xml" /> - <tool file="metag_tools/short_reads_trim_seq.xml" /> - <tool file="metag_tools/megablast_wrapper.xml" /> - <tool file="metag_tools/megablast_xml_parser.xml" /> - </section> - <section name="EMBOSS" id="EMBOSSLite"> - <tool file="emboss_5/emboss_antigenic.xml" /> - <tool file="emboss_5/emboss_backtranseq.xml" /> - <tool file="emboss_5/emboss_banana.xml" /> - <tool file="emboss_5/emboss_biosed.xml" /> - <tool file="emboss_5/emboss_btwisted.xml" /> - <tool file="emboss_5/emboss_cai_custom.xml" /> - <tool file="emboss_5/emboss_cai.xml" /> - <tool file="emboss_5/emboss_chaos.xml" /> - <tool file="emboss_5/emboss_charge.xml" /> - <tool file="emboss_5/emboss_checktrans.xml" /> - <tool file="emboss_5/emboss_chips.xml" /> - <tool file="emboss_5/emboss_cirdna.xml" /> - <tool file="emboss_5/emboss_codcmp.xml" /> - <tool file="emboss_5/emboss_coderet.xml" /> - <tool file="emboss_5/emboss_compseq.xml" /> - <tool file="emboss_5/emboss_cpgplot.xml" /> - <tool file="emboss_5/emboss_cpgreport.xml" /> - <tool file="emboss_5/emboss_cusp.xml" /> - <tool file="emboss_5/emboss_cutseq.xml" /> - <tool file="emboss_5/emboss_dan.xml" /> - <tool file="emboss_5/emboss_degapseq.xml" /> - <tool file="emboss_5/emboss_descseq.xml" /> - <tool file="emboss_5/emboss_diffseq.xml" /> - <tool file="emboss_5/emboss_digest.xml" /> - <tool file="emboss_5/emboss_dotmatcher.xml" /> - <tool file="emboss_5/emboss_dotpath.xml" /> - <tool file="emboss_5/emboss_dottup.xml" /> - <tool file="emboss_5/emboss_dreg.xml" /> - <tool file="emboss_5/emboss_einverted.xml" /> - <tool file="emboss_5/emboss_epestfind.xml" /> - <tool file="emboss_5/emboss_equicktandem.xml" /> - <tool file="emboss_5/emboss_est2genome.xml" /> - <tool file="emboss_5/emboss_etandem.xml" /> - <tool file="emboss_5/emboss_extractfeat.xml" /> - <tool file="emboss_5/emboss_extractseq.xml" /> - <tool file="emboss_5/emboss_freak.xml" /> - <tool file="emboss_5/emboss_fuzznuc.xml" /> - <tool file="emboss_5/emboss_fuzzpro.xml" /> - <tool file="emboss_5/emboss_fuzztran.xml" /> - <tool file="emboss_5/emboss_garnier.xml" /> - <tool file="emboss_5/emboss_geecee.xml" /> - <tool file="emboss_5/emboss_getorf.xml" /> - <tool file="emboss_5/emboss_helixturnhelix.xml" /> - <tool file="emboss_5/emboss_hmoment.xml" /> - <tool file="emboss_5/emboss_iep.xml" /> - <tool file="emboss_5/emboss_infoseq.xml" /> - <tool file="emboss_5/emboss_isochore.xml" /> - <tool file="emboss_5/emboss_lindna.xml" /> - <tool file="emboss_5/emboss_marscan.xml" /> - <tool file="emboss_5/emboss_maskfeat.xml" /> - <tool file="emboss_5/emboss_maskseq.xml" /> - <tool file="emboss_5/emboss_matcher.xml" /> - <tool file="emboss_5/emboss_megamerger.xml" /> - <tool file="emboss_5/emboss_merger.xml" /> - <tool file="emboss_5/emboss_msbar.xml" /> - <tool file="emboss_5/emboss_needle.xml" /> - <tool file="emboss_5/emboss_newcpgreport.xml" /> - <tool file="emboss_5/emboss_newcpgseek.xml" /> - <tool file="emboss_5/emboss_newseq.xml" /> - <tool file="emboss_5/emboss_noreturn.xml" /> - <tool file="emboss_5/emboss_notseq.xml" /> - <tool file="emboss_5/emboss_nthseq.xml" /> - <tool file="emboss_5/emboss_octanol.xml" /> - <tool file="emboss_5/emboss_oddcomp.xml" /> - <tool file="emboss_5/emboss_palindrome.xml" /> - <tool file="emboss_5/emboss_pasteseq.xml" /> - <tool file="emboss_5/emboss_patmatdb.xml" /> - <tool file="emboss_5/emboss_pepcoil.xml" /> - <tool file="emboss_5/emboss_pepinfo.xml" /> - <tool file="emboss_5/emboss_pepnet.xml" /> - <tool file="emboss_5/emboss_pepstats.xml" /> - <tool file="emboss_5/emboss_pepwheel.xml" /> - <tool file="emboss_5/emboss_pepwindow.xml" /> - <tool file="emboss_5/emboss_pepwindowall.xml" /> - <tool file="emboss_5/emboss_plotcon.xml" /> - <tool file="emboss_5/emboss_plotorf.xml" /> - <tool file="emboss_5/emboss_polydot.xml" /> - <tool file="emboss_5/emboss_preg.xml" /> - <tool file="emboss_5/emboss_prettyplot.xml" /> - <tool file="emboss_5/emboss_prettyseq.xml" /> - <tool file="emboss_5/emboss_primersearch.xml" /> - <tool file="emboss_5/emboss_revseq.xml" /> - <tool file="emboss_5/emboss_seqmatchall.xml" /> - <tool file="emboss_5/emboss_seqret.xml" /> - <tool file="emboss_5/emboss_showfeat.xml" /> - <tool file="emboss_5/emboss_shuffleseq.xml" /> - <tool file="emboss_5/emboss_sigcleave.xml" /> - <tool file="emboss_5/emboss_sirna.xml" /> - <tool file="emboss_5/emboss_sixpack.xml" /> - <tool file="emboss_5/emboss_skipseq.xml" /> - <tool file="emboss_5/emboss_splitter.xml" /> - <tool file="emboss_5/emboss_supermatcher.xml" /> - <tool file="emboss_5/emboss_syco.xml" /> - <tool file="emboss_5/emboss_tcode.xml" /> - <tool file="emboss_5/emboss_textsearch.xml" /> - <tool file="emboss_5/emboss_tmap.xml" /> - <tool file="emboss_5/emboss_tranalign.xml" /> - <tool file="emboss_5/emboss_transeq.xml" /> - <tool file="emboss_5/emboss_trimest.xml" /> - <tool file="emboss_5/emboss_trimseq.xml" /> - <tool file="emboss_5/emboss_twofeat.xml" /> - <tool file="emboss_5/emboss_union.xml" /> - <tool file="emboss_5/emboss_vectorstrip.xml" /> - <tool file="emboss_5/emboss_water.xml" /> - <tool file="emboss_5/emboss_wobble.xml" /> - <tool file="emboss_5/emboss_wordcount.xml" /> - <tool file="emboss_5/emboss_wordmatch.xml" /> - </section> -</toolbox>

1 0

[hg] galaxy 2678: Streamline history sharing, add a "Manage shar...
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f0adb6152df9 changeset: 2678:f0adb6152df9 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Sep 10 21:24:06 2009 -0400 description: Streamline history sharing, add a "Manage shared histories" section to the History options menu. Also use a better approach to setting peek on datasets. 5 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/web/controllers/history.py templates/history/sharing.mako templates/root/index.mako test/functional/test_history_functions.py diffs (482 lines): diff -r 96ccd29277be -r f0adb6152df9 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Thu Sep 10 17:48:52 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Thu Sep 10 21:24:06 2009 -0400 @@ -416,8 +416,9 @@ count = 0 file_type = None data_checked = False - for line in file( file_name ): - line = line[:WIDTH] + temp = open( file_name, "U" ) + while count <= LINE_COUNT: + line = temp.readline( WIDTH ) if line and not is_multi_byte and not data_checked: # See if we have a compressed or binary file if line[0:2] == util.gzip_magic: @@ -432,9 +433,8 @@ if file_type in [ 'gzipped', 'binary' ]: break lines.append( line ) - if count == LINE_COUNT: - break count += 1 + temp.close() if file_type in [ 'gzipped', 'binary' ]: text = "%s file" % file_type else: diff -r 96ccd29277be -r f0adb6152df9 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Sep 10 17:48:52 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Sep 10 21:24:06 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.model.mapping import desc from galaxy.model.orm import * from galaxy.util.json import * -import webhelpers, logging +import webhelpers, logging, operator from datetime import datetime from cgi import escape @@ -31,10 +31,12 @@ return "deleted" elif history.users_shared_with: return "shared" + elif history.importable: + return "importable" return "" def get_link( self, trans, grid, item ): - if item.users_shared_with: - return dict( operation="sharing", id=item.id ) + if item.users_shared_with or item.importable: + return dict( operation="sharing" ) return None # Grid definition title = "Stored histories" @@ -55,9 +57,12 @@ operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Share", condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Unshare", condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), - grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ) + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), @@ -99,7 +104,9 @@ ] operations = [ grids.GridOperation( "Clone" ), - grids.GridOperation( "Unshare" ) + grids.GridOperation( "Unshare" ), + grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) ) ] standard_filters = [] def build_initial_query( self, session ): @@ -126,19 +133,19 @@ current_history = trans.get_history() status = message = None if 'operation' in kwargs: - history_ids = util.listify( kwargs.get( 'id', [] ) ) - histories = [] operation = kwargs['operation'].lower() if operation == "share": return self.share( trans, **kwargs ) - elif operation == "rename": + if operation == "rename": return self.rename( trans, **kwargs ) - elif operation == 'sharing': - return self.sharing( trans, id=kwargs['id'] ) + history_ids = util.listify( kwargs.get( 'id', [] ) ) + if operation == "sharing": + return self.sharing( trans, id=history_ids ) # Display no message by default status, message = None, None refresh_history = False # Load the histories and ensure they all belong to the current user + histories = [] for history_id in history_ids: history = get_history( trans, history_id ) if history: @@ -161,6 +168,21 @@ trans.template_context['refresh_frames'] = ['history'] elif operation == "undelete": status, message = self._list_undelete( trans, histories ) + elif operation == "unshare": + for history in histories: + husas = trans.app.model.HistoryUserShareAssociation.filter_by( history=history ).all() + for husa in husas: + husa.delete() + elif operation == "enable import via link": + for history in histories: + if not history.importable: + history.importable = True + elif operation == "disable import via link": + if history_ids: + histories = [ get_history( trans, history_id ) for history_id in history_ids ] + for history in histories: + if history.importable: + history.importable = False trans.sa_session.flush() # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) @@ -237,24 +259,20 @@ msg = util.restore_text( kwargs.get( 'msg', '' ) ) status = message = None if 'operation' in kwargs: - id = kwargs.get( 'id', None ) + ids = util.listify( kwargs.get( 'id', [] ) ) operation = kwargs['operation'].lower() if operation == "clone": - if not id: + if not ids: message = "Select a history to clone" return self.shared_list_grid( trans, status='error', message=message, **kwargs ) # When cloning shared histories, only copy active datasets new_kwargs = { 'clone_choice' : 'active' } return self.clone( trans, id, **new_kwargs ) elif operation == 'unshare': - if not id: + if not ids: message = "Select a history to unshare" return self.shared_list_grid( trans, status='error', message=message, **kwargs ) - ids = util.listify( id ) - histories = [] - for history_id in ids: - history = get_history( trans, history_id, check_ownership=False ) - histories.append( history ) + histories = [ get_history( trans, history_id ) for history_id in ids ] for history in histories: # Current user is the user with which the histories were shared association = trans.app.model.HistoryUserShareAssociation.filter_by( user=trans.user, history=history ).one() @@ -262,6 +280,20 @@ association.flush() message = "Unshared %d shared histories" % len( ids ) status = 'done' + elif operation == "enable import via link": + if ids: + histories = [ get_history( trans, id ) for id in ids ] + for history in histories: + if not history.importable: + history.importable = True + history.flush() + elif operation == "disable import via link": + if ids: + histories = [ get_history( trans, id ) for id in ids ] + for history in histories: + if history.importable: + history.importable = False + history.flush() # Render the list view return self.shared_list_grid( trans, status=status, message=message, **kwargs ) @web.expose @@ -622,7 +654,9 @@ params = util.Params( kwd ) msg = util.restore_text ( params.get( 'msg', '' ) ) if id: - histories = [ get_history( trans, id ) ] + ids = util.listify( id ) + if ids: + histories = [ get_history( trans, history_id ) for history_id in ids ] for history in histories: if params.get( 'enable_import_via_link', False ): history.importable = True @@ -635,14 +669,34 @@ if not user: msg = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email ) return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='error' ) - association = trans.app.model.HistoryUserShareAssociation.filter_by( user=user, history=history ).one() - association.delete() - association.flush() - if not id: - shared_msg = "History (%s) now shared with: %d users. " % ( history.name, len( history.users_shared_with ) ) - msg = '%s%s' % ( shared_msg, msg ) + husas = trans.app.model.HistoryUserShareAssociation.filter_by( user=user, history=history ).all() + if husas: + for husa in husas: + husa.delete() + husa.flush() + histories = [] + # Get all histories that have been shared with others + husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \ + .join( "history" ) \ + .filter( and_( trans.app.model.History.user == trans.user, + trans.app.model.History.deleted == False ) ) \ + .order_by( trans.app.model.History.table.c.name ) \ + .all() + for husa in husas: + history = husa.history + if history not in histories: + histories.append( history ) + # Get all histories that are importable + importables = trans.sa_session.query( trans.app.model.History ) \ + .filter_by( user=trans.user, importable=True, deleted=False ) \ + .order_by( trans.app.model.History.table.c.name ) \ + .all() + for importable in importables: + if importable not in histories: + histories.append( importable ) + # Sort the list of histories by history.name + histories.sort( key=operator.attrgetter( 'name') ) return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='done' ) - @web.expose @web.require_login( "rename histories" ) def rename( self, trans, id=None, name=None, **kwd ): diff -r 96ccd29277be -r f0adb6152df9 templates/history/sharing.mako --- a/templates/history/sharing.mako Thu Sep 10 17:48:52 2009 -0400 +++ b/templates/history/sharing.mako Thu Sep 10 21:24:06 2009 -0400 @@ -1,75 +1,63 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<h2>Public access via link</h2> +##<h2>Import via link</h2> %if msg: ${render_msg( msg, messagetype )} %endif -%for history in histories: - <p> - %if history.importable: - Send the following URL to users as an easy way for them to import the history, making a copy of their own: - <% url = h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id), qualified=True ) %> - <blockquote> - <a href="${url}">${url}</a> - </blockquote> - <br/> - <form action="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ) )}" method="POST"> - <input class="action-button" type="submit" name="disable_import_via_link" value="Disable import via link"> - </form> - %else: - This history is currently restricted (only you and the users listed below - can access it). Enabling the following option will generate a URL that you - can give to a user to allow them to import this history. - <br/> - <form action="${h.url_for( action='sharing', id=trans.security.encode_id(history.id) )}" method="POST"> - <input class="action-button" type="submit" name="enable_import_via_link" value="Enable import via link"> - </form> - %endif - </p> - <h2>Sharing with specific users</h2> - %if history.users_shared_with: - <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id( history.id ) )}"> - <span>Share with another user</span> - </a> - </li> - </ul> - <p> - The following users will see this history in their list of histories - shared with them by others, and they will be able to create their own copy of it: - </p> - <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <tr class="header"> - <th>History '${history.name}' currently shared with</th> - <th></th> - </tr> - %for i, association in enumerate( history.users_shared_with ): - <% user = association.user %> - <tr> - <td> - ${user.email} - <a id="user-${i}-popup" class="popup-arrow" style="display: none;">▼</a> - </td> - <td> - %if len( histories ) == 1: - ## Only allow unsharing if we're dealing with 1 history, otherwise - ## page refreshes screw things up - <div popupmenu="user-${i}-popup"> - <a class="action-button" href="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ), unshare_user=trans.security.encode_id( user.id ) )}">Unshare</a> +<h2>Histories that you've shared with others or enabled to be imported</h2> + +%if not histories: + You have no histories that you've shared with others or enabled to be imported +%else: + %for history in histories: + <div class="toolForm"> + <div class="toolFormTitle">History '${history.name}' shared with</div> + <div class="toolFormBody"> + <div class="form-row"> + <div style="float: right;"> + <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id( history.id ) )}"> + <span>Share with another user</span> + </a> + </div> + </div> + %if history.users_shared_with: + %for i, association in enumerate( history.users_shared_with ): + <% user = association.user %> + <div class="form-row"> + <a class="action-button" href="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ), unshare_user=trans.security.encode_id( user.id ) )}">Unshare</a> + ${user.email} + </div> + %endfor + %endif + %if history.importable: + <div class="form-row"> + <% url = h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id), qualified=True ) %> + <a href="${url}">${url}</a> + <div class="toolParamHelp" style="clear: both;"> + Send the above URL to users as an easy way for them to import the history, making a copy of their own + </div> + </div> + <div class="form-row"> + <form action="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ) )}" method="POST"> + <div class="form-row"> + <input class="action-button" type="submit" name="disable_import_via_link" value="Disable import via link"> </div> - %endif - </td> - </tr> - %endfor - </table> - %else: - <p>You have not shared this history with any users.</p> - <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id(history.id) )}"> - <span>Share with another user</span> - </a> - %endif -%endfor + </form> + </div> + %else: + <form action="${h.url_for( action='sharing', id=trans.security.encode_id(history.id) )}" method="POST"> + <div class="form-row"> + <input class="action-button" type="submit" name="enable_import_via_link" value="Enable import via link"> + <div class="toolParamHelp" style="clear: both;"> + Click to generate a URL that you can give to a user to allow them to import this history, making a copy of their own + </div> + </div> + </form> + %endif + </div> + </div> + %endfor +%endif diff -r 96ccd29277be -r f0adb6152df9 templates/root/index.mako --- a/templates/root/index.mako Thu Sep 10 17:48:52 2009 -0400 +++ b/templates/root/index.mako Thu Sep 10 21:24:06 2009 -0400 @@ -9,9 +9,6 @@ "List your histories": null, "Stored by you": function() { galaxy_main.location = "${h.url_for( controller='history', action='list')}"; - }, - "Shared with you": function() { - galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}"; }, "Current History": null, "Create new": function() { @@ -32,10 +29,19 @@ "Show deleted datasets": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; }, - "Delete": function() { - if ( confirm( "Really delete the current history?" ) ) { + "Delete": function() + { + if ( confirm( "Really delete the current history?" ) ) + { galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; } + }, + "Manage shared histories": null, + "Shared by you": function() { + galaxy_main.location = "${h.url_for( controller='history', action='list', operation='sharing' )}"; + }, + "Shared with you": function() { + galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}"; } }); }); diff -r 96ccd29277be -r f0adb6152df9 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Thu Sep 10 17:48:52 2009 -0400 +++ b/test/functional/test_history_functions.py Thu Sep 10 21:24:06 2009 -0400 @@ -141,14 +141,13 @@ check_str_after_submit='You cannot send histories to yourself.' ) # Share history3 with 1 valid user self.share_current_history( regular_user1.email, - check_str=history3.name, - check_str_after_submit='History (%s) now shared with: 1 users' % history3.name ) + check_str=history3.name ) # Check out list of histories to make sure history3 was shared - self.view_stored_active_histories( check_str='operation=sharing&id=%s">shared' % self.security.encode_id( history3.id ) ) + self.view_stored_active_histories( check_str='operation=sharing">shared' ) # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare', - check_str_after_submit='Send the following URL to users' ) + check_str_after_submit='Send the above URL to users' ) # Make sure history3 is now import-able history3.refresh() if not history3.importable: @@ -159,7 +158,7 @@ check_str_after_submit='You cannot import your own history.' ) # Disable the import link for history3 self.disable_import_via_link( self.security.encode_id( history3.id ), - check_str='Send the following URL to users', + check_str='Send the above URL to users', check_str_after_submit='Enable import via link' ) # Try importing history3 after disabling the URL self.import_history_via_url( self.security.encode_id( history3.id ), @@ -274,12 +273,10 @@ self.upload_file( '2.bed', dbkey='hg18' ) ids = '%s,%s' % ( self.security.encode_id( history3.id ), self.security.encode_id( history4.id ) ) emails = '%s,%s' % ( regular_user2.email, regular_user3.email ) - check_str_after_submit = 'History (%s) now shared with: 3 users.' % history3.name self.share_histories_with_users( ids, emails, check_str1='Share 2 histories', - check_str2=history4.name, - check_str_after_submit=check_str_after_submit ) + check_str2=history4.name ) self.logout() self.login( email=regular_user2.email ) # Shared history3 should be in regular_user2's list of shared histories @@ -342,12 +339,10 @@ """Testing sharing a restricted history by making the datasets public""" # Logged in as admin_user action_check_str = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email - action_check_str_after_submit = 'History (%s) now shared with: 1 users.' % history5.name # Current history is history5 self.share_current_history( regular_user1.email, action='public', - action_check_str=action_check_str, - action_check_str_after_submit=action_check_str_after_submit ) + action_check_str=action_check_str ) self.logout() self.login( email=regular_user1.email ) # Shared history5 should be in regular_user1's list of shared histories @@ -375,12 +370,10 @@ self.upload_file( '2.bed', dbkey='hg18' ) check_str_after_submit = 'The following datasets can be shared with %s with no changes' % regular_user2.email check_str_after_submit2 = 'The following datasets can be shared with %s by updating their permissions' % regular_user2.email - action_check_str_after_submit = 'History (%s) now shared with: 2 users.' % history5.name self.share_current_history( regular_user2.email, check_str_after_submit=check_str_after_submit, check_str_after_submit2=check_str_after_submit2, - action='private', - action_check_str_after_submit=action_check_str_after_submit ) + action='private' ) # We should now have a new sharing role global sharing_role role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user2.email ) @@ -470,12 +463,10 @@ check_str_after_submit = 'The following datasets can be shared with %s with no changes' % email check_str_after_submit2 = 'The following datasets can be shared with %s by updating their permissions' % email # history5 will be shared with regular_user1, regular_user2 and regular_user3 - action_check_str_after_submit = 'History (%s) now shared with: 3 users.' % history5.name self.share_current_history( email, check_str_after_submit=check_str_after_submit, check_str_after_submit2=check_str_after_submit2, - action='share_anyway', - action_check_str_after_submit=action_check_str_after_submit ) + action='share_anyway' ) # Check security on clone of history5 for regular_user2 self.logout() self.login( email=regular_user2.email )

1 0

[hg] galaxy 2677: Merge
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/96ccd29277be changeset: 2677:96ccd29277be user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Sep 10 17:48:52 2009 -0400 description: Merge 0 file(s) affected in this change: diffs (69 lines): diff -r f2e4673d784b -r 96ccd29277be cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample Thu Sep 10 17:48:37 2009 -0400 +++ b/cron/updateucsc.sh.sample Thu Sep 10 17:48:52 2009 -0400 @@ -6,7 +6,8 @@ # Edit this line to refer to galaxy's path: GALAXY=/galaxy/path -export PYTHONPATH=${GALAXY}/lib +PYTHONPATH=${GALAXY}/lib +export PYTHONPATH # setup directories echo "Creating required directories." @@ -32,7 +33,11 @@ python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -42,7 +47,11 @@ python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -52,7 +61,16 @@ python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len ${GALAXY}/tool-data/shared/ucsc/chrom/ + for src in ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len + do + dst=${GALAXY}/tool-data/shared/ucsc/chrom/`basename $src` + diff $src $dst > /dev/null 2>&1 + if [ $? -ne 0 ] + then + echo "cp -f $src $dst" + cp -f $src $dst + fi + done else echo "Failed to update chromInfo tables." >&2 fi diff -r f2e4673d784b -r 96ccd29277be tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Thu Sep 10 17:48:37 2009 -0400 +++ b/tools/new_operations/flanking_features.py Thu Sep 10 17:48:52 2009 -0400 @@ -129,7 +129,7 @@ map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval elif result_up: map(outfields.append, result_up[res_ind].other) - else: + elif result_down: map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields

1 0

[hg] galaxy 2675: Support for (1) ordering tags and (2) page tags.
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2a15e0eca0b9 changeset: 2675:2a15e0eca0b9 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Sep 10 16:48:11 2009 -0400 description: Support for (1) ordering tags and (2) page tags. 5 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py lib/galaxy/tags/tag_handler.py lib/galaxy/web/controllers/tag.py diffs (249 lines): diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/model/__init__.py Thu Sep 10 16:48:11 2009 -0400 @@ -1145,7 +1145,8 @@ return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name ) class ItemTagAssociation ( object ): - def __init__( self, item_id=None, tag_id=None, user_tname=None, value=None ): + def __init__( self, id=None, item_id=None, tag_id=None, user_tname=None, value=None ): + self.id = id self.item_id = item_id self.tag_id = tag_id self.user_tname = user_tname @@ -1165,6 +1166,8 @@ class HistoryDatasetAssociationTagAssociation ( ItemTagAssociation ): pass +class PageTagAssociation ( ItemTagAssociation ): + pass ## ---- Utility methods ------------------------------------------------------- diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/model/mapping.py Thu Sep 10 16:48:11 2009 -0400 @@ -552,6 +552,7 @@ UniqueConstraint( "name" ) ) HistoryTagAssociation.table = Table( "history_tag_association", metadata, + Column( "id", Integer, primary_key=True ), Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), @@ -559,6 +560,7 @@ Column( "user_value", TrimmedString(255), index=True) ) DatasetTagAssociation.table = Table( "dataset_tag_association", metadata, + Column( "id", Integer, primary_key=True ), Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), @@ -566,7 +568,16 @@ Column( "user_value", TrimmedString(255), index=True) ) HistoryDatasetAssociationTagAssociation.table = Table( "history_dataset_association_tag_association", metadata, + Column( "id", Integer, primary_key=True ), Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +PageTagAssociation.table = Table( "page_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), Column( "value", TrimmedString(255), index=True), @@ -672,7 +683,7 @@ visible_children=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ) & ( HistoryDatasetAssociation.table.c.visible == True ) ) ), - tags=relation(HistoryDatasetAssociationTagAssociation, backref='history_tag_associations') + tags=relation(HistoryDatasetAssociationTagAssociation, order_by=HistoryDatasetAssociationTagAssociation.table.c.id, backref='history_tag_associations') ) ) assign_mapper( context, Dataset, Dataset.table, @@ -689,7 +700,7 @@ active_library_associations=relation( LibraryDatasetDatasetAssociation, primaryjoin=( ( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ), - tags=relation(DatasetTagAssociation, backref='datasets') + tags=relation(DatasetTagAssociation, order_by=DatasetTagAssociation.table.c.id, backref='datasets') ) ) assign_mapper( context, HistoryDatasetAssociationDisplayAtAuthorization, HistoryDatasetAssociationDisplayAtAuthorization.table, @@ -709,7 +720,7 @@ properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ), active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), viewonly=True ), - tags=relation(HistoryTagAssociation, backref="histories") + tags=relation(HistoryTagAssociation, order_by=HistoryTagAssociation.table.c.id, backref="histories") ) ) assign_mapper( context, HistoryUserShareAssociation, HistoryUserShareAssociation.table, @@ -967,7 +978,8 @@ primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), latest_revision=relation( PageRevision, post_update=True, primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), - lazy=False ) + lazy=False ), + tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages") ) ) assign_mapper( context, Tag, Tag.table, @@ -988,6 +1000,11 @@ properties=dict( tag=relation(Tag, backref="tagged_history_dataset_associations") ), primary_key=[HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id, HistoryDatasetAssociationTagAssociation.table.c.tag_id] ) + +assign_mapper( context, PageTagAssociation, PageTagAssociation.table, + properties=dict( tag=relation(Tag, backref="tagged_pages") ), + primary_key=[PageTagAssociation.table.c.page_id, PageTagAssociation.table.c.tag_id] + ) def db_next_hid( self ): """ diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Thu Sep 10 16:48:11 2009 -0400 @@ -0,0 +1,116 @@ +""" +This migration script provides support for (a) ordering tags by recency and +(b) tagging pages. This script deletes all existing tags. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +import migrate.changeset + +import datetime +now = datetime.datetime.utcnow + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def display_migration_details(): + print "" + print "This migration script provides support for (a) ordering tags by recency and" + print "(b) tagging pages. This script deletes all existing tags." + +HistoryTagAssociation_table = Table( "history_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +DatasetTagAssociation_table = Table( "dataset_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +PageTagAssociation_table = Table( "page_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +def upgrade(): + display_migration_details() + metadata.reflect() + + # + # Recreate tables. + # + try: + HistoryTagAssociation_table.drop() + HistoryTagAssociation_table.create() + except Exception, e: + print "Recreating history_tag_association table failed: %s" % str( e ) + log.debug( "Recreating history_tag_association table failed: %s" % str( e ) ) + + try: + DatasetTagAssociation_table.drop() + DatasetTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Recreating dataset_tag_association table failed: %s" % str( e ) ) + + try: + HistoryDatasetAssociationTagAssociation_table.drop() + HistoryDatasetAssociationTagAssociation_table.create() + except OperationalError, e: + # Handle error that results from and index name that is too long; this occurs + # in MySQL. + if str(e).find("CREATE INDEX") != -1: + # Manually create index. + i = Index( "ix_hda_ta_history_dataset_association_id", HistoryDatasetAssociationTagAssociation_table.c.history_dataset_association_id ) + try: + i.create() + except Exception, e: + print str(e) + log.debug( "Adding index 'ix_hda_ta_history_dataset_association_id' to table 'history_dataset_association_tag_association' table failed: %s" % str( e ) ) + except Exception, e: + print str(e) + log.debug( "Recreating history_dataset_association_tag_association table failed: %s" % str( e ) ) + + # Create page_tag_association table. + try: + PageTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating page_tag_association table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # No need to downgrade other tagging tables. They work fine with verision 16 code. + + # Drop page_tag_association table. + try: + PageTagAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping page_tag_association table failed: %s" % str( e ) ) diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/tags/tag_handler.py Thu Sep 10 16:48:11 2009 -0400 @@ -1,4 +1,4 @@ -from galaxy.model import Tag, History, HistoryTagAssociation, Dataset, DatasetTagAssociation, HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation +from galaxy.model import Tag import re class TagHandler( object ): diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/web/controllers/tag.py Thu Sep 10 16:48:11 2009 -0400 @@ -1,6 +1,9 @@ """ Tags Controller: handles tagging/untagging of entities and provides autocomplete support. """ + +from galaxy.model import History, HistoryTagAssociation, Dataset, DatasetTagAssociation, \ + HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation, Page, PageTagAssociation from galaxy.web.base.controller import * from galaxy.tags.tag_handler import *

1 0

[hg] galaxy 2676: merge
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f2e4673d784b changeset: 2676:f2e4673d784b user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Sep 10 17:48:37 2009 -0400 description: merge 0 file(s) affected in this change: diffs (151 lines): diff -r 2a15e0eca0b9 -r f2e4673d784b lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Sep 10 16:48:11 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Sep 10 17:48:37 2009 -0400 @@ -502,13 +502,6 @@ context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running - if context.get( 'path', None ): - # The tool can set an alternate output path for the dataset. - try: - shutil.move( context['path'], dataset.file_name ) - except ( IOError, OSError ): - if not context['stderr']: - context['stderr'] = 'This dataset could not be processed' dataset.blurb = 'done' dataset.peek = 'no peek' dataset.info = context['stdout'] + context['stderr'] @@ -707,6 +700,13 @@ sizes.append( ( outfile, os.stat( outfile ).st_size ) ) return sizes def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, **kwds ): + # extension could still be 'auto' if this is the upload tool. + job = model.Job.get( self.job_id ) + for output_dataset_assoc in job.output_datasets: + if output_dataset_assoc.dataset.ext == 'auto': + context = self.get_dataset_finish_context( dict(), output_dataset_assoc.dataset.dataset ) + output_dataset_assoc.dataset.extension = context.get( 'ext', 'data' ) + mapping.context.current.flush() if tmp_dir is None: #this dir should should relative to the exec_dir tmp_dir = self.app.config.new_file_path @@ -716,7 +716,6 @@ config_root = self.app.config.root if datatypes_config is None: datatypes_config = self.app.config.datatypes_config - job = model.Job.get( self.job_id ) return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, config_root = config_root, datatypes_config = datatypes_config, **kwds ) class DefaultJobDispatcher( object ): diff -r 2a15e0eca0b9 -r f2e4673d784b lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Sep 10 16:48:11 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Thu Sep 10 17:48:37 2009 -0400 @@ -144,7 +144,7 @@ job.add_parameter( name, value ) job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) for i, dataset in enumerate( data_list ): - job.add_output_dataset( i, dataset ) + job.add_output_dataset( 'output%i' % i, dataset ) job.state = trans.app.model.Job.states.NEW trans.app.model.flush() diff -r 2a15e0eca0b9 -r f2e4673d784b tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Sep 10 16:48:11 2009 -0400 +++ b/tools/data_source/upload.py Thu Sep 10 17:48:37 2009 -0400 @@ -115,7 +115,14 @@ return ( True, False, test_ext ) return ( True, True, test_ext ) -def add_file( dataset, json_file ): +def parse_outputs( args ): + rval = {} + for arg in args: + id, path = arg.split( ':', 1 ) + rval[int( id )] = path + return rval + +def add_file( dataset, json_file, output_path ): data_type = None line_count = None @@ -229,16 +236,18 @@ ext = dataset.ext if ext == 'auto': ext = 'data' + # Move the dataset to its "real" path + shutil.move( dataset.path, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.path, ext = ext, stdout = 'uploaded %s file' % data_type, name = dataset.name, line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) -def add_composite_file( dataset, json_file ): +def add_composite_file( dataset, json_file, output_path ): if dataset.composite_files: os.mkdir( dataset.extra_files_path ) for name, value in dataset.composite_files.iteritems(): @@ -253,17 +262,21 @@ else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] ) shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( dataset.extra_files_path, name ) ) + # Move the dataset to its "real" path + shutil.move( dataset.primary_file, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.primary_file, stdout = 'uploaded %s file' % dataset.file_type ) json_file.write( to_json_string( info ) + "\n" ) def __main__(): - if len( sys.argv ) != 2: - print >>sys.stderr, 'usage: upload.py <json paramfile>' + if len( sys.argv ) < 2: + print >>sys.stderr, 'usage: upload.py <json paramfile> <output spec> ...' sys.exit( 1 ) + + output_paths = parse_outputs( sys.argv[2:] ) json_file = open( 'galaxy.json', 'w' ) @@ -271,10 +284,16 @@ dataset = from_json_string( line ) dataset = util.bunch.Bunch( **safe_dict( dataset ) ) + try: + output_path = output_paths[int( dataset.dataset_id )] + except: + print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id + sys.exit( 1 ) + if dataset.type == 'composite': - add_composite_file( dataset, json_file ) + add_composite_file( dataset, json_file, output_path ) else: - add_file( dataset, json_file ) + add_file( dataset, json_file, output_path ) # clean up paramfile try: diff -r 2a15e0eca0b9 -r f2e4673d784b tools/data_source/upload.xml --- a/tools/data_source/upload.xml Thu Sep 10 16:48:11 2009 -0400 +++ b/tools/data_source/upload.xml Thu Sep 10 17:48:37 2009 -0400 @@ -7,6 +7,12 @@ <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <command interpreter="python"> upload.py $paramfile + #set $outnum = 0 + #while $varExists('output%i' % $outnum): + #set $output = $getVar('output%i' % $outnum) + #set $outnum += 1 + ${output.dataset.dataset.id}:${output} + #end while </command> <inputs> <param name="file_type" type="select" label="File Format" help="Which format? See help below">

1 0

[hg] galaxy 2674: Bug fix for 'Fetch closest feature' tool.
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0a41293e679a changeset: 2674:0a41293e679a user: guru date: Thu Sep 10 17:35:21 2009 -0400 description: Bug fix for 'Fetch closest feature' tool. 1 file(s) affected in this change: tools/new_operations/flanking_features.py diffs (12 lines): diff -r ce8c57840343 -r 0a41293e679a tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Thu Sep 10 17:31:05 2009 -0400 +++ b/tools/new_operations/flanking_features.py Thu Sep 10 17:35:21 2009 -0400 @@ -129,7 +129,7 @@ map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval elif result_up: map(outfields.append, result_up[res_ind].other) - else: + elif result_down: map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields

1 0

[hg] galaxy 2673: POSIXize/Bournize updateucsc.sh.sample
by Nate Coraor 10 Sep '09

10 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ce8c57840343 changeset: 2673:ce8c57840343 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 10 17:31:05 2009 -0400 description: POSIXize/Bournize updateucsc.sh.sample 1 file(s) affected in this change: cron/updateucsc.sh.sample diffs (57 lines): diff -r d3fe789e3931 -r ce8c57840343 cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample Thu Sep 10 14:52:38 2009 -0400 +++ b/cron/updateucsc.sh.sample Thu Sep 10 17:31:05 2009 -0400 @@ -6,7 +6,8 @@ # Edit this line to refer to galaxy's path: GALAXY=/galaxy/path -export PYTHONPATH=${GALAXY}/lib +PYTHONPATH=${GALAXY}/lib +export PYTHONPATH # setup directories echo "Creating required directories." @@ -32,7 +33,11 @@ python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -42,7 +47,11 @@ python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -52,7 +61,16 @@ python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len ${GALAXY}/tool-data/shared/ucsc/chrom/ + for src in ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len + do + dst=${GALAXY}/tool-data/shared/ucsc/chrom/`basename $src` + diff $src $dst > /dev/null 2>&1 + if [ $? -ne 0 ] + then + echo "cp -f $src $dst" + cp -f $src $dst + fi + done else echo "Failed to update chromInfo tables." >&2 fi

1 0

[hg] galaxy 2672: Get rid of the hacky "alternate path" stuff us...
by Greg Von Kuster 10 Sep '09

10 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d3fe789e3931 changeset: 2672:d3fe789e3931 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 10 14:52:38 2009 -0400 description: Get rid of the hacky "alternate path" stuff used by the upload tool and fix setting metadata when using autodetect and set_metadata_externally 4 file(s) affected in this change: lib/galaxy/jobs/__init__.py lib/galaxy/tools/actions/upload.py tools/data_source/upload.py tools/data_source/upload.xml diffs (151 lines): diff -r dbbc63c0630a -r d3fe789e3931 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Sep 10 14:52:38 2009 -0400 @@ -502,13 +502,6 @@ context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running - if context.get( 'path', None ): - # The tool can set an alternate output path for the dataset. - try: - shutil.move( context['path'], dataset.file_name ) - except ( IOError, OSError ): - if not context['stderr']: - context['stderr'] = 'This dataset could not be processed' dataset.blurb = 'done' dataset.peek = 'no peek' dataset.info = context['stdout'] + context['stderr'] @@ -707,6 +700,13 @@ sizes.append( ( outfile, os.stat( outfile ).st_size ) ) return sizes def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, **kwds ): + # extension could still be 'auto' if this is the upload tool. + job = model.Job.get( self.job_id ) + for output_dataset_assoc in job.output_datasets: + if output_dataset_assoc.dataset.ext == 'auto': + context = self.get_dataset_finish_context( dict(), output_dataset_assoc.dataset.dataset ) + output_dataset_assoc.dataset.extension = context.get( 'ext', 'data' ) + mapping.context.current.flush() if tmp_dir is None: #this dir should should relative to the exec_dir tmp_dir = self.app.config.new_file_path @@ -716,7 +716,6 @@ config_root = self.app.config.root if datatypes_config is None: datatypes_config = self.app.config.datatypes_config - job = model.Job.get( self.job_id ) return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, config_root = config_root, datatypes_config = datatypes_config, **kwds ) class DefaultJobDispatcher( object ): diff -r dbbc63c0630a -r d3fe789e3931 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Thu Sep 10 14:52:38 2009 -0400 @@ -144,7 +144,7 @@ job.add_parameter( name, value ) job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) for i, dataset in enumerate( data_list ): - job.add_output_dataset( i, dataset ) + job.add_output_dataset( 'output%i' % i, dataset ) job.state = trans.app.model.Job.states.NEW trans.app.model.flush() diff -r dbbc63c0630a -r d3fe789e3931 tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Sep 10 10:42:50 2009 -0400 +++ b/tools/data_source/upload.py Thu Sep 10 14:52:38 2009 -0400 @@ -115,7 +115,14 @@ return ( True, False, test_ext ) return ( True, True, test_ext ) -def add_file( dataset, json_file ): +def parse_outputs( args ): + rval = {} + for arg in args: + id, path = arg.split( ':', 1 ) + rval[int( id )] = path + return rval + +def add_file( dataset, json_file, output_path ): data_type = None line_count = None @@ -229,16 +236,18 @@ ext = dataset.ext if ext == 'auto': ext = 'data' + # Move the dataset to its "real" path + shutil.move( dataset.path, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.path, ext = ext, stdout = 'uploaded %s file' % data_type, name = dataset.name, line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) -def add_composite_file( dataset, json_file ): +def add_composite_file( dataset, json_file, output_path ): if dataset.composite_files: os.mkdir( dataset.extra_files_path ) for name, value in dataset.composite_files.iteritems(): @@ -253,17 +262,21 @@ else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] ) shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( dataset.extra_files_path, name ) ) + # Move the dataset to its "real" path + shutil.move( dataset.primary_file, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.primary_file, stdout = 'uploaded %s file' % dataset.file_type ) json_file.write( to_json_string( info ) + "\n" ) def __main__(): - if len( sys.argv ) != 2: - print >>sys.stderr, 'usage: upload.py <json paramfile>' + if len( sys.argv ) < 2: + print >>sys.stderr, 'usage: upload.py <json paramfile> <output spec> ...' sys.exit( 1 ) + + output_paths = parse_outputs( sys.argv[2:] ) json_file = open( 'galaxy.json', 'w' ) @@ -271,10 +284,16 @@ dataset = from_json_string( line ) dataset = util.bunch.Bunch( **safe_dict( dataset ) ) + try: + output_path = output_paths[int( dataset.dataset_id )] + except: + print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id + sys.exit( 1 ) + if dataset.type == 'composite': - add_composite_file( dataset, json_file ) + add_composite_file( dataset, json_file, output_path ) else: - add_file( dataset, json_file ) + add_file( dataset, json_file, output_path ) # clean up paramfile try: diff -r dbbc63c0630a -r d3fe789e3931 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Thu Sep 10 10:42:50 2009 -0400 +++ b/tools/data_source/upload.xml Thu Sep 10 14:52:38 2009 -0400 @@ -7,6 +7,12 @@ <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <command interpreter="python"> upload.py $paramfile + #set $outnum = 0 + #while $varExists('output%i' % $outnum): + #set $output = $getVar('output%i' % $outnum) + #set $outnum += 1 + ${output.dataset.dataset.id}:${output} + #end while </command> <inputs> <param name="file_type" type="select" label="File Format" help="Which format? See help below">

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[hg] galaxy 2671: Updated manual builds will L. major (2005) gen...
by Greg Von Kuster 10 Sep '09

10 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dbbc63c0630a changeset: 2671:dbbc63c0630a user: guru date: Thu Sep 10 10:42:50 2009 -0400 description: Updated manual builds will L. major (2005) genome. 1 file(s) affected in this change: tool-data/shared/ucsc/manual_builds.txt diffs (8 lines): diff -r c3b40f23a0e0 -r dbbc63c0630a tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt Wed Sep 09 14:24:11 2009 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu Sep 10 10:42:50 2009 -0400 @@ -664,3 +664,4 @@ baciAnth_AMES Bacillus anthracis str. Ames chr=5227293 shewOnei Shewanella oneidensis MR-1 plasmid_pMR-1=161613,chr=4969803 15217 Human herpesvirus 1 NC_001806=152261 +lMaj5 Leishmania major 2005 chr1=268984,chr2=355714,chr3=384518,chr4=441313,chr5=465823,chr6=516874,chr7=596348,chr8=574972,chr9=573441,chr10=570864,chr11=582575,chr12=675347,chr13=654604,chr14=622648,chr15=629514,chr16=714659,chr17=684831,chr18=739751,chr19=702212,chr20=742551,chr21=772974,chr22=716608,chr23=772567,chr24=840950,chr25=912849,chr26=1091579,chr27=1130447,chr28=1160128,chr29=1212674,chr30=1403454,chr31=1484336,chr32=1604650,chr33=1583673,chr34=1866754,chr35=2090491,chr36=2682183

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Logging and Debugging
by SHAUN WEBB 10 Sep '09

10 Sep '09

Hi, I am looking for more information on the options in the Logging and Debugging section of the universe_wsgi.ini file, in particular what are specific values to which I can set log_level in the first option "verbosity of log messages". I wish to turn off the debugging messages in the log file. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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