- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by Bitbucket 12 Sep '12

12 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ce64f5d64ff4/ changeset: ce64f5d64ff4 user: carlfeberhard date: 2012-09-12 17:03:17 summary: Client side templates for history panel; IconButtonView in ui.js; copied BaseModel/View into base-mvc.js; stubs for annotations, tags MVC; cleaned up controllers/root.py affected #: 18 files diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -120,9 +120,9 @@ show_hidden = util.string_as_bool( show_hidden ) datasets = self.get_history_datasets( trans, history, show_deleted, show_hidden, show_purged ) + history_panel_template = "root/history.mako" # history panel -> backbone - history_panel_template = "root/history.mako" - #history_panel_template = "root/alternate_history.mako" + ##history_panel_template = "root/alternate_history.mako" return trans.stream_template_mako( history_panel_template, history = history, annotation = self.get_item_annotation_str( trans.sa_session, trans.user, history ), @@ -512,85 +512,3 @@ @web.expose def generate_error( self, trans ): raise Exception( "Fake error!" ) - - - -""" -import galaxy.web.framework.helpers as web_helpers -from functools import wraps -def debug_mako_template( template_fn ): - # Wrap a function that produces a mako template for better debugging - - # http://stackoverflow.com/questions/390409/how-do-you-debug-mako-templates - @wraps( template_fn ) - def wrapper( *args, **kwargs ): - try: - log.debug( 'rendering template' ) - return template_fn( *args, **kwargs ) - log.debug( 'done rendering template' ) - except Exception, ex: - log.error( "Mako Exception: " + str( ex ), exc_info=True ) - return exceptions.html_error_template().render() - return wrapper - -def prep_dataset( hda, trans ): - states = trans.app.model.Dataset.states - print states - STATES_INTERPRETED_AS_QUEUED = [ 'no state', '', None ] - ## dataset is actually a HistoryDatasetAssociation - #ported mostly from history_common - #post: return dictionary form - #??: move out of templates? - #??: gather data from model? - - - #TODO: clean up magic strings - - hda_dict = hda.get_api_value() - #TODO: use hda_dict.update to add these (instead of localvars) - def add_to_hda( **kwargs ): - hda_dict.update( kwargs ) - - # trans - encoded_hda_id = trans.security.encode_id( hda.id ) - add_to_hda( id=encoded_hda_id ) - - add_to_hda( state=hda.state ) - if hda.state in STATES_INTERPRETED_AS_QUEUED: - #TODO: magic string - add_to_hda( state='queued' ) - - # trans - current_user_roles = trans.get_current_user_roles() - add_to_hda( can_edit=( not ( hda.deleted or hda.purged ) ) ) - - # considered accessible if user can access or user isn't admin - # trans - accessible = trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset ) - accessible = trans.user_is_admin() or accessible - add_to_hda( accessible=accessible ) - - #TODO: move urls into js galaxy_paths (decorate) - deleted = hda.deleted - purged = hda.purged - dataset_purged = hda.dataset.purged - if not ( dataset_purged or purged ) and for_editing: - undelete_url = web_helpers.url_for( controller='dataset', action='undelete', dataset_id=encoded_hda_id ) - # trans - if trans.app.config.allow_user_dataset_purge: - purge_url = web_helpers.url_for( controller='dataset', action='purge', dataset_id=encoded_hda_id ) - - if not hda.visible: - unhide_url = web_helpers.url_for( controller='dataset', action='unhide', dataset_id=encoded_hda_id ) - - - print 'dataset:', dataset - - undelete_url = web_helpers.url_for( controller='dataset', action='undelete', dataset_id=encoded_hda_id ) - purge_url = web_helpers.url_for( controller='dataset', action='purge', dataset_id=encoded_hda_id ) - unhide_url = web_helpers.url_for( controller='dataset', action='unhide', dataset_id=encoded_hda_id ) - print 'urls:', '\n'.join( undelete_url, purge_url, unhide_url ) - - return hda_dict - -""" \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/libs/handlebars.full.js --- /dev/null +++ b/static/scripts/libs/handlebars.full.js @@ -0,0 +1,1550 @@ +// lib/handlebars/base.js +var Handlebars = {}; + +Handlebars.VERSION = "1.0.beta.6"; + +Handlebars.helpers = {}; +Handlebars.partials = {}; + +Handlebars.registerHelper = function(name, fn, inverse) { + if(inverse) { fn.not = inverse; } + this.helpers[name] = fn; +}; + +Handlebars.registerPartial = function(name, str) { + this.partials[name] = str; +}; + +Handlebars.registerHelper('helperMissing', function(arg) { + if(arguments.length === 2) { + return undefined; + } else { + throw new Error("Could not find property '" + arg + "'"); + } +}); + +var toString = Object.prototype.toString, functionType = "[object Function]"; + +Handlebars.registerHelper('blockHelperMissing', function(context, options) { + var inverse = options.inverse || function() {}, fn = options.fn; + + + var ret = ""; + var type = toString.call(context); + + if(type === functionType) { context = context.call(this); } + + if(context === true) { + return fn(this); + } else if(context === false || context == null) { + return inverse(this); + } else if(type === "[object Array]") { + if(context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; + } else { + return fn(context); + } +}); + +Handlebars.registerHelper('each', function(context, options) { + var fn = options.fn, inverse = options.inverse; + var ret = ""; + + if(context && context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; +}); + +Handlebars.registerHelper('if', function(context, options) { + var type = toString.call(context); + if(type === functionType) { context = context.call(this); } + + if(!context || Handlebars.Utils.isEmpty(context)) { + return options.inverse(this); + } else { + return options.fn(this); + } +}); + +Handlebars.registerHelper('unless', function(context, options) { + var fn = options.fn, inverse = options.inverse; + options.fn = inverse; + options.inverse = fn; + + return Handlebars.helpers['if'].call(this, context, options); +}); + +Handlebars.registerHelper('with', function(context, options) { + return options.fn(context); +}); + +Handlebars.registerHelper('log', function(context) { + Handlebars.log(context); +}); +; +// lib/handlebars/compiler/parser.js +/* Jison generated parser */ +var handlebars = (function(){ + +var parser = {trace: function trace() { }, +yy: {}, +symbols_: {"error":2,"root":3,"program":4,"EOF":5,"statements":6,"simpleInverse":7,"statement":8,"openInverse":9,"closeBlock":10,"openBlock":11,"mustache":12,"partial":13,"CONTENT":14,"COMMENT":15,"OPEN_BLOCK":16,"inMustache":17,"CLOSE":18,"OPEN_INVERSE":19,"OPEN_ENDBLOCK":20,"path":21,"OPEN":22,"OPEN_UNESCAPED":23,"OPEN_PARTIAL":24,"params":25,"hash":26,"param":27,"STRING":28,"INTEGER":29,"BOOLEAN":30,"hashSegments":31,"hashSegment":32,"ID":33,"EQUALS":34,"pathSegments":35,"SEP":36,"$accept":0,"$end":1}, +terminals_: {2:"error",5:"EOF",14:"CONTENT",15:"COMMENT",16:"OPEN_BLOCK",18:"CLOSE",19:"OPEN_INVERSE",20:"OPEN_ENDBLOCK",22:"OPEN",23:"OPEN_UNESCAPED",24:"OPEN_PARTIAL",28:"STRING",29:"INTEGER",30:"BOOLEAN",33:"ID",34:"EQUALS",36:"SEP"}, +productions_: [0,[3,2],[4,3],[4,1],[4,0],[6,1],[6,2],[8,3],[8,3],[8,1],[8,1],[8,1],[8,1],[11,3],[9,3],[10,3],[12,3],[12,3],[13,3],[13,4],[7,2],[17,3],[17,2],[17,2],[17,1],[25,2],[25,1],[27,1],[27,1],[27,1],[27,1],[26,1],[31,2],[31,1],[32,3],[32,3],[32,3],[32,3],[21,1],[35,3],[35,1]], +performAction: function anonymous(yytext,yyleng,yylineno,yy,yystate,$$,_$) { + +var $0 = $$.length - 1; +switch (yystate) { +case 1: return $$[$0-1] +break; +case 2: this.$ = new yy.ProgramNode($$[$0-2], $$[$0]) +break; +case 3: this.$ = new yy.ProgramNode($$[$0]) +break; +case 4: this.$ = new yy.ProgramNode([]) +break; +case 5: this.$ = [$$[$0]] +break; +case 6: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] +break; +case 7: this.$ = new yy.InverseNode($$[$0-2], $$[$0-1], $$[$0]) +break; +case 8: this.$ = new yy.BlockNode($$[$0-2], $$[$0-1], $$[$0]) +break; +case 9: this.$ = $$[$0] +break; +case 10: this.$ = $$[$0] +break; +case 11: this.$ = new yy.ContentNode($$[$0]) +break; +case 12: this.$ = new yy.CommentNode($$[$0]) +break; +case 13: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 14: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 15: this.$ = $$[$0-1] +break; +case 16: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 17: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], true) +break; +case 18: this.$ = new yy.PartialNode($$[$0-1]) +break; +case 19: this.$ = new yy.PartialNode($$[$0-2], $$[$0-1]) +break; +case 20: +break; +case 21: this.$ = [[$$[$0-2]].concat($$[$0-1]), $$[$0]] +break; +case 22: this.$ = [[$$[$0-1]].concat($$[$0]), null] +break; +case 23: this.$ = [[$$[$0-1]], $$[$0]] +break; +case 24: this.$ = [[$$[$0]], null] +break; +case 25: $$[$0-1].push($$[$0]); this.$ = $$[$0-1]; +break; +case 26: this.$ = [$$[$0]] +break; +case 27: this.$ = $$[$0] +break; +case 28: this.$ = new yy.StringNode($$[$0]) +break; +case 29: this.$ = new yy.IntegerNode($$[$0]) +break; +case 30: this.$ = new yy.BooleanNode($$[$0]) +break; +case 31: this.$ = new yy.HashNode($$[$0]) +break; +case 32: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] +break; +case 33: this.$ = [$$[$0]] +break; +case 34: this.$ = [$$[$0-2], $$[$0]] +break; +case 35: this.$ = [$$[$0-2], new yy.StringNode($$[$0])] +break; +case 36: this.$ = [$$[$0-2], new yy.IntegerNode($$[$0])] +break; +case 37: this.$ = [$$[$0-2], new yy.BooleanNode($$[$0])] +break; +case 38: this.$ = new yy.IdNode($$[$0]) +break; +case 39: $$[$0-2].push($$[$0]); this.$ = $$[$0-2]; +break; +case 40: this.$ = [$$[$0]] +break; +} +}, +table: [{3:1,4:2,5:[2,4],6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{1:[3]},{5:[1,16]},{5:[2,3],7:17,8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,19],20:[2,3],22:[1,13],23:[1,14],24:[1,15]},{5:[2,5],14:[2,5],15:[2,5],16:[2,5],19:[2,5],20:[2,5],22:[2,5],23:[2,5],24:[2,5]},{4:20,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{4:21,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{5:[2,9],14:[2,9],15:[2,9],16:[2,9],19:[2,9],20:[2,9],22:[2,9],23:[2,9],24:[2,9]},{5:[2,10],14:[2,10],15:[2,10],16:[2,10],19:[2,10],20:[2,10],22:[2,10],23:[2,10],24:[2,10]},{5:[2,11],14:[2,11],15:[2,11],16:[2,11],19:[2,11],20:[2,11],22:[2,11],23:[2,11],24:[2,11]},{5:[2,12],14:[2,12],15:[2,12],16:[2,12],19:[2,12],20:[2,12],22:[2,12],23:[2,12],24:[2,12]},{17:22,21:23,33:[1,25],35:24},{17:26,21:23,33:[1,25],35:24},{17:27,21:23,33:[1,25],35:24},{17:28,21:23,33:[1,25],35:24},{21:29,33:[1,25],35:24},{1:[2,1]},{6:30,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{5:[2,6],14:[2,6],15:[2,6],16:[2,6],19:[2,6],20:[2,6],22:[2,6],23:[2,6],24:[2,6]},{17:22,18:[1,31],21:23,33:[1,25],35:24},{10:32,20:[1,33]},{10:34,20:[1,33]},{18:[1,35]},{18:[2,24],21:40,25:36,26:37,27:38,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,38],28:[2,38],29:[2,38],30:[2,38],33:[2,38],36:[1,46]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],36:[2,40]},{18:[1,47]},{18:[1,48]},{18:[1,49]},{18:[1,50],21:51,33:[1,25],35:24},{5:[2,2],8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,2],22:[1,13],23:[1,14],24:[1,15]},{14:[2,20],15:[2,20],16:[2,20],19:[2,20],22:[2,20],23:[2,20],24:[2,20]},{5:[2,7],14:[2,7],15:[2,7],16:[2,7],19:[2,7],20:[2,7],22:[2,7],23:[2,7],24:[2,7]},{21:52,33:[1,25],35:24},{5:[2,8],14:[2,8],15:[2,8],16:[2,8],19:[2,8],20:[2,8],22:[2,8],23:[2,8],24:[2,8]},{14:[2,14],15:[2,14],16:[2,14],19:[2,14],20:[2,14],22:[2,14],23:[2,14],24:[2,14]},{18:[2,22],21:40,26:53,27:54,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,23]},{18:[2,26],28:[2,26],29:[2,26],30:[2,26],33:[2,26]},{18:[2,31],32:55,33:[1,56]},{18:[2,27],28:[2,27],29:[2,27],30:[2,27],33:[2,27]},{18:[2,28],28:[2,28],29:[2,28],30:[2,28],33:[2,28]},{18:[2,29],28:[2,29],29:[2,29],30:[2,29],33:[2,29]},{18:[2,30],28:[2,30],29:[2,30],30:[2,30],33:[2,30]},{18:[2,33],33:[2,33]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],34:[1,57],36:[2,40]},{33:[1,58]},{14:[2,13],15:[2,13],16:[2,13],19:[2,13],20:[2,13],22:[2,13],23:[2,13],24:[2,13]},{5:[2,16],14:[2,16],15:[2,16],16:[2,16],19:[2,16],20:[2,16],22:[2,16],23:[2,16],24:[2,16]},{5:[2,17],14:[2,17],15:[2,17],16:[2,17],19:[2,17],20:[2,17],22:[2,17],23:[2,17],24:[2,17]},{5:[2,18],14:[2,18],15:[2,18],16:[2,18],19:[2,18],20:[2,18],22:[2,18],23:[2,18],24:[2,18]},{18:[1,59]},{18:[1,60]},{18:[2,21]},{18:[2,25],28:[2,25],29:[2,25],30:[2,25],33:[2,25]},{18:[2,32],33:[2,32]},{34:[1,57]},{21:61,28:[1,62],29:[1,63],30:[1,64],33:[1,25],35:24},{18:[2,39],28:[2,39],29:[2,39],30:[2,39],33:[2,39],36:[2,39]},{5:[2,19],14:[2,19],15:[2,19],16:[2,19],19:[2,19],20:[2,19],22:[2,19],23:[2,19],24:[2,19]},{5:[2,15],14:[2,15],15:[2,15],16:[2,15],19:[2,15],20:[2,15],22:[2,15],23:[2,15],24:[2,15]},{18:[2,34],33:[2,34]},{18:[2,35],33:[2,35]},{18:[2,36],33:[2,36]},{18:[2,37],33:[2,37]}], +defaultActions: {16:[2,1],37:[2,23],53:[2,21]}, +parseError: function parseError(str, hash) { + throw new Error(str); +}, +parse: function parse(input) { + var self = this, stack = [0], vstack = [null], lstack = [], table = this.table, yytext = "", yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1; + this.lexer.setInput(input); + this.lexer.yy = this.yy; + this.yy.lexer = this.lexer; + if (typeof this.lexer.yylloc == "undefined") + this.lexer.yylloc = {}; + var yyloc = this.lexer.yylloc; + lstack.push(yyloc); + if (typeof this.yy.parseError === "function") + this.parseError = this.yy.parseError; + function popStack(n) { + stack.length = stack.length - 2 * n; + vstack.length = vstack.length - n; + lstack.length = lstack.length - n; + } + function lex() { + var token; + token = self.lexer.lex() || 1; + if (typeof token !== "number") { + token = self.symbols_[token] || token; + } + return token; + } + var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected; + while (true) { + state = stack[stack.length - 1]; + if (this.defaultActions[state]) { + action = this.defaultActions[state]; + } else { + if (symbol == null) + symbol = lex(); + action = table[state] && table[state][symbol]; + } + if (typeof action === "undefined" || !action.length || !action[0]) { + if (!recovering) { + expected = []; + for (p in table[state]) + if (this.terminals_[p] && p > 2) { + expected.push("'" + this.terminals_[p] + "'"); + } + var errStr = ""; + if (this.lexer.showPosition) { + errStr = "Parse error on line " + (yylineno + 1) + ":\n" + this.lexer.showPosition() + "\nExpecting " + expected.join(", ") + ", got '" + this.terminals_[symbol] + "'"; + } else { + errStr = "Parse error on line " + (yylineno + 1) + ": Unexpected " + (symbol == 1?"end of input":"'" + (this.terminals_[symbol] || symbol) + "'"); + } + this.parseError(errStr, {text: this.lexer.match, token: this.terminals_[symbol] || symbol, line: this.lexer.yylineno, loc: yyloc, expected: expected}); + } + } + if (action[0] instanceof Array && action.length > 1) { + throw new Error("Parse Error: multiple actions possible at state: " + state + ", token: " + symbol); + } + switch (action[0]) { + case 1: + stack.push(symbol); + vstack.push(this.lexer.yytext); + lstack.push(this.lexer.yylloc); + stack.push(action[1]); + symbol = null; + if (!preErrorSymbol) { + yyleng = this.lexer.yyleng; + yytext = this.lexer.yytext; + yylineno = this.lexer.yylineno; + yyloc = this.lexer.yylloc; + if (recovering > 0) + recovering--; + } else { + symbol = preErrorSymbol; + preErrorSymbol = null; + } + break; + case 2: + len = this.productions_[action[1]][1]; + yyval.$ = vstack[vstack.length - len]; + yyval._$ = {first_line: lstack[lstack.length - (len || 1)].first_line, last_line: lstack[lstack.length - 1].last_line, first_column: lstack[lstack.length - (len || 1)].first_column, last_column: lstack[lstack.length - 1].last_column}; + r = this.performAction.call(yyval, yytext, yyleng, yylineno, this.yy, action[1], vstack, lstack); + if (typeof r !== "undefined") { + return r; + } + if (len) { + stack = stack.slice(0, -1 * len * 2); + vstack = vstack.slice(0, -1 * len); + lstack = lstack.slice(0, -1 * len); + } + stack.push(this.productions_[action[1]][0]); + vstack.push(yyval.$); + lstack.push(yyval._$); + newState = table[stack[stack.length - 2]][stack[stack.length - 1]]; + stack.push(newState); + break; + case 3: + return true; + } + } + return true; +} +};/* Jison generated lexer */ +var lexer = (function(){ + +var lexer = ({EOF:1, +parseError:function parseError(str, hash) { + if (this.yy.parseError) { + this.yy.parseError(str, hash); + } else { + throw new Error(str); + } + }, +setInput:function (input) { + this._input = input; + this._more = this._less = this.done = false; + this.yylineno = this.yyleng = 0; + this.yytext = this.matched = this.match = ''; + this.conditionStack = ['INITIAL']; + this.yylloc = {first_line:1,first_column:0,last_line:1,last_column:0}; + return this; + }, +input:function () { + var ch = this._input[0]; + this.yytext+=ch; + this.yyleng++; + this.match+=ch; + this.matched+=ch; + var lines = ch.match(/\n/); + if (lines) this.yylineno++; + this._input = this._input.slice(1); + return ch; + }, +unput:function (ch) { + this._input = ch + this._input; + return this; + }, +more:function () { + this._more = true; + return this; + }, +pastInput:function () { + var past = this.matched.substr(0, this.matched.length - this.match.length); + return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\n/g, ""); + }, +upcomingInput:function () { + var next = this.match; + if (next.length < 20) { + next += this._input.substr(0, 20-next.length); + } + return (next.substr(0,20)+(next.length > 20 ? '...':'')).replace(/\n/g, ""); + }, +showPosition:function () { + var pre = this.pastInput(); + var c = new Array(pre.length + 1).join("-"); + return pre + this.upcomingInput() + "\n" + c+"^"; + }, +next:function () { + if (this.done) { + return this.EOF; + } + if (!this._input) this.done = true; + + var token, + match, + col, + lines; + if (!this._more) { + this.yytext = ''; + this.match = ''; + } + var rules = this._currentRules(); + for (var i=0;i < rules.length; i++) { + match = this._input.match(this.rules[rules[i]]); + if (match) { + lines = match[0].match(/\n.*/g); + if (lines) this.yylineno += lines.length; + this.yylloc = {first_line: this.yylloc.last_line, + last_line: this.yylineno+1, + first_column: this.yylloc.last_column, + last_column: lines ? lines[lines.length-1].length-1 : this.yylloc.last_column + match[0].length} + this.yytext += match[0]; + this.match += match[0]; + this.matches = match; + this.yyleng = this.yytext.length; + this._more = false; + this._input = this._input.slice(match[0].length); + this.matched += match[0]; + token = this.performAction.call(this, this.yy, this, rules[i],this.conditionStack[this.conditionStack.length-1]); + if (token) return token; + else return; + } + } + if (this._input === "") { + return this.EOF; + } else { + this.parseError('Lexical error on line '+(this.yylineno+1)+'. Unrecognized text.\n'+this.showPosition(), + {text: "", token: null, line: this.yylineno}); + } + }, +lex:function lex() { + var r = this.next(); + if (typeof r !== 'undefined') { + return r; + } else { + return this.lex(); + } + }, +begin:function begin(condition) { + this.conditionStack.push(condition); + }, +popState:function popState() { + return this.conditionStack.pop(); + }, +_currentRules:function _currentRules() { + return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules; + }, +topState:function () { + return this.conditionStack[this.conditionStack.length-2]; + }, +pushState:function begin(condition) { + this.begin(condition); + }}); +lexer.performAction = function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) { + +var YYSTATE=YY_START +switch($avoiding_name_collisions) { +case 0: + if(yy_.yytext.slice(-1) !== "\\") this.begin("mu"); + if(yy_.yytext.slice(-1) === "\\") yy_.yytext = yy_.yytext.substr(0,yy_.yyleng-1), this.begin("emu"); + if(yy_.yytext) return 14; + +break; +case 1: return 14; +break; +case 2: this.popState(); return 14; +break; +case 3: return 24; +break; +case 4: return 16; +break; +case 5: return 20; +break; +case 6: return 19; +break; +case 7: return 19; +break; +case 8: return 23; +break; +case 9: return 23; +break; +case 10: yy_.yytext = yy_.yytext.substr(3,yy_.yyleng-5); this.popState(); return 15; +break; +case 11: return 22; +break; +case 12: return 34; +break; +case 13: return 33; +break; +case 14: return 33; +break; +case 15: return 36; +break; +case 16: /*ignore whitespace*/ +break; +case 17: this.popState(); return 18; +break; +case 18: this.popState(); return 18; +break; +case 19: yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2).replace(/\\"/g,'"'); return 28; +break; +case 20: return 30; +break; +case 21: return 30; +break; +case 22: return 29; +break; +case 23: return 33; +break; +case 24: yy_.yytext = yy_.yytext.substr(1, yy_.yyleng-2); return 33; +break; +case 25: return 'INVALID'; +break; +case 26: return 5; +break; +} +}; +lexer.rules = [/^[^\x00]*?(?=(\{\{))/,/^[^\x00]+/,/^[^\x00]{2,}?(?=(\{\{))/,/^\{\{>/,/^\{\{#/,/^\{\{\//,/^\{\{\^/,/^\{\{\s*else\b/,/^\{\{\{/,/^\{\{&/,/^\{\{![\s\S]*?\}\}/,/^\{\{/,/^=/,/^\.(?=[} ])/,/^\.\./,/^[\/.]/,/^\s+/,/^\}\}\}/,/^\}\}/,/^"(\\["]|[^"])*"/,/^true(?=[}\s])/,/^false(?=[}\s])/,/^[0-9]+(?=[}\s])/,/^[a-zA-Z0-9_$-]+(?=[=}\s\/.])/,/^\[[^\]]*\]/,/^./,/^$/]; +lexer.conditions = {"mu":{"rules":[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26],"inclusive":false},"emu":{"rules":[2],"inclusive":false},"INITIAL":{"rules":[0,1,26],"inclusive":true}};return lexer;})() +parser.lexer = lexer; +return parser; +})(); +if (typeof require !== 'undefined' && typeof exports !== 'undefined') { +exports.parser = handlebars; +exports.parse = function () { return handlebars.parse.apply(handlebars, arguments); } +exports.main = function commonjsMain(args) { + if (!args[1]) + throw new Error('Usage: '+args[0]+' FILE'); + if (typeof process !== 'undefined') { + var source = require('fs').readFileSync(require('path').join(process.cwd(), args[1]), "utf8"); + } else { + var cwd = require("file").path(require("file").cwd()); + var source = cwd.join(args[1]).read({charset: "utf-8"}); + } + return exports.parser.parse(source); +} +if (typeof module !== 'undefined' && require.main === module) { + exports.main(typeof process !== 'undefined' ? process.argv.slice(1) : require("system").args); +} +}; +; +// lib/handlebars/compiler/base.js +Handlebars.Parser = handlebars; + +Handlebars.parse = function(string) { + Handlebars.Parser.yy = Handlebars.AST; + return Handlebars.Parser.parse(string); +}; + +Handlebars.print = function(ast) { + return new Handlebars.PrintVisitor().accept(ast); +}; + +Handlebars.logger = { + DEBUG: 0, INFO: 1, WARN: 2, ERROR: 3, level: 3, + + // override in the host environment + log: function(level, str) {} +}; + +Handlebars.log = function(level, str) { Handlebars.logger.log(level, str); }; +; +// lib/handlebars/compiler/ast.js +(function() { + + Handlebars.AST = {}; + + Handlebars.AST.ProgramNode = function(statements, inverse) { + this.type = "program"; + this.statements = statements; + if(inverse) { this.inverse = new Handlebars.AST.ProgramNode(inverse); } + }; + + Handlebars.AST.MustacheNode = function(params, hash, unescaped) { + this.type = "mustache"; + this.id = params[0]; + this.params = params.slice(1); + this.hash = hash; + this.escaped = !unescaped; + }; + + Handlebars.AST.PartialNode = function(id, context) { + this.type = "partial"; + + // TODO: disallow complex IDs + + this.id = id; + this.context = context; + }; + + var verifyMatch = function(open, close) { + if(open.original !== close.original) { + throw new Handlebars.Exception(open.original + " doesn't match " + close.original); + } + }; + + Handlebars.AST.BlockNode = function(mustache, program, close) { + verifyMatch(mustache.id, close); + this.type = "block"; + this.mustache = mustache; + this.program = program; + }; + + Handlebars.AST.InverseNode = function(mustache, program, close) { + verifyMatch(mustache.id, close); + this.type = "inverse"; + this.mustache = mustache; + this.program = program; + }; + + Handlebars.AST.ContentNode = function(string) { + this.type = "content"; + this.string = string; + }; + + Handlebars.AST.HashNode = function(pairs) { + this.type = "hash"; + this.pairs = pairs; + }; + + Handlebars.AST.IdNode = function(parts) { + this.type = "ID"; + this.original = parts.join("."); + + var dig = [], depth = 0; + + for(var i=0,l=parts.length; i<l; i++) { + var part = parts[i]; + + if(part === "..") { depth++; } + else if(part === "." || part === "this") { this.isScoped = true; } + else { dig.push(part); } + } + + this.parts = dig; + this.string = dig.join('.'); + this.depth = depth; + this.isSimple = (dig.length === 1) && (depth === 0); + }; + + Handlebars.AST.StringNode = function(string) { + this.type = "STRING"; + this.string = string; + }; + + Handlebars.AST.IntegerNode = function(integer) { + this.type = "INTEGER"; + this.integer = integer; + }; + + Handlebars.AST.BooleanNode = function(bool) { + this.type = "BOOLEAN"; + this.bool = bool; + }; + + Handlebars.AST.CommentNode = function(comment) { + this.type = "comment"; + this.comment = comment; + }; + +})();; +// lib/handlebars/utils.js +Handlebars.Exception = function(message) { + var tmp = Error.prototype.constructor.apply(this, arguments); + + for (var p in tmp) { + if (tmp.hasOwnProperty(p)) { this[p] = tmp[p]; } + } + + this.message = tmp.message; +}; +Handlebars.Exception.prototype = new Error; + +// Build out our basic SafeString type +Handlebars.SafeString = function(string) { + this.string = string; +}; +Handlebars.SafeString.prototype.toString = function() { + return this.string.toString(); +}; + +(function() { + var escape = { + "<": "<", + ">": ">", + '"': """, + "'": "'", + "`": "`" + }; + + var badChars = /&(?!\w+;)|[<>"'`]/g; + var possible = /[&<>"'`]/; + + var escapeChar = function(chr) { + return escape[chr] || "&"; + }; + + Handlebars.Utils = { + escapeExpression: function(string) { + // don't escape SafeStrings, since they're already safe + if (string instanceof Handlebars.SafeString) { + return string.toString(); + } else if (string == null || string === false) { + return ""; + } + + if(!possible.test(string)) { return string; } + return string.replace(badChars, escapeChar); + }, + + isEmpty: function(value) { + if (typeof value === "undefined") { + return true; + } else if (value === null) { + return true; + } else if (value === false) { + return true; + } else if(Object.prototype.toString.call(value) === "[object Array]" && value.length === 0) { + return true; + } else { + return false; + } + } + }; +})();; +// lib/handlebars/compiler/compiler.js +Handlebars.Compiler = function() {}; +Handlebars.JavaScriptCompiler = function() {}; + +(function(Compiler, JavaScriptCompiler) { + Compiler.OPCODE_MAP = { + appendContent: 1, + getContext: 2, + lookupWithHelpers: 3, + lookup: 4, + append: 5, + invokeMustache: 6, + appendEscaped: 7, + pushString: 8, + truthyOrFallback: 9, + functionOrFallback: 10, + invokeProgram: 11, + invokePartial: 12, + push: 13, + assignToHash: 15, + pushStringParam: 16 + }; + + Compiler.MULTI_PARAM_OPCODES = { + appendContent: 1, + getContext: 1, + lookupWithHelpers: 2, + lookup: 1, + invokeMustache: 3, + pushString: 1, + truthyOrFallback: 1, + functionOrFallback: 1, + invokeProgram: 3, + invokePartial: 1, + push: 1, + assignToHash: 1, + pushStringParam: 1 + }; + + Compiler.DISASSEMBLE_MAP = {}; + + for(var prop in Compiler.OPCODE_MAP) { + var value = Compiler.OPCODE_MAP[prop]; + Compiler.DISASSEMBLE_MAP[value] = prop; + } + + Compiler.multiParamSize = function(code) { + return Compiler.MULTI_PARAM_OPCODES[Compiler.DISASSEMBLE_MAP[code]]; + }; + + Compiler.prototype = { + compiler: Compiler, + + disassemble: function() { + var opcodes = this.opcodes, opcode, nextCode; + var out = [], str, name, value; + + for(var i=0, l=opcodes.length; i<l; i++) { + opcode = opcodes[i]; + + if(opcode === 'DECLARE') { + name = opcodes[++i]; + value = opcodes[++i]; + out.push("DECLARE " + name + " = " + value); + } else { + str = Compiler.DISASSEMBLE_MAP[opcode]; + + var extraParams = Compiler.multiParamSize(opcode); + var codes = []; + + for(var j=0; j<extraParams; j++) { + nextCode = opcodes[++i]; + + if(typeof nextCode === "string") { + nextCode = "\"" + nextCode.replace("\n", "\\n") + "\""; + } + + codes.push(nextCode); + } + + str = str + " " + codes.join(" "); + + out.push(str); + } + } + + return out.join("\n"); + }, + + guid: 0, + + compile: function(program, options) { + this.children = []; + this.depths = {list: []}; + this.options = options; + + // These changes will propagate to the other compiler components + var knownHelpers = this.options.knownHelpers; + this.options.knownHelpers = { + 'helperMissing': true, + 'blockHelperMissing': true, + 'each': true, + 'if': true, + 'unless': true, + 'with': true, + 'log': true + }; + if (knownHelpers) { + for (var name in knownHelpers) { + this.options.knownHelpers[name] = knownHelpers[name]; + } + } + + return this.program(program); + }, + + accept: function(node) { + return this[node.type](node); + }, + + program: function(program) { + var statements = program.statements, statement; + this.opcodes = []; + + for(var i=0, l=statements.length; i<l; i++) { + statement = statements[i]; + this[statement.type](statement); + } + this.isSimple = l === 1; + + this.depths.list = this.depths.list.sort(function(a, b) { + return a - b; + }); + + return this; + }, + + compileProgram: function(program) { + var result = new this.compiler().compile(program, this.options); + var guid = this.guid++; + + this.usePartial = this.usePartial || result.usePartial; + + this.children[guid] = result; + + for(var i=0, l=result.depths.list.length; i<l; i++) { + depth = result.depths.list[i]; + + if(depth < 2) { continue; } + else { this.addDepth(depth - 1); } + } + + return guid; + }, + + block: function(block) { + var mustache = block.mustache; + var depth, child, inverse, inverseGuid; + + var params = this.setupStackForMustache(mustache); + + var programGuid = this.compileProgram(block.program); + + if(block.program.inverse) { + inverseGuid = this.compileProgram(block.program.inverse); + this.declare('inverse', inverseGuid); + } + + this.opcode('invokeProgram', programGuid, params.length, !!mustache.hash); + this.declare('inverse', null); + this.opcode('append'); + }, + + inverse: function(block) { + var params = this.setupStackForMustache(block.mustache); + + var programGuid = this.compileProgram(block.program); + + this.declare('inverse', programGuid); + + this.opcode('invokeProgram', null, params.length, !!block.mustache.hash); + this.declare('inverse', null); + this.opcode('append'); + }, + + hash: function(hash) { + var pairs = hash.pairs, pair, val; + + this.opcode('push', '{}'); + + for(var i=0, l=pairs.length; i<l; i++) { + pair = pairs[i]; + val = pair[1]; + + this.accept(val); + this.opcode('assignToHash', pair[0]); + } + }, + + partial: function(partial) { + var id = partial.id; + this.usePartial = true; + + if(partial.context) { + this.ID(partial.context); + } else { + this.opcode('push', 'depth0'); + } + + this.opcode('invokePartial', id.original); + this.opcode('append'); + }, + + content: function(content) { + this.opcode('appendContent', content.string); + }, + + mustache: function(mustache) { + var params = this.setupStackForMustache(mustache); + + this.opcode('invokeMustache', params.length, mustache.id.original, !!mustache.hash); + + if(mustache.escaped && !this.options.noEscape) { + this.opcode('appendEscaped'); + } else { + this.opcode('append'); + } + }, + + ID: function(id) { + this.addDepth(id.depth); + + this.opcode('getContext', id.depth); + + this.opcode('lookupWithHelpers', id.parts[0] || null, id.isScoped || false); + + for(var i=1, l=id.parts.length; i<l; i++) { + this.opcode('lookup', id.parts[i]); + } + }, + + STRING: function(string) { + this.opcode('pushString', string.string); + }, + + INTEGER: function(integer) { + this.opcode('push', integer.integer); + }, + + BOOLEAN: function(bool) { + this.opcode('push', bool.bool); + }, + + comment: function() {}, + + // HELPERS + pushParams: function(params) { + var i = params.length, param; + + while(i--) { + param = params[i]; + + if(this.options.stringParams) { + if(param.depth) { + this.addDepth(param.depth); + } + + this.opcode('getContext', param.depth || 0); + this.opcode('pushStringParam', param.string); + } else { + this[param.type](param); + } + } + }, + + opcode: function(name, val1, val2, val3) { + this.opcodes.push(Compiler.OPCODE_MAP[name]); + if(val1 !== undefined) { this.opcodes.push(val1); } + if(val2 !== undefined) { this.opcodes.push(val2); } + if(val3 !== undefined) { this.opcodes.push(val3); } + }, + + declare: function(name, value) { + this.opcodes.push('DECLARE'); + this.opcodes.push(name); + this.opcodes.push(value); + }, + + addDepth: function(depth) { + if(depth === 0) { return; } + + if(!this.depths[depth]) { + this.depths[depth] = true; + this.depths.list.push(depth); + } + }, + + setupStackForMustache: function(mustache) { + var params = mustache.params; + + this.pushParams(params); + + if(mustache.hash) { + this.hash(mustache.hash); + } + + this.ID(mustache.id); + + return params; + } + }; + + JavaScriptCompiler.prototype = { + // PUBLIC API: You can override these methods in a subclass to provide + // alternative compiled forms for name lookup and buffering semantics + nameLookup: function(parent, name, type) { + if (/^[0-9]+$/.test(name)) { + return parent + "[" + name + "]"; + } else if (JavaScriptCompiler.isValidJavaScriptVariableName(name)) { + return parent + "." + name; + } + else { + return parent + "['" + name + "']"; + } + }, + + appendToBuffer: function(string) { + if (this.environment.isSimple) { + return "return " + string + ";"; + } else { + return "buffer += " + string + ";"; + } + }, + + initializeBuffer: function() { + return this.quotedString(""); + }, + + namespace: "Handlebars", + // END PUBLIC API + + compile: function(environment, options, context, asObject) { + this.environment = environment; + this.options = options || {}; + + this.name = this.environment.name; + this.isChild = !!context; + this.context = context || { + programs: [], + aliases: { self: 'this' }, + registers: {list: []} + }; + + this.preamble(); + + this.stackSlot = 0; + this.stackVars = []; + + this.compileChildren(environment, options); + + var opcodes = environment.opcodes, opcode; + + this.i = 0; + + for(l=opcodes.length; this.i<l; this.i++) { + opcode = this.nextOpcode(0); + + if(opcode[0] === 'DECLARE') { + this.i = this.i + 2; + this[opcode[1]] = opcode[2]; + } else { + this.i = this.i + opcode[1].length; + this[opcode[0]].apply(this, opcode[1]); + } + } + + return this.createFunctionContext(asObject); + }, + + nextOpcode: function(n) { + var opcodes = this.environment.opcodes, opcode = opcodes[this.i + n], name, val; + var extraParams, codes; + + if(opcode === 'DECLARE') { + name = opcodes[this.i + 1]; + val = opcodes[this.i + 2]; + return ['DECLARE', name, val]; + } else { + name = Compiler.DISASSEMBLE_MAP[opcode]; + + extraParams = Compiler.multiParamSize(opcode); + codes = []; + + for(var j=0; j<extraParams; j++) { + codes.push(opcodes[this.i + j + 1 + n]); + } + + return [name, codes]; + } + }, + + eat: function(opcode) { + this.i = this.i + opcode.length; + }, + + preamble: function() { + var out = []; + + // this register will disambiguate helper lookup from finding a function in + // a context. This is necessary for mustache compatibility, which requires + // that context functions in blocks are evaluated by blockHelperMissing, and + // then proceed as if the resulting value was provided to blockHelperMissing. + this.useRegister('foundHelper'); + + if (!this.isChild) { + var namespace = this.namespace; + var copies = "helpers = helpers || " + namespace + ".helpers;"; + if(this.environment.usePartial) { copies = copies + " partials = partials || " + namespace + ".partials;"; } + out.push(copies); + } else { + out.push(''); + } + + if (!this.environment.isSimple) { + out.push(", buffer = " + this.initializeBuffer()); + } else { + out.push(""); + } + + // track the last context pushed into place to allow skipping the + // getContext opcode when it would be a noop + this.lastContext = 0; + this.source = out; + }, + + createFunctionContext: function(asObject) { + var locals = this.stackVars; + if (!this.isChild) { + locals = locals.concat(this.context.registers.list); + } + + if(locals.length > 0) { + this.source[1] = this.source[1] + ", " + locals.join(", "); + } + + // Generate minimizer alias mappings + if (!this.isChild) { + var aliases = [] + for (var alias in this.context.aliases) { + this.source[1] = this.source[1] + ', ' + alias + '=' + this.context.aliases[alias]; + } + } + + if (this.source[1]) { + this.source[1] = "var " + this.source[1].substring(2) + ";"; + } + + // Merge children + if (!this.isChild) { + this.source[1] += '\n' + this.context.programs.join('\n') + '\n'; + } + + if (!this.environment.isSimple) { + this.source.push("return buffer;"); + } + + var params = this.isChild ? ["depth0", "data"] : ["Handlebars", "depth0", "helpers", "partials", "data"]; + + for(var i=0, l=this.environment.depths.list.length; i<l; i++) { + params.push("depth" + this.environment.depths.list[i]); + } + + if (asObject) { + params.push(this.source.join("\n ")); + + return Function.apply(this, params); + } else { + var functionSource = 'function ' + (this.name || '') + '(' + params.join(',') + ') {\n ' + this.source.join("\n ") + '}'; + Handlebars.log(Handlebars.logger.DEBUG, functionSource + "\n\n"); + return functionSource; + } + }, + + appendContent: function(content) { + this.source.push(this.appendToBuffer(this.quotedString(content))); + }, + + append: function() { + var local = this.popStack(); + this.source.push("if(" + local + " || " + local + " === 0) { " + this.appendToBuffer(local) + " }"); + if (this.environment.isSimple) { + this.source.push("else { " + this.appendToBuffer("''") + " }"); + } + }, + + appendEscaped: function() { + var opcode = this.nextOpcode(1), extra = ""; + this.context.aliases.escapeExpression = 'this.escapeExpression'; + + if(opcode[0] === 'appendContent') { + extra = " + " + this.quotedString(opcode[1][0]); + this.eat(opcode); + } + + this.source.push(this.appendToBuffer("escapeExpression(" + this.popStack() + ")" + extra)); + }, + + getContext: function(depth) { + if(this.lastContext !== depth) { + this.lastContext = depth; + } + }, + + lookupWithHelpers: function(name, isScoped) { + if(name) { + var topStack = this.nextStack(); + + this.usingKnownHelper = false; + + var toPush; + if (!isScoped && this.options.knownHelpers[name]) { + toPush = topStack + " = " + this.nameLookup('helpers', name, 'helper'); + this.usingKnownHelper = true; + } else if (isScoped || this.options.knownHelpersOnly) { + toPush = topStack + " = " + this.nameLookup('depth' + this.lastContext, name, 'context'); + } else { + this.register('foundHelper', this.nameLookup('helpers', name, 'helper')); + toPush = topStack + " = foundHelper || " + this.nameLookup('depth' + this.lastContext, name, 'context'); + } + + toPush += ';'; + this.source.push(toPush); + } else { + this.pushStack('depth' + this.lastContext); + } + }, + + lookup: function(name) { + var topStack = this.topStack(); + this.source.push(topStack + " = (" + topStack + " === null || " + topStack + " === undefined || " + topStack + " === false ? " + + topStack + " : " + this.nameLookup(topStack, name, 'context') + ");"); + }, + + pushStringParam: function(string) { + this.pushStack('depth' + this.lastContext); + this.pushString(string); + }, + + pushString: function(string) { + this.pushStack(this.quotedString(string)); + }, + + push: function(name) { + this.pushStack(name); + }, + + invokeMustache: function(paramSize, original, hasHash) { + this.populateParams(paramSize, this.quotedString(original), "{}", null, hasHash, function(nextStack, helperMissingString, id) { + if (!this.usingKnownHelper) { + this.context.aliases.helperMissing = 'helpers.helperMissing'; + this.context.aliases.undef = 'void 0'; + this.source.push("else if(" + id + "=== undef) { " + nextStack + " = helperMissing.call(" + helperMissingString + "); }"); + if (nextStack !== id) { + this.source.push("else { " + nextStack + " = " + id + "; }"); + } + } + }); + }, + + invokeProgram: function(guid, paramSize, hasHash) { + var inverse = this.programExpression(this.inverse); + var mainProgram = this.programExpression(guid); + + this.populateParams(paramSize, null, mainProgram, inverse, hasHash, function(nextStack, helperMissingString, id) { + if (!this.usingKnownHelper) { + this.context.aliases.blockHelperMissing = 'helpers.blockHelperMissing'; + this.source.push("else { " + nextStack + " = blockHelperMissing.call(" + helperMissingString + "); }"); + } + }); + }, + + populateParams: function(paramSize, helperId, program, inverse, hasHash, fn) { + var needsRegister = hasHash || this.options.stringParams || inverse || this.options.data; + var id = this.popStack(), nextStack; + var params = [], param, stringParam, stringOptions; + + if (needsRegister) { + this.register('tmp1', program); + stringOptions = 'tmp1'; + } else { + stringOptions = '{ hash: {} }'; + } + + if (needsRegister) { + var hash = (hasHash ? this.popStack() : '{}'); + this.source.push('tmp1.hash = ' + hash + ';'); + } + + if(this.options.stringParams) { + this.source.push('tmp1.contexts = [];'); + } + + for(var i=0; i<paramSize; i++) { + param = this.popStack(); + params.push(param); + + if(this.options.stringParams) { + this.source.push('tmp1.contexts.push(' + this.popStack() + ');'); + } + } + + if(inverse) { + this.source.push('tmp1.fn = tmp1;'); + this.source.push('tmp1.inverse = ' + inverse + ';'); + } + + if(this.options.data) { + this.source.push('tmp1.data = data;'); + } + + params.push(stringOptions); + + this.populateCall(params, id, helperId || id, fn, program !== '{}'); + }, + + populateCall: function(params, id, helperId, fn, program) { + var paramString = ["depth0"].concat(params).join(", "); + var helperMissingString = ["depth0"].concat(helperId).concat(params).join(", "); + + var nextStack = this.nextStack(); + + if (this.usingKnownHelper) { + this.source.push(nextStack + " = " + id + ".call(" + paramString + ");"); + } else { + this.context.aliases.functionType = '"function"'; + var condition = program ? "foundHelper && " : "" + this.source.push("if(" + condition + "typeof " + id + " === functionType) { " + nextStack + " = " + id + ".call(" + paramString + "); }"); + } + fn.call(this, nextStack, helperMissingString, id); + this.usingKnownHelper = false; + }, + + invokePartial: function(context) { + params = [this.nameLookup('partials', context, 'partial'), "'" + context + "'", this.popStack(), "helpers", "partials"]; + + if (this.options.data) { + params.push("data"); + } + + this.pushStack("self.invokePartial(" + params.join(", ") + ");"); + }, + + assignToHash: function(key) { + var value = this.popStack(); + var hash = this.topStack(); + + this.source.push(hash + "['" + key + "'] = " + value + ";"); + }, + + // HELPERS + + compiler: JavaScriptCompiler, + + compileChildren: function(environment, options) { + var children = environment.children, child, compiler; + + for(var i=0, l=children.length; i<l; i++) { + child = children[i]; + compiler = new this.compiler(); + + this.context.programs.push(''); // Placeholder to prevent name conflicts for nested children + var index = this.context.programs.length; + child.index = index; + child.name = 'program' + index; + this.context.programs[index] = compiler.compile(child, options, this.context); + } + }, + + programExpression: function(guid) { + if(guid == null) { return "self.noop"; } + + var child = this.environment.children[guid], + depths = child.depths.list; + var programParams = [child.index, child.name, "data"]; + + for(var i=0, l = depths.length; i<l; i++) { + depth = depths[i]; + + if(depth === 1) { programParams.push("depth0"); } + else { programParams.push("depth" + (depth - 1)); } + } + + if(depths.length === 0) { + return "self.program(" + programParams.join(", ") + ")"; + } else { + programParams.shift(); + return "self.programWithDepth(" + programParams.join(", ") + ")"; + } + }, + + register: function(name, val) { + this.useRegister(name); + this.source.push(name + " = " + val + ";"); + }, + + useRegister: function(name) { + if(!this.context.registers[name]) { + this.context.registers[name] = true; + this.context.registers.list.push(name); + } + }, + + pushStack: function(item) { + this.source.push(this.nextStack() + " = " + item + ";"); + return "stack" + this.stackSlot; + }, + + nextStack: function() { + this.stackSlot++; + if(this.stackSlot > this.stackVars.length) { this.stackVars.push("stack" + this.stackSlot); } + return "stack" + this.stackSlot; + }, + + popStack: function() { + return "stack" + this.stackSlot--; + }, + + topStack: function() { + return "stack" + this.stackSlot; + }, + + quotedString: function(str) { + return '"' + str + .replace(/\\/g, '\\\\') + .replace(/"/g, '\\"') + .replace(/\n/g, '\\n') + .replace(/\r/g, '\\r') + '"'; + } + }; + + var reservedWords = ( + "break else new var" + + " case finally return void" + + " catch for switch while" + + " continue function this with" + + " default if throw" + + " delete in try" + + " do instanceof typeof" + + " abstract enum int short" + + " boolean export interface static" + + " byte extends long super" + + " char final native synchronized" + + " class float package throws" + + " const goto private transient" + + " debugger implements protected volatile" + + " double import public let yield" + ).split(" "); + + var compilerWords = JavaScriptCompiler.RESERVED_WORDS = {}; + + for(var i=0, l=reservedWords.length; i<l; i++) { + compilerWords[reservedWords[i]] = true; + } + + JavaScriptCompiler.isValidJavaScriptVariableName = function(name) { + if(!JavaScriptCompiler.RESERVED_WORDS[name] && /^[a-zA-Z_$][0-9a-zA-Z_$]+$/.test(name)) { + return true; + } + return false; + } + +})(Handlebars.Compiler, Handlebars.JavaScriptCompiler); + +Handlebars.precompile = function(string, options) { + options = options || {}; + + var ast = Handlebars.parse(string); + var environment = new Handlebars.Compiler().compile(ast, options); + return new Handlebars.JavaScriptCompiler().compile(environment, options); +}; + +Handlebars.compile = function(string, options) { + options = options || {}; + + var compiled; + function compile() { + var ast = Handlebars.parse(string); + var environment = new Handlebars.Compiler().compile(ast, options); + var templateSpec = new Handlebars.JavaScriptCompiler().compile(environment, options, undefined, true); + return Handlebars.template(templateSpec); + } + + // Template is only compiled on first use and cached after that point. + return function(context, options) { + if (!compiled) { + compiled = compile(); + } + return compiled.call(this, context, options); + }; +}; +; +// lib/handlebars/runtime.js +Handlebars.VM = { + template: function(templateSpec) { + // Just add water + var container = { + escapeExpression: Handlebars.Utils.escapeExpression, + invokePartial: Handlebars.VM.invokePartial, + programs: [], + program: function(i, fn, data) { + var programWrapper = this.programs[i]; + if(data) { + return Handlebars.VM.program(fn, data); + } else if(programWrapper) { + return programWrapper; + } else { + programWrapper = this.programs[i] = Handlebars.VM.program(fn); + return programWrapper; + } + }, + programWithDepth: Handlebars.VM.programWithDepth, + noop: Handlebars.VM.noop + }; + + return function(context, options) { + options = options || {}; + return templateSpec.call(container, Handlebars, context, options.helpers, options.partials, options.data); + }; + }, + + programWithDepth: function(fn, data, $depth) { + var args = Array.prototype.slice.call(arguments, 2); + + return function(context, options) { + options = options || {}; + + return fn.apply(this, [context, options.data || data].concat(args)); + }; + }, + program: function(fn, data) { + return function(context, options) { + options = options || {}; + + return fn(context, options.data || data); + }; + }, + noop: function() { return ""; }, + invokePartial: function(partial, name, context, helpers, partials, data) { + options = { helpers: helpers, partials: partials, data: data }; + + if(partial === undefined) { + throw new Handlebars.Exception("The partial " + name + " could not be found"); + } else if(partial instanceof Function) { + return partial(context, options); + } else if (!Handlebars.compile) { + throw new Handlebars.Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); + } else { + partials[name] = Handlebars.compile(partial); + return partials[name](context, options); + } + } +}; + +Handlebars.template = Handlebars.VM.template; +; diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/annotations.js --- /dev/null +++ b/static/scripts/mvc/annotations.js @@ -0,0 +1,35 @@ +/*============================================================================== +Backbone MV for Annotations + + +TODO: + +==============================================================================*/ +/** Single Tag model + */ +var Annotation = BaseModel.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'Annotation()'; + } +}); + +//------------------------------------------------------------------------------ +/** Single Tag view + */ +var AnnotationView = BaseView.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'AnnotationView()'; + } +}); + +//============================================================================== +/** YAGNI? A collection of Annotations, mainView? + */ diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/base-mvc.js --- /dev/null +++ b/static/scripts/mvc/base-mvc.js @@ -0,0 +1,271 @@ +/** + * Simple base model for any visible element. Includes useful attributes and ability + * to set and track visibility. + */ +var BaseModel = Backbone.RelationalModel.extend({ + defaults: { + name: null, + hidden: false + }, + + show: function() { + this.set("hidden", false); + }, + + hide: function() { + this.set("hidden", true); + }, + + is_visible: function() { + return !this.attributes.hidden; + } +}); + + +/** + * Base view that handles visibility based on model's hidden attribute. + */ +var BaseView = Backbone.View.extend({ + + initialize: function() { + this.model.on("change:hidden", this.update_visible, this); + this.update_visible(); + }, + + update_visible: function() { + if( this.model.attributes.hidden ){ + this.$el.hide(); + } else { + this.$el.show(); + } + } +}); + +//============================================================================== +/** + * Adds logging capabilities to your Models/Views + * can be used with plain browser console (or something more complex like an AJAX logger) + * + * add to your models/views at the definition using chaining: + * var MyModel = BaseModel.extend( LoggableMixin ).extend({ // ... }); + * + * or - more explicitly AFTER the definition: + * var MyModel = BaseModel.extend({ + * logger : console + * // ... + * this.log( '$#%& it! - broken already...' ); + * }) + * _.extend( MyModel.prototype, LoggableMixin ) + * + * NOTE: currently only uses the console.debug log function (as opposed to debug, error, warn, etc.) + */ +var LoggableMixin = { + // replace null with console (if available) to see all logs + logger : null, + + log : function(){ + return ( this.logger )?( this.logger.log.apply( this, arguments ) ) + :( undefined ); + } +}; + + +//============================================================================== +/** + * Base class for template loaders: + * The main interface is loader.getTemplates( templatesToLoad ) + * where templatesToLoad is in the form: + * { + * remoteTemplateFilename1: { + * templateFunctionName1 : templateID1, + * templateFunctionName2 : templateID2, + * ... + * }, + * remoteTemplateFilename2: { + * templateFunctionName3 : templateID3, + * templateFunctionName4 : templateID4, + * ... + * } + * } + * getTemplates will return a map of the templates in the form: + * { + * templateFunctionName1 : compiledTemplateFn1(), + * templateFunctionName2 : compiledTemplateFn2(), + * templateFunctionName3 : compiledTemplateFn3(), + * ... + * } + * + * Generally meant to be called for Backbone views, etc like this: + * BackboneView.templates = CompiledTemplateLoader( templatesToLoad ); + */ +var TemplateLoader = _.extend( {}, LoggableMixin, { + //TODO: incorporate caching of template functions (for use across objects) + //TODO: only require and use 2 level (or some variation) map templatesToLoad for the remote loader + + // comment next line out to suppress logging + //logger : console, + + //cachedTemplates : {}, + + getTemplateLoadFn : function(){ + throw( "There is no templateLoadFn. Make sure you're using a subclass of TemplateLoader" ); + }, + + // loop through templatesToLoad assuming it is a map in the form mentioned above + getTemplates : function( templatesToLoad, forceReload ){ + forceReload = forceReload || false; + this.log( this, 'getTemplates:', templatesToLoad, ', forceReload:', forceReload ); + + //!TODO: cache templates here + var templates = {}, + loader = this, + templateLoadFn = this.getTemplateLoadFn(); + + if( !templatesToLoad ){ return templates; } + jQuery.each( templatesToLoad, function( templateFile, templateData ){ + + //TODO: handle flatter map versions of templatesToLoad ({ name : id }) + jQuery.each( templateData, function( templateName, templateID ){ + loader.log( loader + ', templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID ); + templates[ templateName ] = templateLoadFn.call( loader, templateFile, templateName, templateID ); + }); + }); + return templates; + } +}); + + +//.............................................................................. +/** find the compiled template in Handlebars.templates by templateName + * and return the entire, requested templates map + */ +var CompiledTemplateLoader = _.extend( {}, TemplateLoader, { + getTemplateLoadFn : function(){ return this.loadCompiledHandlebarsTemplate; }, + + // override if new compiler + loadCompiledHandlebarsTemplate : function( templateFile, templateName, templateID ){ + //pre: compiled templates should have been loaded with the mako helper h.templates + // (although these could be dynamically loaded as well?) + this.log( 'getInDomTemplates, templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID ); + + if( !Handlebars.templates || !Handlebars.templates[ templateID ] ){ + throw( 'Template not found: Handlebars.' + templateID + + '. Check your h.templates() call in the mako file that rendered this page' ); + } + this.log( 'found template function:', templateID ); + // really this is just a lookup + return Handlebars.templates[ templateID ]; + } + + //TEST: Handlebars.full NOT runtime + //TEST: no Handlebars + //TEST: bad id + //TEST: Handlebars.runtime, good id +}); + +//.............................................................................. +/** find the NON-compiled template templateID in the DOM, compile it (using Handlebars), + * and return the entire, requested templates map + * (Note: for use with Mako.include and multiple templates) + */ +var InDomTemplateLoader = _.extend( {}, TemplateLoader, { + + // override or change if a new compiler (Underscore, etc.) is being used + compileTemplate : function( templateText ){ + // we'll need the compiler + if( !Handlebars || !Handlebars.compile ){ + throw( 'No Handlebars.compile found. You may only have Handlebars.runtime loaded.' + + 'Include handlebars.full for this to work' ); + } + // copy fn ref to this view under the templateName + this.log( 'compiling template:', templateText ); + return Handlebars.compile( templateText ); + }, + + findTemplateInDom : function( templateFile, templateName, templateID ){ + // assume the last is best + return $( 'script#' + templateID ).last(); + }, + + getTemplateLoadFn : function(){ return this.loadInDomTemplate; }, + + loadInDomTemplate : function( templateFile, templateName, templateID ){ + this.log( 'getInDomTemplate, templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID ); + + // find it in the dom by the id and compile + var template = this.findTemplateInDom( templateFile, templateName, templateID ); + if( !template || !template.length ){ + throw( 'Template not found within the DOM: ' + templateID + + '. Check that this template has been included in the page' ); + } + this.log( 'found template in dom:', template.html() ); + return this.compileTemplate( template.html() ); + } + + //TEST: no compiler + //TEST: good url, good id, in DOM + //TEST: good url, good id, NOT in DOM +}); + +//.............................................................................. +/** HTTP GET the NON-compiled templates, append into the DOM, compile them, + * and return the entire, requested templates map + * (for use with dynamically loaded views) + */ +var RemoteTemplateLoader = _.extend( {}, InDomTemplateLoader, { + templateBaseURL : 'static/scripts/templates/', + + getTemplateLoadFn : function(){ return this.loadViaHttpGet; }, + + loadViaHttpGet : function( templateFile, templateName, templateID ){ + var templateBaseURL = 'static/scripts/templates/'; + this.log( 'loadViaHttpGet, templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID, + 'templateBaseURL:', this.templateBaseURL ); + + //??: possibly not the best pattern here... + // try in-dom first (prevent loading the same templateFile for each of its templates) + var template = null; + try { + template = this.loadInDomTemplate( templateFile, templateName, templateID ); + + // if that didn't work, load the templateFile via GET,... + } catch( exception ){ + this.log( 'getInDomTemplate exception:' + exception ); + // handle no compiler exception + if( !Handlebars.compile ){ throw( exception ); } + //TEST: + + this.log( "Couldn't locate template in DOM: " + templateID ); + var loader = this; + var url = templateBaseURL + templateFile; + //??: async : false may cause problems in the long run + jQuery.ajax( url, { + method : 'GET', + async : false, + success : function( data ){ + loader.log( templateFile + ' loaded via GET. Attempting compile...' ); + //...move the templateFile into the DOM and try that again + $( 'body' ).append( data ); + template = loader.loadInDomTemplate( templateFile, templateName, templateID ); + }, + error : function( data, status, xhr ){ + throw( 'Failed to fetch ' + url + ':' + status ); + } + }); + } + if( !template ){ + throw( "Couldn't load or fetch template: " + templateID ); + } + return template; + } + + //TEST: no compiler + //TEST: good url, good id, already local + //TEST: good url, good id, remote load + //TEST: good url, bad template id + //TEST: bad url, error from ajax +}); diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -1,3 +1,4 @@ +if( console ){ console.debug( 'history mvc loaded' ); } /* Backbone.js implementation of history panel @@ -13,6 +14,8 @@ convert function comments to /** style complete comments + don't draw body until it's first unhide event + as always: where does the model end and the view begin? HistoryPanel HistoryCollection: (collection of History: 'Saved Histories') @@ -30,23 +33,12 @@ poly HistoryItemView on: can/cant_edit */ -_ = _; //============================================================================== -var Loggable = { - // replace null with console (if available) to see all logs - logger : null, - - log : function(){ - return ( this.logger )?( this.logger.debug.apply( this, arguments ) ) - :( undefined ); - } -}; -var LoggingModel = BaseModel.extend( Loggable ); -var LoggingView = BaseView.extend( Loggable ); //============================================================================== //TODO: move to Galaxy obj./namespace, decorate for current page (as GalaxyPaths) +/* var Localizable = { localizedStrings : {}, setLocalizedString : function( str, localizedString ){ @@ -58,6 +50,7 @@ } }; var LocalizableView = LoggingView.extend( Localizable ); +*/ //TODO: wire up to views //============================================================================== @@ -93,7 +86,8 @@ } //============================================================================== -var HistoryItem = LoggingModel.extend({ +//TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted +var HistoryItem = BaseModel.extend( LoggableMixin ).extend({ // a single HDA model // uncomment this out see log messages @@ -141,7 +135,11 @@ }, toString : function(){ - return 'HistoryItem(' + ( this.get( 'name' ) || this.get( 'id' ) || '' ) + ')'; + var nameAndId = this.get( 'id' ) || ''; + if( this.get( 'name' ) ){ + nameAndId += ':"' + this.get( 'name' ) + '"'; + } + return 'HistoryItem(' + nameAndId + ')'; } }); @@ -161,20 +159,19 @@ //============================================================================== -var HistoryItemView = LoggingView.extend({ +var HistoryItemView = BaseView.extend( LoggableMixin ).extend({ // view for HistoryItem model above // uncomment this out see log messages - logger : console, + //logger : console, tagName : "div", className : "historyItemContainer", - // ................................................................................ SET UP initialize : function(){ this.log( this + '.initialize:', this, this.model ); - return this; + }, // ................................................................................ RENDER MAIN @@ -190,12 +187,8 @@ .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) .addClass( 'historyItem-' + state ); - itemWrapper.append( this._render_purgedWarning() ); - itemWrapper.append( this._render_deletionWarning() ); - itemWrapper.append( this._render_visibleWarning() ); - + itemWrapper.append( this._render_warnings() ); itemWrapper.append( this._render_titleBar() ); - this.body = $( this._render_body() ); itemWrapper.append( this.body ); @@ -215,52 +208,9 @@ }, // ................................................................................ RENDER WARNINGS - //TODO: refactor into generalized warning widget/view - //TODO: refactor the three following - too much common ground - _render_purgedWarning : function(){ - // Render warnings for purged - //this.log( this + '_render_purgedWarning' ); - var warning = null; - if( this.model.get( 'purged' ) ){ - warning = $( HistoryItemView.STRINGS.purgedMsg ); - } - //this.log( 'warning:', warning ); - return warning; - }, - - _render_deletionWarning : function(){ - //this.log( this + '_render_deletionWarning' ); - // Render warnings for deleted items (and links: undelete and purge) - //pre: this.model.purge_url will be undefined if trans.app.config.allow_user_dataset_purge=False - var warningElem = null; - if( this.model.get( 'deleted' ) ){ - var warning = ''; - - if( this.model.get( 'undelete_url' ) ){ - warning += HistoryItemView.TEMPLATES.undeleteLink( this.model.attributes ); - } - if( this.model.get( 'purge_url' ) ){ - warning += HistoryItemView.TEMPLATES.purgeLink( this.model.attributes ); - } - // wrap it in the standard warning msg - warningElem = $( HistoryItemView.TEMPLATES.warningMsg({ warning: warning }) ); - } - //this.log( 'warning:', warning ); - return warningElem; - }, - - _render_visibleWarning : function(){ - //this.log( this + '_render_visibleWarning' ); - // Render warnings for hidden items (and link: unhide) - var warningElem = null; - if( !this.model.get( 'visible' ) && this.model.get( 'unhide_url' ) ){ - var warning = HistoryItemView.TEMPLATES.hiddenMsg( this.model.attributes ); - - // wrap it in the standard warning msg - warningElem = $( HistoryItemView.TEMPLATES.warningMsg({ warning: warning }) ); - } - //this.log( 'warning:', warning ); - return warningElem; + _render_warnings : function(){ + // jQ errs on building dom with whitespace - if there are no messages, trim -> '' + return $( jQuery.trim( HistoryItemView.templates.messages( this.model.toJSON() ) ) ); }, // ................................................................................ RENDER TITLEBAR @@ -292,23 +242,21 @@ //TODO: move other data (non-href) into {} in view definition, cycle over those keys in _titlebuttons //TODO: move disabled span data into view def, move logic into _titlebuttons _render_displayButton : function(){ - // render the display icon-button - // show a disabled display if the data's been purged - if( this.model.get( 'purged' ) ){ - return $( '<span class="icon-button display_disabled tooltip" ' + - 'title="Cannot display datasets removed from disk"></span>' ); - } - var id = this.model.get( 'id' ), - displayBtnData = { - //TODO: localized title - title : 'Display data in browser', - //TODO: need generated url here - href : '/datasets/' + id + '/display/?preview=True', - target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( '' ), - classes : [ 'icon-button', 'tooltip', 'display' ], - dataset_id : id - }; - return $( linkHTMLTemplate( displayBtnData ) ); + displayBtnData = ( this.model.get( 'purged' ) )?({ + // show a disabled display if the data's been purged + title : 'Cannot display datasets removed from disk', + icon_class : 'display', + enabled : false, + }):({ + // if not, render the display icon-button with href + title : 'Display data in browser', + //TODO: need generated url here + href : this.model.get( 'display_url' ), + target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( null ), + icon_class : 'display', + }); + this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); + return this.displayButton.render().$el; }, _render_editButton : function(){ @@ -317,44 +265,42 @@ purged = this.model.get( 'purged' ), deleted = this.model.get( 'deleted' ); + var editBtnData = { + title : 'Edit attributes', + href : this.model.get( 'edit_url' ), + target : 'galaxy_main', + icon_class : 'edit' + } + // disable if purged or deleted and explain why in the tooltip + //TODO: if for_editing if( deleted || purged ){ - if( !purged ){ - return $( '<span class="icon-button edit_disabled tooltip" ' + - 'title="Undelete dataset to edit attributes"></span>' ); - } else { - return $( '<span class="icon-button edit_disabled tooltip" ' + - 'title="Cannot edit attributes of datasets removed from disk"></span>' ); - } + editBtnData = { + enabled : false, + icon_class : 'edit' + }; + editBtnData.title = ( !purged )?( 'Undelete dataset to edit attributes' ): + ( 'Cannot edit attributes of datasets removed from disk' ); } - return $( linkHTMLTemplate({ - title : 'Edit attributes', - //TODO: need generated url here - href : '/datasets/' + id + '/edit', - target : 'galaxy_main', - classes : [ 'icon-button', 'tooltip', 'edit' ] - }) ); + this.editButton = new IconButtonView({ model : new IconButton( editBtnData ) }); + return this.editButton.render().$el; }, _render_deleteButton : function(){ - // render the delete icon-button - var id = this.model.get( 'id' ), - purged = this.model.get( 'purged' ), - deleted = this.model.get( 'deleted' ); - - //??: WHAAAA? can_edit == deleted?? - // yes! : (history_common.mako) can_edit=( not ( data.deleted or data.purged ) ) - if( purged || deleted ){ - return $( '<span title="Dataset is already deleted" ' + - 'class="icon-button delete_disabled tooltip"></span>' ); - } - return $( linkHTMLTemplate({ + if( !this.model.get( 'for_editing' ) ){ return null; } + + var deleteBtnData = ( this.model.get( 'delete_url' ) )?({ title : 'Delete', - //TODO: need generated url here - href : '/datasets/' + id + '/delete?show_deleted_on_refresh=False', + href : this.model.get( 'delete_url' ), target : 'galaxy_main', - id : 'historyItemDeleter-' + id, - classes : [ 'icon-button', 'tooltip', 'delete' ] - })); + id : 'historyItemDeleter-' + this.model.get( 'id' ), + icon_class : 'delete' + }):({ + title : 'Dataset is already deleted', + icon_class : 'delete', + enabled : false + }); + this.deleteButton = new IconButtonView({ model : new IconButton( deleteBtnData ) }); + return this.deleteButton.render().$el; }, _render_titleLink : function(){ @@ -441,7 +387,7 @@ }); warningMsgText += 'You may be able to ' + editLink + '.'; } - parent.append( $( HistoryItemView.TEMPLATES.warningMsg({ warning: warningMsgText }) ) ); + parent.append( $( HistoryItemView.templates.warningMsg({ warning: warningMsgText }) ) ); //...render the remaining body as STATES.OK (only diff between these states is the box above) this._render_body_ok( parent ); @@ -497,7 +443,8 @@ // if trans.user if( this.model.get( 'retag_url' ) && this.model.get( 'annotate_url' ) ){ - // tags, annotation buttons and display areas + // tag, annotate buttons + //TODO: move to tag, Annot MV var tagsAnnotationsBtns = $( '<div style="float: right;"></div>' ); tagsAnnotationsBtns.append( $( linkHTMLTemplate({ title : 'Edit dataset tags', @@ -514,17 +461,20 @@ actionBtnDiv.append( tagsAnnotationsBtns ); actionBtnDiv.append( '<div style="clear: both"></div>' ); - var tagArea = $( '<div class="tag-area" style="display: none">' ); - tagArea.append( '<strong>Tags:</strong>' ); - tagArea.append( '<div class="tag-elt"></div>' ); - actionBtnDiv.append( tagArea ); + // tag/annot display areas + this.tagArea = $( '<div class="tag-area" style="display: none">' ); + this.tagArea.append( '<strong>Tags:</strong>' ); + this.tagElt = $( '<div class="tag-elt"></div>' ); + actionBtnDiv.append( this.tagArea.append( this.tagElt ) ); var annotationArea = $( ( '<div id="${dataset_id}-annotation-area"' + ' class="annotation-area" style="display: none">' ) ); + this.annotationArea = annotationArea; annotationArea.append( '<strong>Annotation:</strong>' ); - annotationArea.append( ( '<div id="${dataset_id}-annotation-elt" ' + this.annotationElem = $( '<div id="' + this.model.get( 'id' ) + '-annotation-elt" ' + 'style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" ' - + 'title="Edit dataset annotation"></div>' ) ); + + 'title="Edit dataset annotation"></div>' ); + annotationArea.append( this.annotationElem ); actionBtnDiv.append( annotationArea ); } } @@ -564,10 +514,10 @@ }, _render_body : function(){ - this.log( this + '_render_body' ); + //this.log( this + '_render_body' ); var state = this.model.get( 'state' ), for_editing = this.model.get( 'for_editing' ); - this.log( 'state:', state, 'for_editing', for_editing ); + //this.log( 'state:', state, 'for_editing', for_editing ); //TODO: incorrect id (encoded - use hid?) var body = $( '<div/>' ) @@ -708,10 +658,86 @@ // ................................................................................ EVENTS events : { - 'click .historyItemTitle' : 'toggleBodyVisibility' + 'click .historyItemTitle' : 'toggleBodyVisibility', + 'click a.icon-button.tags' : 'loadAndDisplayTags', + 'click a.icon-button.annotate' : 'loadAndDisplayAnnotation' }, // ................................................................................ STATE CHANGES / MANIPULATION + loadAndDisplayTags : function( event ){ + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this, '.loadAndDisplayTags', event ); + var tagArea = this.tagArea; + var tagElt = this.tagElt; + + // Show or hide tag area; if showing tag area and it's empty, fill it. + if( tagArea.is( ":hidden" ) ){ + if( !tagElt.html() ){ + // Need to fill tag element. + $.ajax({ + url: this.model.get( 'ajax_get_tag_url' ), + error: function() { alert( "Tagging failed" ) }, + success: function(tag_elt_html) { + console.debug( 'tag_elt_html:', tag_elt_html ); + tagElt.html(tag_elt_html); + tagElt.find(".tooltip").tooltip(); + tagArea.slideDown("fast"); + } + }); + } else { + // Tag element is filled; show. + tagArea.slideDown("fast"); + } + + } else { + // Hide. + tagArea.slideUp("fast"); + } + return false; + }, + + loadAndDisplayAnnotation : function( event ){ + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this, '.loadAndDisplayAnnotation', event ); + var annotationArea = this.annotationArea, + annotationElem = this.annotationElem, + setAnnotationUrl = this.model.get( 'ajax_set_annotation_url' ); + + // Show or hide annotation area; if showing annotation area and it's empty, fill it. + this.log( 'annotationArea hidden:', annotationArea.is( ":hidden" ) ); + this.log( 'annotationElem html:', annotationElem.html() ); + if ( annotationArea.is( ":hidden" ) ){ + if( !annotationElem.html() ){ + // Need to fill annotation element. + $.ajax({ + url: this.model.get( 'ajax_get_annotation_url' ), + error: function(){ alert( "Annotations failed" ) }, + success: function( htmlFromAjax ){ + if( htmlFromAjax === "" ){ + htmlFromAjax = "<em>Describe or add notes to dataset</em>"; + } + annotationElem.html( htmlFromAjax ); + annotationArea.find(".tooltip").tooltip(); + + async_save_text( + annotationElem.attr("id"), annotationElem.attr("id"), + setAnnotationUrl, + "new_annotation", 18, true, 4 + ); + annotationArea.slideDown("fast"); + } + }); + } else { + annotationArea.slideDown("fast"); + } + + } else { + // Hide. + annotationArea.slideUp("fast"); + } + return false; + }, + toggleBodyVisibility : function(){ this.log( this + '.toggleBodyVisibility' ); this.$el.find( '.historyItemBody' ).toggle(); @@ -723,30 +749,8 @@ return 'HistoryItemView(' + modelString + ')'; } }); - -//------------------------------------------------------------------------------ HistoryItemView.TEMPLATES = {}; -//TODO: move next one out - doesn't belong -HistoryItemView.TEMPLATES.warningMsg = - _.template( '<div class=warningmessagesmall><strong><%= warning %></strong></div>' ); - - -//??TODO: move into functions? -HistoryItemView.TEMPLATES.undeleteLink = _.template( - 'This dataset has been deleted. ' + - 'Click <a href="<%= undelete_url %>" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" ' + - ' target="galaxy_history">here</a> to undelete it.' ); - -HistoryItemView.TEMPLATES.purgeLink = _.template( - ' or <a href="<%= purge_url %>" class="historyItemPurge" id="historyItemPurger-{{ id }}"' + - ' target="galaxy_history">here</a> to immediately remove it from disk.' ); - -HistoryItemView.TEMPLATES.hiddenMsg = _.template( - 'This dataset has been hidden. ' + - 'Click <a href="<%= unhide_url %>" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" ' + - ' target="galaxy_history">here</a> to unhide it.' ); - //TODO: contains localized strings HistoryItemView.TEMPLATES.hdaSummary = _.template([ '<%= misc_blurb %><br />', @@ -754,13 +758,18 @@ 'database: <%= dbkeyHTML %>' ].join( '' )); - -//------------------------------------------------------------------------------ -HistoryItemView.STRINGS = {}; -HistoryItemView.STRINGS.purgedMsg = HistoryItemView.TEMPLATES.warningMsg( - { warning: 'This dataset has been deleted and removed from disk.' }); - +//============================================================================== +//HistoryItemView.templates = InDomTemplateLoader.getTemplates({ +HistoryItemView.templates = CompiledTemplateLoader.getTemplates({ + 'common-templates.html' : { + warningMsg : 'template-warningmessagesmall', + }, + 'history-templates.html' : { + messages : 'template-history-warning-messages2', + hdaSummary : 'template-history-hdaSummary' + } +}); //============================================================================== var HistoryCollection = Backbone.Collection.extend({ @@ -773,10 +782,10 @@ //============================================================================== -var History = LoggingModel.extend({ +var History = BaseModel.extend( LoggableMixin ).extend({ // uncomment this out see log messages - logger : console, + //logger : console, // values from api (may need more) defaults : { @@ -867,11 +876,11 @@ }); //------------------------------------------------------------------------------ -var HistoryView = LoggingView.extend({ +var HistoryView = BaseView.extend( LoggableMixin ).extend({ // view for the HistoryCollection (as per current right hand panel) // uncomment this out see log messages - logger : console, + //logger : console, // direct attachment to existing element el : 'body.historyPage', @@ -908,8 +917,7 @@ //============================================================================== -//USE_MOCK_DATA = true; -if( window.USE_MOCK_DATA ){ +function createMockHistoryData(){ mockHistory = {}; mockHistory.data = { @@ -986,6 +994,7 @@ notvisible : _.extend( _.clone( mockHistory.data.template ), { visible : false }), + hasDisplayApps : _.extend( _.clone( mockHistory.data.template ), { display_apps : { @@ -1041,7 +1050,8 @@ failed_metadata : _.extend( _.clone( mockHistory.data.template ), { state : HistoryItem.STATES.FAILED_METADATA }) - +/* +*/ }); $( document ).ready( function(){ diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/tags.js --- /dev/null +++ b/static/scripts/mvc/tags.js @@ -0,0 +1,66 @@ +/*============================================================================== +Backbone MV for Tags + + +TODO: +move rendering from tagging_common.py +move functionality from controllers/tag.py +?? - polymorph on class or simply class as attr? + +==============================================================================*/ +/** Single Tag model + */ +var Tag = BaseModel.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + defaults : { + id : null, + itemClass : null + }, + + toString : function(){ + return 'Tag()'; + } +}); + +//------------------------------------------------------------------------------ +/** Single Tag view + */ +var TagView = BaseView.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'TagView()'; + } +}); + +//============================================================================== +/** A collection of Tags + */ +var TagCollection = Backbone.Collection.extend( LoggableMixin ).extend({ + model : Tag, + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'TagCollection()'; + } +}); + +//------------------------------------------------------------------------------ +/** View for a TagCollection (and it's controls) - as per an hda's tag controls on the history panel + */ +var TagList = BaseView.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'TagList()'; + } +}); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -1,41 +1,12 @@ /** * -- Functions for creating large UI elements. -- */ - -/** - * Returns an IconButtonMenuView for the provided configuration. - * Configuration is a list of dictionaries where each dictionary - * defines an icon button. Each dictionary must have the following - * elements: icon_class, title, and on_click. - */ -var create_icon_buttons_menu = function(config, global_config) { - if (!global_config) { global_config = {}; } - - // Create and initialize menu. - var buttons = new IconButtonCollection( - _.map(config, function(button_config) { - return new IconButton(_.extend(button_config, global_config)); - }) - ); - - return new IconButtonMenuView( {collection: buttons} ); -}; - +// ============================================================================= /** * -- Utility models and views for Galaxy objects. -- */ /** - * Necessary Galaxy paths. - */ -var GalaxyPaths = Backbone.Model.extend({ - defaults: { - root_path: "", - image_path: "" - } -}); - -/** * Clickable button represented as an icon. */ var IconButton = Backbone.Model.extend({ @@ -43,14 +14,107 @@ title: "", icon_class: "", on_click: null, - tooltip_config: {} + tooltip_config: {}, + + isMenuButton : true, + id : null, + href : null, + target : null, + enabled : true, + visible : true + } + + //validate : function( attributes ){ + //TODO: validate href or on_click + //TODO: validate icon_class + //} +}); + + +/** + * + */ +var IconButtonView = Backbone.View.extend({ + tagName : 'a', + className : 'icon-button', + + // jsHint.shut( up ) + hrefVoidFn : [ 'javascript', ':void(0)' ].join( '' ), + fadeSpeed : 0, + + initialize : function(){ + // better rendering this way (for me anyway) + this.model.attributes.tooltip_config = { placement : 'bottom' }; + this.model.bind( 'change', this.render, this ); + }, + + render : function(){ + //NOTE: this is meant to be rerendered on a model change + // - since most of the rendering is attributes, it gets complicated + //TODO: template would be faster, more concise - more PITA + var disabled_class = this.model.attributes.icon_class + '_disabled'; + + if( !this.model.attributes.visible ){ + //TODO: fancy - but may not work as you expect + this.$el.fadeOut( this.fadeSpeed ); + } + + if( this.model.attributes.enabled ){ + if( this.$el.hasClass( disabled_class ) ){ + this.$el.removeClass( disabled_class ); + } + this.$el.addClass( this.model.attributes.icon_class ); + } else { + this.$el.removeClass( this.model.attributes.icon_class ); + this.$el.addClass( disabled_class ); + } + + if( this.model.attributes.isMenuButton ){ + this.$el.addClass( 'menu-button' ); + } else { + this.$el.removeClass( 'menu-button' ); + } + + this.$el.data( 'tooltip', false ); + this.$el.attr( 'data-original-title', null ); + this.$el.removeClass( 'tooltip' ); + if( this.model.attributes.title ){ + this.$el.attr( 'title', this.model.attributes.title ).addClass( 'tooltip' ); + this.$el.tooltip( this.model.attributes.tooltip_config ); + } + + this.$el.attr( 'id', ( this.model.attributes.id )?( this.model.attributes.id ):( null ) ); + this.$el.attr( 'target', ( this.model.attributes.target )?( this.model.attributes.target ):( null ) ); + this.$el.attr( 'href', ( this.model.attributes.href && !this.model.attributes.on_click )? + ( this.model.attributes.href ):( this.hrefVoidFn ) ); + + if( this.model.attributes.visible ){ + this.$el.fadeIn( this.fadeSpeed ); + } + return this; + }, + + events : { + 'click' : 'click' + }, + + click : function( event ){ + // if on_click pass to that function + if( this.model.attributes.on_click ){ + this.model.attributes.on_click( event ); + return false; + } + // otherwise, bubble up (to href or whatever) + return true; } }); + var IconButtonCollection = Backbone.Collection.extend({ model: IconButton }); +//------------------------------------------------------------------------------ /** * Menu with multiple icon buttons. Views are not needed nor used for individual buttons. */ @@ -82,6 +146,27 @@ }); /** + * Returns an IconButtonMenuView for the provided configuration. + * Configuration is a list of dictionaries where each dictionary + * defines an icon button. Each dictionary must have the following + * elements: icon_class, title, and on_click. + */ +var create_icon_buttons_menu = function(config, global_config) { + if (!global_config) { global_config = {}; } + + // Create and initialize menu. + var buttons = new IconButtonCollection( + _.map(config, function(button_config) { + return new IconButton(_.extend(button_config, global_config)); + }) + ); + + return new IconButtonMenuView( {collection: buttons} ); +}; + + +// ============================================================================= +/** * */ var Grid = Backbone.Collection.extend({ @@ -95,4 +180,101 @@ }); +// ============================================================================= +/** + * Necessary Galaxy paths. + */ +var GalaxyPaths = Backbone.Model.extend({ + defaults: { + root_path: "", + image_path: "" + } +}); +// ============================================================================= +/** Global string localization object (and global short form alias) + * set with either: + * GalaxyLocalization.setLocalizedString( original, localized ) + * GalaxyLocalization.setLocalizedString({ original1 : localized1, original2 : localized2 }) + * get with either: + * _l( original ) + */ +//TODO: move to Galaxy.Localization +var GalaxyLocalization = jQuery.extend({}, { + aliasName : '_l', + localizedStrings : {}, + + setLocalizedString : function( str_or_obj, localizedString ){ + // pass in either two strings (english, translated) or an obj (map) of english : translated attributes + //console.debug( this + '.setLocalizedString:', str_or_obj, localizedString ); + var self = this; + + // DRY non-duplicate assignment function + var setStringIfNotDuplicate = function( original, localized ){ + // do not set if identical - strcmp expensive but should only happen once per page per word + if( original !== localized ){ + self.localizedStrings[ original ] = localized; + } + }; + + if( jQuery.type( str_or_obj ) === "string" ){ + setStringIfNotDuplicate( str_or_obj, localizedString ); + + } else if( jQuery.type( str_or_obj ) === "object" ){ + jQuery.each( str_or_obj, function( key, val ){ + //console.debug( 'key=>val', key, '=>', val ); + // could recurse here but no reason + setStringIfNotDuplicate( key, val ); + }); + + } else { + throw( 'Localization.setLocalizedString needs either a string or object as the first argument,' + + ' given: ' + str_or_obj ); + } + }, + + localize : function( strToLocalize ){ + //console.debug( this + '.localize:', strToLocalize ); + // return the localized version if it's there, the strToLocalize if not + // try/catch cheaper than if in + try { + //var localized = this.localizedStrings[ strToLocalize ]; + //return localized; + return this.localizedStrings[ strToLocalize ]; + } catch( err ){ + //TODO??: potentially problematic catch all + //console.error( err ); + return strToLocalize; + } + }, + + toString : function(){ return 'GalaxyLocalization'; } +}); + +// global localization alias +window[ GalaxyLocalization.aliasName ] = function( str ){ return GalaxyLocalization.localize( str ); }; + +//TEST: setLocalizedString( string, string ), _l( string ) +//TEST: setLocalizedString( hash ), _l( string ) +//TEST: setLocalizedString( string === string ), _l( string ) +//TEST: _l( non assigned string ) + + +// ============================================================================= +/** UI icon-button (Backbone.View only - no model) + * + */ + + + + + + + + + + + + + + diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/common-templates.html --- /dev/null +++ b/static/scripts/templates/common-templates.html @@ -0,0 +1,3 @@ +<script type="text/template" class="template-common" id="template-warningmessagesmall"> + <div class=warningmessagesmall><strong>{{{warning}}}</strong></div> +</script> diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compile_templates.py --- a/static/scripts/templates/compile_templates.py +++ b/static/scripts/templates/compile_templates.py @@ -3,24 +3,274 @@ # Script requires handlebars compiler be installed; use node package manager # to install handlebars. +"""%prog [options] [ specific .handlebars or .html template file to compile ] + Compiles handlebars templates into javascript for better load times and performance. + + Handlebars compilation errors will print to stderr. + NOTE!: you will need node.js, npm, and handlebars (installed from npm) in order to compile templates + See http://handlebarsjs.com/precompilation.html for more info. + + Should be called from the $GLX_ROOT/static/scripts/templates directory. + Compiled templates will be written to the compiled/ directory. + + If the --multi-ext option is passed a file extension string, the script will: + * search for *.<extension> in the current directory, + * extract each '<script type="text/template"> from the file and write them into a new handlebars file + named using the id of the script tag (eg. id="undeleteMsg" -> undeleteMsg.handlebars) + * these new handlebars scripts will be compiled along with any other handlebars templates in the dir + + additionally for each of those files, the script will: + * extract each '<script type="text/javascript"> from the file and write them ALL into a single js file + named using the prefix 'helpers-' and the basename of the enclosing file + (eg. common-templates.html -> helpers-common-templates.js ) + * these new handlebars scripts will be compiled along with any other handlebars templates in the dir + These files can be included as if they were templates (eg. h.templates( 'helpers-common-templates' ) ) + + This hopefully will allow both multiple templates and their associated Handlebars helper functions to be + included in one file. + + Currently, this works (best?) if: + * the multiple templates are within one html file + * each template is enclosed in a <script> tag with type="text/template" and some id attribute + * each helper fn is enclosed in a <script> tag with type="text/javascript" and some id attribute + e.g. <script type="text/template" id="history-deletedMsg" class="template">Deleted {{ msg }}</script> + +""" +# ------------------------------------------------------------------------------ + +TODO = """ +""" + import sys from glob import glob from subprocess import call from shutil import copyfile from os import path +from optparse import OptionParser +from HTMLParser import HTMLParser -cmd = "handlebars %s -f compiled/%s.js" +import logging +log = logging.getLogger( __name__ ) -# If specific scripts specified on command line, just pack them, otherwise pack -# all. +COMPILED_DIR = 'compiled' +COMPILED_EXT = '.js' +COMPILE_CMD_STR = "handlebars %s -f %s" +COMPILE_MINIMIZE_SWITCH = ' -m' -if len( sys.argv ) > 1: - to_pack = sys.argv[1:] -else: - to_pack = glob( "*.handlebars" ) +# both of these are off by default for backward compat +DEFAULT_MINIMIZATION = False +DEFAULT_MULTI_EXT = None #'.html' + +# ------------------------------------------------------------------------------ +class HTMLMultiTemplateParser( HTMLParser ): + """Parses multiple templates from an HTML file, saving them to a map of: + { id : template_text, ... } + + Templates must: + * be within the TEMPLATE_TAG + * TEMPLATE_TAG must have a type attribute + * that attr must == TEMPLATE_TYPE + * TEMPLATE_TAG cannot be nested within one another + * TEMPLATE_TAG must have an id attribute + """ + TEMPLATE_TAG = 'script' + TEMPLATE_TYPES = [ 'text/template' ] -for fname in to_pack: - fname_base = path.splitext( path.split( fname )[1] )[0] - print "%s --> compiled/%s.js" % ( fname, fname_base ) - out = call( cmd % ( fname, fname_base ), shell=True ) + HELPER_TAG = 'script' + HELPER_TYPES = [ 'text/javascript' ] + + def __init__( self ): + HTMLParser.__init__( self ) + self.templates = {} + self.curr_template_id = None + self.template_data = '' + + self.helpers = {} + self.curr_helper_id = None + self.helper_data = '' + + def is_template_tag( self, tag, attr_dict ): + # both tag and type attr must match + return ( ( tag == self.TEMPLATE_TAG ) + and ( 'type' in attr_dict ) + and ( attr_dict[ 'type' ] in self.TEMPLATE_TYPES ) ) + + def is_helper_tag( self, tag, attr_dict ): + # both tag and type attr must match + return ( ( tag == self.HELPER_TAG ) + and ( 'type' in attr_dict ) + and ( attr_dict[ 'type' ] in self.HELPER_TYPES ) ) + + def handle_starttag( self, tag, attrs ): + attr_dict = dict( attrs ) + if self.is_template_tag( tag, attr_dict ): + log.debug( "\t template tag: %s, %s", tag, str( attr_dict ) ); + + # as far as I know these tags can't/shouldn't nest/overlap + #pre: not already inside a template/helper tag + assert self.curr_template_id == None, "Found nested template tag: %s" % ( self.curr_template_id ) + assert self.curr_helper_id == None, "Found template tag inside helper: %s" % ( self.curr_helper_id ) + #pre: must have an id + assert 'id' in attr_dict, "No id attribute in template: " + str( attr_dict ) + + self.curr_template_id = attr_dict[ 'id' ] + + elif self.is_helper_tag( tag, attr_dict ): + log.debug( "\t helper tag: %s, %s", tag, str( attr_dict ) ); + + #pre: not already inside a template/helper tag + assert self.curr_helper_id == None, "Found nested helper tag: %s" % ( self.curr_helper_id ) + assert self.curr_template_id == None, "Found helper tag inside template: %s" % ( self.curr_template_id ) + #pre: must have an id + assert 'id' in attr_dict, "No id attribute in helper: " + str( attr_dict ) + + self.curr_helper_id = attr_dict[ 'id' ] + + def handle_endtag( self, tag ): + if( ( tag == self.TEMPLATE_TAG ) + and ( self.curr_template_id ) ): + log.debug( "\t ending template tag :", tag, self.curr_template_id ); + + # store the template data by the id + if self.template_data: + self.templates[ self.curr_template_id ] = self.template_data + + #! reset for next template + self.curr_template_id = None + self.template_data = '' + + elif( ( tag == self.HELPER_TAG ) + and ( self.curr_helper_id ) ): + log.debug( "\t ending helper tag :", tag, self.curr_template_id ); + + # store the template data by the id + if self.helper_data: + self.helpers[ self.curr_helper_id ] = self.helper_data + + #! reset for next template + self.curr_helper_id = None + self.helper_data = '' + + def handle_data(self, data): + data = data.strip() + if data: + if self.curr_template_id: + log.debug( "\t template text :", data ); + self.template_data += data + + elif self.curr_helper_id: + log.debug( "\t helper js fn :", data ); + self.helper_data += data + + +# ------------------------------------------------------------------------------ +def break_multi_template( multi_template_filename ): + """parse the multi template, writing each template into a new handlebars tmpl and returning their names""" + template_filenames = [] + parser = HTMLMultiTemplateParser() + + # parse the multi template + print "\nBreaking multi-template file %s into individual templates and helpers:" % ( multi_template_filename ) + with open( multi_template_filename, 'r' ) as multi_template_file: + # wish I could use a gen here + parser.feed( multi_template_file.read() ) + + # after breaking, write each indiv. template and save the names + for template_id, template_text in parser.templates.items(): + handlebar_template_filename = template_id + '.handlebars' + with open( handlebar_template_filename, 'w' ) as handlebar_template_file: + handlebar_template_file.write( template_text ) + + template_filenames.append( handlebar_template_filename ) + + # write all helpers to a 'helper-' prefixed js file in the compilation dir + if parser.helpers: + helper_filename = 'helpers-' + path.splitext( multi_template_filename )[0] + '.js' + helper_filename = path.join( COMPILED_DIR, helper_filename ) + with open( helper_filename, 'w' ) as helper_file: + for helper_fn_name, helper_fn in parser.helpers.items(): + print '(helper)', helper_fn_name + helper_file.write( helper_fn + '\n' ) + + print '\n'.join( template_filenames ) + return template_filenames + + +# ------------------------------------------------------------------------------ +def compile_template( template_filename, minimize=False ): + """compile the given template file (optionally minimizing the js) using subprocess. + + Use the basename of the template file for the outputed js. + """ + template_basename = path.splitext( path.split( template_filename )[1] )[0] + compiled_filename = path.join( COMPILED_DIR, template_basename + COMPILED_EXT ) + + command_string = COMPILE_CMD_STR % ( template_filename, compiled_filename ) + if minimize: + command_string += COMPILE_MINIMIZE_SWITCH + print command_string + return call( command_string, shell=True ) + + +# ------------------------------------------------------------------------------ +def main( options, args ): + """Break multi template files into single templates, compile all single templates. + + If args, compile that as a list of specific handlebars and/or multi template files. + """ + print "(Call this script with the '-h' option for more help)" + + handlebars_templates = [] + # If specific scripts specified on command line, just compile them, + if len( args ) >= 1: + handlebars_templates = filter( lambda( x ): x.endswith( '.handlebars' ), args ) + + # otherwise compile all in the current dir + else: + handlebars_templates = glob( '*.handlebars' ) + + # if desired, break up any passed-in or found multi template files + # adding the names of the new single templates to those needing compilation + if options.multi_ext: + multi_templates = [] + if len( args ) >= 1: + multi_templates = filter( lambda( x ): x.endswith( options.multi_ext ), args ) + else: + multi_templates = glob( '*' + options.multi_ext ) + + for multi_template_filename in multi_templates: + handlebars_templates.extend( break_multi_template( multi_template_filename ) ) + + # unique filenames only (Q&D) + handlebars_templates = list( set( handlebars_templates ) ) + + # compile the templates + print "\nCompiling templates:" + filenames_w_possible_errors = [] + for handlebars_template in handlebars_templates: + shell_ret = compile_template( handlebars_template, options.minimize ) + if shell_ret: + filenames_w_possible_errors.append( handlebars_template ) + + # report any possible errors + if filenames_w_possible_errors: + print "\nThere may have been errors on the following files:" + print ',\n'.join( filenames_w_possible_errors ) + print "\nCall this script with the '-h' for more help" + + +# ------------------------------------------------------------------------------ +if __name__ == '__main__': + optparser = OptionParser( usage=__doc__ ) + optparser.add_option( '-m', '--minimize', dest='minimize', action='store_true', default=DEFAULT_MINIMIZATION, + help=( 'minimize compiled template scripts via handlebars ' + + '(defaults to %s)' % DEFAULT_MINIMIZATION ) ) + optparser.add_option( '--multi-ext', dest='multi_ext', metavar="FILE_EXTENSION", default=DEFAULT_MULTI_EXT, + help=( 'indicates that files ending with the given string contain multiple ' + + 'templates and the script should break those into individual ' + + 'handlebars templates (defaults to "%s")' ) % DEFAULT_MULTI_EXT ) + + ( options, args ) = optparser.parse_args() + sys.exit( main( options, args ) ) + \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compiled/template-history-hdaSummary.js --- /dev/null +++ b/static/scripts/templates/compiled/template-history-hdaSummary.js @@ -0,0 +1,25 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-hdaSummary'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + + + foundHelper = helpers.misc_blurb; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "<br />\nformat: <span class=\""; + foundHelper = helpers.data_type; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.data_type; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span>, ',\ndatabase: "; + foundHelper = helpers.dbkeyHTML; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.dbkeyHTML; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1); + return buffer;}); +})(); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compiled/template-history-warning-messages.js --- /dev/null +++ b/static/scripts/templates/compiled/template-history-warning-messages.js @@ -0,0 +1,87 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-warning-messages'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1; + buffer += "\n<div class=warningmessagesmall><strong>\nThis dataset has been deleted.\n "; + stack1 = depth0.undelete_url; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</strong></div>\n"; + return buffer;} +function program2(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n Click <a href=\""; + foundHelper = helpers.undelete_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.undelete_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" class=\"historyItemUndelete\" id=\"historyItemUndeleter-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; + stack1 = depth0.purge_url; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + return buffer;} +function program3(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n or\n <a href=\""; + foundHelper = helpers.purge_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.purge_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" class=\"historyItemPurge\" id=\"historyItemPurger-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to immediately remove it from disk\n "; + return buffer;} + +function program5(depth0,data) { + + + return "\n<div class=warningmessagesmall><strong>\nThis dataset has been deleted and removed from disk.\n</strong></div>\n";} + +function program7(depth0,data) { + + var buffer = "", stack1; + buffer += "\n<div class=warningmessagesmall><strong>\nThis dataset has been hidden.\n "; + stack1 = depth0.undelete_url; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</strong></div>\n"; + return buffer;} +function program8(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n Click <a href=\""; + foundHelper = helpers.unhide_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.unhide_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" class=\"historyItemUnhide\" id=\"historyItemUnhider-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to unhide it\n "; + return buffer;} + + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.purged; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.visible; + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + return buffer;}); +})(); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compiled/template-warningmessagesmall.js --- /dev/null +++ b/static/scripts/templates/compiled/template-warningmessagesmall.js @@ -0,0 +1,15 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-warningmessagesmall'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function"; + + + buffer += "<div class=warningmessagesmall><strong>"; + foundHelper = helpers.warning; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.warning; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</strong></div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/history-templates.html --- /dev/null +++ b/static/scripts/templates/history-templates.html @@ -0,0 +1,38 @@ +<script type="text/template" class="template-history" id="template-history-warning-messages"> +{{#if deleted}} +<div class=warningmessagesmall><strong> +This dataset has been deleted. + {{#if undelete_url}} + Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" + target="galaxy_history">here</a> to undelete it + {{#if purge_url}} + or + <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" + target="galaxy_history">here</a> to immediately remove it from disk + {{/if}} + {{/if}} +</strong></div> +{{/if}} + +{{#if purged}} +<div class=warningmessagesmall><strong> +This dataset has been deleted and removed from disk. +</strong></div> +{{/if}} + +{{#unless visible}} +<div class=warningmessagesmall><strong> +This dataset has been hidden. + {{#if undelete_url}} + Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" + target="galaxy_history">here</a> to unhide it + {{/if}} +</strong></div> +{{/unless}} +</script> + +<script type="text/template" class="template-history" id="template-history-hdaSummary"> +{{ misc_blurb }}<br /> +format: <span class="{{ data_type }}">{{ data_type }}</span>, ', +database: {{ dbkeyHTML }} +</script> diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/template-history-hdaSummary.handlebars --- /dev/null +++ b/static/scripts/templates/template-history-hdaSummary.handlebars @@ -0,0 +1,3 @@ +{{ misc_blurb }}<br /> +format: <span class="{{ data_type }}">{{ data_type }}</span>, ', +database: {{ dbkeyHTML }} \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/template-history-warning-messages.handlebars --- /dev/null +++ b/static/scripts/templates/template-history-warning-messages.handlebars @@ -0,0 +1,30 @@ +{{#if deleted}} +<div class=warningmessagesmall><strong> +This dataset has been deleted. + {{#if undelete_url}} + Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" + target="galaxy_history">here</a> to undelete it + {{#if purge_url}} + or + <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" + target="galaxy_history">here</a> to immediately remove it from disk + {{/if}} + {{/if}} +</strong></div> +{{/if}} + +{{#if purged}} +<div class=warningmessagesmall><strong> +This dataset has been deleted and removed from disk. +</strong></div> +{{/if}} + +{{#unless visible}} +<div class=warningmessagesmall><strong> +This dataset has been hidden. + {{#if undelete_url}} + Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" + target="galaxy_history">here</a> to unhide it + {{/if}} +</strong></div> +{{/unless}} \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/template-warningmessagesmall.handlebars --- /dev/null +++ b/static/scripts/templates/template-warningmessagesmall.handlebars @@ -0,0 +1,1 @@ +<div class=warningmessagesmall><strong>{{{warning}}}</strong></div> \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -26,7 +26,18 @@ ##  - ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )} + + ${h.js( + "libs/jquery/jquery", + "libs/bootstrap", + "galaxy.base", + "libs/underscore", + "libs/backbone/backbone", + "libs/backbone/backbone-relational", + "libs/handlebars.runtime", + "mvc/ui" + )} + <script type="text/javascript"> // Set up needed paths. var galaxy_paths = new GalaxyPaths({ diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -54,7 +54,7 @@ <%def name="get_urls_for_hda( hda, encoded_data_id, for_editing )"><% from galaxy.datatypes.metadata import FileParameter - + data_dict = {} def add_to_data( **kwargs ): data_dict.update( kwargs ) @@ -79,7 +79,10 @@ #TODO??: better way to do urls (move into js galaxy_paths (decorate) - _not_ dataset specific) deleted = hda.deleted - purged = hda.purged or hda.dataset.purged + purged = hda.purged + + #purged = purged or hda.dataset.purged //?? + # all of these urls are 'datasets/data_id/<action> if not ( dataset_purged or purged ) and for_editing: add_to_data( undelete_url=h.url_for( controller='dataset', action='undelete', dataset_id=encoded_data_id ) ) @@ -106,7 +109,21 @@ display_url = h.url_for( controller='dataset', action='display', dataset_id=encoded_data_id, preview=True, filename='' ) add_to_data( display_url=display_url ) - if app.config.get_bool( 'enable_tracks', False ) and hda.ext in app.datatypes_registry.get_available_tracks(): + # edit attr button + if for_editing: + if not( hda.deleted or hda.purged ): + edit_url = h.url_for( controller='dataset', action='edit', dataset_id=encoded_data_id ) + add_to_data( edit_url=edit_url ) + + # delete button + if for_editing and not ( dataset_purged or purged ): + add_to_data( delete_url=h.url_for( controller='dataset', action='delete', dataset_id=encoded_data_id ) ) + ##TODO: loose end + ##show_deleted_on_refresh=show_deleted_on_refresh ) ) + #show_deleted_on_refresh=False ) ) + + #print app + if hda.ext in app.datatypes_registry.get_available_tracks(): # do these need _localized_ dbkeys? trackster_urls = {} if hda.dbkey != '?': @@ -117,11 +134,21 @@ trackster_urls[ 'hda-url' ] = data_url trackster_urls[ 'action-url' ] = h.url_for( controller='tracks', action='browser', dataset_id=encoded_data_id ) trackster_urls[ 'new-url' ] = h.url_for( controller='tracks', action='index', dataset_id=encoded_data_id, default_dbkey=hda.dbkey ) - add_to_data( trackster_url=trackster_url ) + add_to_data( trackster_url=trackster_urls ) if trans.user: - add_to_data( retag_url=( h.url_for( controller='tag', action='retag', item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) + add_to_data( ajax_get_tag_url=( h.url_for( + controller='tag', action='get_tagging_elt_async', + item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) + add_to_data( retag_url=( h.url_for( + controller='tag', action='retag', + item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) + add_to_data( annotate_url=( h.url_for( controller='dataset', action='annotate', id=encoded_data_id ) ) ) + add_to_data( ajax_get_annotation_url=( h.url_for( + controller='dataset', action='get_annotation_async', id=encoded_data_id ) ) ) + add_to_data( ajax_set_annotation_url=( h.url_for( + controller='/dataset', action='annotate_async', id=encoded_data_id ) ) ) display_type_display_links = {} #TODO: this doesn't seem to get called with the hda I'm using. What would call this? How can I spoof it? @@ -182,8 +209,8 @@ data_dict.update( kwargs ) # trans + add_to_data( non_encoded_id=data.id ) encoded_data_id = trans.security.encode_id( data.id ) - #print data.name, encoded_data_id add_to_data( id=encoded_data_id ) # localize dbkey @@ -205,8 +232,8 @@ add_to_data( accessible=accessible ) url_dict = get_urls_for_hda( data, encoded_data_id, for_editing ) + data_dict.update( url_dict ) #print 'url_dict:', pformat( url_dict, indent=2 ) - data_dict.update( url_dict ) #print 'data_dict:', pformat( data_dict, indent=2 ), "\n" #print data_dict @@ -227,7 +254,7 @@ user_is_admin = trans.user_is_admin() user_roles = trans.get_current_user_roles() prepped_hdas = [ - prep_hda( hda, true ) for hda in datasets ] + prep_hda( hda, True ) for hda in datasets ] context_dict = { 'history' : { @@ -257,74 +284,66 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.templates( "tool_link", "panel_section", "tool_search" )} - ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "bootstrap", "mvc/tools", "mvc/history" )} + + ${h.js( + "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", + ##"libs/handlebars.full", + "galaxy.autocom_tagging", + "mvc/base-mvc", "mvc/ui" + )} + + ${h.templates( + "helpers-common-templates", + "template-warningmessagesmall", + + "template-history-warning-messages", + "template-history-hdaSummary" + )} + + ## if using in-dom templates they need to go here (before the Backbone classes are defined) + ##NOTE: it's impossible(?) to include _ templates in this way bc they use identical delims as mako + ## (without altering Underscore.templateSettings) + ##<%include file="../../static/scripts/templates/common-templates.html" /> + ##<%include file="../../static/scripts/templates/history-templates.html" /> + + ${h.js( + "mvc/history" + ##"mvc/tags", "mvc/annotations" + )} <script type="text/javascript"> - ##//var localization = local( ${ create_localization_json( get_page_localized_strings() ) } ); + GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); + // add needed controller urls to GalaxyPaths + galaxy_paths.set( 'dataset_path', "${h.url_for( controller='dataset' )}" ) + // Init. on document load. var pageData = ${context_to_js()}; - // add needed controller urls to GalaxyPaths - galaxy_paths.set( 'dataset_path', "${h.url_for( controller='dataset' )}" ) + //USE_MOCK_DATA = true; $(function(){ if( console && console.debug ){ console.debug( 'using backbone.js in history panel' ); } - if( window.USE_MOCK_DATA ){ return; } + if( window.USE_MOCK_DATA ){ + if( console && console.debug ){ console.debug( '\t using mock data' ); } + createMockHistoryData(); + return; + } glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ); glx_history_view = new HistoryView({ model: glx_history }); glx_history_view.render(); - //hi = glx_history.items.at( 0 ); - //hi_view = new HistoryItemView({ model: hi }); - //$( 'body' ).append( hi_view.render() ); + hi = glx_history.items.at( 0 ); + hi_view = new HistoryItemView({ model: hi }); + $( 'body' ).append( hi_view.render() ); }); </script> - - <script type='text/javascript'> -function tag_handling(parent_elt) { - $(parent_elt).find("a.icon-button.tags").each( function() { - // Use links parameters but custom URL as ajax URL. - $(this).click( function() { - // Get tag area, tag element. - var history_item = $(this).parents(".historyItem"); - var tag_area = history_item.find(".tag-area"); - var tag_elt = history_item.find(".tag-elt"); - - // Show or hide tag area; if showing tag area and it's empty, fill it. - if ( tag_area.is( ":hidden" ) ) { - if (!tag_elt.html()) { - // Need to fill tag element. - var href_parms = $(this).attr("href").split("?")[1]; - var ajax_url = "${h.url_for( controller='tag', action='get_tagging_elt_async' )}?" + href_parms; - $.ajax({ - url: ajax_url, - error: function() { alert( "Tagging failed" ) }, - success: function(tag_elt_html) { - tag_elt.html(tag_elt_html); - tag_elt.find(".tooltip").tooltip(); - tag_area.slideDown("fast"); - } - }); - } else { - // Tag element is filled; show. - tag_area.slideDown("fast"); - } - } else { - // Hide. - tag_area.slideUp("fast"); - } - return false; - }); - }); -}; - </script></%def><%def name="stylesheets()"> ${parent.stylesheets()} - <style> + ${h.css("base", "history", "autocomplete_tagging" )} + <style>" .historyItemBody { display: none; } https://bitbucket.org/galaxy/galaxy-central/changeset/e2cb958b3f75/ changeset: e2cb958b3f75 user: carlfeberhard date: 2012-09-12 17:09:09 summary: clean debug statements from history.js affected #: 1 file diff -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 -r e2cb958b3f7596744bb08febc858fa25139fd1ac static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -1,4 +1,3 @@ -if( console ){ console.debug( 'history mvc loaded' ); } /* Backbone.js implementation of history panel @@ -678,7 +677,7 @@ url: this.model.get( 'ajax_get_tag_url' ), error: function() { alert( "Tagging failed" ) }, success: function(tag_elt_html) { - console.debug( 'tag_elt_html:', tag_elt_html ); + this.log( 'tag_elt_html:', tag_elt_html ); tagElt.html(tag_elt_html); tagElt.find(".tooltip").tooltip(); tagArea.slideDown("fast"); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Allow for overriding app.config.track_jobs_in_database.
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/244b4cb100d1/ changeset: 244b4cb100d1 user: natefoo date: 2012-09-11 20:58:13 summary: Allow for overriding app.config.track_jobs_in_database. affected #: 2 files diff -r 9a8614de4141be276ab4a416ef7b0def8c5703d2 -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -105,6 +105,7 @@ self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) self.smtp_password = kwargs.get( 'smtp_password', None ) + self.track_jobs_in_database = kwargs.get( 'track_jobs_in_database', None ) self.start_job_runners = kwargs.get( 'start_job_runners', None ) self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', 'False' ) ) # External Service types used in sample tracking @@ -210,9 +211,12 @@ self.job_handlers = [ x.strip() for x in kwargs.get('job_handlers', self.server_name).split(',') ] self.default_job_handlers = [ x.strip() for x in kwargs.get('default_job_handlers', ','.join( self.job_handlers ) ).split(',') ] # Use database for IPC unless this is a standalone server (or multiple servers doing self dispatching in memory) - self.track_jobs_in_database = True - if ( len( self.job_handlers ) == 1 ) and ( self.job_handlers[0] == self.server_name ) and ( self.job_manager == self.server_name ): - self.track_jobs_in_database = False + if self.track_jobs_in_database is None or self.track_jobs_in_database == "None": + self.track_jobs_in_database = True + if ( len( self.job_handlers ) == 1 ) and ( self.job_handlers[0] == self.server_name ) and ( self.job_manager == self.server_name ): + self.track_jobs_in_database = False + else: + self.track_jobs_in_database = string_as_bool( self.track_jobs_in_database ) # Store per-tool runner configs self.tool_handlers = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_handlers', 'name' ) self.tool_runners = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_runners', 'url' ) diff -r 9a8614de4141be276ab4a416ef7b0def8c5703d2 -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -586,6 +586,15 @@ # used for jobs without explicit handlers. #default_job_handlers = main +# In multiprocess configurations, notification between processes about new jobs +# is done via the database. In single process configurations, this is done in +# memory, which is a bit quicker. Galaxy tries to automatically determine +# which method it should used based on your manager/handler configuration +# above, but can't reliably determine if you have multiple processes for web +# servers but only a single process as a manager/handler. In that scenario, +# you can override the tracking method by setting the following to True: +#track_jobs_in_database = None + # This enables splitting of jobs into tasks, if specified by the particular tool config. # This is a new feature and not recommended for production servers yet. #use_tasked_jobs = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: removed console.debug statement from history.mako
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9a8614de4141/ changeset: 9a8614de4141 user: carlfeberhard date: 2012-09-11 19:52:55 summary: removed console.debug statement from history.mako affected #: 1 file diff -r 7b1b6e81b1756234001eb1c3a32d7a9b98da92c3 -r 9a8614de4141be276ab4a416ef7b0def8c5703d2 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -233,7 +233,6 @@ //TODO: hack (github has an issue on this - see how it's resolved) // fix for two line bootstrap tooltips when placement: above $( this ).find( '.tooltip' ).each( function(){ - console.debug( 'tooltip:', this ); var $this = $( this ); // documented method - that doesn't seem to work Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Do not report the disk usage of purged HDAs in history disk usage.
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7b1b6e81b175/ changeset: 7b1b6e81b175 user: natefoo date: 2012-09-11 19:33:20 summary: Do not report the disk usage of purged HDAs in history disk usage. affected #: 1 file diff -r 2b4111248390ae6340f4bec54d0cff29f48665fb -r 7b1b6e81b1756234001eb1c3a32d7a9b98da92c3 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -685,6 +685,7 @@ db_session = object_session( self ) rval = db_session.query( func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset ) .filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + .filter( HistoryDatasetAssociation.purged != True ) .filter( Dataset.purged != True ) .distinct().subquery().c.total_size ) ).first()[0] if rval is None: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Distributed object store fixes for pgcleanup.py.
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2b4111248390/ changeset: 2b4111248390 user: natefoo date: 2012-09-11 18:22:03 summary: Distributed object store fixes for pgcleanup.py. affected #: 1 file diff -r 63cd6402badaf98f26080e71b1f0ed49db30e3ab -r 2b4111248390ae6340f4bec54d0cff29f48665fb scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -31,6 +31,12 @@ log = logging.getLogger() +class MetadataFile(Bunch): + pass + +class Dataset(Bunch): + pass + class Cleanup(object): def __init__(self): self.options = None @@ -199,12 +205,13 @@ log.info("All changes committed") def _remove_metadata_file(self, id, object_store_id, action_name): - metadata_file = Bunch(id=id, object_store_id=object_store_id) + metadata_file = MetadataFile(id=id, object_store_id=object_store_id) try: filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) self._log('Removing from disk: %s' % filename, action_name) - except ObjectNotFound: + except (ObjectNotFound, AttributeError), e: + log.error('Unable to get MetadataFile %s filename: %s' % (id, e)) return if not self.options.dry_run: @@ -656,8 +663,6 @@ """ log.info('Marking purged all Datasets marked deleted that are older than the specified number of days.') - # TODO: force retry option - event_id = self._create_event(inspect.stack()[0][3]) sql = """ @@ -700,15 +705,16 @@ self._log('Marked Dataset purged: %s in Object Store: %s' % (tup[0], tup[1])) # always try to remove the "object store path" - if it's at an external_filename, that file will be untouched anyway (which is what we want) - dataset = Bunch(id=tup[0], object_store_id=tup[1]) + dataset = Dataset(id=tup[0], object_store_id=tup[1]) try: filename = self.object_store.get_filename(dataset) - except ObjectNotFound, AttributeError: + except (ObjectNotFound, AttributeError), e: + log.error('Unable to get Dataset %s filename: %s' % (tup[0], e)) continue try: extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) - except ObjectNotFound, AttributeError: + except (ObjectNotFound, AttributeError): extra_files_dir = None # don't check for existence of the dataset, it should exist Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: historyPanel: temp fix for 2 line tooltips when placement = 'above'
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63cd6402bada/ changeset: 63cd6402bada user: carlfeberhard date: 2012-09-11 17:46:15 summary: historyPanel: temp fix for 2 line tooltips when placement = 'above' affected #: 1 file diff -r 6568368038dc220ce1f66d5566570f32633055d9 -r 63cd6402badaf98f26080e71b1f0ed49db30e3ab templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -45,7 +45,7 @@ error: function() { alert( "Tagging failed" ) }, success: function(tag_elt_html) { tag_elt.html(tag_elt_html); - tag_elt.find(".tooltip").tooltip(); + tag_elt.find(".tooltip").tooltip({ placement : 'bottom' }); tag_area.slideDown("fast"); } }); @@ -86,7 +86,7 @@ annotation = "<em>Describe or add notes to dataset</em>"; } annotation_elt.html(annotation); - annotation_area.find(".tooltip").tooltip(); + annotation_area.find(".tooltip").tooltip({ placement : 'bottom' }); async_save_text( annotation_elt.attr("id"), annotation_elt.attr("id"), "${h.url_for( controller='/dataset', action='annotate_async')}?" + href_parms, @@ -229,6 +229,25 @@ tag_handling(this); annotation_handling(this); + + //TODO: hack (github has an issue on this - see how it's resolved) + // fix for two line bootstrap tooltips when placement: above + $( this ).find( '.tooltip' ).each( function(){ + console.debug( 'tooltip:', this ); + var $this = $( this ); + + // documented method - that doesn't seem to work + //$( this ).tooltip( 'destroy' ); + + $this.data( 'tooltip', false ); + var title = $this.attr( 'data-original-title' ); + $this.attr( 'data-original-title', null ); + $this.attr( 'title', title ); + + // place them on the bottom for now + $this.tooltip({ placement : 'bottom' }); + }); + }); // Trackster links Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 10 Sep '12

10 Sep '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ef7f11e99547/ changeset: ef7f11e99547 user: james_taylor date: 2012-09-10 23:09:09 summary: circster: Allow data_standalone types to work; phyloviz: add tree datatypes to sample conf affected #: 2 files diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r ef7f11e995473293a2e45f5517a627ad7177a3b1 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -198,6 +198,10 @@ <display file="igv/vcf.xml" /><converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/></datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /><datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r ef7f11e995473293a2e45f5517a627ad7177a3b1 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -553,11 +553,14 @@ # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) data_sources = self._get_datasources( trans, dataset ) - indexed_type = data_sources['index']['name'] - - # Get converted dataset and append track's genome data. - converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) - data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) + if 'data_standalone' in data_sources: + indexed_type = data_sources['data_standalone']['name'] + data_provider = get_data_provider( indexed_type )( dataset ) + else: + indexed_type = data_sources['index']['name'] + # Get converted dataset and append track's genome data. + converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) + data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=3, detail_cutoff=0, draw_cutoff=0 ) } https://bitbucket.org/galaxy/galaxy-central/changeset/c71026b3d7ac/ changeset: c71026b3d7ac user: james_taylor date: 2012-09-10 23:40:56 summary: circster: render in entire window, ensure initially entire plot fits in view and is centered affected #: 2 files diff -r ef7f11e995473293a2e45f5517a627ad7177a3b1 -r c71026b3d7ac3c01ed6ee5350962de96b6ca47dd static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -823,26 +823,27 @@ className: 'circster', initialize: function(options) { - this.width = options.width; - this.height = options.height; this.total_gap = options.total_gap; this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; - - // Compute radius start based on model. - this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap); }, render: function() { var self = this, - dataset_arc_height = this.dataset_arc_height; + dataset_arc_height = this.dataset_arc_height, + width = self.$el.width(), + height = self.$el.height(), + // Compute radius start based on model, will be centered + // and fit entirely inside element by default + init_radius_start = ( Math.min(width,height)/2 + - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ); // Set up SVG element. var svg = d3.select(self.$el[0]) .append("svg") - .attr("width", self.width) - .attr("height", self.height) + .attr("width", width) + .attr("height", height) .attr("pointer-events", "all") // Set up zooming, dragging. .append('svg:g') @@ -851,14 +852,14 @@ "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")"); })) - .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")") + .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g') // -- Render each dataset in the visualization. -- this.model.get('tracks').each(function(track, index) { var dataset = track.get('genome_wide_data'), - radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap), + radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), // Layout chromosome arcs. layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ), arcs_layout = new layout_class({ diff -r ef7f11e995473293a2e45f5517a627ad7177a3b1 -r c71026b3d7ac3c01ed6ee5350962de96b6ca47dd templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -69,8 +69,7 @@ var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')) visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), viz_view = new CircsterView({ - width: 700, - height: 700, + el: $('#vis'), // Gap is difficult to set because it very dependent on chromosome size and organization. total_gap: 2 * Math.PI * 0.1, genome: genome, @@ -81,7 +80,7 @@ // -- Render viz. -- viz_view.render(); - $('#vis').append(viz_view.$el); + }); </script></%def> https://bitbucket.org/galaxy/galaxy-central/changeset/6568368038dc/ changeset: 6568368038dc user: james_taylor date: 2012-09-10 23:41:20 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 4 files diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -198,6 +198,10 @@ <display file="igv/vcf.xml" /><converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/></datatype> +  + <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" /> + <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" /> + <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /><datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -553,11 +553,14 @@ # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) data_sources = self._get_datasources( trans, dataset ) - indexed_type = data_sources['index']['name'] - - # Get converted dataset and append track's genome data. - converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) - data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) + if 'data_standalone' in data_sources: + indexed_type = data_sources['data_standalone']['name'] + data_provider = get_data_provider( indexed_type )( dataset ) + else: + indexed_type = data_sources['index']['name'] + # Get converted dataset and append track's genome data. + converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) + data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -823,26 +823,27 @@ className: 'circster', initialize: function(options) { - this.width = options.width; - this.height = options.height; this.total_gap = options.total_gap; this.genome = options.genome; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; - - // Compute radius start based on model. - this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap); }, render: function() { var self = this, - dataset_arc_height = this.dataset_arc_height; + dataset_arc_height = this.dataset_arc_height, + width = self.$el.width(), + height = self.$el.height(), + // Compute radius start based on model, will be centered + // and fit entirely inside element by default + init_radius_start = ( Math.min(width,height)/2 + - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ); // Set up SVG element. var svg = d3.select(self.$el[0]) .append("svg") - .attr("width", self.width) - .attr("height", self.height) + .attr("width", width) + .attr("height", height) .attr("pointer-events", "all") // Set up zooming, dragging. .append('svg:g') @@ -851,14 +852,14 @@ "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")"); })) - .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")") + .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g') // -- Render each dataset in the visualization. -- this.model.get('tracks').each(function(track, index) { var dataset = track.get('genome_wide_data'), - radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap), + radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), // Layout chromosome arcs. layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ), arcs_layout = new layout_class({ diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -69,8 +69,7 @@ var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')) visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), viz_view = new CircsterView({ - width: 700, - height: 700, + el: $('#vis'), // Gap is difficult to set because it very dependent on chromosome size and organization. total_gap: 2 * Math.PI * 0.1, genome: genome, @@ -81,7 +80,7 @@ // -- Render viz. -- viz_view.render(); - $('#vis').append(viz_view.$el); + }); </script></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Bug fixes for pgcleanup.py
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04cd4894e840/ changeset: 04cd4894e840 user: natefoo date: 2012-09-10 22:59:33 summary: Bug fixes for pgcleanup.py affected #: 1 file diff -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 -r 04cd4894e8406028c6acfd521cbcef7a396748b2 scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -25,6 +25,7 @@ import galaxy.config +from galaxy.exceptions import ObjectNotFound from galaxy.objectstore import build_object_store_from_config from galaxy.util.bunch import Bunch @@ -60,6 +61,7 @@ parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config) parser.add_option('-d', '--debug', action='store_true', dest='debug', help='Enable debug logging', default=False) parser.add_option('--dry-run', action='store_true', dest='dry_run', help="Dry run (rollback all transactions)", default=False) + parser.add_option('--force-retry', action='store_true', dest='force_retry', help="Retry file removals (on applicable actions)", default=False) parser.add_option('-o', '--older-than', type='int', dest='days', help='Only perform action(s) on objects that have not been updated since the specified number of days', default=14) parser.add_option('-U', '--no-update-time', action='store_false', dest='update_time', help="Don't set update_time on updated objects", default=True) parser.add_option('-s', '--sequence', dest='sequence', help='Comma-separated sequence of actions, chosen from: %s' % self.action_names, default='') @@ -68,18 +70,11 @@ self.options.sequence = [ x.strip() for x in self.options.sequence.split(',') ] def __setup_logging(self): + format = "%(funcName)s %(levelname)s %(asctime)s %(message)s" if self.options.debug: - log.setLevel('DEBUG') + logging.basicConfig(level=logging.DEBUG, format=format) else: - log.setLevel('INFO') - - format = "%(funcName)s %(levelname)s %(asctime)s %(message)s" - formatter = logging.Formatter(format) - - handler = logging.StreamHandler(sys.stdout) - handler.setFormatter(formatter) - - log.addHandler(handler) + logging.basicConfig(level=logging.INFO, format=format) def __load_config(self): log.info('Reading config from %s' % self.options.config) @@ -203,11 +198,15 @@ self.conn.commit() log.info("All changes committed") - def _remove_metadata_file(self, id, action_name): - metadata_file = Bunch(id=id) - filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) + def _remove_metadata_file(self, id, object_store_id, action_name): + metadata_file = Bunch(id=id, object_store_id=object_store_id) - self._log('Removing from disk: %s' % filename, action_name) + try: + filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) + self._log('Removing from disk: %s' % filename, action_name) + except ObjectNotFound: + return + if not self.options.dry_run: try: os.unlink(filename) @@ -329,7 +328,7 @@ update_time_sql = '' if self.options.update_time: update_time_sql = """, - update_time = NOW()'""" + update_time = NOW()""" sql = sql % (update_time_sql, '%s', '%s') args = (self.options.days, event_id) @@ -356,8 +355,7 @@ WITH purged_hda_ids AS ( UPDATE history_dataset_association SET purged = true%s - WHERE deleted - AND NOT purged + WHERE deleted%s AND update_time < (NOW() - interval '%s days') RETURNING id, history_id), @@ -367,7 +365,8 @@ FROM purged_hda_ids WHERE purged_hda_ids.id = metadata_file.hda_id RETURNING metadata_file.hda_id AS hda_id, - metadata_file.id AS id), + metadata_file.id AS id, + metadata_file.object_store_id AS object_store_id), deleted_icda_ids AS ( UPDATE implicitly_converted_dataset_association SET deleted = true%s @@ -403,6 +402,7 @@ SELECT purged_hda_ids.id, history.user_id, deleted_metadata_file_ids.id, + deleted_metadata_file_ids.object_store_id, deleted_icda_ids.id, deleted_icda_ids.hda_id FROM purged_hda_ids @@ -414,12 +414,19 @@ ON purged_hda_ids.history_id = history.id; """ + force_retry_sql = """ + AND NOT purged""" update_time_sql = "" - if self.options.update_time: - update_time_sql += """, + + if self.options.force_retry: + force_retry_sql = "" + else: + # only update time if not doing force retry (otherwise a lot of things would have their update times reset that were actually purged a long time ago) + if self.options.update_time: + update_time_sql = """, update_time = NOW()""" - sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s') + sql = sql % (update_time_sql, force_retry_sql, '%s', update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s') args = (self.options.days, event_id, event_id, event_id, event_id) cur = self._update(sql, args) self._flush() @@ -430,10 +437,10 @@ if tup[1] is not None and tup[1] not in self.disk_accounting_user_ids: self.disk_accounting_user_ids.append(int(tup[1])) if tup[2] is not None: - self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[0], tup[2])) - self._remove_metadata_file(tup[2], 'purge_deleted_hdas') - if tup[3] is not None: - self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[0], tup[3], tup[4])) + self._log('Purge of HDA %s caused deletion of MetadataFile: %s in Object Store: %s' % (tup[0], tup[2], tup[3])) + self._remove_metadata_file(tup[2], tup[3], 'purge_deleted_hdas') + if tup[4] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[0], tup[4], tup[5])) self._close_logfile() def purge_deleted_histories(self): @@ -449,8 +456,7 @@ WITH purged_history_ids AS ( UPDATE history SET purged = true%s - WHERE deleted - AND NOT purged + WHERE deleted%s AND update_time < (NOW() - interval '%s days') RETURNING id, user_id), @@ -468,7 +474,8 @@ FROM purged_hda_ids WHERE purged_hda_ids.id = metadata_file.hda_id RETURNING metadata_file.hda_id AS hda_id, - metadata_file.id AS id), + metadata_file.id AS id, + metadata_file.object_store_id AS object_store_id), deleted_icda_ids AS ( UPDATE implicitly_converted_dataset_association SET deleted = true%s @@ -510,6 +517,7 @@ purged_history_ids.user_id, purged_hda_ids.id, deleted_metadata_file_ids.id, + deleted_metadata_file_ids.object_store_id, deleted_icda_ids.id, deleted_icda_ids.hda_id FROM purged_history_ids @@ -521,12 +529,18 @@ ON deleted_icda_ids.hda_parent_id = purged_hda_ids.id; """ + force_retry_sql = """ + AND NOT purged""" update_time_sql = "" - if self.options.update_time: - update_time_sql += """, + + if self.options.force_retry: + force_retry_sql = "" + else: + if self.options.update_time: + update_time_sql += """, update_time = NOW()""" - sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s', '%s') + sql = sql % (update_time_sql, force_retry_sql, '%s', update_time_sql, update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s', '%s') args = (self.options.days, event_id, event_id, event_id, event_id, event_id) cur = self._update(sql, args) self._flush() @@ -539,10 +553,10 @@ if tup[2] is not None: self._log('Purge of History %s caused deletion of HistoryDatasetAssociation: %s' % (tup[0], tup[2])) if tup[3] is not None: - self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[1], tup[3])) - self._remove_metadata_file(tup[3], 'purge_deleted_histories') - if tup[4] is not None: - self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[1], tup[4], tup[5])) + self._log('Purge of HDA %s caused deletion of MetadataFile: %s in Object Store: %s' % (tup[1], tup[3], tup[4])) + self._remove_metadata_file(tup[3], tup[4], 'purge_deleted_histories') + if tup[5] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[1], tup[5], tup[6])) self._close_logfile() def delete_exported_histories(self): @@ -559,6 +573,7 @@ SET deleted = true%s FROM job_export_history_archive WHERE job_export_history_archive.dataset_id = dataset.id + AND NOT deleted AND dataset.update_time <= (NOW() - interval '%s days') RETURNING dataset.id), dataset_events @@ -649,38 +664,52 @@ WITH purged_dataset_ids AS ( UPDATE dataset SET purged = true%s - WHERE deleted = true - AND purged = false + WHERE deleted%s AND update_time < (NOW() - interval '%s days') - RETURNING id), + RETURNING id, + object_store_id), dataset_events AS (INSERT INTO cleanup_event_dataset_association (create_time, cleanup_event_id, dataset_id) SELECT NOW(), %s, id FROM purged_dataset_ids) - SELECT id + SELECT id, + object_store_id FROM purged_dataset_ids ORDER BY id; """ + force_retry_sql = """ + AND NOT purged""" update_time_sql = "" - if self.options.update_time: - update_time_sql += """, + + if self.options.force_retry: + force_retry_sql = "" + else: + if self.options.update_time: + update_time_sql = """, update_time = NOW()""" - sql = sql % (update_time_sql, '%s', '%s') + sql = sql % (update_time_sql, force_retry_sql, '%s', '%s') args = (self.options.days, event_id) cur = self._update(sql, args) self._flush() self._open_logfile() for tup in cur: - self._log('Marked Dataset purged: %s' % tup[0]) + self._log('Marked Dataset purged: %s in Object Store: %s' % (tup[0], tup[1])) # always try to remove the "object store path" - if it's at an external_filename, that file will be untouched anyway (which is what we want) - dataset = Bunch(id=tup[0]) - filename = self.object_store.get_filename(dataset) - extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) + dataset = Bunch(id=tup[0], object_store_id=tup[1]) + try: + filename = self.object_store.get_filename(dataset) + except ObjectNotFound, AttributeError: + continue + + try: + extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) + except ObjectNotFound, AttributeError: + extra_files_dir = None # don't check for existence of the dataset, it should exist self._log('Removing from disk: %s' % filename) @@ -691,7 +720,7 @@ self._log('Removal of %s failed with error: %s' % (filename, e)) # extra_files_dir is optional so it's checked first - if os.path.exists(extra_files_dir): + if extra_files_dir is not None and os.path.exists(extra_files_dir): self._log('Removing from disk: %s' % extra_files_dir) if not self.options.dry_run: try: @@ -703,6 +732,10 @@ if __name__ == '__main__': cleanup = Cleanup() - cleanup._run() - cleanup._update_user_disk_usage() + try: + cleanup._run() + if cleanup.disk_accounting_user_ids: + cleanup._update_user_disk_usage() + except: + log.exception('Caught exception in run sequence:') cleanup._shutdown() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 10 Sep '12

10 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5118cb9c05f7/ changeset: 5118cb9c05f7 user: jgoecks date: 2012-09-10 20:12:52 summary: Small fixes to make summary tree compatible with Circster. affected #: 2 files diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -93,8 +93,10 @@ starting_block = self.find_block( start, level ) ending_block = self.find_block( end, level ) for block in range( starting_block, ending_block + 1 ): + val = 0 if block in blocks[ level ]: - results.append( ( block * multiplier, blocks[ level ][ block ] ) ) + val = blocks[ level ][ block ] + results.append( ( block * multiplier, val ) ) return results return None diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -559,7 +559,7 @@ converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) data_provider = get_data_provider( indexed_type )( converted_dataset, dataset ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=3, detail_cutoff=0, draw_cutoff=0 ) } + track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) https://bitbucket.org/galaxy/galaxy-central/changeset/4e69bc5d9e1e/ changeset: 4e69bc5d9e1e user: jgoecks date: 2012-09-10 20:13:09 summary: Merge affected #: 3 files diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -186,6 +186,8 @@ self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) + if self.distributed_object_store_config_file is not None: + self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,6 +19,7 @@ from galaxy.security.validate_user_input import validate_publicname from paste.httpexceptions import * from galaxy.exceptions import * +from galaxy.model import NoConverterException, ConverterDependencyException from Cheetah.Template import Template diff -r 5118cb9c05f700a244b0d091bbb1b28edda3a881 -r 4e69bc5d9e1e02074de22cc6e809c33f3462f587 scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -90,6 +90,7 @@ config_dict = {} for key, value in config_parser.items('app:main'): config_dict[key] = value + config_dict['root_dir'] = galaxy_root self.config = galaxy.config.Configuration(**config_dict) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Bugfix for pgcleanup.py
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6b35719fdcc8/ changeset: 6b35719fdcc8 user: natefoo date: 2012-09-10 20:07:05 summary: Bugfix for pgcleanup.py affected #: 2 files diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r 6b35719fdcc8356267ebe786ecd738d0c14fb52b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -186,6 +186,8 @@ self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) + if self.distributed_object_store_config_file is not None: + self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r 6b35719fdcc8356267ebe786ecd738d0c14fb52b scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -90,6 +90,7 @@ config_dict = {} for key, value in config_parser.items('app:main'): config_dict[key] = value + config_dict['root_dir'] = galaxy_root self.config = galaxy.config.Configuration(**config_dict) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: Datatype conversion exceptions no imported but used in base controller.
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6e79399b38d2/ changeset: 6e79399b38d2 user: james_taylor date: 2012-09-10 20:05:56 summary: Datatype conversion exceptions no imported but used in base controller. affected #: 1 file diff -r 6d3023815cd77ec3045bf81ff15af884b828c38d -r 6e79399b38d22512d8438522d26945c53f95b11a lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,6 +19,7 @@ from galaxy.security.validate_user_input import validate_publicname from paste.httpexceptions import * from galaxy.exceptions import * +from galaxy.model import NoConverterException, ConverterDependencyException from Cheetah.Template import Template Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 10 Sep '12

10 Sep '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b64b57240149/ changeset: b64b57240149 user: nuwan_ag date: 2012-08-23 06:22:13 summary: Modified REST API to support multipart/form-data requests, to enable large file upload. affected #: 2 files diff -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 -r b64b572401493be2b424e7166c67473cf1f298dd lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -28,7 +28,7 @@ local_filename = local_filename ) elif type( f ) == dict and 'filename' and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) - if upload_dataset['url_paste'].strip() != '': + if upload_dataset['url_paste'] and upload_dataset['url_paste'].strip() != '': upload_dataset['url_paste'], is_multi_byte = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" ) else: upload_dataset['url_paste'] = None diff -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 -r b64b572401493be2b424e7166c67473cf1f298dd lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -5,6 +5,7 @@ import pkg_resources import os, sys, time, socket, random, string +import inspect pkg_resources.require( "Cheetah" ) from Cheetah.Template import Template import base @@ -125,9 +126,25 @@ return error trans.set_user( provided_key.user ) if trans.request.body: - try: - payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) - kwargs['payload'] = payload + def extract_payload_from_request(trans, func, kwargs): + content_type = trans.request.headers['content-type'] + if content_type.startswith('multipart/form-data'): + # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body + # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which + # are not a part of the request body. This is a problem because it's not possible to differentiate between values + # which are a part of the request body, and therefore should be a part of the payload, and values which should not be + # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from + # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods. + payload = kwargs.copy() + named_args, _, _, _ = inspect.getargspec(func) + for arg in named_args: + payload.pop(arg, None) + else: + # When it's a non standard request body (e.g. json), the wsgi framework does not parse the request body. So do so manually. + payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) + return payload + try: + kwargs['payload'] = extract_payload_from_request(trans, func, kwargs) except ValueError: error_status = '400 Bad Request' error_message = 'Your request did not appear to be valid JSON, please consult the API documentation' https://bitbucket.org/galaxy/galaxy-central/changeset/5747b665127a/ changeset: 5747b665127a user: nuwan_ag date: 2012-08-23 07:09:20 summary: Also added support for x-www-form-urlencoded REST API requests, for consistencies sake. This way, API clients can post as either JSON, multi-part form data, or standard url form encoding. affected #: 1 file diff -r b64b572401493be2b424e7166c67473cf1f298dd -r 5747b665127a5e4f82e102783048358fca68083b lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -128,7 +128,7 @@ if trans.request.body: def extract_payload_from_request(trans, func, kwargs): content_type = trans.request.headers['content-type'] - if content_type.startswith('multipart/form-data'): + if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'): # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which # are not a part of the request body. This is a problem because it's not possible to differentiate between values @@ -140,7 +140,9 @@ for arg in named_args: payload.pop(arg, None) else: - # When it's a non standard request body (e.g. json), the wsgi framework does not parse the request body. So do so manually. + # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check + # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding + # such as multipart/form-data. Leaving it as is for backward compatibility, just in case. payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) return payload try: https://bitbucket.org/galaxy/galaxy-central/changeset/6d3023815cd7/ changeset: 6d3023815cd7 user: dannon date: 2012-09-10 18:33:01 summary: Merged in nuwan_ag/galaxy-central (pull request #63) affected #: 2 files diff -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f -r 6d3023815cd77ec3045bf81ff15af884b828c38d lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -28,7 +28,7 @@ local_filename = local_filename ) elif type( f ) == dict and 'filename' and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) - if upload_dataset['url_paste'].strip() != '': + if upload_dataset['url_paste'] and upload_dataset['url_paste'].strip() != '': upload_dataset['url_paste'], is_multi_byte = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" ) else: upload_dataset['url_paste'] = None diff -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f -r 6d3023815cd77ec3045bf81ff15af884b828c38d lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -5,6 +5,7 @@ import pkg_resources import os, sys, time, socket, random, string +import inspect pkg_resources.require( "Cheetah" ) from Cheetah.Template import Template import base @@ -125,9 +126,27 @@ return error trans.set_user( provided_key.user ) if trans.request.body: - try: - payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) - kwargs['payload'] = payload + def extract_payload_from_request(trans, func, kwargs): + content_type = trans.request.headers['content-type'] + if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'): + # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body + # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which + # are not a part of the request body. This is a problem because it's not possible to differentiate between values + # which are a part of the request body, and therefore should be a part of the payload, and values which should not be + # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from + # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods. + payload = kwargs.copy() + named_args, _, _, _ = inspect.getargspec(func) + for arg in named_args: + payload.pop(arg, None) + else: + # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check + # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding + # such as multipart/form-data. Leaving it as is for backward compatibility, just in case. + payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) + return payload + try: + kwargs['payload'] = extract_payload_from_request(trans, func, kwargs) except ValueError: error_status = '400 Bad Request' error_message = 'Your request did not appear to be valid JSON, please consult the API documentation' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial.
by Bitbucket 10 Sep '12

10 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e0975c9b9bd2/ changeset: e0975c9b9bd2 user: natefoo date: 2012-09-10 18:03:23 summary: Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial. affected #: 2 files diff -r 9207ba35fa0caad1f8eac717afceb50f5c2a61c0 -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py @@ -0,0 +1,83 @@ +""" +Migration script to add the cleanup_event* tables. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +log = logging.getLogger( __name__ ) +log.setLevel( logging.DEBUG ) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) + +# New table to log cleanup events +CleanupEvent_table = Table( "cleanup_event", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "message", TrimmedString( 1024 ) ) ) + +CleanupEventDatasetAssociation_table = Table( "cleanup_event_dataset_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ) ) + +CleanupEventMetadataFileAssociation_table = Table( "cleanup_event_metadata_file_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "metadata_file_id", Integer, ForeignKey( "metadata_file.id" ), index=True ) ) + +CleanupEventHistoryAssociation_table = Table( "cleanup_event_history_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ) ) + +CleanupEventHistoryDatasetAssociationAssociation_table = Table( "cleanup_event_hda_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ) ) + +CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table = Table( "cleanup_event_icda_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "cleanup_event_id", Integer, ForeignKey( "cleanup_event.id" ), index=True, nullable=True ), + Column( "icda_id", Integer, ForeignKey( "implicitly_converted_dataset_association.id" ), index=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + CleanupEvent_table.create() + CleanupEventDatasetAssociation_table.create() + CleanupEventMetadataFileAssociation_table.create() + CleanupEventHistoryAssociation_table.create() + CleanupEventHistoryDatasetAssociationAssociation_table.create() + CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table.create() + except Exception, e: + log.debug( "Creating table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table.drop() + CleanupEventHistoryDatasetAssociationAssociation_table.drop() + CleanupEventHistoryAssociation_table.drop() + CleanupEventMetadataFileAssociation_table.drop() + CleanupEventDatasetAssociation_table.drop() + CleanupEvent_table.drop() + except Exception, e: + log.debug( "Dropping table failed: %s" % str( e ) ) diff -r 9207ba35fa0caad1f8eac717afceb50f5c2a61c0 -r e0975c9b9bd25d44cfcacc202470bb8037da6d6f scripts/cleanup_datasets/pgcleanup.py --- /dev/null +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -0,0 +1,707 @@ +#!/usr/bin/env python +""" +pgcleanup.py - A script for cleaning up datasets in Galaxy efficiently, by + bypassing the Galaxy model and operating directly on the database. + PostgreSQL 9.1 or greater is required. +""" + +import os +import sys +import shutil +import logging +import inspect +import datetime +from ConfigParser import ConfigParser +from optparse import OptionParser + +galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..')) +sys.path.insert(0, os.path.join(galaxy_root, 'lib')) + +from galaxy import eggs +eggs.require('psycopg2') +eggs.require('SQLAlchemy') +import psycopg2 +from sqlalchemy.engine.url import make_url + +import galaxy.config + +from galaxy.objectstore import build_object_store_from_config +from galaxy.util.bunch import Bunch + +log = logging.getLogger() + +class Cleanup(object): + def __init__(self): + self.options = None + self.args = None + self.config = None + self.conn = None + self.action_names = [] + self.logs = {} + self.disk_accounting_user_ids = [] + self.object_store = None + + self.__cache_action_names() + self.__parse_args() + self.__setup_logging() + self.__load_config() + self.__connect_db() + self.__load_object_store() + + def __cache_action_names(self): + for name, value in inspect.getmembers(self): + if not name.startswith('_') and inspect.ismethod(value): + self.action_names.append(name) + + def __parse_args(self): + default_config = os.path.abspath(os.path.join(galaxy_root, 'universe_wsgi.ini')) + + parser = OptionParser() + parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default=default_config) + parser.add_option('-d', '--debug', action='store_true', dest='debug', help='Enable debug logging', default=False) + parser.add_option('--dry-run', action='store_true', dest='dry_run', help="Dry run (rollback all transactions)", default=False) + parser.add_option('-o', '--older-than', type='int', dest='days', help='Only perform action(s) on objects that have not been updated since the specified number of days', default=14) + parser.add_option('-U', '--no-update-time', action='store_false', dest='update_time', help="Don't set update_time on updated objects", default=True) + parser.add_option('-s', '--sequence', dest='sequence', help='Comma-separated sequence of actions, chosen from: %s' % self.action_names, default='') + ( self.options, self.args ) = parser.parse_args() + + self.options.sequence = [ x.strip() for x in self.options.sequence.split(',') ] + + def __setup_logging(self): + if self.options.debug: + log.setLevel('DEBUG') + else: + log.setLevel('INFO') + + format = "%(funcName)s %(levelname)s %(asctime)s %(message)s" + formatter = logging.Formatter(format) + + handler = logging.StreamHandler(sys.stdout) + handler.setFormatter(formatter) + + log.addHandler(handler) + + def __load_config(self): + log.info('Reading config from %s' % self.options.config) + config_parser = ConfigParser(dict(here = os.getcwd(), + database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE')) + config_parser.read(self.options.config) + + config_dict = {} + for key, value in config_parser.items('app:main'): + config_dict[key] = value + + self.config = galaxy.config.Configuration(**config_dict) + + def __connect_db(self): + url = make_url(self.config.database_connection) + + log.info('Connecting to database with URL: %s' % url) + args = url.translate_connect_args() + args.update(url.query) + + assert url.get_dialect().name == 'postgres', 'This script can only be used with PostgreSQL.' + + self.conn = psycopg2.connect(**args) + + def __load_object_store(self): + self.object_store = build_object_store_from_config(self.config) + + def _open_logfile(self): + action_name = inspect.stack()[1][3] + logname = os.path.join(galaxy_root, 'scripts', 'cleanup_datasets', action_name + '.log') + + if self.options.dry_run: + log.debug('--dry-run specified, logging changes to stdout instead of log file: %s' % logname) + self.logs[action_name] = sys.stdout + else: + log.debug('Opening log file: %s' % logname) + self.logs[action_name] = open(logname, 'a') + + message = '==== Log opened: %s ' % datetime.datetime.now().isoformat() + self.logs[action_name].write(message.ljust(72, '=')) + self.logs[action_name].write('\n') + + def _log(self, message, action_name=None): + if action_name is None: + action_name = inspect.stack()[1][3] + if not message.endswith('\n'): + message += '\n' + self.logs[action_name].write(message) + + def _close_logfile(self): + action_name = inspect.stack()[1][3] + + message = '==== Log closed: %s ' % datetime.datetime.now().isoformat() + self.logs[action_name].write(message.ljust(72, '=')) + self.logs[action_name].write('\n') + + if self.options.dry_run: + log.debug('--dry-run specified, changes were logged to stdout insted of log file') + else: + log.debug('Closing log file: %s' % self.logs[action_name].name) + self.logs[action_name].close() + + del self.logs[action_name] + + def _run(self): + ok = True + for name in self.options.sequence: + if name not in self.action_names: + log.error('Unknown action in sequence: %s' % name) + ok = False + if not ok: + log.critical('Exiting due to previous error(s)') + sys.exit(1) + for name in self.options.sequence: + log.info('Calling %s' % name) + self.__getattribute__(name)() + log.info('Finished %s' % name) + + def _create_event(self, message): + """ + Create a new event in the cleanup_event table. + """ + + sql = """ + INSERT INTO cleanup_event + (create_time, message) + VALUES (NOW(), %s) + RETURNING id; + """ + + log.debug("SQL is: %s" % sql % ("'" + message + "'")) + + args = (message,) + + cur = self.conn.cursor() + log.info("Executing SQL") + cur.execute(sql, args) + log.info('Database status: %s' % cur.statusmessage) + + return cur.fetchone()[0] + + def _update(self, sql, args): + if args is not None: + log.debug('SQL is: %s' % sql % args) + else: + log.debug('SQL is: %s' % sql) + + cur = self.conn.cursor() + log.info('Executing SQL') + cur.execute(sql, args) + log.info('Database status: %s' % cur.statusmessage) + + return cur + + def _flush(self): + if self.options.dry_run: + self.conn.rollback() + log.info("--dry-run specified, all changes rolled back") + else: + self.conn.commit() + log.info("All changes committed") + + def _remove_metadata_file(self, id, action_name): + metadata_file = Bunch(id=id) + filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) + + self._log('Removing from disk: %s' % filename, action_name) + if not self.options.dry_run: + try: + os.unlink(filename) + except Exception, e: + self._log('Removal of %s failed with error: %s' % (filename, e), action_name) + + def _update_user_disk_usage(self): + """ + Any operation that purges a HistoryDatasetAssociation may require + updating a user's disk usage. Rather than attempt to resolve dataset + copies at purge-time, simply maintain a list of users that have had + HDAs purged, and update their usages once all updates are complete. + + This could probably be done more efficiently. + """ + log.info('Recalculating disk usage for users whose HistoryDatasetAssociations were purged') + + for user_id in self.disk_accounting_user_ids: + + # TODO: h.purged = false should be unnecessary once all hdas in purged histories are purged. + sql = """ + UPDATE galaxy_user + SET disk_usage = (SELECT SUM(total_size) + FROM ( SELECT d.total_size + FROM history_dataset_association hda + JOIN history h ON h.id = hda.history_id + JOIN dataset d ON hda.dataset_id = d.id + WHERE h.user_id = %s + AND h.purged = false + AND hda.purged = false + AND d.purged = false + AND d.id NOT IN (SELECT dataset_id + FROM library_dataset_dataset_association) + GROUP BY d.id) sizes) + WHERE id = %s + RETURNING disk_usage; + """ + + args = (user_id, user_id) + cur = self._update(sql, args) + self._flush() + + for tup in cur: + # disk_usage might be None (e.g. user has purged all data) + log.debug('Updated disk usage for user id %i to %s bytes' % (user_id, tup[0])) + + def _shutdown(self): + self.object_store.shutdown() + self.conn.close() + for handle in self.logs.values(): + message = '==== Log closed at shutdown: %s ' % datetime.datetime.now().isoformat() + handle.write(message.ljust(72, '=')) + handle.write('\n') + handle.close() + + def update_hda_purged_flag(self): + """ + The old cleanup script does not mark HistoryDatasetAssociations as purged when deleted Histories are purged. This method can be used to rectify that situation. + """ + log.info('Marking purged all HistoryDatasetAssociations associated with purged Datasets') + + event_id = self._create_event(inspect.stack()[0][3]) + + # update_time is intentionally left unmodified. + sql = """ + WITH purged_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true + FROM dataset + WHERE history_dataset_association.dataset_id = dataset.id + AND dataset.purged + AND NOT history_dataset_association.purged + RETURNING history_dataset_association.id), + hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, id + FROM purged_hda_ids) + SELECT id + FROM purged_hda_ids + ORDER BY id; + """ + + args = (event_id,) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked HistoryDatasetAssociation purged: %s' % tup[0]) + self._close_logfile() + + def delete_userless_histories(self): + """ + Mark deleted all "anonymous" Histories (not owned by a registered user) that are older than the specified number of days. + """ + log.info('Marking deleted all userless Histories older than %i days' % self.options.days) + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH deleted_history_ids + AS ( UPDATE history + SET deleted = true%s + WHERE user_id is null + AND NOT deleted + AND update_time < (NOW() - interval '%s days') + RETURNING id), + history_events + AS (INSERT INTO cleanup_event_history_association + (create_time, cleanup_event_id, history_id) + SELECT NOW(), %s, id + FROM deleted_history_ids) + SELECT id + FROM deleted_history_ids + ORDER BY id; + """ + + update_time_sql = '' + if self.options.update_time: + update_time_sql = """, + update_time = NOW()'""" + + sql = sql % (update_time_sql, '%s', '%s') + args = (self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked userless History deleted: %s' % tup[0]) + self._close_logfile() + + def purge_deleted_hdas(self): + """ + Mark purged all HistoryDatasetAssociations currently marked deleted that are older than the specified number of days. + Mark deleted all MetadataFiles whose hda_id is purged in this step. + Mark deleted all ImplicitlyConvertedDatasetAssociations whose hda_parent_id is purged in this step. + Mark purged all HistoryDatasetAssociations for which an ImplicitlyConvertedDatasetAssociation with matching hda_id is deleted in this step. + """ + log.info('Marking purged all deleted HistoryDatasetAssociations older than %i days' % self.options.days) + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH purged_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + WHERE deleted + AND NOT purged + AND update_time < (NOW() - interval '%s days') + RETURNING id, + history_id), + deleted_metadata_file_ids + AS ( UPDATE metadata_file + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = metadata_file.hda_id + RETURNING metadata_file.hda_id AS hda_id, + metadata_file.id AS id), + deleted_icda_ids + AS ( UPDATE implicitly_converted_dataset_association + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = implicitly_converted_dataset_association.hda_parent_id + RETURNING implicitly_converted_dataset_association.hda_id AS hda_id, + implicitly_converted_dataset_association.hda_parent_id AS hda_parent_id, + implicitly_converted_dataset_association.id AS id), + deleted_icda_purged_child_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + FROM deleted_icda_ids where deleted_icda_ids.hda_id = history_dataset_association.id), + hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, id + FROM purged_hda_ids), + metadata_file_events + AS (INSERT INTO cleanup_event_metadata_file_association + (create_time, cleanup_event_id, metadata_file_id) + SELECT NOW(), %s, id + FROM deleted_metadata_file_ids), + icda_events + AS (INSERT INTO cleanup_event_icda_association + (create_time, cleanup_event_id, icda_id) + SELECT NOW(), %s, id + FROM deleted_icda_ids), + icda_hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, hda_id + FROM deleted_icda_ids) + SELECT purged_hda_ids.id, + history.user_id, + deleted_metadata_file_ids.id, + deleted_icda_ids.id, + deleted_icda_ids.hda_id + FROM purged_hda_ids + LEFT OUTER JOIN deleted_metadata_file_ids + ON deleted_metadata_file_ids.hda_id = purged_hda_ids.id + LEFT OUTER JOIN deleted_icda_ids + ON deleted_icda_ids.hda_parent_id = purged_hda_ids.id + LEFT OUTER JOIN history + ON purged_hda_ids.history_id = history.id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s') + args = (self.options.days, event_id, event_id, event_id, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked HistoryDatasetAssociations purged: %s' % tup[0]) + if tup[1] is not None and tup[1] not in self.disk_accounting_user_ids: + self.disk_accounting_user_ids.append(int(tup[1])) + if tup[2] is not None: + self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[0], tup[2])) + self._remove_metadata_file(tup[2], 'purge_deleted_hdas') + if tup[3] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[0], tup[3], tup[4])) + self._close_logfile() + + def purge_deleted_histories(self): + """ + Mark purged all Histories marked deleted that are older than the specified number of days. + Mark purged all HistoryDatasetAssociations in Histories marked purged in this step (if not already purged). + """ + log.info('Marking purged all deleted histories that are older than the specified number of days.') + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH purged_history_ids + AS ( UPDATE history + SET purged = true%s + WHERE deleted + AND NOT purged + AND update_time < (NOW() - interval '%s days') + RETURNING id, + user_id), + purged_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + FROM purged_history_ids + WHERE purged_history_ids.id = history_dataset_association.history_id + AND NOT history_dataset_association.purged + RETURNING history_dataset_association.history_id AS history_id, + history_dataset_association.id AS id), + deleted_metadata_file_ids + AS ( UPDATE metadata_file + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = metadata_file.hda_id + RETURNING metadata_file.hda_id AS hda_id, + metadata_file.id AS id), + deleted_icda_ids + AS ( UPDATE implicitly_converted_dataset_association + SET deleted = true%s + FROM purged_hda_ids + WHERE purged_hda_ids.id = implicitly_converted_dataset_association.hda_parent_id + RETURNING implicitly_converted_dataset_association.hda_id AS hda_id, + implicitly_converted_dataset_association.hda_parent_id AS hda_parent_id, + implicitly_converted_dataset_association.id AS id), + deleted_icda_purged_child_hda_ids + AS ( UPDATE history_dataset_association + SET purged = true%s + FROM deleted_icda_ids where deleted_icda_ids.hda_id = history_dataset_association.id), + history_events + AS (INSERT INTO cleanup_event_history_association + (create_time, cleanup_event_id, history_id) + SELECT NOW(), %s, id + FROM purged_history_ids), + hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, id + FROM purged_hda_ids), + metadata_file_events + AS (INSERT INTO cleanup_event_metadata_file_association + (create_time, cleanup_event_id, metadata_file_id) + SELECT NOW(), %s, id + FROM deleted_metadata_file_ids), + icda_events + AS (INSERT INTO cleanup_event_icda_association + (create_time, cleanup_event_id, icda_id) + SELECT NOW(), %s, id + FROM deleted_icda_ids), + icda_hda_events + AS (INSERT INTO cleanup_event_hda_association + (create_time, cleanup_event_id, hda_id) + SELECT NOW(), %s, hda_id + FROM deleted_icda_ids) + SELECT purged_history_ids.id, + purged_history_ids.user_id, + purged_hda_ids.id, + deleted_metadata_file_ids.id, + deleted_icda_ids.id, + deleted_icda_ids.hda_id + FROM purged_history_ids + LEFT OUTER JOIN purged_hda_ids + ON purged_history_ids.id = purged_hda_ids.history_id + LEFT OUTER JOIN deleted_metadata_file_ids + ON deleted_metadata_file_ids.hda_id = purged_hda_ids.id + LEFT OUTER JOIN deleted_icda_ids + ON deleted_icda_ids.hda_parent_id = purged_hda_ids.id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', update_time_sql, update_time_sql, update_time_sql, update_time_sql, '%s', '%s', '%s', '%s', '%s') + args = (self.options.days, event_id, event_id, event_id, event_id, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked History purged: %s' % tup[0]) + if tup[1] is not None and tup[1] not in self.disk_accounting_user_ids: + self.disk_accounting_user_ids.append(int(tup[1])) + if tup[2] is not None: + self._log('Purge of History %s caused deletion of HistoryDatasetAssociation: %s' % (tup[0], tup[2])) + if tup[3] is not None: + self._log('Purge of HDA %s caused deletion of MetadataFile: %s' % (tup[1], tup[3])) + self._remove_metadata_file(tup[3], 'purge_deleted_histories') + if tup[4] is not None: + self._log('Purge of HDA %s caused deletion of ImplicitlyConvertedDatasetAssociation: %s and converted HistoryDatasetAssociation: %s' % (tup[1], tup[4], tup[5])) + self._close_logfile() + + def delete_exported_histories(self): + """ + Mark deleted all Datasets that are derivative of JobExportHistoryArchives that are older than the specified number of days. + """ + log.info('Marking deleted all Datasets that are derivative of JobExportHistoryArchives that are older than the specified number of days.') + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH deleted_dataset_ids + AS ( UPDATE dataset + SET deleted = true%s + FROM job_export_history_archive + WHERE job_export_history_archive.dataset_id = dataset.id + AND dataset.update_time <= (NOW() - interval '%s days') + RETURNING dataset.id), + dataset_events + AS (INSERT INTO cleanup_event_dataset_association + (create_time, cleanup_event_id, dataset_id) + SELECT NOW(), %s, id + FROM deleted_dataset_ids) + SELECT id + FROM deleted_dataset_ids + ORDER BY id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', '%s') + args = (self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked Dataset deleted: %s' % tup[0]) + self._close_logfile() + + def delete_datasets(self): + """ + Mark deleted all Datasets whose associations are all marked as deleted (LDDA) or purged (HDA) that are older than the specified number of days. + """ + log.info('Marking deleted all Datasets whose associations are all marked as deleted/purged that are older than the specified number of days.') + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH deleted_dataset_ids + AS ( UPDATE dataset + SET deleted = true%s + WHERE NOT deleted + AND NOT EXISTS (SELECT true + FROM library_dataset_dataset_association + WHERE (NOT deleted + OR update_time >= (NOW() - interval '%s days')) + AND dataset.id = dataset_id) + AND NOT EXISTS (SELECT true + FROM history_dataset_association + WHERE (NOT purged + OR update_time >= (NOW() - interval '%s days')) + AND dataset.id = dataset_id) + RETURNING id), + dataset_events + AS (INSERT INTO cleanup_event_dataset_association + (create_time, cleanup_event_id, dataset_id) + SELECT NOW(), %s, id + FROM deleted_dataset_ids) + SELECT id + FROM deleted_dataset_ids + ORDER BY id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', '%s', '%s') + args = (self.options.days, self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked Dataset deleted: %s' % tup[0]) + self._close_logfile() + + def purge_datasets(self): + """ + Mark purged all Datasets marked deleted that are older than the specified number of days. + """ + log.info('Marking purged all Datasets marked deleted that are older than the specified number of days.') + + # TODO: force retry option + + event_id = self._create_event(inspect.stack()[0][3]) + + sql = """ + WITH purged_dataset_ids + AS ( UPDATE dataset + SET purged = true%s + WHERE deleted = true + AND purged = false + AND update_time < (NOW() - interval '%s days') + RETURNING id), + dataset_events + AS (INSERT INTO cleanup_event_dataset_association + (create_time, cleanup_event_id, dataset_id) + SELECT NOW(), %s, id + FROM purged_dataset_ids) + SELECT id + FROM purged_dataset_ids + ORDER BY id; + """ + + update_time_sql = "" + if self.options.update_time: + update_time_sql += """, + update_time = NOW()""" + + sql = sql % (update_time_sql, '%s', '%s') + args = (self.options.days, event_id) + cur = self._update(sql, args) + self._flush() + + self._open_logfile() + for tup in cur: + self._log('Marked Dataset purged: %s' % tup[0]) + + # always try to remove the "object store path" - if it's at an external_filename, that file will be untouched anyway (which is what we want) + dataset = Bunch(id=tup[0]) + filename = self.object_store.get_filename(dataset) + extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) + + # don't check for existence of the dataset, it should exist + self._log('Removing from disk: %s' % filename) + if not self.options.dry_run: + try: + os.unlink(filename) + except Exception, e: + self._log('Removal of %s failed with error: %s' % (filename, e)) + + # extra_files_dir is optional so it's checked first + if os.path.exists(extra_files_dir): + self._log('Removing from disk: %s' % extra_files_dir) + if not self.options.dry_run: + try: + shutil.rmtree(extra_files_dir) + except Exception, e: + self._log('Removal of %s failed with error: %s' % (extra_files_dir, e)) + + self._close_logfile() + +if __name__ == '__main__': + cleanup = Cleanup() + cleanup._run() + cleanup._update_user_disk_usage() + cleanup._shutdown() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: rmarenco: Added the base.css generated from base.less
by Bitbucket 09 Sep '12

09 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9207ba35fa0c/ changeset: 9207ba35fa0c user: rmarenco date: 2012-09-10 00:24:51 summary: Added the base.css generated from base.less affected #: 1 file diff -r 110a69b0d387228ec7bed84814192b9c99082d7c -r 9207ba35fa0caad1f8eac717afceb50f5c2a61c0 static/june_2007_style/blue/base.css --- /dev/null +++ b/static/june_2007_style/blue/base.css @@ -0,0 +1,914 @@ +article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block;} +audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} +audio:not([controls]){display:none;} +html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} +a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:hover,a:active{outline:0;} +sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} +sup{top:-0.5em;} +sub{bottom:-0.25em;} +img{max-width:100%;vertical-align:middle;border:0;-ms-interpolation-mode:bicubic;} +#map_canvas img{max-width:none;} +button,input,select,textarea{margin:0;font-size:100%;vertical-align:middle;} +button,input{*overflow:visible;line-height:normal;} +button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} +button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;} +input[type="search"]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield;} +input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} +textarea{overflow:auto;vertical-align:top;} +.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";} +.clearfix:after{clear:both;} +.hide-text{font:0/0 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rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;} +.progress.active .bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;-ms-animation:progress-bar-stripes 2s linear infinite;-o-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite;} +.progress-danger .bar{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);} +.progress-danger.progress-striped .bar{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-success .bar{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);} +.progress-success.progress-striped .bar{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-info .bar{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);} +.progress-info.progress-striped .bar{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-warning .bar{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);} +.progress-warning.progress-striped .bar{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.accordion{margin-bottom:16px;} +.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.accordion-heading{border-bottom:0;} +.accordion-heading .accordion-toggle{display:block;padding:8px 15px;} +.accordion-toggle{cursor:pointer;} +.accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5;} +.carousel{position:relative;margin-bottom:16px;line-height:1;} +.carousel-inner{overflow:hidden;width:100%;position:relative;} +.carousel .item{display:none;position:relative;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;} +.carousel .item>img{display:block;line-height:1;} +.carousel .active,.carousel .next,.carousel .prev{display:block;} +.carousel .active{left:0;} +.carousel .next,.carousel .prev{position:absolute;top:0;width:100%;} +.carousel .next{left:100%;} +.carousel .prev{left:-100%;} +.carousel .next.left,.carousel .prev.right{left:0;} +.carousel .active.left{left:-100%;} +.carousel .active.right{left:100%;} +.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#ffffff;text-align:center;background:#222222;border:3px solid #ffffff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:0.5;filter:alpha(opacity=50);opacity:0.5;filter:alpha(opacity=50);}.carousel-control.right{left:auto;right:15px;} +.carousel-control:hover{color:#ffffff;text-decoration:none;opacity:0.9;filter:alpha(opacity=90);opacity:0.9;filter:alpha(opacity=90);} +.carousel-caption{position:absolute;left:0;right:0;bottom:0;padding:10px 15px 5px;background:#333333;background:rgba(0, 0, 0, 0.75);} +.carousel-caption h4,.carousel-caption p{color:#ffffff;} +.hero-unit{padding:60px;margin-bottom:30px;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;} +.hero-unit p{font-size:18px;font-weight:200;line-height:24px;color:inherit;} 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8px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#999999;} +#masthead .navbar-text{margin-bottom:0;line-height:32px;} +#masthead .navbar-link{color:#999999;}#masthead .navbar-link:hover{color:#ffffff;} +#masthead .btn,#masthead .btn-group{margin-top:1px;margin-top:1px;} +#masthead .btn-group .btn{margin:0;} +#masthead .nav{z-index:10000;background-color:#2c3143;} +#masthead .nav>li>a{padding:6px 10px 8px;cursor:pointer;}#masthead .nav>li>a:hover{color:gold;} +#masthead .dropdown-menu a,#masthead .dropdown-menu a:hover{text-decoration:none;} +#masthead .title{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000;}#masthead .title img{display:inline;width:26px;vertical-align:top;} +#masthead .title a{color:white;text-decoration:none;} +#masthead 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+.quota-meter-container{position:absolute;top:0;right:0;height:32px;} +.quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#c1c9e5;} +.quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#969db3;} +.quota-meter-bar-warn{background-color:#ffb400;} +.quota-meter-bar-error{background-color:#ff4343;} +.quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000000;white-space:nowrap;} +div.metadataForm{border:solid #aaaaaa 1px;} +div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px;} +div.metadataFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} +div.metadataFormBody div.metadataFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #dcb790 1px;margin-bottom:5px;} +div.metadataFormDisabled div.metadataFormTitle{background:#eee;border-color:#999;} +div.metadataFormDisabled{border-color:#999;} +div.metadataHelpBody{width:100%;overflow:auto;} +div.titleRow{font-weight:bold;border-bottom:dotted gray 1px;margin-bottom:0.5em;padding-bottom:0.25em;} +div.toolFormBody{background:#ffffff;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} +div.toolFormBody div.toolFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #d8b365 1px;margin-bottom:5px;} +div.toolFormDisabled div.toolFormTitle{background:#eeeeee;border-color:#999999;} +div.toolFormDisabled{border-color:#999999;} +div.toolHelp{margin-top:15px;padding:5px;} +div.toolHelpBody{width:100%;} +.toolForm.toolFormInCanvas{border:solid #d8b365 1px;}.toolForm.toolFormInCanvas 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+div.permissionContainer{padding-left:20px;} +.text-content hr{display:block;background:black;color:black;width:100%;height:1px;border:none;background:#aaa;color:#aaa;} +.text-content table{border-collapse:collapse;border-top:1px solid #ccc;border-left:1px solid #ccc;} +.text-content blockquote{color:#666;} +.text-content fieldset{border-color:#ccc;border:1px solid #ccc;} +.text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} +.text-content th,.text-content td{padding:.8em;} +.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} +.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} +.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} +.tipsy-north{background-position:top center;} 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commit/galaxy-central: rmarenco: Added links to BioStar in the Help Menu and in tool forms + When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in universe
by Bitbucket 09 Sep '12

09 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/110a69b0d387/ changeset: 110a69b0d387 user: rmarenco date: 2012-09-09 23:13:00 summary: Added links to BioStar in the Help Menu and in tool forms + When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in universe affected #: 8 files diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1783,3 +1783,17 @@ .opacity(80); } } + +.icon-button.general-question{ + background: url(question-octagon-frame.png) no-repeat; + float: right; + margin-top: 3px; + margin-right: 4px; +} + +.icon-button.tag-question{ + background: url(question-balloon.png) no-repeat; + float: right; + margin-top: 3px; + margin-right: 4px; +} diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 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-div.permissionContainer{padding-left:20px;} -.text-content hr{display:block;background:black;color:black;width:100%;height:1px;border:none;background:#aaa;color:#aaa;} -.text-content table{border-collapse:collapse;border-top:1px solid #ccc;border-left:1px solid #ccc;} -.text-content blockquote{color:#666;} -.text-content fieldset{border-color:#ccc;border:1px solid #ccc;} -.text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} -.text-content th,.text-content td{padding:.8em;} -.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} -.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} -.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} -.tipsy-north{background-position:top center;} -.tipsy-south{background-position:bottom center;} -.tipsy-east{background-position:right center;} -.tipsy-west{background-position:left center;} -.editable-text{cursor:pointer;} -.editable-text:hover{cursor:text;border:dotted #999999 1px;} -.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} -.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} -body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} -div.historyLinks{margin:5px 5px;} -div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 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-div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} -div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} -div.historyItemButtons{float:right;} -div.historyItemBody div{padding-top:2px;} -pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} -pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} -.toolMenuContainer{color:#303030;background:#dfe5f9;margin-top:5px;} -div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} -div.toolSectionWrapper{margin-bottom:5px;} -div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} -div.toolSectionTitle{font-weight:bold;} -div.toolPanelLabel{padding-top:10px;padding-bottom:5px;font-weight:bold;color:gray;text-transform:uppercase;} -div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} -div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} -div.toolTitleNoSection{padding-bottom:5px;font-weight:bold;} -#tool-search{padding-top:5px;padding-bottom:10px;position:relative;} -#loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;display:none;background:url(largespinner.gif);} -#content_table td{text-align:right;white-space:nowrap;padding:2px 10px;} -#content_table td.stringalign{text-align:left;} -.toolMenuAndView .toolForm{float:left;background-color:white;margin:10px;} -.icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} -.icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} -.icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} -.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -78px;} -.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -104px;} -.icon-button.delete_disabled{background:url(history-buttons.png) no-repeat 0px -130px;} -.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -156px;} -.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -182px;} -.icon-button.edit_disabled{background:url(history-buttons.png) no-repeat 0px -208px;} -.icon-button.tag{background:url(fugue.png) no-repeat 0px 0px;} -.icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;} -.icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} -.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} -.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} -.icon-button.toggle:hover{background:url(fugue.png) no-repeat 0px -130px;} -.icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -156px;} -.icon-button.chevron{background:url(fugue.png) no-repeat 0px -182px;} -.icon-button.bug{background:url(fugue.png) no-repeat 0px -208px;} -.icon-button.disk{background:url(fugue.png) no-repeat 0px -234px;} -.icon-button.information{background:url(fugue.png) no-repeat 0px -260px;} -.icon-button.annotate{background:url(fugue.png) no-repeat 0px -286px;} -.icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -312px;} -.icon-button.import{background:url(fugue.png) no-repeat 0px -338px;} -.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -364px;} -.icon-button.plus-button:hover{background:url(fugue.png) no-repeat 0px -390px;} -.icon-button.gear{background:url(fugue.png) no-repeat 0px -416px;} -.icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -442px;} -.icon-button.disk--arrow{background:url(fugue.png) no-repeat 0px -468px;} -.icon-button.disk--arrow:hover{background:url(fugue.png) no-repeat 0px -494px;} -.icon-button.cross-circle{background:url(fugue.png) no-repeat 0px -520px;} -.icon-button.cross-circle:hover{background:url(fugue.png) no-repeat 0px -546px;} -.icon-button.arrow-split{background:url(fugue.png) no-repeat 0px -572px;} -.icon-button.arrow-split:hover{background:url(fugue.png) no-repeat 0px -598px;} -.icon-button.chevron-expand:hover{background:url(fugue.png) no-repeat 0px -624px;} -.icon-button.chevron-expand{background:url(fugue.png) no-repeat 0px -650px;} -.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -676px;} -div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} -div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} -div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} -.text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.3;filter:alpha(opacity=30);opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c static/june_2007_style/blue/question-balloon.png Binary file static/june_2007_style/blue/question-balloon.png has changed diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c static/june_2007_style/blue/question-octagon-frame.png Binary file static/june_2007_style/blue/question-octagon-frame.png has changed diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -12,7 +12,7 @@ </%def><%def name="javascripts()"> - ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage" )} + ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage", "libs/bootstrap" )} <script type="text/javascript"> $(function() { $(window).bind("refresh_on_change", function() { @@ -282,6 +282,11 @@ tool_url = tool.action[0] + h.url_for(tool.action[1]) %> +<% + # Name of the tool in lower case + low_tool_name = tool.name.lower() +%> + %if tool_id_version_message: ${render_msg( tool_id_version_message, 'warning' )} %endif @@ -289,12 +294,17 @@ <div class="toolForm" id="${tool.id}"><form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> + <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) %elif not tool_version_select_field: - <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> + <div class="toolFormTitle">${tool.name} (version ${tool.version}) %else: - <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()}</div> + <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} %endif +  + <a href="http://slyfox.bx.psu.edu:8080/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="http://slyfox.bx.psu.edu:8080/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> +  + </div><div class="toolFormBody"><input type="hidden" name="refresh" value="refresh"><input type="hidden" name="tool_id" value="${tool.id}"> diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -71,7 +71,8 @@ ## Help tab. <% - menu_options = [ + menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "_blank" ] [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -120,6 +120,7 @@ ## Help tab. <% menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "galaxy_main" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], diff -r 51b24be13e9085b6fda294354e709d844e5da964 -r 110a69b0d387228ec7bed84814192b9c99082d7c universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -263,6 +263,9 @@ # as on the user registration and login forms. #terms_url = None +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +qa_url = http://slyfox.bx.psu.edu:8080/ + # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not # documented individually. You can use these paths (or ones in the proxy Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Circster enhancements: (a) dragging and zooming; and (b) fill complete palette.
by Bitbucket 08 Sep '12

08 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/51b24be13e90/ changeset: 51b24be13e90 user: jgoecks date: 2012-09-08 19:08:33 summary: Circster enhancements: (a) dragging and zooming; and (b) fill complete palette. affected #: 2 files diff -r 108cda8986460298279279fca9ae40661a8e6174 -r 51b24be13e9085b6fda294354e709d844e5da964 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -827,9 +827,11 @@ this.height = options.height; this.total_gap = options.total_gap; this.genome = options.genome; - this.radius_start = options.radius_start; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; + + // Compute radius start based on model. + this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap); }, render: function() { @@ -841,8 +843,17 @@ .append("svg") .attr("width", self.width) .attr("height", self.height) - .append("g") - .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")"); + .attr("pointer-events", "all") + // Set up zooming, dragging. + .append('svg:g') + .call(d3.behavior.zoom().on('zoom', function() { + svg.attr("transform", + "translate(" + d3.event.translate + ")" + + " scale(" + d3.event.scale + ")"); + })) + .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")") + .append('svg:g') + // -- Render each dataset in the visualization. -- this.model.get('tracks').each(function(track, index) { @@ -889,8 +900,8 @@ .style("stroke", block_color) .style("fill", block_color); }); - }); - } + }); + } }); /** diff -r 108cda8986460298279279fca9ae40661a8e6174 -r 51b24be13e9085b6fda294354e709d844e5da964 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -69,14 +69,13 @@ var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')) visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), viz_view = new CircsterView({ - width: 600, - height: 600, + width: 700, + height: 700, // Gap is difficult to set because it very dependent on chromosome size and organization. - total_gap: 2 * Math.PI * 0.2, + total_gap: 2 * Math.PI * 0.1, genome: genome, model: visualization, - radius_start: 100, - dataset_arc_height: 15 + dataset_arc_height: 25 }); // -- Render viz. -- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Enhancements to tool dependency installation when installing with a tool shed repository: multiple environment variables can now be set and a new "make_directory" tag is supported.
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/108cda898646/ changeset: 108cda898646 user: greg date: 2012-09-07 20:49:46 summary: Enhancements to tool dependency installation when installing with a tool shed repository: multiple environment variables can now be set and a new "make_directory" tag is supported. affected #: 3 files diff -r 1475240809a7e9b996aa7b9026b33e20ea9209bd -r 108cda8986460298279279fca9ae40661a8e6174 lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py @@ -17,6 +17,9 @@ return tarfile.is_tarfile( file_path ) def iszip( file_path ): return check_zip( file_path ) +def make_directory( full_path ): + if not os.path.exists( full_path ): + os.makedirs( full_path ) def move_directory_files( current_dir, source_dir, destination_dir ): source_directory = os.path.abspath( os.path.join( current_dir, source_dir ) ) destination_directory = os.path.join( destination_dir ) diff -r 1475240809a7e9b996aa7b9026b33e20ea9209bd -r 108cda8986460298279279fca9ae40661a8e6174 lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -88,7 +88,9 @@ for action_tup in actions[ 1: ]: action_type, action_dict = action_tup current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - if action_type == 'move_directory_files': + if action_type == 'make_directory': + common_util.make_directory( full_path=action_dict[ 'full_path' ] ) + elif action_type == 'move_directory_files': common_util.move_directory_files( current_dir=current_dir, source_dir=os.path.join( action_dict[ 'source_directory' ] ), destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) @@ -98,29 +100,36 @@ destination_dir=os.path.join( action_dict[ 'destination' ] ) ) elif action_type == 'set_environment': # Currently the only action supported in this category is "environment_variable". - env_var_dict = action_dict[ 'environment_variable' ] - env_var_name = env_var_dict[ 'name' ] - env_var_action = env_var_dict[ 'action' ] - env_var_value = env_var_dict[ 'value' ] - if env_var_action == 'prepend_to': - changed_value = '%s:$%s' % ( env_var_value, env_var_name ) - elif env_var_action == 'set_to': - changed_value = '%s' % env_var_value - elif env_var_action == 'append_to': - changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - cmd = "echo '%s=%s; export %s' > %s/env.sh;chmod +x %s/env.sh" % ( env_var_name, - changed_value, - env_var_name, - install_dir, - install_dir ) - output = local( cmd, capture=True ) - log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - if output.return_code: - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = str( output.stderr ) - sa_session.add( tool_dependency ) - sa_session.flush() - return + env_var_dicts = action_dict[ 'environment_variable' ] + for env_var_dict in env_var_dicts: + env_var_name = env_var_dict[ 'name' ] + env_var_action = env_var_dict[ 'action' ] + env_var_value = env_var_dict[ 'value' ] + if env_var_action == 'prepend_to': + changed_value = '%s:$%s' % ( env_var_value, env_var_name ) + elif env_var_action == 'set_to': + changed_value = '%s' % env_var_value + elif env_var_action == 'append_to': + changed_value = '$%s:%s' % ( env_var_name, env_var_value ) + env_shell_file_path = '%s/env.sh' % install_dir + if os.path.exists( env_shell_file_path ): + write_action = '>>' + else: + write_action = '>' + cmd = "echo '%s=%s; export %s' %s %s;chmod +x %s" % ( env_var_name, + changed_value, + env_var_name, + write_action, + env_shell_file_path, + env_shell_file_path ) + output = local( cmd, capture=True ) + log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) + if output.return_code: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = str( output.stderr ) + sa_session.add( tool_dependency ) + sa_session.flush() + return elif action_type == 'shell_command': action = action_dict[ 'command' ] with settings( warn_only=True ): diff -r 1475240809a7e9b996aa7b9026b33e20ea9209bd -r 108cda8986460298279279fca9ae40661a8e6174 lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -113,6 +113,12 @@ action_dict[ 'url' ] = action_elem.text else: continue + elif action_type == 'make_directory': + # <action type="make_directory">$INSTALL_DIR/lib/python</action> + if action_elem.text: + action_dict[ 'full_path' ] = action_elem.text.replace( '$INSTALL_DIR', install_dir ) + else: + continue elif action_type in [ 'move_directory_files', 'move_file' ]: # <action type="move_file"> # <source>misc/some_file</source> @@ -128,15 +134,21 @@ action_dict[ move_elem.tag ] = move_elem_text elif action_type == 'set_environment': # <action type="set_environment"> + # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> # </action> + env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': env_var_name = env_elem.get( 'name', 'PATH' ) env_var_action = env_elem.get( 'action', 'prepend_to' ) env_var_text = env_elem.text.replace( '$INSTALL_DIR', install_dir ) if env_var_text: - action_dict[ env_elem.tag ] = dict( name=env_var_name, action=env_var_action, value=env_var_text ) + env_var_dicts.append( dict( name=env_var_name, action=env_var_action, value=env_var_text ) ) + if env_var_dicts: + action_dict[ env_elem.tag ] = env_var_dicts + else: + continue else: continue actions.append( ( action_type, action_dict ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Added an error message to the repository clone error handling.
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1475240809a7/ changeset: 1475240809a7 user: inithello date: 2012-09-07 17:54:02 summary: Added an error message to the repository clone error handling. affected #: 2 files diff -r 0491c108154248cab0006533d30e462df3ade6f9 -r 1475240809a7e9b996aa7b9026b33e20ea9209bd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -363,7 +363,8 @@ noupdate=False, rev=util.listify( str( ctx_rev ) ) ) return True - except: + except Exception, e: + log.debug( 'Encountered an exception while cloning the repository: %s' % e ) return False def copy_sample_file( app, filename, dest_path=None ): """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data.""" diff -r 0491c108154248cab0006533d30e462df3ade6f9 -r 1475240809a7e9b996aa7b9026b33e20ea9209bd lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -772,15 +772,8 @@ repository_id = kwd[ 'id' ] repository = get_repository( trans, repository_id ) if repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, - trans.model.ToolShedRepository.installation_status.CLONING ]: - message = "The repository '%s' is not yet cloned, please try again..." - status = 'warning' - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='monitor_repository_installation', - **kwd ) ) - if repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: - message = "There was an error installing the repository '%s', please try again..." - status = 'warning' + trans.model.ToolShedRepository.installation_status.CLONING, + trans.model.ToolShedRepository.installation_status.ERROR ]: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', **kwd ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Handle errors when cloning a tool shed repository.
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0491c1081542/ changeset: 0491c1081542 user: inithello date: 2012-09-07 17:22:09 summary: Handle errors when cloning a tool shed repository. affected #: 2 files diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 0491c108154248cab0006533d30e462df3ade6f9 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -355,12 +355,16 @@ return tool_shed_url.rstrip( '/' ) def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" - commands.clone( get_configured_ui(), - str( repository_clone_url ), - dest=str( repository_file_dir ), - pull=True, - noupdate=False, - rev=util.listify( str( ctx_rev ) ) ) + try: + commands.clone( get_configured_ui(), + str( repository_clone_url ), + dest=str( repository_file_dir ), + pull=True, + noupdate=False, + rev=util.listify( str( ctx_rev ) ) ) + return True + except: + return False def copy_sample_file( app, filename, dest_path=None ): """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data.""" if dest_path is None: diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 0491c108154248cab0006533d30e462df3ade6f9 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -64,7 +64,8 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ), + link=( lambda item: iff( item.status == model.ToolShedRepository.installation_status.ERROR, \ + None, dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), attach_popup=True ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), @@ -86,17 +87,29 @@ global_actions = [] operations = [ grids.GridOperation( "Get updates", allow_multiple=False, - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and item.status not in \ + [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='get updates' ) ), grids.GridOperation( "Deactivate or uninstall", allow_multiple=False, - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and item.status not in \ + [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='deactivate or uninstall' ) ), + grids.GridOperation( "Uninstall", + allow_multiple=False, + condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='uninstall' ) ), + grids.GridOperation( "Reset to install", + allow_multiple=False, + condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='reset status to new' ) ), grids.GridOperation( "Activate or reinstall", allow_multiple=False, - condition=( lambda item: item.deleted ), + condition=( lambda item: ( item.deleted or item.uninstalled ) ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='activate or reinstall' ) ) ] standard_filters = [] @@ -342,6 +355,16 @@ return self.manage_repository( trans, **kwd ) if operation == "get updates": return self.check_for_updates( trans, **kwd ) + if operation == "uninstall": + kwd[ 'deactivate_or_uninstall_repository_button' ] = 'Deactivate or Uninstall' + kwd[ 'remove_from_disk' ] = [u'true', u'true'] + return self.deactivate_or_uninstall_repository( trans, **kwd ) + if operation == "reset status to new": + repository = get_repository( trans, kwd[ 'id' ] ) + repository.status = model.ToolShedRepository.installation_status.NEW + repository.deleted = False + repository.uninstalled = True + trans.app.model.context.current.flush() if operation == "activate or reinstall": repository = get_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: @@ -406,7 +429,7 @@ remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) tool_shed_repository = get_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) - repository_install_dir = os.path.abspath ( relative_install_dir ) + repository_install_dir = os.path.abspath ( relative_install_dir ) if relative_install_dir is not None else None errors = '' if params.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools: @@ -426,8 +449,12 @@ log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) ) removed = True except Exception, e: - log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) - removed = False + if repository_install_dir is not None: + removed = False + log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) + else: + log.debug( "Repository installation directory does not exist." ) + removed = True if removed: tool_shed_repository.uninstalled = True # Remove all installed tool dependencies. @@ -610,7 +637,12 @@ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) - clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + result = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + if not result: + update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.ERROR ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + tool_shed_repository_ids=[ trans.security.encode_id( tool_shed_repository.id ) ] ) ) if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) @@ -746,6 +778,12 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', **kwd ) ) + if repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: + message = "There was an error installing the repository '%s', please try again..." + status = 'warning' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + **kwd ) ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: rmarenco: Modified the good files instead of the auto-generated ones
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1a56c4b28c6b/ changeset: 1a56c4b28c6b user: rmarenco date: 2012-09-07 15:54:31 summary: Modified the good files instead of the auto-generated ones affected #: 5 files diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb database/compiled_templates/webapps/galaxy/base_panels.mako.py --- a/database/compiled_templates/webapps/galaxy/base_panels.mako.py +++ /dev/null @@ -1,415 +0,0 @@ -# -*- encoding:ascii -*- -from mako import runtime, filters, cache -UNDEFINED = runtime.UNDEFINED -__M_dict_builtin = dict -__M_locals_builtin = locals -_magic_number = 6 -_modified_time = 1346972736.51736 -_template_filename=u'templates/webapps/galaxy/base_panels.mako' -_template_uri=u'/webapps/galaxy/base_panels.mako' -_template_cache=cache.Cache(__name__, _modified_time) -_source_encoding='ascii' -_exports = ['masthead', 'javascripts', 'title'] - - -def _mako_get_namespace(context, name): - try: - return context.namespaces[(__name__, name)] - except KeyError: - _mako_generate_namespaces(context) - return context.namespaces[(__name__, name)] -def _mako_generate_namespaces(context): - pass -def _mako_inherit(template, context): - _mako_generate_namespaces(context) - return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) -def render_body(context,**pageargs): - context.caller_stack._push_frame() - try: - __M_locals = __M_dict_builtin(pageargs=pageargs) - __M_writer = context.writer() - # SOURCE LINE 1 - __M_writer(u'\n\n') - # SOURCE LINE 4 - __M_writer(u'\n\n') - # SOURCE LINE 8 - __M_writer(u'\n\n') - # SOURCE LINE 232 - __M_writer(u'\n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_masthead(context): - context.caller_stack._push_frame() - try: - AssertionError = context.get('AssertionError', UNDEFINED) - h = context.get('h', UNDEFINED) - app = context.get('app', UNDEFINED) - util = context.get('util', UNDEFINED) - def tab(id,display,href,target='_parent',visible=True,extra_class='',menu_options=None): - context.caller_stack._push_frame() - try: - self = context.get('self', UNDEFINED) - len = context.get('len', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 19 - __M_writer(u'\n') - # SOURCE LINE 22 - __M_writer(u' \n ') - # SOURCE LINE 23 - - cls = "" - a_cls = "" - extra = "" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - if menu_options: - cls += " dropdown" - a_cls += " dropdown-toggle" - extra = "<b class='caret'></b>" - style = "" - if not visible: - style = "display: none;" - - - # SOURCE LINE 38 - __M_writer(u'\n <li class="') - # SOURCE LINE 39 - __M_writer(unicode(cls)) - __M_writer(u'" style="') - __M_writer(unicode(style)) - __M_writer(u'">\n') - # SOURCE LINE 40 - if href: - # SOURCE LINE 41 - __M_writer(u' <a class="') - __M_writer(unicode(a_cls)) - __M_writer(u'" data-toggle="dropdown" target="') - __M_writer(unicode(target)) - __M_writer(u'" href="') - __M_writer(unicode(href)) - __M_writer(u'">') - __M_writer(unicode(display)) - __M_writer(unicode(extra)) - __M_writer(u'</a>\n') - # SOURCE LINE 42 - else: - # SOURCE LINE 43 - __M_writer(u' <a class="') - __M_writer(unicode(a_cls)) - __M_writer(u'" data-toggle="dropdown">') - __M_writer(unicode(display)) - __M_writer(unicode(extra)) - __M_writer(u'</a>\n') - pass - # SOURCE LINE 45 - if menu_options: - # SOURCE LINE 46 - __M_writer(u' <ul class="dropdown-menu">\n') - # SOURCE LINE 47 - for menu_item in menu_options: - # SOURCE LINE 48 - if not menu_item: - # SOURCE LINE 49 - __M_writer(u' <li class="divider"></li>\n') - # SOURCE LINE 50 - else: - # SOURCE LINE 51 - __M_writer(u' <li>\n') - # SOURCE LINE 52 - if len ( menu_item ) == 1: - # SOURCE LINE 53 - __M_writer(u' ') - __M_writer(unicode(menu_item[0])) - __M_writer(u'\n') - # SOURCE LINE 54 - elif len ( menu_item ) == 2: - # SOURCE LINE 55 - __M_writer(u' ') - name, link = menu_item - - __M_writer(u'\n <a href="') - # SOURCE LINE 56 - __M_writer(unicode(link)) - __M_writer(u'">') - __M_writer(unicode(name)) - __M_writer(u'</a>\n') - # SOURCE LINE 57 - else: - # SOURCE LINE 58 - __M_writer(u' ') - name, link, target = menu_item - - __M_writer(u'\n <a target="') - # SOURCE LINE 59 - __M_writer(unicode(target)) - __M_writer(u'" href="') - __M_writer(unicode(link)) - __M_writer(u'">') - __M_writer(unicode(name)) - __M_writer(u'</a>\n') - pass - # SOURCE LINE 61 - __M_writer(u' </li>\n') - pass - pass - # SOURCE LINE 64 - __M_writer(u' </ul>\n') - pass - # SOURCE LINE 66 - __M_writer(u' </li>\n ') - return '' - finally: - context.caller_stack._pop_frame() - trans = context.get('trans', UNDEFINED) - _ = context.get('_', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 11 - __M_writer(u'\n\n') - # SOURCE LINE 14 - __M_writer(u' <div style="position: relative; right: -50%; float: left;">\n <div style="display: block; position: relative; right: 50%;">\n\n <ul class="nav" border="0" cellspacing="0">\n \n ') - # SOURCE LINE 67 - __M_writer(u'\n\n') - # SOURCE LINE 70 - __M_writer(u' ') - __M_writer(unicode(tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 73 - __M_writer(u' ') - __M_writer(unicode(tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 76 - __M_writer(u' ') - - menu_options = [ - [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], - None, - [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], - [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ], - [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ], - [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] - ] - tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) - - - # SOURCE LINE 86 - __M_writer(u'\n \n') - # SOURCE LINE 89 - __M_writer(u' ') - - menu_options = [ - [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ], - [ _('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 or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) - - - # SOURCE LINE 96 - __M_writer(u'\n\n') - # SOURCE LINE 99 - __M_writer(u' ') - - menu_options = [ - [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], - [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] - ] - tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) - - - # SOURCE LINE 105 - __M_writer(u'\n\n') - # SOURCE LINE 108 - if app.config.get_bool( 'enable_cloud_launch', False ): - # SOURCE LINE 109 - __M_writer(u' ') - - menu_options = [ - [_('New Cloud Cluster'), h.url_for( controller='/cloudlaunch', action='index' ) ], - ] - tab( "cloud", _("Cloud"), h.url_for( controller='/cloudlaunch', action='index'), menu_options=menu_options ) - - - # SOURCE LINE 114 - __M_writer(u'\n') - pass - # SOURCE LINE 116 - __M_writer(u'\n') - # SOURCE LINE 118 - __M_writer(u' ') - __M_writer(unicode(tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 121 - __M_writer(u' ') - - menu_options = [ - [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "galaxy_main" ], - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] - ] - if app.config.get( 'terms_url', None ) is not None: - menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) - tab( "help", _("Help"), None, menu_options=menu_options) - - - # SOURCE LINE 132 - __M_writer(u'\n \n') - # SOURCE LINE 135 - __M_writer(u' ') - - # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] - if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - extra_class = "loggedout-only" - visible = ( trans.user == None ) - tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) - - # Menu for user who is logged in. - if trans.user: - email = trans.user.email - else: - email = "" - menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] - if app.config.use_remote_user: - if app.config.remote_user_logout_href: - menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) - else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) - else: - logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) - menu_options.append( None ) - menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - - extra_class = "loggedin-only" - visible = ( trans.user != None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) - - - # SOURCE LINE 172 - __M_writer(u'\n \n') - # SOURCE LINE 176 - __M_writer(u' </ul>\n\n </div>\n </div>\n \n') - # SOURCE LINE 182 - __M_writer(u' <div class="title">\n <a href="') - # SOURCE LINE 183 - __M_writer(unicode(h.url_for( app.config.get( 'logo_url', '/' ) ))) - __M_writer(u'">\n <img border="0" src="') - # SOURCE LINE 184 - __M_writer(unicode(h.url_for('/static/images/galaxyIcon_noText.png'))) - __M_writer(u'">\n Galaxy\n') - # SOURCE LINE 186 - if app.config.brand: - # SOURCE LINE 187 - __M_writer(u' <span>/ ') - __M_writer(unicode(app.config.brand)) - __M_writer(u'</span>\n') - pass - # SOURCE LINE 189 - __M_writer(u' </a>\n </div>\n\n') - # SOURCE LINE 193 - __M_writer(u' ') - - bar_style = "quota-meter-bar" - usage = 0 - percent = 0 - quota = None - try: - usage = trans.app.quota_agent.get_usage( trans=trans ) - quota = trans.app.quota_agent.get_quota( trans.user ) - percent = trans.app.quota_agent.get_percent( usage=usage, quota=quota ) - if percent is not None: - if percent >= 100: - bar_style += " quota-meter-bar-error" - elif percent >= 85: - bar_style += " quota-meter-bar-warn" - else: - percent = 0 - except AssertionError: - pass # Probably no history yet - tooltip = None - if not trans.user and quota and trans.app.config.allow_user_creation: - if trans.app.quota_agent.default_registered_quota is None or trans.app.quota_agent.default_unregistered_quota < trans.app.quota_agent.default_registered_quota: - tooltip = "Your disk quota is %s. You can increase your quota by registering a Galaxy account." % util.nice_size( quota ) - - - # SOURCE LINE 215 - __M_writer(u'\n\n <div class="quota-meter-container">\n') - # SOURCE LINE 218 - if tooltip: - # SOURCE LINE 219 - __M_writer(u' <div id="quota-meter" class="quota-meter tooltip" title="') - __M_writer(unicode(tooltip)) - __M_writer(u'">\n') - # SOURCE LINE 220 - else: - # SOURCE LINE 221 - __M_writer(u' <div id="quota-meter" class="quota-meter">\n') - pass - # SOURCE LINE 223 - __M_writer(u' <div id="quota-meter-bar" class="') - __M_writer(unicode(bar_style)) - __M_writer(u'" style="width: ') - __M_writer(unicode(percent)) - __M_writer(u'px;"></div>\n') - # SOURCE LINE 224 - if quota is not None: - # SOURCE LINE 225 - __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') - __M_writer(unicode(percent)) - __M_writer(u'%</div>\n') - # SOURCE LINE 226 - else: - # SOURCE LINE 227 - __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') - __M_writer(unicode(util.nice_size( usage ))) - __M_writer(u'</div>\n') - pass - # SOURCE LINE 229 - __M_writer(u' </div>\n </div>\n \n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_javascripts(context): - context.caller_stack._push_frame() - try: - parent = context.get('parent', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 6 - __M_writer(u'\n ') - # SOURCE LINE 7 - __M_writer(unicode(parent.javascripts())) - __M_writer(u'\n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_title(context): - context.caller_stack._push_frame() - try: - __M_writer = context.writer() - # SOURCE LINE 4 - __M_writer(u'Galaxy') - return '' - finally: - context.caller_stack._pop_frame() - - diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -71,7 +71,8 @@ ## Help tab. <% - menu_options = [ + menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8081/" ), "_blank" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -120,7 +120,7 @@ ## Help tab. <% menu_options = [ - [_('Galaxy Q&A'), app.config.get( "q&a", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb universe_wsgi.ini --- a/universe_wsgi.ini +++ /dev/null @@ -1,753 +0,0 @@ -# -# Galaxy is configured by default to be useable in a single-user development -# environment. To tune the application for a multi-user production -# environment, see the documentation at: -# -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server -# - -# Throughout this sample configuration file, except where stated otherwise, -# uncommented values override the default if left unset, whereas commented -# values are set to the default value. -# Examples of many of these options are explained in more detail in the wiki: -# -# http://wiki.g2.bx.psu.edu/Admin/Config -# -# Config hackers are encouraged to check there before asking for help. - -# ---- HTTP Server ---------------------------------------------------------- - -# Configuration of the internal HTTP server. - -[server:main] - -# The internal HTTP server to use. Currently only Paste is provided. This -# option is required. -use = egg:Paste#http - -# The port on which to listen. -#port = 8080 - -# The address on which to listen. By default, only listen to localhost (Galaxy -# will not be accessible over the network). Use '0.0.0.0' to listen on all -# available network interfaces. -#host = 127.0.0.1 - -# Use a threadpool for the web server instead of creating a thread for each -# request. -use_threadpool = True - -# Number of threads in the web server thread pool. -#threadpool_workers = 10 - -# ---- Filters -------------------------------------------------------------- - -# Filters sit between Galaxy and the HTTP server. - -# These filters are disabled by default. They can be enabled with -# 'filter-with' in the [app:main] section below. - -# Define the gzip filter. -[filter:gzip] -use = egg:Paste#gzip - -# Define the proxy-prefix filter. -[filter:proxy-prefix] -use = egg:PasteDeploy#prefix -prefix = /galaxy - -# ---- Galaxy --------------------------------------------------------------- - -# Configuration of the Galaxy application. - -[app:main] - -# -- Application and filtering - -# The factory for the WSGI application. This should not be changed. -paste.app_factory = galaxy.web.buildapp:app_factory - -# If not running behind a proxy server, you may want to enable gzip compression -# to decrease the size of data transferred over the network. If using a proxy -# server, please enable gzip compression there instead. -#filter-with = gzip - -# If running behind a proxy server and Galaxy is served from a subdirectory, -# enable the proxy-prefix filter and set the prefix in the -# [filter:proxy-prefix] section above. -#filter-with = proxy-prefix - -# If proxy-prefix is enabled and you're running more than one Galaxy instance -# behind one hostname, you will want to set this to the same path as the prefix -# in the filter above. This value becomes the "path" attribute set in the -# cookie so the cookies from each instance will not clobber each other. -#cookie_path = None - -# -- Database - -# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You -# may use a SQLAlchemy connection string to specify an external database -# instead. This string takes many options which are explained in detail in the -# config file documentation. -#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE - -# If the server logs errors about not having enough database pool connections, -# you will want to increase these values, or consider running more Galaxy -# processes. -#database_engine_option_pool_size = 5 -#database_engine_option_max_overflow = 10 - -# If using MySQL and the server logs the error "MySQL server has gone away", -# you will want to set this to some positive value (7200 should work). -#database_engine_option_pool_recycle = -1 - -# If large database query results are causing memory or response time issues in -# the Galaxy process, leave the result on the server instead. This option is -# only available for PostgreSQL and is highly recommended. -#database_engine_option_server_side_cursors = False - -# Create only one connection to the database per thread, to reduce the -# connection overhead. Recommended when not using SQLite: -#database_engine_option_strategy = threadlocal - -# Log all database transactions, can be useful for debugging and performance -# profiling. Logging is done via Python's 'logging' module under the qualname -# 'galaxy.model.orm.logging_connection_proxy' -#database_query_profiling_proxy = False - -# -- Files and directories - -# Path where genome builds are stored. This defaults to tool-data/genome -#genome_data_path = tool-data/genome - -# URL for rsync server to download pre-built indexes. -#rsync_url = rsync://scofield.bx.psu.edu/indexes - -# Dataset files are stored in this directory. -#file_path = database/files - -# Temporary files are stored in this directory. -#new_file_path = database/tmp - -# Tool config files, defines what tools are available in Galaxy. -# Tools can be locally developed or installed from Galaxy tool sheds. -#tool_config_file = tool_conf.xml,shed_tool_conf.xml - -# Default path to the directory containing the tools defined in tool_conf.xml. -# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. -#tool_path = tools - -# Path to the directory in which managed tool dependencies are placed. To use -# the dependency system, see the documentation at: -# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies -#tool_dependency_dir = None - -# Enable automatic polling of relative tool sheds to see if any updates -# are available for installed repositories. Ideally only one Galaxy -# server process should be able to check for repository updates. The -# setting for hours_between_check should be an integer between 1 and 24. -#enable_tool_shed_check = False -#hours_between_check = 12 - -# Directory where data used by tools is located, see the samples in that -# directory and the wiki for help: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration -#tool_data_path = tool-data - -# Directory where chrom len files are kept, currently mainly used by trackster -#len_file_path = tool-data/shared/ucsc/chrom - -# Datatypes config file, defines what data (file) types are available in -# Galaxy. -#datatypes_config_file = datatypes_conf.xml - -# Each job is given a unique empty directory as its current working directory. -# This option defines in what parent directory those directories will be -# created. -#job_working_directory = database/job_working_directory - -# If using a cluster, Galaxy will write job scripts and stdout/stderr to this -# directory. -#cluster_files_directory = database/pbs - -# External service types config file, defines what types of external_services configurations -# are available in Galaxy. -#external_service_type_config_file = external_service_types_conf.xml - -# Path to the directory containing the external_service_types defined in the config. -#external_service_type_path = external_service_types - -# Tools with a number of outputs not known until runtime can write these -# outputs to a directory for collection by Galaxy when the job is done. -# Previously, this directory was new_file_path, but using one global directory -# can cause performance problems, so using job_working_directory ('.' or cwd -# when a job is run) is encouraged. By default, both are checked to avoid -# breaking existing tools. -#collect_outputs_from = new_file_path,job_working_directory - -# -- Mail and notification - -# Galaxy sends mail for various things: Subscribing users to the mailing list -# if they request it, emailing password resets, notification from the Galaxy -# Sample Tracking system, and reporting dataset errors. To do this, it needs -# to send mail through an SMTP server, which you may define here (host:port). -# Galaxy will automatically try STARTTLS but will continue upon failure. -#smtp_server = None - -# If your SMTP server requires a username and password, you can provide them -# here (password in cleartext here, but if your server supports STARTTLS it -# will be sent over the network encrypted). -#smtp_username = None -#smtp_password = None - -# On the user registration form, users may choose to join the mailing list. -# This is the address of the list they'll be subscribed to. -#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu - -# Datasets in an error state include a link to report the error. Those reports -# will be sent to this address. Error reports are disabled if no address is set. -#error_email_to = None - -# -- Display sites - -# Galaxy can display data at various external browsers. These options specify -# which browsers should be available. URLs and builds available at these -# browsers are defined in the specifield files. - -# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt -#ucsc_display_sites = main,test,archaea,ucla - -# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 - -# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt -#genetrack_display_sites = main,test - -# If use_remote_user = True, display application servers will be denied access -# to Galaxy and so displaying datasets in these sites will fail. -# display_servers contains a list of hostnames which should be allowed to -# bypass security to display datasets. Please be aware that there are security -# implications if this is allowed. More details (including required changes to -# the proxy server config) are available in the Apache proxy documentation on -# the wiki. -# -# The list of servers in this sample config are for the UCSC Main, Test and -# Archaea browsers, but the default if left commented is to not allow any -# display sites to bypass security (you must uncomment the line below to allow -# them). -#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… - -# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. - -use_nglims = False -nglims_config_file = tool-data/nglims.yaml - -# -- UI Localization - -# Append "/{brand}" to the "Galaxy" text in the masthead. -#brand = None - -# The URL linked by the "Galaxy/brand" text. -#logo_url = / - -# The URL linked by the "Galaxy Wiki" link in the "Help" menu. -#wiki_url = http://wiki.g2.bx.psu.edu/ - -# The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.g2.bx.psu.edu/Support - -# The URL linked by the "How to Cite..." link in the "Help" menu. -#citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy - -# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well -# as on the user registration and login forms. -#terms_url = None - -# The URL linked by the "Galaxy Q&A" link in the "Help" menu -qa_url = http://slyfox.bx.psu.edu:8080/ - -# Serve static content, which must be enabled if you're not serving it via a -# proxy server. These options should be self explanatory and so are not -# documented individually. You can use these paths (or ones in the proxy -# server) to point to your own styles. -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue -static_robots_txt = %(here)s/static/robots.txt - -# Pack javascript at launch (/static/scripts/*.js) -# This only happens if the modified timestamp of the source .js is newer -# than the version (if it exists) in /static/scripts/packed/ -# Note that this requires java > 1.4 for executing yuicompressor.jar -#pack_scripts = False - -# Enable Cloud Launch - -#enable_cloud_launch = False - -# -- Advanced proxy features - -# For help on configuring the Advanced proxy features, see: -# http://usegalaxy.org/production - -# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set -# this to True to inform Galaxy that mod_xsendfile is enabled upstream. -#apache_xsendfile = False - -# The same download handling can be done by nginx using X-Accel-Redirect. This -# should be set to the path defined in the nginx config as an internal redirect -# with access to Galaxy's data files (see documentation linked above). -#nginx_x_accel_redirect_base = False - -# nginx can make use of mod_zip to create zip files containing multiple library -# files. If using X-Accel-Redirect, this can be the same value as that option. -#nginx_x_archive_files_base = False - -# If using compression in the upstream proxy server, use this option to disable -# gzipping of library .tar.gz and .zip archives, since the proxy server will do -# it faster on the fly. -#upstream_gzip = False - -# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. -# Configuration for this is complex and explained in detail in the -# documentation linked above. The upload store is a temporary directory in -# which files uploaded by the upload module will be placed. -#nginx_upload_store = False - -# This value overrides the action set on the file upload form, e.g. the web -# path where the nginx_upload_module has been configured to intercept upload -# requests. -#nginx_upload_path = False - -# -- Logging and Debugging - -# Verbosity of console log messages. Acceptable values can be found here: -# http://docs.python.org/library/logging.html#logging-levels -#log_level = DEBUG - -# Print database operations to the server log (warning, quite verbose!). -#database_engine_option_echo = False - -# Print database pool operations to the server log (warning, quite verbose!). -#database_engine_option_echo_pool = False - -# Turn on logging of application events and some user events to the database. -#log_events = True - -# Turn on logging of user actions to the database. Actions currently logged are -# grid views, tool searches, and use of "recently" used tools menu. The -# log_events and log_actions functionality will eventually be merged. -#log_actions = True - -# Sanitize All HTML Tool Output -# By default, all tool output served as 'text/html' will be sanitized -# thoroughly. This can be disabled if you have special tools that require -# unaltered output. -#sanitize_all_html = True - -# Debug enables access to various config options useful for development and -# debugging: use_lint, use_profile, use_printdebug and use_interactive. It -# also causes the files used by PBS/SGE (submission script, output, and error) -# to remain on disk after the job is complete. Debug mode is disabled if -# commented, but is uncommented by default in the sample config. -debug = True - -# Check for WSGI compliance. -#use_lint = False - -# Run the Python profiler on each request. -#use_profile = False - -# Intercept print statements and show them on the returned page. -#use_printdebug = True - -# Enable live debugging in your browser. This should NEVER be enabled on a -# public site. Enabled in the sample config for development. -use_interactive = True - -# Write thread status periodically to 'heartbeat.log', (careful, uses disk -# space rapidly!). Useful to determine why your processes may be consuming a -# lot of CPU. -#use_heartbeat = False - -# Enable the memory debugging interface (careful, negatively impacts server -# performance). -#use_memdump = False - -# -- Data Libraries - -# These library upload options are described in much more detail in the wiki: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files - -# Add an option to the library upload form which allows administrators to -# upload a directory of files. -#library_import_dir = None - -# Add an option to the library upload form which allows authorized -# non-administrators to upload a directory of files. The configured directory -# must contain sub-directories named the same as the non-admin user's Galaxy -# login ( email ). The non-admin user is restricted to uploading files or -# sub-directories of files contained in their directory. -#user_library_import_dir = None - -# Add an option to the admin library upload tool allowing admins to paste -# filesystem paths to files and directories in a box, and these paths will be -# added to a library. Set to True to enable. Please note the security -# implication that this will give Galaxy Admins access to anything your Galaxy -# user has access to. -#allow_library_path_paste = False - -# Users may choose to download multiple files from a library in an archive. By -# default, Galaxy allows users to select from a few different archive formats -# if testing shows that Galaxy is able to create files using these formats. -# Specific formats can be disabled with this option, separate more than one -# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. -#disable_library_comptypes = - -# Some sequencer integration features in beta allow you to automatically -# transfer datasets. This is done using a lightweight transfer manager which -# runs outside of Galaxy (but is spawned by it automatically). Galaxy will -# communicate with this manager over the port specified here. -#transfer_manager_port = 8163 - -# Search data libraries with whoosh -#enable_whoosh_library_search = True -# Whoosh indexes are stored in this directory. -#whoosh_index_dir = database/whoosh_indexes - -# Search data libraries with lucene -#enable_lucene_library_search = False -# maxiumum file size to index for searching, in MB -#fulltext_max_size = 500 -#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger -# base URL of server providing search functionality using lucene -#fulltext_url = http://localhost:8081 - -# -- Users and Security - -# Galaxy encodes various internal values when these values will be output in -# some format (for example, in a URL or cookie). You should set a key to be -# used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. -#id_secret = USING THE DEFAULT IS NOT SECURE! - -# User authentication can be delegated to an upstream proxy server (usually -# Apache). The upstream proxy should set a REMOTE_USER header in the request. -# Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy -#use_remote_user = False - -# If use_remote_user is enabled and your external authentication -# method just returns bare usernames, set a default mail domain to be appended -# to usernames, to become your Galaxy usernames (email addresses). -#remote_user_maildomain = None - -# If use_remote_user is enabled, you can set this to a URL that will log your -# users out. -#remote_user_logout_href = None - -# Administrative users - set this to a comma-separated list of valid Galaxy -# users (email addresses). These users will have access to the Admin section -# of the server, and will have access to create users, groups, roles, -# libraries, and more. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Interface -#admin_users = None - -# Force everyone to log in (disable anonymous access). -#require_login = False - -# Allow unregistered users to create new accounts (otherwise, they will have to -# be created by an admin). -#allow_user_creation = True - -# Allow administrators to delete accounts. -#allow_user_deletion = False - -# Allow administrators to log in as other users (useful for debugging) -#allow_user_impersonation = False - -# Allow users to remove their datasets from disk immediately (otherwise, -# datasets will be removed after a time period specified by an administrator in -# the cleanup scripts run via cron) -#allow_user_dataset_purge = False - -# By default, users' data will be public, but setting this to True will cause -# it to be private. Does not affect existing users and data, only ones created -# after this option is set. Users may still change their default back to -# public. -#new_user_dataset_access_role_default_private = False - -# -- Beta features - -# Object store mode (valid options are: disk, s3, swift, distributed, hierarchical) -#object_store = disk -#os_access_key = <your cloud object store access key> -#os_secret_key = <your cloud object store secret key> -#os_bucket_name = <name of an existing object store bucket or container> -# If using 'swift' object store, you must specify the following connection properties -#os_host = swift.rc.nectar.org.au -#os_port = 8888 -#os_is_secure = False -#os_conn_path = / -# Reduced redundancy can be used only with the 's3' object store -#os_use_reduced_redundancy = False -# Size (in GB) that the cache used by object store should be limited to. -# If the value is not specified, the cache size will be limited only by the -# file system size. The file system location of the cache is considered the -# configuration of the ``file_path`` directive defined above. -#object_store_cache_size = 100 - -# Configuration file for the distributed object store, if object_store = -# distributed. See the sample at distributed_object_store_conf.xml.sample -#distributed_object_store_config_file = None - -# Enable Galaxy to communicate directly with a sequencer -#enable_sequencer_communication = False - -# Enable authentication via OpenID. Allows users to log in to their Galaxy -# account by authenticating with an OpenID provider. -#enable_openid = False -#openid_config_file = openid_conf.xml - -# Optional list of email addresses of API users who can make calls on behalf of -# other users -#api_allow_run_as = None - -# Enable tool tags (associating tools with tags). This has its own option -# since its implementation has a few performance implications on startup for -# large servers. -#enable_tool_tags = False - -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - -# The URL to the myExperiment instance being used (omit scheme but include port) -#myexperiment_url = www.myexperiment.org:80 - -# Enable Galaxy's "Upload via FTP" interface. You'll need to install and -# configure an FTP server (we've used ProFTPd since it can use Galaxy's -# database for authentication) and set the following two options. - -# This should point to a directory containing subdirectories matching users' -# email addresses, where Galaxy will look for files. -#ftp_upload_dir = None - -# This should be the hostname of your FTP server, which will be provided to -# users in the help text. -#ftp_upload_site = None - -# Enable enforcement of quotas. Quotas can be set from the Admin interface. -#enable_quotas = False - -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - -# -- Job Execution - -# To increase performance of job execution and the web interface, you can -# separate Galaxy into multiple processes. There are more than one way to do -# this, and they are explained in detail in the documentation: -# -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… -# -# By default, Galaxy manages and executes jobs from within a single process and -# notifies itself of new jobs via in-memory queues. If you change job_manager -# and job_handlers from their default values, notification will instead be done -# using the `state` and `handler` columns of the job table in the database. - -# Identify the server_name (the string following server: at the top of this -# file) which should be designated as the job manager (only one): -#job_manager = main - -# Identify the server_name(s) which should be designated as job handlers -# (responsible for starting, tracking, finishing, and cleaning up jobs) as a -# comma-separated list. -#job_handlers = main - -# By default, a handler from job_handlers will be selected at random if the -# tool to run does specify a handler below in [galaxy:tool_handlers]. If you -# want certain handlers to only handle jobs for tools/params explicitly -# assigned below, use default_job_handlers to specify which handlers should be -# used for jobs without explicit handlers. -#default_job_handlers = main - -# This enables splitting of jobs into tasks, if specified by the particular tool config. -# This is a new feature and not recommended for production servers yet. -#use_tasked_jobs = False -#local_task_queue_workers = 2 - -# Enable job recovery (if Galaxy is restarted while cluster jobs are running, -# it can "recover" them when it starts). This is not safe to use if you are -# running more than one Galaxy server using the same database. -#enable_job_recovery = True - -# Setting metadata on job outputs to in a separate process (or if using a -# cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the -# hefty expense that setting metadata incurs, your Galaxy process may become -# unresponsive when this operation occurs internally. -#set_metadata_externally = False - -# Although it is fairly reliable, setting metadata can occasionally fail. In -# these instances, you can choose to retry setting it internally or leave it in -# a failed state (since retrying internally may cause the Galaxy process to be -# unresponsive). If this option is set to False, the user will be given the -# option to retry externally, or set metadata manually (when possible). -#retry_metadata_internally = True - -# If (for example) you run on a cluster and your datasets (by default, -# database/files/) are mounted read-only, this option will override tool output -# paths to write outputs to the working directory instead, and the job manager -# will move the outputs to their proper place in the dataset directory on the -# Galaxy server after the job completes. -#outputs_to_working_directory = False - -# If your network filesystem's caching prevents the Galaxy server from seeing -# the job's stdout and stderr files when it completes, you can retry reading -# these files. The job runner will retry the number of times specified below, -# waiting 1 second between tries. For NFS, you may want to try the -noac mount -# option (Linux) or -actimeo=0 (Solaris). -#retry_job_output_collection = 0 - -# Clean up various bits of jobs left on the filesystem after completion. These -# bits include the job working directory, external metadata temporary files, -# and DRM stdout and stderr files (if using a DRM). Possible values are: -# always, onsuccess, never -#cleanup_job = always - -# Number of concurrent jobs to run (local job runner) -#local_job_queue_workers = 5 - -# Jobs can be killed after a certain amount of execution time. Format is in -# hh:mm:ss. Currently only implemented for PBS. -#job_walltime = None - -# Jobs can be killed if any of their outputs grow over a certain size (in -# bytes). 0 for no limit. -#output_size_limit = 0 - -# Jobs can be held back from submission to a runner if a user already has more -# jobs queued or running than the number specified below. This prevents a -# single user from stuffing the queue and preventing other users from being -# able to run jobs. -#user_job_limit = None - -# Clustering Galaxy is not a straightforward process and requires some -# pre-configuration. See the the wiki before attempting to set any of these -# options: -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster - -# Comma-separated list of job runners to start. local is always started. If -# left commented, no jobs will be run on the cluster, even if a cluster URL is -# explicitly defined in the [galaxy:tool_runners] section below. The runners -# currently available are 'pbs' and 'drmaa'. -#start_job_runners = None - -# For sites where all users in Galaxy match users on the system on which Galaxy -# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the -# actual user instead of as the user running the Galaxy server process. For -# details on these options, see the documentation at: -# -# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster -# -#drmaa_external_runjob_script = scripts/drmaa_external_runner.py -#drmaa_external_killjob_script = scripts/drmaa_external_killer.py -#external_chown_script = scripts/external_chown_script.py - -# File to source to set up the environment when running jobs. By default, the -# environment in which the Galaxy server starts is used when running jobs -# locally, and the environment set up per the DRM's submission method and -# policy is used when running jobs on a cluster (try testing with `qsub` on the -# command line). environment_setup_file can be set to the path of a file on -# the cluster that should be sourced by the user to set up the environment -# prior to running tools. This can be especially useful for running jobs as -# the actual user, to remove the need to configure each user's environment -# individually. This only affects cluster jobs, not local jobs. -#environment_setup_file = None - -# The URL for the default runner to use when a tool doesn't explicitly define a -# runner below. -#default_cluster_job_runner = local:/// - -# The cluster runners have their own thread pools used to prepare and finish -# jobs (so that these sometimes lengthy operations do not block normal queue -# operation). The value here is the number of worker threads available to each -# started runner. -#cluster_job_queue_workers = 3 - -# These options are only used when using file staging with PBS. -#pbs_application_server = -#pbs_stage_path = -#pbs_dataset_server = - -# This option allows users to see the full path of datasets via the "View -# Details" option in the history. Administrators can always see this. -#expose_dataset_path = False - -# ---- Per-Tool Job Management ---------------------------------------------- - -# Per-tool job handler and runner overrides. Parameters can be included to define multiple -# runners per tool. E.g. to run Cufflinks jobs initiated from Trackster -# differently than standard Cufflinks jobs: -# -# cufflinks = local:/// -# cufflinks[source@trackster] = local:/// - -[galaxy:tool_handlers] - -# By default, Galaxy will select a handler at random from the list of -# job_handlers set above. You can override as in the following examples: -# -#upload1 = upload_handler -#cufflinks[source@trackster] = realtime_handler - -[galaxy:tool_runners] - -# If not listed here, a tool will run with the runner defined with -# default_cluster_job_runner. These overrides for local:/// are done because -# these tools can fetch data from remote sites, which may not be suitable to -# run on a cluster (if it does not have access to the Internet, for example). - -biomart = local:/// -encode_db1 = local:/// -hbvar = local:/// -microbial_import1 = local:/// -ucsc_table_direct1 = local:/// -ucsc_table_direct_archaea1 = local:/// -ucsc_table_direct_test1 = local:/// -upload1 = local:/// - -# ---- Galaxy Message Queue ------------------------------------------------- - -# Galaxy uses AMQ protocol to receive messages from external sources like -# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -# For Galaxy to receive messages from a message queue the RabbitMQ server has -# to be set up with a user account and other parameters listed below. The 'host' -# and 'port' fields should point to where the RabbitMQ server is running. - -[galaxy_amqp] - -#host = 127.0.0.1 -#port = 5672 -#userid = galaxy -#password = galaxy -#virtual_host = galaxy_messaging_engine -#queue = galaxy_queue -#exchange = galaxy_exchange -#routing_key = bar_code_scanner -#rabbitmqctl_path = /path/to/rabbitmqctl - diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -263,6 +263,9 @@ # as on the user registration and login forms. #terms_url = None +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +qa_url = http://slyfox.bx.psu.edu:8080/ + # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not # documented individually. You can use these paths (or ones in the proxy Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: rmarenco: When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in unverse
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/95d98a265183/ changeset: 95d98a265183 user: rmarenco date: 2012-09-07 02:55:35 summary: When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in unverse affected #: 3 files diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd database/compiled_templates/webapps/galaxy/base_panels.mako.py --- /dev/null +++ b/database/compiled_templates/webapps/galaxy/base_panels.mako.py @@ -0,0 +1,415 @@ +# -*- encoding:ascii -*- +from mako import runtime, filters, cache +UNDEFINED = runtime.UNDEFINED +__M_dict_builtin = dict +__M_locals_builtin = locals +_magic_number = 6 +_modified_time = 1346972736.51736 +_template_filename=u'templates/webapps/galaxy/base_panels.mako' +_template_uri=u'/webapps/galaxy/base_panels.mako' +_template_cache=cache.Cache(__name__, _modified_time) +_source_encoding='ascii' +_exports = ['masthead', 'javascripts', 'title'] + + +def _mako_get_namespace(context, name): + try: + return context.namespaces[(__name__, name)] + except KeyError: + _mako_generate_namespaces(context) + return context.namespaces[(__name__, name)] +def _mako_generate_namespaces(context): + pass +def _mako_inherit(template, context): + _mako_generate_namespaces(context) + return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) +def render_body(context,**pageargs): + context.caller_stack._push_frame() + try: + __M_locals = __M_dict_builtin(pageargs=pageargs) + __M_writer = context.writer() + # SOURCE LINE 1 + __M_writer(u'\n\n') + # SOURCE LINE 4 + __M_writer(u'\n\n') + # SOURCE LINE 8 + __M_writer(u'\n\n') + # SOURCE LINE 232 + __M_writer(u'\n') + return '' + finally: + context.caller_stack._pop_frame() + + +def render_masthead(context): + context.caller_stack._push_frame() + try: + AssertionError = context.get('AssertionError', UNDEFINED) + h = context.get('h', UNDEFINED) + app = context.get('app', UNDEFINED) + util = context.get('util', UNDEFINED) + def tab(id,display,href,target='_parent',visible=True,extra_class='',menu_options=None): + context.caller_stack._push_frame() + try: + self = context.get('self', UNDEFINED) + len = context.get('len', UNDEFINED) + __M_writer = context.writer() + # SOURCE LINE 19 + __M_writer(u'\n') + # SOURCE LINE 22 + __M_writer(u' \n ') + # SOURCE LINE 23 + + cls = "" + a_cls = "" + extra = "" + if extra_class: + cls += " " + extra_class + if self.active_view == id: + cls += " active" + if menu_options: + cls += " dropdown" + a_cls += " dropdown-toggle" + extra = "<b class='caret'></b>" + style = "" + if not visible: + style = "display: none;" + + + # SOURCE LINE 38 + __M_writer(u'\n <li class="') + # SOURCE LINE 39 + __M_writer(unicode(cls)) + __M_writer(u'" style="') + __M_writer(unicode(style)) + __M_writer(u'">\n') + # SOURCE LINE 40 + if href: + # SOURCE LINE 41 + __M_writer(u' <a class="') + __M_writer(unicode(a_cls)) + __M_writer(u'" data-toggle="dropdown" target="') + __M_writer(unicode(target)) + __M_writer(u'" href="') + __M_writer(unicode(href)) + __M_writer(u'">') + __M_writer(unicode(display)) + __M_writer(unicode(extra)) + __M_writer(u'</a>\n') + # SOURCE LINE 42 + else: + # SOURCE LINE 43 + __M_writer(u' <a class="') + __M_writer(unicode(a_cls)) + __M_writer(u'" data-toggle="dropdown">') + __M_writer(unicode(display)) + __M_writer(unicode(extra)) + __M_writer(u'</a>\n') + pass + # SOURCE LINE 45 + if menu_options: + # SOURCE LINE 46 + __M_writer(u' <ul class="dropdown-menu">\n') + # SOURCE LINE 47 + for menu_item in menu_options: + # SOURCE LINE 48 + if not menu_item: + # SOURCE LINE 49 + __M_writer(u' <li class="divider"></li>\n') + # SOURCE LINE 50 + else: + # SOURCE LINE 51 + __M_writer(u' <li>\n') + # SOURCE LINE 52 + if len ( menu_item ) == 1: + # SOURCE LINE 53 + __M_writer(u' ') + __M_writer(unicode(menu_item[0])) + __M_writer(u'\n') + # SOURCE LINE 54 + elif len ( menu_item ) == 2: + # SOURCE LINE 55 + __M_writer(u' ') + name, link = menu_item + + __M_writer(u'\n <a href="') + # SOURCE LINE 56 + __M_writer(unicode(link)) + __M_writer(u'">') + __M_writer(unicode(name)) + __M_writer(u'</a>\n') + # SOURCE LINE 57 + else: + # SOURCE LINE 58 + __M_writer(u' ') + name, link, target = menu_item + + __M_writer(u'\n <a target="') + # SOURCE LINE 59 + __M_writer(unicode(target)) + __M_writer(u'" href="') + __M_writer(unicode(link)) + __M_writer(u'">') + __M_writer(unicode(name)) + __M_writer(u'</a>\n') + pass + # SOURCE LINE 61 + __M_writer(u' </li>\n') + pass + pass + # SOURCE LINE 64 + __M_writer(u' </ul>\n') + pass + # SOURCE LINE 66 + __M_writer(u' </li>\n ') + return '' + finally: + context.caller_stack._pop_frame() + trans = context.get('trans', UNDEFINED) + _ = context.get('_', UNDEFINED) + __M_writer = context.writer() + # SOURCE LINE 11 + __M_writer(u'\n\n') + # SOURCE LINE 14 + __M_writer(u' <div style="position: relative; right: -50%; float: left;">\n <div style="display: block; position: relative; right: 50%;">\n\n <ul class="nav" border="0" cellspacing="0">\n \n ') + # SOURCE LINE 67 + __M_writer(u'\n\n') + # SOURCE LINE 70 + __M_writer(u' ') + __M_writer(unicode(tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) ))) + __M_writer(u'\n \n') + # SOURCE LINE 73 + __M_writer(u' ') + __M_writer(unicode(tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) ))) + __M_writer(u'\n \n') + # SOURCE LINE 76 + __M_writer(u' ') + + menu_options = [ + [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], + None, + [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], + [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ], + [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ], + [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] + ] + tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) + + + # SOURCE LINE 86 + __M_writer(u'\n \n') + # SOURCE LINE 89 + __M_writer(u' ') + + menu_options = [ + [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ], + [ _('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 or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) + + + # SOURCE LINE 96 + __M_writer(u'\n\n') + # SOURCE LINE 99 + __M_writer(u' ') + + menu_options = [ + [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] + ] + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) + + + # SOURCE LINE 105 + __M_writer(u'\n\n') + # SOURCE LINE 108 + if app.config.get_bool( 'enable_cloud_launch', False ): + # SOURCE LINE 109 + __M_writer(u' ') + + menu_options = [ + [_('New Cloud Cluster'), h.url_for( controller='/cloudlaunch', action='index' ) ], + ] + tab( "cloud", _("Cloud"), h.url_for( controller='/cloudlaunch', action='index'), menu_options=menu_options ) + + + # SOURCE LINE 114 + __M_writer(u'\n') + pass + # SOURCE LINE 116 + __M_writer(u'\n') + # SOURCE LINE 118 + __M_writer(u' ') + __M_writer(unicode(tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) ))) + __M_writer(u'\n \n') + # SOURCE LINE 121 + __M_writer(u' ') + + menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "galaxy_main" ], + [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], + [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], + [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], + [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + ] + if app.config.get( 'terms_url', None ) is not None: + menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) + tab( "help", _("Help"), None, menu_options=menu_options) + + + # SOURCE LINE 132 + __M_writer(u'\n \n') + # SOURCE LINE 135 + __M_writer(u' ') + + # Menu for user who is not logged in. + menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] + if app.config.allow_user_creation: + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + extra_class = "loggedout-only" + visible = ( trans.user == None ) + tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) + + # Menu for user who is logged in. + if trans.user: + email = trans.user.email + else: + email = "" + menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] + if app.config.use_remote_user: + if app.config.remote_user_logout_href: + menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) + else: + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) + if app.config.require_login: + logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) + else: + logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' ) + menu_options.append( [ 'Logout', logout_url, "_top" ] ) + menu_options.append( None ) + menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) + menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) + menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) + menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + if app.config.use_remote_user: + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + + extra_class = "loggedin-only" + visible = ( trans.user != None ) + tab( "user", "User", None, visible=visible, menu_options=menu_options ) + + + # SOURCE LINE 172 + __M_writer(u'\n \n') + # SOURCE LINE 176 + __M_writer(u' </ul>\n\n </div>\n </div>\n \n') + # SOURCE LINE 182 + __M_writer(u' <div class="title">\n <a href="') + # SOURCE LINE 183 + __M_writer(unicode(h.url_for( app.config.get( 'logo_url', '/' ) ))) + __M_writer(u'">\n <img border="0" src="') + # SOURCE LINE 184 + __M_writer(unicode(h.url_for('/static/images/galaxyIcon_noText.png'))) + __M_writer(u'">\n Galaxy\n') + # SOURCE LINE 186 + if app.config.brand: + # SOURCE LINE 187 + __M_writer(u' <span>/ ') + __M_writer(unicode(app.config.brand)) + __M_writer(u'</span>\n') + pass + # SOURCE LINE 189 + __M_writer(u' </a>\n </div>\n\n') + # SOURCE LINE 193 + __M_writer(u' ') + + bar_style = "quota-meter-bar" + usage = 0 + percent = 0 + quota = None + try: + usage = trans.app.quota_agent.get_usage( trans=trans ) + quota = trans.app.quota_agent.get_quota( trans.user ) + percent = trans.app.quota_agent.get_percent( usage=usage, quota=quota ) + if percent is not None: + if percent >= 100: + bar_style += " quota-meter-bar-error" + elif percent >= 85: + bar_style += " quota-meter-bar-warn" + else: + percent = 0 + except AssertionError: + pass # Probably no history yet + tooltip = None + if not trans.user and quota and trans.app.config.allow_user_creation: + if trans.app.quota_agent.default_registered_quota is None or trans.app.quota_agent.default_unregistered_quota < trans.app.quota_agent.default_registered_quota: + tooltip = "Your disk quota is %s. You can increase your quota by registering a Galaxy account." % util.nice_size( quota ) + + + # SOURCE LINE 215 + __M_writer(u'\n\n <div class="quota-meter-container">\n') + # SOURCE LINE 218 + if tooltip: + # SOURCE LINE 219 + __M_writer(u' <div id="quota-meter" class="quota-meter tooltip" title="') + __M_writer(unicode(tooltip)) + __M_writer(u'">\n') + # SOURCE LINE 220 + else: + # SOURCE LINE 221 + __M_writer(u' <div id="quota-meter" class="quota-meter">\n') + pass + # SOURCE LINE 223 + __M_writer(u' <div id="quota-meter-bar" class="') + __M_writer(unicode(bar_style)) + __M_writer(u'" style="width: ') + __M_writer(unicode(percent)) + __M_writer(u'px;"></div>\n') + # SOURCE LINE 224 + if quota is not None: + # SOURCE LINE 225 + __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') + __M_writer(unicode(percent)) + __M_writer(u'%</div>\n') + # SOURCE LINE 226 + else: + # SOURCE LINE 227 + __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') + __M_writer(unicode(util.nice_size( usage ))) + __M_writer(u'</div>\n') + pass + # SOURCE LINE 229 + __M_writer(u' </div>\n </div>\n \n') + return '' + finally: + context.caller_stack._pop_frame() + + +def render_javascripts(context): + context.caller_stack._push_frame() + try: + parent = context.get('parent', UNDEFINED) + __M_writer = context.writer() + # SOURCE LINE 6 + __M_writer(u'\n ') + # SOURCE LINE 7 + __M_writer(unicode(parent.javascripts())) + __M_writer(u'\n') + return '' + finally: + context.caller_stack._pop_frame() + + +def render_title(context): + context.caller_stack._push_frame() + try: + __M_writer = context.writer() + # SOURCE LINE 4 + __M_writer(u'Galaxy') + return '' + finally: + context.caller_stack._pop_frame() + + diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -302,8 +302,8 @@ ${tool.name} ${tool_version_select_field.get_html()} %endif  - <a href="http://slyfox.bx.psu.edu:8081/new/post/" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> - <a href="http://slyfox.bx.psu.edu:8081/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> + <a href="http://slyfox.bx.psu.edu:8080/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="http://slyfox.bx.psu.edu:8080/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a></div><div class="toolFormBody"> diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd universe_wsgi.ini --- /dev/null +++ b/universe_wsgi.ini @@ -0,0 +1,753 @@ +# +# Galaxy is configured by default to be useable in a single-user development +# environment. To tune the application for a multi-user production +# environment, see the documentation at: +# +# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server +# + +# Throughout this sample configuration file, except where stated otherwise, +# uncommented values override the default if left unset, whereas commented +# values are set to the default value. +# Examples of many of these options are explained in more detail in the wiki: +# +# http://wiki.g2.bx.psu.edu/Admin/Config +# +# Config hackers are encouraged to check there before asking for help. + +# ---- HTTP Server ---------------------------------------------------------- + +# Configuration of the internal HTTP server. + +[server:main] + +# The internal HTTP server to use. Currently only Paste is provided. This +# option is required. +use = egg:Paste#http + +# The port on which to listen. +#port = 8080 + +# The address on which to listen. By default, only listen to localhost (Galaxy +# will not be accessible over the network). Use '0.0.0.0' to listen on all +# available network interfaces. +#host = 127.0.0.1 + +# Use a threadpool for the web server instead of creating a thread for each +# request. +use_threadpool = True + +# Number of threads in the web server thread pool. +#threadpool_workers = 10 + +# ---- Filters -------------------------------------------------------------- + +# Filters sit between Galaxy and the HTTP server. + +# These filters are disabled by default. They can be enabled with +# 'filter-with' in the [app:main] section below. + +# Define the gzip filter. +[filter:gzip] +use = egg:Paste#gzip + +# Define the proxy-prefix filter. +[filter:proxy-prefix] +use = egg:PasteDeploy#prefix +prefix = /galaxy + +# ---- Galaxy --------------------------------------------------------------- + +# Configuration of the Galaxy application. + +[app:main] + +# -- Application and filtering + +# The factory for the WSGI application. This should not be changed. +paste.app_factory = galaxy.web.buildapp:app_factory + +# If not running behind a proxy server, you may want to enable gzip compression +# to decrease the size of data transferred over the network. If using a proxy +# server, please enable gzip compression there instead. +#filter-with = gzip + +# If running behind a proxy server and Galaxy is served from a subdirectory, +# enable the proxy-prefix filter and set the prefix in the +# [filter:proxy-prefix] section above. +#filter-with = proxy-prefix + +# If proxy-prefix is enabled and you're running more than one Galaxy instance +# behind one hostname, you will want to set this to the same path as the prefix +# in the filter above. This value becomes the "path" attribute set in the +# cookie so the cookies from each instance will not clobber each other. +#cookie_path = None + +# -- Database + +# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You +# may use a SQLAlchemy connection string to specify an external database +# instead. This string takes many options which are explained in detail in the +# config file documentation. +#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# If the server logs errors about not having enough database pool connections, +# you will want to increase these values, or consider running more Galaxy +# processes. +#database_engine_option_pool_size = 5 +#database_engine_option_max_overflow = 10 + +# If using MySQL and the server logs the error "MySQL server has gone away", +# you will want to set this to some positive value (7200 should work). +#database_engine_option_pool_recycle = -1 + +# If large database query results are causing memory or response time issues in +# the Galaxy process, leave the result on the server instead. This option is +# only available for PostgreSQL and is highly recommended. +#database_engine_option_server_side_cursors = False + +# Create only one connection to the database per thread, to reduce the +# connection overhead. Recommended when not using SQLite: +#database_engine_option_strategy = threadlocal + +# Log all database transactions, can be useful for debugging and performance +# profiling. Logging is done via Python's 'logging' module under the qualname +# 'galaxy.model.orm.logging_connection_proxy' +#database_query_profiling_proxy = False + +# -- Files and directories + +# Path where genome builds are stored. This defaults to tool-data/genome +#genome_data_path = tool-data/genome + +# URL for rsync server to download pre-built indexes. +#rsync_url = rsync://scofield.bx.psu.edu/indexes + +# Dataset files are stored in this directory. +#file_path = database/files + +# Temporary files are stored in this directory. +#new_file_path = database/tmp + +# Tool config files, defines what tools are available in Galaxy. +# Tools can be locally developed or installed from Galaxy tool sheds. +#tool_config_file = tool_conf.xml,shed_tool_conf.xml + +# Default path to the directory containing the tools defined in tool_conf.xml. +# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. +#tool_path = tools + +# Path to the directory in which managed tool dependencies are placed. To use +# the dependency system, see the documentation at: +# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies +#tool_dependency_dir = None + +# Enable automatic polling of relative tool sheds to see if any updates +# are available for installed repositories. Ideally only one Galaxy +# server process should be able to check for repository updates. The +# setting for hours_between_check should be an integer between 1 and 24. +#enable_tool_shed_check = False +#hours_between_check = 12 + +# Directory where data used by tools is located, see the samples in that +# directory and the wiki for help: +# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration +#tool_data_path = tool-data + +# Directory where chrom len files are kept, currently mainly used by trackster +#len_file_path = tool-data/shared/ucsc/chrom + +# Datatypes config file, defines what data (file) types are available in +# Galaxy. +#datatypes_config_file = datatypes_conf.xml + +# Each job is given a unique empty directory as its current working directory. +# This option defines in what parent directory those directories will be +# created. +#job_working_directory = database/job_working_directory + +# If using a cluster, Galaxy will write job scripts and stdout/stderr to this +# directory. +#cluster_files_directory = database/pbs + +# External service types config file, defines what types of external_services configurations +# are available in Galaxy. +#external_service_type_config_file = external_service_types_conf.xml + +# Path to the directory containing the external_service_types defined in the config. +#external_service_type_path = external_service_types + +# Tools with a number of outputs not known until runtime can write these +# outputs to a directory for collection by Galaxy when the job is done. +# Previously, this directory was new_file_path, but using one global directory +# can cause performance problems, so using job_working_directory ('.' or cwd +# when a job is run) is encouraged. By default, both are checked to avoid +# breaking existing tools. +#collect_outputs_from = new_file_path,job_working_directory + +# -- Mail and notification + +# Galaxy sends mail for various things: Subscribing users to the mailing list +# if they request it, emailing password resets, notification from the Galaxy +# Sample Tracking system, and reporting dataset errors. To do this, it needs +# to send mail through an SMTP server, which you may define here (host:port). +# Galaxy will automatically try STARTTLS but will continue upon failure. +#smtp_server = None + +# If your SMTP server requires a username and password, you can provide them +# here (password in cleartext here, but if your server supports STARTTLS it +# will be sent over the network encrypted). +#smtp_username = None +#smtp_password = None + +# On the user registration form, users may choose to join the mailing list. +# This is the address of the list they'll be subscribed to. +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu + +# Datasets in an error state include a link to report the error. Those reports +# will be sent to this address. Error reports are disabled if no address is set. +#error_email_to = None + +# -- Display sites + +# Galaxy can display data at various external browsers. These options specify +# which browsers should be available. URLs and builds available at these +# browsers are defined in the specifield files. + +# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt +#ucsc_display_sites = main,test,archaea,ucla + +# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt +#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 + +# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt +#genetrack_display_sites = main,test + +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + +# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. + +use_nglims = False +nglims_config_file = tool-data/nglims.yaml + +# -- UI Localization + +# Append "/{brand}" to the "Galaxy" text in the masthead. +#brand = None + +# The URL linked by the "Galaxy/brand" text. +#logo_url = / + +# The URL linked by the "Galaxy Wiki" link in the "Help" menu. +#wiki_url = http://wiki.g2.bx.psu.edu/ + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.g2.bx.psu.edu/Support + +# The URL linked by the "How to Cite..." link in the "Help" menu. +#citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy + +# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well +# as on the user registration and login forms. +#terms_url = None + +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +qa_url = http://slyfox.bx.psu.edu:8080/ + +# Serve static content, which must be enabled if you're not serving it via a +# proxy server. These options should be self explanatory and so are not +# documented individually. You can use these paths (or ones in the proxy +# server) to point to your own styles. +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue +static_robots_txt = %(here)s/static/robots.txt + +# Pack javascript at launch (/static/scripts/*.js) +# This only happens if the modified timestamp of the source .js is newer +# than the version (if it exists) in /static/scripts/packed/ +# Note that this requires java > 1.4 for executing yuicompressor.jar +#pack_scripts = False + +# Enable Cloud Launch + +#enable_cloud_launch = False + +# -- Advanced proxy features + +# For help on configuring the Advanced proxy features, see: +# http://usegalaxy.org/production + +# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set +# this to True to inform Galaxy that mod_xsendfile is enabled upstream. +#apache_xsendfile = False + +# The same download handling can be done by nginx using X-Accel-Redirect. This +# should be set to the path defined in the nginx config as an internal redirect +# with access to Galaxy's data files (see documentation linked above). +#nginx_x_accel_redirect_base = False + +# nginx can make use of mod_zip to create zip files containing multiple library +# files. If using X-Accel-Redirect, this can be the same value as that option. +#nginx_x_archive_files_base = False + +# If using compression in the upstream proxy server, use this option to disable +# gzipping of library .tar.gz and .zip archives, since the proxy server will do +# it faster on the fly. +#upstream_gzip = False + +# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. +# Configuration for this is complex and explained in detail in the +# documentation linked above. The upload store is a temporary directory in +# which files uploaded by the upload module will be placed. +#nginx_upload_store = False + +# This value overrides the action set on the file upload form, e.g. the web +# path where the nginx_upload_module has been configured to intercept upload +# requests. +#nginx_upload_path = False + +# -- Logging and Debugging + +# Verbosity of console log messages. Acceptable values can be found here: +# http://docs.python.org/library/logging.html#logging-levels +#log_level = DEBUG + +# Print database operations to the server log (warning, quite verbose!). +#database_engine_option_echo = False + +# Print database pool operations to the server log (warning, quite verbose!). +#database_engine_option_echo_pool = False + +# Turn on logging of application events and some user events to the database. +#log_events = True + +# Turn on logging of user actions to the database. Actions currently logged are +# grid views, tool searches, and use of "recently" used tools menu. The +# log_events and log_actions functionality will eventually be merged. +#log_actions = True + +# Sanitize All HTML Tool Output +# By default, all tool output served as 'text/html' will be sanitized +# thoroughly. This can be disabled if you have special tools that require +# unaltered output. +#sanitize_all_html = True + +# Debug enables access to various config options useful for development and +# debugging: use_lint, use_profile, use_printdebug and use_interactive. It +# also causes the files used by PBS/SGE (submission script, output, and error) +# to remain on disk after the job is complete. Debug mode is disabled if +# commented, but is uncommented by default in the sample config. +debug = True + +# Check for WSGI compliance. +#use_lint = False + +# Run the Python profiler on each request. +#use_profile = False + +# Intercept print statements and show them on the returned page. +#use_printdebug = True + +# Enable live debugging in your browser. This should NEVER be enabled on a +# public site. Enabled in the sample config for development. +use_interactive = True + +# Write thread status periodically to 'heartbeat.log', (careful, uses disk +# space rapidly!). Useful to determine why your processes may be consuming a +# lot of CPU. +#use_heartbeat = False + +# Enable the memory debugging interface (careful, negatively impacts server +# performance). +#use_memdump = False + +# -- Data Libraries + +# These library upload options are described in much more detail in the wiki: +# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files + +# Add an option to the library upload form which allows administrators to +# upload a directory of files. +#library_import_dir = None + +# Add an option to the library upload form which allows authorized +# non-administrators to upload a directory of files. The configured directory +# must contain sub-directories named the same as the non-admin user's Galaxy +# login ( email ). The non-admin user is restricted to uploading files or +# sub-directories of files contained in their directory. +#user_library_import_dir = None + +# Add an option to the admin library upload tool allowing admins to paste +# filesystem paths to files and directories in a box, and these paths will be +# added to a library. Set to True to enable. Please note the security +# implication that this will give Galaxy Admins access to anything your Galaxy +# user has access to. +#allow_library_path_paste = False + +# Users may choose to download multiple files from a library in an archive. By +# default, Galaxy allows users to select from a few different archive formats +# if testing shows that Galaxy is able to create files using these formats. +# Specific formats can be disabled with this option, separate more than one +# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. +#disable_library_comptypes = + +# Some sequencer integration features in beta allow you to automatically +# transfer datasets. This is done using a lightweight transfer manager which +# runs outside of Galaxy (but is spawned by it automatically). Galaxy will +# communicate with this manager over the port specified here. +#transfer_manager_port = 8163 + +# Search data libraries with whoosh +#enable_whoosh_library_search = True +# Whoosh indexes are stored in this directory. +#whoosh_index_dir = database/whoosh_indexes + +# Search data libraries with lucene +#enable_lucene_library_search = False +# maxiumum file size to index for searching, in MB +#fulltext_max_size = 500 +#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger +# base URL of server providing search functionality using lucene +#fulltext_url = http://localhost:8081 + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +#id_secret = USING THE DEFAULT IS NOT SECURE! + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy +#use_remote_user = False + +# If use_remote_user is enabled and your external authentication +# method just returns bare usernames, set a default mail domain to be appended +# to usernames, to become your Galaxy usernames (email addresses). +#remote_user_maildomain = None + +# If use_remote_user is enabled, you can set this to a URL that will log your +# users out. +#remote_user_logout_href = None + +# Administrative users - set this to a comma-separated list of valid Galaxy +# users (email addresses). These users will have access to the Admin section +# of the server, and will have access to create users, groups, roles, +# libraries, and more. For more information, see: +# http://wiki.g2.bx.psu.edu/Admin/Interface +#admin_users = None + +# Force everyone to log in (disable anonymous access). +#require_login = False + +# Allow unregistered users to create new accounts (otherwise, they will have to +# be created by an admin). +#allow_user_creation = True + +# Allow administrators to delete accounts. +#allow_user_deletion = False + +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + +# Allow users to remove their datasets from disk immediately (otherwise, +# datasets will be removed after a time period specified by an administrator in +# the cleanup scripts run via cron) +#allow_user_dataset_purge = False + +# By default, users' data will be public, but setting this to True will cause +# it to be private. Does not affect existing users and data, only ones created +# after this option is set. Users may still change their default back to +# public. +#new_user_dataset_access_role_default_private = False + +# -- Beta features + +# Object store mode (valid options are: disk, s3, swift, distributed, hierarchical) +#object_store = disk +#os_access_key = <your cloud object store access key> +#os_secret_key = <your cloud object store secret key> +#os_bucket_name = <name of an existing object store bucket or container> +# If using 'swift' object store, you must specify the following connection properties +#os_host = swift.rc.nectar.org.au +#os_port = 8888 +#os_is_secure = False +#os_conn_path = / +# Reduced redundancy can be used only with the 's3' object store +#os_use_reduced_redundancy = False +# Size (in GB) that the cache used by object store should be limited to. +# If the value is not specified, the cache size will be limited only by the +# file system size. The file system location of the cache is considered the +# configuration of the ``file_path`` directive defined above. +#object_store_cache_size = 100 + +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + +# Enable Galaxy to communicate directly with a sequencer +#enable_sequencer_communication = False + +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False +#openid_config_file = openid_conf.xml + +# Optional list of email addresses of API users who can make calls on behalf of +# other users +#api_allow_run_as = None + +# Enable tool tags (associating tools with tags). This has its own option +# since its implementation has a few performance implications on startup for +# large servers. +#enable_tool_tags = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# The URL to the myExperiment instance being used (omit scheme but include port) +#myexperiment_url = www.myexperiment.org:80 + +# Enable Galaxy's "Upload via FTP" interface. You'll need to install and +# configure an FTP server (we've used ProFTPd since it can use Galaxy's +# database for authentication) and set the following two options. + +# This should point to a directory containing subdirectories matching users' +# email addresses, where Galaxy will look for files. +#ftp_upload_dir = None + +# This should be the hostname of your FTP server, which will be provided to +# users in the help text. +#ftp_upload_site = None + +# Enable enforcement of quotas. Quotas can be set from the Admin interface. +#enable_quotas = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# -- Job Execution + +# To increase performance of job execution and the web interface, you can +# separate Galaxy into multiple processes. There are more than one way to do +# this, and they are explained in detail in the documentation: +# +# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… +# +# By default, Galaxy manages and executes jobs from within a single process and +# notifies itself of new jobs via in-memory queues. If you change job_manager +# and job_handlers from their default values, notification will instead be done +# using the `state` and `handler` columns of the job table in the database. + +# Identify the server_name (the string following server: at the top of this +# file) which should be designated as the job manager (only one): +#job_manager = main + +# Identify the server_name(s) which should be designated as job handlers +# (responsible for starting, tracking, finishing, and cleaning up jobs) as a +# comma-separated list. +#job_handlers = main + +# By default, a handler from job_handlers will be selected at random if the +# tool to run does specify a handler below in [galaxy:tool_handlers]. If you +# want certain handlers to only handle jobs for tools/params explicitly +# assigned below, use default_job_handlers to specify which handlers should be +# used for jobs without explicit handlers. +#default_job_handlers = main + +# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This is a new feature and not recommended for production servers yet. +#use_tasked_jobs = False +#local_task_queue_workers = 2 + +# Enable job recovery (if Galaxy is restarted while cluster jobs are running, +# it can "recover" them when it starts). This is not safe to use if you are +# running more than one Galaxy server using the same database. +#enable_job_recovery = True + +# Setting metadata on job outputs to in a separate process (or if using a +# cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the +# hefty expense that setting metadata incurs, your Galaxy process may become +# unresponsive when this operation occurs internally. +#set_metadata_externally = False + +# Although it is fairly reliable, setting metadata can occasionally fail. In +# these instances, you can choose to retry setting it internally or leave it in +# a failed state (since retrying internally may cause the Galaxy process to be +# unresponsive). If this option is set to False, the user will be given the +# option to retry externally, or set metadata manually (when possible). +#retry_metadata_internally = True + +# If (for example) you run on a cluster and your datasets (by default, +# database/files/) are mounted read-only, this option will override tool output +# paths to write outputs to the working directory instead, and the job manager +# will move the outputs to their proper place in the dataset directory on the +# Galaxy server after the job completes. +#outputs_to_working_directory = False + +# If your network filesystem's caching prevents the Galaxy server from seeing +# the job's stdout and stderr files when it completes, you can retry reading +# these files. The job runner will retry the number of times specified below, +# waiting 1 second between tries. For NFS, you may want to try the -noac mount +# option (Linux) or -actimeo=0 (Solaris). +#retry_job_output_collection = 0 + +# Clean up various bits of jobs left on the filesystem after completion. These +# bits include the job working directory, external metadata temporary files, +# and DRM stdout and stderr files (if using a DRM). Possible values are: +# always, onsuccess, never +#cleanup_job = always + +# Number of concurrent jobs to run (local job runner) +#local_job_queue_workers = 5 + +# Jobs can be killed after a certain amount of execution time. Format is in +# hh:mm:ss. Currently only implemented for PBS. +#job_walltime = None + +# Jobs can be killed if any of their outputs grow over a certain size (in +# bytes). 0 for no limit. +#output_size_limit = 0 + +# Jobs can be held back from submission to a runner if a user already has more +# jobs queued or running than the number specified below. This prevents a +# single user from stuffing the queue and preventing other users from being +# able to run jobs. +#user_job_limit = None + +# Clustering Galaxy is not a straightforward process and requires some +# pre-configuration. See the the wiki before attempting to set any of these +# options: +# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster + +# Comma-separated list of job runners to start. local is always started. If +# left commented, no jobs will be run on the cluster, even if a cluster URL is +# explicitly defined in the [galaxy:tool_runners] section below. The runners +# currently available are 'pbs' and 'drmaa'. +#start_job_runners = None + +# For sites where all users in Galaxy match users on the system on which Galaxy +# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the +# actual user instead of as the user running the Galaxy server process. For +# details on these options, see the documentation at: +# +# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster +# +#drmaa_external_runjob_script = scripts/drmaa_external_runner.py +#drmaa_external_killjob_script = scripts/drmaa_external_killer.py +#external_chown_script = scripts/external_chown_script.py + +# File to source to set up the environment when running jobs. By default, the +# environment in which the Galaxy server starts is used when running jobs +# locally, and the environment set up per the DRM's submission method and +# policy is used when running jobs on a cluster (try testing with `qsub` on the +# command line). environment_setup_file can be set to the path of a file on +# the cluster that should be sourced by the user to set up the environment +# prior to running tools. This can be especially useful for running jobs as +# the actual user, to remove the need to configure each user's environment +# individually. This only affects cluster jobs, not local jobs. +#environment_setup_file = None + +# The URL for the default runner to use when a tool doesn't explicitly define a +# runner below. +#default_cluster_job_runner = local:/// + +# The cluster runners have their own thread pools used to prepare and finish +# jobs (so that these sometimes lengthy operations do not block normal queue +# operation). The value here is the number of worker threads available to each +# started runner. +#cluster_job_queue_workers = 3 + +# These options are only used when using file staging with PBS. +#pbs_application_server = +#pbs_stage_path = +#pbs_dataset_server = + +# This option allows users to see the full path of datasets via the "View +# Details" option in the history. Administrators can always see this. +#expose_dataset_path = False + +# ---- Per-Tool Job Management ---------------------------------------------- + +# Per-tool job handler and runner overrides. Parameters can be included to define multiple +# runners per tool. E.g. to run Cufflinks jobs initiated from Trackster +# differently than standard Cufflinks jobs: +# +# cufflinks = local:/// +# cufflinks[source@trackster] = local:/// + +[galaxy:tool_handlers] + +# By default, Galaxy will select a handler at random from the list of +# job_handlers set above. You can override as in the following examples: +# +#upload1 = upload_handler +#cufflinks[source@trackster] = realtime_handler + +[galaxy:tool_runners] + +# If not listed here, a tool will run with the runner defined with +# default_cluster_job_runner. These overrides for local:/// are done because +# these tools can fetch data from remote sites, which may not be suitable to +# run on a cluster (if it does not have access to the Internet, for example). + +biomart = local:/// +encode_db1 = local:/// +hbvar = local:/// +microbial_import1 = local:/// +ucsc_table_direct1 = local:/// +ucsc_table_direct_archaea1 = local:/// +ucsc_table_direct_test1 = local:/// +upload1 = local:/// + +# ---- Galaxy Message Queue ------------------------------------------------- + +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +[galaxy_amqp] + +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +#rabbitmqctl_path = /path/to/rabbitmqctl + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rmarenco: Added links to BioStar in the Help Menu and in tool forms
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2f684dfa8d47/ changeset: 2f684dfa8d47 user: rmarenco date: 2012-09-07 01:08:27 summary: Added links to BioStar in the Help Menu and in tool forms affected #: 6 files diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1783,3 +1783,17 @@ .opacity(80); } } + +.icon-button.general-question{ + background: url(question-octagon-frame.png) no-repeat 0px 0px; + margin-top: 3px; + margin-right: 4px; + float: right; +} + +.icon-button.tag-question{ + background: url(question-balloon.png) no-repeat 0px 0px; + margin-top: 3px; + margin-right: 4px; + float: right; +} diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -910,3 +910,5 @@ div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} .text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.3;filter:alpha(opacity=30);opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} +.icon-button.general-question{background:url(question-octagon-frame.png) no-repeat 0px 0px;margin-top:3px;margin-right:4px;float:right;} +.icon-button.tag-question{background:url(question-balloon.png) no-repeat 0px 0px;margin-top:3px;margin-right:4px;float:right;} diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/blue/question-balloon.png Binary file static/june_2007_style/blue/question-balloon.png has changed diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/blue/question-octagon-frame.png Binary file static/june_2007_style/blue/question-octagon-frame.png has changed diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -12,7 +12,7 @@ </%def><%def name="javascripts()"> - ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage" )} + ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage", "libs/bootstrap" )} <script type="text/javascript"> $(function() { $(window).bind("refresh_on_change", function() { @@ -282,19 +282,30 @@ tool_url = tool.action[0] + h.url_for(tool.action[1]) %> +<% + # Set the tool name in lower case + low_tool_name = tool.name.lower() +%> + %if tool_id_version_message: ${render_msg( tool_id_version_message, 'warning' )} %endif <div class="toolForm" id="${tool.id}"><form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> - %elif not tool_version_select_field: - <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> - %else: - <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()}</div> - %endif + <div class="toolFormTitle"> + %if tool.has_multiple_pages: + ${tool.name} (step ${tool_state.page+1} of ${tool.npages}) + %elif not tool_version_select_field: + ${tool.name} (version ${tool.version}) + %else: + ${tool.name} ${tool_version_select_field.get_html()} + %endif +  + <a href="http://slyfox.bx.psu.edu:8081/new/post/" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="http://slyfox.bx.psu.edu:8081/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> +  + </div><div class="toolFormBody"><input type="hidden" name="refresh" value="refresh"><input type="hidden" name="tool_id" value="${tool.id}"> diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -120,6 +120,7 @@ ## Help tab. <% menu_options = [ + [_('Galaxy Q&A'), app.config.get( "q&a", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix bug introduced 2 commits ago.
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5c09dfcc62c2/ changeset: 5c09dfcc62c2 user: greg date: 2012-09-06 22:27:35 summary: Fix bug introduced 2 commits ago. affected #: 1 file diff -r f0fe84f46793708dc5eac02442e2e9a72e1d9c70 -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1427,10 +1427,7 @@ tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) invalid_file_tups = [] - if tool is None: - if not valid: - invalid_file_tups = [ ( name, error_message ) ] - else: + if tool: invalid_file_tups = check_tool_input_params( trans.app, repository.repo_path, tool_config, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix a mis-named variable.
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f0fe84f46793/ changeset: f0fe84f46793 user: greg date: 2012-09-06 22:22:57 summary: Fix a mis-named variable. affected #: 1 file diff -r 42e544d00e75be44887b17f6985bcb251573e1de -r f0fe84f46793708dc5eac02442e2e9a72e1d9c70 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -266,7 +266,7 @@ if name.endswith( '.sample' ): relative_path = os.path.join( root, name ) copy_sample_file( trans.app, relative_path, dest_path=dest_path ) - sample_files_copied.append( name ) + sample_files.append( name ) return sample_files def copy_file_from_disk( filename, repo_dir, dir ): file_path = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for displaying error messages when displaying invalid tools in tool shed repository changeset revisions.
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/42e544d00e75/ changeset: 42e544d00e75 user: greg date: 2012-09-06 22:17:15 summary: Fixes for displaying error messages when displaying invalid tools in tool shed repository changeset revisions. affected #: 2 files diff -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d -r 42e544d00e75be44887b17f6985bcb251573e1de lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -248,6 +248,34 @@ except: pass return converter_path, display_path +def can_generate_tool_dependency_metadata( root, metadata_dict ): + """ + Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml + file is defined in the <requirement> tag for at least one tool in the repository. + """ + can_generate_dependency_metadata = False + for elem in root: + can_generate_dependency_metadata = False + tool_dependency_name = elem.get( 'name', None ) + tool_dependency_version = elem.get( 'version', None ) + tool_dependency_type = elem.tag + if tool_dependency_name and tool_dependency_version and tool_dependency_type: + for tool_dict in metadata_dict[ 'tools' ]: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_version = requirement_dict.get( 'version', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name==tool_dependency_name and req_version==tool_dependency_version and req_type==tool_dependency_type: + can_generate_dependency_metadata = True + break + if requirements and not can_generate_dependency_metadata: + # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> + # tag for any tool in the repository. + break + if not can_generate_dependency_metadata: + break + return can_generate_dependency_metadata def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files, webapp='galaxy' ): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make @@ -512,34 +540,6 @@ if tool_dependencies_dict: metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict return metadata_dict -def can_generate_tool_dependency_metadata( root, metadata_dict ): - """ - Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml - file is defined in the <requirement> tag for at least one tool in the repository. - """ - can_generate_dependency_metadata = False - for elem in root: - can_generate_dependency_metadata = False - tool_dependency_name = elem.get( 'name', None ) - tool_dependency_version = elem.get( 'version', None ) - tool_dependency_type = elem.tag - if tool_dependency_name and tool_dependency_version and tool_dependency_type: - for tool_dict in metadata_dict[ 'tools' ]: - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - req_name = requirement_dict.get( 'name', None ) - req_version = requirement_dict.get( 'version', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==tool_dependency_name and req_version==tool_dependency_version and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - if not can_generate_dependency_metadata: - break - return can_generate_dependency_metadata def generate_metadata_for_changeset_revision( app, repository_clone_url, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, webapp='galaxy' ): """ @@ -597,50 +597,53 @@ # Find all tool configs. if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): full_path = os.path.abspath( os.path.join( root, name ) ) - if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] - or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) - element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' - except Exception, e: - print "Error parsing %s", full_path, ", exception: ", str( e ) - is_tool = False - if is_tool: - tool, valid, error_message = load_tool_from_config( app, full_path ) - if tool is None: - if not valid: - invalid_file_tups.append( ( name, error_message ) ) - else: - invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths, webapp=webapp ) - can_set_metadata = True - for tup in invalid_files_and_errors_tups: - if name in tup: - can_set_metadata = False - invalid_tool_configs.append( name ) - break - if can_set_metadata: - if resetting_all_metadata_on_repository: - full_path_to_tool_config = os.path.join( root, name ) - stripped_path_to_tool_config = full_path_to_tool_config.replace( work_dir, '' ) - if stripped_path_to_tool_config.startswith( '/' ): - stripped_path_to_tool_config = stripped_path_to_tool_config[ 1: ] - relative_path_to_tool_config = os.path.join( relative_install_dir, stripped_path_to_tool_config ) + if os.path.getsize( full_path ) > 0: + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + # Make sure we're looking at a tool config and not a display application config or something else. + element_tree = util.parse_xml( full_path ) + element_tree_root = element_tree.getroot() + is_tool = element_tree_root.tag == 'tool' + except Exception, e: + print "Error parsing %s", full_path, ", exception: ", str( e ) + is_tool = False + if is_tool: + tool, valid, error_message = load_tool_from_config( app, full_path ) + if tool is None: + if not valid: + invalid_file_tups.append( ( name, error_message ) ) + else: + invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths, webapp=webapp ) + can_set_metadata = True + for tup in invalid_files_and_errors_tups: + if name in tup: + can_set_metadata = False + invalid_tool_configs.append( name ) + break + if can_set_metadata: + if resetting_all_metadata_on_repository: + full_path_to_tool_config = os.path.join( root, name ) + stripped_path_to_tool_config = full_path_to_tool_config.replace( work_dir, '' ) + if stripped_path_to_tool_config.startswith( '/' ): + stripped_path_to_tool_config = stripped_path_to_tool_config[ 1: ] + relative_path_to_tool_config = os.path.join( relative_install_dir, stripped_path_to_tool_config ) + else: + relative_path_to_tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( relative_path_to_tool_config, tool, repository_clone_url, metadata_dict ) else: - relative_path_to_tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( relative_path_to_tool_config, tool, repository_clone_url, metadata_dict ) - else: - invalid_file_tups.extend( invalid_files_and_errors_tups ) + for tup in invalid_files_and_errors_tups: + invalid_file_tups.append( tup ) # Find all exported workflows elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) - fp = open( relative_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) + if os.path.getsize( os.path.abspath( relative_path ) ) > 0: + fp = open( relative_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) if 'tools' in metadata_dict: # This step must be done after metadata for tools has been defined. tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) diff -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d -r 42e544d00e75be44887b17f6985bcb251573e1de lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1426,9 +1426,22 @@ repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) + invalid_file_tups = [] + if tool is None: + if not valid: + invalid_file_tups = [ ( name, error_message ) ] + else: + invalid_file_tups = check_tool_input_params( trans.app, + repository.repo_path, + tool_config, + tool, + [], + webapp=webapp ) + if invalid_file_tups: + message = generate_message_for_invalid_tools( invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True ) + elif error_message: + message = error_message try: - if error_message: - message = error_message return trans.fill_template( "/webapps/community/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, @@ -1439,7 +1452,7 @@ message=message, status='error' ) except Exception, e: - message = "This tool is invalid because: %s." % str( e ) + message = "Exception thrown attempting to display tool: %s." % str( e ) if webapp == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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