galaxy-commits February 2015

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305 discussions

commit/galaxy-central: natefoo: Remove escaping of quotes in the slurm cli status checks, I don't think they should be there (the format args should in fact be quoted).
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d02053706169/ Changeset: d02053706169 User: natefoo Date: 2015-02-09 15:59:36+00:00 Summary: Remove escaping of quotes in the slurm cli status checks, I don't think they should be there (the format args should in fact be quoted). Affected #: 1 file diff -r bb9de7bc465630eb3f8d055df573a9007f670914 -r d020537061694aabfc7d3786aeec419a0ed318de lib/galaxy/jobs/runners/util/cli/job/slurm.py --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -7,7 +7,7 @@ except ImportError: # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum - job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') + job_states = enum(RUNNING='running', OK='complete', QUEUED='queued', ERROR="failed") from ..job import BaseJobExec @@ -59,10 +59,10 @@ return 'scancel %s' % job_id def get_status(self, job_ids=None): - return 'squeue -a -o \\"%A %t\\"' + return "squeue -a -o '%A %t'" def get_single_status(self, job_id): - return 'squeue -a -o \\"%A %t\\" -j ' + job_id + return "squeue -a -o '%A %t' -j " + job_id def parse_status(self, status, job_ids): # Get status for each job, skipping header. @@ -80,6 +80,7 @@ # Job still on cluster and has state. id, state = status[1].split() return self._get_job_state(state) + # else line like "slurm_load_jobs error: Invalid job id specified" return job_states.OK def _get_job_state(self, state): 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: Dataproviders, column: allow filtering data by parsed column values (numeric, list, and string)
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bb9de7bc4656/ Changeset: bb9de7bc4656 User: carlfeberhard Date: 2015-02-09 15:36:43+00:00 Summary: Dataproviders, column: allow filtering data by parsed column values (numeric, list, and string) Affected #: 1 file diff -r 9d795f2108c14bb7b8486be0b949b251cb0fd94c -r bb9de7bc465630eb3f8d055df573a9007f670914 lib/galaxy/datatypes/dataproviders/column.py --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -3,6 +3,9 @@ is further subdivided into multiple data (e.g. columns from a line). """ +import urllib +import re + import line _TODO = """ @@ -34,12 +37,13 @@ 'column_count' : 'int', 'column_types' : 'list:str', 'parse_columns' : 'bool', - 'deliminator' : 'str' + 'deliminator' : 'str', + 'filters' : 'list:str' } def __init__( self, source, indeces=None, column_count=None, column_types=None, parsers=None, parse_columns=True, - deliminator='\t', **kwargs ): + deliminator='\t', filters=None, **kwargs ): """ :param indeces: a list of indeces of columns to gather from each row Optional: will default to `None`. @@ -103,6 +107,104 @@ # overwrite with user desired parsers self.parsers.update( parsers or {} ) + filters = filters or [] + self.column_filters = [] + for filter_ in filters: + parsed = self.parse_filter( filter_ ) + #TODO: might be better to error on bad filter/None here + if callable( parsed ): + self.column_filters.append( parsed ) + + def parse_filter( self, filter_param_str ): + split = filter_param_str.split( '-', 3 ) + if not len( split ) == 3: + return None + column, op, val = split + + # better checking v. len and indeces + column = int( column ) + if column > len( self.column_types ): + return None + if self.column_types[ column ] in ( 'float', 'int' ): + return self.create_numeric_filter( column, op, val ) + if self.column_types[ column ] in ( 'str' ): + return self.create_string_filter( column, op, val ) + if self.column_types[ column ] in ( 'list' ): + return self.create_list_filter( column, op, val ) + return None + + def create_numeric_filter( self, column, op, val ): + """ + Return an anonymous filter function that will be passed the array + of parsed columns. Return None if no filter function can be + created for the given params. + + The function will compare the column at index `column` against `val` + using the given op where op is one of: + lt: less than, le: less than or equal to, + eq: equal to, ne: not equal to, + ge: greather than or equal to, gt: greater than + + `val` is cast as float here and will return None if there's a parsing error. + """ + try: + val = float( val ) + except ValueError: + return None + if 'lt' == op: + return lambda d: d[column] < val + elif 'le' == op: + return lambda d: d[column] <= val + elif 'eq' == op: + return lambda d: d[column] == val + elif 'ne' == op: + return lambda d: d[column] != val + elif 'ge' == op: + return lambda d: d[column] >= val + elif 'gt' == op: + return lambda d: d[column] > val + return None + + def create_string_filter( self, column, op, val ): + """ + Return an anonymous filter function that will be passed the array + of parsed columns. Return None if no filter function can be + created for the given params. + + The function will compare the column at index `column` against `val` + using the given op where op is one of: + eq: exactly matches, + has: the column contains the substring `val`, + re: the column matches the regular expression in `val` + """ + if 'eq' == op: + return lambda d: d[column] == val + elif 'has' == op: + return lambda d: val in d[column] + elif 're' == op: + val = urllib.unquote_plus( val ) + val = re.compile( val ) + return lambda d: val.match( d[column] ) is not None + return None + + def create_list_filter( self, column, op, val ): + """ + Return an anonymous filter function that will be passed the array + of parsed columns. Return None if no filter function can be + created for the given params. + + The function will compare the column at index `column` against `val` + using the given op where op is one of: + eq: the list `val` exactly matches the list in the column, + has: the list in the column contains the sublist `val`, + """ + if 'eq' == op: + val = self.parse_value( val, 'list' ) + return lambda d: d[column] == val + elif 'has' == op: + return lambda d: val in d[column] + return None + def get_default_parsers( self ): """ Return parser dictionary keyed for each columnar type @@ -140,6 +242,39 @@ #'gffstrand': # -, +, ?, or '.' for None, etc. } + def filter( self, line ): + line = super( ColumnarDataProvider, self ).filter( line ) + if line == None: + return line + columns = self.parse_columns_from_line( line ) + return self.filter_by_columns( columns ) + + def parse_columns_from_line( self, line ): + """ + Returns a list of the desired, parsed columns. + :param line: the line to parse + :type line: str + """ + #TODO: too much going on in this loop - the above should all be precomputed AMAP... + all_columns = line.split( self.deliminator ) + # if no indeces were passed to init, return all columns + selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) ) + parsed_columns = [] + for parser_index, column_index in enumerate( selected_indeces ): + parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) ) + return parsed_columns + + def parse_column_at_index( self, columns, parser_index, index ): + """ + Get the column type for the parser from `self.column_types` or `None` + if the type is unavailable. + """ + try: + return self.parse_value( columns[ index ], self.get_column_type( parser_index ) ) + # if a selected index is not within columns, return None + except IndexError, index_err: + return None + def parse_value( self, val, type ): """ Attempt to parse and return the given value based on the given type. @@ -173,51 +308,11 @@ except IndexError, ind_err: return None - def parse_column_at_index( self, columns, parser_index, index ): - """ - Get the column type for the parser from `self.column_types` or `None` - if the type is unavailable. - """ - try: - return self.parse_value( columns[ index ], self.get_column_type( parser_index ) ) - # if a selected index is not within columns, return None - except IndexError, index_err: - return None - - def parse_columns_from_line( self, line ): - """ - Returns a list of the desired, parsed columns. - :param line: the line to parse - :type line: str - """ - #TODO: too much going on in this loop - the above should all be precomputed AMAP... - all_columns = line.split( self.deliminator ) - # if no indeces were passed to init, return all columns - selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) ) - parsed_columns = [] - for parser_index, column_index in enumerate( selected_indeces ): - parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) ) - return parsed_columns - - def __iter__( self ): - parent_gen = super( ColumnarDataProvider, self ).__iter__() - for line in parent_gen: - columns = self.parse_columns_from_line( line ) - yield columns - - #TODO: implement column filters here and not below - flatten hierarchy - -class FilteredByColumnDataProvider( ColumnarDataProvider ): - """ - Data provider that provide a list of columns from the lines of its source - _only_ if they pass a given filter function. - - e.g. column #3 is type int and > N - """ - # TODO: how to do this and still have limit and offset work? - def __init__( self, source, **kwargs ): - raise NotImplementedError() - super( FilteredByColumnDataProvider, self ).__init__( source, **kwargs ) + def filter_by_columns( self, columns ): + for filter_fn in self.column_filters: + if not filter_fn( columns ): + return None + return columns class DictDataProvider( ColumnarDataProvider ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Add a _future_expose_api_raw_anonymous_and_sessionless to restore functionality
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d795f2108c1/ Changeset: 9d795f2108c1 User: natefoo Date: 2015-02-09 15:17:53+00:00 Summary: Add a _future_expose_api_raw_anonymous_and_sessionless to restore functionality that was previously available with _future_expose_api_raw_anonymous. Affected #: 3 files diff -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 -r 9d795f2108c14bb7b8486be0b949b251cb0fd94c lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -19,6 +19,7 @@ from framework.decorators import _future_expose_api_raw from framework.decorators import _future_expose_api_raw_anonymous from framework.decorators import _future_expose_api_anonymous_and_sessionless +from framework.decorators import _future_expose_api_raw_anonymous_and_sessionless from framework.formbuilder import form from framework.formbuilder import FormBuilder diff -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 -r 9d795f2108c14bb7b8486be0b949b251cb0fd94c lib/galaxy/web/framework/decorators.py --- a/lib/galaxy/web/framework/decorators.py +++ b/lib/galaxy/web/framework/decorators.py @@ -344,3 +344,6 @@ def _future_expose_api_raw_anonymous( func ): return _future_expose_api( func, to_json=False, user_required=False ) + +def _future_expose_api_raw_anonymous_and_sessionless( func ): + return _future_expose_api( func, to_json=False, user_required=False, user_or_session_required=False ) diff -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 -r 9d795f2108c14bb7b8486be0b949b251cb0fd94c lib/galaxy/webapps/galaxy/api/job_files.py --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -8,8 +8,8 @@ from galaxy import util from galaxy import model from galaxy.web.base.controller import BaseAPIController -from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous +from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless +from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless import logging @@ -28,7 +28,7 @@ security model for tool execution. """ - @expose_api_raw_anonymous + @expose_api_raw_anonymous_and_sessionless def index( self, trans, job_id, **kwargs ): """ index( self, trans, job_id, **kwargs ) @@ -54,7 +54,7 @@ path = kwargs.get("path", None) return open(path, 'rb') - @expose_api_anonymous + @expose_api_anonymous_and_sessionless def create( self, trans, job_id, payload, **kwargs ): """ create( self, trans, job_id, payload, **kwargs ) 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: guerler: ToolForm: Set missing values to null
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/48f8adbdab6e/ Changeset: 48f8adbdab6e User: guerler Date: 2015-02-09 14:15:25+00:00 Summary: ToolForm: Set missing values to null Affected #: 6 files diff -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -34,8 +34,7 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - ((this.default_value === undefined) || - ((this.field.validate && !this.field.validate()) || !v || + (((this.field.validate && !this.field.validate()) || !v || (v == this.default_value) || (Number(v) == Number(this.default_value)) || (JSON.stringify(v) == JSON.stringify(this.default_value))))); diff -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -294,17 +294,20 @@ // get id var id = input_def.id; + // add regular/default value if missing + if (input_def.value === undefined) { + input_def.value = null; + } + if (input_def.default_value === undefined) { + input_def.default_value = input_def.value; + } + // create input field var field = this._createField(input_def); // add to field list this.app.field_list[id] = field; - // fix default value if missing - if (input_def.default_value === undefined) { - input_def.default_value = input_def.value; - } - // create input field wrapper var input_element = new InputElement(this.app, { label : input_def.label, diff -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -34,8 +34,7 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - ((this.default_value === undefined) || - ((this.field.validate && !this.field.validate()) || !v || + (((this.field.validate && !this.field.validate()) || !v || (v == this.default_value) || (Number(v) == Number(this.default_value)) || (JSON.stringify(v) == JSON.stringify(this.default_value))))); diff -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -294,17 +294,20 @@ // get id var id = input_def.id; + // add regular/default value if missing + if (input_def.value === undefined) { + input_def.value = null; + } + if (input_def.default_value === undefined) { + input_def.default_value = input_def.value; + } + // create input field var field = this._createField(input_def); // add to field list this.app.field_list[id] = field; - // fix default value if missing - if (input_def.default_value === undefined) { - input_def.default_value = input_def.value; - } - // create input field wrapper var input_element = new InputElement(this.app, { label : input_def.label, diff -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((this.default_value===undefined)||((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 -r 48f8adbdab6e2b66fe563be547da9db9627b1a94 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;var l=new c.View({title:p.title,title_new:p.title,min:p.min,max:p.max,onnew:function(){n(p.inputs);s.app.trigger("refresh")}});function n(i){var t=p.id+"-section-"+(q++);var u=new g(s.app,{inputs:i});l.add({id:t,$el:u.$el,ondel:function(){l.del(t);s.app.trigger("refresh")}})}var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o)}var k=new f(this.app,{label:p.title,help:p.help,field:l});this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);l.append($("<div/>").addClass("ui-table-form-info").html(i.help));var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;if(i.default_value===undefined){i.default_value=i.value}var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;var l=new c.View({title:p.title,title_new:p.title,min:p.min,max:p.max,onnew:function(){n(p.inputs);s.app.trigger("refresh")}});function n(i){var t=p.id+"-section-"+(q++);var u=new g(s.app,{inputs:i});l.add({id:t,$el:u.$el,ondel:function(){l.del(t);s.app.trigger("refresh")}})}var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o)}var k=new f(this.app,{label:p.title,help:p.help,field:l});this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);l.append($("<div/>").addClass("ui-table-form-info").html(i.help));var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;if(i.value===undefined){i.value=null}if(i.default_value===undefined){i.default_value=i.value}var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file 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

[galaxyproject/usegalaxy-playbook] 34a9d0: Swapped out Prestige server and SupAgro event from...
by GitHub 09 Feb '15

09 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 34a9d0483ff49564998b838e5e47f7b8421d0041 https://github.com/galaxyproject/usegalaxy-playbook/commit/34a9d0483ff49564… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2015-02-08 (Sun, 08 Feb 2015) Changed paths: A files/galaxy/common/static/welcome_img/GalaxyAdmins201502.png A files/galaxy/common/static/welcome_img/kmerSVMGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Swapped out Prestige server and SupAgro event from slide deck. Add GalaxyAdmins Feb meetup, and kmer-SVM Galaxy server.

1 0

commit/galaxy-central: guerler: Parameters: Fix initial value for drill downs, Workflow/ToolForm: Move module building to api
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/de8fa2d2312e/ Changeset: de8fa2d2312e User: guerler Date: 2015-02-09 04:49:24+00:00 Summary: Parameters: Fix initial value for drill downs, Workflow/ToolForm: Move module building to api Affected #: 14 files diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -275,10 +275,16 @@ /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { + // link self + var self = this; + // create the request dictionary - var self = this; - var current_state = this.tree.finalize(); - + var current_state = { + tool_id : this.options.id, + tool_version : this.options.version, + inputs : this.tree.finalize() + } + // log tool state console.debug('tools-form-workflow::_refreshForm() - Refreshing states.'); console.debug(current_state); @@ -287,11 +293,11 @@ var process_id = this.deferred.register(); // build model url for request - var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; + var model_url = galaxy_config.root + 'api/workflows/build_module'; // post job Utils.request({ - type : 'GET', + type : 'POST', url : model_url, data : current_state, success : function(data) { diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -10,13 +10,13 @@ initialize: function(app) { this.app = app; }, - + /** Convert dictionary representation into tool api specific flat dictionary format. */ finalize: function(patch) { // link this var self = this; - + // dictionary with api specific identifiers this.map_dict = {}; @@ -24,24 +24,24 @@ if (!this.app.section) { return {}; } - + // ensure that dictionary with patching functions exists patch = patch || {}; - + // dictionary formatted for job submission or tool form update var result_dict = {}; // prepare full dictionary var dict = {}; - + // fill dictionary from dom this._iterate(this.app.section.$el, dict); - + // add identifier and value to job definition function add(job_input_id, input_id, input_value) { // add entry to result dictionary result_dict[job_input_id] = input_value; - + // backup id mapping self.map_dict[job_input_id] = input_id; }; @@ -53,21 +53,21 @@ if (node.input) { // get node var input = node.input; - + // create identifier var job_input_id = identifier; if (identifier != '') { job_input_id += '|'; } job_input_id += input.name; - + // process input type switch (input.type) { // handle repeats case 'repeat': // section identifier var section_label = 'section-'; - + // collect repeat block identifiers var block_indices = []; var block_prefix = null; @@ -81,10 +81,10 @@ } } } - + // sort repeat blocks block_indices.sort(function(a,b) { return a - b; }); - + // add to response dictionary in created order var index = 0; for (var i in block_indices) { @@ -98,10 +98,10 @@ if (patch[input.test_param.type]) { value = patch[input.test_param.type](value); } - + // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); - + // identify selected case var selectedCase = self.matchCase(input, value); if (selectedCase != -1) { @@ -116,22 +116,17 @@ // get field var field = self.app.field_list[input.id]; if (field && field.value) { + // validate field value + var value = field.value(); + if (field.validate && !field.validate()) { + value = null; + } + // get and patch field value - var value = field.value(); if (patch[input.type]) { value = patch[input.type](value); } - // validate field value - if (field.skip) { - continue; - } - - // validate field value - if (field.validate && !field.validate()) { - value = null; - } - // ignore certain values if (input.ignore === undefined || (value !== null && input.ignore != value)) { // add value to submission @@ -149,20 +144,20 @@ } } } - + // start conversion convert('', dict); - + // return result return result_dict; }, - + /** Match job definition identifier to input element identifier */ match: function (job_input_id) { return this.map_dict && this.map_dict[job_input_id]; }, - + /** Match conditional values to selected cases */ matchCase: function(input, value) { @@ -174,27 +169,27 @@ value = input.test_param.falsevalue || 'false'; } } - + // find selected case for (var i in input.cases) { if (input.cases[i].value == value) { return i; } } - + // selected case not found return -1; }, - + /** Matches identifier from api model to input elements */ matchModel: function(model, callback) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { for (var i in head) { @@ -224,23 +219,23 @@ } } } - + // match all ids and return messages search('', model.inputs); // return matched results return result; }, - + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { if (typeof head === 'string') { @@ -262,14 +257,14 @@ } } } - + // match all ids and return messages search('', response); - + // return matched results return result; }, - + /** Iterate through the tool form dom and map it to the dictionary. */ _iterate: function(parent, dict) { @@ -279,15 +274,15 @@ children.each(function() { // get child element var child = this; - + // get id var id = $(child).attr('id'); - + // create new branch if ($(child).hasClass('section-row')) { // create sub dictionary dict[id] = {}; - + // add input element if it exists var input = self.app.input_list[id]; if (input) { @@ -295,7 +290,7 @@ input : input } } - + // fill sub dictionary self._iterate(child, dict[id]); } else { diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2250,13 +2250,12 @@ return tool_dict - def to_json (self, trans, **kwd): + def to_json (self, trans, kwd={}, is_dynamic=True): """ Recursively creates a tool dictionary containing repeats, dynamic options and updated states. """ job_id = kwd.get('__job_id__', None) dataset_id = kwd.get('__dataset_id__', None) - is_dynamic = string_as_bool(kwd.get('__is_dynamic__', True)) # load job details if provided job = None diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1618,6 +1618,8 @@ return UnvalidatedValue( None ) initial_values = [] recurse_options( initial_values, self.get_options( trans=trans, other_values=context ) ) + if len( initial_values ) == 0: + initial_values = None return initial_values def value_to_display_text( self, value, app ): diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -76,14 +76,10 @@ GET /api/tools/{tool_id}/build Returns a tool model including dynamic parameters and updated values, repeats block etc. """ - tool_id = urllib.unquote_plus( id ) tool_version = kwd.get( 'tool_version', None ) - tool = self.app.toolbox.get_tool( tool_id, tool_version ) - if not tool: - trans.response.status = 500 - return { 'error': 'Could not find tool with id \'%s\'' % tool_id } - return tool.to_json(trans, **kwd) - + tool = self._get_tool( id, tool_version=tool_version, user=trans.user ) + return tool.to_json(trans, kwd) + @_future_expose_api @web.require_admin def reload( self, trans, tool_id, **kwd ): diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,6 +6,8 @@ import uuid import logging +import copy +import urllib from sqlalchemy import desc, or_, and_ from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations @@ -17,6 +19,7 @@ from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke, queue_invoke from galaxy.workflow.run_request import build_workflow_run_config +from galaxy.workflow.modules import module_factory log = logging.getLogger(__name__) @@ -305,6 +308,52 @@ raise exceptions.RequestParameterInvalidException( message ) return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" ) + @expose_api + def build_module( self, trans, payload={}): + """ + POST /api/workflows/build_module + Builds module details including a tool model for the workflow editor. + """ + tool_id = payload.get( 'tool_id', None ) + tool_version = payload.get( 'tool_version', None ) + tool_inputs = payload.get( 'inputs', None ) + annotation = payload.get( 'annotation', '' ) + + # load tool + tool = self._get_tool( tool_id, tool_version=tool_version, user=trans.user ) + + # initialize module + trans.workflow_building_mode = True + module = module_factory.from_dict( trans, { + 'type' : 'tool', + 'tool_id' : tool.id, + 'tool_state' : None + } ) + + # create tool model and default tool state (if missing) + tool_model = module.tool.to_json(trans, tool_inputs, is_dynamic=False) + module.state.inputs = copy.deepcopy(tool_model['state_inputs']) + return { + 'tool_model' : tool_model, + 'tool_state' : module.get_state(), + 'data_inputs' : module.get_data_inputs(), + 'data_outputs' : module.get_data_outputs(), + 'tool_errors' : module.get_errors(), + 'form_html' : module.get_config_form(), + 'annotation' : annotation, + 'post_job_actions' : module.get_post_job_actions(tool_inputs) + } + + # + # -- Helper methods -- + # + def _get_tool( self, id, tool_version=None, user=None ): + id = urllib.unquote_plus( id ) + tool = self.app.toolbox.get_tool( id, tool_version ) + if not tool or not tool.allow_user_access( user ): + raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) + return tool + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -217,6 +217,7 @@ webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' ) webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) + webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" ) webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -609,7 +609,6 @@ This is used for the form shown in the right pane when a node is selected. """ - tool_state = incoming.pop('tool_state', None) trans.workflow_building_mode = True module = module_factory.from_dict( trans, { @@ -617,22 +616,7 @@ 'tool_id': tool_id, 'tool_state': tool_state } ) - - # create tool model and default tool state (if missing) - if type == 'tool' and not tool_state: - tool_model = module.tool.to_json(trans, **incoming) - module.state.inputs = copy.deepcopy(tool_model['state_inputs']) - return { - 'tool_model': tool_model, - 'tool_state': module.get_state(), - 'data_inputs': module.get_data_inputs(), - 'data_outputs': module.get_data_outputs(), - 'tool_errors': module.get_errors(), - 'form_html': module.get_config_form(), - 'annotation': annotation, - 'post_job_actions': module.get_post_job_actions(incoming) - } - + # update module state module.update_state( incoming ) @@ -669,7 +653,8 @@ module = module_factory.new( trans, type, **kwargs ) tool_model = None if type == 'tool': - tool_model = module.tool.to_json(trans) + tool_model = module.tool.to_json(trans, is_dynamic=False) + module.state.inputs = copy.deepcopy(tool_model['state_inputs']) return { 'type': module.type, 'name': module.get_name(), diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -275,10 +275,16 @@ /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { + // link self + var self = this; + // create the request dictionary - var self = this; - var current_state = this.tree.finalize(); - + var current_state = { + tool_id : this.options.id, + tool_version : this.options.version, + inputs : this.tree.finalize() + } + // log tool state console.debug('tools-form-workflow::_refreshForm() - Refreshing states.'); console.debug(current_state); @@ -287,11 +293,11 @@ var process_id = this.deferred.register(); // build model url for request - var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; + var model_url = galaxy_config.root + 'api/workflows/build_module'; // post job Utils.request({ - type : 'GET', + type : 'POST', url : model_url, data : current_state, success : function(data) { diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -10,13 +10,13 @@ initialize: function(app) { this.app = app; }, - + /** Convert dictionary representation into tool api specific flat dictionary format. */ finalize: function(patch) { // link this var self = this; - + // dictionary with api specific identifiers this.map_dict = {}; @@ -24,24 +24,24 @@ if (!this.app.section) { return {}; } - + // ensure that dictionary with patching functions exists patch = patch || {}; - + // dictionary formatted for job submission or tool form update var result_dict = {}; // prepare full dictionary var dict = {}; - + // fill dictionary from dom this._iterate(this.app.section.$el, dict); - + // add identifier and value to job definition function add(job_input_id, input_id, input_value) { // add entry to result dictionary result_dict[job_input_id] = input_value; - + // backup id mapping self.map_dict[job_input_id] = input_id; }; @@ -53,21 +53,21 @@ if (node.input) { // get node var input = node.input; - + // create identifier var job_input_id = identifier; if (identifier != '') { job_input_id += '|'; } job_input_id += input.name; - + // process input type switch (input.type) { // handle repeats case 'repeat': // section identifier var section_label = 'section-'; - + // collect repeat block identifiers var block_indices = []; var block_prefix = null; @@ -81,10 +81,10 @@ } } } - + // sort repeat blocks block_indices.sort(function(a,b) { return a - b; }); - + // add to response dictionary in created order var index = 0; for (var i in block_indices) { @@ -98,10 +98,10 @@ if (patch[input.test_param.type]) { value = patch[input.test_param.type](value); } - + // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); - + // identify selected case var selectedCase = self.matchCase(input, value); if (selectedCase != -1) { @@ -116,22 +116,17 @@ // get field var field = self.app.field_list[input.id]; if (field && field.value) { + // validate field value + var value = field.value(); + if (field.validate && !field.validate()) { + value = null; + } + // get and patch field value - var value = field.value(); if (patch[input.type]) { value = patch[input.type](value); } - // validate field value - if (field.skip) { - continue; - } - - // validate field value - if (field.validate && !field.validate()) { - value = null; - } - // ignore certain values if (input.ignore === undefined || (value !== null && input.ignore != value)) { // add value to submission @@ -149,20 +144,20 @@ } } } - + // start conversion convert('', dict); - + // return result return result_dict; }, - + /** Match job definition identifier to input element identifier */ match: function (job_input_id) { return this.map_dict && this.map_dict[job_input_id]; }, - + /** Match conditional values to selected cases */ matchCase: function(input, value) { @@ -174,27 +169,27 @@ value = input.test_param.falsevalue || 'false'; } } - + // find selected case for (var i in input.cases) { if (input.cases[i].value == value) { return i; } } - + // selected case not found return -1; }, - + /** Matches identifier from api model to input elements */ matchModel: function(model, callback) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { for (var i in head) { @@ -224,23 +219,23 @@ } } } - + // match all ids and return messages search('', model.inputs); // return matched results return result; }, - + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { if (typeof head === 'string') { @@ -262,14 +257,14 @@ } } } - + // match all ids and return messages search('', response); - + // return matched results return result; }, - + /** Iterate through the tool form dom and map it to the dictionary. */ _iterate: function(parent, dict) { @@ -279,15 +274,15 @@ children.each(function() { // get child element var child = this; - + // get id var id = $(child).attr('id'); - + // create new branch if ($(child).hasClass('section-row')) { // create sub dictionary dict[id] = {}; - + // add input element if it exists var input = self.app.input_list[id]; if (input) { @@ -295,7 +290,7 @@ input : input } } - + // fill sub dictionary self._iterate(child, dict[id]); } else { diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e={tool_id:this.options.id,tool_version:this.options.version,inputs:this.tree.finalize()};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(t.skip){continue}if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(t.validate&&!t.validate()){v=null}if(g[u.type]){v=g[u.type](v)}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -10,7 +10,7 @@ ## This avoids making two separate requests since the classic form requires the mako anyway. params = dict(trans.request.params) params['__dataset_id__'] = params.get('id', None) - self.form_config = tool.to_json(trans, **params) + self.form_config = tool.to_json(trans, params) self.form_config.update({ 'id' : tool.id, 'job_id' : trans.security.encode_id( job.id ) if job else None, diff -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 -r de8fa2d2312eaad8178fe9aa39a2278bae7da239 templates/webapps/galaxy/workflow/editor_tool_form.mako --- a/templates/webapps/galaxy/workflow/editor_tool_form.mako +++ b/templates/webapps/galaxy/workflow/editor_tool_form.mako @@ -6,11 +6,9 @@ ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. ## This avoids making two separate requests since the classic form requires the mako anyway. from galaxy.tools.parameters import params_to_incoming - incoming = { - '__is_dynamic__' : False - } + incoming = {} params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app, to_html=False) - self.form_config = tool.to_json(trans, **incoming) + self.form_config = tool.to_json(trans, incoming, is_dynamic=False) self.form_config.update({ 'id' : tool.id, 'job_id' : trans.security.encode_id( job.id ) if job else 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.

1 0

commit/galaxy-central: jmchilton: Link to "easiest ways to start" card in CONTRIBUTING.md.
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/28126538ef19/ Changeset: 28126538ef19 User: jmchilton Date: 2015-02-08 23:17:10+00:00 Summary: Link to "easiest ways to start" card in CONTRIBUTING.md. Affected #: 1 file diff -r 7ad7c739fd195596fec28531fe55830cf7a3039e -r 28126538ef19e8dc9d5a5dede2ccf3080ccdf603 CONTRIBUTING.md --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -81,6 +81,13 @@ * A description of how to test the change. +## Ideas + +Galaxy's [Trello board](http://bit.ly/gxytrello) is filled with bugs and ideas +for enhancements, but we maintain a [card](https://trello.com/c/eFdPIdIB) with +links to smaller issues we believe would make the best entry points for new +developers. + ## A Quick Note about Tools For the most part, Galaxy tools should be published to the 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: 2 new changesets
by commits-noreply＠bitbucket.org 08 Feb '15

08 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/edc4b7ae61b6/ Changeset: edc4b7ae61b6 User: jmchilton Date: 2015-02-08 20:29:02+00:00 Summary: Add link to actual presentation slides to CONTRIBUTING.md. For people who want to follow along with Dannon at home. Affected #: 1 file diff -r 2c93bedd4898c21ccaa0de413ffedcba91220bb1 -r edc4b7ae61b6036b2fdcbe032d35ae3f0a3115f0 CONTRIBUTING.md --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,12 +1,13 @@ # Contributing This document briefly describes how to contribute to the -galaxy-central core project - also checkout the video of our [2013 -Galaxy Community Conference -presentation](http://vimeo.com/channels/581875/73486255) on the -topic. For information on contributing more broadly to the Galaxy -ecosystem and a deeper discussion of some of these points - please see -the [Develop](https://wiki.galaxyproject.org/Develop/) section of the +galaxy-central core project - also checkout our 2013 Galaxy Community +Conference presentation] on the topic +([video](http://vimeo.com/channels/581875/73486255), +[presentation](https://wiki.galaxyproject.org/Documents/Presentations/GCC2013?action=AttachFile&do=view&target=BakerContribute.pdf)). For +information on contributing more broadly to the Galaxy ecosystem and a +deeper discussion of some of these points - please see the +[Develop](https://wiki.galaxyproject.org/Develop/) section of the [Galaxy Wiki](https://wiki.galaxyproject.org/). ## Before you Begin https://bitbucket.org/galaxy/galaxy-central/commits/7ad7c739fd19/ Changeset: 7ad7c739fd19 User: jmchilton Date: 2015-02-08 20:31:45+00:00 Summary: Merge. Affected #: 3 files diff -r edc4b7ae61b6036b2fdcbe032d35ae3f0a3115f0 -r 7ad7c739fd195596fec28531fe55830cf7a3039e lib/galaxy/forms/forms.py --- a/lib/galaxy/forms/forms.py +++ b/lib/galaxy/forms/forms.py @@ -50,7 +50,7 @@ #load fields fields = [] fields_elem = elem.find( 'fields' ) - if fields_elem: + if fields_elem is not None: for field_elem in fields_elem.findall( 'field' ): field_type = field_elem.get( 'type' ) assert field_type in self.field_type_factories, 'Invalid form field type ( %s ).' % field_type diff -r edc4b7ae61b6036b2fdcbe032d35ae3f0a3115f0 -r 7ad7c739fd195596fec28531fe55830cf7a3039e lib/galaxy/sample_tracking/external_service_types.py --- a/lib/galaxy/sample_tracking/external_service_types.py +++ b/lib/galaxy/sample_tracking/external_service_types.py @@ -96,9 +96,9 @@ def parse_run_details( self, root ): self.run_details = {} run_details_elem = root.find( 'run_details' ) - if run_details_elem: + if run_details_elem is not None: results_elem = run_details_elem.find( 'results' ) - if results_elem: + if results_elem is not None: # Get the list of resulting datatypes # TODO: the 'results_urls' attribute is only useful if the transfer protocol is http(s), so check if that is the case. self.run_details[ 'results' ], self.run_details[ 'results_urls' ] = self.parse_run_details_results( results_elem ) diff -r edc4b7ae61b6036b2fdcbe032d35ae3f0a3115f0 -r 7ad7c739fd195596fec28531fe55830cf7a3039e lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -31,11 +31,11 @@ self.app = app self.__job_config = app.job_config self.workflow_schedulers = {} - self.active_workflow_schedulers = {} # Passive workflow schedulers - # won't need to be monitored I - # guess. + self.active_workflow_schedulers = {} + # Passive workflow schedulers won't need to be monitored I guess. + self.request_monitor = None - + self.__plugin_classes = self.__plugins_dict() self.__init_schedulers() @@ -67,7 +67,7 @@ try: self.request_monitor.shutdown() except Exception: - log.exception( "Failed to shutdown worklfow request monitor." ) + log.exception( "Failed to shutdown workflow request monitor." ) def queue( self, workflow_invocation, request_params ): workflow_invocation.state = model.WorkflowInvocation.states.NEW @@ -112,8 +112,7 @@ def __init_schedulers_for_element( self, plugins_element ): plugins_kwds = dict( plugins_element.items() ) self.default_scheduler_id = plugins_kwds.get( 'default', DEFAULT_SCHEDULER_ID ) - - for plugin_element in plugins_element.getchildren(): + for plugin_element in plugins_element: plugin_type = plugin_element.tag plugin_kwds = dict( plugin_element.items() ) workflow_scheduler_id = plugin_kwds.get( 'id', None ) @@ -134,7 +133,7 @@ self.workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler if isinstance( workflow_scheduler, galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin ): self.active_workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler - + def __start_request_monitor( self ): self.request_monitor = WorkflowRequestMonitor( self.app, self ) 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: 3 new changesets
by commits-noreply＠bitbucket.org 08 Feb '15

08 Feb '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b654710d5844/ Changeset: b654710d5844 User: dannon Date: 2015-02-08 16:16:14+00:00 Summary: Fix a few instances of incorrect (deprecated) use of value instead of identity testing in xml parsing. Affected #: 3 files diff -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 -r b654710d58445917baae8e3ec8f78acc745ef262 lib/galaxy/forms/forms.py --- a/lib/galaxy/forms/forms.py +++ b/lib/galaxy/forms/forms.py @@ -50,7 +50,7 @@ #load fields fields = [] fields_elem = elem.find( 'fields' ) - if fields_elem: + if fields_elem is not None: for field_elem in fields_elem.findall( 'field' ): field_type = field_elem.get( 'type' ) assert field_type in self.field_type_factories, 'Invalid form field type ( %s ).' % field_type diff -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 -r b654710d58445917baae8e3ec8f78acc745ef262 lib/galaxy/sample_tracking/external_service_types.py --- a/lib/galaxy/sample_tracking/external_service_types.py +++ b/lib/galaxy/sample_tracking/external_service_types.py @@ -96,9 +96,9 @@ def parse_run_details( self, root ): self.run_details = {} run_details_elem = root.find( 'run_details' ) - if run_details_elem: + if run_details_elem is not None: results_elem = run_details_elem.find( 'results' ) - if results_elem: + if results_elem is not None: # Get the list of resulting datatypes # TODO: the 'results_urls' attribute is only useful if the transfer protocol is http(s), so check if that is the case. self.run_details[ 'results' ], self.run_details[ 'results_urls' ] = self.parse_run_details_results( results_elem ) diff -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 -r b654710d58445917baae8e3ec8f78acc745ef262 lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -112,8 +112,7 @@ def __init_schedulers_for_element( self, plugins_element ): plugins_kwds = dict( plugins_element.items() ) self.default_scheduler_id = plugins_kwds.get( 'default', DEFAULT_SCHEDULER_ID ) - - for plugin_element in plugins_element.getchildren(): + for plugin_element in plugins_element: plugin_type = plugin_element.tag plugin_kwds = dict( plugin_element.items() ) workflow_scheduler_id = plugin_kwds.get( 'id', None ) https://bitbucket.org/galaxy/galaxy-central/commits/a02abac7d68d/ Changeset: a02abac7d68d User: dannon Date: 2015-02-08 16:21:42+00:00 Summary: Minor formatting, spelling in workflow scheduling_manager. Affected #: 1 file diff -r b654710d58445917baae8e3ec8f78acc745ef262 -r a02abac7d68dd4decd91e5a24022dc6648bf011c lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -31,11 +31,11 @@ self.app = app self.__job_config = app.job_config self.workflow_schedulers = {} - self.active_workflow_schedulers = {} # Passive workflow schedulers - # won't need to be monitored I - # guess. + self.active_workflow_schedulers = {} + # Passive workflow schedulers won't need to be monitored I guess. + self.request_monitor = None - + self.__plugin_classes = self.__plugins_dict() self.__init_schedulers() @@ -67,7 +67,7 @@ try: self.request_monitor.shutdown() except Exception: - log.exception( "Failed to shutdown worklfow request monitor." ) + log.exception( "Failed to shutdown workflow request monitor." ) def queue( self, workflow_invocation, request_params ): workflow_invocation.state = model.WorkflowInvocation.states.NEW @@ -133,7 +133,7 @@ self.workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler if isinstance( workflow_scheduler, galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin ): self.active_workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler - + def __start_request_monitor( self ): self.request_monitor = WorkflowRequestMonitor( self.app, self ) https://bitbucket.org/galaxy/galaxy-central/commits/ea23071cf22e/ Changeset: ea23071cf22e User: dannon Date: 2015-02-08 20:09:23+00:00 Summary: Merge. Affected #: 1 file diff -r a02abac7d68dd4decd91e5a24022dc6648bf011c -r ea23071cf22ea78b699264e04b59e3adf88ec619 CONTRIBUTING.md --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,93 @@ +# Contributing + +This document briefly describes how to contribute to the +galaxy-central core project - also checkout the video of our [2013 +Galaxy Community Conference +presentation](http://vimeo.com/channels/581875/73486255) on the +topic. For information on contributing more broadly to the Galaxy +ecosystem and a deeper discussion of some of these points - please see +the [Develop](https://wiki.galaxyproject.org/Develop/) section of the +[Galaxy Wiki](https://wiki.galaxyproject.org/). + +## Before you Begin + +If you have an idea for a feature to add or an approach for a bugfix - +it is best to communicate with Galaxy developers early. The most +common venue for this is the [Galaxy Trello +board](https://wiki.galaxyproject.org/Issues). Browse through existing +cards [here](http://bit.ly/gxytrello) and if one seems related comment +on it. If no existing cards seem appropriate, a new issue can be +opened using [this form](http://galaxyproject.org/trello). Galaxy +developers are also generally available via +[IRC](https://wiki.galaxyproject.org/GetInvolved#IRC_Channel) and on +the [development mailing list](http://dev.list.galaxyproject.org/). + +## How to Contribute + +* If you are new to Mercurial - please check out this [official + tutorial](http://mercurial.selenic.com/wiki/Tutorial) + +* Make sure you have a free [Bitbucket + account](https://bitbucket.org/account/signup/) + +* Fork the galaxy-central repository on + [Bitbucket](https://bitbucket.org/galaxy/galaxy-central/fork) to + make your changes. (Many Galaxy instances target + [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist) - but active + development happens on galaxy-central and this is where pull + requests should be made). + +* Choose the correct Mercurial branch to develop your changes against. + + * Additions to the code base should be pushed to the `default` + branch (`hg checkout default`). + + * Most bug fixes to previously release components (things in + galaxy-dist) should be pushed to the `stable` branch (`hg checkout + stable`). + + * Serious security problems should not be fixed via pull request - + please responsibly disclose these by e-mailing them (with or + without patches) to galaxy-lab(a)bx.psu.edu. The Galaxy core + development team will issue patches to public servers before + announcing the issue to ensure there is time to patch and + highlight these fixes widely. We will provide you credit for the + discovery when publicly disclosing the issue. + +* If your changes modify code - please ensure the resulting files + conform to Galaxy [style + guidelines](https://wiki.galaxyproject.org/Develop/BestPractices). + +* Galaxy contains hundreds of tests of different types and complexity + and running each is difficult and probably not reasonable at this + time (someday we will provide a holistic test procedure to make this + possible). For now, please just review the [running tests + documentation](https://wiki.galaxyproject.org/Admin/RunningTests) + and run any that seem relevant. Developers reviewing your pull + request will be happy to help guide you to running the most relevant + tests as part of the pull request review process and may request the + output of these tests. + +* Commit and push your changes to your Bitbucket fork. + +* Open a [pull + request](https://confluence.atlassian.com/display/BITBUCKET/Fork+a+Repo,+Co… + with these changes. You pull request message should include: + + * A description of why the change should be made. + + * A description of implementation of the change. + + * A description of how to test the change. + +## A Quick Note about Tools + + For the most part, Galaxy tools should be published to the + [ToolShed](https://wiki.galaxyproject.org/ToolShed) and not in this + repository directly. If you are looking to supply fixes for migrated + core tools that used to exist in this repository - please checkout + the [tools-devteam](https://github.com/galaxyproject/tools-devteam) + repository on GitHub. + + More information about tool development can be found [on the + wiki](https://wiki.galaxyproject.org/Develop). 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: jmchilton: First crack at a CONTRIBUTING file for galaxy-central.
by commits-noreply＠bitbucket.org 08 Feb '15

08 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c93bedd4898/ Changeset: 2c93bedd4898 User: jmchilton Date: 2015-02-08 20:02:54+00:00 Summary: First crack at a CONTRIBUTING file for galaxy-central. Ideally this would come in through a pull request but I am trying to rush through documentation related to Galaxy development ahead of a GSOC application - by all means I would encourage comments related to this commit as well as well as direct modifications. CONTRIBUTING files are meant to encourge developers to contribute to open source projects by spelling out how to contribute and what is expected from contributions. More resources related to CONTRIBUTION files include: - http://contribute.md/ - https://github.com/blog/1184-contributing-guidelines This isn't coming at the expense of wiki documentation - I have already made dozens of enhancements to the Develop section of the wiki today and I am planning a huge walkthrough of how to contribute and learn about various aspect of the broader Galaxy community from a new developer perspective. Having this file in place though I feel is an important part of that however. Affected #: 1 file diff -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 -r 2c93bedd4898c21ccaa0de413ffedcba91220bb1 CONTRIBUTING.md --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,93 @@ +# Contributing + +This document briefly describes how to contribute to the +galaxy-central core project - also checkout the video of our [2013 +Galaxy Community Conference +presentation](http://vimeo.com/channels/581875/73486255) on the +topic. For information on contributing more broadly to the Galaxy +ecosystem and a deeper discussion of some of these points - please see +the [Develop](https://wiki.galaxyproject.org/Develop/) section of the +[Galaxy Wiki](https://wiki.galaxyproject.org/). + +## Before you Begin + +If you have an idea for a feature to add or an approach for a bugfix - +it is best to communicate with Galaxy developers early. The most +common venue for this is the [Galaxy Trello +board](https://wiki.galaxyproject.org/Issues). Browse through existing +cards [here](http://bit.ly/gxytrello) and if one seems related comment +on it. If no existing cards seem appropriate, a new issue can be +opened using [this form](http://galaxyproject.org/trello). Galaxy +developers are also generally available via +[IRC](https://wiki.galaxyproject.org/GetInvolved#IRC_Channel) and on +the [development mailing list](http://dev.list.galaxyproject.org/). + +## How to Contribute + +* If you are new to Mercurial - please check out this [official + tutorial](http://mercurial.selenic.com/wiki/Tutorial) + +* Make sure you have a free [Bitbucket + account](https://bitbucket.org/account/signup/) + +* Fork the galaxy-central repository on + [Bitbucket](https://bitbucket.org/galaxy/galaxy-central/fork) to + make your changes. (Many Galaxy instances target + [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist) - but active + development happens on galaxy-central and this is where pull + requests should be made). + +* Choose the correct Mercurial branch to develop your changes against. + + * Additions to the code base should be pushed to the `default` + branch (`hg checkout default`). + + * Most bug fixes to previously release components (things in + galaxy-dist) should be pushed to the `stable` branch (`hg checkout + stable`). + + * Serious security problems should not be fixed via pull request - + please responsibly disclose these by e-mailing them (with or + without patches) to galaxy-lab(a)bx.psu.edu. The Galaxy core + development team will issue patches to public servers before + announcing the issue to ensure there is time to patch and + highlight these fixes widely. We will provide you credit for the + discovery when publicly disclosing the issue. + +* If your changes modify code - please ensure the resulting files + conform to Galaxy [style + guidelines](https://wiki.galaxyproject.org/Develop/BestPractices). + +* Galaxy contains hundreds of tests of different types and complexity + and running each is difficult and probably not reasonable at this + time (someday we will provide a holistic test procedure to make this + possible). For now, please just review the [running tests + documentation](https://wiki.galaxyproject.org/Admin/RunningTests) + and run any that seem relevant. Developers reviewing your pull + request will be happy to help guide you to running the most relevant + tests as part of the pull request review process and may request the + output of these tests. + +* Commit and push your changes to your Bitbucket fork. + +* Open a [pull + request](https://confluence.atlassian.com/display/BITBUCKET/Fork+a+Repo,+Co… + with these changes. You pull request message should include: + + * A description of why the change should be made. + + * A description of implementation of the change. + + * A description of how to test the change. + +## A Quick Note about Tools + + For the most part, Galaxy tools should be published to the + [ToolShed](https://wiki.galaxyproject.org/ToolShed) and not in this + repository directly. If you are looking to supply fixes for migrated + core tools that used to exist in this repository - please checkout + the [tools-devteam](https://github.com/galaxyproject/tools-devteam) + repository on GitHub. + + More information about tool development can be found [on the + wiki](https://wiki.galaxyproject.org/Develop). 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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