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commit/galaxy-central: guerler: SelectToolParameter: Fix type check before split operation.
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20882e294f92/ Changeset: 20882e294f92 User: guerler Date: 2014-10-16 17:42:17+00:00 Summary: SelectToolParameter: Fix type check before split operation. Affected #: 1 file diff -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 -r 20882e294f925cb4c895e194d508bc15306e4403 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -818,7 +818,7 @@ if value == '': value = None else: - if not isinstance( value, list ): + if isinstance( value, basestring ): # Split on all whitespace. This not only provides flexibility # in interpreting values but also is needed because many browsers # use \r\n to separate lines. 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: Update tag latest_2014.10.06 for changeset e1404e285ccb
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78c9a97be4b6/ Changeset: 78c9a97be4b6 Branch: stable User: natefoo Date: 2014-10-16 17:00:13+00:00 Summary: Update tag latest_2014.10.06 for changeset e1404e285ccb Affected #: 1 file diff -r e1404e285ccb9e52bd09c5827934cd0da1974acc -r 78c9a97be4b6bfe55136b055477fd1b9f22fd848 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -1744b7d8e9ab619d78c0516f9ccb093b0a814163 latest_2014.10.06 +e1404e285ccb9e52bd09c5827934cd0da1974acc latest_2014.10.06 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: Move dictionary building methods from mako to api.
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d44e35432ab/ Changeset: 0d44e35432ab User: guerler Date: 2014-10-16 16:43:39+00:00 Summary: ToolForm: Move dictionary building methods from mako to api. Affected #: 15 files diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -22,7 +22,7 @@ // get history summary Utils.get({ - url : self.base_url + '?deleted=false', + url : self.base_url + '?deleted=false&state=ok', success : function(response) { // backup summary self.summary = response; diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -27,10 +27,8 @@ this.modal = new Ui.Modal.View(); } - // link model/inputs and all options - this.options = options; - this.model = options.model; - this.inputs = options.model.inputs; + // link options + this.options = options; // set element this.setElement('<div/>'); @@ -53,9 +51,13 @@ // reset input element list, which contains the dom elements of each input element (includes also the input field) this.element_list = {}; - // initialize contents + // for now the initial tool model is parsed through the mako + this.model = this.options; + this.inputs = this.options.inputs; + + // request history content and build form this.content = new ToolContent({ - history_id : this.options.history_id, + history_id : self.options.history_id, success : function() { self._buildForm(); } @@ -89,6 +91,51 @@ console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); }, + // build tool model through api call + _buildModel: function() { + // link this + var self = this; + + // construct url + var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build?'; + if (this.options.job_id) { + model_url += 'job_id=' + this.options.job_id; + } else { + if (this.options.dataset_id) { + model_url += 'dataset_id=' + this.options.dataset_id; + } else { + var loc = top.location.href; + var pos = loc.indexOf('?'); + if (loc.indexOf('tool_id=') != -1 && pos !== -1) { + model_url += loc.slice(pos + 1); + } + } + } + + // get initial model + Utils.request({ + type : 'GET', + url : model_url, + success : function(response) { + // link model data update options + self.options = $.extend(self.options, response); + self.model = response; + self.inputs = response.inputs; + + // log success + console.debug('tools-form::initialize() - Initial tool model ready.'); + console.debug(response); + + // build form + self._buildForm(); + }, + error : function(response) { + console.debug('tools-form::initialize() - Initial tool model request failed.'); + console.debug(response); + } + }); + }, + // refresh form data _refreshForm: function() { // link this @@ -111,7 +158,7 @@ // post job Utils.request({ type : 'GET', - url : galaxy_config.root + 'tool_runner/index?tool_id=' + this.options.id + '&form_refresh=True', + url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -106,17 +106,17 @@ value : function (dict) { // update current value if (dict !== undefined) { - if (dict.values.length > 0 && dict.values[0] && dict.values[0].src) { + try { + // set source + this.current = dict.values[0].src; + this.refresh(); + // create list var list = []; for (var i in dict.values) { list.push(dict.values[i].id); } - // set source - this.current = dict.values[0].src; - this.refresh(); - // identify select element switch(this.current) { case 'hda': @@ -126,6 +126,8 @@ this.select_collection.value(list[0]); break; } + } catch (err) { + console.debug('tools-select-content::value() - Skipped.'); } } diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2175,7 +2175,7 @@ for expanded_incoming in expanded_incomings: state, state_new = self.__fetch_state( trans, expanded_incoming, history, all_pages=all_pages ) all_states.append( state ) - if state_new and "form_refresh" not in incoming: + if state_new: # This feels a bit like a hack. It allows forcing full processing # of inputs even when there is no state in the incoming dictionary # by providing either 'runtool_btn' (the name of the submit button @@ -2358,7 +2358,7 @@ message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) - def populate_state( self, trans, inputs, state, incoming, history, source, prefix="", context=None ): + def populate_state( self, trans, inputs, state, incoming, history=None, source="html", prefix="", context=None ): errors = dict() # Push this level onto the context stack context = ExpressionContext( state, context ) diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -10,8 +10,13 @@ from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import dumps from galaxy.visualization.data_providers.genome import * - +from galaxy.tools.parameters import params_to_incoming +from galaxy.tools.parameters import visit_input_values +from galaxy.tools.parameters.meta import expand_meta_parameters from galaxy.managers.collections_util import dictify_dataset_collection_instance +from galaxy.model import HistoryDatasetAssociation +from galaxy.util.expressions import ExpressionContext +from collections import Iterable import galaxy.queue_worker @@ -61,6 +66,15 @@ tool = self._get_tool( id ) return tool.to_dict( trans, io_details=io_details, link_details=link_details ) + @_future_expose_api_anonymous + def build( self, trans, id, **kwd ): + """ + GET /api/tools/{tool_id}/build + Returns a tool model including dynamic parameters and updated values, repeats block etc. + """ + tool = self._get_tool( id ) + return self._build_dict(trans, tool, kwd) + @_future_expose_api @web.require_admin def reload( self, trans, tool_id, **kwd ): @@ -464,3 +478,174 @@ dataset_dict[ 'id' ] = trans.security.encode_id( dataset_dict[ 'id' ] ) dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset ) return dataset_dict + + def _build_dict(self, trans, tool, kwd={}): + """ + 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) + + # load job details if provided + job = None + if job_id: + try: + job_id = trans.security.decode_id( job_id ) + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) + except Exception, exception: + trans.response.status = 500 + return { 'error': 'Failed to retrieve job.' } + elif dataset_id: + try: + dataset_id = trans.security.decode_id( dataset_id ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ): + trans.response.status = 500 + return { 'error': 'User has no access to dataset.' } + job = data.creating_job + if not job: + trans.response.status = 500 + return { 'error': 'Creating job not found.' } + except Exception, exception: + trans.response.status = 500 + return { 'error': 'Failed to get job information.' } + + # check if job was identified + if job: + try: + job_params = job.get_param_values( trans.app, ignore_errors = True ) + job_messages = tool.check_and_update_param_values( job_params, trans, update_values=False ) + params_to_incoming( kwd, tool.inputs, job_params, trans.app ) + except Exception, exception: + trans.response.status = 500 + return { 'error': str( exception ) } + + # create parameter object + params = galaxy.util.Params( kwd, sanitize = False ) + + # convert value to jsonifiable value + def convert(v): + # check if value is numeric + isnumber = False + try: + float(v) + isnumber = True + except Exception: + pass + + # fix hda parsing + if isinstance(v, HistoryDatasetAssociation): + return { + 'id' : trans.security.encode_id(v.id), + 'src' : 'hda' + } + elif isinstance(v, basestring) or isnumber: + return v + else: + return None + + # ensures that input dictionary is jsonifiable + def sanitize(dict): + # get current value + value = dict['value'] if 'value' in dict else None + + # identify lists + if dict['type'] == 'data': + if isinstance(value, list): + value = [ convert(v) for v in value ] + else: + value = [ convert(value) ] + value = { + 'batch' : dict['multiple'], + 'values' : value + } + elif isinstance(value, list): + value = [ convert(v) for v in value ] + else: + value = convert(value) + + # update and return + dict['value'] = value + return dict + + # build model + def iterate(group_inputs, inputs, tool_state, errors, other_values=None): + other_values = ExpressionContext( tool_state, other_values ) + for input_index, input in enumerate( inputs.itervalues() ): + # create model dictionary + group_inputs[input_index] = input.to_dict(trans) + + # identify stat for subsection/group + group_state = tool_state[input.name] + + # iterate and update values + if input.type == 'repeat': + group_cache = group_inputs[input_index]['cache'] = {} + for i in range( len( group_state ) ): + group_cache[i] = {} + group_errors = errors[input.name][i] if input.name in errors else dict() + iterate( group_cache[i], input.inputs, group_state[i], group_errors, other_values ) + elif input.type == 'conditional': + # TODO: loop over all cases + try: + test_param = group_inputs[input_index]['test_param'] + test_param['value'] = group_state[test_param['name']] + except Exception: + pass + i = group_state['__current_case__'] + group_errors = errors.get( input.name, {} ) + iterate(group_inputs[input_index]['cases'][i]['inputs'], input.cases[i].inputs, group_state, group_errors, other_values) + else: + # create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options + try: + group_inputs[input_index] = input.to_dict(trans, other_values=other_values) + except Exception: + pass + + # update input value from tool state + try: + group_inputs[input_index]['value'] = tool_state[group_inputs[input_index]['name']] + except Exception: + pass + + # sanitize if value exists + if group_inputs[input_index]['value']: + group_inputs[input_index] = sanitize(group_inputs[input_index]) + + # do param translation here, used by datasource tools + if tool.input_translator: + tool.input_translator.translate( params ) + + # create tool state + state = tool.new_state(trans, all_pages=True) + errors = tool.populate_state( trans, tool.inputs, state.inputs, params.__dict__ ) + + # create basic tool model + tool_model = tool.to_dict(trans) + tool_model['inputs'] = {} + + # build tool model + iterate(tool_model['inputs'], tool.inputs, state.inputs, errors, '') + + # load tool help + tool_help = '' + if tool.help: + tool_help = tool.help + tool_help = tool_help.render( static_path=web.url_for( '/static' ), host_url=web.url_for('/', qualified=True) ) + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + + # check if citations exist + tool_citations = False + if tool.citations: + tool_citations = True + + # add additional properties + tool_model.update({ + 'help' : tool_help, + 'citations' : tool_citations, + 'biostar_url' : trans.app.config.biostar_url + }) + + # return enriched tool model + return tool_model diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -180,6 +180,7 @@ webapp.mapper.resource( 'ftp_file', 'ftp_files', path_prefix='/api' ) webapp.mapper.resource( 'group', 'groups', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.mapper.connect( '/api/tools/{id:.+?}/build', action='build', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/reload', action='reload', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}/download', action='download', controller="tools" ) diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -60,9 +60,6 @@ # so the default selected option should be the most recent version of the tool. The following # check will mae sure this occurs. refreshed_on_change = kwd.get( 'refresh', False ) - # This is the new tool forms equivalent to the 'refresh' parameter of the classic tool form - form_refresh = kwd.get( 'form_refresh', False ) - process_state = "populate" if form_refresh else "update" tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, @@ -90,7 +87,7 @@ # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. history = tool.get_default_history_by_trans( trans, create=True ) - template, vars = tool.handle_input( trans, params.__dict__, process_state=process_state) + template, vars = tool.handle_input( trans, params.__dict__ ) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) add_frame = AddFrameData() @@ -98,8 +95,6 @@ if from_noframe is not None: add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True - if form_refresh: - template = "tool_form_refresh.mako" return trans.fill_template( template, history=history, toolbox=self.get_toolbox(), diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 static/scripts/mvc/tools/tools-content.js --- a/static/scripts/mvc/tools/tools-content.js +++ b/static/scripts/mvc/tools/tools-content.js @@ -22,7 +22,7 @@ // get history summary Utils.get({ - url : self.base_url + '?deleted=false', + url : self.base_url + '?deleted=false&state=ok', success : function(response) { // backup summary self.summary = response; diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -27,10 +27,8 @@ this.modal = new Ui.Modal.View(); } - // link model/inputs and all options - this.options = options; - this.model = options.model; - this.inputs = options.model.inputs; + // link options + this.options = options; // set element this.setElement('<div/>'); @@ -53,9 +51,13 @@ // reset input element list, which contains the dom elements of each input element (includes also the input field) this.element_list = {}; - // initialize contents + // for now the initial tool model is parsed through the mako + this.model = this.options; + this.inputs = this.options.inputs; + + // request history content and build form this.content = new ToolContent({ - history_id : this.options.history_id, + history_id : self.options.history_id, success : function() { self._buildForm(); } @@ -89,6 +91,51 @@ console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); }, + // build tool model through api call + _buildModel: function() { + // link this + var self = this; + + // construct url + var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build?'; + if (this.options.job_id) { + model_url += 'job_id=' + this.options.job_id; + } else { + if (this.options.dataset_id) { + model_url += 'dataset_id=' + this.options.dataset_id; + } else { + var loc = top.location.href; + var pos = loc.indexOf('?'); + if (loc.indexOf('tool_id=') != -1 && pos !== -1) { + model_url += loc.slice(pos + 1); + } + } + } + + // get initial model + Utils.request({ + type : 'GET', + url : model_url, + success : function(response) { + // link model data update options + self.options = $.extend(self.options, response); + self.model = response; + self.inputs = response.inputs; + + // log success + console.debug('tools-form::initialize() - Initial tool model ready.'); + console.debug(response); + + // build form + self._buildForm(); + }, + error : function(response) { + console.debug('tools-form::initialize() - Initial tool model request failed.'); + console.debug(response); + } + }); + }, + // refresh form data _refreshForm: function() { // link this @@ -111,7 +158,7 @@ // post job Utils.request({ type : 'GET', - url : galaxy_config.root + 'tool_runner/index?tool_id=' + this.options.id + '&form_refresh=True', + url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -106,17 +106,17 @@ value : function (dict) { // update current value if (dict !== undefined) { - if (dict.values.length > 0 && dict.values[0] && dict.values[0].src) { + try { + // set source + this.current = dict.values[0].src; + this.refresh(); + // create list var list = []; for (var i in dict.values) { list.push(dict.values[i].id); } - // set source - this.current = dict.values[0].src; - this.refresh(); - // identify select element switch(this.current) { case 'hda': @@ -126,6 +126,8 @@ this.select_collection.value(list[0]); break; } + } catch (err) { + console.debug('tools-select-content::value() - Skipped.'); } } diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 static/scripts/packed/mvc/tools/tools-content.js --- a/static/scripts/packed/mvc/tools/tools-content.js +++ b/static/scripts/packed/mvc/tools/tools-content.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false&state=ok",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(this.options.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.model=this.options;this.inputs=this.options.inputs;this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(this.options.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.content.filterType({src:"hda",extensions:h.extensions});var k=[];for(var j in l){k.push({label:l[j].hid+": "+l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.content.filterType({src:"hdca",extensions:h.extensions});var f=[];for(var j in m){f.push({label:m[j].hid+": "+m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(k){if(k!==undefined){if(k.values.length>0&&k.values[0]&&k.values[0].src){var j=[];for(var g in k.values){j.push(k.values[g].id)}this.current=k.values[0].src;this.refresh();switch(this.current){case"hda":this.select_datasets.value(j);break;case"hdca":this.select_collection.value(j[0]);break}}}var h=this._select().value();if(!(h instanceof Array)){h=[h]}var f={batch:!this.options.multiple,values:[]};for(var g in h){f.values.push({id:h[g],src:this.current})}return f},validate:function(){return this._select().validate()},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}},_select:function(){switch(this.current){case"hdca":return this.select_collection;default:return this.select_datasets}}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.content.filterType({src:"hda",extensions:h.extensions});var k=[];for(var j in l){k.push({label:l[j].hid+": "+l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.content.filterType({src:"hdca",extensions:h.extensions});var f=[];for(var j in m){f.push({label:m[j].hid+": "+m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(l){if(l!==undefined){try{this.current=l.values[0].src;this.refresh();var k=[];for(var g in l.values){k.push(l.values[g].id)}switch(this.current){case"hda":this.select_datasets.value(k);break;case"hdca":this.select_collection.value(k[0]);break}}catch(j){console.debug("tools-select-content::value() - Skipped.")}}var h=this._select().value();if(!(h instanceof Array)){h=[h]}var f={batch:!this.options.multiple,values:[]};for(var g in h){f.values.push({id:h[g],src:this.current})}return f},validate:function(){return this._select().validate()},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}},_select:function(){switch(this.current){case"hdca":return this.select_collection;default:return this.select_datasets}}});return{View:d}}); \ No newline at end of file diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -1,16 +1,27 @@ <%inherit file="/base.mako"/> -## initialize configuration -<%namespace name="tool_form_refresh" file="./webapps/galaxy/tool_form_refresh.mako" import="*" /> -${tool_form_refresh.init()} - ## new tool form +<% + ## 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.webapps.galaxy.api.tools import ToolsController + controller = ToolsController(trans.app) + params = dict(trans.request.params) + if 'id' in params: + params['dataset_id'] = params['id'] + self.form_config = controller._build_dict(trans, tool, params) + self.form_config.update({ + 'id' : tool.id, + 'job_id' : trans.security.encode_id( job.id ) if job else None, + 'history_id' : trans.security.encode_id( trans.history.id ) + }) +%> ${h.js("libs/bibtex", "libs/jquery/jquery-ui")} ${h.css('base', 'jquery-ui/smoothness/jquery-ui')} <script> require(['mvc/tools/tools-form'], function(ToolsForm){ $(function(){ - var form = new ToolsForm.View(${ h.dumps(tool_form_refresh.form_config) }); + var form = new ToolsForm.View(${ h.dumps(self.form_config) }); }); }); </script> diff -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 -r 0d44e35432abe4071aa073d1eb4cad074b7fc067 templates/webapps/galaxy/tool_form_refresh.mako --- a/templates/webapps/galaxy/tool_form_refresh.mako +++ /dev/null @@ -1,138 +0,0 @@ -<%def name="init()"> -<% - ## create basic tool model - tool_model = tool.to_dict(trans) - tool_model['inputs'] = {} - - ## convert value to jsonifiable value - def convert(v): - # check if value is numeric - isnumber = False - try: - float(v) - isnumber = True - except Exception: - pass - - ## fix hda parsing - if isinstance(v, HistoryDatasetAssociation): - return { - 'id' : trans.security.encode_id(v.id), - 'src' : 'hda' - } - elif isinstance(v, basestring) or isnumber: - return v - else: - return None - - ## ensures that input dictionary is jsonifiable - from collections import Iterable - from galaxy.model import HistoryDatasetAssociation - def sanitize(dict): - ## quotations for Infinity so its jsonifiable - for name in dict: - if dict[name] == Infinity: - dict[name] = 'Infinity' - - ## get current value - value = dict['value'] if 'value' in dict else None - - ## identify lists - if dict['type'] == 'data': - if isinstance(value, list): - value = [ convert(v) for v in value ] - else: - value = [ convert(value) ] - value = { - 'batch' : dict['multiple'], - 'values' : value - } - elif isinstance(value, list): - value = [ convert(v) for v in value ] - else: - value = convert(value) - - ## update and return - dict['value'] = value - return dict - - ## build model - def build(group_inputs, inputs, tool_state, errors, other_values=None): - from galaxy.util.expressions import ExpressionContext - other_values = ExpressionContext( tool_state, other_values ) - for input_index, input in enumerate( inputs.itervalues() ): - ## create model dictionary - group_inputs[input_index] = input.to_dict(trans) - - ## identify stat for subsection/group - group_state = tool_state[input.name] - - ## iterate and update values - if input.type == "repeat": - group_cache = group_inputs[input_index]['cache'] = {} - for i in range( len( group_state ) ): - group_cache[i] = {} - group_errors = errors[input.name][i] if input.name in errors else dict() - build( group_cache[i], input.inputs, group_state[i], group_errors, other_values ) - elif input.type == "conditional": - try: - test_param = group_inputs[input_index]['test_param'] - test_param['value'] = group_state[test_param['name']] - except Exception: - pass - i = group_state['__current_case__'] - group_errors = errors.get( input.name, {} ) - build(group_inputs[input_index]['cases'][i]['inputs'], input.cases[i].inputs, group_state, group_errors, other_values) - else: - ## create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options - try: - group_inputs[input_index] = input.to_dict(trans, other_values=other_values) - except Exception: - pass - - ## update input value from tool state - try: - group_inputs[input_index]['value'] = tool_state[group_inputs[input_index]['name']] - group_inputs[input_index] = sanitize(group_inputs[input_index]) - except Exception: - pass - endif - endfor - build(tool_model['inputs'], tool.inputs, tool_state.inputs, errors, "") - - # load tool help - tool_help = '' - if tool.help: - if tool.has_multiple_pages: - tool_help = tool.help_by_page[tool_state.page] - else: - tool_help = tool.help - - # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) - - # Convert to unicode to display non-ascii characters. - if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') - endif - - # check if citations exist - tool_citations = False - if tool.citations: - tool_citations = True - - # form configuration - self.form_config = { - 'id' : tool.id, - 'model' : tool_model, - 'help' : tool_help, - 'citations' : tool_citations, - 'biostar_url' : trans.app.config.biostar_url, - 'history_id' : trans.security.encode_id( trans.history.id ), - 'job_id' : trans.security.encode_id( job.id ) if job else None - } -%> -</%def> - -${ init() } -${ h.dumps(self.form_config) } \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix for datatypes consuming output extra files path for the change in d781366.
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e1404e285ccb/ Changeset: e1404e285ccb Branch: stable User: jmchilton Date: 2014-10-15 16:57:10+00:00 Summary: Fix for datatypes consuming output extra files path for the change in d781366. That change forced $output.extra_files_path to be the same thing as $output.files_path. See rational in changeset. Some datatypes however consume this path when generated metadata - post d781366 these datatypes would be accessing the wrong directory. This fixes them. The suggested best practice I would put forward is $input.extra_files_path and $output.files_path. $output.extra_files_path redirects to $output.files_path for newer Galaxy versions (August 2014+) so that Galaxy configurations requiring this directory be in the jobs working directory work. Datatypes consuming dataset.extra_files_path for these outputs will be broken when used with $output.files_path for the August release of Galaxy - but if this changeset is back-ported to the October 2014 release then these types and tools will work going forward (without modification). It can be verified that the older releases are broken with the following existing test (fixed with this changeset). ./run_functional_tests.sh -framework -id composite_output Affected #: 2 files diff -r cdd3a8a9cd7d5d71705843d2fa448462c7ed0675 -r e1404e285ccb9e52bd09c5827934cd0da1974acc lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1332,6 +1332,7 @@ self.purged = False self.purgable = purgable self.external_filename = external_filename + self.external_extra_files_path = None self._extra_files_path = extra_files_path self.file_size = file_size if uuid is None: @@ -1355,9 +1356,20 @@ else: self.external_filename = filename file_name = property( get_file_name, set_file_name ) - @property - def extra_files_path( self ): - return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) + def get_extra_files_path( self ): + # Unlike get_file_name - extrnal_extra_files_path is not backed by an + # actual database column so if SA instantiates this object - the + # attribute won't exist yet. + if not getattr( self, "external_extra_files_path", None ): + return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) + else: + return os.path.abspath( self.external_extra_files_path ) + def set_extra_files_path( self, extra_files_path ): + if not extra_files_path: + self.external_extra_files_path = None + else: + self.external_extra_files_path = extra_files_path + extra_files_path = property( get_extra_files_path, set_extra_files_path) def _calculate_size( self ): if self.external_filename: try: diff -r cdd3a8a9cd7d5d71705843d2fa448462c7ed0675 -r e1404e285ccb9e52bd09c5827934cd0da1974acc scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -120,6 +120,8 @@ dataset = cPickle.load( open( filename_in ) ) # load DatasetInstance if dataset_filename_override: dataset.dataset.external_filename = dataset_filename_override + files_path = os.path.abspath(os.path.join( tool_job_working_directory, "dataset_%s_files" % (dataset.dataset.id) )) + dataset.dataset.external_extra_files_path = files_path if dataset.dataset.id in existing_job_metadata_dict: dataset.extension = existing_job_metadata_dict[ dataset.dataset.id ].get( 'ext', dataset.extension ) # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles 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: Fix options menu
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b09297ed0db/ Changeset: 9b09297ed0db User: guerler Date: 2014-10-16 14:48:18+00:00 Summary: ToolForm: Fix options menu Affected #: 3 files diff -r 6e605c5d9feff984bfb5e67f2c36a400abdcae85 -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -135,25 +135,28 @@ tooltip : 'Click to see a list of options.' }); - // add question option - menu.addMenu({ - icon : 'fa-question-circle', - title : 'Question?', - tooltip : 'Ask a question about this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/p/new/post/'); - } - }); - - // create search button - menu.addMenu({ - icon : 'fa-search', - title : 'Search', - tooltip : 'Search help for this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); - } - }); + // configure button selection + if(this.options.biostar_url) { + // add question option + menu.addMenu({ + icon : 'fa-question-circle', + title : 'Question?', + tooltip : 'Ask a question about this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/p/new/post/'); + } + }); + + // create search button + menu.addMenu({ + icon : 'fa-search', + title : 'Search', + tooltip : 'Search help for this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); + } + }); + }; // create share button menu.addMenu({ @@ -213,12 +216,6 @@ } }); - // configure button selection - if(!this.options.biostar_url) { - button_question.$el.hide(); - button_search.$el.hide(); - } - // append form this.$el.append(this.portlet.$el); diff -r 6e605c5d9feff984bfb5e67f2c36a400abdcae85 -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -135,25 +135,28 @@ tooltip : 'Click to see a list of options.' }); - // add question option - menu.addMenu({ - icon : 'fa-question-circle', - title : 'Question?', - tooltip : 'Ask a question about this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/p/new/post/'); - } - }); - - // create search button - menu.addMenu({ - icon : 'fa-search', - title : 'Search', - tooltip : 'Search help for this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); - } - }); + // configure button selection + if(this.options.biostar_url) { + // add question option + menu.addMenu({ + icon : 'fa-question-circle', + title : 'Question?', + tooltip : 'Ask a question about this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/p/new/post/'); + } + }); + + // create search button + menu.addMenu({ + icon : 'fa-search', + title : 'Search', + tooltip : 'Search help for this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); + } + }); + }; // create share button menu.addMenu({ @@ -213,12 +216,6 @@ } }); - // configure button selection - if(!this.options.biostar_url) { - button_question.$el.hide(); - button_search.$el.hide(); - } - // append form this.$el.append(this.portlet.$el); diff -r 6e605c5d9feff984bfb5e67f2c36a400abdcae85 -r 9b09297ed0dbf506d5de13b6f91bbbd334b86238 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!this.options.biostar_url){button_question.$el.hide();button_search.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(this.options.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ 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.

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commit/galaxy-central: guerler: ToolForm: Fix sorting of content labels
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6e605c5d9fef/ Changeset: 6e605c5d9fef User: guerler Date: 2014-10-15 22:38:07+00:00 Summary: ToolForm: Fix sorting of content labels Affected #: 3 files diff -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 -r 6e605c5d9feff984bfb5e67f2c36a400abdcae85 client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -27,6 +27,11 @@ // backup summary self.summary = response; + // sort by id + self.summary.sort(function(a, b) { + return a.hid > b.hid ? -1 : (a.hid < b.hid ? 1 : 0); + }); + // log console.debug('tools-content::initialize() - Completed.'); diff -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 -r 6e605c5d9feff984bfb5e67f2c36a400abdcae85 static/scripts/mvc/tools/tools-content.js --- a/static/scripts/mvc/tools/tools-content.js +++ b/static/scripts/mvc/tools/tools-content.js @@ -27,6 +27,11 @@ // backup summary self.summary = response; + // sort by id + self.summary.sort(function(a, b) { + return a.hid > b.hid ? -1 : (a.hid < b.hid ? 1 : 0); + }); + // log console.debug('tools-content::initialize() - Completed.'); diff -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 -r 6e605c5d9feff984bfb5e67f2c36a400abdcae85 static/scripts/packed/mvc/tools/tools-content.js --- a/static/scripts/packed/mvc/tools/tools-content.js +++ b/static/scripts/packed/mvc/tools/tools-content.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ 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.

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commit/galaxy-central: guerler: ToolForm: Highlight first error only
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a100c09d3e3a/ Changeset: a100c09d3e3a User: guerler Date: 2014-10-15 20:43:42+00:00 Summary: ToolForm: Highlight first error only Affected #: 6 files diff -r d94ef8154c63145b0e2928b099017324097d4352 -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -132,7 +132,7 @@ // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', - tooltip : 'Click to see a list of available operations.' + tooltip : 'Click to see a list of options.' }); // add question option diff -r d94ef8154c63145b0e2928b099017324097d4352 -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -55,6 +55,7 @@ var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); + break; } } else { // show error message with details diff -r d94ef8154c63145b0e2928b099017324097d4352 -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -132,7 +132,7 @@ // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', - tooltip : 'Click to see a list of available operations.' + tooltip : 'Click to see a list of options.' }); // add question option diff -r d94ef8154c63145b0e2928b099017324097d4352 -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -55,6 +55,7 @@ var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); + break; } } else { // show error message with details diff -r d94ef8154c63145b0e2928b099017324097d4352 -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of available operations."});p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!this.options.biostar_url){button_question.$el.hide();button_search.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!this.options.biostar_url){button_question.$el.hide();button_search.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file diff -r d94ef8154c63145b0e2928b099017324097d4352 -r a100c09d3e3ad5d8df2747384d3d6b22c3658cb9 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ 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

commit/galaxy-central: dannon: Merged in jmchilton/galaxy-central-fork-1 (pull request #530)
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d94ef8154c63/ Changeset: d94ef8154c63 User: dannon Date: 2014-10-15 20:30:56+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #530) Implement creating tool shed repository revisions via API tarball upload. Affected #: 5 files diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -30,7 +30,7 @@ f.file.close() upload_dataset['file_data'] = dict( filename=f.filename, local_filename=local_filename ) - elif type( f ) == dict and 'filename' and 'local_filename' not in f: + elif type( f ) == dict and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) 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_" ) diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -2,11 +2,15 @@ import logging import os import tarfile +import StringIO import tempfile from time import strftime +from cgi import FieldStorage + from galaxy import util from galaxy import web +from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest @@ -16,10 +20,14 @@ from tool_shed.metadata import repository_metadata_manager from tool_shed.repository_types import util as rt_util +from tool_shed.dependencies import attribute_handlers + from tool_shed.util import basic_util +from tool_shed.util import commit_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import repository_util +from tool_shed.util import repository_content_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -568,3 +576,108 @@ action='show', id=trans.security.encode_id( repository.id ) ) return repository_dict + + @web.expose_api + def create_changeset_revision( self, trans, id, payload, **kwd ): + """ + POST /api/repositories/{encoded_repository_id}/changeset_revision + + Create a new tool shed repository commit - leaving PUT on parent + resource open for updating meta-attirbutes of the repository (and + Galaxy doesn't allow PUT multipart data anyway + https://trello.com/c/CQwmCeG6) + + :param id: the encoded id of the Repository object + + The following parameters may be included in the payload. + :param commit_message: hg commit message for update. + """ + + # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135 + rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) + tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) + + repository = suc.get_repository_in_tool_shed( trans.app, id ) + repo_dir = repository.repo_path( trans.app ) + repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) + + upload_point = commit_util.get_upload_point( repository, **kwd ) + tip = repository.tip( trans.app ) + + file_data = payload.get('file') + # Code stolen from gx's upload_common.py + if isinstance( file_data, FieldStorage ): + assert not isinstance( file_data.file, StringIO.StringIO ) + assert file_data.file.name != '<fdopen>' + local_filename = util.mkstemp_ln( file_data.file.name, 'upload_file_data_' ) + file_data.file.close() + file_data = dict( filename=file_data.filename, + local_filename=local_filename ) + elif type( file_data ) == dict and 'local_filename' not in file_data: + raise Exception( 'Uploaded file was encoded in a way not understood.' ) + + commit_message = kwd.get( 'commit_message', 'Uploaded' ) + + uploaded_file = open(file_data['local_filename'], 'rb') + uploaded_file_name = file_data['local_filename'] + + isgzip = False + isbz2 = False + isgzip = checkers.is_gzip( uploaded_file_name ) + if not isgzip: + isbz2 = checkers.is_bz2( uploaded_file_name ) + if ( isgzip or isbz2 ): + # Open for reading with transparent compression. + tar = tarfile.open( uploaded_file_name, 'r:*' ) + else: + tar = tarfile.open( uploaded_file_name ) + + new_repo_alert = False + remove_repo_files_not_in_tar = True + + ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + repository_content_util.upload_tar( + trans, + rdah, + tdah, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert + ) + if ok: + # Update the repository files for browsing. + hg_util.update_repository( repo ) + # Get the new repository tip. + if tip == repository.tip( trans.app ): + trans.response.status = 400 + message = 'No changes to repository.' + ok = False + else: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = \ + rmm.set_repository_metadata_due_to_new_tip( trans.request.host, + content_alert_str=content_alert_str, + **kwd ) + if error_message: + ok = False + trans.response.status = 500 + message = error_message + else: + trans.response.status = 500 + + if not ok: + return { + "err_msg": message, + "content_alert": content_alert_str + } + else: + return { + "message": message, + "content_alert": content_alert_str + } diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -119,6 +119,12 @@ name_prefix='user_', path_prefix='/api', parent_resources=dict( member_name='user', collection_name='users' ) ) + webapp.mapper.connect( 'repository_create_changeset_revision', + '/api/repositories/:id/changeset_revision', + controller='repositories', + action='create_changeset_revision', + conditions=dict( method=[ "POST" ] ) ) + webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -20,6 +20,7 @@ from tool_shed.util import commit_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc +from tool_shed.util import repository_content_util from tool_shed.util import xml_util from galaxy import eggs @@ -129,16 +130,18 @@ istar = False if istar: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ - self.upload_tar( trans, - rdah, - tdah, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message, - new_repo_alert ) + repository_content_util.upload_tar( + trans, + rdah, + tdah, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert + ) elif uploaded_directory: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ self.upload_directory( trans, @@ -407,69 +410,3 @@ commit_message, undesirable_dirs_removed, undesirable_files_removed ) - - def upload_tar( self, trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, - commit_message, new_repo_alert ): - # Upload a tar archive of files. - repo_dir = repository.repo_path( trans.app ) - repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) - undesirable_dirs_removed = 0 - undesirable_files_removed = 0 - ok, message = commit_util.check_archive( repository, tar ) - if not ok: - tar.close() - uploaded_file.close() - return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed - else: - if upload_point is not None: - full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) - else: - full_path = os.path.abspath( repo_dir ) - filenames_in_archive = [] - for tarinfo_obj in tar.getmembers(): - ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES - if ok: - for file_path_item in tarinfo_obj.name.split( '/' ): - if file_path_item in commit_util.UNDESIRABLE_DIRS: - undesirable_dirs_removed += 1 - ok = False - break - else: - undesirable_files_removed += 1 - if ok: - filenames_in_archive.append( tarinfo_obj.name ) - # Extract the uploaded tar to the load_point within the repository hierarchy. - tar.extractall( path=full_path ) - tar.close() - uploaded_file.close() - for filename in filenames_in_archive: - uploaded_file_name = os.path.join( full_path, filename ) - if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if toolshed or changeset_revision attributes - # are missing and if so, set them appropriately. - altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) - if error_message: - return False, error_message, [], '', [], [] - elif altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) - elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if toolshed or changeset_revision - # attributes are missing and if so, set them appropriately. - altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) - if error_message: - return False, error_message, [], '', [], [] - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) - return commit_util.handle_directory_changes( trans.app, - trans.request.host, - trans.user.username, - repository, - full_path, - filenames_in_archive, - remove_repo_files_not_in_tar, - new_repo_alert, - commit_message, - undesirable_dirs_removed, - undesirable_files_removed ) diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/tool_shed/util/repository_content_util.py --- /dev/null +++ b/lib/tool_shed/util/repository_content_util.py @@ -0,0 +1,75 @@ +import os +import shutil + +from tool_shed.util import commit_util +from tool_shed.util import hg_util +from tool_shed.util import xml_util + +import tool_shed.repository_types.util as rt_util + + +def upload_tar( trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, + commit_message, new_repo_alert ): + # Upload a tar archive of files. + repo_dir = repository.repo_path( trans.app ) + hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + ok, message = commit_util.check_archive( repository, tar ) + if not ok: + tar.close() + uploaded_file.close() + return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed + else: + if upload_point is not None: + full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) + else: + full_path = os.path.abspath( repo_dir ) + filenames_in_archive = [] + for tarinfo_obj in tar.getmembers(): + ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in commit_util.UNDESIRABLE_DIRS: + undesirable_dirs_removed += 1 + ok = False + break + else: + undesirable_files_removed += 1 + if ok: + filenames_in_archive.append( tarinfo_obj.name ) + # Extract the uploaded tar to the load_point within the repository hierarchy. + tar.extractall( path=full_path ) + tar.close() + uploaded_file.close() + for filename in filenames_in_archive: + uploaded_file_name = os.path.join( full_path, filename ) + if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + return False, error_message, [], '', [], [] + elif altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + return False, error_message, [], '', [], [] + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + return commit_util.handle_directory_changes( trans.app, + trans.request.host, + trans.user.username, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d6059c7194ef/ Changeset: d6059c7194ef User: jmchilton Date: 2014-10-14 20:30:27+00:00 Summary: Implement creating tool shed repository revisions via API tarball upload. Affected #: 4 files diff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac -r d6059c7194effc68dbfae4a459bd456c82fe8478 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -2,11 +2,15 @@ import logging import os import tarfile +import StringIO import tempfile from time import strftime +from cgi import FieldStorage + from galaxy import util from galaxy import web +from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest @@ -16,10 +20,14 @@ from tool_shed.metadata import repository_metadata_manager from tool_shed.repository_types import util as rt_util +from tool_shed.dependencies import attribute_handlers + from tool_shed.util import basic_util +from tool_shed.util import commit_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import repository_util +from tool_shed.util import repository_content_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -568,3 +576,109 @@ action='show', id=trans.security.encode_id( repository.id ) ) return repository_dict + + @web.expose_api + def create_changeset_revision( self, trans, id, payload, **kwd ): + """ + POST /api/repositories/{encoded_repository_id}/changeset_revision + + Create a new tool shed repository commit - leaving PUT on parent + resource open for updating meta-attirbutes of the repository (and + Galaxy doesn't allow PUT multipart data anyway + https://trello.com/c/CQwmCeG6) + + :param id: the encoded id of the Repository object + + The following parameters may be included in the payload. + :param commit_message: hg commit message for update. + """ + + # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135 + rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) + tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) + + repository = suc.get_repository_in_tool_shed( trans.app, id ) + repo_dir = repository.repo_path( trans.app ) + repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) + + upload_point = commit_util.get_upload_point( repository, **kwd ) + tip = repository.tip( trans.app ) + + file_data = payload.get('file') + # Code stolen from gx's upload_common.py + if isinstance( file_data, FieldStorage ): + assert not isinstance( file_data.file, StringIO.StringIO ) + assert file_data.file.name != '<fdopen>' + local_filename = util.mkstemp_ln( file_data.file.name, 'upload_file_data_' ) + file_data.file.close() + file_data = dict( filename=file_data.filename, + local_filename=local_filename ) + elif type( file_data ) == dict and 'filename' and 'local_filename' not in file_data: + raise Exception( 'Uploaded file was encoded in a way not understood.' ) + + commit_message = kwd.get( 'commit_message', 'Uploaded' ) + + uploaded_file = open(file_data['local_filename'], 'rb') + uploaded_file_name = file_data['local_filename'] + + ok = True + isgzip = False + isbz2 = False + isgzip = checkers.is_gzip( uploaded_file_name ) + if not isgzip: + isbz2 = checkers.is_bz2( uploaded_file_name ) + if ( isgzip or isbz2 ): + # Open for reading with transparent compression. + tar = tarfile.open( uploaded_file_name, 'r:*' ) + else: + tar = tarfile.open( uploaded_file_name ) + + new_repo_alert = False + remove_repo_files_not_in_tar = True + + ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + repository_content_util.upload_tar( + trans, + rdah, + tdah, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert + ) + if ok: + # Update the repository files for browsing. + hg_util.update_repository( repo ) + # Get the new repository tip. + if tip == repository.tip( trans.app ): + trans.response.status = 400 + message = 'No changes to repository.' + ok = False + else: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = \ + rmm.set_repository_metadata_due_to_new_tip( trans.request.host, + content_alert_str=content_alert_str, + **kwd ) + if error_message: + ok = False + trans.response.status = 500 + message = error_message + else: + trans.response.status = 500 + + if not ok: + return { + "err_msg": message, + "content_alert": content_alert_str + } + else: + return { + "message": message, + "content_alert": content_alert_str + } diff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac -r d6059c7194effc68dbfae4a459bd456c82fe8478 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -119,6 +119,12 @@ name_prefix='user_', path_prefix='/api', parent_resources=dict( member_name='user', collection_name='users' ) ) + webapp.mapper.connect( 'repository_create_changeset_revision', + '/api/repositories/:id/changeset_revision', + controller='repositories', + action='create_changeset_revision', + conditions=dict( method=[ "POST" ] ) ) + webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac -r d6059c7194effc68dbfae4a459bd456c82fe8478 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -20,6 +20,7 @@ from tool_shed.util import commit_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc +from tool_shed.util import repository_content_util from tool_shed.util import xml_util from galaxy import eggs @@ -129,16 +130,18 @@ istar = False if istar: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ - self.upload_tar( trans, - rdah, - tdah, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message, - new_repo_alert ) + repository_content_util.upload_tar( + trans, + rdah, + tdah, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert + ) elif uploaded_directory: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ self.upload_directory( trans, @@ -407,69 +410,3 @@ commit_message, undesirable_dirs_removed, undesirable_files_removed ) - - def upload_tar( self, trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, - commit_message, new_repo_alert ): - # Upload a tar archive of files. - repo_dir = repository.repo_path( trans.app ) - repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) - undesirable_dirs_removed = 0 - undesirable_files_removed = 0 - ok, message = commit_util.check_archive( repository, tar ) - if not ok: - tar.close() - uploaded_file.close() - return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed - else: - if upload_point is not None: - full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) - else: - full_path = os.path.abspath( repo_dir ) - filenames_in_archive = [] - for tarinfo_obj in tar.getmembers(): - ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES - if ok: - for file_path_item in tarinfo_obj.name.split( '/' ): - if file_path_item in commit_util.UNDESIRABLE_DIRS: - undesirable_dirs_removed += 1 - ok = False - break - else: - undesirable_files_removed += 1 - if ok: - filenames_in_archive.append( tarinfo_obj.name ) - # Extract the uploaded tar to the load_point within the repository hierarchy. - tar.extractall( path=full_path ) - tar.close() - uploaded_file.close() - for filename in filenames_in_archive: - uploaded_file_name = os.path.join( full_path, filename ) - if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if toolshed or changeset_revision attributes - # are missing and if so, set them appropriately. - altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) - if error_message: - return False, error_message, [], '', [], [] - elif altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) - elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if toolshed or changeset_revision - # attributes are missing and if so, set them appropriately. - altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) - if error_message: - return False, error_message, [], '', [], [] - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) - return commit_util.handle_directory_changes( trans.app, - trans.request.host, - trans.user.username, - repository, - full_path, - filenames_in_archive, - remove_repo_files_not_in_tar, - new_repo_alert, - commit_message, - undesirable_dirs_removed, - undesirable_files_removed ) diff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac -r d6059c7194effc68dbfae4a459bd456c82fe8478 lib/tool_shed/util/repository_content_util.py --- /dev/null +++ b/lib/tool_shed/util/repository_content_util.py @@ -0,0 +1,75 @@ +import os +import shutil + +from tool_shed.util import commit_util +from tool_shed.util import hg_util +from tool_shed.util import xml_util + +import tool_shed.repository_types.util as rt_util + + +def upload_tar( trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, + commit_message, new_repo_alert ): + # Upload a tar archive of files. + repo_dir = repository.repo_path( trans.app ) + hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + ok, message = commit_util.check_archive( repository, tar ) + if not ok: + tar.close() + uploaded_file.close() + return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed + else: + if upload_point is not None: + full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) + else: + full_path = os.path.abspath( repo_dir ) + filenames_in_archive = [] + for tarinfo_obj in tar.getmembers(): + ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in commit_util.UNDESIRABLE_DIRS: + undesirable_dirs_removed += 1 + ok = False + break + else: + undesirable_files_removed += 1 + if ok: + filenames_in_archive.append( tarinfo_obj.name ) + # Extract the uploaded tar to the load_point within the repository hierarchy. + tar.extractall( path=full_path ) + tar.close() + uploaded_file.close() + for filename in filenames_in_archive: + uploaded_file_name = os.path.join( full_path, filename ) + if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + return False, error_message, [], '', [], [] + elif altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + return False, error_message, [], '', [], [] + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + return commit_util.handle_directory_changes( trans.app, + trans.request.host, + trans.user.username, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) https://bitbucket.org/galaxy/galaxy-central/commits/7d8d1396b7ca/ Changeset: 7d8d1396b7ca User: jmchilton Date: 2014-10-15 19:27:23+00:00 Summary: Fixes to tool shed tar upload API enhancement. Thanks to Bjoern and Dannon for the comments. Affected #: 2 files diff -r d6059c7194effc68dbfae4a459bd456c82fe8478 -r 7d8d1396b7cad129e9d89677a8c10d5bc9b2f1f4 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -30,7 +30,7 @@ f.file.close() upload_dataset['file_data'] = dict( filename=f.filename, local_filename=local_filename ) - elif type( f ) == dict and 'filename' and 'local_filename' not in f: + elif type( f ) == dict and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) 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_" ) diff -r d6059c7194effc68dbfae4a459bd456c82fe8478 -r 7d8d1396b7cad129e9d89677a8c10d5bc9b2f1f4 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -613,7 +613,7 @@ file_data.file.close() file_data = dict( filename=file_data.filename, local_filename=local_filename ) - elif type( file_data ) == dict and 'filename' and 'local_filename' not in file_data: + elif type( file_data ) == dict and 'local_filename' not in file_data: raise Exception( 'Uploaded file was encoded in a way not understood.' ) commit_message = kwd.get( 'commit_message', 'Uploaded' ) @@ -621,7 +621,6 @@ uploaded_file = open(file_data['local_filename'], 'rb') uploaded_file_name = file_data['local_filename'] - ok = True isgzip = False isbz2 = False isgzip = checkers.is_gzip( uploaded_file_name ) https://bitbucket.org/galaxy/galaxy-central/commits/d94ef8154c63/ Changeset: d94ef8154c63 User: dannon Date: 2014-10-15 20:30:56+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #530) Implement creating tool shed repository revisions via API tarball upload. Affected #: 5 files diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -30,7 +30,7 @@ f.file.close() upload_dataset['file_data'] = dict( filename=f.filename, local_filename=local_filename ) - elif type( f ) == dict and 'filename' and 'local_filename' not in f: + elif type( f ) == dict and 'local_filename' not in f: raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) 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_" ) diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -2,11 +2,15 @@ import logging import os import tarfile +import StringIO import tempfile from time import strftime +from cgi import FieldStorage + from galaxy import util from galaxy import web +from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest @@ -16,10 +20,14 @@ from tool_shed.metadata import repository_metadata_manager from tool_shed.repository_types import util as rt_util +from tool_shed.dependencies import attribute_handlers + from tool_shed.util import basic_util +from tool_shed.util import commit_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import repository_util +from tool_shed.util import repository_content_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -568,3 +576,108 @@ action='show', id=trans.security.encode_id( repository.id ) ) return repository_dict + + @web.expose_api + def create_changeset_revision( self, trans, id, payload, **kwd ): + """ + POST /api/repositories/{encoded_repository_id}/changeset_revision + + Create a new tool shed repository commit - leaving PUT on parent + resource open for updating meta-attirbutes of the repository (and + Galaxy doesn't allow PUT multipart data anyway + https://trello.com/c/CQwmCeG6) + + :param id: the encoded id of the Repository object + + The following parameters may be included in the payload. + :param commit_message: hg commit message for update. + """ + + # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135 + rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) + tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) + + repository = suc.get_repository_in_tool_shed( trans.app, id ) + repo_dir = repository.repo_path( trans.app ) + repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) + + upload_point = commit_util.get_upload_point( repository, **kwd ) + tip = repository.tip( trans.app ) + + file_data = payload.get('file') + # Code stolen from gx's upload_common.py + if isinstance( file_data, FieldStorage ): + assert not isinstance( file_data.file, StringIO.StringIO ) + assert file_data.file.name != '<fdopen>' + local_filename = util.mkstemp_ln( file_data.file.name, 'upload_file_data_' ) + file_data.file.close() + file_data = dict( filename=file_data.filename, + local_filename=local_filename ) + elif type( file_data ) == dict and 'local_filename' not in file_data: + raise Exception( 'Uploaded file was encoded in a way not understood.' ) + + commit_message = kwd.get( 'commit_message', 'Uploaded' ) + + uploaded_file = open(file_data['local_filename'], 'rb') + uploaded_file_name = file_data['local_filename'] + + isgzip = False + isbz2 = False + isgzip = checkers.is_gzip( uploaded_file_name ) + if not isgzip: + isbz2 = checkers.is_bz2( uploaded_file_name ) + if ( isgzip or isbz2 ): + # Open for reading with transparent compression. + tar = tarfile.open( uploaded_file_name, 'r:*' ) + else: + tar = tarfile.open( uploaded_file_name ) + + new_repo_alert = False + remove_repo_files_not_in_tar = True + + ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + repository_content_util.upload_tar( + trans, + rdah, + tdah, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert + ) + if ok: + # Update the repository files for browsing. + hg_util.update_repository( repo ) + # Get the new repository tip. + if tip == repository.tip( trans.app ): + trans.response.status = 400 + message = 'No changes to repository.' + ok = False + else: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = \ + rmm.set_repository_metadata_due_to_new_tip( trans.request.host, + content_alert_str=content_alert_str, + **kwd ) + if error_message: + ok = False + trans.response.status = 500 + message = error_message + else: + trans.response.status = 500 + + if not ok: + return { + "err_msg": message, + "content_alert": content_alert_str + } + else: + return { + "message": message, + "content_alert": content_alert_str + } diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -119,6 +119,12 @@ name_prefix='user_', path_prefix='/api', parent_resources=dict( member_name='user', collection_name='users' ) ) + webapp.mapper.connect( 'repository_create_changeset_revision', + '/api/repositories/:id/changeset_revision', + controller='repositories', + action='create_changeset_revision', + conditions=dict( method=[ "POST" ] ) ) + webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -20,6 +20,7 @@ from tool_shed.util import commit_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc +from tool_shed.util import repository_content_util from tool_shed.util import xml_util from galaxy import eggs @@ -129,16 +130,18 @@ istar = False if istar: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ - self.upload_tar( trans, - rdah, - tdah, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message, - new_repo_alert ) + repository_content_util.upload_tar( + trans, + rdah, + tdah, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert + ) elif uploaded_directory: ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ self.upload_directory( trans, @@ -407,69 +410,3 @@ commit_message, undesirable_dirs_removed, undesirable_files_removed ) - - def upload_tar( self, trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, - commit_message, new_repo_alert ): - # Upload a tar archive of files. - repo_dir = repository.repo_path( trans.app ) - repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) - undesirable_dirs_removed = 0 - undesirable_files_removed = 0 - ok, message = commit_util.check_archive( repository, tar ) - if not ok: - tar.close() - uploaded_file.close() - return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed - else: - if upload_point is not None: - full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) - else: - full_path = os.path.abspath( repo_dir ) - filenames_in_archive = [] - for tarinfo_obj in tar.getmembers(): - ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES - if ok: - for file_path_item in tarinfo_obj.name.split( '/' ): - if file_path_item in commit_util.UNDESIRABLE_DIRS: - undesirable_dirs_removed += 1 - ok = False - break - else: - undesirable_files_removed += 1 - if ok: - filenames_in_archive.append( tarinfo_obj.name ) - # Extract the uploaded tar to the load_point within the repository hierarchy. - tar.extractall( path=full_path ) - tar.close() - uploaded_file.close() - for filename in filenames_in_archive: - uploaded_file_name = os.path.join( full_path, filename ) - if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if toolshed or changeset_revision attributes - # are missing and if so, set them appropriately. - altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) - if error_message: - return False, error_message, [], '', [], [] - elif altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) - elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Inspect the contents of the file to see if toolshed or changeset_revision - # attributes are missing and if so, set them appropriately. - altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) - if error_message: - return False, error_message, [], '', [], [] - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) - return commit_util.handle_directory_changes( trans.app, - trans.request.host, - trans.user.username, - repository, - full_path, - filenames_in_archive, - remove_repo_files_not_in_tar, - new_repo_alert, - commit_message, - undesirable_dirs_removed, - undesirable_files_removed ) diff -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 -r d94ef8154c63145b0e2928b099017324097d4352 lib/tool_shed/util/repository_content_util.py --- /dev/null +++ b/lib/tool_shed/util/repository_content_util.py @@ -0,0 +1,75 @@ +import os +import shutil + +from tool_shed.util import commit_util +from tool_shed.util import hg_util +from tool_shed.util import xml_util + +import tool_shed.repository_types.util as rt_util + + +def upload_tar( trans, rdah, tdah, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, + commit_message, new_repo_alert ): + # Upload a tar archive of files. + repo_dir = repository.repo_path( trans.app ) + hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + ok, message = commit_util.check_archive( repository, tar ) + if not ok: + tar.close() + uploaded_file.close() + return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed + else: + if upload_point is not None: + full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) + else: + full_path = os.path.abspath( repo_dir ) + filenames_in_archive = [] + for tarinfo_obj in tar.getmembers(): + ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in commit_util.UNDESIRABLE_DIRS: + undesirable_dirs_removed += 1 + ok = False + break + else: + undesirable_files_removed += 1 + if ok: + filenames_in_archive.append( tarinfo_obj.name ) + # Extract the uploaded tar to the load_point within the repository hierarchy. + tar.extractall( path=full_path ) + tar.close() + uploaded_file.close() + for filename in filenames_in_archive: + uploaded_file_name = os.path.join( full_path, filename ) + if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + return False, error_message, [], '', [], [] + elif altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + return False, error_message, [], '', [], [] + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + return commit_util.handle_directory_changes( trans.app, + trans.request.host, + trans.user.username, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History structure: found a way to sync SVG and DOM when expanding/collapsing jobs and datasets in the vertical layout
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9728fcd5167c/ Changeset: 9728fcd5167c User: carlfeberhard Date: 2014-10-15 20:21:51+00:00 Summary: History structure: found a way to sync SVG and DOM when expanding/collapsing jobs and datasets in the vertical layout Affected #: 9 files diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 client/galaxy/scripts/mvc/history/history-structure-view.js --- a/client/galaxy/scripts/mvc/history/history-structure-view.js +++ b/client/galaxy/scripts/mvc/history/history-structure-view.js @@ -52,14 +52,22 @@ //this.debug( job.outputCollection ); // create the bbone view for the job (to be positioned later accrd. to the layout) and cache - var li = new JOB_LI.JobListItemView({ model: job, expanded: true }); + var li = new JOB_LI.JobListItemView({ model: job }); //var li = new JOB_LI.JobListItemView({ model: job }); - li.$el.appendTo( view.$el ); + li.render( 0 ).$el.appendTo( view.$el ); view._jobLiMap[ job.id ] = li; + view._setUpJobListeners( li ); + }); return view.jobs; }, + _setUpJobListeners : function( jobLi ){ + // update the layout during expansion and collapsing of job and output li's + jobLi.on( 'expanding expanded collapsing collapsed', this.render, this ); + jobLi.foldout.on( 'view:expanding view:expanded view:collapsing view:collapsed', this.render, this ); + }, + layoutDefaults : { paddingTop : 8, paddingLeft : 20, @@ -131,32 +139,32 @@ }, render : function( options ){ - this.log( this + '.renderComponent:', options ); + this.debug( this + '.render:', options ); var view = this; - view.component.eachVertex( function( v ){ - //TODO:? liMap needed - can't we attach to vertex? - var li = view._jobLiMap[ v.name ]; - if( !li.$el.is( ':visible' ) ){ - li.render( 0 ); - } - }); + function _render(){ + view._updateLayout(); + // set up the display containers + view.$el + .width( view.layout.el.width ) + .height( view.layout.el.height ); + view.renderSVG(); - view._updateLayout(); - // set up the display containers - view.$el - .width( view.layout.el.width ) - .height( view.layout.el.height ); - this.renderSVG(); - - // position the job views accrd. to the layout - view.component.eachVertex( function( v ){ - //TODO:? liMap needed - can't we attach to vertex? - var li = view._jobLiMap[ v.name ], - position = view.layout.nodeMap[ li.model.id ]; - //this.debug( position ); - li.$el.css({ top: position.y, left: position.x }); - }); + // position the job views accrd. to the layout + view.component.eachVertex( function( v ){ +//TODO:? liMap needed - can't we attach to vertex? + var li = view._jobLiMap[ v.name ], + position = view.layout.nodeMap[ li.model.id ]; + //this.debug( position ); + li.$el.css({ top: position.y, left: position.x }); + }); + } +//TODO: hack - li's invisible in updateLayout without this delay + if( !this.$el.is( ':visible' ) ){ + _.delay( _render, 0 ); + } else { + _render(); + } return this; }, @@ -195,7 +203,7 @@ .on( 'mouseover', highlightConnect ) .on( 'mouseout', unhighlightConnect ); - connections.transition() + connections .attr( 'd', function( d ){ return view._connectionPath( d ); }); //TODO: ? can we use tick here to update the links? @@ -256,7 +264,7 @@ */ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({ - logger : console, + //logger : console, className : HistoryStructureComponent.prototype.className + ' vertical', @@ -376,8 +384,8 @@ _createComponent : function( component ){ this.log( this + '._createComponent:', component ); - return new HistoryStructureComponent({ - //return new VerticalHistoryStructureComponent({ + //return new HistoryStructureComponent({ + return new VerticalHistoryStructureComponent({ model : this.model, component : component }); diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 client/galaxy/scripts/mvc/job/job-li.js --- a/client/galaxy/scripts/mvc/job/job-li.js +++ b/client/galaxy/scripts/mvc/job/job-li.js @@ -30,7 +30,6 @@ /** where should pages from links be displayed? (default to new tab/window) */ this.linkTarget = attributes.linkTarget || '_blank'; - this._setUpListeners(); }, /** In this override, add the state as a class for use with state-based CSS */ diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 client/galaxy/scripts/mvc/list/list-item.js --- a/client/galaxy/scripts/mvc/list/list-item.js +++ b/client/galaxy/scripts/mvc/list/list-item.js @@ -17,7 +17,7 @@ /** are the details of this view expanded/shown or not? */ this.expanded = attributes.expanded || false; this.log( '\t expanded:', this.expanded ); - this.fxSpeed = attributes.fxSpeed || this.fxSpeed; + this.fxSpeed = attributes.fxSpeed !== undefined? attributes.fxSpeed : this.fxSpeed; }, // ........................................................................ render main @@ -119,15 +119,8 @@ */ expand : function(){ var view = this; - return view._fetchModelDetails() - .always(function(){ - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); + return view._fetchModelDetails().always( function(){ + view._expand(); }); }, @@ -141,6 +134,24 @@ return jQuery.when(); }, + /** Inner fn called when expand (public) has fetched the details */ + _expand : function(){ + var view = this, + $newDetails = view._renderDetails(); + view.$details().replaceWith( $newDetails ); + // needs to be set after the above or the slide will not show + view.expanded = true; + view.$details().slideDown({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'expanding', view ); + }, + complete: function(){ + view.trigger( 'expanded', view ); + } + }); + }, + /** Hide the body/details of an HDA. * @fires collapsed when a body has been collapsed */ @@ -148,8 +159,14 @@ this.debug( this + '(ExpandableView).collapse' ); var view = this; view.expanded = false; - this.$details().slideUp( view.fxSpeed, function(){ - view.trigger( 'collapsed', view ); + this.$details().slideUp({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'collapsing', view ); + }, + complete: function(){ + view.trigger( 'collapsed', view ); + } }); } @@ -377,11 +394,13 @@ * disrespect attributes.expanded if drilldown */ initialize : function( attributes ){ - ListItemView.prototype.initialize.call( this, attributes ); //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ this.expanded = false; } this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle; this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass; + + ListItemView.prototype.initialize.call( this, attributes ); + this.foldout = this._createFoldoutPanel(); }, //TODO:?? override to exclude foldout scope? @@ -395,7 +414,7 @@ //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ return $(); } var $newDetails = ListItemView.prototype._renderDetails.call( this ); - return this._attachFoldout( this._createFoldoutPanel(), $newDetails ); + return this._attachFoldout( this.foldout, $newDetails ); }, /** In this override, handle collection expansion. */ @@ -419,7 +438,8 @@ _getFoldoutPanelOptions : function(){ return { // propagate foldout style down - foldoutStyle : this.foldoutStyle + foldoutStyle : this.foldoutStyle, + fxSpeed : this.fxSpeed }; }, @@ -438,25 +458,13 @@ return view._fetchModelDetails() .always(function(){ if( view.foldoutStyle === 'foldout' ){ - view._expandByFoldout(); + view._expand(); } else if( view.foldoutStyle === 'drilldown' ){ view._expandByDrilldown(); } }); }, - /** For foldout, call render details then slide down */ - _expandByFoldout : function(){ - var view = this; - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); - }, - /** For drilldown, set up close handler and fire expanded:drilldown * containing views can listen to this and handle other things * (like hiding themselves) by listening for expanded/collapsed:drilldown @@ -464,7 +472,6 @@ _expandByDrilldown : function(){ var view = this; // attachment and rendering done by listener - view.foldout = this._createFoldoutPanel(); view.foldout.on( 'close', function(){ view.trigger( 'collapsed:drilldown', view, view.foldout ); }); diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 static/scripts/mvc/history/history-structure-view.js --- a/static/scripts/mvc/history/history-structure-view.js +++ b/static/scripts/mvc/history/history-structure-view.js @@ -52,14 +52,22 @@ //this.debug( job.outputCollection ); // create the bbone view for the job (to be positioned later accrd. to the layout) and cache - var li = new JOB_LI.JobListItemView({ model: job, expanded: true }); + var li = new JOB_LI.JobListItemView({ model: job }); //var li = new JOB_LI.JobListItemView({ model: job }); - li.$el.appendTo( view.$el ); + li.render( 0 ).$el.appendTo( view.$el ); view._jobLiMap[ job.id ] = li; + view._setUpJobListeners( li ); + }); return view.jobs; }, + _setUpJobListeners : function( jobLi ){ + // update the layout during expansion and collapsing of job and output li's + jobLi.on( 'expanding expanded collapsing collapsed', this.render, this ); + jobLi.foldout.on( 'view:expanding view:expanded view:collapsing view:collapsed', this.render, this ); + }, + layoutDefaults : { paddingTop : 8, paddingLeft : 20, @@ -131,32 +139,32 @@ }, render : function( options ){ - this.log( this + '.renderComponent:', options ); + this.debug( this + '.render:', options ); var view = this; - view.component.eachVertex( function( v ){ - //TODO:? liMap needed - can't we attach to vertex? - var li = view._jobLiMap[ v.name ]; - if( !li.$el.is( ':visible' ) ){ - li.render( 0 ); - } - }); + function _render(){ + view._updateLayout(); + // set up the display containers + view.$el + .width( view.layout.el.width ) + .height( view.layout.el.height ); + view.renderSVG(); - view._updateLayout(); - // set up the display containers - view.$el - .width( view.layout.el.width ) - .height( view.layout.el.height ); - this.renderSVG(); - - // position the job views accrd. to the layout - view.component.eachVertex( function( v ){ - //TODO:? liMap needed - can't we attach to vertex? - var li = view._jobLiMap[ v.name ], - position = view.layout.nodeMap[ li.model.id ]; - //this.debug( position ); - li.$el.css({ top: position.y, left: position.x }); - }); + // position the job views accrd. to the layout + view.component.eachVertex( function( v ){ +//TODO:? liMap needed - can't we attach to vertex? + var li = view._jobLiMap[ v.name ], + position = view.layout.nodeMap[ li.model.id ]; + //this.debug( position ); + li.$el.css({ top: position.y, left: position.x }); + }); + } +//TODO: hack - li's invisible in updateLayout without this delay + if( !this.$el.is( ':visible' ) ){ + _.delay( _render, 0 ); + } else { + _render(); + } return this; }, @@ -195,7 +203,7 @@ .on( 'mouseover', highlightConnect ) .on( 'mouseout', unhighlightConnect ); - connections.transition() + connections .attr( 'd', function( d ){ return view._connectionPath( d ); }); //TODO: ? can we use tick here to update the links? @@ -256,7 +264,7 @@ */ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({ - logger : console, + //logger : console, className : HistoryStructureComponent.prototype.className + ' vertical', @@ -376,8 +384,8 @@ _createComponent : function( component ){ this.log( this + '._createComponent:', component ); - return new HistoryStructureComponent({ - //return new VerticalHistoryStructureComponent({ + //return new HistoryStructureComponent({ + return new VerticalHistoryStructureComponent({ model : this.model, component : component }); diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 static/scripts/mvc/job/job-li.js --- a/static/scripts/mvc/job/job-li.js +++ b/static/scripts/mvc/job/job-li.js @@ -30,7 +30,6 @@ /** where should pages from links be displayed? (default to new tab/window) */ this.linkTarget = attributes.linkTarget || '_blank'; - this._setUpListeners(); }, /** In this override, add the state as a class for use with state-based CSS */ diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 static/scripts/mvc/list/list-item.js --- a/static/scripts/mvc/list/list-item.js +++ b/static/scripts/mvc/list/list-item.js @@ -17,7 +17,7 @@ /** are the details of this view expanded/shown or not? */ this.expanded = attributes.expanded || false; this.log( '\t expanded:', this.expanded ); - this.fxSpeed = attributes.fxSpeed || this.fxSpeed; + this.fxSpeed = attributes.fxSpeed !== undefined? attributes.fxSpeed : this.fxSpeed; }, // ........................................................................ render main @@ -119,15 +119,8 @@ */ expand : function(){ var view = this; - return view._fetchModelDetails() - .always(function(){ - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); + return view._fetchModelDetails().always( function(){ + view._expand(); }); }, @@ -141,6 +134,24 @@ return jQuery.when(); }, + /** Inner fn called when expand (public) has fetched the details */ + _expand : function(){ + var view = this, + $newDetails = view._renderDetails(); + view.$details().replaceWith( $newDetails ); + // needs to be set after the above or the slide will not show + view.expanded = true; + view.$details().slideDown({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'expanding', view ); + }, + complete: function(){ + view.trigger( 'expanded', view ); + } + }); + }, + /** Hide the body/details of an HDA. * @fires collapsed when a body has been collapsed */ @@ -148,8 +159,14 @@ this.debug( this + '(ExpandableView).collapse' ); var view = this; view.expanded = false; - this.$details().slideUp( view.fxSpeed, function(){ - view.trigger( 'collapsed', view ); + this.$details().slideUp({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'collapsing', view ); + }, + complete: function(){ + view.trigger( 'collapsed', view ); + } }); } @@ -377,11 +394,13 @@ * disrespect attributes.expanded if drilldown */ initialize : function( attributes ){ - ListItemView.prototype.initialize.call( this, attributes ); //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ this.expanded = false; } this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle; this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass; + + ListItemView.prototype.initialize.call( this, attributes ); + this.foldout = this._createFoldoutPanel(); }, //TODO:?? override to exclude foldout scope? @@ -395,7 +414,7 @@ //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ return $(); } var $newDetails = ListItemView.prototype._renderDetails.call( this ); - return this._attachFoldout( this._createFoldoutPanel(), $newDetails ); + return this._attachFoldout( this.foldout, $newDetails ); }, /** In this override, handle collection expansion. */ @@ -419,7 +438,8 @@ _getFoldoutPanelOptions : function(){ return { // propagate foldout style down - foldoutStyle : this.foldoutStyle + foldoutStyle : this.foldoutStyle, + fxSpeed : this.fxSpeed }; }, @@ -438,25 +458,13 @@ return view._fetchModelDetails() .always(function(){ if( view.foldoutStyle === 'foldout' ){ - view._expandByFoldout(); + view._expand(); } else if( view.foldoutStyle === 'drilldown' ){ view._expandByDrilldown(); } }); }, - /** For foldout, call render details then slide down */ - _expandByFoldout : function(){ - var view = this; - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); - }, - /** For drilldown, set up close handler and fire expanded:drilldown * containing views can listen to this and handle other things * (like hiding themselves) by listening for expanded/collapsed:drilldown @@ -464,7 +472,6 @@ _expandByDrilldown : function(){ var view = this; // attachment and rendering done by listener - view.foldout = this._createFoldoutPanel(); view.foldout.on( 'close', function(){ view.trigger( 'collapsed:drilldown', view, view.foldout ); }); diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 static/scripts/packed/mvc/history/history-structure-view.js --- a/static/scripts/packed/mvc/history/history-structure-view.js +++ b/static/scripts/packed/mvc/history/history-structure-view.js @@ -1,1 +1,1 @@ -define(["mvc/job/job-model","mvc/job/job-li","mvc/history/history-content-model","mvc/history/job-dag","mvc/base-mvc","utils/localization","libs/d3"],function(e,f,i,c,h,a){var b=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure-component",initialize:function(j){this.log(this+"(HistoryStructureComponent).initialize:",j);this.component=j.component;this._jobLiMap={};this._createJobModels();this.layout=this._createLayout(j.layoutOptions)},_createJobModels:function(){var j=this;j.component.eachVertex(function(o){var n=o.data.job,m=new e.Job(n);var l=_.map(m.get("outputs"),function(p){var r=p.src==="hda"?"dataset":"dataset_collection",q=i.typeIdStr(r,p.id);return j.model.contents.get(q)});m.outputCollection.reset(l);m.outputCollection.historyId=j.model.id;var k=new f.JobListItemView({model:m,expanded:true});k.$el.appendTo(j.$el);j._jobLiMap[m.id]=k});return j.jobs},layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobHeight:308,jobWidthSpacing:320,linkAdjX:4,linkAdjY:0},_createLayout:function(l){l=_.defaults(_.clone(l||{}),this.layoutDefaults);var j=this,k=_.values(j.component.vertices),m=_.extend(l,{nodeMap:{},links:[],el:{width:0,height:0},svg:{width:0,height:0,top:0,left:0}});k.forEach(function(n,o){var p={name:n.name,x:0,y:0};m.nodeMap[n.name]=p});j.component.edges(function(o){var n={source:o.source,target:o.target};m.links.push(n)});return m},_updateLayout:function(){var k=this,l=k.layout;l.svg.height=l.paddingTop+(l.linkSpacing*_.size(l.nodeMap));l.el.height=l.svg.height+l.jobHeight;var j=l.paddingLeft,m=l.svg.height;_.each(l.nodeMap,function(o,n){o.x=j;o.y=m;j+=l.jobWidthSpacing});l.el.width=l.svg.width=Math.max(l.el.width,j);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY});return this.layout},render:function(k){this.log(this+".renderComponent:",k);var j=this;j.component.eachVertex(function(m){var l=j._jobLiMap[m.name];if(!l.$el.is(":visible")){l.render(0)}});j._updateLayout();j.$el.width(j.layout.el.width).height(j.layout.el.height);this.renderSVG();j.component.eachVertex(function(n){var m=j._jobLiMap[n.name],l=j.layout.nodeMap[m.model.id];m.$el.css({top:l.y,left:l.x})});return this},renderSVG:function(){var j=this,o=j.layout;var k=d3.select(this.el).select("svg");if(k.empty()){k=d3.select(this.el).append("svg")}k.attr("width",o.svg.width).attr("height",o.svg.height);function m(p){d3.select(this).classed("highlighted",true);j._jobLiMap[p.source].$el.addClass("highlighted");j._jobLiMap[p.target].$el.addClass("highlighted")}function l(p){d3.select(this).classed("highlighted",false);j._jobLiMap[p.source].$el.removeClass("highlighted");j._jobLiMap[p.target].$el.removeClass("highlighted")}var n=k.selectAll(".connection").data(o.links);n.enter().append("path").attr("class","connection").attr("id",function(p){return p.source+"-"+p.target}).on("mouseover",m).on("mouseout",l);n.transition().attr("d",function(p){return j._connectionPath(p)});return k.node()},_connectionPath:function(k){var l=0,j=((k.x2-k.x1)/this.layout.svg.width)*this.layout.svg.height;return["M",k.x1,",",k.y1," ","C",k.x1+l,",",k.y1-j," ",k.x2-l,",",k.y2-j," ",k.x2,",",k.y2].join("")},events:{"mouseover .job.list-item":function(j){this.highlightConnected(j.currentTarget,true)},"mouseout .job.list-item":function(j){this.highlightConnected(j.currentTarget,false)}},highlightConnected:function(p,k){k=k!==undefined?k:true;var j=this,l=j.component,n=k?jQuery.prototype.addClass:jQuery.prototype.removeClass,m=k?"connection highlighted":"connection";var o=n.call($(p),"highlighted"),q=o.attr("id").replace("job-","");l.edges({target:q}).forEach(function(r){n.call(j.$("#job-"+r.source),"highlighted");j.$("#"+r.source+"-"+q).attr("class",m)});l.vertices[q].eachEdge(function(r){n.call(j.$("#job-"+r.target),"highlighted");j.$("#"+q+"-"+r.target).attr("class",m)})},toString:function(){return"HistoryStructureComponent("+this.model.id+")"}});var g=b.extend({logger:console,className:b.prototype.className+" vertical",layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobWidth:308,jobHeight:308,initialSpacing:64,jobSpacing:16,linkAdjX:0,linkAdjY:4},_updateLayout:function(){var k=this,l=k.layout;l.svg.width=l.paddingLeft+(l.linkSpacing*_.size(l.nodeMap));l.el.width=l.svg.width+l.jobWidth;l.el.height=0;var j=l.svg.width,m=l.paddingTop;_.each(l.nodeMap,function(p,o){p.x=j;p.y=m;var n=k._jobLiMap[o];if(n.$el.is(":visible")){m+=n.$el.height()+l.jobSpacing}else{m+=l.initialSpacing+l.jobSpacing}});l.el.height=l.svg.height=Math.max(l.el.height,m);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY;k.debug("link:",n.x1,n.y1,n.x2,n.y2,n)});k.debug("el:",l.el);k.debug("svg:",l.svg);return l},_connectionPath:function(l){var k=0,j=((l.y2-l.y1)/this.layout.svg.height)*this.layout.svg.width;return["M",l.x1,",",l.y1," ","C",l.x1-j,",",l.y1+k," ",l.x2-j,",",l.y2-k," ",l.x2,",",l.y2].join("")},toString:function(){return"VerticalHistoryStructureComponent("+this.model.id+")"}});var d=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure",initialize:function(j){this.log(this+"(HistoryStructureView).initialize:",j,this.model);this.jobs=j.jobs;this._createDAG()},_createDAG:function(){this.dag=new c({historyContents:this.model.contents.toJSON(),jobs:this.jobs,excludeSetMetadata:true,excludeErroredJobs:true});this.log(this+".dag:",this.dag);this._createComponents()},_createComponents:function(){this.log(this+"._createComponents");var j=this;j.componentViews=j.dag.weakComponentGraphArray().map(function(k){return j._createComponent(k)})},_createComponent:function(j){this.log(this+"._createComponent:",j);return new b({model:this.model,component:j})},render:function(k){this.log(this+".render:",k);var j=this;j.$el.html(['<div class="controls"></div>','<div class="components"></div>'].join(""));j.componentViews.forEach(function(l){l.render().$el.appendTo(j.$components())});return j},$components:function(){return this.$(".components")},toString:function(){return"HistoryStructureView()"}});return d}); \ No newline at end of file +define(["mvc/job/job-model","mvc/job/job-li","mvc/history/history-content-model","mvc/history/job-dag","mvc/base-mvc","utils/localization","libs/d3"],function(e,f,i,c,h,a){var b=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure-component",initialize:function(j){this.log(this+"(HistoryStructureComponent).initialize:",j);this.component=j.component;this._jobLiMap={};this._createJobModels();this.layout=this._createLayout(j.layoutOptions)},_createJobModels:function(){var j=this;j.component.eachVertex(function(o){var n=o.data.job,m=new e.Job(n);var l=_.map(m.get("outputs"),function(p){var r=p.src==="hda"?"dataset":"dataset_collection",q=i.typeIdStr(r,p.id);return j.model.contents.get(q)});m.outputCollection.reset(l);m.outputCollection.historyId=j.model.id;var k=new f.JobListItemView({model:m});k.render(0).$el.appendTo(j.$el);j._jobLiMap[m.id]=k;j._setUpJobListeners(k)});return j.jobs},_setUpJobListeners:function(j){j.on("expanding expanded collapsing collapsed",this.render,this);j.foldout.on("view:expanding view:expanded view:collapsing view:collapsed",this.render,this)},layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobHeight:308,jobWidthSpacing:320,linkAdjX:4,linkAdjY:0},_createLayout:function(l){l=_.defaults(_.clone(l||{}),this.layoutDefaults);var j=this,k=_.values(j.component.vertices),m=_.extend(l,{nodeMap:{},links:[],el:{width:0,height:0},svg:{width:0,height:0,top:0,left:0}});k.forEach(function(n,o){var p={name:n.name,x:0,y:0};m.nodeMap[n.name]=p});j.component.edges(function(o){var n={source:o.source,target:o.target};m.links.push(n)});return m},_updateLayout:function(){var k=this,l=k.layout;l.svg.height=l.paddingTop+(l.linkSpacing*_.size(l.nodeMap));l.el.height=l.svg.height+l.jobHeight;var j=l.paddingLeft,m=l.svg.height;_.each(l.nodeMap,function(o,n){o.x=j;o.y=m;j+=l.jobWidthSpacing});l.el.width=l.svg.width=Math.max(l.el.width,j);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY});return this.layout},render:function(k){this.debug(this+".render:",k);var j=this;function l(){j._updateLayout();j.$el.width(j.layout.el.width).height(j.layout.el.height);j.renderSVG();j.component.eachVertex(function(o){var n=j._jobLiMap[o.name],m=j.layout.nodeMap[n.model.id];n.$el.css({top:m.y,left:m.x})})}if(!this.$el.is(":visible")){_.delay(l,0)}else{l()}return this},renderSVG:function(){var j=this,o=j.layout;var k=d3.select(this.el).select("svg");if(k.empty()){k=d3.select(this.el).append("svg")}k.attr("width",o.svg.width).attr("height",o.svg.height);function m(p){d3.select(this).classed("highlighted",true);j._jobLiMap[p.source].$el.addClass("highlighted");j._jobLiMap[p.target].$el.addClass("highlighted")}function l(p){d3.select(this).classed("highlighted",false);j._jobLiMap[p.source].$el.removeClass("highlighted");j._jobLiMap[p.target].$el.removeClass("highlighted")}var n=k.selectAll(".connection").data(o.links);n.enter().append("path").attr("class","connection").attr("id",function(p){return p.source+"-"+p.target}).on("mouseover",m).on("mouseout",l);n.attr("d",function(p){return j._connectionPath(p)});return k.node()},_connectionPath:function(k){var l=0,j=((k.x2-k.x1)/this.layout.svg.width)*this.layout.svg.height;return["M",k.x1,",",k.y1," ","C",k.x1+l,",",k.y1-j," ",k.x2-l,",",k.y2-j," ",k.x2,",",k.y2].join("")},events:{"mouseover .job.list-item":function(j){this.highlightConnected(j.currentTarget,true)},"mouseout .job.list-item":function(j){this.highlightConnected(j.currentTarget,false)}},highlightConnected:function(p,k){k=k!==undefined?k:true;var j=this,l=j.component,n=k?jQuery.prototype.addClass:jQuery.prototype.removeClass,m=k?"connection highlighted":"connection";var o=n.call($(p),"highlighted"),q=o.attr("id").replace("job-","");l.edges({target:q}).forEach(function(r){n.call(j.$("#job-"+r.source),"highlighted");j.$("#"+r.source+"-"+q).attr("class",m)});l.vertices[q].eachEdge(function(r){n.call(j.$("#job-"+r.target),"highlighted");j.$("#"+q+"-"+r.target).attr("class",m)})},toString:function(){return"HistoryStructureComponent("+this.model.id+")"}});var g=b.extend({className:b.prototype.className+" vertical",layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobWidth:308,jobHeight:308,initialSpacing:64,jobSpacing:16,linkAdjX:0,linkAdjY:4},_updateLayout:function(){var k=this,l=k.layout;l.svg.width=l.paddingLeft+(l.linkSpacing*_.size(l.nodeMap));l.el.width=l.svg.width+l.jobWidth;l.el.height=0;var j=l.svg.width,m=l.paddingTop;_.each(l.nodeMap,function(p,o){p.x=j;p.y=m;var n=k._jobLiMap[o];if(n.$el.is(":visible")){m+=n.$el.height()+l.jobSpacing}else{m+=l.initialSpacing+l.jobSpacing}});l.el.height=l.svg.height=Math.max(l.el.height,m);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY;k.debug("link:",n.x1,n.y1,n.x2,n.y2,n)});k.debug("el:",l.el);k.debug("svg:",l.svg);return l},_connectionPath:function(l){var k=0,j=((l.y2-l.y1)/this.layout.svg.height)*this.layout.svg.width;return["M",l.x1,",",l.y1," ","C",l.x1-j,",",l.y1+k," ",l.x2-j,",",l.y2-k," ",l.x2,",",l.y2].join("")},toString:function(){return"VerticalHistoryStructureComponent("+this.model.id+")"}});var d=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure",initialize:function(j){this.log(this+"(HistoryStructureView).initialize:",j,this.model);this.jobs=j.jobs;this._createDAG()},_createDAG:function(){this.dag=new c({historyContents:this.model.contents.toJSON(),jobs:this.jobs,excludeSetMetadata:true,excludeErroredJobs:true});this.log(this+".dag:",this.dag);this._createComponents()},_createComponents:function(){this.log(this+"._createComponents");var j=this;j.componentViews=j.dag.weakComponentGraphArray().map(function(k){return j._createComponent(k)})},_createComponent:function(j){this.log(this+"._createComponent:",j);return new g({model:this.model,component:j})},render:function(k){this.log(this+".render:",k);var j=this;j.$el.html(['<div class="controls"></div>','<div class="components"></div>'].join(""));j.componentViews.forEach(function(l){l.render().$el.appendTo(j.$components())});return j},$components:function(){return this.$(".components")},toString:function(){return"HistoryStructureView()"}});return d}); \ No newline at end of file diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 static/scripts/packed/mvc/job/job-li.js --- a/static/scripts/packed/mvc/job/job-li.js +++ b/static/scripts/packed/mvc/job/job-li.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/dataset/dataset-list","mvc/base-mvc","utils/localization"],function(d,f,b,c){var e=d.FoldoutListItemView;var a=e.extend({className:e.prototype.className+" job",id:function(){return["job",this.model.get("id")].join("-")},foldoutPanelClass:f.DatasetList,initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);e.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_swapNewRender:function(g){e.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_getFoldoutPanelOptions:function(){var g=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(g,{collection:this.model.outputCollection,selecting:false})},toString:function(){return"JobListItemView("+this.model+")"}});a.prototype.templates=(function(){var g=b.wrapTemplate(['<div class="list-element">','<div class="id"><%= model.id %></div>','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var h=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- job.tool_id %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"job");return _.extend({},e.prototype.templates,{titleBar:h,})}());return{JobListItemView:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/dataset/dataset-list","mvc/base-mvc","utils/localization"],function(d,f,b,c){var e=d.FoldoutListItemView;var a=e.extend({className:e.prototype.className+" job",id:function(){return["job",this.model.get("id")].join("-")},foldoutPanelClass:f.DatasetList,initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);e.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank"},_swapNewRender:function(g){e.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_getFoldoutPanelOptions:function(){var g=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(g,{collection:this.model.outputCollection,selecting:false})},toString:function(){return"JobListItemView("+this.model+")"}});a.prototype.templates=(function(){var g=b.wrapTemplate(['<div class="list-element">','<div class="id"><%= model.id %></div>','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var h=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- job.tool_id %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"job");return _.extend({},e.prototype.templates,{titleBar:h,})}());return{JobListItemView:a}}); \ No newline at end of file diff -r 78124761ad558e4670c338fdbdbf371acb6b91bd -r 9728fcd5167c2aceb8e0b72d3d8b9dc6fd5435b7 static/scripts/packed/mvc/list/list-item.js --- a/static/scripts/packed/mvc/list/list-item.js +++ b/static/scripts/packed/mvc/list/list-item.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(b,d){var e=Backbone.View.extend(b.LoggableMixin).extend({initialize:function(f){this.expanded=f.expanded||false;this.log("\t expanded:",this.expanded);this.fxSpeed=f.fxSpeed||this.fxSpeed},fxSpeed:"fast",render:function(g){var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){var f=$(this.templates.el(this.model.toJSON(),this));if(this.expanded){this.$details(f).replaceWith(this._renderDetails().show())}return f},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){this.trigger("rendered",f);i()}])},_swapNewRender:function(f){return this.$el.empty().attr("class",_.isFunction(this.className)?this.className():this.className).append(f.children())},_setUpBehaviors:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},$details:function(f){f=f||this.$el;return f.find("> .details")},_renderDetails:function(){var f=$(this.templates.details(this.model.toJSON(),this));this._setUpBehaviors(f);return f},toggleExpanded:function(f){f=(f===undefined)?(!this.expanded):(f);if(f){this.expand()}else{this.collapse()}return this},expand:function(){var f=this;return f._fetchModelDetails().always(function(){var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})})},_fetchModelDetails:function(){if(!this.model.hasDetails()){return this.model.fetch()}return jQuery.when()},collapse:function(){this.debug(this+"(ExpandableView).collapse");var f=this;f.expanded=false;this.$details().slideUp(f.fxSpeed,function(){f.trigger("collapsed",f)})}});var a=e.extend(b.mixin(b.SelectableViewMixin,b.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(f){e.prototype.initialize.call(this,f);b.SelectableViewMixin.initialize.call(this,f);b.DraggableViewMixin.initialize.call(this,f);this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}},this);return this},_buildNewRender:function(){var f=e.prototype._buildNewRender.call(this);f.children(".warnings").replaceWith(this._renderWarnings());f.children(".title-bar").replaceWith(this._renderTitleBar());f.children(".primary-actions").append(this._renderPrimaryActions());f.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle());return f},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.selectable){this.showSelector(0)}if(this.draggable){this.draggableOn()}return this.$el},_renderWarnings:function(){var f=this,h=$('<div class="warnings"></div>'),g=f.model.toJSON();_.each(f.templates.warnings,function(i){h.append($(i(g,f)))});return h},_renderTitleBar:function(){return $(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(f){f.stopPropagation();if(f.altKey){this.toggleSelect(f);if(!this.selectable){this.showSelector()}}else{this.toggleExpanded()}},_keyDownTitleBar:function(h){var f=32,g=13;if(h&&(h.type==="keydown")&&(h.keyCode===f||h.keyCode===g)){this.toggleExpanded();h.stopPropagation();return false}return true},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"ListItemView("+f+")"}}));a.prototype.templates=(function(){var h=b.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var f={};var i=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");var j=b.wrapTemplate(['<div class="subtitle"></div>']);var g=b.wrapTemplate(['<div class="details"></div>']);return{el:h,warnings:f,titleBar:i,subtitle:j,details:g}}());var c=a.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(f){a.prototype.initialize.call(this,f);if(this.foldoutStyle==="drilldown"){this.expanded=false}this.foldoutStyle=f.foldoutStyle||this.foldoutStyle;this.foldoutPanelClass=f.foldoutPanelClass||this.foldoutPanelClass},_renderDetails:function(){if(this.foldoutStyle==="drilldown"){return $()}var f=a.prototype._renderDetails.call(this);return this._attachFoldout(this._createFoldoutPanel(),f)},_createFoldoutPanel:function(){var h=this.model;var i=this._getFoldoutPanelClass(h),g=this._getFoldoutPanelOptions(h),f=new i(_.extend(g,{model:h}));return f},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle}},_attachFoldout:function(f,g){g=g||this.$("> .details");this.foldout=f.render(0);f.$("> .controls").hide();return g.append(f.$el)},expand:function(){var f=this;return f._fetchModelDetails().always(function(){if(f.foldoutStyle==="foldout"){f._expandByFoldout()}else{if(f.foldoutStyle==="drilldown"){f._expandByDrilldown()}}})},_expandByFoldout:function(){var f=this;var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})},_expandByDrilldown:function(){var f=this;f.foldout=this._createFoldoutPanel();f.foldout.on("close",function(){f.trigger("collapsed:drilldown",f,f.foldout)});f.trigger("expanded:drilldown",f,f.foldout)}});c.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="details">',"</div>"],"collection");return _.extend({},a.prototype.templates,{details:f})}());return{ExpandableView:e,ListItemView:a,FoldoutListItemView:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(b,d){var e=Backbone.View.extend(b.LoggableMixin).extend({initialize:function(f){this.expanded=f.expanded||false;this.log("\t expanded:",this.expanded);this.fxSpeed=f.fxSpeed!==undefined?f.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(g){var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){var f=$(this.templates.el(this.model.toJSON(),this));if(this.expanded){this.$details(f).replaceWith(this._renderDetails().show())}return f},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){this.trigger("rendered",f);i()}])},_swapNewRender:function(f){return this.$el.empty().attr("class",_.isFunction(this.className)?this.className():this.className).append(f.children())},_setUpBehaviors:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},$details:function(f){f=f||this.$el;return f.find("> .details")},_renderDetails:function(){var f=$(this.templates.details(this.model.toJSON(),this));this._setUpBehaviors(f);return f},toggleExpanded:function(f){f=(f===undefined)?(!this.expanded):(f);if(f){this.expand()}else{this.collapse()}return this},expand:function(){var f=this;return f._fetchModelDetails().always(function(){f._expand()})},_fetchModelDetails:function(){if(!this.model.hasDetails()){return this.model.fetch()}return jQuery.when()},_expand:function(){var f=this,g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown({duration:f.fxSpeed,step:function(){f.trigger("expanding",f)},complete:function(){f.trigger("expanded",f)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var f=this;f.expanded=false;this.$details().slideUp({duration:f.fxSpeed,step:function(){f.trigger("collapsing",f)},complete:function(){f.trigger("collapsed",f)}})}});var a=e.extend(b.mixin(b.SelectableViewMixin,b.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(f){e.prototype.initialize.call(this,f);b.SelectableViewMixin.initialize.call(this,f);b.DraggableViewMixin.initialize.call(this,f);this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}},this);return this},_buildNewRender:function(){var f=e.prototype._buildNewRender.call(this);f.children(".warnings").replaceWith(this._renderWarnings());f.children(".title-bar").replaceWith(this._renderTitleBar());f.children(".primary-actions").append(this._renderPrimaryActions());f.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle());return f},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.selectable){this.showSelector(0)}if(this.draggable){this.draggableOn()}return this.$el},_renderWarnings:function(){var f=this,h=$('<div class="warnings"></div>'),g=f.model.toJSON();_.each(f.templates.warnings,function(i){h.append($(i(g,f)))});return h},_renderTitleBar:function(){return $(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(f){f.stopPropagation();if(f.altKey){this.toggleSelect(f);if(!this.selectable){this.showSelector()}}else{this.toggleExpanded()}},_keyDownTitleBar:function(h){var f=32,g=13;if(h&&(h.type==="keydown")&&(h.keyCode===f||h.keyCode===g)){this.toggleExpanded();h.stopPropagation();return false}return true},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"ListItemView("+f+")"}}));a.prototype.templates=(function(){var h=b.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var f={};var i=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");var j=b.wrapTemplate(['<div class="subtitle"></div>']);var g=b.wrapTemplate(['<div class="details"></div>']);return{el:h,warnings:f,titleBar:i,subtitle:j,details:g}}());var c=a.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(f){if(this.foldoutStyle==="drilldown"){this.expanded=false}this.foldoutStyle=f.foldoutStyle||this.foldoutStyle;this.foldoutPanelClass=f.foldoutPanelClass||this.foldoutPanelClass;a.prototype.initialize.call(this,f);this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if(this.foldoutStyle==="drilldown"){return $()}var f=a.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,f)},_createFoldoutPanel:function(){var h=this.model;var i=this._getFoldoutPanelClass(h),g=this._getFoldoutPanelOptions(h),f=new i(_.extend(g,{model:h}));return f},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(f,g){g=g||this.$("> .details");this.foldout=f.render(0);f.$("> .controls").hide();return g.append(f.$el)},expand:function(){var f=this;return f._fetchModelDetails().always(function(){if(f.foldoutStyle==="foldout"){f._expand()}else{if(f.foldoutStyle==="drilldown"){f._expandByDrilldown()}}})},_expandByDrilldown:function(){var f=this;f.foldout.on("close",function(){f.trigger("collapsed:drilldown",f,f.foldout)});f.trigger("expanded:drilldown",f,f.foldout)}});c.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="details">',"</div>"],"collection");return _.extend({},a.prototype.templates,{details:f})}());return{ExpandableView:e,ListItemView:a,FoldoutListItemView:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Activate rerun feature for new tool form, fix sliders, fix content labels
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78124761ad55/ Changeset: 78124761ad55 User: guerler Date: 2014-10-15 20:06:03+00:00 Summary: ToolForm: Activate rerun feature for new tool form, fix sliders, fix content labels Affected #: 20 files diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -97,7 +97,7 @@ // finalize data var current_state = this.tree.finalize({ data : function(dict) { - if (dict.values.length > 0 && dict.values[0].src === 'hda') { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { return self.content.get({id: dict.values[0].id}).dataset_id; } return null; @@ -185,11 +185,11 @@ }); // switch to classic tool form mako if the form definition is incompatible - //if (this.incompatible) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; - //} + } // create portlet this.portlet = new Portlet.View({ diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -37,7 +37,7 @@ console.debug(job_def); // show progress modal - this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: { 'Close' : function () {self.app.modal.hide();} }}); + this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }}); // post job Utils.request({ @@ -59,6 +59,15 @@ } else { // show error message with details console.debug(response); + self.app.modal.show({ + title : 'Job submission failed', + body : ToolTemplate.error(job_def), + buttons : { + 'Close' : function() { + self.app.modal.hide(); + } + } + }); } } }); diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd 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 @@ -529,22 +529,12 @@ /** Slider field */ _fieldSlider: function(input_def) { - // set min/max - input_def.min = input_def.min || 0; - input_def.max = input_def.max || 100000; - - // calculate step size - var step = 1; - if (input_def.type == 'float') { - step = (input_def.max - input_def.min) / 10000; - } - // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, + precise : input_def.type == 'float', min : input_def.min, - max : input_def.max, - step : step + max : input_def.max }); }, diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -40,7 +40,7 @@ var dataset_options = []; for (var i in datasets) { dataset_options.push({ - label: datasets[i].name, + label: datasets[i].hid + ': ' + datasets[i].name, value: datasets[i].id }); } @@ -67,7 +67,7 @@ var collection_options = []; for (var i in collections) { collection_options.push({ - label: collections[i].name, + label: collections[i].hid + ': ' + collections[i].name, value: collections[i].id }); } @@ -103,20 +103,34 @@ }, /** Return the currently selected dataset values */ - value : function () { - // identify select element - var select = null; - switch(this.current) { - case 'hda': - select = this.select_datasets; - break; - case 'hdca': - select = this.select_collection; - break; + value : function (dict) { + // update current value + if (dict !== undefined) { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src) { + // create list + var list = []; + for (var i in dict.values) { + list.push(dict.values[i].id); + } + + // set source + this.current = dict.values[0].src; + this.refresh(); + + // identify select element + switch(this.current) { + case 'hda': + this.select_datasets.value(list); + break; + case 'hdca': + this.select_collection.value(list[0]); + break; + } + } } // transform into an array - var id_list = select.value(); + var id_list = this._select().value(); if (!(id_list instanceof Array)) { id_list = [id_list]; } @@ -142,12 +156,7 @@ /** Validate current selection */ validate: function() { - switch(this.current) { - case 'hda': - return this.select_datasets.validate(); - case 'hdca': - return this.select_collection.validate(); - } + return this._select().validate(); }, /** Refreshes data selection view */ @@ -162,6 +171,16 @@ this.select_collection.$el.fadeIn(); break; } + }, + + /** Assists in selecting the current field */ + _select: function() { + switch(this.current) { + case 'hdca': + return this.select_collection; + default: + return this.select_datasets; + } } }); diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -49,7 +49,7 @@ error: function(job_def) { return '<div>' + '<p>' + - 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + JSON.stringify(job_def, undefined, 4) + diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd client/galaxy/scripts/mvc/ui/ui-slider.js --- a/client/galaxy/scripts/mvc/ui/ui-slider.js +++ b/client/galaxy/scripts/mvc/ui/ui-slider.js @@ -6,9 +6,11 @@ // options optionsDefault: { value : '', - min : 1, - max : 100, - step : 1 + min : null, + max : null, + step : null, + precise : false, + split : 10000 }, // initialize @@ -18,19 +20,35 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); - + // create new element this.setElement(this._template(this.options)); - // backup slider - this.$slider = this.$el.find('#slider'); + // determine wether to use the slider + this.useslider = this.options.max !== null && this.options.min !== null && this.options.max > this.options.min; + + // set default step size + if (this.options.step === null) { + this.options.step = 1; + if (this.options.precise && this.useslider) { + this.options.step = (this.options.max - this.options.min) / this.options.split; + } + } + + // create slider if min and max are defined properly + if (this.useslider) { + this.$slider = this.$el.find('#slider'); + this.$slider.slider(this.options); + this.$slider.on('slide', function (event, ui) { + self.value(ui.value); + }); + } else { + this.$el.find('.ui-form-slider-text').css('width', '100%'); + } // backup integer field this.$text = this.$el.find('#text'); - // load slider plugin - this.$slider.slider(this.options); - // add text field event this.$text.on('change', function () { self.value($(this).val()); @@ -39,24 +57,23 @@ // add text field event this.$text.on('keydown', function (event) { var v = event.which; - console.log(v); if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57) - || (self.options.step != 1 && $(this).val().indexOf('.') == -1) && v == 190)) { + || (self.options.precise && $(this).val().indexOf('.') == -1) && v == 190)) { event.preventDefault(); } }); - - // add slider event - this.$slider.on('slide', function (event, ui) { - self.value(ui.value); - }); }, // value value : function (new_val) { if (new_val !== undefined) { - // limit - new_val = Math.max(Math.min(new_val, this.options.max), this.options.min); + // apply limit + if (this.options.max !== null) { + new_val = Math.min(new_val, this.options.max); + } + if (this.options.min !== null) { + new_val = Math.max(new_val, this.options.min); + } // trigger on change event if (this.options.onchange) { @@ -64,7 +81,7 @@ } // set values - this.$slider.slider('value', new_val); + this.$slider && this.$slider.slider('value', new_val); this.$text.val(new_val); } diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1278,7 +1278,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ): # call parent to_dict - d = super( ColumnListParameter, self ).to_dict( trans, other_values ) + d = super( ColumnListParameter, self ).to_dict( trans, other_values=other_values) # add data reference d['data_ref'] = self.data_ref @@ -1432,7 +1432,10 @@ call_other_values = { '__trans__': trans, '__value__': value } if other_values: call_other_values.update( other_values.dict ) - return eval( self.dynamic_options, self.tool.code_namespace, call_other_values ) + try: + return eval( self.dynamic_options, self.tool.code_namespace, call_other_values ) + except Exception: + return [] def get_options( self, trans=None, value=None, other_values={} ): if self.is_dynamic: diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -97,7 +97,7 @@ // finalize data var current_state = this.tree.finalize({ data : function(dict) { - if (dict.values.length > 0 && dict.values[0].src === 'hda') { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { return self.content.get({id: dict.values[0].id}).dataset_id; } return null; @@ -185,11 +185,11 @@ }); // switch to classic tool form mako if the form definition is incompatible - //if (this.incompatible) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; - //} + } // create portlet this.portlet = new Portlet.View({ diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -37,7 +37,7 @@ console.debug(job_def); // show progress modal - this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: { 'Close' : function () {self.app.modal.hide();} }}); + this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }}); // post job Utils.request({ @@ -59,6 +59,15 @@ } else { // show error message with details console.debug(response); + self.app.modal.show({ + title : 'Job submission failed', + body : ToolTemplate.error(job_def), + buttons : { + 'Close' : function() { + self.app.modal.hide(); + } + } + }); } } }); diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -529,22 +529,12 @@ /** Slider field */ _fieldSlider: function(input_def) { - // set min/max - input_def.min = input_def.min || 0; - input_def.max = input_def.max || 100000; - - // calculate step size - var step = 1; - if (input_def.type == 'float') { - step = (input_def.max - input_def.min) / 10000; - } - // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, + precise : input_def.type == 'float', min : input_def.min, - max : input_def.max, - step : step + max : input_def.max }); }, diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -40,7 +40,7 @@ var dataset_options = []; for (var i in datasets) { dataset_options.push({ - label: datasets[i].name, + label: datasets[i].hid + ': ' + datasets[i].name, value: datasets[i].id }); } @@ -67,7 +67,7 @@ var collection_options = []; for (var i in collections) { collection_options.push({ - label: collections[i].name, + label: collections[i].hid + ': ' + collections[i].name, value: collections[i].id }); } @@ -103,20 +103,34 @@ }, /** Return the currently selected dataset values */ - value : function () { - // identify select element - var select = null; - switch(this.current) { - case 'hda': - select = this.select_datasets; - break; - case 'hdca': - select = this.select_collection; - break; + value : function (dict) { + // update current value + if (dict !== undefined) { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src) { + // create list + var list = []; + for (var i in dict.values) { + list.push(dict.values[i].id); + } + + // set source + this.current = dict.values[0].src; + this.refresh(); + + // identify select element + switch(this.current) { + case 'hda': + this.select_datasets.value(list); + break; + case 'hdca': + this.select_collection.value(list[0]); + break; + } + } } // transform into an array - var id_list = select.value(); + var id_list = this._select().value(); if (!(id_list instanceof Array)) { id_list = [id_list]; } @@ -142,12 +156,7 @@ /** Validate current selection */ validate: function() { - switch(this.current) { - case 'hda': - return this.select_datasets.validate(); - case 'hdca': - return this.select_collection.validate(); - } + return this._select().validate(); }, /** Refreshes data selection view */ @@ -162,6 +171,16 @@ this.select_collection.$el.fadeIn(); break; } + }, + + /** Assists in selecting the current field */ + _select: function() { + switch(this.current) { + case 'hdca': + return this.select_collection; + default: + return this.select_datasets; + } } }); diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -49,7 +49,7 @@ error: function(job_def) { return '<div>' + '<p>' + - 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + JSON.stringify(job_def, undefined, 4) + diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/mvc/ui/ui-slider.js --- a/static/scripts/mvc/ui/ui-slider.js +++ b/static/scripts/mvc/ui/ui-slider.js @@ -6,9 +6,11 @@ // options optionsDefault: { value : '', - min : 1, - max : 100, - step : 1 + min : null, + max : null, + step : null, + precise : false, + split : 10000 }, // initialize @@ -18,19 +20,35 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); - + // create new element this.setElement(this._template(this.options)); - // backup slider - this.$slider = this.$el.find('#slider'); + // determine wether to use the slider + this.useslider = this.options.max !== null && this.options.min !== null && this.options.max > this.options.min; + + // set default step size + if (this.options.step === null) { + this.options.step = 1; + if (this.options.precise && this.useslider) { + this.options.step = (this.options.max - this.options.min) / this.options.split; + } + } + + // create slider if min and max are defined properly + if (this.useslider) { + this.$slider = this.$el.find('#slider'); + this.$slider.slider(this.options); + this.$slider.on('slide', function (event, ui) { + self.value(ui.value); + }); + } else { + this.$el.find('.ui-form-slider-text').css('width', '100%'); + } // backup integer field this.$text = this.$el.find('#text'); - // load slider plugin - this.$slider.slider(this.options); - // add text field event this.$text.on('change', function () { self.value($(this).val()); @@ -39,24 +57,23 @@ // add text field event this.$text.on('keydown', function (event) { var v = event.which; - console.log(v); if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57) - || (self.options.step != 1 && $(this).val().indexOf('.') == -1) && v == 190)) { + || (self.options.precise && $(this).val().indexOf('.') == -1) && v == 190)) { event.preventDefault(); } }); - - // add slider event - this.$slider.on('slide', function (event, ui) { - self.value(ui.value); - }); }, // value value : function (new_val) { if (new_val !== undefined) { - // limit - new_val = Math.max(Math.min(new_val, this.options.max), this.options.min); + // apply limit + if (this.options.max !== null) { + new_val = Math.min(new_val, this.options.max); + } + if (this.options.min !== null) { + new_val = Math.max(new_val, this.options.min); + } // trigger on change event if (this.options.onchange) { @@ -64,7 +81,7 @@ } // set values - this.$slider.slider('value', new_val); + this.$slider && this.$slider.slider('value', new_val); this.$text.val(new_val); } diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of available operations."});p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});this.$el.hide();$("#tool-form-classic").show();return;this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!this.options.biostar_url){button_question.$el.hide();button_search.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of available operations."});p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!this.options.biostar_url){button_question.$el.hide();button_search.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd 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/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.content.filterType({src:"hda",extensions:h.extensions});var k=[];for(var j in l){k.push({label:l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.content.filterType({src:"hdca",extensions:h.extensions});var f=[];for(var j in m){f.push({label:m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(){var g=null;switch(this.current){case"hda":g=this.select_datasets;break;case"hdca":g=this.select_collection;break}var j=g.value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.current})}return f},validate:function(){switch(this.current){case"hda":return this.select_datasets.validate();case"hdca":return this.select_collection.validate()}},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.content.filterType({src:"hda",extensions:h.extensions});var k=[];for(var j in l){k.push({label:l[j].hid+": "+l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.content.filterType({src:"hdca",extensions:h.extensions});var f=[];for(var j in m){f.push({label:m[j].hid+": "+m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(k){if(k!==undefined){if(k.values.length>0&&k.values[0]&&k.values[0].src){var j=[];for(var g in k.values){j.push(k.values[g].id)}this.current=k.values[0].src;this.refresh();switch(this.current){case"hda":this.select_datasets.value(j);break;case"hdca":this.select_collection.value(j[0]);break}}}var h=this._select().value();if(!(h instanceof Array)){h=[h]}var f={batch:!this.options.multiple,values:[]};for(var g in h){f.values.push({id:h[g],src:this.current})}return f},validate:function(){return this._select().validate()},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}},_select:function(){switch(this.current){case"hdca":return this.select_collection;default:return this.select_datasets}}});return{View:d}}); \ No newline at end of file diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd static/scripts/packed/mvc/ui/ui-slider.js --- a/static/scripts/packed/mvc/ui/ui-slider.js +++ b/static/scripts/packed/mvc/ui/ui-slider.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100,step:1},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$slider=this.$el.find("#slider");this.$text=this.$el.find("#text");this.$slider.slider(this.options);this.$text.on("change",function(){c.value($(this).val())});this.$text.on("keydown",function(f){var e=f.which;console.log(e);if(!(e==8||e==9||e==13||e==37||e==39||e==189||(e>=48&&e<=57)||(c.options.step!=1&&$(this).val().indexOf(".")==-1)&&e==190)){f.preventDefault()}});this.$slider.on("slide",function(e,f){c.value(f.value)})},value:function(c){if(c!==undefined){c=Math.max(Math.min(c,this.options.max),this.options.min);if(this.options.onchange){this.options.onchange(c)}this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(e,f){c.value(f.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");this.$text.on("change",function(){c.value($(this).val())});this.$text.on("keydown",function(f){var e=f.which;if(!(e==8||e==9||e==13||e==37||e==39||e==189||(e>=48&&e<=57)||(c.options.precise&&$(this).val().indexOf(".")==-1)&&e==190)){f.preventDefault()}})},value:function(c){if(c!==undefined){if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ No newline at end of file diff -r a83921df0dc2047c6874c6daeddbe3047c86cd4e -r 78124761ad558e4670c338fdbdbf371acb6b91bd templates/webapps/galaxy/tool_form_refresh.mako --- a/templates/webapps/galaxy/tool_form_refresh.mako +++ b/templates/webapps/galaxy/tool_form_refresh.mako @@ -4,30 +4,55 @@ tool_model = tool.to_dict(trans) tool_model['inputs'] = {} - ## sanitize + ## convert value to jsonifiable value + def convert(v): + # check if value is numeric + isnumber = False + try: + float(v) + isnumber = True + except Exception: + pass + + ## fix hda parsing + if isinstance(v, HistoryDatasetAssociation): + return { + 'id' : trans.security.encode_id(v.id), + 'src' : 'hda' + } + elif isinstance(v, basestring) or isnumber: + return v + else: + return None + + ## ensures that input dictionary is jsonifiable from collections import Iterable from galaxy.model import HistoryDatasetAssociation def sanitize(dict): - # quotations for Infinity so its jsonifiable + ## quotations for Infinity so its jsonifiable for name in dict: if dict[name] == Infinity: dict[name] = 'Infinity' - value = dict['value'] if 'value' in dict else None; - # check if value is numeric - def isnumber(s): - try: - float(s) - return True - except Exception: - return False - # fix hda parsing - if isinstance(value, HistoryDatasetAssociation): + + ## get current value + value = dict['value'] if 'value' in dict else None + + ## identify lists + if dict['type'] == 'data': + if isinstance(value, list): + value = [ convert(v) for v in value ] + else: + value = [ convert(value) ] value = { - 'id' : trans.security.encode_id(value.dataset_id), - 'src' : 'hda' + 'batch' : dict['multiple'], + 'values' : value } - elif value and not (isinstance(value, basestring) or isnumber(value) or isinstance(value, Iterable)): - value = 'Unsupported' + elif isinstance(value, list): + value = [ convert(v) for v in value ] + else: + value = convert(value) + + ## update and return dict['value'] = value return dict @@ -52,7 +77,7 @@ elif input.type == "conditional": try: test_param = group_inputs[input_index]['test_param'] - test_param['value'] = tool_state[test_param['name']] + test_param['value'] = group_state[test_param['name']] except Exception: pass i = group_state['__current_case__'] @@ -65,7 +90,7 @@ except Exception: pass - ## update input value from tool state and sanitize dictionary + ## update input value from tool state try: group_inputs[input_index]['value'] = tool_state[group_inputs[input_index]['name']] group_inputs[input_index] = sanitize(group_inputs[input_index]) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix to 8f8341a
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a83921df0dc2/ Changeset: a83921df0dc2 User: carlfeberhard Date: 2014-10-15 18:12:14+00:00 Summary: Fix to 8f8341a Affected #: 3 files diff -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 -r a83921df0dc2047c6874c6daeddbe3047c86cd4e client/galaxy/scripts/mvc/history/history-structure-view.js --- a/client/galaxy/scripts/mvc/history/history-structure-view.js +++ b/client/galaxy/scripts/mvc/history/history-structure-view.js @@ -48,7 +48,7 @@ }); // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls) job.outputCollection.reset( outputModels ); - job.outputCollection.historyId = structure.model.id; + job.outputCollection.historyId = view.model.id; //this.debug( job.outputCollection ); // create the bbone view for the job (to be positioned later accrd. to the layout) and cache diff -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 -r a83921df0dc2047c6874c6daeddbe3047c86cd4e static/scripts/mvc/history/history-structure-view.js --- a/static/scripts/mvc/history/history-structure-view.js +++ b/static/scripts/mvc/history/history-structure-view.js @@ -48,7 +48,7 @@ }); // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls) job.outputCollection.reset( outputModels ); - job.outputCollection.historyId = structure.model.id; + job.outputCollection.historyId = view.model.id; //this.debug( job.outputCollection ); // create the bbone view for the job (to be positioned later accrd. to the layout) and cache diff -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 -r a83921df0dc2047c6874c6daeddbe3047c86cd4e static/scripts/packed/mvc/history/history-structure-view.js --- a/static/scripts/packed/mvc/history/history-structure-view.js +++ b/static/scripts/packed/mvc/history/history-structure-view.js @@ -1,1 +1,1 @@ -define(["mvc/job/job-model","mvc/job/job-li","mvc/history/history-content-model","mvc/history/job-dag","mvc/base-mvc","utils/localization","libs/d3"],function(e,f,i,c,h,a){var b=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure-component",initialize:function(j){this.log(this+"(HistoryStructureComponent).initialize:",j);this.component=j.component;this._jobLiMap={};this._createJobModels();this.layout=this._createLayout(j.layoutOptions)},_createJobModels:function(){var j=this;j.component.eachVertex(function(o){var n=o.data.job,m=new e.Job(n);var l=_.map(m.get("outputs"),function(p){var r=p.src==="hda"?"dataset":"dataset_collection",q=i.typeIdStr(r,p.id);return j.model.contents.get(q)});m.outputCollection.reset(l);m.outputCollection.historyId=structure.model.id;var k=new f.JobListItemView({model:m,expanded:true});k.$el.appendTo(j.$el);j._jobLiMap[m.id]=k});return j.jobs},layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobHeight:308,jobWidthSpacing:320,linkAdjX:4,linkAdjY:0},_createLayout:function(l){l=_.defaults(_.clone(l||{}),this.layoutDefaults);var j=this,k=_.values(j.component.vertices),m=_.extend(l,{nodeMap:{},links:[],el:{width:0,height:0},svg:{width:0,height:0,top:0,left:0}});k.forEach(function(n,o){var p={name:n.name,x:0,y:0};m.nodeMap[n.name]=p});j.component.edges(function(o){var n={source:o.source,target:o.target};m.links.push(n)});return m},_updateLayout:function(){var k=this,l=k.layout;l.svg.height=l.paddingTop+(l.linkSpacing*_.size(l.nodeMap));l.el.height=l.svg.height+l.jobHeight;var j=l.paddingLeft,m=l.svg.height;_.each(l.nodeMap,function(o,n){o.x=j;o.y=m;j+=l.jobWidthSpacing});l.el.width=l.svg.width=Math.max(l.el.width,j);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY});return this.layout},render:function(k){this.log(this+".renderComponent:",k);var j=this;j.component.eachVertex(function(m){var l=j._jobLiMap[m.name];if(!l.$el.is(":visible")){l.render(0)}});j._updateLayout();j.$el.width(j.layout.el.width).height(j.layout.el.height);this.renderSVG();j.component.eachVertex(function(n){var m=j._jobLiMap[n.name],l=j.layout.nodeMap[m.model.id];m.$el.css({top:l.y,left:l.x})});return this},renderSVG:function(){var j=this,o=j.layout;var k=d3.select(this.el).select("svg");if(k.empty()){k=d3.select(this.el).append("svg")}k.attr("width",o.svg.width).attr("height",o.svg.height);function m(p){d3.select(this).classed("highlighted",true);j._jobLiMap[p.source].$el.addClass("highlighted");j._jobLiMap[p.target].$el.addClass("highlighted")}function l(p){d3.select(this).classed("highlighted",false);j._jobLiMap[p.source].$el.removeClass("highlighted");j._jobLiMap[p.target].$el.removeClass("highlighted")}var n=k.selectAll(".connection").data(o.links);n.enter().append("path").attr("class","connection").attr("id",function(p){return p.source+"-"+p.target}).on("mouseover",m).on("mouseout",l);n.transition().attr("d",function(p){return j._connectionPath(p)});return k.node()},_connectionPath:function(k){var l=0,j=((k.x2-k.x1)/this.layout.svg.width)*this.layout.svg.height;return["M",k.x1,",",k.y1," ","C",k.x1+l,",",k.y1-j," ",k.x2-l,",",k.y2-j," ",k.x2,",",k.y2].join("")},events:{"mouseover .job.list-item":function(j){this.highlightConnected(j.currentTarget,true)},"mouseout .job.list-item":function(j){this.highlightConnected(j.currentTarget,false)}},highlightConnected:function(p,k){k=k!==undefined?k:true;var j=this,l=j.component,n=k?jQuery.prototype.addClass:jQuery.prototype.removeClass,m=k?"connection highlighted":"connection";var o=n.call($(p),"highlighted"),q=o.attr("id").replace("job-","");l.edges({target:q}).forEach(function(r){n.call(j.$("#job-"+r.source),"highlighted");j.$("#"+r.source+"-"+q).attr("class",m)});l.vertices[q].eachEdge(function(r){n.call(j.$("#job-"+r.target),"highlighted");j.$("#"+q+"-"+r.target).attr("class",m)})},toString:function(){return"HistoryStructureComponent("+this.model.id+")"}});var g=b.extend({logger:console,className:b.prototype.className+" vertical",layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobWidth:308,jobHeight:308,initialSpacing:64,jobSpacing:16,linkAdjX:0,linkAdjY:4},_updateLayout:function(){var k=this,l=k.layout;l.svg.width=l.paddingLeft+(l.linkSpacing*_.size(l.nodeMap));l.el.width=l.svg.width+l.jobWidth;l.el.height=0;var j=l.svg.width,m=l.paddingTop;_.each(l.nodeMap,function(p,o){p.x=j;p.y=m;var n=k._jobLiMap[o];if(n.$el.is(":visible")){m+=n.$el.height()+l.jobSpacing}else{m+=l.initialSpacing+l.jobSpacing}});l.el.height=l.svg.height=Math.max(l.el.height,m);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY;k.debug("link:",n.x1,n.y1,n.x2,n.y2,n)});k.debug("el:",l.el);k.debug("svg:",l.svg);return l},_connectionPath:function(l){var k=0,j=((l.y2-l.y1)/this.layout.svg.height)*this.layout.svg.width;return["M",l.x1,",",l.y1," ","C",l.x1-j,",",l.y1+k," ",l.x2-j,",",l.y2-k," ",l.x2,",",l.y2].join("")},toString:function(){return"VerticalHistoryStructureComponent("+this.model.id+")"}});var d=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure",initialize:function(j){this.log(this+"(HistoryStructureView).initialize:",j,this.model);this.jobs=j.jobs;this._createDAG()},_createDAG:function(){this.dag=new c({historyContents:this.model.contents.toJSON(),jobs:this.jobs,excludeSetMetadata:true,excludeErroredJobs:true});this.log(this+".dag:",this.dag);this._createComponents()},_createComponents:function(){this.log(this+"._createComponents");var j=this;j.componentViews=j.dag.weakComponentGraphArray().map(function(k){return j._createComponent(k)})},_createComponent:function(j){this.log(this+"._createComponent:",j);return new b({model:this.model,component:j})},render:function(k){this.log(this+".render:",k);var j=this;j.$el.html(['<div class="controls"></div>','<div class="components"></div>'].join(""));j.componentViews.forEach(function(l){l.render().$el.appendTo(j.$components())});return j},$components:function(){return this.$(".components")},toString:function(){return"HistoryStructureView()"}});return d}); \ No newline at end of file +define(["mvc/job/job-model","mvc/job/job-li","mvc/history/history-content-model","mvc/history/job-dag","mvc/base-mvc","utils/localization","libs/d3"],function(e,f,i,c,h,a){var b=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure-component",initialize:function(j){this.log(this+"(HistoryStructureComponent).initialize:",j);this.component=j.component;this._jobLiMap={};this._createJobModels();this.layout=this._createLayout(j.layoutOptions)},_createJobModels:function(){var j=this;j.component.eachVertex(function(o){var n=o.data.job,m=new e.Job(n);var l=_.map(m.get("outputs"),function(p){var r=p.src==="hda"?"dataset":"dataset_collection",q=i.typeIdStr(r,p.id);return j.model.contents.get(q)});m.outputCollection.reset(l);m.outputCollection.historyId=j.model.id;var k=new f.JobListItemView({model:m,expanded:true});k.$el.appendTo(j.$el);j._jobLiMap[m.id]=k});return j.jobs},layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobHeight:308,jobWidthSpacing:320,linkAdjX:4,linkAdjY:0},_createLayout:function(l){l=_.defaults(_.clone(l||{}),this.layoutDefaults);var j=this,k=_.values(j.component.vertices),m=_.extend(l,{nodeMap:{},links:[],el:{width:0,height:0},svg:{width:0,height:0,top:0,left:0}});k.forEach(function(n,o){var p={name:n.name,x:0,y:0};m.nodeMap[n.name]=p});j.component.edges(function(o){var n={source:o.source,target:o.target};m.links.push(n)});return m},_updateLayout:function(){var k=this,l=k.layout;l.svg.height=l.paddingTop+(l.linkSpacing*_.size(l.nodeMap));l.el.height=l.svg.height+l.jobHeight;var j=l.paddingLeft,m=l.svg.height;_.each(l.nodeMap,function(o,n){o.x=j;o.y=m;j+=l.jobWidthSpacing});l.el.width=l.svg.width=Math.max(l.el.width,j);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY});return this.layout},render:function(k){this.log(this+".renderComponent:",k);var j=this;j.component.eachVertex(function(m){var l=j._jobLiMap[m.name];if(!l.$el.is(":visible")){l.render(0)}});j._updateLayout();j.$el.width(j.layout.el.width).height(j.layout.el.height);this.renderSVG();j.component.eachVertex(function(n){var m=j._jobLiMap[n.name],l=j.layout.nodeMap[m.model.id];m.$el.css({top:l.y,left:l.x})});return this},renderSVG:function(){var j=this,o=j.layout;var k=d3.select(this.el).select("svg");if(k.empty()){k=d3.select(this.el).append("svg")}k.attr("width",o.svg.width).attr("height",o.svg.height);function m(p){d3.select(this).classed("highlighted",true);j._jobLiMap[p.source].$el.addClass("highlighted");j._jobLiMap[p.target].$el.addClass("highlighted")}function l(p){d3.select(this).classed("highlighted",false);j._jobLiMap[p.source].$el.removeClass("highlighted");j._jobLiMap[p.target].$el.removeClass("highlighted")}var n=k.selectAll(".connection").data(o.links);n.enter().append("path").attr("class","connection").attr("id",function(p){return p.source+"-"+p.target}).on("mouseover",m).on("mouseout",l);n.transition().attr("d",function(p){return j._connectionPath(p)});return k.node()},_connectionPath:function(k){var l=0,j=((k.x2-k.x1)/this.layout.svg.width)*this.layout.svg.height;return["M",k.x1,",",k.y1," ","C",k.x1+l,",",k.y1-j," ",k.x2-l,",",k.y2-j," ",k.x2,",",k.y2].join("")},events:{"mouseover .job.list-item":function(j){this.highlightConnected(j.currentTarget,true)},"mouseout .job.list-item":function(j){this.highlightConnected(j.currentTarget,false)}},highlightConnected:function(p,k){k=k!==undefined?k:true;var j=this,l=j.component,n=k?jQuery.prototype.addClass:jQuery.prototype.removeClass,m=k?"connection highlighted":"connection";var o=n.call($(p),"highlighted"),q=o.attr("id").replace("job-","");l.edges({target:q}).forEach(function(r){n.call(j.$("#job-"+r.source),"highlighted");j.$("#"+r.source+"-"+q).attr("class",m)});l.vertices[q].eachEdge(function(r){n.call(j.$("#job-"+r.target),"highlighted");j.$("#"+q+"-"+r.target).attr("class",m)})},toString:function(){return"HistoryStructureComponent("+this.model.id+")"}});var g=b.extend({logger:console,className:b.prototype.className+" vertical",layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobWidth:308,jobHeight:308,initialSpacing:64,jobSpacing:16,linkAdjX:0,linkAdjY:4},_updateLayout:function(){var k=this,l=k.layout;l.svg.width=l.paddingLeft+(l.linkSpacing*_.size(l.nodeMap));l.el.width=l.svg.width+l.jobWidth;l.el.height=0;var j=l.svg.width,m=l.paddingTop;_.each(l.nodeMap,function(p,o){p.x=j;p.y=m;var n=k._jobLiMap[o];if(n.$el.is(":visible")){m+=n.$el.height()+l.jobSpacing}else{m+=l.initialSpacing+l.jobSpacing}});l.el.height=l.svg.height=Math.max(l.el.height,m);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY;k.debug("link:",n.x1,n.y1,n.x2,n.y2,n)});k.debug("el:",l.el);k.debug("svg:",l.svg);return l},_connectionPath:function(l){var k=0,j=((l.y2-l.y1)/this.layout.svg.height)*this.layout.svg.width;return["M",l.x1,",",l.y1," ","C",l.x1-j,",",l.y1+k," ",l.x2-j,",",l.y2-k," ",l.x2,",",l.y2].join("")},toString:function(){return"VerticalHistoryStructureComponent("+this.model.id+")"}});var d=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure",initialize:function(j){this.log(this+"(HistoryStructureView).initialize:",j,this.model);this.jobs=j.jobs;this._createDAG()},_createDAG:function(){this.dag=new c({historyContents:this.model.contents.toJSON(),jobs:this.jobs,excludeSetMetadata:true,excludeErroredJobs:true});this.log(this+".dag:",this.dag);this._createComponents()},_createComponents:function(){this.log(this+"._createComponents");var j=this;j.componentViews=j.dag.weakComponentGraphArray().map(function(k){return j._createComponent(k)})},_createComponent:function(j){this.log(this+"._createComponent:",j);return new b({model:this.model,component:j})},render:function(k){this.log(this+".render:",k);var j=this;j.$el.html(['<div class="controls"></div>','<div class="components"></div>'].join(""));j.componentViews.forEach(function(l){l.render().$el.appendTo(j.$components())});return j},$components:function(){return this.$(".components")},toString:function(){return"HistoryStructureView()"}});return d}); \ 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.

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commit/galaxy-central: carlfeberhard: History structure: documentation and clean up
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8f8341ac47cd/ Changeset: 8f8341ac47cd User: carlfeberhard Date: 2014-10-15 18:05:18+00:00 Summary: History structure: documentation and clean up Affected #: 13 files diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 client/galaxy/scripts/mvc/history/history-structure-view.js --- a/client/galaxy/scripts/mvc/history/history-structure-view.js +++ b/client/galaxy/scripts/mvc/history/history-structure-view.js @@ -13,6 +13,9 @@ */ // ============================================================================ +/** + * + */ var HistoryStructureComponent = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ //logger : console, @@ -151,7 +154,6 @@ //TODO:? liMap needed - can't we attach to vertex? var li = view._jobLiMap[ v.name ], position = view.layout.nodeMap[ li.model.id ]; - console.debug( li.$el.is( ':visible' ) ); //this.debug( position ); li.$el.css({ top: position.y, left: position.x }); }); @@ -249,6 +251,9 @@ // ============================================================================ +/** + * + */ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({ logger : console, @@ -288,7 +293,6 @@ node.y = y; var li = view._jobLiMap[ jobId ]; if( li.$el.is( ':visible' ) ){ - console.debug( 'li is visible, adj. by:', li.$el.height() ); y += li.$el.height() + layout.jobSpacing; } else { y += layout.initialSpacing + layout.jobSpacing; @@ -331,6 +335,9 @@ // ============================================================================ +/** + * + */ var HistoryStructureView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ //logger : console, @@ -351,7 +358,7 @@ excludeSetMetadata : true, excludeErroredJobs : true }); -window.dag = this.dag; +//window.dag = this.dag; this.log( this + '.dag:', this.dag ); this._createComponents(); @@ -360,7 +367,7 @@ _createComponents : function(){ this.log( this + '._createComponents' ); var structure = this; -window.structure = structure; +//window.structure = structure; structure.componentViews = structure.dag.weakComponentGraphArray().map( function( componentGraph ){ return structure._createComponent( componentGraph ); @@ -402,8 +409,5 @@ // ============================================================================ - //return { - // HistoryStructureView : HistoryStructureView - //}; return HistoryStructureView; }); diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 client/galaxy/scripts/mvc/history/job-dag.js --- a/client/galaxy/scripts/mvc/history/job-dag.js +++ b/client/galaxy/scripts/mvc/history/job-dag.js @@ -4,6 +4,10 @@ ],function( GRAPH, addLogging ){ // ============================================================================ var _super = GRAPH.Graph; +/** A Directed acyclic Graph built from a history's job data. + * Reads in job json, filters and process that json, and builds a graph + * using the connections between job inputs and outputs. + */ var JobDAG = function( options ){ var self = this; //this.logger = console; @@ -25,9 +29,12 @@ }; JobDAG.prototype = new GRAPH.Graph(); JobDAG.prototype.constructor = JobDAG; + +// add logging ability - turn off/on using the this.logger statement above addLogging( JobDAG ); // ---------------------------------------------------------------------------- +/** process jobs, options, filters, and any history data, then create the graph */ JobDAG.prototype.init = function _init( options ){ options = options || {}; _super.prototype.init.call( this, options ); @@ -52,6 +59,7 @@ return self; }; +/** add job filters based on options */ JobDAG.prototype._initFilters = function __initFilters(){ var self = this, filters = []; @@ -84,6 +92,7 @@ return filters; }; +/** sort the jobs and cache any that pass all filters into _idMap by job.id */ JobDAG.prototype.preprocessJobs = function _preprocessJobs( jobs ){ this.info( 'processing jobs' ); @@ -98,6 +107,7 @@ return self; }; +/** sort the jobs based on update time */ JobDAG.prototype.sort = function _sort( jobs ){ function cmpCreate( a, b ){ if( a.update_time > b.update_time ){ return 1; } @@ -107,6 +117,7 @@ return jobs.sort( cmpCreate ); }; +/** proces input/output, filter based on job data returning data if passing, null if not */ JobDAG.prototype.preprocessJob = function _preprocessJob( job, index ){ //this.info( 'preprocessJob', job, index ); var self = this, @@ -138,6 +149,9 @@ return jobData; }; +/** make verbose input/output lists more concise, sanity checking along the way + * processFn is called on each input/output and passed the dataset obj (id,src) and the input/output name. + */ JobDAG.prototype.datasetMapToIdArray = function _datasetMapToIdArray( datasetMap, processFn ){ var self = this; return _.map( datasetMap, function( dataset, nameInJob ){ @@ -152,6 +166,9 @@ }); }; +/** Walk all the jobs (vertices), attempting to find connections + * between datasets used as both inputs and outputs (edges) + */ JobDAG.prototype.createGraph = function _createGraph(){ var self = this; self.debug( 'connections:' ); @@ -183,6 +200,7 @@ return self; }; +/** Override to re-sort (ugh) jobs in each component by update time */ Graph.prototype.weakComponentGraphArray = function(){ return this.weakComponents().map( function( component ){ //TODO: this seems to belong above (in sort) - why isn't it preserved? @@ -198,7 +216,4 @@ // ============================================================================ return JobDAG; - //return { - // jobDAG : jobDAG - //}; }); diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 client/galaxy/scripts/mvc/job/job-li.js --- a/client/galaxy/scripts/mvc/job/job-li.js +++ b/client/galaxy/scripts/mvc/job/job-li.js @@ -6,7 +6,8 @@ ], function( LIST_ITEM, DATASET_LIST, BASE_MVC, _l ){ //============================================================================== var _super = LIST_ITEM.FoldoutListItemView; -/** @class +/** @class A job view used from within a larger list of jobs. + * Each job itself is a foldout panel of history contents displaying the outputs of this job. */ var JobListItemView = _super.extend(/** @lends JobListItemView.prototype */{ diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 client/galaxy/scripts/mvc/job/job-model.js --- a/client/galaxy/scripts/mvc/job/job-model.js +++ b/client/galaxy/scripts/mvc/job/job-model.js @@ -7,7 +7,7 @@ ], function( HISTORY_CONTENTS, STATES, AJAX_QUEUE, BASE_MVC, _l ){ //============================================================================== var searchableMixin = BASE_MVC.SearchableModelMixin; -/** @class +/** @class Represents a job running or ran on the server job handlers. */ var Job = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( BASE_MVC.mixin( searchableMixin, /** @lends Job.prototype */{ @@ -126,6 +126,7 @@ }, // ........................................................................ ajax + /** fetches all details for each job in the collection using a queue */ queueDetailFetching : function(){ var collection = this, queue = new AJAX_QUEUE.AjaxQueue( this.map( function( job ){ @@ -179,7 +180,7 @@ //----------------------------------------------------------------------------- class vars }, { - + /** class level fn for fetching the job details for all jobs in a history */ fromHistory : function( historyId ){ console.debug( this ); var Collection = this, diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 client/galaxy/scripts/utils/graph.js --- a/client/galaxy/scripts/utils/graph.js +++ b/client/galaxy/scripts/utils/graph.js @@ -2,10 +2,10 @@ ],function(){ /* ============================================================================ TODO: - edges can't retain data ============================================================================ */ //TODO: go ahead and move to underscore... +/** call fn on each key/value in d */ function each( d, fn ){ for( var k in d ){ if( d.hasOwnProperty( k ) ){ @@ -14,6 +14,7 @@ } } +/** copy key/values from d2 to d overwriting if present */ function extend( d, d2 ){ for( var k in d2 ){ if( d2.hasOwnProperty( k ) ){ @@ -23,6 +24,7 @@ return d; } +/** deep equal of two dictionaries */ function matches( d, d2 ){ for( var k in d2 ){ if( d2.hasOwnProperty( k ) ){ @@ -34,6 +36,10 @@ return true; } +/** map key/values in obj + * if propsOrFn is an object, return only those k/v that match the object + * if propsOrFn is function, call the fn and returned the mapped values from it + */ function iterate( obj, propsOrFn ){ var fn = typeof propsOrFn === 'function'? propsOrFn : undefined, props = typeof propsOrFn === 'object'? propsOrFn : undefined, @@ -60,6 +66,8 @@ // ============================================================================ +/** A graph edge containing the name/id of both source and target and optional data + */ function Edge( source, target, data ){ var self = this; self.source = source !== undefined? source : null; @@ -70,10 +78,12 @@ //} return self; } +/** String representation */ Edge.prototype.toString = function(){ return this.source + '->' + this.target; }; +/** Return a plain object representing this edge */ Edge.prototype.toJSON = function(){ //TODO: this is safe in most browsers (fns will be stripped) - alter tests to incorporate this in order to pass data //return this; @@ -88,6 +98,9 @@ }; // ============================================================================ +/** A graph vertex with a (unique) name/id and optional data. + * A vertex contains a list of Edges (whose sources are this vertex) and maintains the degree. + */ function Vertex( name, data ){ var self = this; self.name = name !== undefined? name : '(unnamed)'; @@ -96,16 +109,19 @@ self.degree = 0; return self; } -window.Vertex = Vertex; + +/** String representation */ Vertex.prototype.toString = function(){ return 'Vertex(' + this.name + ')'; }; //TODO: better name w no collision for either this.eachEdge or this.edges +/** Iterate over each edge from this vertex */ Vertex.prototype.eachEdge = function( propsOrFn ){ return iterate( this.edges, propsOrFn ); }; +/** Return a plain object representing this vertex */ Vertex.prototype.toJSON = function(){ //return this; return { @@ -116,6 +132,10 @@ // ============================================================================ +/** Base (abstract) class for Graph search algorithms. + * Pass in the graph to search + * and an optional dictionary containing the 3 vertex/edge processing fns listed below. + */ var GraphSearch = function( graph, processFns ){ var self = this; self.graph = graph; @@ -136,6 +156,9 @@ return self; }; +/** Search interface where start is the vertex (or the name/id of the vertex) to begin the search at + * This public interface caches searches and returns the cached version if it's already been done. + */ GraphSearch.prototype.search = function _search( start ){ var self = this; if( start in self._cache ){ return self._cache[ start ]; } @@ -143,6 +166,22 @@ return ( self._cache[ start.name ] = self._search( start ) ); }; +/** Actual search (private) function (abstract here) */ +GraphSearch.prototype._search = function __search( start, search ){ + search = search || { + discovered : {}, + //parents : {}, + edges : [] + }; + return search; +}; + +/** Searches graph from start and returns a search tree of the results */ +GraphSearch.prototype.searchTree = function _searchTree( start ){ + return this._searchTree( this.search( start ) ); +}; + +/** Helper fn that returns a graph (a search tree) based on the search object passed in (does not actually search) */ GraphSearch.prototype._searchTree = function __searchTree( search ){ var self = this; return new Graph( true, { @@ -153,11 +192,10 @@ }); }; -GraphSearch.prototype.searchTree = function _searchTree( start ){ - return this._searchTree( this.search( start ) ); -}; // ============================================================================ +/** Breadth first search algo. + */ var BreadthFirstSearch = function( graph, processFns ){ var self = this; GraphSearch.call( this, graph, processFns ); @@ -166,6 +204,7 @@ BreadthFirstSearch.prototype = new GraphSearch(); BreadthFirstSearch.prototype.constructor = BreadthFirstSearch; +/** (Private) implementation of BFS */ BreadthFirstSearch.prototype._search = function __search( start, search ){ search = search || { discovered : {}, @@ -205,6 +244,8 @@ // ============================================================================ +/** Depth first search algorithm. + */ var DepthFirstSearch = function( graph, processFns ){ var self = this; GraphSearch.call( this, graph, processFns ); @@ -213,6 +254,7 @@ DepthFirstSearch.prototype = new GraphSearch(); DepthFirstSearch.prototype.constructor = DepthFirstSearch; +/** (Private) implementation of DFS */ DepthFirstSearch.prototype._search = function( start, search ){ //console.debug( 'depthFirstSearch:', start ); search = search || { @@ -258,6 +300,8 @@ // ============================================================================ +/** A directed/non-directed graph object. + */ function Graph( directed, data, options ){ //TODO: move directed to options this.directed = directed || false; @@ -265,7 +309,7 @@ } window.Graph = Graph; - +/** Set up options and instance variables */ Graph.prototype.init = function( options ){ options = options || {}; var self = this; @@ -277,6 +321,7 @@ return self; }; +/** Read data from the plain object data - both in d3 form (nodes and links) or vertices and edges */ Graph.prototype.read = function( data ){ if( !data ){ return this; } var self = this; @@ -286,6 +331,7 @@ }; //TODO: the next two could be combined +/** Create the graph using a list of nodes and a list of edges (where source and target are indeces into nodes) */ Graph.prototype.readNodesAndLinks = function( data ){ if( !( data && data.hasOwnProperty( 'nodes' ) ) ){ return this; } //console.debug( 'readNodesAndLinks:', data ); @@ -306,6 +352,7 @@ return self; }; +/** Create the graph using a list of nodes and a list of edges (where source and target are names of nodes) */ Graph.prototype.readVerticesAndEdges = function( data ){ if( !( data && data.hasOwnProperty( 'vertices' ) ) ){ return this; } //console.debug( 'readVerticesAndEdges:', data ); @@ -324,12 +371,16 @@ return self; }; +/** Return the vertex with name, creating it if necessary */ Graph.prototype.createVertex = function( name, data ){ //console.debug( 'createVertex:', name, data ); if( this.vertices[ name ] ){ return this.vertices[ name ]; } return ( this.vertices[ name ] = new Vertex( name, data ) ); }; +/** Create an edge in vertex named sourceName to targetName (optionally adding data to it) + * If directed is false, create a second edge from targetName to sourceName. + */ Graph.prototype.createEdge = function( sourceName, targetName, directed, data ){ //note: allows multiple 'equivalent' edges (to/from same source/target) //console.debug( 'createEdge:', source, target, directed ); @@ -359,16 +410,19 @@ return edge; }; +/** Walk over all the edges of the graph using the vertex.eachEdge iterator */ Graph.prototype.edges = function( propsOrFn ){ return Array.prototype.concat.apply( [], this.eachVertex( function( vertex ){ return vertex.eachEdge( propsOrFn ); })); }; +/** Iterate over all the vertices in the graph */ Graph.prototype.eachVertex = function( propsOrFn ){ return iterate( this.vertices, propsOrFn ); }; +/** Return a list of the vertices adjacent to vertex */ Graph.prototype.adjacent = function( vertex ){ var self = this; return iterate( vertex.edges, function( edge ){ @@ -376,6 +430,7 @@ }); }; +/** Call fn on each vertex adjacent to vertex */ Graph.prototype.eachAdjacent = function( vertex, fn ){ var self = this; return iterate( vertex.edges, function( edge ){ @@ -384,6 +439,7 @@ }); }; +/** Print the graph to the console (debugging) */ Graph.prototype.print = function(){ var self = this; console.log( 'Graph has ' + Object.keys( self.vertices ).length + ' vertices' ); @@ -396,6 +452,7 @@ return self; }; +/** Return a DOT format string of this graph */ Graph.prototype.toDOT = function(){ var self = this, strings = []; @@ -407,6 +464,7 @@ return strings.join( '\n' ); }; +/** Return vertices and edges of this graph in d3 node/link format */ Graph.prototype.toNodesAndLinks = function(){ var self = this, indeces = {}; @@ -424,6 +482,7 @@ }; }; +/** Return vertices and edges of this graph where edges use the name/id as source and target */ Graph.prototype.toVerticesAndEdges = function(){ var self = this; return { @@ -436,18 +495,22 @@ }; }; +/** Search this graph using BFS */ Graph.prototype.breadthFirstSearch = function( start, processFns ){ return new BreadthFirstSearch( this ).search( start ); }; +/** Return a searchtree of this graph using BFS */ Graph.prototype.breadthFirstSearchTree = function( start, processFns ){ return new BreadthFirstSearch( this ).searchTree( start ); }; +/** Search this graph using DFS */ Graph.prototype.depthFirstSearch = function( start, processFns ){ return new DepthFirstSearch( this ).search( start ); }; +/** Return a searchtree of this graph using DFS */ Graph.prototype.depthFirstSearchTree = function( start, processFns ){ return new DepthFirstSearch( this ).searchTree( start ); }; @@ -465,6 +528,7 @@ //Graph.prototype.isBipartite = function(){ //}; +/** Return an array of weakly connected (no edges between) sub-graphs in this graph */ Graph.prototype.weakComponents = function(){ //TODO: alternately, instead of returning graph-like objects: // - could simply decorate the vertices (vertex.component = componentIndex), or clone the graph and do that @@ -515,6 +579,7 @@ return components; }; +/** Return a single graph containing the weakly connected components in this graph */ Graph.prototype.weakComponentGraph = function(){ //note: although this can often look like the original graph - edges can be lost var components = this.weakComponents(); @@ -528,6 +593,7 @@ }); }; +/** Return an array of graphs of the weakly connected components in this graph */ Graph.prototype.weakComponentGraphArray = function(){ //note: although this can often look like the original graph - edges can be lost return this.weakComponents().map( function( component ){ @@ -537,10 +603,8 @@ // ============================================================================ - - - -// ============================================================================ +/** Create a random graph with numVerts vertices and numEdges edges (for testing) + */ function randGraph( directed, numVerts, numEdges ){ //console.debug( 'randGraph', directed, numVerts, numEdges ); var data = { nodes : [], links : [] }; diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 static/scripts/mvc/history/history-structure-view.js --- a/static/scripts/mvc/history/history-structure-view.js +++ b/static/scripts/mvc/history/history-structure-view.js @@ -13,6 +13,9 @@ */ // ============================================================================ +/** + * + */ var HistoryStructureComponent = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ //logger : console, @@ -151,7 +154,6 @@ //TODO:? liMap needed - can't we attach to vertex? var li = view._jobLiMap[ v.name ], position = view.layout.nodeMap[ li.model.id ]; - console.debug( li.$el.is( ':visible' ) ); //this.debug( position ); li.$el.css({ top: position.y, left: position.x }); }); @@ -249,6 +251,9 @@ // ============================================================================ +/** + * + */ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({ logger : console, @@ -288,7 +293,6 @@ node.y = y; var li = view._jobLiMap[ jobId ]; if( li.$el.is( ':visible' ) ){ - console.debug( 'li is visible, adj. by:', li.$el.height() ); y += li.$el.height() + layout.jobSpacing; } else { y += layout.initialSpacing + layout.jobSpacing; @@ -331,6 +335,9 @@ // ============================================================================ +/** + * + */ var HistoryStructureView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ //logger : console, @@ -351,7 +358,7 @@ excludeSetMetadata : true, excludeErroredJobs : true }); -window.dag = this.dag; +//window.dag = this.dag; this.log( this + '.dag:', this.dag ); this._createComponents(); @@ -360,7 +367,7 @@ _createComponents : function(){ this.log( this + '._createComponents' ); var structure = this; -window.structure = structure; +//window.structure = structure; structure.componentViews = structure.dag.weakComponentGraphArray().map( function( componentGraph ){ return structure._createComponent( componentGraph ); @@ -402,8 +409,5 @@ // ============================================================================ - //return { - // HistoryStructureView : HistoryStructureView - //}; return HistoryStructureView; }); diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 static/scripts/mvc/history/job-dag.js --- a/static/scripts/mvc/history/job-dag.js +++ b/static/scripts/mvc/history/job-dag.js @@ -4,6 +4,10 @@ ],function( GRAPH, addLogging ){ // ============================================================================ var _super = GRAPH.Graph; +/** A Directed acyclic Graph built from a history's job data. + * Reads in job json, filters and process that json, and builds a graph + * using the connections between job inputs and outputs. + */ var JobDAG = function( options ){ var self = this; //this.logger = console; @@ -25,9 +29,12 @@ }; JobDAG.prototype = new GRAPH.Graph(); JobDAG.prototype.constructor = JobDAG; + +// add logging ability - turn off/on using the this.logger statement above addLogging( JobDAG ); // ---------------------------------------------------------------------------- +/** process jobs, options, filters, and any history data, then create the graph */ JobDAG.prototype.init = function _init( options ){ options = options || {}; _super.prototype.init.call( this, options ); @@ -52,6 +59,7 @@ return self; }; +/** add job filters based on options */ JobDAG.prototype._initFilters = function __initFilters(){ var self = this, filters = []; @@ -84,6 +92,7 @@ return filters; }; +/** sort the jobs and cache any that pass all filters into _idMap by job.id */ JobDAG.prototype.preprocessJobs = function _preprocessJobs( jobs ){ this.info( 'processing jobs' ); @@ -98,6 +107,7 @@ return self; }; +/** sort the jobs based on update time */ JobDAG.prototype.sort = function _sort( jobs ){ function cmpCreate( a, b ){ if( a.update_time > b.update_time ){ return 1; } @@ -107,6 +117,7 @@ return jobs.sort( cmpCreate ); }; +/** proces input/output, filter based on job data returning data if passing, null if not */ JobDAG.prototype.preprocessJob = function _preprocessJob( job, index ){ //this.info( 'preprocessJob', job, index ); var self = this, @@ -138,6 +149,9 @@ return jobData; }; +/** make verbose input/output lists more concise, sanity checking along the way + * processFn is called on each input/output and passed the dataset obj (id,src) and the input/output name. + */ JobDAG.prototype.datasetMapToIdArray = function _datasetMapToIdArray( datasetMap, processFn ){ var self = this; return _.map( datasetMap, function( dataset, nameInJob ){ @@ -152,6 +166,9 @@ }); }; +/** Walk all the jobs (vertices), attempting to find connections + * between datasets used as both inputs and outputs (edges) + */ JobDAG.prototype.createGraph = function _createGraph(){ var self = this; self.debug( 'connections:' ); @@ -183,6 +200,7 @@ return self; }; +/** Override to re-sort (ugh) jobs in each component by update time */ Graph.prototype.weakComponentGraphArray = function(){ return this.weakComponents().map( function( component ){ //TODO: this seems to belong above (in sort) - why isn't it preserved? @@ -198,7 +216,4 @@ // ============================================================================ return JobDAG; - //return { - // jobDAG : jobDAG - //}; }); diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 static/scripts/mvc/job/job-li.js --- a/static/scripts/mvc/job/job-li.js +++ b/static/scripts/mvc/job/job-li.js @@ -6,7 +6,8 @@ ], function( LIST_ITEM, DATASET_LIST, BASE_MVC, _l ){ //============================================================================== var _super = LIST_ITEM.FoldoutListItemView; -/** @class +/** @class A job view used from within a larger list of jobs. + * Each job itself is a foldout panel of history contents displaying the outputs of this job. */ var JobListItemView = _super.extend(/** @lends JobListItemView.prototype */{ diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 static/scripts/mvc/job/job-model.js --- a/static/scripts/mvc/job/job-model.js +++ b/static/scripts/mvc/job/job-model.js @@ -7,7 +7,7 @@ ], function( HISTORY_CONTENTS, STATES, AJAX_QUEUE, BASE_MVC, _l ){ //============================================================================== var searchableMixin = BASE_MVC.SearchableModelMixin; -/** @class +/** @class Represents a job running or ran on the server job handlers. */ var Job = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( BASE_MVC.mixin( searchableMixin, /** @lends Job.prototype */{ @@ -126,6 +126,7 @@ }, // ........................................................................ ajax + /** fetches all details for each job in the collection using a queue */ queueDetailFetching : function(){ var collection = this, queue = new AJAX_QUEUE.AjaxQueue( this.map( function( job ){ @@ -179,7 +180,7 @@ //----------------------------------------------------------------------------- class vars }, { - + /** class level fn for fetching the job details for all jobs in a history */ fromHistory : function( historyId ){ console.debug( this ); var Collection = this, diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 static/scripts/packed/mvc/history/history-structure-view.js --- a/static/scripts/packed/mvc/history/history-structure-view.js +++ b/static/scripts/packed/mvc/history/history-structure-view.js @@ -1,1 +1,1 @@ -define(["mvc/job/job-model","mvc/job/job-li","mvc/history/history-content-model","mvc/history/job-dag","mvc/base-mvc","utils/localization","libs/d3"],function(e,f,i,c,h,a){var b=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure-component",initialize:function(j){this.log(this+"(HistoryStructureComponent).initialize:",j);this.component=j.component;this._jobLiMap={};this._createJobModels();this.layout=this._createLayout(j.layoutOptions)},_createJobModels:function(){var j=this;j.component.eachVertex(function(o){var n=o.data.job,m=new e.Job(n);var l=_.map(m.get("outputs"),function(p){var r=p.src==="hda"?"dataset":"dataset_collection",q=i.typeIdStr(r,p.id);return j.model.contents.get(q)});m.outputCollection.reset(l);m.outputCollection.historyId=structure.model.id;var k=new f.JobListItemView({model:m,expanded:true});k.$el.appendTo(j.$el);j._jobLiMap[m.id]=k});return j.jobs},layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobHeight:308,jobWidthSpacing:320,linkAdjX:4,linkAdjY:0},_createLayout:function(l){l=_.defaults(_.clone(l||{}),this.layoutDefaults);var j=this,k=_.values(j.component.vertices),m=_.extend(l,{nodeMap:{},links:[],el:{width:0,height:0},svg:{width:0,height:0,top:0,left:0}});k.forEach(function(n,o){var p={name:n.name,x:0,y:0};m.nodeMap[n.name]=p});j.component.edges(function(o){var n={source:o.source,target:o.target};m.links.push(n)});return m},_updateLayout:function(){var k=this,l=k.layout;l.svg.height=l.paddingTop+(l.linkSpacing*_.size(l.nodeMap));l.el.height=l.svg.height+l.jobHeight;var j=l.paddingLeft,m=l.svg.height;_.each(l.nodeMap,function(o,n){o.x=j;o.y=m;j+=l.jobWidthSpacing});l.el.width=l.svg.width=Math.max(l.el.width,j);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY});return this.layout},render:function(k){this.log(this+".renderComponent:",k);var j=this;j.component.eachVertex(function(m){var l=j._jobLiMap[m.name];if(!l.$el.is(":visible")){l.render(0)}});j._updateLayout();j.$el.width(j.layout.el.width).height(j.layout.el.height);this.renderSVG();j.component.eachVertex(function(n){var m=j._jobLiMap[n.name],l=j.layout.nodeMap[m.model.id];console.debug(m.$el.is(":visible"));m.$el.css({top:l.y,left:l.x})});return this},renderSVG:function(){var j=this,o=j.layout;var k=d3.select(this.el).select("svg");if(k.empty()){k=d3.select(this.el).append("svg")}k.attr("width",o.svg.width).attr("height",o.svg.height);function m(p){d3.select(this).classed("highlighted",true);j._jobLiMap[p.source].$el.addClass("highlighted");j._jobLiMap[p.target].$el.addClass("highlighted")}function l(p){d3.select(this).classed("highlighted",false);j._jobLiMap[p.source].$el.removeClass("highlighted");j._jobLiMap[p.target].$el.removeClass("highlighted")}var n=k.selectAll(".connection").data(o.links);n.enter().append("path").attr("class","connection").attr("id",function(p){return p.source+"-"+p.target}).on("mouseover",m).on("mouseout",l);n.transition().attr("d",function(p){return j._connectionPath(p)});return k.node()},_connectionPath:function(k){var l=0,j=((k.x2-k.x1)/this.layout.svg.width)*this.layout.svg.height;return["M",k.x1,",",k.y1," ","C",k.x1+l,",",k.y1-j," ",k.x2-l,",",k.y2-j," ",k.x2,",",k.y2].join("")},events:{"mouseover .job.list-item":function(j){this.highlightConnected(j.currentTarget,true)},"mouseout .job.list-item":function(j){this.highlightConnected(j.currentTarget,false)}},highlightConnected:function(p,k){k=k!==undefined?k:true;var j=this,l=j.component,n=k?jQuery.prototype.addClass:jQuery.prototype.removeClass,m=k?"connection highlighted":"connection";var o=n.call($(p),"highlighted"),q=o.attr("id").replace("job-","");l.edges({target:q}).forEach(function(r){n.call(j.$("#job-"+r.source),"highlighted");j.$("#"+r.source+"-"+q).attr("class",m)});l.vertices[q].eachEdge(function(r){n.call(j.$("#job-"+r.target),"highlighted");j.$("#"+q+"-"+r.target).attr("class",m)})},toString:function(){return"HistoryStructureComponent("+this.model.id+")"}});var g=b.extend({logger:console,className:b.prototype.className+" vertical",layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobWidth:308,jobHeight:308,initialSpacing:64,jobSpacing:16,linkAdjX:0,linkAdjY:4},_updateLayout:function(){var k=this,l=k.layout;l.svg.width=l.paddingLeft+(l.linkSpacing*_.size(l.nodeMap));l.el.width=l.svg.width+l.jobWidth;l.el.height=0;var j=l.svg.width,m=l.paddingTop;_.each(l.nodeMap,function(p,o){p.x=j;p.y=m;var n=k._jobLiMap[o];if(n.$el.is(":visible")){console.debug("li is visible, adj. by:",n.$el.height());m+=n.$el.height()+l.jobSpacing}else{m+=l.initialSpacing+l.jobSpacing}});l.el.height=l.svg.height=Math.max(l.el.height,m);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY;k.debug("link:",n.x1,n.y1,n.x2,n.y2,n)});k.debug("el:",l.el);k.debug("svg:",l.svg);return l},_connectionPath:function(l){var k=0,j=((l.y2-l.y1)/this.layout.svg.height)*this.layout.svg.width;return["M",l.x1,",",l.y1," ","C",l.x1-j,",",l.y1+k," ",l.x2-j,",",l.y2-k," ",l.x2,",",l.y2].join("")},toString:function(){return"VerticalHistoryStructureComponent("+this.model.id+")"}});var d=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure",initialize:function(j){this.log(this+"(HistoryStructureView).initialize:",j,this.model);this.jobs=j.jobs;this._createDAG()},_createDAG:function(){this.dag=new c({historyContents:this.model.contents.toJSON(),jobs:this.jobs,excludeSetMetadata:true,excludeErroredJobs:true});window.dag=this.dag;this.log(this+".dag:",this.dag);this._createComponents()},_createComponents:function(){this.log(this+"._createComponents");var j=this;window.structure=j;j.componentViews=j.dag.weakComponentGraphArray().map(function(k){return j._createComponent(k)})},_createComponent:function(j){this.log(this+"._createComponent:",j);return new b({model:this.model,component:j})},render:function(k){this.log(this+".render:",k);var j=this;j.$el.html(['<div class="controls"></div>','<div class="components"></div>'].join(""));j.componentViews.forEach(function(l){l.render().$el.appendTo(j.$components())});return j},$components:function(){return this.$(".components")},toString:function(){return"HistoryStructureView()"}});return d}); \ No newline at end of file +define(["mvc/job/job-model","mvc/job/job-li","mvc/history/history-content-model","mvc/history/job-dag","mvc/base-mvc","utils/localization","libs/d3"],function(e,f,i,c,h,a){var b=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure-component",initialize:function(j){this.log(this+"(HistoryStructureComponent).initialize:",j);this.component=j.component;this._jobLiMap={};this._createJobModels();this.layout=this._createLayout(j.layoutOptions)},_createJobModels:function(){var j=this;j.component.eachVertex(function(o){var n=o.data.job,m=new e.Job(n);var l=_.map(m.get("outputs"),function(p){var r=p.src==="hda"?"dataset":"dataset_collection",q=i.typeIdStr(r,p.id);return j.model.contents.get(q)});m.outputCollection.reset(l);m.outputCollection.historyId=structure.model.id;var k=new f.JobListItemView({model:m,expanded:true});k.$el.appendTo(j.$el);j._jobLiMap[m.id]=k});return j.jobs},layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobHeight:308,jobWidthSpacing:320,linkAdjX:4,linkAdjY:0},_createLayout:function(l){l=_.defaults(_.clone(l||{}),this.layoutDefaults);var j=this,k=_.values(j.component.vertices),m=_.extend(l,{nodeMap:{},links:[],el:{width:0,height:0},svg:{width:0,height:0,top:0,left:0}});k.forEach(function(n,o){var p={name:n.name,x:0,y:0};m.nodeMap[n.name]=p});j.component.edges(function(o){var n={source:o.source,target:o.target};m.links.push(n)});return m},_updateLayout:function(){var k=this,l=k.layout;l.svg.height=l.paddingTop+(l.linkSpacing*_.size(l.nodeMap));l.el.height=l.svg.height+l.jobHeight;var j=l.paddingLeft,m=l.svg.height;_.each(l.nodeMap,function(o,n){o.x=j;o.y=m;j+=l.jobWidthSpacing});l.el.width=l.svg.width=Math.max(l.el.width,j);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY});return this.layout},render:function(k){this.log(this+".renderComponent:",k);var j=this;j.component.eachVertex(function(m){var l=j._jobLiMap[m.name];if(!l.$el.is(":visible")){l.render(0)}});j._updateLayout();j.$el.width(j.layout.el.width).height(j.layout.el.height);this.renderSVG();j.component.eachVertex(function(n){var m=j._jobLiMap[n.name],l=j.layout.nodeMap[m.model.id];m.$el.css({top:l.y,left:l.x})});return this},renderSVG:function(){var j=this,o=j.layout;var k=d3.select(this.el).select("svg");if(k.empty()){k=d3.select(this.el).append("svg")}k.attr("width",o.svg.width).attr("height",o.svg.height);function m(p){d3.select(this).classed("highlighted",true);j._jobLiMap[p.source].$el.addClass("highlighted");j._jobLiMap[p.target].$el.addClass("highlighted")}function l(p){d3.select(this).classed("highlighted",false);j._jobLiMap[p.source].$el.removeClass("highlighted");j._jobLiMap[p.target].$el.removeClass("highlighted")}var n=k.selectAll(".connection").data(o.links);n.enter().append("path").attr("class","connection").attr("id",function(p){return p.source+"-"+p.target}).on("mouseover",m).on("mouseout",l);n.transition().attr("d",function(p){return j._connectionPath(p)});return k.node()},_connectionPath:function(k){var l=0,j=((k.x2-k.x1)/this.layout.svg.width)*this.layout.svg.height;return["M",k.x1,",",k.y1," ","C",k.x1+l,",",k.y1-j," ",k.x2-l,",",k.y2-j," ",k.x2,",",k.y2].join("")},events:{"mouseover .job.list-item":function(j){this.highlightConnected(j.currentTarget,true)},"mouseout .job.list-item":function(j){this.highlightConnected(j.currentTarget,false)}},highlightConnected:function(p,k){k=k!==undefined?k:true;var j=this,l=j.component,n=k?jQuery.prototype.addClass:jQuery.prototype.removeClass,m=k?"connection highlighted":"connection";var o=n.call($(p),"highlighted"),q=o.attr("id").replace("job-","");l.edges({target:q}).forEach(function(r){n.call(j.$("#job-"+r.source),"highlighted");j.$("#"+r.source+"-"+q).attr("class",m)});l.vertices[q].eachEdge(function(r){n.call(j.$("#job-"+r.target),"highlighted");j.$("#"+q+"-"+r.target).attr("class",m)})},toString:function(){return"HistoryStructureComponent("+this.model.id+")"}});var g=b.extend({logger:console,className:b.prototype.className+" vertical",layoutDefaults:{paddingTop:8,paddingLeft:20,linkSpacing:16,jobWidth:308,jobHeight:308,initialSpacing:64,jobSpacing:16,linkAdjX:0,linkAdjY:4},_updateLayout:function(){var k=this,l=k.layout;l.svg.width=l.paddingLeft+(l.linkSpacing*_.size(l.nodeMap));l.el.width=l.svg.width+l.jobWidth;l.el.height=0;var j=l.svg.width,m=l.paddingTop;_.each(l.nodeMap,function(p,o){p.x=j;p.y=m;var n=k._jobLiMap[o];if(n.$el.is(":visible")){m+=n.$el.height()+l.jobSpacing}else{m+=l.initialSpacing+l.jobSpacing}});l.el.height=l.svg.height=Math.max(l.el.height,m);l.links.forEach(function(n){var o=l.nodeMap[n.source],p=l.nodeMap[n.target];n.x1=o.x+l.linkAdjX;n.y1=o.y+l.linkAdjY;n.x2=p.x+l.linkAdjX;n.y2=p.y+l.linkAdjY;k.debug("link:",n.x1,n.y1,n.x2,n.y2,n)});k.debug("el:",l.el);k.debug("svg:",l.svg);return l},_connectionPath:function(l){var k=0,j=((l.y2-l.y1)/this.layout.svg.height)*this.layout.svg.width;return["M",l.x1,",",l.y1," ","C",l.x1-j,",",l.y1+k," ",l.x2-j,",",l.y2-k," ",l.x2,",",l.y2].join("")},toString:function(){return"VerticalHistoryStructureComponent("+this.model.id+")"}});var d=Backbone.View.extend(h.LoggableMixin).extend({className:"history-structure",initialize:function(j){this.log(this+"(HistoryStructureView).initialize:",j,this.model);this.jobs=j.jobs;this._createDAG()},_createDAG:function(){this.dag=new c({historyContents:this.model.contents.toJSON(),jobs:this.jobs,excludeSetMetadata:true,excludeErroredJobs:true});this.log(this+".dag:",this.dag);this._createComponents()},_createComponents:function(){this.log(this+"._createComponents");var j=this;j.componentViews=j.dag.weakComponentGraphArray().map(function(k){return j._createComponent(k)})},_createComponent:function(j){this.log(this+"._createComponent:",j);return new b({model:this.model,component:j})},render:function(k){this.log(this+".render:",k);var j=this;j.$el.html(['<div class="controls"></div>','<div class="components"></div>'].join(""));j.componentViews.forEach(function(l){l.render().$el.appendTo(j.$components())});return j},$components:function(){return this.$(".components")},toString:function(){return"HistoryStructureView()"}});return d}); \ No newline at end of file diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 static/scripts/packed/utils/graph.js --- a/static/scripts/packed/utils/graph.js +++ b/static/scripts/packed/utils/graph.js @@ -1,1 +1,1 @@ -define([],function(){function l(r,q){for(var p in r){if(r.hasOwnProperty(p)){q(r[p],p,r)}}}function i(r,q){for(var p in q){if(q.hasOwnProperty(p)){r[p]=q[p]}}return r}function f(r,q){for(var p in q){if(q.hasOwnProperty(p)){if(!r.hasOwnProperty(p)||r[p]!==q[p]){return false}}}return true}function c(w,p){var t=typeof p==="function"?p:undefined,s=typeof p==="object"?p:undefined,u=[],q=0;for(var r in w){if(w.hasOwnProperty(r)){var v=w[r];if(t){u.push(t.call(v,v,r,q))}else{if(s){if(typeof v==="object"&&f(v,s)){u.push(v)}}else{u.push(v)}}q+=1}}return u}function g(r,s,q){var p=this;p.source=r!==undefined?r:null;p.target=s!==undefined?s:null;p.data=q||null;return p}g.prototype.toString=function(){return this.source+"->"+this.target};g.prototype.toJSON=function(){var p={source:this.source,target:this.target};if(this.data){p.data=this.data}return p};function m(q,r){var p=this;p.name=q!==undefined?q:"(unnamed)";p.data=r||null;p.edges={};p.degree=0;return p}window.Vertex=m;m.prototype.toString=function(){return"Vertex("+this.name+")"};m.prototype.eachEdge=function(p){return c(this.edges,p)};m.prototype.toJSON=function(){return{name:this.name,data:this.data}};var k=function(r,q){var p=this;p.graph=r;p.processFns=q||{vertexEarly:function(t,s){},edge:function(u,t,s){},vertexLate:function(t,s){}};p._cache={};return p};k.prototype.search=function e(q){var p=this;if(q in p._cache){return p._cache[q]}if(!(q instanceof m)){q=p.graph.vertices[q]}return(p._cache[q.name]=p._search(q))};k.prototype._searchTree=function a(q){var p=this;return new j(true,{edges:q.edges,vertices:Object.keys(q.discovered).map(function(r){return p.graph.vertices[r].toJSON()})})};k.prototype.searchTree=function b(p){return this._searchTree(this.search(p))};var n=function(r,q){var p=this;k.call(this,r,q);return p};n.prototype=new k();n.prototype.constructor=n;n.prototype._search=function d(u,s){s=s||{discovered:{},edges:[]};var r=this,p=[];function q(v,w){var x=this;if(r.processFns.edge){r.processFns.edge.call(r,x,w,s)}if(!s.discovered[v.name]){s.discovered[v.name]=true;s.edges.push({source:x.name,target:v.name});p.push(v)}}s.discovered[u.name]=true;p.push(u);while(p.length){var t=p.shift();if(r.processFns.vertexEarly){r.processFns.vertexEarly.call(r,t,s)}r.graph.eachAdjacent(t,q);if(r.processFns.vertexLate){r.processFns.vertexLate.call(r,t,s)}}return s};var h=function(r,q){var p=this;k.call(this,r,q);return p};h.prototype=new k();h.prototype.constructor=h;h.prototype._search=function(u,q){q=q||{discovered:{},edges:[],entryTimes:{},exitTimes:{}};var p=this,t=0;function s(w,x){var v=this;if(p.processFns.edge){p.processFns.edge.call(p,v,x,q)}if(!q.discovered[w.name]){q.edges.push({source:v.name,target:w.name});r(w)}}function r(v){q.discovered[v.name]=true;if(p.processFns.vertexEarly){p.processFns.vertexEarly.call(p,v,q)}q.entryTimes[v.name]=t++;p.graph.eachAdjacent(v,s);if(p.processFns.vertexLate){p.processFns.vertexLate.call(p,v,q)}q.exitTimes[v.name]=t++}r(u);return q};function j(q,r,p){this.directed=q||false;return this.init(p).read(r)}window.Graph=j;j.prototype.init=function(q){q=q||{};var p=this;p.allowReflexiveEdges=q.allowReflexiveEdges||false;p.vertices={};p.numEdges=0;return p};j.prototype.read=function(q){if(!q){return this}var p=this;if(q.hasOwnProperty("nodes")){return p.readNodesAndLinks(q)}if(q.hasOwnProperty("vertices")){return p.readVerticesAndEdges(q)}return p};j.prototype.readNodesAndLinks=function(q){if(!(q&&q.hasOwnProperty("nodes"))){return this}var p=this;q.nodes.forEach(function(r){p.createVertex(r.name,r.data)});(q.links||[]).forEach(function(u,s){var r=q.nodes[u.source].name,t=q.nodes[u.target].name;p.createEdge(r,t,p.directed)});return p};j.prototype.readVerticesAndEdges=function(q){if(!(q&&q.hasOwnProperty("vertices"))){return this}var p=this;q.vertices.forEach(function(r){p.createVertex(r.name,r.data)});(q.edges||[]).forEach(function(s,r){p.createEdge(s.source,s.target,p.directed)});return p};j.prototype.createVertex=function(p,q){if(this.vertices[p]){return this.vertices[p]}return(this.vertices[p]=new m(p,q))};j.prototype.createEdge=function(q,r,t,u){var v=q===r;if(!this.allowReflexiveEdges&&v){return null}sourceVertex=this.vertices[q];targetVertex=this.vertices[r];if(!(sourceVertex&&targetVertex)){return null}var p=this,s=new g(q,r,u);sourceVertex.edges[r]=s;sourceVertex.degree+=1;p.numEdges+=1;if(!v&&!t){p.createEdge(r,q,true)}return s};j.prototype.edges=function(p){return Array.prototype.concat.apply([],this.eachVertex(function(q){return q.eachEdge(p)}))};j.prototype.eachVertex=function(p){return c(this.vertices,p)};j.prototype.adjacent=function(q){var p=this;return c(q.edges,function(r){return p.vertices[r.target]})};j.prototype.eachAdjacent=function(r,q){var p=this;return c(r.edges,function(t){var s=p.vertices[t.target];return q.call(r,s,t)})};j.prototype.print=function(){var p=this;console.log("Graph has "+Object.keys(p.vertices).length+" vertices");p.eachVertex(function(q){console.log(q.toString());q.eachEdge(function(r){console.log("\t "+r)})});return p};j.prototype.toDOT=function(){var q=this,p=[];p.push("graph bler {");q.edges(function(r){p.push("\t"+r.from+" -- "+r.to+";")});p.push("}");return p.join("\n")};j.prototype.toNodesAndLinks=function(){var p=this,q={};return{nodes:p.eachVertex(function(t,s,r){q[t.name]=r;return t.toJSON()}),links:p.edges(function(s){var r=s.toJSON();r.source=q[s.source];r.target=q[s.target];return r})}};j.prototype.toVerticesAndEdges=function(){var p=this;return{vertices:p.eachVertex(function(r,q){return r.toJSON()}),edges:p.edges(function(q){return q.toJSON()})}};j.prototype.breadthFirstSearch=function(q,p){return new n(this).search(q)};j.prototype.breadthFirstSearchTree=function(q,p){return new n(this).searchTree(q)};j.prototype.depthFirstSearch=function(q,p){return new h(this).search(q)};j.prototype.depthFirstSearchTree=function(q,p){return new h(this).searchTree(q)};j.prototype.weakComponents=function(){var r=this,u=this,q,t=[];function p(v){var w=new h(u)._search(v);q=q.filter(function(x){return !(x in w.discovered)});return{vertices:Object.keys(w.discovered).map(function(x){return r.vertices[x].toJSON()}),edges:w.edges.map(function(y){var x=r.vertices[y.target].edges[y.source]!==undefined;if(r.directed&&x){var z=y.source;y.source=y.target;y.target=z}return y})}}if(r.directed){u=new j(false,r.toNodesAndLinks())}q=Object.keys(u.vertices);while(q.length){var s=u.vertices[q.shift()];t.push(p(s))}return t};j.prototype.weakComponentGraph=function(){var p=this.weakComponents();return new j(this.directed,{vertices:p.reduce(function(r,q){return r.concat(q.vertices)},[]),edges:p.reduce(function(r,q){return r.concat(q.edges)},[])})};j.prototype.weakComponentGraphArray=function(){return this.weakComponents().map(function(p){return new j(this.directed,p)})};function o(s,p,r){var u={nodes:[],links:[]};function t(v){return Math.floor(Math.random()*v)}for(var q=0;q<p;q++){u.nodes.push({name:q})}for(q=0;q<r;q++){u.links.push({source:t(p),target:t(p)})}return new j(s,u)}return{Vertex:m,Edge:g,BreadthFirstSearch:n,DepthFirstSearch:h,Graph:j,randGraph:o}}); \ No newline at end of file +define([],function(){function l(r,q){for(var p in r){if(r.hasOwnProperty(p)){q(r[p],p,r)}}}function i(r,q){for(var p in q){if(q.hasOwnProperty(p)){r[p]=q[p]}}return r}function f(r,q){for(var p in q){if(q.hasOwnProperty(p)){if(!r.hasOwnProperty(p)||r[p]!==q[p]){return false}}}return true}function c(w,p){var t=typeof p==="function"?p:undefined,s=typeof p==="object"?p:undefined,u=[],q=0;for(var r in w){if(w.hasOwnProperty(r)){var v=w[r];if(t){u.push(t.call(v,v,r,q))}else{if(s){if(typeof v==="object"&&f(v,s)){u.push(v)}}else{u.push(v)}}q+=1}}return u}function g(r,s,q){var p=this;p.source=r!==undefined?r:null;p.target=s!==undefined?s:null;p.data=q||null;return p}g.prototype.toString=function(){return this.source+"->"+this.target};g.prototype.toJSON=function(){var p={source:this.source,target:this.target};if(this.data){p.data=this.data}return p};function m(q,r){var p=this;p.name=q!==undefined?q:"(unnamed)";p.data=r||null;p.edges={};p.degree=0;return p}m.prototype.toString=function(){return"Vertex("+this.name+")"};m.prototype.eachEdge=function(p){return c(this.edges,p)};m.prototype.toJSON=function(){return{name:this.name,data:this.data}};var k=function(r,q){var p=this;p.graph=r;p.processFns=q||{vertexEarly:function(t,s){},edge:function(u,t,s){},vertexLate:function(t,s){}};p._cache={};return p};k.prototype.search=function e(q){var p=this;if(q in p._cache){return p._cache[q]}if(!(q instanceof m)){q=p.graph.vertices[q]}return(p._cache[q.name]=p._search(q))};k.prototype._search=function d(q,p){p=p||{discovered:{},edges:[]};return p};k.prototype.searchTree=function b(p){return this._searchTree(this.search(p))};k.prototype._searchTree=function a(q){var p=this;return new j(true,{edges:q.edges,vertices:Object.keys(q.discovered).map(function(r){return p.graph.vertices[r].toJSON()})})};var n=function(r,q){var p=this;k.call(this,r,q);return p};n.prototype=new k();n.prototype.constructor=n;n.prototype._search=function d(u,s){s=s||{discovered:{},edges:[]};var r=this,p=[];function q(v,w){var x=this;if(r.processFns.edge){r.processFns.edge.call(r,x,w,s)}if(!s.discovered[v.name]){s.discovered[v.name]=true;s.edges.push({source:x.name,target:v.name});p.push(v)}}s.discovered[u.name]=true;p.push(u);while(p.length){var t=p.shift();if(r.processFns.vertexEarly){r.processFns.vertexEarly.call(r,t,s)}r.graph.eachAdjacent(t,q);if(r.processFns.vertexLate){r.processFns.vertexLate.call(r,t,s)}}return s};var h=function(r,q){var p=this;k.call(this,r,q);return p};h.prototype=new k();h.prototype.constructor=h;h.prototype._search=function(u,q){q=q||{discovered:{},edges:[],entryTimes:{},exitTimes:{}};var p=this,t=0;function s(w,x){var v=this;if(p.processFns.edge){p.processFns.edge.call(p,v,x,q)}if(!q.discovered[w.name]){q.edges.push({source:v.name,target:w.name});r(w)}}function r(v){q.discovered[v.name]=true;if(p.processFns.vertexEarly){p.processFns.vertexEarly.call(p,v,q)}q.entryTimes[v.name]=t++;p.graph.eachAdjacent(v,s);if(p.processFns.vertexLate){p.processFns.vertexLate.call(p,v,q)}q.exitTimes[v.name]=t++}r(u);return q};function j(q,r,p){this.directed=q||false;return this.init(p).read(r)}window.Graph=j;j.prototype.init=function(q){q=q||{};var p=this;p.allowReflexiveEdges=q.allowReflexiveEdges||false;p.vertices={};p.numEdges=0;return p};j.prototype.read=function(q){if(!q){return this}var p=this;if(q.hasOwnProperty("nodes")){return p.readNodesAndLinks(q)}if(q.hasOwnProperty("vertices")){return p.readVerticesAndEdges(q)}return p};j.prototype.readNodesAndLinks=function(q){if(!(q&&q.hasOwnProperty("nodes"))){return this}var p=this;q.nodes.forEach(function(r){p.createVertex(r.name,r.data)});(q.links||[]).forEach(function(u,s){var r=q.nodes[u.source].name,t=q.nodes[u.target].name;p.createEdge(r,t,p.directed)});return p};j.prototype.readVerticesAndEdges=function(q){if(!(q&&q.hasOwnProperty("vertices"))){return this}var p=this;q.vertices.forEach(function(r){p.createVertex(r.name,r.data)});(q.edges||[]).forEach(function(s,r){p.createEdge(s.source,s.target,p.directed)});return p};j.prototype.createVertex=function(p,q){if(this.vertices[p]){return this.vertices[p]}return(this.vertices[p]=new m(p,q))};j.prototype.createEdge=function(q,r,t,u){var v=q===r;if(!this.allowReflexiveEdges&&v){return null}sourceVertex=this.vertices[q];targetVertex=this.vertices[r];if(!(sourceVertex&&targetVertex)){return null}var p=this,s=new g(q,r,u);sourceVertex.edges[r]=s;sourceVertex.degree+=1;p.numEdges+=1;if(!v&&!t){p.createEdge(r,q,true)}return s};j.prototype.edges=function(p){return Array.prototype.concat.apply([],this.eachVertex(function(q){return q.eachEdge(p)}))};j.prototype.eachVertex=function(p){return c(this.vertices,p)};j.prototype.adjacent=function(q){var p=this;return c(q.edges,function(r){return p.vertices[r.target]})};j.prototype.eachAdjacent=function(r,q){var p=this;return c(r.edges,function(t){var s=p.vertices[t.target];return q.call(r,s,t)})};j.prototype.print=function(){var p=this;console.log("Graph has "+Object.keys(p.vertices).length+" vertices");p.eachVertex(function(q){console.log(q.toString());q.eachEdge(function(r){console.log("\t "+r)})});return p};j.prototype.toDOT=function(){var q=this,p=[];p.push("graph bler {");q.edges(function(r){p.push("\t"+r.from+" -- "+r.to+";")});p.push("}");return p.join("\n")};j.prototype.toNodesAndLinks=function(){var p=this,q={};return{nodes:p.eachVertex(function(t,s,r){q[t.name]=r;return t.toJSON()}),links:p.edges(function(s){var r=s.toJSON();r.source=q[s.source];r.target=q[s.target];return r})}};j.prototype.toVerticesAndEdges=function(){var p=this;return{vertices:p.eachVertex(function(r,q){return r.toJSON()}),edges:p.edges(function(q){return q.toJSON()})}};j.prototype.breadthFirstSearch=function(q,p){return new n(this).search(q)};j.prototype.breadthFirstSearchTree=function(q,p){return new n(this).searchTree(q)};j.prototype.depthFirstSearch=function(q,p){return new h(this).search(q)};j.prototype.depthFirstSearchTree=function(q,p){return new h(this).searchTree(q)};j.prototype.weakComponents=function(){var r=this,u=this,q,t=[];function p(v){var w=new h(u)._search(v);q=q.filter(function(x){return !(x in w.discovered)});return{vertices:Object.keys(w.discovered).map(function(x){return r.vertices[x].toJSON()}),edges:w.edges.map(function(y){var x=r.vertices[y.target].edges[y.source]!==undefined;if(r.directed&&x){var z=y.source;y.source=y.target;y.target=z}return y})}}if(r.directed){u=new j(false,r.toNodesAndLinks())}q=Object.keys(u.vertices);while(q.length){var s=u.vertices[q.shift()];t.push(p(s))}return t};j.prototype.weakComponentGraph=function(){var p=this.weakComponents();return new j(this.directed,{vertices:p.reduce(function(r,q){return r.concat(q.vertices)},[]),edges:p.reduce(function(r,q){return r.concat(q.edges)},[])})};j.prototype.weakComponentGraphArray=function(){return this.weakComponents().map(function(p){return new j(this.directed,p)})};function o(s,p,r){var u={nodes:[],links:[]};function t(v){return Math.floor(Math.random()*v)}for(var q=0;q<p;q++){u.nodes.push({name:q})}for(q=0;q<r;q++){u.links.push({source:t(p),target:t(p)})}return new j(s,u)}return{Vertex:m,Edge:g,BreadthFirstSearch:n,DepthFirstSearch:h,Graph:j,randGraph:o}}); \ No newline at end of file diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 static/scripts/utils/graph.js --- a/static/scripts/utils/graph.js +++ b/static/scripts/utils/graph.js @@ -2,10 +2,10 @@ ],function(){ /* ============================================================================ TODO: - edges can't retain data ============================================================================ */ //TODO: go ahead and move to underscore... +/** call fn on each key/value in d */ function each( d, fn ){ for( var k in d ){ if( d.hasOwnProperty( k ) ){ @@ -14,6 +14,7 @@ } } +/** copy key/values from d2 to d overwriting if present */ function extend( d, d2 ){ for( var k in d2 ){ if( d2.hasOwnProperty( k ) ){ @@ -23,6 +24,7 @@ return d; } +/** deep equal of two dictionaries */ function matches( d, d2 ){ for( var k in d2 ){ if( d2.hasOwnProperty( k ) ){ @@ -34,6 +36,10 @@ return true; } +/** map key/values in obj + * if propsOrFn is an object, return only those k/v that match the object + * if propsOrFn is function, call the fn and returned the mapped values from it + */ function iterate( obj, propsOrFn ){ var fn = typeof propsOrFn === 'function'? propsOrFn : undefined, props = typeof propsOrFn === 'object'? propsOrFn : undefined, @@ -60,6 +66,8 @@ // ============================================================================ +/** A graph edge containing the name/id of both source and target and optional data + */ function Edge( source, target, data ){ var self = this; self.source = source !== undefined? source : null; @@ -70,10 +78,12 @@ //} return self; } +/** String representation */ Edge.prototype.toString = function(){ return this.source + '->' + this.target; }; +/** Return a plain object representing this edge */ Edge.prototype.toJSON = function(){ //TODO: this is safe in most browsers (fns will be stripped) - alter tests to incorporate this in order to pass data //return this; @@ -88,6 +98,9 @@ }; // ============================================================================ +/** A graph vertex with a (unique) name/id and optional data. + * A vertex contains a list of Edges (whose sources are this vertex) and maintains the degree. + */ function Vertex( name, data ){ var self = this; self.name = name !== undefined? name : '(unnamed)'; @@ -96,16 +109,19 @@ self.degree = 0; return self; } -window.Vertex = Vertex; + +/** String representation */ Vertex.prototype.toString = function(){ return 'Vertex(' + this.name + ')'; }; //TODO: better name w no collision for either this.eachEdge or this.edges +/** Iterate over each edge from this vertex */ Vertex.prototype.eachEdge = function( propsOrFn ){ return iterate( this.edges, propsOrFn ); }; +/** Return a plain object representing this vertex */ Vertex.prototype.toJSON = function(){ //return this; return { @@ -116,6 +132,10 @@ // ============================================================================ +/** Base (abstract) class for Graph search algorithms. + * Pass in the graph to search + * and an optional dictionary containing the 3 vertex/edge processing fns listed below. + */ var GraphSearch = function( graph, processFns ){ var self = this; self.graph = graph; @@ -136,6 +156,9 @@ return self; }; +/** Search interface where start is the vertex (or the name/id of the vertex) to begin the search at + * This public interface caches searches and returns the cached version if it's already been done. + */ GraphSearch.prototype.search = function _search( start ){ var self = this; if( start in self._cache ){ return self._cache[ start ]; } @@ -143,6 +166,22 @@ return ( self._cache[ start.name ] = self._search( start ) ); }; +/** Actual search (private) function (abstract here) */ +GraphSearch.prototype._search = function __search( start, search ){ + search = search || { + discovered : {}, + //parents : {}, + edges : [] + }; + return search; +}; + +/** Searches graph from start and returns a search tree of the results */ +GraphSearch.prototype.searchTree = function _searchTree( start ){ + return this._searchTree( this.search( start ) ); +}; + +/** Helper fn that returns a graph (a search tree) based on the search object passed in (does not actually search) */ GraphSearch.prototype._searchTree = function __searchTree( search ){ var self = this; return new Graph( true, { @@ -153,11 +192,10 @@ }); }; -GraphSearch.prototype.searchTree = function _searchTree( start ){ - return this._searchTree( this.search( start ) ); -}; // ============================================================================ +/** Breadth first search algo. + */ var BreadthFirstSearch = function( graph, processFns ){ var self = this; GraphSearch.call( this, graph, processFns ); @@ -166,6 +204,7 @@ BreadthFirstSearch.prototype = new GraphSearch(); BreadthFirstSearch.prototype.constructor = BreadthFirstSearch; +/** (Private) implementation of BFS */ BreadthFirstSearch.prototype._search = function __search( start, search ){ search = search || { discovered : {}, @@ -205,6 +244,8 @@ // ============================================================================ +/** Depth first search algorithm. + */ var DepthFirstSearch = function( graph, processFns ){ var self = this; GraphSearch.call( this, graph, processFns ); @@ -213,6 +254,7 @@ DepthFirstSearch.prototype = new GraphSearch(); DepthFirstSearch.prototype.constructor = DepthFirstSearch; +/** (Private) implementation of DFS */ DepthFirstSearch.prototype._search = function( start, search ){ //console.debug( 'depthFirstSearch:', start ); search = search || { @@ -258,6 +300,8 @@ // ============================================================================ +/** A directed/non-directed graph object. + */ function Graph( directed, data, options ){ //TODO: move directed to options this.directed = directed || false; @@ -265,7 +309,7 @@ } window.Graph = Graph; - +/** Set up options and instance variables */ Graph.prototype.init = function( options ){ options = options || {}; var self = this; @@ -277,6 +321,7 @@ return self; }; +/** Read data from the plain object data - both in d3 form (nodes and links) or vertices and edges */ Graph.prototype.read = function( data ){ if( !data ){ return this; } var self = this; @@ -286,6 +331,7 @@ }; //TODO: the next two could be combined +/** Create the graph using a list of nodes and a list of edges (where source and target are indeces into nodes) */ Graph.prototype.readNodesAndLinks = function( data ){ if( !( data && data.hasOwnProperty( 'nodes' ) ) ){ return this; } //console.debug( 'readNodesAndLinks:', data ); @@ -306,6 +352,7 @@ return self; }; +/** Create the graph using a list of nodes and a list of edges (where source and target are names of nodes) */ Graph.prototype.readVerticesAndEdges = function( data ){ if( !( data && data.hasOwnProperty( 'vertices' ) ) ){ return this; } //console.debug( 'readVerticesAndEdges:', data ); @@ -324,12 +371,16 @@ return self; }; +/** Return the vertex with name, creating it if necessary */ Graph.prototype.createVertex = function( name, data ){ //console.debug( 'createVertex:', name, data ); if( this.vertices[ name ] ){ return this.vertices[ name ]; } return ( this.vertices[ name ] = new Vertex( name, data ) ); }; +/** Create an edge in vertex named sourceName to targetName (optionally adding data to it) + * If directed is false, create a second edge from targetName to sourceName. + */ Graph.prototype.createEdge = function( sourceName, targetName, directed, data ){ //note: allows multiple 'equivalent' edges (to/from same source/target) //console.debug( 'createEdge:', source, target, directed ); @@ -359,16 +410,19 @@ return edge; }; +/** Walk over all the edges of the graph using the vertex.eachEdge iterator */ Graph.prototype.edges = function( propsOrFn ){ return Array.prototype.concat.apply( [], this.eachVertex( function( vertex ){ return vertex.eachEdge( propsOrFn ); })); }; +/** Iterate over all the vertices in the graph */ Graph.prototype.eachVertex = function( propsOrFn ){ return iterate( this.vertices, propsOrFn ); }; +/** Return a list of the vertices adjacent to vertex */ Graph.prototype.adjacent = function( vertex ){ var self = this; return iterate( vertex.edges, function( edge ){ @@ -376,6 +430,7 @@ }); }; +/** Call fn on each vertex adjacent to vertex */ Graph.prototype.eachAdjacent = function( vertex, fn ){ var self = this; return iterate( vertex.edges, function( edge ){ @@ -384,6 +439,7 @@ }); }; +/** Print the graph to the console (debugging) */ Graph.prototype.print = function(){ var self = this; console.log( 'Graph has ' + Object.keys( self.vertices ).length + ' vertices' ); @@ -396,6 +452,7 @@ return self; }; +/** Return a DOT format string of this graph */ Graph.prototype.toDOT = function(){ var self = this, strings = []; @@ -407,6 +464,7 @@ return strings.join( '\n' ); }; +/** Return vertices and edges of this graph in d3 node/link format */ Graph.prototype.toNodesAndLinks = function(){ var self = this, indeces = {}; @@ -424,6 +482,7 @@ }; }; +/** Return vertices and edges of this graph where edges use the name/id as source and target */ Graph.prototype.toVerticesAndEdges = function(){ var self = this; return { @@ -436,18 +495,22 @@ }; }; +/** Search this graph using BFS */ Graph.prototype.breadthFirstSearch = function( start, processFns ){ return new BreadthFirstSearch( this ).search( start ); }; +/** Return a searchtree of this graph using BFS */ Graph.prototype.breadthFirstSearchTree = function( start, processFns ){ return new BreadthFirstSearch( this ).searchTree( start ); }; +/** Search this graph using DFS */ Graph.prototype.depthFirstSearch = function( start, processFns ){ return new DepthFirstSearch( this ).search( start ); }; +/** Return a searchtree of this graph using DFS */ Graph.prototype.depthFirstSearchTree = function( start, processFns ){ return new DepthFirstSearch( this ).searchTree( start ); }; @@ -465,6 +528,7 @@ //Graph.prototype.isBipartite = function(){ //}; +/** Return an array of weakly connected (no edges between) sub-graphs in this graph */ Graph.prototype.weakComponents = function(){ //TODO: alternately, instead of returning graph-like objects: // - could simply decorate the vertices (vertex.component = componentIndex), or clone the graph and do that @@ -515,6 +579,7 @@ return components; }; +/** Return a single graph containing the weakly connected components in this graph */ Graph.prototype.weakComponentGraph = function(){ //note: although this can often look like the original graph - edges can be lost var components = this.weakComponents(); @@ -528,6 +593,7 @@ }); }; +/** Return an array of graphs of the weakly connected components in this graph */ Graph.prototype.weakComponentGraphArray = function(){ //note: although this can often look like the original graph - edges can be lost return this.weakComponents().map( function( component ){ @@ -537,10 +603,8 @@ // ============================================================================ - - - -// ============================================================================ +/** Create a random graph with numVerts vertices and numEdges edges (for testing) + */ function randGraph( directed, numVerts, numEdges ){ //console.debug( 'randGraph', directed, numVerts, numEdges ); var data = { nodes : [], links : [] }; diff -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 -r 8f8341ac47cd276cf0a2aa3d1c1098f7d3d58c75 templates/webapps/galaxy/history/structure.mako --- a/templates/webapps/galaxy/history/structure.mako +++ b/templates/webapps/galaxy/history/structure.mako @@ -95,9 +95,6 @@ <script type="text/javascript"> /* TODO: - components should be graphs? - as it is they're verts+edges - in-panel view of anc desc show datasets when job not expanded @@ -119,8 +116,8 @@ controls: (optionally) filter all deleted (optionally) filter all hidden - (optionally) filter __SET_METADATA__ - (optionally) filter error'd jobs + //(optionally) filter __SET_METADATA__ + //(optionally) filter error'd jobs vertical layout will not allow expansion of jobs/datasets easily @@ -141,8 +138,6 @@ would need to update as jquery was expanding foreignObject/dom */ - - define( 'app', function(){ require([ 'mvc/job/job-model', @@ -151,18 +146,14 @@ ], function( JOB, HISTORY, StructureView ){ var historyModel = new HISTORY.History( bootstrapped.history, bootstrapped.hdas ); -window.historymodel = history; -window.jobs = bootstrapped.jobs; +//window.historymodel = history; +//window.jobs = bootstrapped.jobs; var structure = new StructureView({ model : historyModel, jobs : bootstrapped.jobs }); - structure.$el.appendTo( 'body' ); - console.debug( 'structure visible?', structure.$el.is( ':visible' ) ); - structure.render(); -window.structure = structure; - + structure.render().$el.appendTo( 'body' ); }); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History structure: (<root>/history/structure) horizontal layout of job/history DAG separated into components (a work in progress) and associated qunit tests; Job model and list-item; rudimentary js graph library and tests; Qunit: allow import of test-data; minor fixes
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eacfa5a1a3f2/ Changeset: eacfa5a1a3f2 User: carlfeberhard Date: 2014-10-15 17:11:30+00:00 Summary: History structure: (<root>/history/structure) horizontal layout of job/history DAG separated into components (a work in progress) and associated qunit tests; Job model and list-item; rudimentary js graph library and tests; Qunit: allow import of test-data; minor fixes Affected #: 32 files diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 client/galaxy/scripts/mvc/collection/collection-li.js --- a/client/galaxy/scripts/mvc/collection/collection-li.js +++ b/client/galaxy/scripts/mvc/collection/collection-li.js @@ -100,8 +100,6 @@ /** add the DCE class to the list item */ className : ListItemView.prototype.className + " dataset-collection-element", - /** jq fx speed for this view */ - fxSpeed : 'fast', /** set up */ initialize : function( attributes ){ diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 client/galaxy/scripts/mvc/history/history-structure-view.js --- /dev/null +++ b/client/galaxy/scripts/mvc/history/history-structure-view.js @@ -0,0 +1,409 @@ +define([ + 'mvc/job/job-model', + 'mvc/job/job-li', + 'mvc/history/history-content-model', + 'mvc/history/job-dag', + 'mvc/base-mvc', + 'utils/localization', + 'libs/d3' +], function( JOB, JOB_LI, HISTORY_CONTENT, JobDAG, BASE_MVC, _l ){ +// ============================================================================ +/* TODO: +change component = this to something else + +*/ +// ============================================================================ +var HistoryStructureComponent = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + //logger : console, + + className : 'history-structure-component', + + initialize : function( attributes ){ + this.log( this + '(HistoryStructureComponent).initialize:', attributes ); + this.component = attributes.component; + + this._jobLiMap = {}; + this._createJobModels(); + + this.layout = this._createLayout( attributes.layoutOptions ); + }, + + _createJobModels : function(){ + var view = this; + view.component.eachVertex( function( vertex ){ + var jobJSON = vertex.data.job, + job = new JOB.Job( jobJSON ); + + // get the models of the outputs for this job from the history + var outputModels = _.map( job.get( 'outputs' ), function( output ){ + //note: output is { src: 'hda/dataset_collection', id: <some id> } + // job output doesn't *quite* match up to normal typeId + var type = output.src === 'hda'? 'dataset' : 'dataset_collection', + typeId = HISTORY_CONTENT.typeIdStr( type, output.id ); + return view.model.contents.get( typeId ); + }); + // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls) + job.outputCollection.reset( outputModels ); + job.outputCollection.historyId = structure.model.id; + //this.debug( job.outputCollection ); + + // create the bbone view for the job (to be positioned later accrd. to the layout) and cache + var li = new JOB_LI.JobListItemView({ model: job, expanded: true }); + //var li = new JOB_LI.JobListItemView({ model: job }); + li.$el.appendTo( view.$el ); + view._jobLiMap[ job.id ] = li; + }); + return view.jobs; + }, + + layoutDefaults : { + paddingTop : 8, + paddingLeft : 20, + linkSpacing : 16, + jobHeight : 308, + jobWidthSpacing : 320, + linkAdjX : 4, + linkAdjY : 0 + }, + + _createLayout : function( options ){ + options = _.defaults( _.clone( options || {} ), this.layoutDefaults ); + var view = this, + vertices = _.values( view.component.vertices ), + layout = _.extend( options, { + nodeMap : {}, + links : [], + el : { width: 0, height: 0 }, + svg : { width: 0, height: 0, top: 0, left: 0 } + }); + + vertices.forEach( function( v, j ){ + var node = { name: v.name, x: 0, y: 0 }; + layout.nodeMap[ v.name ] = node; + }); + + view.component.edges( function( e ){ + var link = { + source: e.source, + target: e.target + }; + layout.links.push( link ); + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + return layout; + }, + + _updateLayout : function(){ + var view = this, + layout = view.layout; + + layout.svg.height = layout.paddingTop + ( layout.linkSpacing * _.size( layout.nodeMap ) ); + layout.el.height = layout.svg.height + layout.jobHeight; + +//TODO:?? can't we just alter the component v and e's directly? + // layout the job views putting jobWidthSpacing btwn each + var x = layout.paddingLeft, + y = layout.svg.height; + _.each( layout.nodeMap, function( node, jobId ){ + //this.debug( node, jobId ); + node.x = x; + node.y = y; + x += layout.jobWidthSpacing; + }); + layout.el.width = layout.svg.width = Math.max( layout.el.width, x ); + + // layout the links - connecting each job by it's main coords (currently) +//TODO: somehow adjust the svg height based on the largest distance the longest connection needs + layout.links.forEach( function( link ){ + var source = layout.nodeMap[ link.source ], + target = layout.nodeMap[ link.target ]; + link.x1 = source.x + layout.linkAdjX; + link.y1 = source.y + layout.linkAdjY; + link.x2 = target.x + layout.linkAdjX; + link.y2 = target.y + layout.linkAdjY; + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + return this.layout; + }, + + render : function( options ){ + this.log( this + '.renderComponent:', options ); + var view = this; + + view.component.eachVertex( function( v ){ + //TODO:? liMap needed - can't we attach to vertex? + var li = view._jobLiMap[ v.name ]; + if( !li.$el.is( ':visible' ) ){ + li.render( 0 ); + } + }); + + view._updateLayout(); + // set up the display containers + view.$el + .width( view.layout.el.width ) + .height( view.layout.el.height ); + this.renderSVG(); + + // position the job views accrd. to the layout + view.component.eachVertex( function( v ){ + //TODO:? liMap needed - can't we attach to vertex? + var li = view._jobLiMap[ v.name ], + position = view.layout.nodeMap[ li.model.id ]; + console.debug( li.$el.is( ':visible' ) ); + //this.debug( position ); + li.$el.css({ top: position.y, left: position.x }); + }); + return this; + }, + + renderSVG : function(){ + var view = this, + layout = view.layout; + + var svg = d3.select( this.el ).select( 'svg' ); + if( svg.empty() ){ + svg = d3.select( this.el ).append( 'svg' ); + } + + svg + .attr( 'width', layout.svg.width ) + .attr( 'height', layout.svg.height ); + + function highlightConnect( d ){ + d3.select( this ).classed( 'highlighted', true ); + view._jobLiMap[ d.source ].$el.addClass( 'highlighted' ); + view._jobLiMap[ d.target ].$el.addClass( 'highlighted' ); + } + + function unhighlightConnect( d ){ + d3.select( this ).classed( 'highlighted', false ); + view._jobLiMap[ d.source ].$el.removeClass( 'highlighted' ); + view._jobLiMap[ d.target ].$el.removeClass( 'highlighted' ); + } + + var connections = svg.selectAll( '.connection' ) + .data( layout.links ); + + connections + .enter().append( 'path' ) + .attr( 'class', 'connection' ) + .attr( 'id', function( d ){ return d.source + '-' + d.target; }) + .on( 'mouseover', highlightConnect ) + .on( 'mouseout', unhighlightConnect ); + + connections.transition() + .attr( 'd', function( d ){ return view._connectionPath( d ); }); + +//TODO: ? can we use tick here to update the links? + + return svg.node(); + }, + + _connectionPath : function( d ){ + var CURVE_X = 0, + controlY = ( ( d.x2 - d.x1 ) / this.layout.svg.width ) * this.layout.svg.height; + return [ + 'M', d.x1, ',', d.y1, ' ', + 'C', + d.x1 + CURVE_X, ',', d.y1 - controlY, ' ', + d.x2 - CURVE_X, ',', d.y2 - controlY, ' ', + d.x2, ',', d.y2 + ].join( '' ); + }, + + events : { + 'mouseover .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, true ); }, + 'mouseout .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, false ); } + }, + + highlightConnected : function( jobElement, highlight ){ + highlight = highlight !== undefined? highlight : true; + + var view = this, + component = view.component, + jobClassFn = highlight? jQuery.prototype.addClass : jQuery.prototype.removeClass, + connectionClass = highlight? 'connection highlighted' : 'connection'; + + //console.debug( 'mouseover', this ); + var $jobs = jobClassFn.call( $( jobElement ), 'highlighted' ), + id = $jobs.attr( 'id' ).replace( 'job-', '' ); + + // immed. ancestors + component.edges({ target: id }).forEach( function( edge ){ + jobClassFn.call( view.$( '#job-' + edge.source ), 'highlighted' ); + view.$( '#' + edge.source + '-' + id ).attr( 'class', connectionClass ); + }); + // descendants + component.vertices[ id ].eachEdge( function( edge ){ + jobClassFn.call( view.$( '#job-' + edge.target ), 'highlighted' ); + view.$( '#' + id + '-' + edge.target ).attr( 'class', connectionClass ); + }); + }, + + toString : function(){ + return 'HistoryStructureComponent(' + this.model.id + ')'; + } +}); + + +// ============================================================================ +var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({ + + logger : console, + + className : HistoryStructureComponent.prototype.className + ' vertical', + + layoutDefaults : { + paddingTop : 8, + paddingLeft : 20, + linkSpacing : 16, + jobWidth : 308, + jobHeight : 308, + initialSpacing : 64, + jobSpacing : 16, + linkAdjX : 0, + linkAdjY : 4 + }, + +//TODO: how can we use the dom height of the job li's - they're not visible when this is called? + _updateLayout : function(){ + var view = this, + layout = view.layout; + //this.info( this.cid, '_updateLayout' ) + + layout.svg.width = layout.paddingLeft + ( layout.linkSpacing * _.size( layout.nodeMap ) ); + layout.el.width = layout.svg.width + layout.jobWidth; + + // reset height - we'll get the max Y below to assign to it + layout.el.height = 0; + +//TODO:?? can't we just alter the component v and e's directly? + var x = layout.svg.width, + y = layout.paddingTop; + _.each( layout.nodeMap, function( node, jobId ){ + //this.debug( node, jobId ); + node.x = x; + node.y = y; + var li = view._jobLiMap[ jobId ]; + if( li.$el.is( ':visible' ) ){ + console.debug( 'li is visible, adj. by:', li.$el.height() ); + y += li.$el.height() + layout.jobSpacing; + } else { + y += layout.initialSpacing + layout.jobSpacing; + } + }); + layout.el.height = layout.svg.height = Math.max( layout.el.height, y ); + + // layout the links - connecting each job by it's main coords (currently) + layout.links.forEach( function( link ){ + var source = layout.nodeMap[ link.source ], + target = layout.nodeMap[ link.target ]; + link.x1 = source.x + layout.linkAdjX; + link.y1 = source.y + layout.linkAdjY; + link.x2 = target.x + layout.linkAdjX; + link.y2 = target.y + layout.linkAdjY; + view.debug( 'link:', link.x1, link.y1, link.x2, link.y2, link ); + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + view.debug( 'el:', layout.el ); + view.debug( 'svg:', layout.svg ); + return layout; + }, + + _connectionPath : function( d ){ + var CURVE_Y = 0, + controlX = ( ( d.y2 - d.y1 ) / this.layout.svg.height ) * this.layout.svg.width; + return [ + 'M', d.x1, ',', d.y1, ' ', + 'C', + d.x1 - controlX, ',', d.y1 + CURVE_Y, ' ', + d.x2 - controlX, ',', d.y2 - CURVE_Y, ' ', + d.x2, ',', d.y2 + ].join( '' ); + }, + + toString : function(){ + return 'VerticalHistoryStructureComponent(' + this.model.id + ')'; + } +}); + + +// ============================================================================ +var HistoryStructureView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + //logger : console, + + className : 'history-structure', + + initialize : function( attributes ){ + this.log( this + '(HistoryStructureView).initialize:', attributes, this.model ); +//TODO: to model + this.jobs = attributes.jobs; + this._createDAG(); + }, + + _createDAG : function(){ + this.dag = new JobDAG({ + historyContents : this.model.contents.toJSON(), + jobs : this.jobs, + excludeSetMetadata : true, + excludeErroredJobs : true + }); +window.dag = this.dag; + this.log( this + '.dag:', this.dag ); + + this._createComponents(); + }, + + _createComponents : function(){ + this.log( this + '._createComponents' ); + var structure = this; +window.structure = structure; + + structure.componentViews = structure.dag.weakComponentGraphArray().map( function( componentGraph ){ + return structure._createComponent( componentGraph ); + }); + }, + + _createComponent : function( component ){ + this.log( this + '._createComponent:', component ); + return new HistoryStructureComponent({ + //return new VerticalHistoryStructureComponent({ + model : this.model, + component : component + }); + }, + + render : function( options ){ + this.log( this + '.render:', options ); + var structure = this; + + structure.$el.html([ + '<div class="controls"></div>', + '<div class="components"></div>' + ].join( '' )); + + structure.componentViews.forEach( function( component ){ + component.render().$el.appendTo( structure.$components() ); + }); + return structure; + }, + + $components : function(){ + return this.$( '.components' ); + }, + + toString : function(){ + return 'HistoryStructureView(' + ')'; + } +}); + + +// ============================================================================ + //return { + // HistoryStructureView : HistoryStructureView + //}; + return HistoryStructureView; +}); diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 client/galaxy/scripts/mvc/history/job-dag.js --- /dev/null +++ b/client/galaxy/scripts/mvc/history/job-dag.js @@ -0,0 +1,204 @@ +define([ + 'utils/graph', + 'utils/add-logging' +],function( GRAPH, addLogging ){ +// ============================================================================ +var _super = GRAPH.Graph; +var JobDAG = function( options ){ + var self = this; + //this.logger = console; + + // instance vars +//TODO: needed? + self._historyContentsMap = {}; + self.filters = []; + + self._idMap = {}; + self.noInputJobs = []; + self.noOutputJobs = []; + +//TODO: save these? + self.filteredSetMetadata = []; + self.filteredErroredJobs = []; + + _super.call( self, true, null, options ); +}; +JobDAG.prototype = new GRAPH.Graph(); +JobDAG.prototype.constructor = JobDAG; +addLogging( JobDAG ); + +// ---------------------------------------------------------------------------- +JobDAG.prototype.init = function _init( options ){ + options = options || {}; + _super.prototype.init.call( this, options ); + + var self = this, + historyContentsJSON = options.historyContents || []; + jobsJSON = options.jobs || []; + + historyContentsJSON.forEach( function( content, i ){ + self._historyContentsMap[ content.id ] = _.clone( content ); + }); + + self.options = _.defaults( _.omit( options, 'historyContents', 'jobs' ), { + excludeSetMetadata : false + }); + self.filters = self._initFilters(); + +//TODO: O( 3N ) + self.preprocessJobs( _.clone( jobsJSON ) ); + self.createGraph(); + + return self; +}; + +JobDAG.prototype._initFilters = function __initFilters(){ + var self = this, + filters = []; + + if( self.options.excludeSetMetadata ){ + self.filteredSetMetadata = []; + filters.push( function filterSetMetadata( jobData ){ + if( jobData.job.tool_id !== '__SET_METADATA__' ){ return true; } + self.filteredSetMetadata.push( jobData.job.id ); + return false; + }); + } + + if( self.options.excludeErroredJobs ){ + self.filteredErroredJobs = []; + filters.push( function filterErrored( jobData ){ + if( jobData.job.state !== 'error' ){ return true; } + self.filteredErroredJobs.push( jobData.job.id ); + return false; + }); + } + + // all outputs deleted + // all outputs hidden + + if( _.isArray( self.options.filters ) ){ + filters = filters.concat( self.options.filters ); + } + self.debug( 'filters len:', filters.length ); + return filters; +}; + +JobDAG.prototype.preprocessJobs = function _preprocessJobs( jobs ){ + this.info( 'processing jobs' ); + + var self = this; +//TODO:? sorting neccessary? + self.sort( jobs ).forEach( function( job, i ){ + var jobData = self.preprocessJob( job, i ); + if( jobData ){ + self._idMap[ job.id ] = jobData; + } + }); + return self; +}; + +JobDAG.prototype.sort = function _sort( jobs ){ + function cmpCreate( a, b ){ + if( a.update_time > b.update_time ){ return 1; } + if( a.update_time < b.update_time ){ return -1; } + return 0; + } + return jobs.sort( cmpCreate ); +}; + +JobDAG.prototype.preprocessJob = function _preprocessJob( job, index ){ + //this.info( 'preprocessJob', job, index ); + var self = this, + jobData = { index: index, job: job }; + + jobData.inputs = self.datasetMapToIdArray( job.inputs, function( dataset, nameInJob ){ + //TODO:? store output name in self._datasets[ output.id ] from creating job? + }); + if( jobData.inputs.length === 0 ){ + self.noInputJobs.push( job.id ); + } + jobData.outputs = self.datasetMapToIdArray( job.outputs, function( dataset, nameInJob ){ + + }); + if( jobData.outputs.length === 0 ){ + self.noOutputJobs.push( job.id ); + } + + //self.debug( JSON.stringify( jobData, null, ' ' ) ); + // apply filters after processing job allowing access to the additional data above in the filters + for( var i=0; i<self.filters.length; i++ ){ + if( !self.filters[i].call( self, jobData ) ){ + self.debug( 'job', job.id, ' has been filtered out by function:\n', self.filters[i] ); + return null; + } + } + + //self.info( 'preprocessJob returning', jobData ); + return jobData; +}; + +JobDAG.prototype.datasetMapToIdArray = function _datasetMapToIdArray( datasetMap, processFn ){ + var self = this; + return _.map( datasetMap, function( dataset, nameInJob ){ + if( !dataset.id ){ + throw new Error( 'No id on datasetMap: ', JSON.stringify( dataset ) ); + } + if( !dataset.src || dataset.src !== 'hda' ){ + throw new Error( 'Bad src on datasetMap: ', JSON.stringify( dataset ) ); + } + processFn.call( self, dataset, nameInJob ); + return dataset.id; + }); +}; + +JobDAG.prototype.createGraph = function _createGraph(){ + var self = this; + self.debug( 'connections:' ); + + _.each( self._idMap, function( sourceJobData, sourceJobId ){ + self.debug( '\t', sourceJobId, sourceJobData ); + self.createVertex( sourceJobId, sourceJobData ); + + sourceJobData.usedIn = []; + _.each( sourceJobData.outputs, function( outputDatasetId ){ +//TODO: O(n^2) + _.each( self._idMap, function( targetJobData, targetJobId ){ + if( targetJobData === sourceJobData ){ return; } + + if( targetJobData.inputs.indexOf( outputDatasetId ) !== -1 ){ + self.info( '\t\t\t found connection: ', sourceJobId, targetJobId ); + sourceJobData.usedIn.push({ job: targetJobId, output: outputDatasetId }); + + self.createVertex( targetJobId, targetJobData ); + + self.createEdge( sourceJobId, targetJobId, self.directed, { + dataset : outputDatasetId + }); + } + }); + }); + }); + self.debug( 'job data: ', JSON.stringify( self._idMap, null, ' ' ) ); + return self; +}; + +Graph.prototype.weakComponentGraphArray = function(){ + return this.weakComponents().map( function( component ){ +//TODO: this seems to belong above (in sort) - why isn't it preserved? + component.vertices.sort( function cmpCreate( a, b ){ + if( a.data.job.update_time > b.data.job.update_time ){ return 1; } + if( a.data.job.update_time < b.data.job.update_time ){ return -1; } + return 0; + }); + return new Graph( this.directed, component ); + }); +}; + + +// ============================================================================ + return JobDAG; + //return { + // jobDAG : jobDAG + //}; +}); diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 client/galaxy/scripts/mvc/job/job-li.js --- /dev/null +++ b/client/galaxy/scripts/mvc/job/job-li.js @@ -0,0 +1,129 @@ +define([ + 'mvc/list/list-item', + 'mvc/dataset/dataset-list', + "mvc/base-mvc", + "utils/localization" +], function( LIST_ITEM, DATASET_LIST, BASE_MVC, _l ){ +//============================================================================== +var _super = LIST_ITEM.FoldoutListItemView; +/** @class + */ +var JobListItemView = _super.extend(/** @lends JobListItemView.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + + className : _super.prototype.className + " job", + id : function(){ + return [ 'job', this.model.get( 'id' ) ].join( '-' ); + }, + + foldoutPanelClass : DATASET_LIST.DatasetList, + + /** Set up: instance vars, options, and event handlers */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( this + '.initialize:', attributes ); + _super.prototype.initialize.call( this, attributes ); + + /** where should pages from links be displayed? (default to new tab/window) */ + this.linkTarget = attributes.linkTarget || '_blank'; + this._setUpListeners(); + }, + + /** In this override, add the state as a class for use with state-based CSS */ + _swapNewRender : function( $newRender ){ + _super.prototype._swapNewRender.call( this, $newRender ); + if( this.model.has( 'state' ) ){ + this.$el.addClass( 'state-' + this.model.get( 'state' ) ); + } + return this.$el; + }, + + /** Stub to return proper foldout panel options */ + _getFoldoutPanelOptions : function(){ + var options = _super.prototype._getFoldoutPanelOptions.call( this ); + return _.extend( options, { + collection : this.model.outputCollection, + selecting : false + }); + }, + + // ........................................................................ misc + /** String representation */ + toString : function(){ + return 'JobListItemView(' + this.model + ')'; + } +}); + +// ............................................................................ TEMPLATES +/** underscore templates */ +JobListItemView.prototype.templates = (function(){ +//TODO: move to require text! plugin + + var elTemplate = BASE_MVC.wrapTemplate([ + '<div class="list-element">', + '<div class="id"><%= model.id %></div>', + // errors, messages, etc. + '<div class="warnings"></div>', + + // multi-select checkbox + '<div class="selector">', + '<span class="fa fa-2x fa-square-o"></span>', + '</div>', + // space for title bar buttons - gen. floated to the right + '<div class="primary-actions"></div>', + '<div class="title-bar"></div>', + + // expandable area for more details + '<div class="details"></div>', + '</div>' + ]); + + var titleBarTemplate = BASE_MVC.wrapTemplate([ + // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display + '<div class="title-bar clear" tabindex="0">', + //'<span class="state-icon"></span>', + '<div class="title">', + '<span class="name"><%- job.tool_id %></span>', + '</div>', + '<div class="subtitle"></div>', + '</div>' + ], 'job' ); + + //var subtitleTemplate = BASE_MVC.wrapTemplate([ + // // override this + // '<div class="subtitle">', + // _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ', + // _l( 'Updated' ), ': <%= new Date( job.update_time ).toString() %>', + // '</div>' + //], 'job' ); + // + //var detailsTemplate = BASE_MVC.wrapTemplate([ + // '<div class="details">', + // '<div class="params">', + // '<% _.each( job.params, function( param, paramName ){ %>', + // '<div class="param">', + // '<label class="prompt"><%= paramName %></label>', + // '<span class="value"><%= param %></span>', + // '</div>', + // '<% }) %>', + // '</div>', + // '</div>' + //], 'job' ); + + return _.extend( {}, _super.prototype.templates, { + //el : elTemplate, + titleBar : titleBarTemplate, + //subtitle : subtitleTemplate, + //details : detailsTemplate + }); +}()); + + +//============================================================================= + return { + JobListItemView : JobListItemView + }; +}); diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 client/galaxy/scripts/mvc/job/job-model.js --- /dev/null +++ b/client/galaxy/scripts/mvc/job/job-model.js @@ -0,0 +1,202 @@ +define([ + "mvc/history/history-contents", + "mvc/dataset/states", + "utils/ajax-queue", + "mvc/base-mvc", + "utils/localization" +], function( HISTORY_CONTENTS, STATES, AJAX_QUEUE, BASE_MVC, _l ){ +//============================================================================== +var searchableMixin = BASE_MVC.SearchableModelMixin; +/** @class + */ +var Job = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( + BASE_MVC.mixin( searchableMixin, /** @lends Job.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** default attributes for a model */ + defaults : { + model_class : 'Job', + + tool : null, + exit_code : null, + + inputs : {}, + outputs : {}, + params : {}, + + create_time : null, + update_time : null, + state : STATES.NEW + }, + + /** instance vars and listeners */ + initialize : function( attributes, options ){ + this.debug( this + '(Job).initialize', attributes, options ); + this.outputCollection = attributes.outputCollection || new HISTORY_CONTENTS.HistoryContents([]); + this._setUpListeners(); + }, + + /** set up any event listeners + * event: state:ready fired when this DA moves into/is already in a ready state + */ + _setUpListeners : function(){ + // if the state has changed and the new state is a ready state, fire an event + this.on( 'change:state', function( currModel, newState ){ + this.log( this + ' has changed state:', currModel, newState ); + if( this.inReadyState() ){ + this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); + } + }); + }, + + // ........................................................................ common queries + /** Is this job in a 'ready' state; where 'Ready' states are states where no + * processing is left to do on the server. + */ + inReadyState : function(){ + return _.contains( STATES.READY_STATES, this.get( 'state' ) ); + }, + + /** Does this model already contain detailed data (as opposed to just summary level data)? */ + hasDetails : function(){ + //?? this may not be reliable + return _.isEmpty( this.get( 'outputs' ) ); + }, + + // ........................................................................ ajax + /** root api url */ + urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs', + //url : function(){ return this.urlRoot; }, + + // ........................................................................ searching + // see base-mvc, SearchableModelMixin + /** what attributes of an Job will be used in a text search */ + searchAttributes : [ + 'tool' + ], + + // ........................................................................ misc + /** String representation */ + toString : function(){ + return [ 'Job(', this.get( 'id' ), ':', this.get( 'tool_id' ), ')' ].join( '' ); + } +})); + + +//============================================================================== +/** @class Backbone collection for Jobs. + */ +var JobCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends JobCollection.prototype */{ + model : Job, + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** root api url */ + urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs', + url : function(){ return this.urlRoot; }, + + intialize : function( models, options ){ + console.debug( models, options ); + }, + + // ........................................................................ common queries + /** Get the ids of every item in this collection + * @returns array of encoded ids + */ + ids : function(){ + return this.map( function( item ){ return item.get( 'id' ); }); + }, + + /** Get jobs that are not ready + * @returns array of content models + */ + notReady : function(){ + return this.filter( function( job ){ + return !job.inReadyState(); + }); + }, + + /** return true if any jobs don't have details */ + haveDetails : function(){ + return this.all( function( job ){ return job.hasDetails(); }); + }, + + // ........................................................................ ajax + queueDetailFetching : function(){ + var collection = this, + queue = new AJAX_QUEUE.AjaxQueue( this.map( function( job ){ + return function(){ + return job.fetch({ silent: true }); + }; + })); + queue.done( function(){ + collection.trigger( 'details-loaded' ); + }); + return queue; + }, + + //toDAG : function(){ + // return new JobDAG( this.toJSON() ); + //}, + + // ........................................................................ sorting/filtering + /** return a new collection of jobs whose attributes contain the substring matchesWhat */ + matches : function( matchesWhat ){ + return this.filter( function( job ){ + return job.matches( matchesWhat ); + }); + }, + + // ........................................................................ misc + /** override to get a correct/smarter merge when incoming data is partial */ + set : function( models, options ){ + // arrrrrrrrrrrrrrrrrg... + // (e.g. stupid backbone) + // w/o this partial models from the server will fill in missing data with model defaults + // and overwrite existing data on the client + // see Backbone.Collection.set and _prepareModel + var collection = this; + models = _.map( models, function( model ){ + if( !collection.get( model.id ) ){ return model; } + + // merge the models _BEFORE_ calling the superclass version + var merged = existing.toJSON(); + _.extend( merged, model ); + return merged; + }); + // now call superclass when the data is filled + Backbone.Collection.prototype.set.call( this, models, options ); + }, + + /** String representation. */ + toString : function(){ + return ([ 'JobCollection(', this.length, ')' ].join( '' )); + } + +//----------------------------------------------------------------------------- class vars +}, { + + fromHistory : function( historyId ){ + console.debug( this ); + var Collection = this, + collection = new Collection([]); + collection.fetch({ data: { history_id: historyId }}) + .done( function(){ + window.queue = collection.queueDetailFetching(); + + }); + return collection; + } +}); + + +//============================================================================= + return { + Job : Job, + JobCollection : JobCollection + }; +}); diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 client/galaxy/scripts/mvc/list/list-item.js --- a/client/galaxy/scripts/mvc/list/list-item.js +++ b/client/galaxy/scripts/mvc/list/list-item.js @@ -16,7 +16,7 @@ initialize : function( attributes ){ /** are the details of this view expanded/shown or not? */ this.expanded = attributes.expanded || false; - //this.log( '\t expanded:', this.expanded ); + this.log( '\t expanded:', this.expanded ); this.fxSpeed = attributes.fxSpeed || this.fxSpeed; }, @@ -70,7 +70,9 @@ /** empty out the current el, move the $newRender's children in */ _swapNewRender : function( $newRender ){ - return this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); + return this.$el.empty() + .attr( 'class', _.isFunction( this.className )? this.className(): this.className ) + .append( $newRender.children() ); }, /** set up js behaviors, event handlers for elements within the given container @@ -204,7 +206,7 @@ $newRender.children( '.warnings' ).replaceWith( this._renderWarnings() ); $newRender.children( '.title-bar' ).replaceWith( this._renderTitleBar() ); $newRender.children( '.primary-actions' ).append( this._renderPrimaryActions() ); - $newRender.find( '.title-bar .subtitle' ).replaceWith( this._renderSubtitle() ); + $newRender.find( '> .title-bar .subtitle' ).replaceWith( this._renderSubtitle() ); return $newRender; }, diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 client/galaxy/scripts/utils/graph.js --- /dev/null +++ b/client/galaxy/scripts/utils/graph.js @@ -0,0 +1,573 @@ +define([ +],function(){ +/* ============================================================================ +TODO: + edges can't retain data + +============================================================================ */ +//TODO: go ahead and move to underscore... +function each( d, fn ){ + for( var k in d ){ + if( d.hasOwnProperty( k ) ){ + fn( d[ k ], k, d ); + } + } +} + +function extend( d, d2 ){ + for( var k in d2 ){ + if( d2.hasOwnProperty( k ) ){ + d[ k ] = d2[ k ]; + } + } + return d; +} + +function matches( d, d2 ){ + for( var k in d2 ){ + if( d2.hasOwnProperty( k ) ){ + if( !d.hasOwnProperty( k ) || d[ k ] !== d2[ k ] ){ + return false; + } + } + } + return true; +} + +function iterate( obj, propsOrFn ){ + var fn = typeof propsOrFn === 'function'? propsOrFn : undefined, + props = typeof propsOrFn === 'object'? propsOrFn : undefined, + returned = [], + index = 0; + for( var key in obj ){ + if( obj.hasOwnProperty( key ) ){ + var value = obj[ key ]; + if( fn ){ + returned.push( fn.call( value, value, key, index ) ); + } else if( props ){ +//TODO: break out to sep? + if( typeof value === 'object' && matches( value, props ) ){ + returned.push( value ); + } + } else { + returned.push( value ); + } + index += 1; + } + } + return returned; +} + + +// ============================================================================ +function Edge( source, target, data ){ + var self = this; + self.source = source !== undefined? source : null; + self.target = target !== undefined? target : null; + self.data = data || null; + //if( typeof data === 'object' ){ + // extend( self, data ); + //} + return self; +} +Edge.prototype.toString = function(){ + return this.source + '->' + this.target; +}; + +Edge.prototype.toJSON = function(){ + //TODO: this is safe in most browsers (fns will be stripped) - alter tests to incorporate this in order to pass data + //return this; + var json = { + source : this.source, + target : this.target + }; + if( this.data ){ + json.data = this.data; + } + return json; +}; + +// ============================================================================ +function Vertex( name, data ){ + var self = this; + self.name = name !== undefined? name : '(unnamed)'; + self.data = data || null; + self.edges = {}; + self.degree = 0; + return self; +} +window.Vertex = Vertex; +Vertex.prototype.toString = function(){ + return 'Vertex(' + this.name + ')'; +}; + +//TODO: better name w no collision for either this.eachEdge or this.edges +Vertex.prototype.eachEdge = function( propsOrFn ){ + return iterate( this.edges, propsOrFn ); +}; + +Vertex.prototype.toJSON = function(){ + //return this; + return { + name : this.name, + data : this.data + }; +}; + + +// ============================================================================ +var GraphSearch = function( graph, processFns ){ + var self = this; + self.graph = graph; + + self.processFns = processFns || { + vertexEarly : function( vertex, search ){ + //console.debug( 'processing vertex:', vertex.name, vertex ); + }, + edge : function( from, edge, search ){ + //console.debug( this, 'edge:', from, edge, search ); + }, + vertexLate : function( vertex, search ){ + //console.debug( this, 'vertexLate:', vertex, search ); + } + }; + + self._cache = {}; + return self; +}; + +GraphSearch.prototype.search = function _search( start ){ + var self = this; + if( start in self._cache ){ return self._cache[ start ]; } + if( !( start instanceof Vertex ) ){ start = self.graph.vertices[ start ]; } + return ( self._cache[ start.name ] = self._search( start ) ); +}; + +GraphSearch.prototype._searchTree = function __searchTree( search ){ + var self = this; + return new Graph( true, { + edges: search.edges, + vertices: Object.keys( search.discovered ).map( function( key ){ + return self.graph.vertices[ key ].toJSON(); + }) + }); +}; + +GraphSearch.prototype.searchTree = function _searchTree( start ){ + return this._searchTree( this.search( start ) ); +}; + +// ============================================================================ +var BreadthFirstSearch = function( graph, processFns ){ + var self = this; + GraphSearch.call( this, graph, processFns ); + return self; +}; +BreadthFirstSearch.prototype = new GraphSearch(); +BreadthFirstSearch.prototype.constructor = BreadthFirstSearch; + +BreadthFirstSearch.prototype._search = function __search( start, search ){ + search = search || { + discovered : {}, + //parents : {}, + edges : [] + }; + + var self = this, + queue = []; + + function discoverAdjacent( adj, edge ){ + var source = this; + if( self.processFns.edge ){ self.processFns.edge.call( self, source, edge, search ); } + if( !search.discovered[ adj.name ] ){ + //console.debug( '\t\t\t', adj.name, 'is undiscovered:', search.discovered[ adj.name ] ); + search.discovered[ adj.name ] = true; + //search.parents[ adj.name ] = source; + search.edges.push({ source: source.name, target: adj.name }); + //console.debug( '\t\t\t queuing undiscovered: ', adj ); + queue.push( adj ); + } + } + + //console.debug( 'BFS starting. start:', start ); + search.discovered[ start.name ] = true; + queue.push( start ); + while( queue.length ){ + var vertex = queue.shift(); + //console.debug( '\t Queue is shifting. Current:', vertex, 'queue:', queue ); + if( self.processFns.vertexEarly ){ self.processFns.vertexEarly.call( self, vertex, search ); } + self.graph.eachAdjacent( vertex, discoverAdjacent ); + if( self.processFns.vertexLate ){ self.processFns.vertexLate.call( self, vertex, search ); } + } + //console.debug( 'search.edges:', JSON.stringify( search.edges ) ); + return search; +}; + + +// ============================================================================ +var DepthFirstSearch = function( graph, processFns ){ + var self = this; + GraphSearch.call( this, graph, processFns ); + return self; +}; +DepthFirstSearch.prototype = new GraphSearch(); +DepthFirstSearch.prototype.constructor = DepthFirstSearch; + +DepthFirstSearch.prototype._search = function( start, search ){ + //console.debug( 'depthFirstSearch:', start ); + search = search || { + discovered : {}, + //parents : {}, + edges : [], + entryTimes : {}, + exitTimes : {} + }; + var self = this, + time = 0; + + // discover verts adjacent to the source (this): + // processing each edge, saving the edge to the tree, and caching the reverse path with parents + function discoverAdjacentVertices( adjacent, edge ){ + //console.debug( '\t\t adjacent:', adjacent, 'edge:', edge ); + var sourceVertex = this; + if( self.processFns.edge ){ self.processFns.edge.call( self, sourceVertex, edge, search ); } + if( !search.discovered[ adjacent.name ] ){ + //search.parents[ adjacent.name ] = sourceVertex; + search.edges.push({ source: sourceVertex.name, target: adjacent.name }); + recurse( adjacent ); + } + } + + // use function stack for DFS stack process verts, times, and discover adjacent verts (recursing into them) + function recurse( vertex ){ + //console.debug( '\t recursing into: ', vertex ); + search.discovered[ vertex.name ] = true; + if( self.processFns.vertexEarly ){ self.processFns.vertexEarly.call( self, vertex, search ); } + search.entryTimes[ vertex.name ] = time++; + + self.graph.eachAdjacent( vertex, discoverAdjacentVertices ); + + if( self.processFns.vertexLate ){ self.processFns.vertexLate.call( self, vertex, search ); } + search.exitTimes[ vertex.name ] = time++; + } + // begin recursion with the desired start + recurse( start ); + + return search; +}; + + +// ============================================================================ +function Graph( directed, data, options ){ +//TODO: move directed to options + this.directed = directed || false; + return this.init( options ).read( data ); +} +window.Graph = Graph; + + +Graph.prototype.init = function( options ){ + options = options || {}; + var self = this; + + self.allowReflexiveEdges = options.allowReflexiveEdges || false; + + self.vertices = {}; + self.numEdges = 0; + return self; +}; + +Graph.prototype.read = function( data ){ + if( !data ){ return this; } + var self = this; + if( data.hasOwnProperty( 'nodes' ) ){ return self.readNodesAndLinks( data ); } + if( data.hasOwnProperty( 'vertices' ) ){ return self.readVerticesAndEdges( data ); } + return self; +}; + +//TODO: the next two could be combined +Graph.prototype.readNodesAndLinks = function( data ){ + if( !( data && data.hasOwnProperty( 'nodes' ) ) ){ return this; } + //console.debug( 'readNodesAndLinks:', data ); + //console.debug( 'data:\n' + JSON.stringify( data, null, ' ' ) ); + var self = this; + data.nodes.forEach( function( node ){ + self.createVertex( node.name, node.data ); + }); + //console.debug( JSON.stringify( self.vertices, null, ' ' ) ); + + ( data.links || [] ).forEach( function( edge, i ){ + var sourceName = data.nodes[ edge.source ].name, + targetName = data.nodes[ edge.target ].name; + self.createEdge( sourceName, targetName, self.directed ); + }); + //self.print(); + //console.debug( JSON.stringify( self.toNodesAndLinks(), null, ' ' ) ); + return self; +}; + +Graph.prototype.readVerticesAndEdges = function( data ){ + if( !( data && data.hasOwnProperty( 'vertices' ) ) ){ return this; } + //console.debug( 'readVerticesAndEdges:', data ); + //console.debug( 'data:\n' + JSON.stringify( data, null, ' ' ) ); + var self = this; + data.vertices.forEach( function( node ){ + self.createVertex( node.name, node.data ); + }); + //console.debug( JSON.stringify( self.vertices, null, ' ' ) ); + + ( data.edges || [] ).forEach( function( edge, i ){ + self.createEdge( edge.source, edge.target, self.directed ); + }); + //self.print(); + //console.debug( JSON.stringify( self.toNodesAndLinks(), null, ' ' ) ); + return self; +}; + +Graph.prototype.createVertex = function( name, data ){ + //console.debug( 'createVertex:', name, data ); + if( this.vertices[ name ] ){ return this.vertices[ name ]; } + return ( this.vertices[ name ] = new Vertex( name, data ) ); +}; + +Graph.prototype.createEdge = function( sourceName, targetName, directed, data ){ + //note: allows multiple 'equivalent' edges (to/from same source/target) + //console.debug( 'createEdge:', source, target, directed ); + var isReflexive = sourceName === targetName; + if( !this.allowReflexiveEdges && isReflexive ){ return null; } + + sourceVertex = this.vertices[ sourceName ]; + targetVertex = this.vertices[ targetName ]; + //note: silently ignores edges from/to unknown vertices + if( !( sourceVertex && targetVertex ) ){ return null; } + +//TODO: prob. move to vertex + var self = this, + edge = new Edge( sourceName, targetName, data ); + sourceVertex.edges[ targetName ] = edge; + sourceVertex.degree += 1; + self.numEdges += 1; + + //TODO:! don't like having duplicate edges for non-directed graphs + // mirror edges (reversing source and target) in non-directed graphs + // but only if not reflexive + if( !isReflexive && !directed ){ + // flip directed to prevent recursion loop + self.createEdge( targetName, sourceName, true ); + } + + return edge; +}; + +Graph.prototype.edges = function( propsOrFn ){ + return Array.prototype.concat.apply( [], this.eachVertex( function( vertex ){ + return vertex.eachEdge( propsOrFn ); + })); +}; + +Graph.prototype.eachVertex = function( propsOrFn ){ + return iterate( this.vertices, propsOrFn ); +}; + +Graph.prototype.adjacent = function( vertex ){ + var self = this; + return iterate( vertex.edges, function( edge ){ + return self.vertices[ edge.target ]; + }); +}; + +Graph.prototype.eachAdjacent = function( vertex, fn ){ + var self = this; + return iterate( vertex.edges, function( edge ){ + var adj = self.vertices[ edge.target ]; + return fn.call( vertex, adj, edge ); + }); +}; + +Graph.prototype.print = function(){ + var self = this; + console.log( 'Graph has ' + Object.keys( self.vertices ).length + ' vertices' ); + self.eachVertex( function( vertex ){ + console.log( vertex.toString() ); + vertex.eachEdge( function( edge ){ + console.log( '\t ' + edge ); + }); + }); + return self; +}; + +Graph.prototype.toDOT = function(){ + var self = this, + strings = []; + strings.push( 'graph bler {' ); + self.edges( function( edge ){ + strings.push( '\t' + edge.from + ' -- ' + edge.to + ';' ); + }); + strings.push( '}' ); + return strings.join( '\n' ); +}; + +Graph.prototype.toNodesAndLinks = function(){ + var self = this, + indeces = {}; + return { + nodes : self.eachVertex( function( vertex, key, i ){ + indeces[ vertex.name ] = i; + return vertex.toJSON(); + }), + links : self.edges( function( edge ){ + var json = edge.toJSON(); + json.source = indeces[ edge.source ]; + json.target = indeces[ edge.target ]; + return json; + }) + }; +}; + +Graph.prototype.toVerticesAndEdges = function(){ + var self = this; + return { + vertices : self.eachVertex( function( vertex, key ){ + return vertex.toJSON(); + }), + edges : self.edges( function( edge ){ + return edge.toJSON(); + }) + }; +}; + +Graph.prototype.breadthFirstSearch = function( start, processFns ){ + return new BreadthFirstSearch( this ).search( start ); +}; + +Graph.prototype.breadthFirstSearchTree = function( start, processFns ){ + return new BreadthFirstSearch( this ).searchTree( start ); +}; + +Graph.prototype.depthFirstSearch = function( start, processFns ){ + return new DepthFirstSearch( this ).search( start ); +}; + +Graph.prototype.depthFirstSearchTree = function( start, processFns ){ + return new DepthFirstSearch( this ).searchTree( start ); +}; + + +//Graph.prototype.shortestPath = function( start, end ){ +//}; +// +//Graph.prototype.articulationVertices = function(){ +//}; +// +//Graph.prototype.isAcyclic = function(){ +//}; +// +//Graph.prototype.isBipartite = function(){ +//}; + +Graph.prototype.weakComponents = function(){ +//TODO: alternately, instead of returning graph-like objects: +// - could simply decorate the vertices (vertex.component = componentIndex), or clone the graph and do that + var self = this, + searchGraph = this, + undiscovered, + components = []; + + function getComponent( undiscoveredVertex ){ +//TODO: better interface on dfs (search v. searchTree) + var search = new DepthFirstSearch( searchGraph )._search( undiscoveredVertex ); + + // remove curr discovered from undiscovered + undiscovered = undiscovered.filter( function( name ){ + return !( name in search.discovered ); + }); + + return { + vertices : Object.keys( search.discovered ).map( function( vertexName ){ + return self.vertices[ vertexName ].toJSON(); + }), + edges : search.edges.map( function( edge ){ + // restore any reversed edges + var hasBeenReversed = self.vertices[ edge.target ].edges[ edge.source ] !== undefined; + if( self.directed && hasBeenReversed ){ + var swap = edge.source; + edge.source = edge.target; + edge.target = swap; + } + return edge; + }) + }; + } + + if( self.directed ){ + // if directed - convert to undirected for search + searchGraph = new Graph( false, self.toNodesAndLinks() ); + } + undiscovered = Object.keys( searchGraph.vertices ); + //console.debug( '(initial) undiscovered:', undiscovered ); + while( undiscovered.length ){ + var undiscoveredVertex = searchGraph.vertices[ undiscovered.shift() ]; + components.push( getComponent( undiscoveredVertex ) ); + //console.debug( 'undiscovered now:', undiscovered ); + } + + //console.debug( 'components:\n', JSON.stringify( components, null, ' ' ) ); + return components; +}; + +Graph.prototype.weakComponentGraph = function(){ + //note: although this can often look like the original graph - edges can be lost + var components = this.weakComponents(); + return new Graph( this.directed, { + vertices : components.reduce( function( reduction, curr ){ + return reduction.concat( curr.vertices ); + }, [] ), + edges : components.reduce( function( reduction, curr ){ + return reduction.concat( curr.edges ); + }, [] ) + }); +}; + +Graph.prototype.weakComponentGraphArray = function(){ + //note: although this can often look like the original graph - edges can be lost + return this.weakComponents().map( function( component ){ + return new Graph( this.directed, component ); + }); +}; + + +// ============================================================================ + + + +// ============================================================================ +function randGraph( directed, numVerts, numEdges ){ + //console.debug( 'randGraph', directed, numVerts, numEdges ); + var data = { nodes : [], links : [] }; + function randRange( range ){ + return Math.floor( Math.random() * range ); + } + for( var i=0; i<numVerts; i++ ){ + data.nodes.push({ name: i }); + } + for( i=0; i<numEdges; i++ ){ + data.links.push({ + source : randRange( numVerts ), + target : randRange( numVerts ) + }); + } + //console.debug( JSON.stringify( data, null, ' ' ) ); + return new Graph( directed, data ); +} + + +// ============================================================================ + return { + Vertex : Vertex, + Edge : Edge, + BreadthFirstSearch : BreadthFirstSearch, + DepthFirstSearch : DepthFirstSearch, + Graph : Graph, + randGraph : randGraph + }; +}); diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -529,6 +529,27 @@ return trans.fill_template( "history/display_structured.mako", items=items, history=history ) @web.expose + def structure( self, trans, id=None ): + """ + """ + if not id: + id = trans.security.encode_id( trans.history.id ) + + history_to_view = self.get_history( trans, id, check_ownership=False, check_accessible=True ) + history_data = self.mgrs.histories._get_history_data( trans, history_to_view ) + history_dictionary = history_data[ 'history' ] + hda_dictionaries = history_data[ 'contents' ] + + jobs = ( trans.sa_session.query( trans.app.model.Job ) + .filter( trans.app.model.Job.user == trans.user ) + .filter( trans.app.model.Job.history_id == trans.security.decode_id( id ) ) ).all() + + jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs ) + + return trans.fill_template( "history/structure.mako", historyId=history_dictionary[ 'id' ], + history=history_dictionary, hdas=hda_dictionaries, jobs=jobs ) + + @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): """ View a history. If a history is importable, then it is viewable by any user. diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r eacfa5a1a3f2e9fc516bea159c16ddb36067a220 static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -100,8 +100,6 @@ /** add the DCE class to the list item */ className : ListItemView.prototype.className + " dataset-collection-element", - /** jq fx speed for this view */ - fxSpeed : 'fast', /** set up */ initialize : function( attributes ){ This diff is so big that we needed to truncate the remainder. 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: dannon: Move handler startup to immediately following full creation and association of the JobManager.
by commits-noreply＠bitbucket.org 15 Oct '14

15 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9f5491972e72/ Changeset: 9f5491972e72 User: dannon Date: 2014-10-15 14:21:13+00:00 Summary: Move handler startup to immediately following full creation and association of the JobManager. Affected #: 2 files diff -r d43121eccec2fa0aa28e4d8ff60204742f6b23af -r 9f5491972e72ee38e011d49e891303e47bca29d9 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -134,6 +134,7 @@ # Start the job manager from galaxy.jobs import manager self.job_manager = manager.JobManager( self ) + self.job_manager.start() # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue self.job_stop_queue = self.job_manager.job_stop_queue diff -r d43121eccec2fa0aa28e4d8ff60204742f6b23af -r 9f5491972e72ee38e011d49e891303e47bca29d9 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -27,6 +27,8 @@ self.job_handler = NoopHandler() self.job_queue = self.job_stop_queue = NoopQueue() self.job_lock = False + + def start( self ): self.job_handler.start() def shutdown( 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: dannon: Update docstring to refer to correct resource from PR529/tool_data endpoint.
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d43121eccec2/ Changeset: d43121eccec2 User: dannon Date: 2014-10-14 22:32:33+00:00 Summary: Update docstring to refer to correct resource from PR529/tool_data endpoint. Affected #: 1 file diff -r 1e7840610ca307c53916b0e6568b0883450c8bab -r d43121eccec2fa0aa28e4d8ff60204742f6b23af lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -1,11 +1,10 @@ - from galaxy import web from galaxy.web.base.controller import BaseAPIController class ToolData( BaseAPIController ): """ - RESTful controller for interactions with tools. + RESTful controller for interactions with tool data """ @web.require_admin 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: dannon: Remove unused import from PR529/ tool_data endpoint.
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e7840610ca3/ Changeset: 1e7840610ca3 User: dannon Date: 2014-10-14 22:31:22+00:00 Summary: Remove unused import from PR529/ tool_data endpoint. Affected #: 1 file diff -r 46a1b41a275dc29dad7dd012d881239625c85154 -r 1e7840610ca307c53916b0e6568b0883450c8bab lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -1,5 +1,5 @@ -from galaxy import web, util +from galaxy import web from galaxy.web.base.controller import BaseAPIController 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: dannon: Branch prune.
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/03c8aa8709cf/ Changeset: 03c8aa8709cf Branch: tool-data-api User: dannon Date: 2014-10-14 22:19:17+00:00 Summary: Branch prune. Affected #: 0 files 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: dannon: Merged in kellrott/galaxy-farm/tool-data-api (pull request #529)
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46a1b41a275d/ Changeset: 46a1b41a275d User: dannon Date: 2014-10-14 22:18:25+00:00 Summary: Merged in kellrott/galaxy-farm/tool-data-api (pull request #529) Adding Tool-Data API Affected #: 3 files diff -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 -r 46a1b41a275dc29dad7dd012d881239625c85154 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -15,6 +15,8 @@ from galaxy import util from galaxy.util.odict import odict +from galaxy.model.item_attrs import Dictifiable + log = logging.getLogger( __name__ ) DEFAULT_TABLE_TYPE = 'tabular' @@ -223,7 +225,7 @@ return self._update_version() -class TabularToolDataTable( ToolDataTable ): +class TabularToolDataTable( ToolDataTable, Dictifiable ): """ Data stored in a tabular / separated value format on disk, allows multiple files to be merged but all must have the same column definitions:: @@ -235,6 +237,7 @@ </table> """ + dict_collection_visible_keys = [ 'name' ] type_key = 'tabular' @@ -514,10 +517,17 @@ else: replace = " " return map( lambda x: x.replace( separator, replace ), fields ) - + @property def xml_string( self ): return util.xml_to_string( self.config_element ) + def to_dict(self, view='collection'): + rval = super(TabularToolDataTable, self).to_dict() + if view == 'element': + rval['columns'] = sorted(self.columns.keys(), key=lambda x:self.columns[x]) + rval['fields'] = self.get_fields() + return rval + # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) diff -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 -r 46a1b41a275dc29dad7dd012d881239625c85154 lib/galaxy/webapps/galaxy/api/tool_data.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -0,0 +1,23 @@ + +from galaxy import web, util +from galaxy.web.base.controller import BaseAPIController + + +class ToolData( BaseAPIController ): + """ + RESTful controller for interactions with tools. + """ + + @web.require_admin + @web.expose_api + def index( self, trans, **kwds ): + """ + GET /api/tool_data: returns a list tool_data tables:: + + """ + return list( a.to_dict() for a in trans.app.tool_data_tables.data_tables.values() ) + + @web.require_admin + @web.expose_api + def show( self, trans, id, **kwds ): + return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') diff -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 -r 46a1b41a275dc29dad7dd012d881239625c85154 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -170,6 +170,7 @@ path_prefix='/api/histories/:history_id/contents/:history_content_id' ) webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) + webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) 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: 4 new changesets
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/224188b46163/ Changeset: 224188b46163 Branch: tool-data-api User: kell...(a)gmail.com Date: 2014-10-13 17:27:15+00:00 Summary: Adding in tool-data API point Affected #: 3 files diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 224188b4616365fb1b9e20e8f1bd8c70d21d63af lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -514,10 +514,17 @@ else: replace = " " return map( lambda x: x.replace( separator, replace ), fields ) - + @property def xml_string( self ): return util.xml_to_string( self.config_element ) + def to_dict(self): + rval = dict( + columns=sorted(self.columns.keys(), key=lambda x:self.columns[x]), + fields=self.get_fields() + ) + return rval + # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 224188b4616365fb1b9e20e8f1bd8c70d21d63af lib/galaxy/webapps/galaxy/api/tool_data.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -0,0 +1,31 @@ + +from galaxy import exceptions +from galaxy import web, util +from galaxy.web import _future_expose_api_anonymous +from galaxy.web import _future_expose_api +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesVisualizationMixin +from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.visualization.genomes import GenomeRegion +from galaxy.util.json import dumps +from galaxy.visualization.data_providers.genome import * + +from galaxy.managers.collections_util import dictify_dataset_collection_instance + + +class ToolData( BaseAPIController ): + """ + RESTful controller for interactions with tools. + """ + + @web.expose_api + def index( self, trans, **kwds ): + """ + GET /api/tool_data: returns a list tool_data tables:: + + """ + return trans.app.tool_data_tables.data_tables.keys() + + @web.expose_api + def show( self, trans, id, **kwds ): + return trans.app.tool_data_tables.data_tables[id].to_dict() diff -r 04015a2bc7375f1179950a3f698353d033fc3a5d -r 224188b4616365fb1b9e20e8f1bd8c70d21d63af lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -170,6 +170,7 @@ path_prefix='/api/histories/:history_id/contents/:history_content_id' ) webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) + webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) https://bitbucket.org/galaxy/galaxy-central/commits/3e978842fac2/ Changeset: 3e978842fac2 Branch: tool-data-api User: kellrott Date: 2014-10-13 20:36:50+00:00 Summary: Making the tool_data api use normal to_dict calls Affected #: 2 files diff -r 224188b4616365fb1b9e20e8f1bd8c70d21d63af -r 3e978842fac25ea4702c8e5b09da0818c74bd028 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -15,6 +15,8 @@ from galaxy import util from galaxy.util.odict import odict +from galaxy.model.item_attrs import Dictifiable + log = logging.getLogger( __name__ ) DEFAULT_TABLE_TYPE = 'tabular' @@ -223,7 +225,7 @@ return self._update_version() -class TabularToolDataTable( ToolDataTable ): +class TabularToolDataTable( ToolDataTable, Dictifiable ): """ Data stored in a tabular / separated value format on disk, allows multiple files to be merged but all must have the same column definitions:: @@ -235,6 +237,7 @@ </table> """ + dict_collection_visible_keys = [ 'name' ] type_key = 'tabular' @@ -519,11 +522,11 @@ def xml_string( self ): return util.xml_to_string( self.config_element ) - def to_dict(self): - rval = dict( - columns=sorted(self.columns.keys(), key=lambda x:self.columns[x]), - fields=self.get_fields() - ) + def to_dict(self, view='collection'): + rval = super(TabularToolDataTable, self).to_dict() + if view == 'element': + rval['columns'] = sorted(self.columns.keys(), key=lambda x:self.columns[x]) + rval['fields'] = self.get_fields() return rval # Registry of tool data types by type_key diff -r 224188b4616365fb1b9e20e8f1bd8c70d21d63af -r 3e978842fac25ea4702c8e5b09da0818c74bd028 lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -24,8 +24,8 @@ GET /api/tool_data: returns a list tool_data tables:: """ - return trans.app.tool_data_tables.data_tables.keys() + return list( a.to_dict() for a in trans.app.tool_data_tables.data_tables.values() ) @web.expose_api def show( self, trans, id, **kwds ): - return trans.app.tool_data_tables.data_tables[id].to_dict() + return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') https://bitbucket.org/galaxy/galaxy-central/commits/8f7128937f08/ Changeset: 8f7128937f08 Branch: tool-data-api User: kellrott Date: 2014-10-13 22:48:50+00:00 Summary: Removing unneeded imports and limiting access to admin for ToolData api Affected #: 1 file diff -r 3e978842fac25ea4702c8e5b09da0818c74bd028 -r 8f7128937f08776c8714aae6a3ee3b22d27c0601 lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -1,16 +1,6 @@ -from galaxy import exceptions from galaxy import web, util -from galaxy.web import _future_expose_api_anonymous -from galaxy.web import _future_expose_api from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesVisualizationMixin -from galaxy.web.base.controller import UsesHistoryMixin -from galaxy.visualization.genomes import GenomeRegion -from galaxy.util.json import dumps -from galaxy.visualization.data_providers.genome import * - -from galaxy.managers.collections_util import dictify_dataset_collection_instance class ToolData( BaseAPIController ): @@ -18,6 +8,7 @@ RESTful controller for interactions with tools. """ + @web.require_admin @web.expose_api def index( self, trans, **kwds ): """ @@ -26,6 +17,7 @@ """ return list( a.to_dict() for a in trans.app.tool_data_tables.data_tables.values() ) + @web.require_admin @web.expose_api def show( self, trans, id, **kwds ): return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') https://bitbucket.org/galaxy/galaxy-central/commits/46a1b41a275d/ Changeset: 46a1b41a275d User: dannon Date: 2014-10-14 22:18:25+00:00 Summary: Merged in kellrott/galaxy-farm/tool-data-api (pull request #529) Adding Tool-Data API Affected #: 3 files diff -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 -r 46a1b41a275dc29dad7dd012d881239625c85154 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -15,6 +15,8 @@ from galaxy import util from galaxy.util.odict import odict +from galaxy.model.item_attrs import Dictifiable + log = logging.getLogger( __name__ ) DEFAULT_TABLE_TYPE = 'tabular' @@ -223,7 +225,7 @@ return self._update_version() -class TabularToolDataTable( ToolDataTable ): +class TabularToolDataTable( ToolDataTable, Dictifiable ): """ Data stored in a tabular / separated value format on disk, allows multiple files to be merged but all must have the same column definitions:: @@ -235,6 +237,7 @@ </table> """ + dict_collection_visible_keys = [ 'name' ] type_key = 'tabular' @@ -514,10 +517,17 @@ else: replace = " " return map( lambda x: x.replace( separator, replace ), fields ) - + @property def xml_string( self ): return util.xml_to_string( self.config_element ) + def to_dict(self, view='collection'): + rval = super(TabularToolDataTable, self).to_dict() + if view == 'element': + rval['columns'] = sorted(self.columns.keys(), key=lambda x:self.columns[x]) + rval['fields'] = self.get_fields() + return rval + # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) diff -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 -r 46a1b41a275dc29dad7dd012d881239625c85154 lib/galaxy/webapps/galaxy/api/tool_data.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -0,0 +1,23 @@ + +from galaxy import web, util +from galaxy.web.base.controller import BaseAPIController + + +class ToolData( BaseAPIController ): + """ + RESTful controller for interactions with tools. + """ + + @web.require_admin + @web.expose_api + def index( self, trans, **kwds ): + """ + GET /api/tool_data: returns a list tool_data tables:: + + """ + return list( a.to_dict() for a in trans.app.tool_data_tables.data_tables.values() ) + + @web.require_admin + @web.expose_api + def show( self, trans, id, **kwds ): + return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') diff -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 -r 46a1b41a275dc29dad7dd012d881239625c85154 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -170,6 +170,7 @@ path_prefix='/api/histories/:history_id/contents/:history_content_id' ) webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) + webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) 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: Parses dynamic options and rerun states to tool model
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f31f262f9f42/ Changeset: f31f262f9f42 User: guerler Date: 2014-10-14 21:57:01+00:00 Summary: ToolForm: Parses dynamic options and rerun states to tool model Affected #: 33 files diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -83,6 +83,12 @@ return result; }, + /** Returns matched content from summary. + */ + get: function(options) { + return _.findWhere(this.summary, options) || {}; + }, + /** Get details of a content by id. */ getDetails: function(options) { diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -7,13 +7,6 @@ function(Utils, Portlet, Ui, CitationModel, CitationView, Tools, ToolTemplate, ToolContent, ToolSection, ToolTree, ToolJobs) { - // create tool model - var Model = Backbone.Model.extend({ - initialize: function (options) { - this.url = galaxy_config.root + 'api/tools/' + options.id + '?io_details=true'; - } - }); - // create form view var View = Backbone.View.extend({ // base element @@ -21,6 +14,9 @@ // initialize initialize: function(options) { + // log options + console.debug(options); + // link this var self = this; @@ -31,8 +27,10 @@ this.modal = new Ui.Modal.View(); } - // link options - this.options = options; + // link model/inputs and all options + this.options = options; + this.model = options.model; + this.inputs = options.model.inputs; // set element this.setElement('<div/>'); @@ -40,11 +38,6 @@ // add to main element $(this.container).append(this.$el); - // load tool model - this.model = new Model({ - id : options.id - }); - // creates a tree/json structure from the input form this.tree = new ToolTree(this); @@ -64,7 +57,7 @@ this.content = new ToolContent({ history_id : this.options.history_id, success : function() { - self._initializeToolForm(); + self._buildForm(); } }); }, @@ -96,33 +89,37 @@ console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); }, - // initialize tool form - _initializeToolForm: function() { + // refresh form data + _refreshForm: function() { // link this var self = this; - // fetch model and render form - this.model.fetch({ - error: function(response) { - console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.'); + // finalize data + var current_state = this.tree.finalize({ + data : function(dict) { + if (dict.values.length > 0 && dict.values[0].src === 'hda') { + return self.content.get({id: dict.values[0].id}).dataset_id; + } + return null; + } + }); + + // log tool state + console.debug('tools-form::_refreshForm() - Refreshing inputs/states.'); + console.debug(current_state); + + // post job + Utils.request({ + type : 'GET', + url : galaxy_config.root + 'tool_runner/index?tool_id=' + this.options.id + '&form_refresh=True', + data : current_state, + success : function(response) { + console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); + console.debug(response); }, - success: function() { - // backup inputs - self.inputs = self.model.get('inputs'); - - // update inputs with job parameters - if (self.options.job_id) { - Utils.get({ - url: galaxy_config.root + 'api/jobs/' + self.options.job_id, - success: function(parameters) { - // TODO: Update input parameters - //self._updateInputs(self.inputs, parameters); - self._buildForm(); - } - }); - } else { - self._buildForm(); - } + error : function(response) { + console.debug('tools-form::_refreshForm() - Refresh request failed.'); + console.debug(response); } }); }, @@ -132,8 +129,14 @@ // link this var self = this; - // create question button - var button_question = new Ui.ButtonIcon({ + // button menu + var menu = new Ui.ButtonMenu({ + icon : 'fa-gear', + tooltip : 'Click to see a list of available operations.' + }); + + // add question option + menu.addMenu({ icon : 'fa-question-circle', title : 'Question?', tooltip : 'Ask a question about this tool (Biostar)', @@ -143,7 +146,7 @@ }); // create search button - var button_search = new Ui.ButtonIcon({ + menu.addMenu({ icon : 'fa-search', title : 'Search', tooltip : 'Search help for this tool (Biostar)', @@ -153,7 +156,7 @@ }); // create share button - var button_share = new Ui.ButtonIcon({ + menu.addMenu({ icon : 'fa-share', title : 'Share', tooltip : 'Share this tool', @@ -162,17 +165,10 @@ } }); - // default operations - var operations = { - button_question: button_question, - button_search: button_search, - button_share: button_share - } - // add admin operations if (Galaxy.currUser.get('is_admin')) { // create download button - operations['button_download'] = new Ui.ButtonIcon({ + menu.addMenu({ icon : 'fa-download', title : 'Download', tooltip : 'Download this tool', @@ -189,25 +185,28 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible) { + //if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; - } + //} // create portlet this.portlet = new Portlet.View({ icon : 'fa-wrench', - title: '<b>' + this.model.get('name') + '</b> ' + this.model.get('description'), - operations: operations, + title: '<b>' + this.model.name + '</b> ' + this.model.description, + operations: { + menu : menu + }, buttons: { - execute: new Ui.Button({ + execute : new Ui.Button({ icon : 'fa-check', tooltip : 'Execute the tool', title : 'Execute', cls : 'btn btn-primary', floating : 'clear', onclick : function() { + //self._refreshForm(); self.job_handler.submit(); } }) diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -58,7 +58,6 @@ } } else { // show error message with details - console.debug(job_def); console.debug(response); } } diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 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 @@ -115,41 +115,53 @@ // block index var block_index = 0; + // helper function to create new repeat blocks + function create (inputs, deleteable) { + // create id tag + var sub_section_id = input_def.id + '-section-' + (block_index++); + + // enable/disable repeat delete button + var ondel = null; + if (deleteable) { + ondel = function() { + // delete repeat block + repeat.del(sub_section_id); + + // retitle repeat block + repeat.retitle(input_def.title); + + // trigger refresh + self.app.refresh(); + } + } + + // create sub section + var sub_section = new View(self.app, { + inputs : inputs, + cls : 'ui-table-plain' + }); + + // add tab + repeat.add({ + id : sub_section_id, + title : input_def.title, + $el : sub_section.$el, + ondel : ondel + }); + + // retitle repeat block + repeat.retitle(input_def.title); + } + // - // create tab field + // create repeat block element // var repeat = new Repeat.View({ title_new : input_def.title, max : input_def.max, onnew : function() { - // create id tag - var sub_section_id = input_def.id + '-section-' + (block_index++); - - // create sub section - var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' - }); - - // add new tab - repeat.add({ - id : sub_section_id, - title : input_def.title, - $el : sub_section.$el, - ondel : function() { - // delete repeat block - repeat.del(sub_section_id); - - // retitle repeat block - repeat.retitle(input_def.title); - - // trigger refresh - self.app.refresh(); - } - }); - - // retitle repeat blocks - repeat.retitle(input_def.title); + // create + create(input_def.inputs, true); // trigger refresh self.app.refresh(); @@ -157,29 +169,23 @@ }); // - // add min number of repeat blocks + // add parsed/minimum number of repeat blocks // - for (var i = 0; i < input_def.min; i++) { - // create id tag - var sub_section_id = input_def.id + '-section-' + (block_index++); - - // create sub section - var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' - }); + var n_min = input_def.min; + var n_cache = _.size(input_def.cache); + for (var i = 0; i < Math.max(n_cache, n_min); i++) { + // select input source + var inputs = null; + if (i < n_cache) { + inputs = input_def.cache[i]; + } else { + inputs = input_def.inputs; + } - // add tab - repeat.add({ - id : sub_section_id, - title : input_def.title, - $el : sub_section.$el - }); + // create repeat block + create(inputs, i >= n_min); } - // retitle repeat block - repeat.retitle(input_def.title); - // create input field wrapper var input_element = new InputElement({ label : input_def.title, diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -16,6 +16,12 @@ }, success: function(response) { + // check + if (!response.jobs || !response.jobs.length) { + console.debug('tools-template::success() - Failed jobs.'); + return; + } + // number of jobs var njobs = response.jobs.length; diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 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 @@ -32,7 +32,10 @@ /** Convert dictionary representation into tool api specific flat dictionary format. */ - finalize: function() { + finalize: function(patch) { + // initialize + patch = patch || {}; + // link this var self = this; @@ -110,12 +113,20 @@ } break; default: - // get conditional value + // get field var field = self.app.field_list[input.id]; + // get value + var value = field.value(); + + // patch value + if (patch[input.type]) { + value = patch[input.type](value); + } + // handle default value if (!field.skip) { - add (job_input_id, input.id, field.value()); + add (job_input_id, input.id, value); } } } diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 client/galaxy/scripts/mvc/ui/ui-button-menu.js --- a/client/galaxy/scripts/mvc/ui/ui-button-menu.js +++ b/client/galaxy/scripts/mvc/ui/ui-button-menu.js @@ -13,7 +13,7 @@ floating : 'right', icon : null, onclick : null, - cls : 'icon-btn', + cls : 'ui-button-icon ui-button-menu', tooltip : '', // additional options @@ -121,7 +121,7 @@ // fill template header _templateMenuItem: function (options) { var tmpl = '<li>' + - '<a href="' + options.href + '" target="' + options.target + '">'; + '<a class="dropdown-item" href="' + options.href + '" target="' + options.target + '">'; if (options.icon) tmpl += '<i class="fa ' + options.icon + '"></i>'; @@ -143,25 +143,28 @@ // element _template: function(options) { - // width + // TODO: width/margin should be set in css var width = ''; + var margin = ''; if (options.title) { width = 'width: auto;'; + } else { + margin = 'margin: 0px;'; } - // string - var str = '<div id="' + options.id + '" style="float: ' + options.floating + '; ' + width + '" class="ui-button-icon dropdown ' + options.cls + '">'; - + // create base string + var str = '<div id="' + options.id + '" style="float: ' + options.floating + '; ' + width + '" class="dropdown ' + options.cls + '">' + + '<div class="root button dropdown-toggle" data-toggle="dropdown" style="' + margin + '">' + + '<i class="icon fa ' + options.icon + '"/>'; + // title if (options.title) { - str += '<div class="root button dropdown-toggle" data-toggle="dropdown">' + - '<i class="icon fa ' + options.icon + '"/> ' + - '<span class="title">' + options.title + '</span>' + - '</div>'; - } else { - str += '<i class="icon fa ' + options.icon + '"/>'; + str += ' <span class="title">' + options.title + '</span>'; } - str += '</div>'; + + // finalize + str += '</div>' + + '</div>'; return str; } }); diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 client/galaxy/scripts/utils/utils.js --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -68,6 +68,14 @@ // make request $.ajax(ajaxConfig) .done(function(response) { + if (typeof response === 'string') { + try { + response = response.replace('Infinity,', '"Infinity",'); + response = jQuery.parseJSON(response); + } catch (e) { + console.debug(e); + } + } options.success && options.success(response); }) .fail(function(response) { diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely 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options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. 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Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart 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h=D.yScale().invert(i.mouseY),p=Math.abs(D.yScale().domain()[0]-D.yScale().domain()[1]),d=.03*p,m=e.nearestValueIndex(c.map(function(e){return e.value}),h,d);m!==null&&(c[m].highlight=!0)}var g=n.tickFormat()(D.x()(s,f),f);o.tooltip.position({left:l+u.left,top:i.mouseY+u.top}).chartContainer(A.parentNode).enabled(v).valueFormatter(function(e,t){return r.tickFormat()(e)}).data({value:g,series:c})(),o.renderGuideLine(l)}),o.dispatch.on("elementMouseout",function(e){k.tooltipHide(),t.clearHighlights()}),k.on("tooltipShow",function(e){v&&_(e,A.parentNode)}),k.on("changeState",function(e){typeof e.disabled!="undefined"&&(b.forEach(function(t,n){t.disabled=e.disabled[n]}),x.disabled=e.disabled),typeof e.index!="undefined"&&(M.i=e.index,M.x=O(M.i),x.index=e.index,tt.data([M])),typeof e.rescaleY!="undefined"&&(y=e.rescaleY),D.update()})}),D}function P(e,n){return n.map(function(n,r){if(!n.values)return n;var i=n.values[e];if(i==null)return n;var s=t.y()(i,e);return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],k.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){k.tooltipHide(e)}),k.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),D.dispatch=k,D.lines=t,D.legend=i,D.xAxis=n,D.yAxis=r,D.interactiveLayer=o,d3.rebind(D,t,"defined","isArea","x","y","xScale","yScale","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id"),D.options=e.utils.optionsFunc.bind(D),D.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,D):u},D.width=function(e){return arguments.length?(f=e,D):f},D.height=function(e){return arguments.length?(l=e,D):l},D.color=function(t){return 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e.y},f=[0],l=e.utils.defaultColor(),c=!1,h=d3.format(",.2f"),p,d,v,m,g=d3.dispatch("chartClick","elementClick","elementDblClick","elementMouseover","elementMouseout"),y="discreteBar",b,w;return E.dispatch=g,E.options=e.utils.optionsFunc.bind(E),E.x=function(e){return arguments.length?(u=e,E):u},E.y=function(e){return arguments.length?(a=e,E):a},E.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,E):t},E.width=function(e){return arguments.length?(n=e,E):n},E.height=function(e){return arguments.length?(r=e,E):r},E.xScale=function(e){return arguments.length?(s=e,E):s},E.yScale=function(e){return arguments.length?(o=e,E):o},E.xDomain=function(e){return arguments.length?(p=e,E):p},E.yDomain=function(e){return arguments.length?(d=e,E):d},E.xRange=function(e){return arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var A=d3.select(this),_=this,D=(a||parseInt(A.style("width"))||960)-u.left-u.right,P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom;M.update=function(){A.call(M)},M.container=this,S.disabled=y.map(function(e){return!!e.disabled});if(!x){var H;x={};for(H in S)S[H]instanceof Array?x[H]=S[H].slice(0):x[H]=S[H]}if(!y||!y.length||!y.filter(function(e){return e.values.length}).length){var B=A.selectAll(".nv-noData").data([T]);return B.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),B.attr("x",u.left+D/2).attr("y",u.top+P/2).text(function(e){return e}),M}A.selectAll(".nv-noData").remove(),b=t.xScale(),w=t.yScale();var j=A.selectAll("g.nv-wrap.nv-stackedAreaChart").data([y]),F=j.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedAreaChart").append("g"),I=j.select("g");F.append("rect").style("opacity",0),F.append("g").attr("class","nv-x nv-axis"),F.append("g").attr("class","nv-y 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U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100,step:1},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$slider=this.$el.find("#slider"),this.$text=this.$el.find("#text"),this.$slider.slider(this.options),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;console.log(t),t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.step!=1&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()}),this.$slider.on("slide",function(e,t){n.value(t.value)})},value:function(e){return e!==undefined&&(e=Math.max(Math.min(e,this.options.max),this.options.min),this.options.onchange&&this.options.onchange(e),this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),empty:"No data available"},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$error=$(this._templateError(t)),this.$options=$(this._template(t)),this.$el.append(this.$error),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if(e[t]==="null")return!1;return!0},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){var e=this.$el.find(".ui-option").length;e==0?(this.$error.show(),this.$options.hide()):(this.$error.hide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_templateError:function(e){return'<div class="ui-error" style="display: none;">'+e.empty+"</div>"}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new 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title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2175,7 +2175,7 @@ for expanded_incoming in expanded_incomings: state, state_new = self.__fetch_state( trans, expanded_incoming, history, all_pages=all_pages ) all_states.append( state ) - if state_new: + if state_new and "form_refresh" not in incoming: # This feels a bit like a hack. It allows forcing full processing # of inputs even when there is no state in the incoming dictionary # by providing either 'runtool_btn' (the name of the submit button diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -984,13 +984,13 @@ else: return [] - def to_dict( self, trans, view='collection', value_mapper=None ): + def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ): d = super( SelectToolParameter, self ).to_dict( trans ) # Get options, value. options = [] try: - options = self.get_options( trans, {} ) + options = self.get_options( trans, other_values ) except AssertionError: # we dont/cant set other_values (the {} above), so params that require other params to be filled will error: # required dependency in filter_options @@ -1276,9 +1276,9 @@ # No late validation return False - def to_dict( self, trans, view='collection', value_mapper=None ): + def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ): # call parent to_dict - d = super( ColumnListParameter, self ).to_dict( trans ) + d = super( ColumnListParameter, self ).to_dict( trans, other_values ) # add data reference d['data_ref'] = self.data_ref diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -135,6 +135,7 @@ return { 'id' : encoded_id, 'history_id' : encoded_history_id, + 'dataset_id' : hda.dataset_id, 'name' : hda.name, 'type' : api_type, 'state' : hda.dataset.state, diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -60,6 +60,9 @@ # so the default selected option should be the most recent version of the tool. The following # check will mae sure this occurs. refreshed_on_change = kwd.get( 'refresh', False ) + # This is the new tool forms equivalent to the 'refresh' parameter of the classic tool form + form_refresh = kwd.get( 'form_refresh', False ) + process_state = "populate" if form_refresh else "update" tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, @@ -87,7 +90,7 @@ # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. history = tool.get_default_history_by_trans( trans, create=True ) - template, vars = tool.handle_input( trans, params.__dict__ ) + template, vars = tool.handle_input( trans, params.__dict__, process_state=process_state) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) add_frame = AddFrameData() @@ -95,6 +98,8 @@ if from_noframe is not None: add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True + if form_refresh: + template = "tool_form_refresh.mako" return trans.fill_template( template, history=history, toolbox=self.get_toolbox(), diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/mvc/tools/tools-content.js --- a/static/scripts/mvc/tools/tools-content.js +++ b/static/scripts/mvc/tools/tools-content.js @@ -83,6 +83,12 @@ return result; }, + /** Returns matched content from summary. + */ + get: function(options) { + return _.findWhere(this.summary, options) || {}; + }, + /** Get details of a content by id. */ getDetails: function(options) { diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -7,13 +7,6 @@ function(Utils, Portlet, Ui, CitationModel, CitationView, Tools, ToolTemplate, ToolContent, ToolSection, ToolTree, ToolJobs) { - // create tool model - var Model = Backbone.Model.extend({ - initialize: function (options) { - this.url = galaxy_config.root + 'api/tools/' + options.id + '?io_details=true'; - } - }); - // create form view var View = Backbone.View.extend({ // base element @@ -21,6 +14,9 @@ // initialize initialize: function(options) { + // log options + console.debug(options); + // link this var self = this; @@ -31,8 +27,10 @@ this.modal = new Ui.Modal.View(); } - // link options - this.options = options; + // link model/inputs and all options + this.options = options; + this.model = options.model; + this.inputs = options.model.inputs; // set element this.setElement('<div/>'); @@ -40,11 +38,6 @@ // add to main element $(this.container).append(this.$el); - // load tool model - this.model = new Model({ - id : options.id - }); - // creates a tree/json structure from the input form this.tree = new ToolTree(this); @@ -64,7 +57,7 @@ this.content = new ToolContent({ history_id : this.options.history_id, success : function() { - self._initializeToolForm(); + self._buildForm(); } }); }, @@ -96,33 +89,37 @@ console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); }, - // initialize tool form - _initializeToolForm: function() { + // refresh form data + _refreshForm: function() { // link this var self = this; - // fetch model and render form - this.model.fetch({ - error: function(response) { - console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.'); + // finalize data + var current_state = this.tree.finalize({ + data : function(dict) { + if (dict.values.length > 0 && dict.values[0].src === 'hda') { + return self.content.get({id: dict.values[0].id}).dataset_id; + } + return null; + } + }); + + // log tool state + console.debug('tools-form::_refreshForm() - Refreshing inputs/states.'); + console.debug(current_state); + + // post job + Utils.request({ + type : 'GET', + url : galaxy_config.root + 'tool_runner/index?tool_id=' + this.options.id + '&form_refresh=True', + data : current_state, + success : function(response) { + console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); + console.debug(response); }, - success: function() { - // backup inputs - self.inputs = self.model.get('inputs'); - - // update inputs with job parameters - if (self.options.job_id) { - Utils.get({ - url: galaxy_config.root + 'api/jobs/' + self.options.job_id, - success: function(parameters) { - // TODO: Update input parameters - //self._updateInputs(self.inputs, parameters); - self._buildForm(); - } - }); - } else { - self._buildForm(); - } + error : function(response) { + console.debug('tools-form::_refreshForm() - Refresh request failed.'); + console.debug(response); } }); }, @@ -132,8 +129,14 @@ // link this var self = this; - // create question button - var button_question = new Ui.ButtonIcon({ + // button menu + var menu = new Ui.ButtonMenu({ + icon : 'fa-gear', + tooltip : 'Click to see a list of available operations.' + }); + + // add question option + menu.addMenu({ icon : 'fa-question-circle', title : 'Question?', tooltip : 'Ask a question about this tool (Biostar)', @@ -143,7 +146,7 @@ }); // create search button - var button_search = new Ui.ButtonIcon({ + menu.addMenu({ icon : 'fa-search', title : 'Search', tooltip : 'Search help for this tool (Biostar)', @@ -153,7 +156,7 @@ }); // create share button - var button_share = new Ui.ButtonIcon({ + menu.addMenu({ icon : 'fa-share', title : 'Share', tooltip : 'Share this tool', @@ -162,17 +165,10 @@ } }); - // default operations - var operations = { - button_question: button_question, - button_search: button_search, - button_share: button_share - } - // add admin operations if (Galaxy.currUser.get('is_admin')) { // create download button - operations['button_download'] = new Ui.ButtonIcon({ + menu.addMenu({ icon : 'fa-download', title : 'Download', tooltip : 'Download this tool', @@ -189,25 +185,28 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible) { + //if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; - } + //} // create portlet this.portlet = new Portlet.View({ icon : 'fa-wrench', - title: '<b>' + this.model.get('name') + '</b> ' + this.model.get('description'), - operations: operations, + title: '<b>' + this.model.name + '</b> ' + this.model.description, + operations: { + menu : menu + }, buttons: { - execute: new Ui.Button({ + execute : new Ui.Button({ icon : 'fa-check', tooltip : 'Execute the tool', title : 'Execute', cls : 'btn btn-primary', floating : 'clear', onclick : function() { + //self._refreshForm(); self.job_handler.submit(); } }) diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -58,7 +58,6 @@ } } else { // show error message with details - console.debug(job_def); console.debug(response); } } diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -115,41 +115,53 @@ // block index var block_index = 0; + // helper function to create new repeat blocks + function create (inputs, deleteable) { + // create id tag + var sub_section_id = input_def.id + '-section-' + (block_index++); + + // enable/disable repeat delete button + var ondel = null; + if (deleteable) { + ondel = function() { + // delete repeat block + repeat.del(sub_section_id); + + // retitle repeat block + repeat.retitle(input_def.title); + + // trigger refresh + self.app.refresh(); + } + } + + // create sub section + var sub_section = new View(self.app, { + inputs : inputs, + cls : 'ui-table-plain' + }); + + // add tab + repeat.add({ + id : sub_section_id, + title : input_def.title, + $el : sub_section.$el, + ondel : ondel + }); + + // retitle repeat block + repeat.retitle(input_def.title); + } + // - // create tab field + // create repeat block element // var repeat = new Repeat.View({ title_new : input_def.title, max : input_def.max, onnew : function() { - // create id tag - var sub_section_id = input_def.id + '-section-' + (block_index++); - - // create sub section - var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' - }); - - // add new tab - repeat.add({ - id : sub_section_id, - title : input_def.title, - $el : sub_section.$el, - ondel : function() { - // delete repeat block - repeat.del(sub_section_id); - - // retitle repeat block - repeat.retitle(input_def.title); - - // trigger refresh - self.app.refresh(); - } - }); - - // retitle repeat blocks - repeat.retitle(input_def.title); + // create + create(input_def.inputs, true); // trigger refresh self.app.refresh(); @@ -157,29 +169,23 @@ }); // - // add min number of repeat blocks + // add parsed/minimum number of repeat blocks // - for (var i = 0; i < input_def.min; i++) { - // create id tag - var sub_section_id = input_def.id + '-section-' + (block_index++); - - // create sub section - var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' - }); + var n_min = input_def.min; + var n_cache = _.size(input_def.cache); + for (var i = 0; i < Math.max(n_cache, n_min); i++) { + // select input source + var inputs = null; + if (i < n_cache) { + inputs = input_def.cache[i]; + } else { + inputs = input_def.inputs; + } - // add tab - repeat.add({ - id : sub_section_id, - title : input_def.title, - $el : sub_section.$el - }); + // create repeat block + create(inputs, i >= n_min); } - // retitle repeat block - repeat.retitle(input_def.title); - // create input field wrapper var input_element = new InputElement({ label : input_def.title, diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -16,6 +16,12 @@ }, success: function(response) { + // check + if (!response.jobs || !response.jobs.length) { + console.debug('tools-template::success() - Failed jobs.'); + return; + } + // number of jobs var njobs = response.jobs.length; diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -32,7 +32,10 @@ /** Convert dictionary representation into tool api specific flat dictionary format. */ - finalize: function() { + finalize: function(patch) { + // initialize + patch = patch || {}; + // link this var self = this; @@ -110,12 +113,20 @@ } break; default: - // get conditional value + // get field var field = self.app.field_list[input.id]; + // get value + var value = field.value(); + + // patch value + if (patch[input.type]) { + value = patch[input.type](value); + } + // handle default value if (!field.skip) { - add (job_input_id, input.id, field.value()); + add (job_input_id, input.id, value); } } } diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/mvc/ui/ui-button-menu.js --- a/static/scripts/mvc/ui/ui-button-menu.js +++ b/static/scripts/mvc/ui/ui-button-menu.js @@ -13,7 +13,7 @@ floating : 'right', icon : null, onclick : null, - cls : 'icon-btn', + cls : 'ui-button-icon ui-button-menu', tooltip : '', // additional options @@ -121,7 +121,7 @@ // fill template header _templateMenuItem: function (options) { var tmpl = '<li>' + - '<a href="' + options.href + '" target="' + options.target + '">'; + '<a class="dropdown-item" href="' + options.href + '" target="' + options.target + '">'; if (options.icon) tmpl += '<i class="fa ' + options.icon + '"></i>'; @@ -143,25 +143,28 @@ // element _template: function(options) { - // width + // TODO: width/margin should be set in css var width = ''; + var margin = ''; if (options.title) { width = 'width: auto;'; + } else { + margin = 'margin: 0px;'; } - // string - var str = '<div id="' + options.id + '" style="float: ' + options.floating + '; ' + width + '" class="ui-button-icon dropdown ' + options.cls + '">'; - + // create base string + var str = '<div id="' + options.id + '" style="float: ' + options.floating + '; ' + width + '" class="dropdown ' + options.cls + '">' + + '<div class="root button dropdown-toggle" data-toggle="dropdown" style="' + margin + '">' + + '<i class="icon fa ' + options.icon + '"/>'; + // title if (options.title) { - str += '<div class="root button dropdown-toggle" data-toggle="dropdown">' + - '<i class="icon fa ' + options.icon + '"/> ' + - '<span class="title">' + options.title + '</span>' + - '</div>'; - } else { - str += '<i class="icon fa ' + options.icon + '"/>'; + str += ' <span class="title">' + options.title + '</span>'; } - str += '</div>'; + + // finalize + str += '</div>' + + '</div>'; return str; } }); diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/packed/mvc/tools/tools-content.js --- a/static/scripts/packed/mvc/tools/tools-content.js +++ b/static/scripts/packed/mvc/tools/tools-content.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(j,i,m,k,a,f,d,g,l,c,h){var e=Backbone.Model.extend({initialize:function(n){this.url=galaxy_config.root+"api/tools/"+n.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(o){var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:o.id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){n._initializeToolForm()}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},refresh:function(){this.tree.refresh();for(var n in this.field_list){this.field_list[n].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;this.model.fetch({error:function(o){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");if(n.options.job_id){j.get({url:galaxy_config.root+"api/jobs/"+n.options.job_id,success:function(o){n._buildForm()}})}else{n._buildForm()}}})},_buildForm:function(){var p=this;var r=new m.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/p/new/post/")}});var s=new m.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/t/"+p.options.id+"/")}});var n=new m.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+p.options.id)}});var q={button_question:r,button_search:s,button_share:n};if(Galaxy.currUser.get("is_admin")){q.button_download=new m.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+p.options.id+"/download"}})}this.section=new l.View(p,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new i.View({icon:"fa-wrench",title:"<b>"+this.model.get("name")+"</b> "+this.model.get("description"),operations:q,buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){p.job_handler.submit()}})}});if(!this.options.biostar_url){r.$el.hide();s.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var o=new k.ToolCitationCollection();o.tool_id=this.options.id;var t=new a.CitationListView({collection:o});t.render();o.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.model=n.model;this.inputs=n.model.inputs;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.content=new f({history_id:this.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"tool_runner/index?tool_id="+this.options.id+"&form_refresh=True",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of available operations."});p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});this.$el.hide();$("#tool-form-classic").show();return;this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!this.options.biostar_url){button_question.$el.hide();button_search.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 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/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,field:m});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 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([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var o=e.input;var h=j;if(j!=""){h+="|"}h+=o.name;switch(o.type){case"repeat":var d="section-";var r=[];var l=null;for(var q in e){var k=q.indexOf(d);if(k!=-1){k+=d.length;r.push(parseInt(q.substr(k)));if(!l){l=q.substr(0,k)}}}r.sort(function(s,i){return s-i});var g=0;for(var f in r){b(h+"_"+g++,e[l+r[f]])}break;case"conditional":var p=a.app.field_list[o.id].value();c(h+"|"+o.test_param.name,o.id,p);for(var f in o.cases){if(o.cases[f].value==p){b(h,m[o.id+"-section-"+f]);break}}break;default:var n=a.app.field_list[o.id];if(!n.skip){c(h,o.id,n.value())}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/packed/mvc/ui/ui-button-menu.js --- a/static/scripts/packed/mvc/ui/ui-button-menu.js +++ b/static/scripts/packed/mvc/ui/ui-button-menu.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:true,tag:""},$menu:null,initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement($(this._template(this.options)));var d=$(this.el).find(".root");var b=this;d.on("click",function(f){$(".tooltip").hide();f.preventDefault();if(b.options.onclick){b.options.onclick()}});if(!this.options.visible){this.hide()}d.tooltip({title:c.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(c){var d={title:"",target:"",href:"",onclick:null,divider:false,icon:null,cls:"button-menu btn-group"};d=a.merge(c,d);if(!this.$menu){$(this.el).append(this._templateMenu());this.$menu=$(this.el).find(".menu")}var b=$(this._templateMenuItem(d));b.on("click",function(f){f.preventDefault();if(d.onclick){d.onclick()}});this.$menu.append(b);if(d.divider){this.$menu.append($(this._templateDivider()))}},_templateMenuItem:function(c){var b='<li><a href="'+c.href+'" target="'+c.target+'">';if(c.icon){b+='<i class="fa '+c.icon+'"></i>'}b+=" "+c.title+"</a></li>";return b},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(b){var c="";if(b.title){c="width: auto;"}var d='<div id="'+b.id+'" style="float: '+b.floating+"; "+c+'" class="ui-button-icon dropdown '+b.cls+'">';if(b.title){d+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+b.icon+'"/> <span class="title">'+b.title+"</span></div>"}else{d+='<i class="icon fa '+b.icon+'"/>'}d+="</div>";return d}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:true,tag:""},$menu:null,initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement($(this._template(this.options)));var d=$(this.el).find(".root");var b=this;d.on("click",function(f){$(".tooltip").hide();f.preventDefault();if(b.options.onclick){b.options.onclick()}});if(!this.options.visible){this.hide()}d.tooltip({title:c.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(c){var d={title:"",target:"",href:"",onclick:null,divider:false,icon:null,cls:"button-menu btn-group"};d=a.merge(c,d);if(!this.$menu){$(this.el).append(this._templateMenu());this.$menu=$(this.el).find(".menu")}var b=$(this._templateMenuItem(d));b.on("click",function(f){f.preventDefault();if(d.onclick){d.onclick()}});this.$menu.append(b);if(d.divider){this.$menu.append($(this._templateDivider()))}},_templateMenuItem:function(c){var b='<li><a class="dropdown-item" href="'+c.href+'" target="'+c.target+'">';if(c.icon){b+='<i class="fa '+c.icon+'"></i>'}b+=" "+c.title+"</a></li>";return b},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(b){var c="";var d="";if(b.title){c="width: auto;"}else{d="margin: 0px;"}var e='<div id="'+b.id+'" style="float: '+b.floating+"; "+c+'" class="dropdown '+b.cls+'"><div class="root button dropdown-toggle" data-toggle="dropdown" style="'+d+'"><i class="icon fa '+b.icon+'"/>';if(b.title){e+=' <span class="title">'+b.title+"</span>"}e+="</div></div>";return e}})}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(j){function d(k){top.__utils__get__=top.__utils__get__||{};if(k.cache&&top.__utils__get__[k.url]){k.success&&k.success(top.__utils__get__[k.url]);console.debug("utils.js::get() - Fetching from cache ["+k.url+"].")}else{g({url:k.url,data:k.data,success:function(l){top.__utils__get__[k.url]=l;k.success&&k.success(l)},error:function(l){k.error&&k.error(l)}})}}function g(l){var k={contentType:"application/json",type:l.type||"GET",data:l.data||{},url:l.url};if(k.type=="GET"||k.type=="DELETE"){if(k.url.indexOf("?")==-1){k.url+="?"}else{k.url+="&"}k.url=k.url+$.param(k.data);k.data=null}else{k.dataType="json";k.url=k.url;k.data=JSON.stringify(k.data)}$.ajax(k).done(function(m){l.success&&l.success(m)}).fail(function(n){var m=null;try{m=jQuery.parseJSON(n.responseText)}catch(o){m=n.responseText}l.error&&l.error(m,n)})}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file +define(["libs/underscore"],function(j){function d(k){top.__utils__get__=top.__utils__get__||{};if(k.cache&&top.__utils__get__[k.url]){k.success&&k.success(top.__utils__get__[k.url]);console.debug("utils.js::get() - Fetching from cache ["+k.url+"].")}else{g({url:k.url,data:k.data,success:function(l){top.__utils__get__[k.url]=l;k.success&&k.success(l)},error:function(l){k.error&&k.error(l)}})}}function g(l){var k={contentType:"application/json",type:l.type||"GET",data:l.data||{},url:l.url};if(k.type=="GET"||k.type=="DELETE"){if(k.url.indexOf("?")==-1){k.url+="?"}else{k.url+="&"}k.url=k.url+$.param(k.data);k.data=null}else{k.dataType="json";k.url=k.url;k.data=JSON.stringify(k.data)}$.ajax(k).done(function(m){if(typeof m==="string"){try{m=m.replace("Infinity,",'"Infinity",');m=jQuery.parseJSON(m)}catch(n){console.debug(n)}}l.success&&l.success(m)}).fail(function(n){var m=null;try{m=jQuery.parseJSON(n.responseText)}catch(o){m=n.responseText}l.error&&l.error(m,n)})}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -68,6 +68,14 @@ // make request $.ajax(ajaxConfig) .done(function(response) { + if (typeof response === 'string') { + try { + response = response.replace('Infinity,', '"Infinity",'); + response = jQuery.parseJSON(response); + } catch (e) { + console.debug(e); + } + } options.success && options.success(response); }) .fail(function(response) { diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1297,6 +1297,8 @@ .ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px} .ui-button-icon .button{margin-right:5px;margin-left:5px}.ui-button-icon .button .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px} .ui-button-icon .button.disabled{filter:alpha(opacity=65);opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65)} +.ui-button-menu .dropdown-menu{min-width:50px} +.ui-button-menu .dropdown-item{text-align:left} .ui-button-icon-plain{border:none !important;background:none !important;height:inherit !important;width:inherit !important;padding-right:3px !important} .ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} .ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -90,14 +90,12 @@ .ui-button-icon { &:extend(.icon-btn); &:extend(.no-highlight); - margin-right: 5px; ul { i { font-size: 1.2em; margin-right: 5px; position: relative; top: 1px; } } - .button { margin-right: 5px; margin-left: 5px; @@ -109,12 +107,20 @@ top: -1px; } } - .button.disabled { .opacity(.65); } } +.ui-button-menu { + .dropdown-menu { + min-width: 50px; + } + .dropdown-item { + text-align: left; + } +} + .ui-button-icon-plain { &:extend(.icon-btn); border: none !important; diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -1,42 +1,16 @@ <%inherit file="/base.mako"/> -<% - # load tool help - tool_help = '' - if tool.help: - if tool.has_multiple_pages: - tool_help = tool.help_by_page[tool_state.page] - else: - tool_help = tool.help - # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) +## initialize configuration +<%namespace name="tool_form_refresh" file="./webapps/galaxy/tool_form_refresh.mako" import="*" /> +${tool_form_refresh.init()} - # Convert to unicode to display non-ascii characters. - if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') - endif - - # check if citations exist - tool_citations = False - if tool.citations: - tool_citations = True - - # form configuration - self.form_config = { - 'id' : tool.id, - 'help' : tool_help, - 'citations' : tool_citations, - 'biostar_url' : trans.app.config.biostar_url, - 'history_id' : trans.security.encode_id( trans.history.id ), - 'job_id' : trans.security.encode_id( job.id ) if job else None - } -%> +## new tool form ${h.js("libs/bibtex", "libs/jquery/jquery-ui")} ${h.css('base', 'jquery-ui/smoothness/jquery-ui')} <script> require(['mvc/tools/tools-form'], function(ToolsForm){ $(function(){ - var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + var form = new ToolsForm.View(${ h.dumps(tool_form_refresh.form_config) }); }); }); </script> diff -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a -r f31f262f9f42a3f7ce37d276edbdd5f516d4ff29 templates/webapps/galaxy/tool_form_refresh.mako --- /dev/null +++ b/templates/webapps/galaxy/tool_form_refresh.mako @@ -0,0 +1,113 @@ +<%def name="init()"> +<% + ## create basic tool model + tool_model = tool.to_dict(trans) + tool_model['inputs'] = {} + + ## sanitize + from collections import Iterable + from galaxy.model import HistoryDatasetAssociation + def sanitize(dict): + # quotations for Infinity so its jsonifiable + for name in dict: + if dict[name] == Infinity: + dict[name] = 'Infinity' + value = dict['value'] if 'value' in dict else None; + # check if value is numeric + def isnumber(s): + try: + float(s) + return True + except Exception: + return False + # fix hda parsing + if isinstance(value, HistoryDatasetAssociation): + value = { + 'id' : trans.security.encode_id(value.dataset_id), + 'src' : 'hda' + } + elif value and not (isinstance(value, basestring) or isnumber(value) or isinstance(value, Iterable)): + value = 'Unsupported' + dict['value'] = value + return dict + + ## build model + def build(group_inputs, inputs, tool_state, errors, other_values=None): + from galaxy.util.expressions import ExpressionContext + other_values = ExpressionContext( tool_state, other_values ) + for input_index, input in enumerate( inputs.itervalues() ): + ## create model dictionary + group_inputs[input_index] = input.to_dict(trans) + + ## identify stat for subsection/group + group_state = tool_state[input.name] + + ## iterate and update values + if input.type == "repeat": + group_cache = group_inputs[input_index]['cache'] = {} + for i in range( len( group_state ) ): + group_cache[i] = {} + group_errors = errors[input.name][i] if input.name in errors else dict() + build( group_cache[i], input.inputs, group_state[i], group_errors, other_values ) + elif input.type == "conditional": + try: + test_param = group_inputs[input_index]['test_param'] + test_param['value'] = tool_state[test_param['name']] + except Exception: + pass + i = group_state['__current_case__'] + group_errors = errors.get( input.name, {} ) + build(group_inputs[input_index]['cases'][i]['inputs'], input.cases[i].inputs, group_state, group_errors, other_values) + else: + ## create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options + try: + group_inputs[input_index] = input.to_dict(trans, other_values=other_values) + except Exception: + pass + + ## update input value from tool state and sanitize dictionary + try: + group_inputs[input_index]['value'] = tool_state[group_inputs[input_index]['name']] + group_inputs[input_index] = sanitize(group_inputs[input_index]) + except Exception: + pass + endif + endfor + build(tool_model['inputs'], tool.inputs, tool_state.inputs, errors, "") + + # load tool help + tool_help = '' + if tool.help: + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help + + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + endif + + # check if citations exist + tool_citations = False + if tool.citations: + tool_citations = True + + # form configuration + self.form_config = { + 'id' : tool.id, + 'model' : tool_model, + 'help' : tool_help, + 'citations' : tool_citations, + 'biostar_url' : trans.app.config.biostar_url, + 'history_id' : trans.security.encode_id( trans.history.id ), + 'job_id' : trans.security.encode_id( job.id ) if job else None + } +%> +</%def> + +${ init() } +${ h.dumps(self.form_config) } \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d8fef0600148/ Changeset: d8fef0600148 User: jmchilton Date: 2014-10-14 19:25:54+00:00 Summary: Save one extra database hit per API query. Honestly I can see the query no longer being emitted but I was unable to detect any difference in performance. Affected #: 1 file diff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac -r d8fef0600148c4b6f4ed7d6a95ba4681d07a67a8 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -23,6 +23,7 @@ eggs.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import and_ from sqlalchemy.orm.exc import NoResultFound +from sqlalchemy.orm import joinedload from galaxy.exceptions import MessageException @@ -337,7 +338,7 @@ # Retrieve the galaxy_session id via the unique session_key galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, #noqa - self.app.model.GalaxySession.table.c.is_valid==True ) ).first() #noqa + self.app.model.GalaxySession.table.c.is_valid==True ) ).options( joinedload( "user" ) ).first() #noqa # If remote user is in use it can invalidate the session and in some # cases won't have a cookie set above, so we need to to check some # things now. https://bitbucket.org/galaxy/galaxy-central/commits/6cd78dca65d1/ Changeset: 6cd78dca65d1 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Less aggressive test polling. Affected #: 1 file diff -r d8fef0600148c4b6f4ed7d6a95ba4681d07a67a8 -r 6cd78dca65d15db75cd98a2733e2dd22db800561 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2441,7 +2441,7 @@ return self.wait_for(lambda: self.get_running_datasets(), **kwds) def wait_for( self, func, **kwd ): - sleep_amount = 0.1 + sleep_amount = 0.2 slept = 0 walltime_exceeded = 86400 while slept <= walltime_exceeded: https://bitbucket.org/galaxy/galaxy-central/commits/b6cb3aabfba4/ Changeset: b6cb3aabfba4 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Fix set_metadata.py for environmental set Galaxy properties. At least for the local job runner. This variant of property loading does correctly interpolate %(here) so there is no longer a need to catch those exceptions and object store related properties can use %(here). Affected #: 1 file diff -r 6cd78dca65d15db75cd98a2733e2dd22db800561 -r b6cb3aabfba4ec844f346fb2d363e47822a3d989 scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -35,6 +35,7 @@ from galaxy.objectstore import build_object_store_from_config from galaxy import config import ConfigParser +from galaxy.util.properties import load_app_properties def set_meta_with_tool_provided( dataset_instance, file_dict, set_meta_kwds ): @@ -63,18 +64,7 @@ # Set up reference to object store # First, read in the main config file for Galaxy; this is required because # the object store configuration is stored there - conf = ConfigParser.ConfigParser() - conf.read(config_file_name) - conf_dict = {} - for section in conf.sections(): - for option in conf.options(section): - try: - conf_dict[option] = conf.get(section, option) - except ConfigParser.InterpolationMissingOptionError: - # Because this is not called from Paste Script, %(here)s variable - # is not initialized in the config file so skip those fields - - # just need not to use any such fields for the object store conf... - log.debug("Did not load option %s from %s" % (option, config_file_name)) + conf_dict = load_app_properties( ini_file=config_file_name ) # config object is required by ObjectStore class so create it now universe_config = config.Configuration(**conf_dict) universe_config.ensure_tempdir() https://bitbucket.org/galaxy/galaxy-central/commits/f94766d53345/ Changeset: f94766d53345 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Switch local runner to set metadata externally by default. Affected #: 1 file diff -r b6cb3aabfba4ec844f346fb2d363e47822a3d989 -r f94766d533450d6e69f6c14000719082f40f84e6 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -23,7 +23,7 @@ DEFAULT_POOL_SLEEP_TIME = 1 # TODO: Set to false and just get rid of this option. It would simplify this # class nicely. -John -DEFAULT_EMBED_METADATA_IN_JOB = False +DEFAULT_EMBED_METADATA_IN_JOB = True class LocalJobRunner( BaseJobRunner ): https://bitbucket.org/galaxy/galaxy-central/commits/5238a1e029e9/ Changeset: 5238a1e029e9 User: jmchilton Date: 2014-10-14 19:25:55+00:00 Summary: Add ability to disable asynchronous data uploads in tool tests. Honestly - need to find a way to make this the default if sqlite is the target. Affected #: 1 file diff -r f94766d533450d6e69f6c14000719082f40f84e6 -r 5238a1e029e9fa4f736ac2ab2ed260c559177d2a test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -21,6 +21,7 @@ # and result in sqlite errors on larger tests or larger numbers of # tests. VERBOSE_ERRORS = util.asbool( os.environ.get( "GALAXY_TEST_VERBOSE_ERRORS", False ) ) +UPLOAD_ASYNC = util.asbool( os.environ.get( "GALAXY_TEST_UPLOAD_ASYNC", True ) ) ERROR_MESSAGE_DATASET_SEP = "--------------------------------------" @@ -33,10 +34,15 @@ # Upload any needed files upload_waits = [] - for test_data in all_test_data: - upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) ) - for upload_wait in upload_waits: - upload_wait() + if UPLOAD_ASYNC: + for test_data in all_test_data: + upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) ) + for upload_wait in upload_waits: + upload_wait() + else: + for test_data in all_test_data: + upload_wait = galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) + upload_wait() class GalaxyInteractorApi( object ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Revert old test polling behavior with respect to 'new' state.
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42cd5d55755a/ Changeset: 42cd5d55755a User: jmchilton Date: 2014-10-14 17:21:12+00:00 Summary: Revert old test polling behavior with respect to 'new' state. So that upload failures don't cause test to hang indefinitely. Affected #: 1 file diff -r c465fdbdbdb2db64e08c31e8eb0084c20e9e50ff -r 42cd5d55755a729dd2f19ccd1ed20649ed29f6ac test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1296,7 +1296,7 @@ history_id = loads( self.last_page() )[0][ 'id' ] self.visit_url( '/api/histories/%s' % history_id ) jsondata = loads( self.last_page() ) - return jsondata[ 'state' ] in [ 'new', 'queued', 'running' ] + return jsondata[ 'state' ] in [ 'queued', 'running' ] def get_tags( self, item_id, item_class ): self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" % \ 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: Optimization of API polling during tool testing.
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c465fdbdbdb2/ Changeset: c465fdbdbdb2 User: jmchilton Date: 2014-10-14 16:56:50+00:00 Summary: Optimization of API polling during tool testing. Not the kind of optimization where you take something reasonable and brilliantly streamline it - but the kind of optimization where you take something ridiculus and make it less so. Oh past @jmchilton there is just no hope for you... Affected #: 1 file diff -r dbee027f74101741533851ce2634b60adca4c454 -r c465fdbdbdb2db64e08c31e8eb0084c20e9e50ff test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1294,14 +1294,9 @@ def get_running_datasets( self ): self.visit_url( '/api/histories' ) history_id = loads( self.last_page() )[0][ 'id' ] - self.visit_url( '/api/histories/%s/contents' % history_id ) + self.visit_url( '/api/histories/%s' % history_id ) jsondata = loads( self.last_page() ) - for history_item in jsondata: - self.visit_url( history_item[ 'url' ] ) - item_json = loads( self.last_page() ) - if item_json[ 'state' ] in [ 'queued', 'running', 'paused' ]: - return True - return False + return jsondata[ 'state' ] in [ 'new', 'queued', 'running' ] def get_tags( self, item_id, item_class ): self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" % \ 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: Update tag latest_2014.10.06 for changeset 1744b7d8e9ab
by commits-noreply＠bitbucket.org 14 Oct '14

14 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cdd3a8a9cd7d/ Changeset: cdd3a8a9cd7d Branch: stable User: natefoo Date: 2014-10-14 13:00:24+00:00 Summary: Update tag latest_2014.10.06 for changeset 1744b7d8e9ab Affected #: 1 file diff -r 1744b7d8e9ab619d78c0516f9ccb093b0a814163 -r cdd3a8a9cd7d5d71705843d2fa448462c7ed0675 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 +1744b7d8e9ab619d78c0516f9ccb093b0a814163 latest_2014.10.06 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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