galaxy-dev February 2010

galaxy-dev@lists.galaxyproject.org

32 participants
180 discussions

[hg] galaxy 3342: Sanitize HTML in annotations and update annota...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/207298b5ea39 changeset: 3342:207298b5ea39 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 15:28:03 2010 -0500 description: Sanitize HTML in annotations and update annotations via ajax to show sanitation results. diffstat: lib/galaxy/web/controllers/history.py | 8 +++++--- lib/galaxy/web/controllers/root.py | 5 ++++- lib/galaxy/web/controllers/workflow.py | 19 ++++++++++--------- static/scripts/galaxy.base.js | 4 ++-- 4 files changed, 21 insertions(+), 15 deletions(-) diffs (128 lines): diff -r 12789b4ba919 -r 207298b5ea39 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Feb 05 14:25:38 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Fri Feb 05 15:28:03 2010 -0500 @@ -4,6 +4,7 @@ from galaxy.model.mapping import desc from galaxy.model.orm import * from galaxy.util.json import * +from galaxy.util.sanitize_html import sanitize_html from galaxy.tags.tag_handler import TagHandler from sqlalchemy.sql.expression import ClauseElement import webhelpers, logging, operator @@ -355,17 +356,18 @@ history.name = new_name trans.sa_session.add( history ) trans.sa_session.flush() + return history.name @web.expose @web.require_login( "use Galaxy histories" ) def annotate_async( self, trans, id, new_annotation=None, **kwargs ): history = self.get_history( trans, id ) if new_annotation: + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans, history, new_annotation ) trans.sa_session.flush() - return - else: - return "failed" + return new_annotation @web.expose @web.json diff -r 12789b4ba919 -r 207298b5ea39 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Fri Feb 05 14:25:38 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Fri Feb 05 15:28:03 2010 -0500 @@ -5,6 +5,7 @@ from cgi import escape, FieldStorage from galaxy import util, datatypes, jobs, web, util from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * log = logging.getLogger( __name__ ) @@ -305,7 +306,9 @@ else: setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) ) data.datatype.after_setting_metadata( data ) - self.add_item_annotation( trans, data, params.annotation ) + # Sanitize annotation before adding it. + annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, data, annotation ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' trans.sa_session.flush() diff -r 12789b4ba919 -r 207298b5ea39 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Fri Feb 05 14:25:38 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Fri Feb 05 15:28:03 2010 -0500 @@ -11,6 +11,7 @@ from galaxy.datatypes.data import Data from galaxy.util.odict import odict from galaxy.util.bunch import Bunch +from galaxy.util.sanitize_html import sanitize_html from galaxy.util.topsort import topsort, topsort_levels, CycleError from galaxy.workflow.modules import * from galaxy.model.mapping import desc @@ -317,8 +318,9 @@ # Rename workflow. stored.name = kwargs[ 'name' ] if 'annotation' in kwargs: - # Set workflow annotation. - self.add_item_annotation( trans, stored, kwargs[ 'annotation' ] ) + # Set workflow annotation; sanitize annotation before adding it. + annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) + self.add_item_annotation( trans, stored, annotation ) trans.sa_session.flush() return trans.fill_template( 'workflow/edit_attributes.mako', @@ -350,20 +352,18 @@ if new_name: stored.name = new_name trans.sa_session.flush() - return - else: - return "failed" + return stored.name @web.expose @web.require_login( "use Galaxy workflows" ) def annotate_async( self, trans, id, new_annotation=None, **kwargs ): stored = get_stored_workflow( trans, id ) if new_annotation: + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans, stored, new_annotation ) trans.sa_session.flush() - return - else: - return "failed" + return new_annotation @web.expose @web.require_login( "use Galaxy workflows" ) @@ -643,7 +643,8 @@ step.temp_input_connections = step_dict['input_connections'] # Save step annotation. - self.add_item_annotation( trans, step, step_dict[ 'annotation' ] ) + annotation = sanitize_html( step_dict[ 'annotation' ], 'utf-8', 'text/html' ) + self.add_item_annotation( trans, step, annotation ) # Second pass to deal with connections between steps for step in steps: # Input connections diff -r 12789b4ba919 -r 207298b5ea39 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Feb 05 14:25:38 2010 -0500 +++ b/static/scripts/galaxy.base.js Fri Feb 05 15:28:03 2010 -0500 @@ -249,9 +249,9 @@ alert( "Text editing for elt " + text_elt_id + " failed" ); // TODO: call finish or no? For now, let's not because error occurred. }, - success: function() { + success: function(processed_text) { // Set new text and call finish method. - $("#" + text_elt_id).text( new_text ); + $("#" + text_elt_id).text( processed_text ); if (on_finish != null) on_finish(t); }

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[hg] galaxy 3341: Add path to OS X HYPHY for buildbot
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/30c0d321bcbd changeset: 3341:30c0d321bcbd user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Feb 05 15:27:38 2010 -0500 description: Add path to OS X HYPHY for buildbot diffstat: buildbot_setup.sh | 9 +++++++++ 1 files changed, 9 insertions(+), 0 deletions(-) diffs (19 lines): diff -r 12789b4ba919 -r 30c0d321bcbd buildbot_setup.sh --- a/buildbot_setup.sh Fri Feb 05 14:25:38 2010 -0500 +++ b/buildbot_setup.sh Fri Feb 05 15:27:38 2010 -0500 @@ -10,6 +10,15 @@ kernel=`uname -r | cut -f1,2 -d.` HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy" ;; + darwin*) + this_minor=`uname -r | awk -F. '{print ($1-4)}'` + machine=`machine` + for minor in `jot - 3 $this_minor 1`; do + HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy" + [ -d "$HYPHY" ] && break + done + [ ! -d "$HYPHY" ] && unset HYPHY + ;; esac LINKS="

1 0

[hg] galaxy 3340: Forms UI improvements
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/12789b4ba919 changeset: 3340:12789b4ba919 user: rc date: Fri Feb 05 14:25:38 2010 -0500 description: Forms UI improvements diffstat: lib/galaxy/web/controllers/forms.py | 8 +++++--- templates/display_common.mako | 34 +++++++++++++++++++--------------- 2 files changed, 24 insertions(+), 18 deletions(-) diffs (76 lines): diff -r 9e2ba4cf4494 -r 12789b4ba919 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Fri Feb 05 14:18:37 2010 -0500 +++ b/lib/galaxy/web/controllers/forms.py Fri Feb 05 14:25:38 2010 -0500 @@ -135,7 +135,9 @@ return trans.response.send_redirect( web.url_for( controller='forms', action='new', msg=msg, - messagetype='error' ) ) + messagetype='error', + name=util.restore_text( params.get( 'name', '' ) ), + description=util.restore_text( params.get( 'description', '' ) ) ) ) self.__get_saved_form( fd ) if self.__imported_from_file: return trans.response.send_redirect( web.url_for( controller='forms', @@ -151,8 +153,8 @@ name=fd.name, description=fd.desc, form_type_selectbox=fd.type ) ) - inputs = [ ( 'Name', TextField( 'name', 40, 'New Form' ) ), - ( 'Description', TextField( 'description', 40, '' ) ), + inputs = [ ( 'Name', TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ), + ( 'Description', TextField( 'description', 40, util.restore_text( params.get( 'description', '' ) ) ) ), ( 'Type', self.__form_types_widget(trans, selected=params.get( 'form_type', 'none' )) ), ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ] return trans.fill_template( '/admin/forms/create_form.mako', diff -r 9e2ba4cf4494 -r 12789b4ba919 templates/display_common.mako --- a/templates/display_common.mako Fri Feb 05 14:18:37 2010 -0500 +++ b/templates/display_common.mako Fri Feb 05 14:25:38 2010 -0500 @@ -30,6 +30,8 @@ ## Start with exceptions, end with default. if a_class is model.History: return "Histories" + elif a_class is model.FormDefinitionCurrent: + return "Forms" else: return get_class_display_name( a_class ) + "s" %> @@ -55,21 +57,23 @@ ## Get plural term for class. <%def name="get_class_plural( a_class )"> - <% - if a_class == model.History: - class_plural = "Histories" - elif a_class == model.StoredWorkflow: - class_plural = "Workflows" - elif a_class == model.Page: - class_plural = "Pages" - elif a_class == model.Library: - class_plural = "Libraries" - elif a_class == model.HistoryDatasetAssociation: - class_plural = "Datasets" - else: - class_plural = a_class.__name__ + "s" - return class_plural - %> +<% + if a_class == model.History: + class_plural = "Histories" + elif a_class == model.StoredWorkflow: + class_plural = "Workflows" + elif a_class == model.Page: + class_plural = "Pages" + elif a_class == model.Library: + class_plural = "Libraries" + elif a_class == model.HistoryDatasetAssociation: + class_plural = "Datasets" + elif a_class == model.FormDefinitionCurrent: + class_plural = "Forms" + else: + class_plural = a_class.__name__ + "s" + return class_plural +%> </%def> ## Returns the controller name for an item based on its class.

1 0

[hg] galaxy 3339: UI improvements for history panel and tags: (1...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9e2ba4cf4494 changeset: 3339:9e2ba4cf4494 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 14:18:37 2010 -0500 description: UI improvements for history panel and tags: (1) added icons for tags, annotations; (2) added tooltips for editable text; (3) added tooltips for tags. diffstat: static/images/sticky-note-text.png | 0 static/images/tag-label.png | 0 static/june_2007_style/base.css.tmpl | 47 ++++++++++++++++++- static/june_2007_style/blue/base.css | 9 +++- static/scripts/galaxy.base.js | 13 +++- static/scripts/packed/galaxy.base.js | 2 +- templates/root/history.mako | 88 ++++++++++++++++++++-------------- templates/tagging_common.mako | 23 +++++--- 8 files changed, 129 insertions(+), 53 deletions(-) diffs (266 lines): diff -r 7163a2128267 -r 9e2ba4cf4494 static/images/sticky-note-text.png Binary file static/images/sticky-note-text.png has changed diff -r 7163a2128267 -r 9e2ba4cf4494 static/images/tag-label.png Binary file static/images/tag-label.png has changed diff -r 7163a2128267 -r 9e2ba4cf4494 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Feb 05 11:53:06 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Fri Feb 05 14:18:37 2010 -0500 @@ -697,4 +697,49 @@ .icon-button.edit:hover { -sprite-group: history-buttons; -sprite-image: pencil_icon_dark.png; -} \ No newline at end of file +} + +.icon-button.tag { + background-image:url(/static/images/tag-label.png); + background-repeat:no-repeat; + background-position:center; + padding: 0px 0px 0px 0px; +} + +.icon-button.annotate { + background-image:url(/static/images/sticky-note-text.png); + background-repeat:no-repeat; + background-position:center; + padding: 0px 0px 0px 0px; +} + +.tooltip { + position: relative; + cursor: pointer; +} + +.tooltip span.tip { + display: none +} + +.tooltip:hover span.tip { + font-size: 90%; + display: block; + position: absolute; + right:2em;top:-1.75em; + width: inherit; + background-color: black; + color: white; + text-align: center; + padding: 0.25em 0.5em; +} + +.editable-text { + cursor:pointer; +} + +.editable-text:hover{ + background-image:url(); + background-repeat:no-repeat; + background-position:right; +} diff -r 7163a2128267 -r 9e2ba4cf4494 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Feb 05 11:53:06 2010 -0500 +++ b/static/june_2007_style/blue/base.css Fri Feb 05 14:18:37 2010 -0500 @@ -116,4 +116,11 @@ .icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.delete{background:url(history-buttons.png) no-repeat 0px -104px;} -.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;} \ No newline at end of file +.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;} +.icon-button.tag{background-image:url(/static/images/tag-label.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} +.icon-button.annotate{background-image:url(/static/images/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} +.tooltip {position: relative; cursor: pointer} +.tooltip span.tip{display: none;} +.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;right:2em;top:-1.75em; width: inherit; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;} +.editable-text{cursor:pointer} +.editable-text:hover{background-image:url();background-repeat:no-repeat;background-position:right} \ No newline at end of file diff -r 7163a2128267 -r 9e2ba4cf4494 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Feb 05 11:53:06 2010 -0500 +++ b/static/scripts/galaxy.base.js Fri Feb 05 14:18:37 2010 -0500 @@ -211,14 +211,21 @@ // // Edit and save text asynchronously. // -function async_save_text(click_to_edit_elt, text_elt_id, save_url, text_parm_name, use_textarea, num_rows, on_start, on_finish) +function async_save_text(click_to_edit_elt, text_elt_id, save_url, text_parm_name, num_cols, use_textarea, num_rows, on_start, on_finish) { + // Set defaults if necessary. + if (num_cols == null) + num_cols = 30; + if (num_rows == null) + num_rows = 4 + + // Set up input element. $("#" + click_to_edit_elt).click( function() { var old_text = $("#" + text_elt_id).text() if (use_textarea) - var t = $("<textarea rows='" + num_rows + "'>" + old_text + "</textarea>" ); + var t = $("<textarea rows='" + num_rows + "' cols='" + num_cols + "'>" + old_text + "</textarea>" ); else - var t = $("<input type='text' value='" + old_text + "'></input>" ); + var t = $("<input type='text' value='" + old_text + "' size='" + num_cols + "'></input>" ); t.blur( function() { $(this).remove(); $("#" + text_elt_id).show(); diff -r 7163a2128267 -r 9e2ba4cf4494 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Feb 05 11:53:06 2010 -0500 +++ b/static/scripts/packed/galaxy.base.js Fri Feb 05 14:18:37 2010 -0500 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i. attr("value","?")}}}})}};function async_save_text(d,c,a,e,f,b){$("#"+d).click(function(){var h=$("#"+c).text();if(f){var g=$("<textarea rows='"+b+"'>"+h+"</textarea>")}else{var g=$("<input type='text' value='"+h+"'></input>")}g.blur(function(){$(this).remove();$("#"+c).show()});g.keyup(function(j){if(j.keyCode==27){$(this).trigger("blur")}else{if(j.keyCode==13){new_text=this.value;$(this).trigger("blur");var i=new Object();i[e]=new_text;$.ajax({url:a,data:i,error:function(){alert("Text editing for elt "+c+" failed")},success:function(){$("#"+c).text(new_text)}})}}});$("#"+c).hide();g.insertAfter($("#"+c));g.focus();g.select();return false})}; \ No newline at end of file +$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i. attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var k=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+k+"</textarea>")}else{var j=$("<input type='text' value='"+k+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(b!=null){b(j)}});j.keyup(function(m){if(m.keyCode==27){$(this).trigger("blur")}else{if(m.keyCode==13){new_text=this.value;$(this).trigger("blur");var l=new Object();l[a]=new_text;$.ajax({url:e,data:l,error:function(){alert("Text editing for elt "+f+" failed")},success:function(){$("#"+f).text(new_text);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();return false})}; \ No newline at end of file diff -r 7163a2128267 -r 9e2ba4cf4494 templates/root/history.mako --- a/templates/root/history.mako Fri Feb 05 11:53:06 2010 -0500 +++ b/templates/root/history.mako Fri Feb 05 14:18:37 2010 -0500 @@ -42,19 +42,22 @@ $.jStore.remove("history_expand_state"); })); - // Rename async. - async_save_text("history-rename", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name"); + // Rename management. + async_save_text("history-name", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); - // Annotation async. - // Tag async. Simply have the workflow tag element generate a click on the tag element to activate tagging. - $('#workflow-tag').click( function() + // Tag management. + $('#history-tag').click( function() { - $('.tag-area').click(); + $('#history-tag-area').toggle("fast"); return false; }); - - // Annotate async. - async_save_text("history-annotate", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", true, 4); + + // Annotation management. + $('#history-annotate').click( function() { + $('#history-annotation-area').toggle("fast"); + return false; + }); + async_save_text("history-annotation", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4); // Updater updater({ @@ -273,10 +276,24 @@ | <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> %endif </div> - + <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold;"> - <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> - <div id="history-name">${history.get_display_name() | h}</div> + <table width="100%" cellpadding="0" cellspacing="0"> + <tr> + <td align="left"> + <div id="history-name-container" class="editable-text tooltip"> + <span id="history-name">${history.get_display_name() | h}</span> + <span class="tip">Click to edit</span></a> + </div> + </td> + <td align="right"> + <div style="float: right"> + <a id="history-tag" title="Tag" class="icon-button tag tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='tag' )}"></a> + <a id="history-annotate" title="Annotate" class="icon-button annotate" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a> + </div> + </td> + </tr> + </table> </div> %if history.deleted: @@ -291,33 +308,30 @@ %if trans.get_user() is not None: <div style="margin: 0px 0px 5px 10px"> - <a href="#" onclick="$('#tags-and-annotation').toggle('fast')">Edit Tags and Annotation/Notes</a> - <div id="tags-and-annotation" style="display: none"> - ## Tagging elt. - <div class="form-row"> - <label>Tags:</label> - <div style="float: right"><a id="workflow-tag" title="Tag" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div> - <style> - .tag-area { - border: none; - } - </style> - ${render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20", render_add_tag_button=False)} - <div style="clear: both"></div> - </div> - - ## Annotation elt. - <div id="history-annotation-area" class="form-row"> - <label>Annotation / Notes:</label> - <div style="float: right"><a id="history-annotate" title="Annotate" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='annotate_async' )}"></a></div> - %if annotation: - <div id="history-annotation">${annotation | h}</div> - %else: - <div id="history-annotation"></div> - %endif - <div style="clear: both"></div> + ## Tagging elt. + <div id="history-tag-area" class="form-row" style="display: none"> + <label>Tags:</label> + <style> + .tag-area { + border: none; + } + </style> + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20")} + </div> + + ## Annotation elt. + <div id="history-annotation-area" class="form-row" style="display: none"> + <label>Annotation / Notes:</label> + <div class="tooltip"> + %if annotation: + <span id="history-annotation">${annotation | h}</span> + %else: + <span id="history-annotation">None</span> + %endif + <span class="tip">Click to edit annotation</span> </div> </div> + </div> %endif diff -r 7163a2128267 -r 9e2ba4cf4494 templates/tagging_common.mako --- a/templates/tagging_common.mako Fri Feb 05 11:53:06 2010 -0500 +++ b/templates/tagging_common.mako Fri Feb 05 14:18:37 2010 -0500 @@ -72,17 +72,20 @@ %endfor ## Add tag input field. If element is in form, tag input is a textarea; otherwise element is a input type=text. - %if editable: - %if in_form: - <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> - %else: - <input class="tag-input" type='text' size='${input_size}'/> + <div class="tooltip"> + %if editable: + %if in_form: + <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> + %else: + <input class="tag-input" type='text' size='${input_size}'/> + %endif + ## Add "add tag" button. + %if render_add_tag_button: + <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> + %endif %endif - ## Add "add tag" button. - %if render_add_tag_button: - <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> - %endif - %endif + <span class="tip">Click to add tags</span> + </div> </div> </div> </%def>

1 0

[hg] galaxy 3338: Have sam2interval provide a (partial) header s...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7163a2128267 changeset: 3338:7163a2128267 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 11:53:06 2010 -0500 description: Have sam2interval provide a (partial) header so that strand is automatically set in metadata. diffstat: test-data/sam2interval_noprintAll.dat | 1 + test-data/sam2interval_printAll.dat | 1 + tools/samtools/sam2interval.py | 2 ++ 3 files changed, 4 insertions(+), 0 deletions(-) diffs (28 lines): diff -r 8b3c1f064bef -r 7163a2128267 test-data/sam2interval_noprintAll.dat --- a/test-data/sam2interval_noprintAll.dat Fri Feb 05 11:49:51 2010 -0500 +++ b/test-data/sam2interval_noprintAll.dat Fri Feb 05 11:53:06 2010 -0500 @@ -1,3 +1,4 @@ +#chrom start end strand ref 6 22 + ref 8 19 + ref 8 14 + diff -r 8b3c1f064bef -r 7163a2128267 test-data/sam2interval_printAll.dat --- a/test-data/sam2interval_printAll.dat Fri Feb 05 11:49:51 2010 -0500 +++ b/test-data/sam2interval_printAll.dat Fri Feb 05 11:53:06 2010 -0500 @@ -1,3 +1,4 @@ +#chrom start end strand ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 diff -r 8b3c1f064bef -r 7163a2128267 tools/samtools/sam2interval.py --- a/tools/samtools/sam2interval.py Fri Feb 05 11:49:51 2010 -0500 +++ b/tools/samtools/sam2interval.py Fri Feb 05 11:53:06 2010 -0500 @@ -76,6 +76,8 @@ cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' ) + print '#chrom\tstart\tend\tstrand' # provide a (partial) header so that strand is automatically set in metadata + for line in infile: line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ) and not line.startswith( '@' ) :

1 0

[hg] galaxy 3337: Fix Twill Test Framework: diffs were no longer...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8b3c1f064bef changeset: 3337:8b3c1f064bef user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 11:49:51 2010 -0500 description: Fix Twill Test Framework: diffs were no longer being reported (all functional tests not writing to stderr were passing regardless of failure). diffstat: test/base/twilltestcase.py | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r 22c1284782fb -r 8b3c1f064bef test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Feb 05 11:20:13 2010 -0500 +++ b/test/base/twilltestcase.py Fri Feb 05 11:49:51 2010 -0500 @@ -82,6 +82,7 @@ for char in line: if ord( char ) > 128: raise AssertionError( "Binary data detected, not displaying diff" ) + raise AssertionError( "".join( diff_slice ) ) def get_filename( self, filename ): full = os.path.join( self.file_dir, filename)

1 0

[hg] galaxy 3336: upgrading pexpect to v2.4
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/22c1284782fb changeset: 3336:22c1284782fb user: rc date: Fri Feb 05 11:20:13 2010 -0500 description: upgrading pexpect to v2.4 diffstat: eggs.ini | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r b4ba343d3540 -r 22c1284782fb eggs.ini --- a/eggs.ini Fri Feb 05 10:04:04 2010 -0500 +++ b/eggs.ini Fri Feb 05 11:20:13 2010 -0500 @@ -40,7 +40,7 @@ Paste = 1.6 PasteDeploy = 1.3.3 PasteScript = 1.7.3 -pexpect = 2.3 +pexpect = 2.4 Routes = 1.11 simplejson = 1.5 SQLAlchemy = 0.5.6 @@ -73,7 +73,7 @@ DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz -pexpect = http://pexpect.sourceforge.net/pexpect-2.3.tar.gz +pexpect = http://pypi.python.org/packages/source/p/pexpect/pexpect-2.4.tar.gz psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2 pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz pysam = http://bitbucket.org/kanwei/kanwei-pysam/get/e3c601a062fd.gz

1 0

[hg] galaxy 3335: Add (most of) Assaf Gordon's patch for allowin...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b4ba343d3540 changeset: 3335:b4ba343d3540 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Feb 05 10:04:04 2010 -0500 description: Add (most of) Assaf Gordon's patch for allowing SGE options in the runner url, and add the same support to PBS. Please note that this should be considered a temporary implementation, and will be removed in the future. diffstat: lib/galaxy/jobs/__init__.py | 9 +++++ lib/galaxy/jobs/runners/pbs.py | 69 +++++++++++++++++++++++++---------------- lib/galaxy/jobs/runners/sge.py | 35 +++++++++++++++++---- 3 files changed, 79 insertions(+), 34 deletions(-) diffs (188 lines): diff -r 51a1369fdf96 -r b4ba343d3540 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Feb 05 09:23:19 2010 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Feb 05 10:04:04 2010 -0500 @@ -719,6 +719,7 @@ for outfile in [ str( o ) for o in output_paths ]: 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, set_extension = True, **kwds ): # extension could still be 'auto' if this is the upload tool. job = self.sa_session.query( model.Job ).get( self.job_id ) @@ -747,6 +748,14 @@ job_metadata = os.path.join( self.working_directory, TOOL_PROVIDED_JOB_METADATA_FILE ), **kwds ) + @property + def user( self ): + job = self.sa_session.query( model.Job ).get( self.job_id ) + if job.history.user is None: + return 'anonymous@' + job.galaxy_session.remote_addr.split()[-1] + else: + return job.history.user.email + class DefaultJobDispatcher( object ): def __init__( self, app ): self.app = app diff -r 51a1369fdf96 -r b4ba343d3540 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Fri Feb 05 09:23:19 2010 -0500 +++ b/lib/galaxy/jobs/runners/pbs.py Fri Feb 05 10:04:04 2010 -0500 @@ -124,12 +124,27 @@ def determine_pbs_queue( self, url ): """Determine what PBS queue we are submitting to""" - url_split = url.split("/") - queue = url_split[3] - if queue == "": - # None == server's default queue - queue = None - return queue + try: + return url.split('/')[3] or None + except: + return None + + def determine_pbs_options( self, url ): + try: + opts = url.split('/')[4].strip().lstrip('-').split(' -') + assert opts != [''] + except: + return [] + rval = [] + for opt in opts: + name, value = opt.split( None, 1 ) + if name == 'l': + resource_attrs = value.split(',') + for j, ( res, val ) in enumerate( [ a.split('=', 1) for a in resource_attrs ] ): + rval.append( dict( name = pbs.ATTR_l, value = val, resource = res ) ) + else: + rval.append( dict( name = getattr( pbs, 'ATTR_' + name ), value = value ) ) + return rval def run_next( self ): """ @@ -175,6 +190,7 @@ ( pbs_server_name, runner_url ) = self.determine_pbs_server( runner_url, rewrite = True ) pbs_queue_name = self.determine_pbs_queue( runner_url ) + pbs_options = self.determine_pbs_options( runner_url ) c = pbs.pbs_connect( pbs_server_name ) if c <= 0: job_wrapper.fail( "Unable to queue job for execution. Resubmitting the job may succeed." ) @@ -185,7 +201,6 @@ ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id) efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id) - output_fnames = job_wrapper.get_output_fnames() # If an application server is set, we're staging @@ -195,28 +210,28 @@ output_files = [ str( o ) for o in output_fnames ] stagein = self.get_stage_in_out( job_wrapper.get_input_fnames() + output_files, symlink=True ) stageout = self.get_stage_in_out( output_files ) - job_attrs = pbs.new_attropl(5) - job_attrs[0].name = pbs.ATTR_o - job_attrs[0].value = pbs_ofile - job_attrs[1].name = pbs.ATTR_e - job_attrs[1].value = pbs_efile - job_attrs[2].name = pbs.ATTR_stagein - job_attrs[2].value = stagein - job_attrs[3].name = pbs.ATTR_stageout - job_attrs[3].value = stageout - job_attrs[4].name = pbs.ATTR_N - job_attrs[4].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) - exec_dir = os.path.abspath( job_wrapper.working_directory ) + attrs = [ + dict( name = pbs.ATTR_o, value = pbs_ofile ), + dict( name = pbs.ATTR_e, value = pbs_efile ), + dict( name = pbs.ATTR_stagein, value = stagein ), + dict( name = pbs.ATTR_stageout, value = stageout ), + ] # If not, we're using NFS else: - job_attrs = pbs.new_attropl(3) - job_attrs[0].name = pbs.ATTR_o - job_attrs[0].value = ofile - job_attrs[1].name = pbs.ATTR_e - job_attrs[1].value = efile - job_attrs[2].name = pbs.ATTR_N - job_attrs[2].value = "%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) - exec_dir = os.path.abspath( job_wrapper.working_directory ) + attrs = [ + dict( name = pbs.ATTR_o, value = ofile ), + dict( name = pbs.ATTR_e, value = efile ), + ] + + # define PBS job options + attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) ) + job_attrs = pbs.new_attropl( len( attrs ) + len( pbs_options ) ) + for i, attr in enumerate( attrs + pbs_options ): + job_attrs[i].name = attr['name'] + job_attrs[i].value = attr['value'] + if 'resource' in attr: + job_attrs[i].resource = attr['resource'] + exec_dir = os.path.abspath( job_wrapper.working_directory ) # write the job script if self.app.config.pbs_stage_path != '': diff -r 51a1369fdf96 -r b4ba343d3540 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Fri Feb 05 09:23:19 2010 -0500 +++ b/lib/galaxy/jobs/runners/sge.py Fri Feb 05 10:04:04 2010 -0500 @@ -94,12 +94,24 @@ def determine_sge_queue( self, url ): """Determine what SGE queue we are submitting to""" - url_split = url.split("/") - queue = url_split[3] - if queue == "": - # None == server's default queue - queue = None - return queue + try: + return url.split('/')[3] or None + except: + return None + + def determine_sge_project( self, url ): + """Determine what SGE project we are submitting to""" + try: + return url.split('/')[4] or None + except: + return None + + def determine_sge_tool_parameters( self, url ): + """Determine what are the tool's specific paramters""" + try: + return url.split('/')[5] or None + except: + return None def queue_job( self, job_wrapper ): """Create SGE script for a job and submit it to the SGE queue""" @@ -132,6 +144,8 @@ # TODO: support multiple cells log.warning( "(%s) Using multiple SGE cells is not supported. This job will be submitted to the default cell." % job_wrapper.job_id ) sge_queue_name = self.determine_sge_queue( runner_url ) + sge_project_name = self.determine_sge_project( runner_url ) + sge_extra_params = self.determine_sge_tool_parameters ( runner_url ) # define job attributes ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.job_id) @@ -140,8 +154,15 @@ jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.job_id) jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile + nativeSpec = [] if sge_queue_name is not None: - jt.setNativeSpecification( "-q %s" % sge_queue_name ) + nativeSpec.append( "-q '%s'" % sge_queue_name ) + if sge_project_name is not None: + nativeSpec.append( "-P '%s'" % sge_project_name) + if sge_extra_params is not None: + nativeSpec.append( sge_extra_params ) + if len(nativeSpec)>0: + jt.nativeSpecification = ' '.join(nativeSpec) script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) fh = file( jt.remoteCommand, "w" )

1 0

[hg] galaxy 3334: Update GeneTrack to provide tool_id as part of...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/51a1369fdf96 changeset: 3334:51a1369fdf96 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 09:23:19 2010 -0500 description: Update GeneTrack to provide tool_id as part of GALAXY_URL and rename provided 'id' to destination name of 'input'. diffstat: lib/galaxy/datatypes/tracks.py | 13 ++++++------- 1 files changed, 6 insertions(+), 7 deletions(-) diffs (33 lines): diff -r 7af418485514 -r 51a1369fdf96 lib/galaxy/datatypes/tracks.py --- a/lib/galaxy/datatypes/tracks.py Thu Feb 04 17:00:46 2010 -0500 +++ b/lib/galaxy/datatypes/tracks.py Fri Feb 05 09:23:19 2010 -0500 @@ -6,7 +6,7 @@ from galaxy import util from galaxy.web import url_for from galaxy.util.hash_util import hmac_new -import urllib +from urllib import quote_plus log = logging.getLogger(__name__) @@ -23,15 +23,14 @@ if hda.has_data: # Get the disk file name and data id file_name = hda.dataset.get_file_name() - data_id = urllib.quote_plus( str( hda.id ) ) #can we name this 'input' in the passed params instead of 'id' to prevent GT from having to map 'id' to 'input'? - galaxy_url = urllib.quote_plus( "%s%s" % ( base_url, url_for( controller = 'tool_runner' ) ) ) - tool_id = urllib.quote_plus( 'predict2genetrack' ) + data_id = quote_plus( str( hda.id ) ) + galaxy_url = quote_plus( "%s%s" % ( base_url, url_for( controller = 'tool_runner', tool_id='predict2genetrack' ) ) ) # Make it secure - hashkey = urllib.quote_plus( hmac_new( app.config.tool_secret, file_name ) ) - encoded = urllib.quote_plus( binascii.hexlify( file_name ) ) + hashkey = quote_plus( hmac_new( app.config.tool_secret, file_name ) ) + encoded = quote_plus( binascii.hexlify( file_name ) ) for name, url in util.get_genetrack_sites(): if name.lower() in app.config.genetrack_display_sites: # send both parameters filename and hashkey - link = "%s?filename=%s&hashkey=%s&id=%s&GALAXY_URL=%s&tool_id=%s" % ( url, encoded, hashkey, data_id, galaxy_url, tool_id ) + link = "%s?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, galaxy_url ) ret_val.append( ( name, link ) ) return ret_val

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[hg] galaxy 3333: LIMS data acquisition: now the data transfer u...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7af418485514 changeset: 3333:7af418485514 user: rc date: Thu Feb 04 17:00:46 2010 -0500 description: LIMS data acquisition: now the data transfer user logs out after the transfer is complete diffstat: lib/galaxy/web/controllers/requests_admin.py | 13 +++++++++-- scripts/galaxy_messaging/server/data_transfer.py | 26 +++++++++++++++++------ templates/admin/requests/show_request.mako | 2 +- 3 files changed, 30 insertions(+), 11 deletions(-) diffs (104 lines): diff -r ef0622415211 -r 7af418485514 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu Feb 04 16:23:32 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Feb 04 17:00:46 2010 -0500 @@ -1449,8 +1449,14 @@ dataset_files=sample.dataset_files) elif params.get( 'start_transfer_button', False ): for f in files_list: - sample.dataset_files.append([os.path.join(folder_path, f), - sample.transfer_status.NOT_STARTED]) + if f[-1] == os.sep: + # the selected item is a folder so transfer all the + # folder contents + sample.dataset_files.append([os.path.join(folder_path, f), + sample.transfer_status.NOT_STARTED]) + else: + sample.dataset_files.append([os.path.join(folder_path, f), + sample.transfer_status.NOT_STARTED]) trans.sa_session.add( sample ) trans.sa_session.flush() return self.__start_datatx(trans, sample) @@ -1547,7 +1553,8 @@ trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_datatx_page', - sample_id=trans.security.encode_id(sample.id))) + sample_id=trans.security.encode_id(sample.id), + folder_path=os.path.dirname(dfile))) diff -r ef0622415211 -r 7af418485514 scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py Thu Feb 04 16:23:32 2010 -0500 +++ b/scripts/galaxy_messaging/server/data_transfer.py Thu Feb 04 17:00:46 2010 -0500 @@ -44,6 +44,13 @@ logging.basicConfig(filename=logfile, level=logging.DEBUG, format="%(asctime)s [%(levelname)s] %(message)s") +class DataTransferException(Exception): + def __init__(self, value): + self.msg = value + def __str__(self): + return repr(self.msg) + + class DataTransfer(object): def __init__(self, host, username, password, remote_file, sample_id, @@ -102,14 +109,14 @@ self.error_and_exit() - def error_and_exit(self): + def error_and_exit(self, msg=''): ''' This method is called any exception is raised. This prints the traceback and terminates this script ''' logging.error(traceback.format_exc()) - logging.error('FATAL ERROR') - self.update_status('Error') + logging.error('FATAL ERROR.'+msg) + self.update_status('Error.'+msg) sys.exit(1) def transfer_file(self): @@ -159,7 +166,7 @@ url = "%s/user/create?email=%s&username=%s&password=%s&confirm=%s&create_user_button=Submit" % ( base_url, email, email, password, password ) f = opener.open(url) if f.read().find("Now logged in as "+email) == -1: - raise Exception + raise DataTransferException("The "+email+" user could not login to Galaxy") # after login, add dataset to the library params = urllib.urlencode(dict( cntrller='library_admin', tool_id='upload1', @@ -177,9 +184,14 @@ logging.debug(url) logging.debug(params) f = opener.open(url, params) - #print f.read() - except: - self.error_and_exit() + if f.read().find("Data Library") == -1: + raise DataTransferException("Dataset could not be uploaded to the data library") + # finally logout + f = opener.open(base_url+'/user/logout') + if f.read().find("You are no longer logged in.") == -1: + raise DataTransferException("The "+email+" user could not logout of Galaxy") + except DataTransferException, (e): + self.error_and_exit(e.msg) def update_status(self, status): ''' diff -r ef0622415211 -r 7af418485514 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Thu Feb 04 16:23:32 2010 -0500 +++ b/templates/admin/requests/show_request.mako Thu Feb 04 17:00:46 2010 -0500 @@ -43,7 +43,7 @@ </script> <style type="text/css"> .msg_head { - padding: 15px 0px; + padding: 10px 0px; cursor: pointer; }

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galaxy-dev February 2010