Skip to content

Commit

Permalink
Allow to execute any tool
Browse files Browse the repository at this point in the history
  • Loading branch information
@guerler
guerler committed Aug 22, 2016
1 parent fdad129 commit 9228213
Show file tree
Hide file tree
Showing 7 changed files with 43 additions and 37 deletions.
4 changes: 2 additions & 2 deletions config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
View file
@@ -1,7 +1,7 @@
define( [ 'plugin/charts/jqplot/common/wrapper', 'plugin/charts/utilities/tabular-jobs', 'plugin/charts/utilities/tabular-utilities' ], function( Plot, Jobs, Utilities ) {
define( [ 'plugin/charts/jqplot/common/wrapper', 'plugin/components/jobs', 'plugin/charts/utilities/tabular-utilities' ], function( Plot, Jobs, Utilities ) {
return Backbone.View.extend({
initialize: function( app, options ) {
Jobs.request( app, 'boxplot', function( dataset ) {
Jobs.request( app, Utilities.buildJobDictionary( 'boxplot', app.chart ), function( dataset ) {
var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id );
var chart = options.chart;
var index = 0;
Expand Down
4 changes: 2 additions & 2 deletions config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
View file
@@ -1,7 +1,7 @@
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/charts/utilities/tabular-jobs', 'plugin/charts/jqplot/common/wrapper' ], function( Utilities, Jobs, Plot ) {
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/jqplot/common/wrapper' ], function( Utilities, Jobs, Plot ) {
return Backbone.Model.extend({
initialize: function( app, options ) {
Jobs.request( app, 'histogramdiscrete', function( dataset ) {
Jobs.request( app, Utilities.buildJobDictionary( 'histogramdiscrete', app.chart ), function( dataset ) {
var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id );
var index = 1;
var tmp_dict = { id : request_dictionary.id, groups : [] };
Expand Down
4 changes: 2 additions & 2 deletions config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
View file
@@ -1,7 +1,7 @@
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/charts/utilities/tabular-jobs', 'plugin/charts/nvd3/common/wrapper' ], function( Utilities, Jobs, NVD3 ) {
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/nvd3/common/wrapper' ], function( Utilities, Jobs, NVD3 ) {
return Backbone.Model.extend({
initialize: function( app, options ) {
Jobs.request( app, 'histogram', function( dataset ) {
Jobs.request( app, Utilities.buildJobDictionary( 'histogram', app.chart ), function( dataset ) {
options.request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id );
var index = 1;
_.each( options.request_dictionary.groups, function( group ) {
Expand Down
4 changes: 2 additions & 2 deletions config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
View file
@@ -1,7 +1,7 @@
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/charts/utilities/tabular-jobs', 'plugin/charts/nvd3/common/wrapper' ], function( Utilities, Jobs, NVD3 ) {
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/nvd3/common/wrapper' ], function( Utilities, Jobs, NVD3 ) {
return Backbone.Model.extend({
initialize: function( app, options ) {
Jobs.request( app, 'histogramdiscrete', function( dataset ) {
Jobs.request( app, Utilities.buildJobDictionary( 'histogramdiscrete', app.chart ), function( dataset ) {
var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id );
var index = 1;
var tmp_dict = { id : request_dictionary.id, groups : [] };
Expand Down
4 changes: 2 additions & 2 deletions config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
View file
@@ -1,7 +1,7 @@
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/charts/utilities/tabular-jobs', 'plugin/charts/others/heatmap/heatmap-plugin' ], function( Utilities, Jobs, HeatMap ) {
define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/others/heatmap/heatmap-plugin' ], function( Utilities, Jobs, HeatMap ) {
return Backbone.View.extend({
initialize: function(app, options) {
Jobs.request( app, 'heatmap', function( dataset ) {
Jobs.request( app, Utilities.buildJobDictionary( 'heatmap', app.chart ), function( dataset ) {
var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id );
var index = 0;
var tmp_dict = { id : request_dictionary.id, groups : [] };
Expand Down
31 changes: 31 additions & 0 deletions config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
View file
Expand Up @@ -18,6 +18,36 @@ define( [ 'utils/utils', 'plugin/charts/utilities/tabular-datasets' ], function(
return result;
};

/** build job dictionary */
function buildJobDictionary( module, chart ) {
var settings_string = '';
var columns_string = '';
var group_index = 0;
for ( key in chart.settings.attributes ) {
settings_string += key + ':' + chart.settings.get( key ) + ', ';
};
settings_string = settings_string.substring( 0, settings_string.length - 2 )
chart.groups.each( function( group ) {
group_index++;
_.each( group.get( '__data_columns' ), function( data_columns, name ) {
columns_string += name + '_' + group_index + ':' + ( parseInt( group.get( name ) ) + 1 ) + ', ';
});
});
columns_string = columns_string.substring( 0, columns_string.length - 2 );
return {
'tool_id' : 'charts',
'inputs' : {
'input' : {
'id' : chart.get( 'dataset_id' ),
'src' : 'hda'
},
'module' : module,
'columns' : columns_string,
'settings' : settings_string
}
}
};

/** Assists in assigning the viewport panels */
function panelHelper( options ) {
var self = this;
Expand Down Expand Up @@ -276,6 +306,7 @@ define( [ 'utils/utils', 'plugin/charts/utilities/tabular-datasets' ], function(

return {
buildRequestDictionary : buildRequestDictionary,
buildJobDictionary : buildJobDictionary,
panelHelper : panelHelper,
makeCategories : makeCategories,
makeUniqueCategories : makeUniqueCategories,
Expand Down
29 changes: 2 additions & 27 deletions ...s/static/charts/utilities/tabular-jobs.js → ...izations/charts/static/components/jobs.js
View file
Expand Up @@ -5,22 +5,8 @@ define( [ 'utils/utils' ], function( Utils ) {
var WAITTIME = 1000;

/** Submit job request to charts tool */
var request = function( app, module, success, error ) {
var request = function( app, parameters, success, error ) {
var chart = app.chart;
var settings_string = '';
var columns_string = '';
var group_index = 0;
for ( key in chart.settings.attributes ) {
settings_string += key + ':' + chart.settings.get( key ) + ', ';
};
settings_string = settings_string.substring( 0, settings_string.length - 2 )
chart.groups.each( function( group ) {
group_index++;
_.each( group.get( '__data_columns' ), function( data_columns, name ) {
columns_string += name + '_' + group_index + ':' + ( parseInt( group.get( name ) ) + 1 ) + ', ';
});
});
columns_string = columns_string.substring( 0, columns_string.length - 2 );
chart.state( 'wait', 'Requesting job results...' );
if ( chart.get( 'modified' ) ) {
cleanup( chart );
Expand All @@ -37,18 +23,7 @@ define( [ 'utils/utils' ], function( Utils ) {
Utils.request({
type : 'POST',
url : Galaxy.root + 'api/tools',
data : {
'tool_id' : 'charts',
'inputs' : {
'input' : {
'id' : chart.get('dataset_id'),
'src' : 'hda'
},
'module' : module,
'columns' : columns_string,
'settings' : settings_string
}
},
data : parameters,
success : function( response ) {
if ( !response.outputs || response.outputs.length == 0 ) {
chart.state( 'failed', 'Job submission failed. No response.' );
Expand Down

0 comments on commit 9228213

Please sign in to comment.