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galaxy-dist commit 7327a60e3396: pbs_deljob bugfix from Glen Beane.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288287803 14400 # Node ID 7327a60e33968cb067edf6541cc84643f970180d # Parent 0b278c24c19f0a0f7a57b8a33bd6d992461c04c3 pbs_deljob bugfix from Glen Beane. --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -563,7 +563,7 @@ class PBSJobRunner( object ): if c <= 0: log.debug("(%s/%s) Connection to PBS server for job delete failed" % ( job.id, job.job_runner_external_id ) ) return - pbs.pbs_deljob( c, str( job.job_runner_external_id ), 'NULL' ) + pbs.pbs_deljob( c, str( job.job_runner_external_id ), '' ) pbs.pbs_disconnect( c ) log.debug( "(%s/%s) Removed from PBS queue before job completion" % ( job.id, job.job_runner_external_id ) )

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galaxy-dist commit 9c6040ab75a8: Fix for refresh_on_change javascript.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Daniel Blankenberg <dan(a)bx.psu.edu> # Date 1288196760 14400 # Node ID 9c6040ab75a8397a5708cfec4edfe216927b8220 # Parent a2e4d36c4318bc4ce73af9df869ae4071af33d55 Fix for refresh_on_change javascript. --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -290,8 +290,8 @@ function replace_big_select_inputs(min_l var try_refresh_fn = function() { // Get new value and see if it can be matched. var new_value = select_mapping[text_input_elt.attr('value')]; - if (new_value !== null && new_value !== undefined) { - if ($.inArray(new_value, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + if (last_selected_value !== new_value && new_value !== null && new_value !== undefined) { + if (ref_on_change_vals !== undefined && $.inArray(new_value, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { return; } text_input_elt.attr('value', new_value); --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.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")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#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,$(document).scr ollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).bind("click",c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d);return a}function show_hide_popupmenu_options(d,c,a){var a=(a===undefined?true:a);var b=new 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h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c. attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(n!==null&&n!==undefined){if($.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).rem ove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" 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h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c =$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.lo g_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{Cancel:function(){d.hide_modal()},"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c) ===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); +if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.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")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#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,$(document).scr ollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).bind("click",c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d);return a}function show_hide_popupmenu_options(d,c,a){var a=(a===undefined?true:a);var b=new RegExp(c);$(d).find("li").each(function(){if(b.exec($(this).text())){if(a){$(this).show()}else{$(this).hide()}}})}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("ta rget");c[$(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"));a.find("a").bind("click",function(b){b.stopPropagation();return true});make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c. attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(l!==n&&n!==null&&n!==undefined){if(h!==undefined&&$.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur( function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" 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h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function rese t_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};Ga laxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{Cancel:function(){d.hide_modal()},"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_val 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galaxy-dist commit 6a97d4fc4268: Update test data for GFF-to-BED to accomodate change made in 4475:aaacde471f03.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288198736 14400 # Node ID 6a97d4fc4268493480a0a3e7462e91f48d926a72 # Parent 121be69ca30675593dc9fc247a4b10a118fed227 Update test data for GFF-to-BED to accomodate change made in 4475:aaacde471f03. --- a/test-data/gff2bed_out2.bed +++ b/test-data/gff2bed_out2.bed @@ -1,3 +1,3 @@ -chr1 3204562 3661579 Xkr4 0 - 3204562 3204562 0 3 2487,200,947 0,207220,456070 -chr1 4481008 4486494 Sox17 0 - 4481008 4481008 0 5 1741,367,92,807,123 0,2172,2844,4208,5363 -chr1 4763278 4775807 Mrpl15 0 - 4763278 4763278 0 5 3604,124,166,155,154 0,4327,9370,10753,12375 +chr1 3204562 3661579 Xkr4 0 - 3204562 3661579 0 3 2487,200,947 0,207220,456070 +chr1 4481008 4486494 Sox17 0 - 4481008 4486494 0 5 1741,367,92,807,123 0,2172,2844,4208,5363 +chr1 4763278 4775807 Mrpl15 0 - 4763278 4775807 0 5 3604,124,166,155,154 0,4327,9370,10753,12375

1 0

galaxy-dist commit 243d80d9905a: adding setup_rabbitmq.sh script.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288197416 14400 # Node ID 243d80d9905af9121452f1a0955b2b49c076d66e # Parent 9c6040ab75a8397a5708cfec4edfe216927b8220 adding setup_rabbitmq.sh script. web api minor code fixes --- a/scripts/api/common.py +++ b/scripts/api/common.py @@ -91,7 +91,10 @@ def submit( api_key, url, data, return_f except urllib2.HTTPError, e: print e print e.read( 1024 ) - sys.exit( 1 ) + if return_formatted: + sys.exit( 1 ) + else: + return 'Error. '+ str( e ) if not return_formatted: return r print 'Response' --- /dev/null +++ b/setup_rabbitmq.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0` +python scripts/galaxy_messaging/server/setup_rabbitmq.py universe_wsgi.ini --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -184,10 +184,11 @@ class DataTransfer(object): url = "http://%s:%s/api/libraries/%s/contents" % ( self.server_host, self.server_port, api.encode_id( self.config_id_secret, self.library_id ) ) - log.debug(str((self.api_key, url, data))) + log.debug( str( ( self.api_key, url, data ) ) ) retval = api.submit( self.api_key, url, data, return_formatted=False ) - except: - self.error_and_exit(str(e)) + log.debug( str( retval ) ) + except Exception, e: + self.error_and_exit( str( e ) ) def update_status(self, status, dataset_id='All', msg=''): ''' @@ -212,7 +213,7 @@ class DataTransfer(object): api.encode_id( self.config_id_secret, self.request_id ) ) log.debug(str((self.api_key, url, data))) retval = api.update( self.api_key, url, data, return_formatted=False ) - log.debug('done.') + log.debug( str( retval ) ) except urllib2.URLError, e: log.debug( 'ERROR(sample_dataset_transfer_status (%s)): %s' % ( url, str(e) ) ) log.error(traceback.format_exc()) --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -11,13 +11,17 @@ import os, sys, csv, ConfigParser def main( config_file ): - config = ConfigParser.ConfigParser() - config.read( config_file ) - rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) - username = config.get( 'galaxy_amqp', 'userid' ) - password = config.get( 'galaxy_amqp', 'password' ) - virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) - + try: + config = ConfigParser.ConfigParser() + config.read( config_file ) + rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) + username = config.get( 'galaxy_amqp', 'userid' ) + password = config.get( 'galaxy_amqp', 'password' ) + virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) + except Exception, e: + print 'Fatal error:', str(e) + sys.exit(1) + cmd_list = [ 'add_user %s %s' % ( username, password ), 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ),

1 0

galaxy-dist commit 522c99a05163: fixed Lab menu access bug
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288298593 14400 # Node ID 522c99a05163c1816e9fe3be4c0b4ad05bff3ea0 # Parent 7327a60e33968cb067edf6541cc84643f970180d fixed Lab menu access bug fixed rabbitmq setup script bug --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -84,7 +84,7 @@ [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and trans.user.requests ) ) + tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.user.accessible_request_types() ) ) ) %> ## Visualization menu. --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -25,7 +25,7 @@ def main( config_file ): cmd_list = [ 'add_user %s %s' % ( username, password ), 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ), - 'set_permissions -p %s %s "%s.*" ".*" ".*"' % ( virtual_host, username, username ) + 'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username ) ] for cmd in cmd_list:

1 0

galaxy-dist commit a2e4d36c4318: Make fastx_barcode_splitter_galaxy_wrapper.sh invoke bash rather than sh.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1288189891 14400 # Node ID a2e4d36c4318bc4ce73af9df869ae4071af33d55 # Parent 0185bb614c7721d6edf6822ad973e589620b91f5 Make fastx_barcode_splitter_galaxy_wrapper.sh invoke bash rather than sh. --- a/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh +++ b/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009 A. Gordon (gordon(a)cshl.edu)

1 0

galaxy-dist commit 121be69ca306: Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1288197699 14400 # Node ID 121be69ca30675593dc9fc247a4b10a118fed227 # Parent 243d80d9905af9121452f1a0955b2b49c076d66e Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test. --- /dev/null +++ b/test-data/cuffdiff_out8.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out9.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out11.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out6.txt @@ -0,0 +1,88 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +XLOC_000001 - - - - chr1:3204754-3204833 0 0 0 0 0 0 +XLOC_000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +XLOC_000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +XLOC_000004 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +XLOC_000005 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +XLOC_000006 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +XLOC_000007 - - - - chr1:3189810-3190789 343500 342328 344672 947555 680603 1.21451e+06 +XLOC_000008 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +XLOC_000009 - - - - chr1:3191512-3192077 345096 343921 346271 1.07827e+06 822433 1.33412e+06 +XLOC_000010 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +XLOC_000011 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +XLOC_000012 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +XLOC_000013 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +XLOC_000014 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +XLOC_000015 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +XLOC_000016 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +XLOC_000017 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +XLOC_000018 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +XLOC_000019 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +XLOC_000020 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +XLOC_000021 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +XLOC_000022 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +XLOC_000023 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +XLOC_000024 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +XLOC_000025 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +XLOC_000026 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +XLOC_000027 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +XLOC_000028 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +XLOC_000029 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +XLOC_000030 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +XLOC_000031 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +XLOC_000032 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +XLOC_000033 - - - - chr1:3211521-3211561 0 0 0 0 0 0 +XLOC_000034 - - - - chr1:3212213-3212292 0 0 0 0 0 0 +XLOC_000035 - - - - chr1:3212367-3212439 0 0 0 0 0 0 +XLOC_000036 - - - - chr1:3212717-3212801 0 0 0 0 0 0 +XLOC_000037 - - - - chr1:3213095-3213192 0 0 0 0 0 0 +XLOC_000038 - - - - chr1:3240606-3240633 0 0 0 0 0 0 +XLOC_000039 - - - - chr1:3242479-3242512 0 0 0 0 0 0 +XLOC_000040 - - - - chr1:3242633-3242923 0 0 0 0 0 0 +XLOC_000041 - - - - chr1:3242924-3243005 0 0 0 0 0 0 +XLOC_000042 - - - - chr1:3243018-3243079 0 0 0 0 0 0 +XLOC_000043 - - - - chr1:3243108-3243154 0 0 0 0 0 0 +XLOC_000044 - - - - chr1:3243347-3243401 0 0 0 0 0 0 +XLOC_000045 - - - - chr1:3254079-3254106 0 0 0 0 0 0 +XLOC_000046 - - - - chr1:3256974-3257011 0 0 0 0 0 0 +XLOC_000047 - - - - chr1:3277155-3277182 0 0 0 0 0 0 +XLOC_000048 - - - - chr1:3277190-3277218 0 0 0 0 0 0 +XLOC_000049 - - - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +XLOC_000050 - - - - chr1:3280117-3280144 0 0 0 0 0 0 +XLOC_000051 - - - - chr1:3280498-3280525 0 0 0 0 0 0 +XLOC_000052 - - - - chr1:3280686-3280741 0 0 0 0 0 0 +XLOC_000053 - - - - chr1:3282504-3282531 0 0 0 0 0 0 +XLOC_000054 - - - - chr1:3282650-3282677 0 0 0 0 0 0 +XLOC_000055 - - - - chr1:3282760-3282832 0 0 0 0 0 0 +XLOC_000056 - - - - chr1:3284966-3284993 0 0 0 0 0 0 +XLOC_000057 - - - - chr1:3290488-3290553 0 0 0 0 0 0 +XLOC_000058 - - - - chr1:3290798-3290859 0 0 0 0 0 0 +XLOC_000059 - - - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +XLOC_000060 - - - - chr1:3299443-3299664 0 0 0 0 0 0 +XLOC_000061 - - - - chr1:3299691-3299733 0 0 0 0 0 0 +XLOC_000062 - - - - chr1:3300051-3300078 0 0 0 0 0 0 +XLOC_000063 - - - - chr1:3307748-3307775 0 0 0 0 0 0 +XLOC_000064 - - - - chr1:3318620-3318647 0 0 0 0 0 0 +XLOC_000065 - - - - chr1:3318999-3319051 0 0 0 0 0 0 +XLOC_000066 - - - - chr1:3330527-3330554 0 0 0 0 0 0 +XLOC_000067 - - - - chr1:3351240-3351311 0 0 0 0 0 0 +XLOC_000068 - - - - chr1:3355887-3356119 0 0 0 0 0 0 +XLOC_000069 - - - - chr1:3356180-3356225 0 0 0 0 0 0 +XLOC_000070 - - - - chr1:3363076-3363176 0 0 0 0 0 0 +XLOC_000071 - - - - chr1:3363214-3363278 0 0 0 0 0 0 +XLOC_000072 - - - - chr1:3363387-3363446 0 0 0 0 0 0 +XLOC_000073 - - - - chr1:3363753-3363849 0 0 0 0 0 0 +XLOC_000074 - - - - chr1:3364871-3364919 0 0 0 0 0 0 +XLOC_000075 - - - - chr1:3367135-3367162 0 0 0 0 0 0 +XLOC_000076 - - - - chr1:3367210-3367237 0 0 0 0 0 0 +XLOC_000077 - - - - chr1:3367333-3367382 0 0 0 0 0 0 +XLOC_000078 - - - - chr1:3369580-3369607 0 0 0 0 0 0 +XLOC_000079 - - - - chr1:3375001-3375028 0 0 0 0 0 0 +XLOC_000080 - - - - chr1:3377211-3377262 0 0 0 0 0 0 +XLOC_000081 - - - - chr1:3379888-3379915 0 0 0 0 0 0 +XLOC_000082 - - - - chr1:3386739-3386836 0 0 0 0 0 0 +XLOC_000083 - - - - chr1:3391325-3391352 0 0 0 0 0 0 +XLOC_000084 - - - - chr1:3435841-3435880 0 0 0 0 0 0 +XLOC_000085 - - - - chr1:3447761-3447788 0 0 0 0 0 0 +XLOC_000086 - - - - chr1:3450906-3450965 0 0 0 0 0 0 +XLOC_000087 - - - - chr1:3451051-3451109 0 0 0 0 0 0 --- /dev/null +++ b/test-data/cuffdiff_out10.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out7.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out1.txt @@ -0,0 +1,99 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +TCONS_00000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +TCONS_00000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +TCONS_00000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +TCONS_00000004 - chr1:3189810-3190789 q1 q2 OK 0 645918 6.95322e-310 1.79769e+308 0 yes +TCONS_00000005 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000006 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000007 - chr1:3191512-3192077 q1 q2 OK 0 704881 6.95322e-310 1.79769e+308 0 yes +TCONS_00000008 - chr1:3191512-3192077 q1 q2 OK 0 0 0 0 1 no +TCONS_00000009 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +TCONS_00000010 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +TCONS_00000011 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +TCONS_00000012 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +TCONS_00000013 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +TCONS_00000014 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +TCONS_00000015 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +TCONS_00000016 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +TCONS_00000017 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +TCONS_00000018 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000019 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +TCONS_00000020 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +TCONS_00000021 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000022 - chr1:3201077-3201481 q1 q2 OK 0 155328 0 1.79769e+308 0 yes +TCONS_00000023 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +TCONS_00000024 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +TCONS_00000025 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +TCONS_00000026 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +TCONS_00000027 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +TCONS_00000028 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +TCONS_00000029 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +TCONS_00000030 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +TCONS_00000031 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +TCONS_00000032 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 no +TCONS_00000033 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +TCONS_00000034 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +TCONS_00000035 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000036 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000037 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000038 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +TCONS_00000039 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +TCONS_00000040 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000041 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +TCONS_00000042 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +TCONS_00000043 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +TCONS_00000044 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +TCONS_00000045 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +TCONS_00000046 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000047 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +TCONS_00000048 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +TCONS_00000049 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +TCONS_00000050 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no +TCONS_00000051 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +TCONS_00000052 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +TCONS_00000053 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +TCONS_00000054 - chr1:3189810-3190789 q1 q2 OK 343500 303241 -0.124659 2.28891 0.0220846 no +TCONS_00000055 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +TCONS_00000056 - chr1:3191512-3192077 q1 q2 OK 345096 376320 0.0866161 -1.17079 0.241685 no +TCONS_00000057 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +TCONS_00000058 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +TCONS_00000059 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000060 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +TCONS_00000061 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +TCONS_00000062 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +TCONS_00000063 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 no +TCONS_00000064 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +TCONS_00000065 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +TCONS_00000066 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +TCONS_00000067 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +TCONS_00000068 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +TCONS_00000069 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +TCONS_00000070 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +TCONS_00000071 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +TCONS_00000072 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +TCONS_00000073 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +TCONS_00000074 - chr1:3277913-3278390 q1 q2 OK 165459 0 0 2.22507e-308 0 yes +TCONS_00000075 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +TCONS_00000076 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +TCONS_00000077 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +TCONS_00000078 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +TCONS_00000079 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +TCONS_00000080 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +TCONS_00000081 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +TCONS_00000082 - chr1:3290919-3291273 q1 q2 OK 163613 0 0 2.22507e-308 0 yes +TCONS_00000083 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000084 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000085 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +TCONS_00000086 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +TCONS_00000087 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +TCONS_00000088 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +TCONS_00000089 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000090 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +TCONS_00000091 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +TCONS_00000092 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +TCONS_00000093 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +TCONS_00000094 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +TCONS_00000095 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +TCONS_00000096 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +TCONS_00000097 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +TCONS_00000098 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -73,11 +73,21 @@ <param name="min_mapqual" value="0" ftype="sam" /><param name="min_alignment_count" value="0" ftype="sam" /><param name="sPaired" value="single" ftype="sam" /> - -  -  + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/> + <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> + <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="8"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="4"/> + <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> + <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> + <output name="splicing_diff" file="cuffdiff_out9.txt"/> + <output name="promoters_diff" file="cuffdiff_out10.txt"/> + <output name="cds_diff" file="cuffdiff_out11.txt"/></test></tests> --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -111,13 +111,13 @@ def __main__(): shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds_exp.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_promoters.diff" ), options.promoters_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) except Exception, e: stop_err( 'Error in cuffdiff:\n' + str( e ) ) finally: --- /dev/null +++ b/test-data/cuffdiff_out5.txt @@ -0,0 +1,99 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 0 0 0 +TCONS_00000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +TCONS_00000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +TCONS_00000004 - - - - chr1:3189810-3190789 0 0 0 645918 357201 934636 +TCONS_00000005 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000006 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000007 - - - - chr1:3191512-3192077 0 0 0 704881 400219 1.00954e+06 +TCONS_00000008 - - - - chr1:3191512-3192077 0 0 0 0 0 0 +TCONS_00000009 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +TCONS_00000010 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +TCONS_00000011 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +TCONS_00000012 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +TCONS_00000013 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +TCONS_00000014 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +TCONS_00000015 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +TCONS_00000016 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +TCONS_00000017 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +TCONS_00000018 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +TCONS_00000019 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +TCONS_00000020 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +TCONS_00000021 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +TCONS_00000022 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +TCONS_00000023 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +TCONS_00000024 i Xkr4 - - chr1:3212213-3212292 0 0 0 0 0 0 +TCONS_00000025 i Xkr4 - - chr1:3212367-3212439 0 0 0 0 0 0 +TCONS_00000026 i Xkr4 - - chr1:3213095-3213192 0 0 0 0 0 0 +TCONS_00000027 i Xkr4 - - chr1:3242633-3242923 0 0 0 0 0 0 +TCONS_00000028 i Xkr4 - - chr1:3243018-3243079 0 0 0 0 0 0 +TCONS_00000029 i Xkr4 - - chr1:3243347-3243401 0 0 0 0 0 0 +TCONS_00000030 i Xkr4 - - chr1:3256974-3257011 0 0 0 0 0 0 +TCONS_00000031 i Xkr4 - - chr1:3277190-3277218 0 0 0 0 0 0 +TCONS_00000032 i Xkr4 - - chr1:3277913-3278390 0 0 0 0 0 0 +TCONS_00000033 i Xkr4 - - chr1:3280686-3280741 0 0 0 0 0 0 +TCONS_00000034 i Xkr4 - - chr1:3290488-3290553 0 0 0 0 0 0 +TCONS_00000035 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000036 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000037 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000038 i Xkr4 - - chr1:3300051-3300078 0 0 0 0 0 0 +TCONS_00000039 i Xkr4 - - chr1:3318999-3319051 0 0 0 0 0 0 +TCONS_00000040 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000041 i Xkr4 - - chr1:3363214-3363278 0 0 0 0 0 0 +TCONS_00000042 i Xkr4 - - chr1:3363753-3363849 0 0 0 0 0 0 +TCONS_00000043 i Xkr4 - - chr1:3367135-3367162 0 0 0 0 0 0 +TCONS_00000044 i Xkr4 - - chr1:3367333-3367382 0 0 0 0 0 0 +TCONS_00000045 i Xkr4 - - chr1:3377211-3377262 0 0 0 0 0 0 +TCONS_00000046 i Xkr4 - - chr1:3391325-3391352 0 0 0 0 0 0 +TCONS_00000047 i Xkr4 - - chr1:3435841-3435880 0 0 0 0 0 0 +TCONS_00000048 i Xkr4 - - chr1:3447761-3447788 0 0 0 0 0 0 +TCONS_00000049 i Xkr4 - - chr1:3450906-3450965 0 0 0 0 0 0 +TCONS_00000050 i Xkr4 - - chr1:3451051-3451109 0 0 0 0 0 0 +TCONS_00000051 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +TCONS_00000052 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +TCONS_00000053 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +TCONS_00000054 - - - - chr1:3189810-3190789 343500 342328 344672 303241 270227 336255 +TCONS_00000055 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +TCONS_00000056 - - - - chr1:3191512-3192077 345096 343921 346271 376320 320653 431986 +TCONS_00000057 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +TCONS_00000058 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +TCONS_00000059 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +TCONS_00000060 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +TCONS_00000061 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +TCONS_00000062 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +TCONS_00000063 - - - - chr1:3201077-3201481 0 0 0 0 0 0 +TCONS_00000064 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +TCONS_00000065 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +TCONS_00000066 i Xkr4 - - chr1:3211521-3211561 0 0 0 0 0 0 +TCONS_00000067 i Xkr4 - - chr1:3212717-3212801 0 0 0 0 0 0 +TCONS_00000068 i Xkr4 - - chr1:3240606-3240633 0 0 0 0 0 0 +TCONS_00000069 i Xkr4 - - chr1:3242479-3242512 0 0 0 0 0 0 +TCONS_00000070 i Xkr4 - - chr1:3242924-3243005 0 0 0 0 0 0 +TCONS_00000071 i Xkr4 - - chr1:3243108-3243154 0 0 0 0 0 0 +TCONS_00000072 i Xkr4 - - chr1:3254079-3254106 0 0 0 0 0 0 +TCONS_00000073 i Xkr4 - - chr1:3277155-3277182 0 0 0 0 0 0 +TCONS_00000074 i Xkr4 - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +TCONS_00000075 i Xkr4 - - chr1:3280117-3280144 0 0 0 0 0 0 +TCONS_00000076 i Xkr4 - - chr1:3280498-3280525 0 0 0 0 0 0 +TCONS_00000077 i Xkr4 - - chr1:3282504-3282531 0 0 0 0 0 0 +TCONS_00000078 i Xkr4 - - chr1:3282650-3282677 0 0 0 0 0 0 +TCONS_00000079 i Xkr4 - - chr1:3282760-3282832 0 0 0 0 0 0 +TCONS_00000080 i Xkr4 - - chr1:3284966-3284993 0 0 0 0 0 0 +TCONS_00000081 i Xkr4 - - chr1:3290798-3290859 0 0 0 0 0 0 +TCONS_00000082 i Xkr4 - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +TCONS_00000083 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000084 i Xkr4 - - chr1:3299691-3299733 0 0 0 0 0 0 +TCONS_00000085 i Xkr4 - - chr1:3307748-3307775 0 0 0 0 0 0 +TCONS_00000086 i Xkr4 - - chr1:3318620-3318647 0 0 0 0 0 0 +TCONS_00000087 i Xkr4 - - chr1:3330527-3330554 0 0 0 0 0 0 +TCONS_00000088 i Xkr4 - - chr1:3351240-3351311 0 0 0 0 0 0 +TCONS_00000089 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000090 i Xkr4 - - chr1:3356180-3356225 0 0 0 0 0 0 +TCONS_00000091 i Xkr4 - - chr1:3363076-3363176 0 0 0 0 0 0 +TCONS_00000092 i Xkr4 - - chr1:3363387-3363446 0 0 0 0 0 0 +TCONS_00000093 i Xkr4 - - chr1:3364871-3364919 0 0 0 0 0 0 +TCONS_00000094 i Xkr4 - - chr1:3367210-3367237 0 0 0 0 0 0 +TCONS_00000095 i Xkr4 - - chr1:3369580-3369607 0 0 0 0 0 0 +TCONS_00000096 i Xkr4 - - chr1:3375001-3375028 0 0 0 0 0 0 +TCONS_00000097 i Xkr4 - - chr1:3379888-3379915 0 0 0 0 0 0 +TCONS_00000098 i Xkr4 - - chr1:3386739-3386836 0 0 0 0 0 0 --- a/test-data/cuffdiff_out5.tracking +++ /dev/null @@ -1,2 +0,0 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q0_FPKM q0_conf_lo q0_conf_hi q1_FPKM q1_conf_lo q1_conf_hi -TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 67745 0 163551 --- /dev/null +++ b/test-data/cuffdiff_out2.txt @@ -0,0 +1,88 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 343500 949159 1.01639 -7.54436 4.55191e-14 yes +XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 345096 1.0812e+06 1.142 -9.91597 0 yes +XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 155328 6.95322e-310 1.79769e+308 0 yes +XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 165459 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 163613 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no +XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no --- /dev/null +++ b/test-data/cuffdiff_out3.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out4.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant

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galaxy-dist commit 49c7938d5827: sample tracking web api cleaned up
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288122647 14400 # Node ID 49c7938d582799125a89f0d6ba38be0ddc6f4b4f # Parent d73fa5f14b013333b2e49bfbf775db8dd0197e2b sample tracking web api cleaned up - added a samples controller --- /dev/null +++ b/lib/galaxy/web/api/samples.py @@ -0,0 +1,44 @@ +""" +API operations on a sample tracking system. +""" +import logging, os, string, shutil, urllib, re, socket +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 * +from galaxy.util.bunch import Bunch + +log = logging.getLogger( __name__ ) + +class SamplesController( BaseController ): + + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/requests/{encoded_request_id}/samples + Displays a collection (list) of sample of a sequencing request. + """ + try: + request_id = trans.security.decode_id( kwd[ 'request_id' ] ) + except TypeError: + trans.response.status = 400 + return "Malformed request id ( %s ) specified, unable to decode." % str( encoded_request_id ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + rval = [] + for sample in request.samples: + item = sample.get_api_value() + item['url'] = url_for( 'samples', + request_id=trans.security.encode_id( request_id ), + id=trans.security.encode_id( sample.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + rval.append( item ) + return rval + + --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1767,6 +1767,7 @@ class RequestTypePermissions( object ): class Sample( object ): bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) + api_collection_visible_keys = ( 'id', 'name' ) def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None): self.name = name self.desc = desc @@ -1818,6 +1819,18 @@ class Sample( object ): pexpect.TIMEOUT:print_ticks}, timeout=10) return output.replace(filepath, '').strip() + def get_api_value( self, view='collection' ): + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[key] = self.__getattribute__( key ) + except AttributeError: + rval[key] = None + return rval class SampleState( object ): def __init__(self, name=None, desc=None, request_type=None): --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -104,8 +104,15 @@ def app_factory( global_conf, **kwargs ) # If enabled, add the web API if asbool( kwargs.get( 'enable_api', False ) ): add_api_controllers( webapp, app ) - webapp.api_mapper.resource( 'content', 'contents', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'content', + 'contents', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) + webapp.api_mapper.resource( 'sample', + 'samples', + path_prefix='/api/requests/:request_id', + parent_resources=dict( member_name='request', collection_name='requests' ) ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware --- a/lib/galaxy/web/api/requests.py +++ b/lib/galaxy/web/api/requests.py @@ -22,23 +22,57 @@ class RequestsController( BaseController GET /api/requests Displays a collection (list) of sequencing requests. """ - query = trans.sa_session.query( trans.app.model.Request )\ - .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ - and trans.app.model.Request.table.c.deleted == False ) ) \ - .all() + # if admin user then return all requests + if trans.user_is_admin(): + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( trans.app.model.Request.table.c.deleted == False )\ + .all() + else: + query = trans.sa_session.query( trans.app.model.Request )\ + .filter( and_( trans.app.model.Request.table.c.user_id == trans.user.id \ + and trans.app.model.Request.table.c.deleted == False ) ) \ + .all() rval = [] for request in query: item = request.get_api_value() item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) item['id'] = trans.security.encode_id( item['id'] ) + if trans.user_is_admin(): + item['user'] = request.user.email rval.append( item ) return rval - + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/requests/{encoded_request_id} + Displays details of a sequencing request. + """ + try: + request_id = trans.security.decode_id( id ) + except TypeError: + trans.response.status = 400 + return "Malformed %s id ( %s ) specified, unable to decode." % ( update_type, str( id ) ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( request_id ) + except: + request = None + if not request or not ( trans.user_is_admin() or request.user.id == trans.user.id ): + trans.response.status = 400 + return "Invalid request id ( %s ) specified." % str( request_id ) + item = request.get_api_value() + item['url'] = url_for( 'requests', id=trans.security.encode_id( request.id ) ) + item['id'] = trans.security.encode_id( item['id'] ) + item['user'] = request.user.email + item['num_of_samples'] = len(request.samples) + return item + @web.expose_api def update( self, trans, id, key, payload, **kwd ): """ PUT /api/requests/{encoded_request_id} - Displays information about a sequencing request. + Updates a request state, sample state or sample dataset transfer status + depending on the update_type """ params = util.Params( kwd ) update_type = None @@ -124,7 +158,3 @@ class RequestsController( BaseController new_status=new_status, error_msg=error_msg ) return status, output - - - -

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galaxy-dist commit e5f90080a2db: Merge with 29157e97e95453c5f9022d9c571527a6de4032e1
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288149696 14400 # Node ID e5f90080a2db9c16bad2300c5ef0b5c49a558638 # Parent 61c786bd2efb6f9cc4d5fa4d43dfb056ed99b909 # Parent 29157e97e95453c5f9022d9c571527a6de4032e1 Merge with 29157e97e95453c5f9022d9c571527a6de4032e1

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galaxy-dist commit 29157e97e954: Added setup script to configure RabbitMQ
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1288148662 14400 # Node ID 29157e97e95453c5f9022d9c571527a6de4032e1 # Parent af2d04e3568078d8d7ad94e229a17983f8282e20 Added setup script to configure RabbitMQ --- a/transfer_datasets.ini.sample +++ b/transfer_datasets.ini.sample @@ -3,13 +3,8 @@ [data_transfer_user_login_info] #email = datatx(a)bx.psu.edu #password = datatx - -# The following section contains 4 config variables neede for the data transfer. -# Please copy the exact values for each of these variables from the universe_wsgi.ini -# configuration file for this installation +#api_key = Generate it from the User menu in Galaxy [universe_wsgi_config] -#host = 127.0.0.1 -#port = -#database_connection = -#library_import_dir = +# The http server section name in the Galaxy config file (universe_wsgi.ini) +#http_server_section = server:main --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -420,4 +420,4 @@ upload1 = local:/// #queue = galaxy_queue #exchange = galaxy_exchange #routing_key = bar_code_scanner - +#rabbitmqctl_path = /path/to/rabbitmqctl --- /dev/null +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -0,0 +1,34 @@ +# +# Configuration script for RabbitMQ in Galaxy +# +# Requirements: +# - set the rabbitmqctl_path variable in the 'galaxy_amqp' section in Galaxy config file +# +# Usage: +# $ python setup_rabbitmq.py <Galaxy config file> +# + +import os, sys, csv, ConfigParser + +def main( config_file ): + config = ConfigParser.ConfigParser() + config.read( config_file ) + rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) + username = config.get( 'galaxy_amqp', 'userid' ) + password = config.get( 'galaxy_amqp', 'password' ) + virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) + + cmd_list = [ + 'add_user %s %s' % ( username, password ), + 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ), + 'set_permissions -p %s %s "%s.*" ".*" ".*"' % ( virtual_host, username, username ) + ] + + for cmd in cmd_list: + retval = os.system( rabbitmqctl_path + ' ' + cmd ) + if retval: + print "Failed command: %s" % cmd + sys.exit(1) + +if __name__ == '__main__': + main( sys.argv[1] )

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