[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8166f7585484/ changeset: 8166f7585484 user: natefoo date: 2011-06-08 19:25:45 summary: Don't provde the output filename to the upload tool if it's outside Galaxy's files_path, since this means we're only linking data and the output paths are not used (and may contain non-shell-safe characters). Fixes issue #533. affected #: 1 file (299 bytes) --- a/tools/data_source/upload.xml Wed Jun 08 12:46:11 2011 -0400 +++ b/tools/data_source/upload.xml Wed Jun 08 13:25:45 2011 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.1.2"> +<tool name="Upload File" id="upload1" version="1.1.3"><description> from your computer </description> @@ -11,7 +11,12 @@ #while $varExists('output%i' % $outnum): #set $output = $getVar('output%i' % $outnum) #set $outnum += 1 - ${output.dataset.dataset.id}:${output.files_path}:${output} + #set $file_name = $output.file_name + ## FIXME: This is not future-proof for other uses of external_filename (other than for use by the library upload's "link data" feature) + #if $output.dataset.dataset.external_filename: + #set $file_name = "None" + #end if + ${output.dataset.dataset.id}:${output.files_path}:${file_name} #end while </command><inputs nginx_upload="true"> http://bitbucket.org/galaxy/galaxy-central/changeset/b2fa1535d02e/ changeset: b2fa1535d02e user: natefoo date: 2011-06-08 19:26:06 summary: merge. affected #: 6 files (2.7 KB) --- a/lib/galaxy/tools/__init__.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jun 08 13:26:06 2011 -0400 @@ -756,13 +756,14 @@ case.inputs = self.parse_input_elem( ElementTree.XML( "<when>%s</when>" % case_inputs ), enctypes, context ) else: - case.inputs = {} + case.inputs = odict() group.cases.append( case ) else: # Should have one child "input" which determines the case input_elem = elem.find( "param" ) assert input_elem is not None, "<conditional> must have a child <param>" group.test_param = self.parse_param_elem( input_elem, enctypes, context ) + possible_cases = list( group.test_param.legal_values ) #store possible cases, undefined whens will have no inputs # Must refresh when test_param changes group.test_param.refresh_on_change = True # And a set of possible cases @@ -771,6 +772,16 @@ case.value = case_elem.get( "value" ) case.inputs = self.parse_input_elem( case_elem, enctypes, context ) group.cases.append( case ) + try: + possible_cases.remove( case.value ) + except: + log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) ) + for unspecified_case in possible_cases: + log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) ) + case = ConditionalWhen() + case.value = unspecified_case + case.inputs = odict() + group.cases.append( case ) rval[group.name] = group elif elem.tag == "upload_dataset": group = UploadDataset() --- a/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:26:06 2011 -0400 @@ -318,7 +318,7 @@ checked = self.checked if value is not None: checked = form_builder.CheckboxField.is_checked( value ) - return form_builder.CheckboxField( self.name, checked ) + return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) def to_python( self, value, app ): @@ -330,6 +330,9 @@ return self.truevalue else: return self.falsevalue + @property + def legal_values( self ): + return [ self.truevalue, self.falsevalue ] class FileToolParameter( ToolParameter ): """ --- a/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:26:06 2011 -0400 @@ -414,7 +414,10 @@ return "Conditional (%s)" % self.name def get_current_case( self, value, trans ): # Convert value to user representation - str_value = self.test_param.filter_value( value, trans ) + if isinstance( value, bool ): + str_value = self.test_param.to_param_dict_string( value ) + else: + str_value = self.test_param.filter_value( value, trans ) # Find the matching case for index, case in enumerate( self.cases ): if str_value == case.value: --- a/lib/galaxy/web/form_builder.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Jun 08 13:26:06 2011 -0400 @@ -88,9 +88,17 @@ >>> print CheckboxField( "bar", checked="yes" ).get_html() <input type="checkbox" id="bar" name="bar" value="true" checked="checked"><input type="hidden" name="bar" value="true"> """ - def __init__( self, name, checked=None ): + def __init__( self, name, checked=None, refresh_on_change = False, refresh_on_change_values = None ): self.name = name self.checked = ( checked == True ) or ( isinstance( checked, basestring ) and ( checked.lower() in ( "yes", "true", "on" ) ) ) + self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values or [] + if self.refresh_on_change: + self.refresh_on_change_text = ' refresh_on_change="true" ' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s" ' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) + else: + self.refresh_on_change_text = '' def get_html( self, prefix="", disabled=False ): if self.checked: checked_text = ' checked="checked"' @@ -102,8 +110,8 @@ # parsing the request, the value 'true' in the hidden field actually means it is NOT checked. # See the is_checked() method below. The prefix is necessary in each case to ensure functional # correctness when the param is inside a conditional. - return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \ - % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), prefix, self.name, self.get_disabled_str( disabled ) ) + return '<input type="checkbox" id="%s" name="%s" value="true"%s%s%s><input type="hidden" name="%s%s" value="true"%s>' \ + % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), self.refresh_on_change_text, prefix, self.name, self.get_disabled_str( disabled ) ) @staticmethod def is_checked( value ): if value == True: @@ -253,7 +261,7 @@ <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div><div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ): + def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None ): self.name = name self.multiple = multiple or False self.size = size @@ -266,7 +274,7 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change - self.refresh_on_change_values = refresh_on_change_values + self.refresh_on_change_values = refresh_on_change_values or [] if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' if self.refresh_on_change_values: --- a/static/scripts/galaxy.base.js Wed Jun 08 13:25:45 2011 -0400 +++ b/static/scripts/galaxy.base.js Wed Jun 08 13:26:06 2011 -0400 @@ -588,6 +588,23 @@ select_field.get(0).form.submit(); }); + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']").click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + // Links with confirmation $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); --- a/static/scripts/packed/galaxy.base.js Wed Jun 08 13:25:45 2011 -0400 +++ b/static/scripts/packed/galaxy.base.js Wed Jun 08 13:26:06 2011 -0400 @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return 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async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+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");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStorage.deleteKey("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id,h=$(this).children("div.historyItemBody"),i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){var k;if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){k=$.jStorage.get("history_expand_state");if(k){delete k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};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}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("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");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(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);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file Repository URL: 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