galaxy-commits June 2010

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galaxy-dist commit 48ec25db21c3: Fix model_class typo.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275923167 14400 # Node ID 48ec25db21c3bd76b52bcd68a1301f777eea280e # Parent f47ab71b2df3c27c7d231522c848b5e5ee2d2fe7 Fix model_class typo. --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -129,7 +129,7 @@ class HistoryDatasetAssociationSelection model_class = model.HistoryDatasetAssociation columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", "tags", model_class=model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),

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galaxy-dist commit f08dff0dd4ac: Allow disabling of library download compression types
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275924310 14400 # Node ID f08dff0dd4ac92c5d9b75792c2c5c38eb280e81b # Parent 4fb747f317d0b2c36ffb5fbf4b815caf4cb6ace1 Allow disabling of library download compression types --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -109,6 +109,13 @@ class LibraryCommon( BaseController ): comptypes_t = comptypes if trans.app.config.nginx_x_archive_files_base: comptypes_t = ['ngxzip'] + for comptype in trans.app.config.disable_library_comptypes: + # TODO: do this once, not every time (we're gonna raise an + # exception every time after the first time) + try: + comptypes_t.remove( comptype ) + except: + pass return trans.fill_template( '/library/common/browse_library.mako', cntrller=cntrller, use_panels=use_panels, --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -98,6 +98,7 @@ class Configuration( object ): if self.user_library_import_dir is not None and not os.path.exists( self.user_library_import_dir ): raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) + self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) # Configuration options for taking advantage of nginx features self.upstream_gzip = string_as_bool( kwargs.get( 'upstream_gzip', False ) ) self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False )

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galaxy-dist commit f47ab71b2df3: Fix autocomplete select not closing after dragging text inside, and holding arrow keys not triggering multiple times in firefox. Cleanup JS
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1275864909 14400 # Node ID f47ab71b2df3c27c7d231522c848b5e5ee2d2fe7 # Parent 9114bd0887769b9ffe570b71f90ab95be68baa44 Fix autocomplete select not closing after dragging text inside, and holding arrow keys not triggering multiple times in firefox. Cleanup JS --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -147,7 +147,7 @@ function naturalSort(a, b){ // Replace select box with a text input box + autocomplete. function replace_big_select_inputs(min_length) { // To do replace, jQuery's autocomplete plugin must be loaded. - if (typeof jQuery().autocomplete == "undefined") + if (!jQuery().autocomplete) return; // Set default for min_length. @@ -174,10 +174,10 @@ function replace_big_select_inputs(min_l text_input_elt.attr('id', select_elt.attr('id')); text_input_elt.click( function() { // Show all. Also provide note that load is happening since this can be slow. - var cur_value = $(this).attr('value'); - $(this).attr('value', 'Loading...'); + var cur_value = $(this).val(); + $(this).val('Loading...'); $(this).showAllInCache(); - $(this).attr('value', cur_value); + $(this).val(cur_value); $(this).select(); }); --- a/static/scripts/jquery.autocomplete.js +++ b/static/scripts/jquery.autocomplete.js @@ -17,819 +17,817 @@ String.prototype.endsWith = function(str var return_key_pressed_for_autocomplete = false; ;(function($) { - + $.fn.extend({ - autocomplete: function(urlOrData, options) { - var isUrl = typeof urlOrData == "string"; - options = $.extend({}, $.Autocompleter.defaults, { - url: isUrl ? urlOrData : null, - data: isUrl ? null : urlOrData, - delay: isUrl ? $.Autocompleter.defaults.delay : 10, - max: options && !options.scroll ? 10 : 150 - }, options); - - // if highlight is set to false, replace it with a do-nothing function - options.highlight = options.highlight || function(value) { return value; }; - - // if the formatMatch option is not specified, then use formatItem for backwards compatibility - options.formatMatch = options.formatMatch || options.formatItem; - - return this.each(function() { - new $.Autocompleter(this, options); - }); - }, - result: function(handler) { - return this.bind("result", handler); - }, - search: function(handler) { - return this.trigger("search", [handler]); - }, - flushCache: function() { + autocomplete: function(urlOrData, options) { + var isUrl = typeof urlOrData == "string"; + options = $.extend({}, $.Autocompleter.defaults, { + url: isUrl ? urlOrData : null, + data: isUrl ? null : urlOrData, + delay: isUrl ? $.Autocompleter.defaults.delay : 10, + max: options && !options.scroll ? 10 : 150 + }, options); + + // if highlight is set to false, replace it with a do-nothing function + options.highlight = options.highlight || function(value) { return value; }; + + // if the formatMatch option is not specified, then use formatItem for backwards compatibility + options.formatMatch = options.formatMatch || options.formatItem; + + return this.each(function() { + new $.Autocompleter(this, options); + }); + }, + result: function(handler) { + return this.bind("result", handler); + }, + search: function(handler) { + return this.trigger("search", [handler]); + }, + flushCache: function() { return this.trigger("flushCache"); - }, - setOptions: function(options){ - return this.trigger("setOptions", [options]); - }, - unautocomplete: function() { - return this.trigger("unautocomplete"); - }, - // JG: add method to show all data in cache. + }, + setOptions: function(options){ + return this.trigger("setOptions", [options]); + }, + unautocomplete: function() { + return this.trigger("unautocomplete"); + }, + // JG: add method to show all data in cache. showAllInCache: function() { - return this.trigger("showAllInCache"); - } + return this.trigger("showAllInCache"); + } }); $.Autocompleter = function(input, options) { - var KEY = { - UP: 38, - DOWN: 40, - DEL: 46, - TAB: 9, - RETURN: 13, - ESC: 27, - COMMA: 188, - PAGEUP: 33, - PAGEDOWN: 34, - BACKSPACE: 8, - COLON: 16 - }; + var KEY = { + UP: 38, + DOWN: 40, + DEL: 46, + TAB: 9, + RETURN: 13, + ESC: 27, + COMMA: 188, + PAGEUP: 33, + PAGEDOWN: 34, + BACKSPACE: 8, + COLON: 16 + }; - // Create $ object for input element - var $input = $(input).attr("autocomplete", "off").addClass(options.inputClass); + // Create $ object for input element + var $input = $(input).attr("autocomplete", "off").addClass(options.inputClass); - var timeout; - var previousValue = ""; - var cache = $.Autocompleter.Cache(options); - var hasFocus = 0; - var lastKeyPressCode; - var config = { - mouseDownOnSelect: false - }; - var select = $.Autocompleter.Select(options, input, selectCurrent, config); - - var blockSubmit; - - // prevent form submit in opera when selecting with return key - $.browser.opera && $(input.form).bind("submit.autocomplete", function() { - if (blockSubmit) { - blockSubmit = false; - return false; - } - }); - - // only opera doesn't trigger keydown multiple times while pressed, others don't work with keypress at all - $input.bind(($.browser.opera ? "keypress" : "keydown") + ".autocomplete", function(event) { - // track last key pressed - lastKeyPressCode = event.keyCode; - switch(event.keyCode) { - - case KEY.UP: - event.preventDefault(); - if ( select.visible() ) { - select.prev(); - } else { - onChange(0, true); - } - break; - - case KEY.DOWN: - event.preventDefault(); - if ( select.visible() ) { - select.next(); - } else { - onChange(0, true); - } - break; - - case KEY.PAGEUP: - event.preventDefault(); - if ( select.visible() ) { - select.pageUp(); - } else { - onChange(0, true); - } - break; - - case KEY.PAGEDOWN: - event.preventDefault(); - if ( select.visible() ) { - select.pageDown(); - } else { - onChange(0, true); - } - break; - - // matches also semicolon - case options.multiple && $.trim(options.multipleSeparator) == "," && KEY.COMMA: - case KEY.TAB: - case KEY.RETURN: - if (event.keyCode == KEY.RETURN) - return_key_pressed_for_autocomplete = false; - if( selectCurrent() ) { - // stop default to prevent a form submit, Opera needs special handling - event.preventDefault(); - blockSubmit = true; - - // JG: set flag to indicate that a selection just occurred using the return key. FYI: - // event.stopPropagation() does not work. - if (event.keyCode == KEY.RETURN) - return_key_pressed_for_autocomplete = true; - - return false; - } - - case KEY.ESC: - select.hide(); - break; - case KEY.COLON: - break; - - default: - clearTimeout(timeout); - timeout = setTimeout(onChange, options.delay); - break; - } - }).focus(function(){ - // track whether the field has focus, we shouldn't process any - // results if the field no longer has focus - hasFocus++; - }).blur(function() { - hasFocus = 0; - if (!config.mouseDownOnSelect) { - // JG: if blur and user is not selecting with mouse, hide - // object. - select.hide(); - } - return this; - }).click(function() { - // show select when clicking in a focused field - if ( hasFocus++ > 1 && !select.visible() ) { - onChange(0, true); - } - return this; - }).bind("search", function() { - // TODO why not just specifying both arguments? - var fn = (arguments.length > 1) ? arguments[1] : null; - function findValueCallback(q, data) { - var result; - if( data && data.length ) { - for (var i=0; i < data.length; i++) { - if( data[i].result.toLowerCase() == q.toLowerCase() ) { - result = data[i]; - break; - } - } - } - if( typeof fn == "function" ) fn(result); - else $input.trigger("result", result && [result.data, result.value]); - } - $.each(trimWords($input.val()), function(i, value) { - request(value, findValueCallback, findValueCallback); - }); + var timeout; + var previousValue = ""; + var cache = $.Autocompleter.Cache(options); + var hasFocus = 0; + var lastKeyPressCode; + var config = { + mouseDownOnSelect: false + }; + var select = $.Autocompleter.Select(options, input, selectCurrent, config); + + var blockSubmit; + + // prevent form submit in opera when selecting with return key + $.browser.opera && $(input.form).bind("submit.autocomplete", function() { + if (blockSubmit) { + blockSubmit = false; + return false; + } + }); + + // Firefox only triggers holding down a key with keypress + $input.bind(($.browser.mozilla ? "keypress" : "keydown") + ".autocomplete", function(event) { + // track last key pressed + lastKeyPressCode = event.keyCode; + switch(event.keyCode) { + + case KEY.UP: + event.preventDefault(); + if ( select.visible() ) { + select.prev(); + } else { + onChange(0, true); + } + break; + + case KEY.DOWN: + event.preventDefault(); + if ( select.visible() ) { + select.next(); + } else { + onChange(0, true); + } + break; + + case KEY.PAGEUP: + event.preventDefault(); + if ( select.visible() ) { + select.pageUp(); + } else { + onChange(0, true); + } + break; + + case KEY.PAGEDOWN: + event.preventDefault(); + if ( select.visible() ) { + select.pageDown(); + } else { + onChange(0, true); + } + break; + + // matches also semicolon + case options.multiple && $.trim(options.multipleSeparator) == "," && KEY.COMMA: + case KEY.TAB: + case KEY.RETURN: + if (event.keyCode == KEY.RETURN) + return_key_pressed_for_autocomplete = false; + if( selectCurrent() ) { + // stop default to prevent a form submit, Opera needs special handling + event.preventDefault(); + blockSubmit = true; + + // JG: set flag to indicate that a selection just occurred using the return key. FYI: + // event.stopPropagation() does not work. + if (event.keyCode == KEY.RETURN) + return_key_pressed_for_autocomplete = true; + + return false; + } + + case KEY.ESC: + select.hide(); + break; + case KEY.COLON: + break; + + default: + clearTimeout(timeout); + timeout = setTimeout(onChange, options.delay); + break; + } + }).focus(function(){ + // track whether the field has focus, we shouldn't process any + // results if the field no longer has focus + hasFocus++; + }).blur(function() { + hasFocus = 0; + if (!config.mouseDownOnSelect) { + // JG: if blur and user is not selecting with mouse, hide + // object. + select.hide(); + } + return this; + }).click(function() { + // show select when clicking in a focused field + if ( hasFocus++ > 1 && !select.visible() ) { + onChange(0, true); + } + return this; + }).bind("search", function() { + // TODO why not just specifying both arguments? + var fn = (arguments.length > 1) ? arguments[1] : null; + function findValueCallback(q, data) { + var result; + if( data && data.length ) { + for (var i=0; i < data.length; i++) { + if( data[i].result.toLowerCase() == q.toLowerCase() ) { + result = data[i]; + break; + } + } + } + if( typeof fn == "function" ) fn(result); + else $input.trigger("result", result && [result.data, result.value]); + } + $.each(trimWords($input.val()), function(i, value) { + request(value, findValueCallback, findValueCallback); + }); - return this; - }).bind("flushCache", function() { - cache.flush(); - }).bind("setOptions", function() { - $.extend(options, arguments[1]); - // if we've updated the data, repopulate - if ( "data" in arguments[1] ) - cache.populate(); - }).bind("unautocomplete", function() { - select.unbind(); - $input.unbind(); - $(input.form).unbind(".autocomplete"); - }) - // JG: Show all data in cache. - .bind("showAllInCache", function() { - receiveData('', cache.load('')); - }); - - - function selectCurrent() { - var selected = select.selected(); - if( !selected ) - return false; - - var v = selected.result; - previousValue = v; - - if ( options.multiple ) { - var words = trimWords($input.val()); - if ( words.length > 1 ) { - v = words.slice(0, words.length - 1).join( options.multipleSeparator ) + options.multipleSeparator + v; - } - v += options.multipleSeparator; - } - - $input.val(v); - hideResultsNow(); - $input.trigger("result", [selected.data, selected.value]); - return true; - } - - function onChange(crap, skipPrevCheck) { - if( lastKeyPressCode == KEY.DEL ) { - select.hide(); - return; - } + return this; + }).bind("flushCache", function() { + cache.flush(); + }).bind("setOptions", function() { + $.extend(options, arguments[1]); + // if we've updated the data, repopulate + if ( "data" in arguments[1] ) + cache.populate(); + }).bind("unautocomplete", function() { + select.unbind(); + $input.unbind(); + $(input.form).unbind(".autocomplete"); + }) + // JG: Show all data in cache. + .bind("showAllInCache", function() { + receiveData('', cache.load('')); + }); + + function selectCurrent() { + var selected = select.selected(); + if( !selected ) + return false; + + var v = selected.result; + previousValue = v; + + if ( options.multiple ) { + var words = trimWords($input.val()); + if ( words.length > 1 ) { + v = words.slice(0, words.length - 1).join( options.multipleSeparator ) + options.multipleSeparator + v; + } + v += options.multipleSeparator; + } + + $input.val(v); + hideResultsNow(); + $input.trigger("result", [selected.data, selected.value]); + return true; + } + + function onChange(crap, skipPrevCheck) { + if( lastKeyPressCode == KEY.DEL ) { + select.hide(); + return; + } - var currentValue = $input.val(); - - if ( !skipPrevCheck && currentValue == previousValue ) - return; - - previousValue = currentValue; - - currentValue = lastWord(currentValue); - if ( currentValue.length >= options.minChars) { - $input.addClass(options.loadingClass); - if (!options.matchCase) - currentValue = currentValue.toLowerCase(); - request(currentValue, receiveData, hideResultsNow); - } else { - stopLoading(); - select.hide(); - } - }; - - function trimWords(value) { - if ( !value ) { - return [""]; - } - var words = value.split( options.multipleSeparator ); - var result = []; - $.each(words, function(i, value) { - if ( $.trim(value) ) - result[i] = $.trim(value); - }); - return result; - } - - function lastWord(value) { - if ( !options.multiple ) - return value; - var words = trimWords(value); - return words[words.length - 1]; - } - - // fills in the input box w/the first match (assumed to be the best match) - // q: the term entered - // sValue: the first matching result - function autoFill(q, sValue){ - // autofill in the complete box w/the first match as long as the user hasn't entered in more data - // if the last user key pressed was backspace, don't autofill - if( options.autoFill && (lastWord($input.val()).toLowerCase() == q.toLowerCase()) && lastKeyPressCode != KEY.BACKSPACE ) { - // fill in the value (keep the case the user has typed) - $input.val($input.val() + sValue.substring(lastWord(previousValue).length)); - // select the portion of the value not typed by the user (so the next character will erase) - $.Autocompleter.Selection(input, previousValue.length, previousValue.length + sValue.length); - } - }; + var currentValue = $input.val(); + + if ( !skipPrevCheck && currentValue == previousValue ) + return; + + previousValue = currentValue; + + currentValue = lastWord(currentValue); + if ( currentValue.length >= options.minChars) { + $input.addClass(options.loadingClass); + if (!options.matchCase) + currentValue = currentValue.toLowerCase(); + request(currentValue, receiveData, hideResultsNow); + } else { + stopLoading(); + select.hide(); + } + }; + + function trimWords(value) { + if ( !value ) { + return [""]; + } + var words = value.split( options.multipleSeparator ); + var result = []; + $.each(words, function(i, value) { + if ( $.trim(value) ) + result[i] = $.trim(value); + }); + return result; + } + + function lastWord(value) { + if ( !options.multiple ) + return value; + var words = trimWords(value); + return words[words.length - 1]; + } + + // fills in the input box w/the first match (assumed to be the best match) + // q: the term entered + // sValue: the first matching result + function autoFill(q, sValue){ + // autofill in the complete box w/the first match as long as the user hasn't entered in more data + // if the last user key pressed was backspace, don't autofill + if( options.autoFill && (lastWord($input.val()).toLowerCase() == q.toLowerCase()) && lastKeyPressCode != KEY.BACKSPACE ) { + // fill in the value (keep the case the user has typed) + $input.val($input.val() + sValue.substring(lastWord(previousValue).length)); + // select the portion of the value not typed by the user (so the next character will erase) + $.Autocompleter.Selection(input, previousValue.length, previousValue.length + sValue.length); + } + }; - function hideResults() { - clearTimeout(timeout); - timeout = setTimeout(hideResultsNow, 200); - }; + function hideResults() { + clearTimeout(timeout); + timeout = setTimeout(hideResultsNow, 200); + }; - function hideResultsNow() { - var wasVisible = select.visible(); - select.hide(); - clearTimeout(timeout); - stopLoading(); - if (options.mustMatch) { - // call search and run callback - $input.search( - function (result){ - // if no value found, clear the input box - if( !result ) { - if (options.multiple) { - var words = trimWords($input.val()).slice(0, -1); - $input.val( words.join(options.multipleSeparator) + (words.length ? options.multipleSeparator : "") ); - } - else - $input.val( "" ); - } - } - ); - } - if (wasVisible) - // position cursor at end of input field - $.Autocompleter.Selection(input, input.value.length, input.value.length); - }; + function hideResultsNow() { + var wasVisible = select.visible(); + select.hide(); + clearTimeout(timeout); + stopLoading(); + if (options.mustMatch) { + // call search and run callback + $input.search( + function (result){ + // if no value found, clear the input box + if( !result ) { + if (options.multiple) { + var words = trimWords($input.val()).slice(0, -1); + $input.val( words.join(options.multipleSeparator) + (words.length ? options.multipleSeparator : "") ); + } + else + $input.val( "" ); + } + } + ); + } + if (wasVisible) + // position cursor at end of input field + $.Autocompleter.Selection(input, input.value.length, input.value.length); + }; - function receiveData(q, data) { - if ( data && data.length && hasFocus ) { - stopLoading(); - select.display(data, q); - autoFill(q, data[0].value); - select.show(); - } else { - hideResultsNow(); - } - }; + function receiveData(q, data) { + if ( data && data.length && hasFocus ) { + stopLoading(); + select.display(data, q); + autoFill(q, data[0].value); + select.show(); + } else { + hideResultsNow(); + } + }; - function request(term, success, failure) { - if (!options.matchCase) - term = term.toLowerCase(); - var data = cache.load(term); + function request(term, success, failure) { + if (!options.matchCase) + term = term.toLowerCase(); + var data = cache.load(term); - // JG: hack: if term ends with ':', kill data to force an ajax request. - if (term.endsWith(":")) - data = null; + // JG: hack: if term ends with ':', kill data to force an ajax request. + if (term.endsWith(":")) + data = null; - // recieve the cached data - if (data && data.length) { - success(term, data); - // if an AJAX url has been supplied, try loading the data now - } else if( (typeof options.url == "string") && (options.url.length > 0) ){ - var extraParams = { - timestamp: +new Date() - }; - $.each(options.extraParams, function(key, param) { - extraParams[key] = typeof param == "function" ? param() : param; - }); - - $.ajax({ - // try to leverage ajaxQueue plugin to abort previous requests - mode: "abort", - // limit abortion to this input - port: "autocomplete" + input.name, - dataType: options.dataType, - url: options.url, - data: $.extend({ - q: lastWord(term), - limit: options.max - }, extraParams), - success: function(data) { - var parsed = options.parse && options.parse(data) || parse(data); - cache.add(term, parsed); - success(term, parsed); - } - }); - } else { - // if we have a failure, we need to empty the list -- this prevents the the [TAB] key from selecting the last successful match - select.emptyList(); - failure(term); - } - }; - - function parse(data) { - var parsed = []; - var rows = data.split("\n"); - for (var i=0; i < rows.length; i++) { - var row = $.trim(rows[i]); - if (row) { - row = row.split("|"); - parsed[parsed.length] = { - data: row, - value: row[0], - result: options.formatResult && options.formatResult(row, row[0]) || row[0] - }; - } - } - return parsed; - }; + // recieve the cached data + if (data && data.length) { + success(term, data); + // if an AJAX url has been supplied, try loading the data now + } else if( (typeof options.url == "string") && (options.url.length > 0) ){ + var extraParams = { + timestamp: +new Date() + }; + $.each(options.extraParams, function(key, param) { + extraParams[key] = typeof param == "function" ? param() : param; + }); + + $.ajax({ + // try to leverage ajaxQueue plugin to abort previous requests + mode: "abort", + // limit abortion to this input + port: "autocomplete" + input.name, + dataType: options.dataType, + url: options.url, + data: $.extend({ + q: lastWord(term), + limit: options.max + }, extraParams), + success: function(data) { + var parsed = options.parse && options.parse(data) || parse(data); + cache.add(term, parsed); + success(term, parsed); + } + }); + } else { + // if we have a failure, we need to empty the list -- this prevents the the [TAB] key from selecting the last successful match + select.emptyList(); + failure(term); + } + }; + + function parse(data) { + var parsed = []; + var rows = data.split("\n"); + for (var i=0; i < rows.length; i++) { + var row = $.trim(rows[i]); + if (row) { + row = row.split("|"); + parsed[parsed.length] = { + data: row, + value: row[0], + result: options.formatResult && options.formatResult(row, row[0]) || row[0] + }; + } + } + return parsed; + }; - function stopLoading() { - $input.removeClass(options.loadingClass); - }; + function stopLoading() { + $input.removeClass(options.loadingClass); + }; }; $.Autocompleter.defaults = { - inputClass: "ac_input", - resultsClass: "ac_results", - loadingClass: "ac_loading", - minChars: 1, - delay: 400, - matchCase: false, - matchSubset: true, - matchContains: false, - cacheLength: 10, - max: 100, - mustMatch: false, - extraParams: {}, - selectFirst: true, - formatItem: function(row) { return row[0]; }, - formatMatch: null, - autoFill: false, - width: 0, - multiple: false, - multipleSeparator: ", ", - highlight: function(value, term) { - // JG: short-circuit highlighting if term is empty string. - if (term == "") - return value; - return value.replace(new RegExp("(?![^&;]+;)(?!<[^<>]*)(" + term.replace(/([\^\$\[\]\{\}\*\.\+\?\|\\])/gi, "\\$1") + ")(?![^<>]*>)(?![^&;]+;)", "gi"), "<strong>$1</strong>"); - }, + inputClass: "ac_input", + resultsClass: "ac_results", + loadingClass: "ac_loading", + minChars: 1, + delay: 400, + matchCase: false, + matchSubset: true, + matchContains: false, + cacheLength: 10, + max: 100, + mustMatch: false, + extraParams: {}, + selectFirst: true, + formatItem: function(row) { return row[0]; }, + formatMatch: null, + autoFill: false, + width: 0, + multiple: false, + multipleSeparator: ", ", + highlight: function(value, term) { + // JG: short-circuit highlighting if term is empty string. + if (term == "") + return value; + return value.replace(new RegExp("(?![^&;]+;)(?!<[^<>]*)(" + term.replace(/([\^\$\[\]\{\}\*\.\+\?\|\\])/gi, "\\$1") + ")(?![^<>]*>)(?![^&;]+;)", "gi"), "<strong>$1</strong>"); + }, scroll: true, scrollHeight: 180 }; $.Autocompleter.Cache = function(options) { - var data = {}; - var length = 0; + var data = {}; + var length = 0; - function matchSubset(s, sub) { - if (!options.matchCase) - s = s.toLowerCase(); - var i = s.indexOf(sub); - if (i == -1) return false; - return i == 0 || options.matchContains; - }; - - function add(q, value) { - if (length > options.cacheLength){ - flush(); - } - if (!data[q]){ - length++; - } - data[q] = value; - } - - function populate(){ - if( !options.data ) return false; - // track the matches - var stMatchSets = {}, - nullData = 0; + function matchSubset(s, sub) { + if (!options.matchCase) + s = s.toLowerCase(); + var i = s.indexOf(sub); + if (i == -1) return false; + return i == 0 || options.matchContains; + }; + + function add(q, value) { + if (length > options.cacheLength){ + flush(); + } + if (!data[q]){ + length++; + } + data[q] = value; + } + + function populate(){ + if( !options.data ) return false; + // track the matches + var stMatchSets = {}, + nullData = 0; - // no url was specified, we need to adjust the cache length to make sure it fits the local data store - if( !options.url ) options.cacheLength = 1; - - // track all options for minChars = 0 - stMatchSets[""] = []; - - // loop through the array and create a lookup structure - for ( var i = 0, ol = options.data.length; i < ol; i++ ) { - var rawValue = options.data[i]; - // if rawValue is a string, make an array otherwise just reference the array - rawValue = (typeof rawValue == "string") ? [rawValue] : rawValue; - - var value = options.formatMatch(rawValue, i+1, options.data.length); - if ( value === false ) - continue; - - var firstChar = value.charAt(0).toLowerCase(); - // if no lookup array for this character exists, look it up now - if( !stMatchSets[firstChar] ) - stMatchSets[firstChar] = []; + // no url was specified, we need to adjust the cache length to make sure it fits the local data store + if( !options.url ) options.cacheLength = 1; + + // track all options for minChars = 0 + stMatchSets[""] = []; + + // loop through the array and create a lookup structure + for ( var i = 0, ol = options.data.length; i < ol; i++ ) { + var rawValue = options.data[i]; + // if rawValue is a string, make an array otherwise just reference the array + rawValue = (typeof rawValue == "string") ? [rawValue] : rawValue; + + var value = options.formatMatch(rawValue, i+1, options.data.length); + if ( value === false ) + continue; + + var firstChar = value.charAt(0).toLowerCase(); + // if no lookup array for this character exists, look it up now + if( !stMatchSets[firstChar] ) + stMatchSets[firstChar] = []; - // if the match is a string - var row = { - value: value, - data: rawValue, - result: options.formatResult && options.formatResult(rawValue) || value - }; - - // push the current match into the set list - stMatchSets[firstChar].push(row); + // if the match is a string + var row = { + value: value, + data: rawValue, + result: options.formatResult && options.formatResult(rawValue) || value + }; + + // push the current match into the set list + stMatchSets[firstChar].push(row); - // keep track of minChars zero items - if ( nullData++ < options.max ) { - stMatchSets[""].push(row); - } - }; + // keep track of minChars zero items + if ( nullData++ < options.max ) { + stMatchSets[""].push(row); + } + }; - // add the data items to the cache - $.each(stMatchSets, function(i, value) { - // increase the cache size - options.cacheLength++; - // add to the cache - add(i, value); - }); - } - - // populate any existing data - setTimeout(populate, 25); - - function flush(){ - data = {}; - length = 0; - } - - return { - flush: flush, - add: add, - populate: populate, - load: function(q) { - if (!options.cacheLength || !length) - return null; + // add the data items to the cache + $.each(stMatchSets, function(i, value) { + // increase the cache size + options.cacheLength++; + // add to the cache + add(i, value); + }); + } + + // populate any existing data + setTimeout(populate, 25); + + function flush(){ + data = {}; + length = 0; + } + + return { + flush: flush, + add: add, + populate: populate, + load: function(q) { + if (!options.cacheLength || !length) + return null; - /* - * if dealing w/local data and matchContains than we must make sure - * to loop through all the data collections looking for matches - */ - if( !options.url && options.matchContains ){ - // track all matches - var csub = []; - // loop through all the data grids for matches - for( var k in data ){ - // don't search through the stMatchSets[""] (minChars: 0) cache - // this prevents duplicates - if( k.length > 0 ){ - var c = data[k]; - $.each(c, function(i, x) { - // if we've got a match, add it to the array - if (matchSubset(x.value, q)) { - csub.push(x); - } - }); - } - } - return csub; - } else - // if the exact item exists, use it - if (data[q]){ - return data[q]; - } else - if (options.matchSubset) { - for (var i = q.length - 1; i >= options.minChars; i--) { - var c = data[q.substr(0, i)]; - if (c) { - var csub = []; - $.each(c, function(i, x) { - if ( (x.data.indexOf("#Header") == 0) || - (matchSubset(x.value, q)) ) { - csub[csub.length] = x; - } - }); - return csub; - } - } + /* + * if dealing w/local data and matchContains than we must make sure + * to loop through all the data collections looking for matches + */ + if( !options.url && options.matchContains ) { + // track all matches + var csub = []; + // loop through all the data grids for matches + for( var k in data ) { + // don't search through the stMatchSets[""] (minChars: 0) cache + // this prevents duplicates + if( k.length > 0 ){ + var c = data[k]; + $.each(c, function(i, x) { + // if we've got a match, add it to the array + if (matchSubset(x.value, q)) { + csub.push(x); + } + }); + } + } + return csub; + } else + // if the exact item exists, use it + if (data[q]) { + return data[q]; + } else + if (options.matchSubset) { + for (var i = q.length - 1; i >= options.minChars; i--) { + var c = data[q.substr(0, i)]; + if (c) { + var csub = []; + $.each(c, function(i, x) { + if ( (x.data.indexOf("#Header") == 0) || + (matchSubset(x.value, q)) ) { + csub[csub.length] = x; + } + }); + return csub; + } + } - } - return null; - } - }; + } + return null; + } + }; }; $.Autocompleter.Select = function (options, input, select, config) { - var CLASSES = { - ACTIVE: "ac_over" - }; - - var listItems, - active = -1, - data, - term = "", - needsInit = true, - element, - list; - - // Create results - function init() { - if (!needsInit) - return; - element = $("<div/>") - .hide() - .addClass(options.resultsClass) - .css("position", "absolute") - .appendTo(document.body); - - list = $("<ul/>").appendTo(element).mouseover( function(event) { - if(target(event).nodeName && target(event).nodeName.toUpperCase() == 'LI') { - active = $("li", list).removeClass(CLASSES.ACTIVE).index(target(event)); - // JG: Only add active class if target is not a header. - if (!headerAtPosition(active)) - $(target(event)).addClass(CLASSES.ACTIVE); - } - }).click(function(event) { - // JG: Ignore click on header. - active = $("li", list).index(target(event)); - if (headerAtPosition(active)) - return; + var CLASSES = { + ACTIVE: "ac_over" + }; + + var listItems, + active = -1, + data, + term = "", + needsInit = true, + element, + list; + + // Create results + function init() { + if (!needsInit) + return; + + element = $("<div/>") + .hide() + .addClass(options.resultsClass) + .css("position", "absolute") + .bind("mouseleave", function() { + element.hide(); + }) + .appendTo(document.body); - // Handle click on autocomplete options. - $(target(event)).addClass(CLASSES.ACTIVE); - select(); - // TODO provide option to avoid setting focus again after selection? useful for cleanup-on-focus - input.focus(); - return false; - }).mousedown(function() { - config.mouseDownOnSelect = true; - }).mouseup(function() { - config.mouseDownOnSelect = false; - }); - - if( options.width > 0 ) - element.css("width", options.width); - - needsInit = false; - } - - function target(event) { - var element = event.target; - while(element && element.tagName != "LI") - element = element.parentNode; - // more fun with IE, sometimes event.target is empty, just ignore it then - if(!element) - return []; - return element; - } + list = $("<ul/>").appendTo(element).mouseover( function(event) { + if(target(event).nodeName && target(event).nodeName.toUpperCase() == 'LI') { + active = $("li", list).removeClass(CLASSES.ACTIVE).index(target(event)); + // JG: Only add active class if target is not a header. + if (!headerAtPosition(active)) + $(target(event)).addClass(CLASSES.ACTIVE); + } + }).click(function(event) { + // JG: Ignore click on header. + active = $("li", list).index(target(event)); + if (headerAtPosition(active)) + return; - // JG: Returns true iff there is a header element at the given position. - function headerAtPosition(position) - { - dataAtPosition = data[position].data; - return (dataAtPosition[0].indexOf("#Header") == 0); - } + // Handle click on autocomplete options. + $(target(event)).addClass(CLASSES.ACTIVE); + select(); + // TODO provide option to avoid setting focus again after selection? useful for cleanup-on-focus + input.focus(); + return false; + }).mousedown(function() { + config.mouseDownOnSelect = true; + }).mouseup(function() { + config.mouseDownOnSelect = false; + }); - function moveSelect(step) { - listItems.slice(active, active + 1).removeClass(CLASSES.ACTIVE); - // JG: while active item is a header, continue stepping. - var isHeader = false; - do - { - movePosition(step); - isHeader = headerAtPosition(active); - } - while (isHeader); - var activeItem = listItems.slice(active, active + 1).addClass(CLASSES.ACTIVE); + if( options.width > 0 ) + element.css("width", options.width); + needsInit = false; + } + + function target(event) { + var element = event.target; + while(element && element.tagName != "LI") + element = element.parentNode; + // more fun with IE, sometimes event.target is empty, just ignore it then + if(!element) + return []; + return element; + } + + // JG: Returns true iff there is a header element at the given position. + function headerAtPosition(position) { + dataAtPosition = data[position].data; + return (dataAtPosition[0].indexOf("#Header") == 0); + } + + function moveSelect(step) { + listItems.slice(active, active + 1).removeClass(CLASSES.ACTIVE); + // JG: while active item is a header, continue stepping. + var isHeader = false; + do { + movePosition(step); + isHeader = headerAtPosition(active); + } + while (isHeader); + var activeItem = listItems.slice(active, active + 1).addClass(CLASSES.ACTIVE); if(options.scroll) { var offset = 0; listItems.slice(0, active).each(function() { - offset += this.offsetHeight; - }); + offset += this.offsetHeight; + }); if((offset + activeItem[0].offsetHeight - list.scrollTop()) > list[0].clientHeight) { list.scrollTop(offset + activeItem[0].offsetHeight - list.innerHeight()); } else if(offset < list.scrollTop()) { list.scrollTop(offset); } } - }; - - function movePosition(step) { - active += step; - if (active < 0) { - active = listItems.size() - 1; - } else if (active >= listItems.size()) { - active = 0; - } - } - - function limitNumberOfItems(available) { - return options.max && options.max < available - ? options.max - : available; - } - - function fillList() { - list.empty(); - var max = limitNumberOfItems(data.length); - for (var i=0; i < max; i++) { - if (!data[i]) - continue; - var formatted = options.formatItem(data[i].data, i+1, max, data[i].value, term); - if ( formatted === false ) - continue; + }; + + function movePosition(step) { + active += step; + if (active < 0) { + active = listItems.size() - 1; + } else if (active >= listItems.size()) { + active = 0; + } + } + + function limitNumberOfItems(available) { + return options.max && options.max < available + ? options.max + : available; + } + + function fillList() { + list.empty(); + var max = limitNumberOfItems(data.length); + for (var i=0; i < max; i++) { + if (!data[i]) + continue; + + var formatted = options.formatItem(data[i].data, i+1, max, data[i].value, term); + if ( formatted === false ) + continue; - // JG: Build list item by formatting the item and choosing a CSS class. - if (headerAtPosition(i)) - { - // Found header element; only add header if there are subsequent elements. - if (i != max-1) - var li = $("<li/>").html(data[i].data[1]).addClass("ac_header").appendTo(list)[0]; - } - else - { - // Found completion element. - var li = $("<li/>").html(options.highlight(formatted, term)).addClass(i%2 == 0 ? "ac_even" : "ac_odd").appendTo(list)[0]; - } + // JG: Build list item by formatting the item and choosing a CSS class. + if (headerAtPosition(i)) { + // Found header element; only add header if there are subsequent elements. + if (i != max-1) + var li = $("<li/>").html(data[i].data[1]).addClass("ac_header").appendTo(list)[0]; + } else { + // Found completion element. + var li = $("<li/>").html(options.highlight(formatted, term)).addClass(i%2 == 0 ? "ac_even" : "ac_odd").appendTo(list)[0]; + } - $.data(li, "ac_data", data[i]); - } - listItems = list.find("li"); - if ( options.selectFirst ) { - listItems.slice(0, 1).addClass(CLASSES.ACTIVE); - active = 0; - } - // apply bgiframe if available - if ( $.fn.bgiframe ) - list.bgiframe(); - } - - return { - display: function(d, q) { - init(); - data = d; - term = q; - fillList(); - }, - next: function() { - moveSelect(1); - }, - prev: function() { - moveSelect(-1); - }, - pageUp: function() { - if (active != 0 && active - 8 < 0) { - moveSelect( -active ); - } else { - moveSelect(-8); - } - }, - pageDown: function() { - if (active != listItems.size() - 1 && active + 8 > listItems.size()) { - moveSelect( listItems.size() - 1 - active ); - } else { - moveSelect(8); - } - }, - hide: function() { - element && element.hide(); - listItems && listItems.removeClass(CLASSES.ACTIVE); - active = -1; - }, - visible : function() { - return element && element.is(":visible"); - }, - current: function() { - return this.visible() && (listItems.filter("." + CLASSES.ACTIVE)[0] || options.selectFirst && listItems[0]); - }, - show: function() { - var offset = $(input).offset(); - element.css({ - width: typeof options.width == "string" || options.width > 0 ? options.width : $(input).width(), - top: offset.top + input.offsetHeight, - left: offset.left - }).show(); + $.data(li, "ac_data", data[i]); + } + listItems = list.find("li"); + if ( options.selectFirst ) { + listItems.slice(0, 1).addClass(CLASSES.ACTIVE); + active = 0; + } + // apply bgiframe if available + if ( $.fn.bgiframe ) + list.bgiframe(); + } + + return { + display: function(d, q) { + init(); + data = d; + term = q; + fillList(); + }, + next: function() { + moveSelect(1); + }, + prev: function() { + moveSelect(-1); + }, + pageUp: function() { + if (active != 0 && active - 8 < 0) { + moveSelect( -active ); + } else { + moveSelect(-8); + } + }, + pageDown: function() { + if (active != listItems.size() - 1 && active + 8 > listItems.size()) { + moveSelect( listItems.size() - 1 - active ); + } else { + moveSelect(8); + } + }, + hide: function() { + element && element.hide(); + listItems && listItems.removeClass(CLASSES.ACTIVE); + active = -1; + }, + visible : function() { + return element && element.is(":visible"); + }, + current: function() { + return this.visible() && (listItems.filter("." + CLASSES.ACTIVE)[0] || options.selectFirst && listItems[0]); + }, + show: function() { + var offset = $(input).offset(); + element.css({ + width: typeof options.width == "string" || options.width > 0 ? options.width : $(input).width(), + top: offset.top + input.offsetHeight, + left: offset.left + }).show(); if(options.scroll) { list.scrollTop(0); list.css({ - maxHeight: options.scrollHeight, - overflow: 'auto' - }); - + maxHeight: options.scrollHeight, + overflow: 'auto' + }); + if($.browser.msie && typeof document.body.style.maxHeight === "undefined") { - var listHeight = 0; - listItems.each(function() { - listHeight += this.offsetHeight; - }); - var scrollbarsVisible = listHeight > options.scrollHeight; + var listHeight = 0; + listItems.each(function() { + listHeight += this.offsetHeight; + }); + var scrollbarsVisible = listHeight > options.scrollHeight; list.css('height', scrollbarsVisible ? options.scrollHeight : listHeight ); - if (!scrollbarsVisible) { - // IE doesn't recalculate width when scrollbar disappears - listItems.width( list.width() - parseInt(listItems.css("padding-left")) - parseInt(listItems.css("padding-right")) ); - } + if (!scrollbarsVisible) { + // IE doesn't recalculate width when scrollbar disappears + listItems.width( list.width() - parseInt(listItems.css("padding-left")) - parseInt(listItems.css("padding-right")) ); + } } } - }, - selected: function() { - var selected = listItems && listItems.filter("." + CLASSES.ACTIVE).removeClass(CLASSES.ACTIVE); - return selected && selected.length && $.data(selected[0], "ac_data"); - }, - emptyList: function (){ - list && list.empty(); - }, - unbind: function() { - element && element.remove(); - } - }; + }, + selected: function() { + var selected = listItems && listItems.filter("." + CLASSES.ACTIVE).removeClass(CLASSES.ACTIVE); + return selected && selected.length && $.data(selected[0], "ac_data"); + }, + emptyList: function (){ + list && list.empty(); + }, + unbind: function() { + element && element.remove(); + } + }; }; $.Autocompleter.Selection = function(field, start, end) { - if( field.createTextRange ){ - var selRange = field.createTextRange(); - selRange.collapse(true); - selRange.moveStart("character", start); - selRange.moveEnd("character", end); - selRange.select(); - } else if( field.setSelectionRange ){ - field.setSelectionRange(start, end); - } else { - if( field.selectionStart ){ - field.selectionStart = start; - field.selectionEnd = end; - } - } - field.focus(); + if( field.createTextRange ){ + var selRange = field.createTextRange(); + selRange.collapse(true); + selRange.moveStart("character", start); + selRange.moveEnd("character", end); + selRange.select(); + } else if( field.setSelectionRange ){ + field.setSelectionRange(start, end); + } else { + if( field.selectionStart ){ + field.selectionStart = start; + field.selectionEnd = end; + } + } + field.focus(); }; })(jQuery); --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(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).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)}function make_popupmenu (c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(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 array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString().t oLowerCase()||"",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){if(typeof 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1 0

galaxy-dist commit 21ddc9f843be: Prevent workflow forms from being submitted twice when dynamic options are refreshed, resulting in AJAX error and inability to savewq
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1275690470 14400 # Node ID 21ddc9f843be29515ea6f260a73a710288606104 # Parent 56e2793886dc2d1547bb86f32a13d0e365f8fecd Prevent workflow forms from being submitted twice when dynamic options are refreshed, resulting in AJAX error and inability to savewq --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -328,6 +328,7 @@ type: 'POST', dataType: 'json', success: function( data ) { + workflow.active_form_has_changes = false; node.update_field_data( data ); }, beforeSubmit: function( data ) {

1 0

galaxy-dist commit 56e2793886dc: Fix for library dataset information page, link to history items using hda.history_id rather than hda.history.id.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275688990 14400 # Node ID 56e2793886dc2d1547bb86f32a13d0e365f8fecd # Parent 5610a35bf9a67b0e43f02a433163232ab3f7a998 Fix for library dataset information page, link to history items using hda.history_id rather than hda.history.id. --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -148,7 +148,7 @@ </thead> %for hda in associated_hdas: <tr> - <td><a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda.history.id ) )}">${hda.history.get_display_name()}</a></td> + <td><a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda.history_id ) )}">${hda.history.get_display_name()}</a></td><td>${hda.get_display_name()}</td><td>${time_ago( hda.update_time )}</td><td>

1 0

galaxy-dist commit 9114bd088776: Better handling of return key in search+select.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275753610 14400 # Node ID 9114bd0887769b9ffe570b71f90ab95be68baa44 # Parent 21ddc9f843be29515ea6f260a73a710288606104 Better handling of return key in search+select. --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -287,9 +287,16 @@ function replace_big_select_inputs(min_l // case a user may have manually entered a value that needs to be refreshed). text_input_elt.bind("result", try_refresh_fn); text_input_elt.keyup( function(e) { - try_refresh_fn(); + if ( e.keyCode === 13 ) // Return key + try_refresh_fn(); }); - + + // Disable return key so that it does not submit the form automatically. This is done because elememnt should behave like a + // select (enter = select), not text input (enter = submit form). + text_input_elt.keydown( function(e) { + if ( e.keyCode === 13 ) // Return key + return false; + }); } }); } --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.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 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galaxy-dist commit 5610a35bf9a6: Add the CBI Rice Mart data source tool to the distribution.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275680998 14400 # Node ID 5610a35bf9a67b0e43f02a433163232ab3f7a998 # Parent 84880085415b7b53ead611ccffee39b0ab9e0d4b Add the CBI Rice Mart data source tool to the distribution. --- /dev/null +++ b/tools/data_source/cbi_rice_mart.xml @@ -0,0 +1,39 @@ +<?xml version="1.0"?> + +<tool name="CBI Rice Mart" id="cbi_rice_mart" tool_type="data_source" version="1.0.1"> + <description>rice mart</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://ricemart.cbi.edu.cn/biomart/martview/" check_values="false" method="get" target="_top"> + <display>go to RMap rice mart $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <append_param separator="&" first_separator="?" join="="> + <value name="_export" missing="1" /> + <value name="GALAXY_URL" missing="0" /> + </append_param> + </request_param> + <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" > + <value_translation> + <value galaxy_value="tabular" remote_value="TSV" /> + </value_translation> + </request_param> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" /> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <request_param galaxy_name="table" remote_name="table" missing="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="Rice mart query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -9,6 +9,7 @@ <tool file="data_source/microbial_import.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/biomart_test.xml" /> + <tool file="data_source/cbi_rice_mart.xml" /><tool file="data_source/gramene_mart.xml" /><tool file="data_source/fly_modencode.xml" /><tool file="data_source/flymine.xml" />

1 0

galaxy-dist commit 84880085415b: Add the ratmine datasource tool to main's tool config.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275677102 14400 # Node ID 84880085415b7b53ead611ccffee39b0ab9e0d4b # Parent 6dde140d0cfd53820f9cbb83bbb44338ac8bd6aa Add the ratmine datasource tool to main's tool config. --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -10,6 +10,7 @@ <tool file="data_source/gramene_mart.xml" /><tool file="data_source/flymine.xml" /><tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/ratmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" />

1 0

galaxy-dist commit 6dde140d0cfd: I forgot to change the disk file size from 0 back to 4 gb for the systems report before may last commit.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275676257 14400 # Node ID 6dde140d0cfd53820f9cbb83bbb44338ac8bd6aa # Parent a76d05bb41e1c1f1eeaa93a18289eeed1213199b I forgot to change the disk file size from 0 back to 4 gb for the systems report before may last commit. --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -170,8 +170,7 @@ class System( BaseController ): def disk_usage( self, trans, **kwd ): file_path = trans.app.config.file_path disk_usage = self.get_disk_usage( file_path ) - #min_file_size = 2**32 # 4 Gb - min_file_size = 0 + min_file_size = 2**32 # 4 Gb file_size_str = nice_size( min_file_size ) datasets = trans.sa_session.query( model.Dataset ) \ .filter( and_( model.Dataset.table.c.purged == False,

1 0

galaxy-dist commit dd69c382eff1: lims: added new feature where the datasets are be automatically renamed using a setting with the request_type. This makes solves the same dataset name problem on SOLiD
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1275671936 14400 # Node ID dd69c382eff1d3c0c160bc3ec392b06671317fd0 # Parent d01207f24908bc3f6d5323689f0aa46557f4d254 lims: added new feature where the datasets are be automatically renamed using a setting with the request_type. This makes solves the same dataset name problem on SOLiD --- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -70,6 +70,15 @@ <input type="text" name="data_dir" value="" size="40"/></div><div class="form-row"> + <label>Add experiment name and the sample name to the dataset name?</label> + ${rename_dataset_selectbox.get_html()} + <div class="toolParamHelp" style="clear: both;"> + The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This + makes sure that dataset names remain unique in Galaxy even when they have the + same name in the sequencer. + </div> + </div> + <div class="form-row"><div style="float: left; width: 250px; margin-right: 10px;"><input type="hidden" name="new" value="submitted" size="40"/></div> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1476,6 +1476,9 @@ class RequestEvent( object ): self.comment = comment class RequestType( object ): + rename_dataset_options = Bunch( NO = 'Do not rename', + SAMPLE_NAME = 'Preprend sample name', + EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment and sample name') permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' ) def __init__(self, name=None, desc=None, request_form=None, sample_form=None, datatx_info=None): --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -62,6 +62,15 @@ <input type="text" name="data_dir" value="${request_type.datatx_info.get('data_dir', '')}" size="40"/></div><div class="form-row"> + <label>Add experiment name and the sample name to the dataset name?</label> + ${rename_dataset_selectbox.get_html()} + <div class="toolParamHelp" style="clear: both;"> + The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This + makes sure that dataset names remain unique in Galaxy even when they have the + same name in the sequencer. + </div> + </div> + <div class="form-row"><input type="submit" name="save_changes" value="Save changes"/></div></form> --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -221,7 +221,6 @@ class RequestsAdmin( BaseController ): @web.json def get_file_details( self, trans, id=None, file=None, folder_path=None ): - print >> sys.stderr, 'get_file_details', id, file def print_ticks(d): pass # Avoid caching @@ -1623,7 +1622,7 @@ class RequestsAdmin( BaseController ): else: sample.dataset_files.append(dict(filepath=filepath, status=sample.transfer_status.NOT_STARTED, - name=filepath.split('/')[-1], + name=self.__dataset_name(sample, filepath.split('/')[-1]), error_msg='', size=sample.dataset_size(filepath))) trans.sa_session.add( sample ) @@ -1638,7 +1637,16 @@ class RequestsAdmin( BaseController ): action='show_datatx_page', sample_id=trans.security.encode_id(sample.id), folder_path=folder_path)) - + + def __dataset_name(self, sample, filepath): + name = filepath.split('/')[-1] + opt = sample.request.type.datatx_info.get('rename_dataset', sample.request.type.rename_dataset_options.NO) + if opt == sample.request.type.rename_dataset_options.NO: + return name + elif opt == sample.request.type.rename_dataset_options.SAMPLE_NAME: + return sample.name+'_'+name + elif opt == sample.request.type.rename_dataset_options.EXPERIMENT_AND_SAMPLE_NAME: + return sample.request.name+'_'+sample.name+'_'+name def __setup_datatx_user(self, trans, library, folder): ''' This method sets up the datatx user: @@ -1830,7 +1838,8 @@ class RequestsAdmin( BaseController ): return trans.fill_template( '/admin/requests/view_request_type.mako', request_type=rt, forms=get_all_forms( trans ), - states_list=rt.states ) + states_list=rt.states, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans, rt) ) def __view_form(self, trans, **kwd): try: fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id(kwd['id']) ) @@ -1855,7 +1864,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) elif params.get( 'remove_state_button', False ): rt_info, rt_states = self.__create_request_type_form(trans, **kwd) index = int(params.get( 'remove_state_button', '' ).split(" ")[2]) @@ -1864,7 +1874,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) elif params.get( 'save_request_type', False ): rt, message = self.__save_request_type(trans, **kwd) if not rt: @@ -1888,7 +1899,8 @@ class RequestsAdmin( BaseController ): rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=params.get( 'password', '' ), - data_dir=util.restore_text( params.get( 'data_dir', '' ) )) + data_dir=util.restore_text( params.get( 'data_dir', '' ) ), + rename_dataset=util.restore_text( params.get('rename_dataset', False) )) trans.sa_session.add( rt ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -1903,7 +1915,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) def __create_request_type_form(self, trans, **kwd): request_forms=get_all_forms( trans, filter=dict(deleted=False), @@ -1949,6 +1962,19 @@ class RequestsAdmin( BaseController ): break return rt_info, rt_states + def __rename_dataset_selectbox(self, trans, rt=None): + if rt: + sel_opt = rt.datatx_info.get('rename_dataset', trans.app.model.RequestType.rename_dataset_options.NO) + else: + sel_opt = trans.app.model.RequestType.rename_dataset_options.NO + rename_dataset_selectbox = SelectField('rename_dataset') + for opt, opt_name in trans.app.model.RequestType.rename_dataset_options.items(): + if sel_opt == opt_name: + rename_dataset_selectbox.add_option(opt_name, opt_name, selected=True) + else: + rename_dataset_selectbox.add_option(opt_name, opt_name) + return rename_dataset_selectbox + def __save_request_type(self, trans, **kwd): params = util.Params( kwd ) rt = trans.app.model.RequestType() @@ -1960,7 +1986,8 @@ class RequestsAdmin( BaseController ): rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=params.get( 'password', '' ), - data_dir=util.restore_text( params.get( 'data_dir', '' ) )) + data_dir=util.restore_text( params.get( 'data_dir', '' ) ), + rename_dataset=util.restore_text( params.get('rename_dataset', '') )) trans.sa_session.add( rt ) trans.sa_session.flush() # set sample states --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -55,6 +55,8 @@ <h2>Data transfer from Sequencer</h2><h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3> +<br/> +<br/><ul class="manage-table-actions"> %if sample.request.submitted() and sample.inprogress_dataset_files(): @@ -131,7 +133,7 @@ <input type="submit" name="open_folder" value="Open folder"/><input type="submit" name="folder_up" value="Up"/></div> - <div class="form-row"> + <div class="form-row"><select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple> %for index, f in enumerate(files): <option value="${f}">${f}</option>

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galaxy-commits June 2010