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commit/galaxy-central: martenson: add logging when password reset fails; stop retreving message form the request - we never need it
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/104537c5219c/ Changeset: 104537c5219c User: martenson Date: 2014-11-24 18:26:24+00:00 Summary: add logging when password reset fails; stop retreving message form the request - we never need it Affected #: 1 file diff -r 7d97ff9d4bef1a92adf5be7e61c5b4a3007a76fd -r 104537c5219c83b8124956f237caedeb07c7164e lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1119,22 +1119,22 @@ """Reset the user's password. Send an email with the new password.""" if trans.app.config.smtp_server is None: return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) - message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) ) + message = '' status = 'done' if kwd.get( 'reset_password_button', False ): reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() user = trans.get_user() if reset_user: if user and user.id != reset_user.id: - message = "You may only reset your own password" + message = "You may only reset your own password." status = 'error' else: chars = string.letters + string.digits new_pass = "" reset_password_length = getattr( trans.app.config, "reset_password_length", 15 ) - for i in range(reset_password_length): - new_pass = new_pass + random.choice(chars) - host = trans.request.host.split(':')[0] + for i in range( reset_password_length ): + new_pass = new_pass + random.choice( chars ) + host = trans.request.host.split( ':' )[ 0 ] if host == 'localhost': host = socket.getfqdn() body = 'Your password on %s has been reset to:\n\n %s\n' % ( host, new_pass ) @@ -1148,10 +1148,11 @@ trans.log_event( "User reset password: %s" % email ) message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: + status = 'error' message = 'Failed to reset password: %s' % str( e ) - status = 'error' + log.exception( 'Unable to reset password: ' + str( e ) ) elif email is not None: - message = "The specified user does not exist" + message = "The specified user does not exist." status = 'error' elif email is None: email = "" 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: Tool test - verify that if 'batch' meta-parameter is False - matching is not attempted.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7d97ff9d4bef/ Changeset: 7d97ff9d4bef User: jmchilton Date: 2014-11-24 18:02:18+00:00 Summary: Tool test - verify that if 'batch' meta-parameter is False - matching is not attempted. Affected #: 1 file diff -r 7b7dd8f82126b3c18e9d311305edae85adeea659 -r 7d97ff9d4bef1a92adf5be7e61c5b4a3007a76fd test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -273,6 +273,15 @@ self._check_repeat_multirun( history_id, inputs ) @skip_without_tool( "cat1" ) + def test_multirun_in_repeat_mismatch( self ): + history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun( ) + inputs = { + "input1": {'batch': False, 'values': [ common_dataset ] }, + 'queries_0|input2': { 'batch': True, 'values': repeat_datasets }, + } + self._check_repeat_multirun( history_id, inputs ) + + @skip_without_tool( "cat1" ) def test_multirun_on_multiple_inputs_legacy( self ): history_id, first_two, second_two = self._setup_two_multiruns() inputs = { 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: Tool API test for mixing batch and non-batch input datasets.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b7dd8f82126/ Changeset: 7b7dd8f82126 User: jmchilton Date: 2014-11-24 17:56:05+00:00 Summary: Tool API test for mixing batch and non-batch input datasets. Affected #: 1 file diff -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed -r 7b7dd8f82126b3c18e9d311305edae85adeea659 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -255,26 +255,22 @@ assert sorted( map( lambda c: len( c.split( "\n" ) ), outputs_contents ) ) == [ 1, 2, 3 ] @skip_without_tool( "cat1" ) + def test_multirun_in_repeat_legacy( self ): + history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun( ) + inputs = { + "input1": common_dataset, + 'queries_0|input2|__multirun__': repeat_datasets, + } + self._check_repeat_multirun( history_id, inputs ) + + @skip_without_tool( "cat1" ) def test_multirun_in_repeat( self ): - history_id = self.dataset_populator.new_history() - new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) - new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) - common_dataset = self.dataset_populator.new_dataset( history_id, content='Common' ) + history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun( ) inputs = { - "input1": dataset_to_param( common_dataset ), - 'queries_0|input2|__multirun__': [ - dataset_to_param( new_dataset1 ), - dataset_to_param( new_dataset2 ), - ], + "input1": common_dataset, + 'queries_0|input2': { 'batch': True, 'values': repeat_datasets }, } - outputs = self._cat1_outputs( history_id, inputs=inputs ) - self.assertEquals( len( outputs ), 2 ) - output1 = outputs[ 0 ] - output2 = outputs[ 1 ] - output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) - output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) - self.assertEquals( output1_content.strip(), "Common\n123" ) - self.assertEquals( output2_content.strip(), "Common\n456" ) + self._check_repeat_multirun( history_id, inputs ) @skip_without_tool( "cat1" ) def test_multirun_on_multiple_inputs_legacy( self ): @@ -317,6 +313,27 @@ assert "123\n0ab" in outputs_contents assert "456\n789" in outputs_contents + def _setup_repeat_multirun( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) + new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) + common_dataset = self.dataset_populator.new_dataset( history_id, content='Common' ) + return ( + history_id, + dataset_to_param( common_dataset ), + [ dataset_to_param( new_dataset1 ), dataset_to_param( new_dataset2 ) ] + ) + + def _check_repeat_multirun( self, history_id, inputs ): + outputs = self._cat1_outputs( history_id, inputs=inputs ) + self.assertEquals( len( outputs ), 2 ) + output1 = outputs[ 0 ] + output2 = outputs[ 1 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) + self.assertEquals( output1_content.strip(), "Common\n123" ) + self.assertEquals( output2_content.strip(), "Common\n456" ) + def _setup_two_multiruns( self ): history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) 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: Allow 1 to n selection for batch mode fields
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6cc3b0c515bc/ Changeset: 6cc3b0c515bc User: guerler Date: 2014-11-24 17:30:29+00:00 Summary: ToolForm: Allow 1 to n selection for batch mode fields Affected #: 3 files diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed 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 @@ -145,12 +145,14 @@ } // check number of inputs - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); - return false; + if (n > 1) { + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + return false; + } } } } diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -145,12 +145,14 @@ } // check number of inputs - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); - return false; + if (n > 1) { + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + return false; + } } } } diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed 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]);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(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</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(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(g>1){if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number or a single input for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</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.

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commit/galaxy-central: jmchilton: Allow passing extra parameter to docker run command in job_conf.xml.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ebceda0721f3/ Changeset: ebceda0721f3 User: jmchilton Date: 2014-11-24 17:24:21+00:00 Summary: Allow passing extra parameter to docker run command in job_conf.xml. As request in the following thread http://dev.list.galaxyproject.org/more-control-over-the-quot-docker-quot-co…. Affected #: 3 files diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -204,6 +204,9 @@ remote job user. Leave empty to not use the -u argument with Docker. --> +  + <!-- Following can be used to connect to docke server in different diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -245,6 +245,7 @@ net=prop("net", "none"), # By default, docker instance has networking disabled auto_rm=asbool(prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)), set_user=prop("set_user", docker_util.DEFAULT_SET_USER), + run_extra_arguments=prop("run_extra_arguments", docker_util.DEFAULT_RUN_EXTRA_ARGUMENTS), **docker_host_props ) return "%s\n%s" % (cache_command, run_command) diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 lib/galaxy/tools/deps/docker_util.py --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -11,6 +11,7 @@ DEFAULT_VOLUMES_FROM = None DEFAULT_AUTO_REMOVE = True DEFAULT_SET_USER = "$UID" +DEFAULT_RUN_EXTRA_ARGUMENTS = None class DockerVolume(object): @@ -116,6 +117,7 @@ working_directory=DEFAULT_WORKING_DIRECTORY, name=None, net=DEFAULT_NET, + run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS, docker_cmd=DEFAULT_DOCKER_COMMAND, sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, @@ -148,6 +150,8 @@ command_parts.extend(["--net", net]) if auto_rm: command_parts.append("--rm") + if run_extra_arguments: + command_parts.append(run_extra_arguments) if set_user: user = set_user if set_user == DEFAULT_SET_USER: 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 optional parameters, add select2 fields, fix style
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3edc85f4761b/ Changeset: 3edc85f4761b User: guerler Date: 2014-11-24 17:08:46+00:00 Summary: ToolForm: Fix optional parameters, add select2 fields, fix style Affected #: 24 files diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 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 @@ -84,14 +84,12 @@ // refreshes input states i.e. for dynamic parameters refresh: function() { // only refresh the state if the form contains dynamic parameters - if (!this.is_dynamic) { - return; - } - - // place refresh process into deferred queue - var self = this; - this.deferred.reset(); - this.deferred.execute(function(){self._updateModel()}); + // by using/reseting the deferred ajax queue the number of redundant calls is reduced + if (this.is_dynamic) { + var self = this; + this.deferred.reset(); + this.deferred.execute(function(){self._updateModel()}); + }; }, // build tool model through api call @@ -141,10 +139,8 @@ // request a new model and update the form inputs _updateModel: function() { - // link this + // create the request dictionary var self = this; - - // finalize data var current_state = this.tree.finalize({ data : function(dict) { if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { @@ -332,8 +328,9 @@ // create portlet this.portlet = new Portlet.View({ - icon : 'fa-wrench', - title: '<b>' + this.model.name + '</b> ' + this.model.description, + icon : 'fa-wrench', + title : '<b>' + this.model.name + '</b> ' + this.model.description, + cls : 'ui-portlet-slim', operations: { menu : menu }, diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -25,12 +25,8 @@ // add field element this.$field.prepend(this.field.$el); - // hide optional field on initialization - if (options.optional) { - this.field.skip = true; - } else { - this.field.skip = false; - } + // start with enabled optional fields + this.field.skip = false; // refresh view this._refresh(); diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 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 @@ -108,15 +108,21 @@ var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; var input_def = this.app.input_list[input_id]; - - // check basic field validation - if (input_def && input_field && input_field.validate && !input_field.validate()) { + + // check if objects where properly identified + if (!input_id || !input_def || !input_field) { + console.debug('tools-jobs::_validation - Retrieving input objects failed.'); + continue; + } + + // validate non-optional fields + if (!input_def.optional && input_field.validate && !input_field.validate()) { this._foundError(input_id); return false; } // check if input field is in batch mode - if (input_value.batch) { + if (input_value && input_value.batch) { // get values var n = input_value.values.length; @@ -148,7 +154,6 @@ } } } - } // return validation result diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 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 @@ -334,6 +334,7 @@ // genome field case 'genomebuild': + input_def.searchable = true; field = this._fieldSelect(input_def); break; @@ -406,10 +407,11 @@ // select field var self = this; return new SelectClass.View({ - id : 'field-' + input_def.id, - data : options, - multiple: input_def.multiple, - onchange: function() { + id : 'field-' + input_def.id, + data : options, + multiple : input_def.multiple, + searchable : input_def.searchable, + onchange : function() { self.app.refresh(); } }); diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 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 @@ -98,8 +98,11 @@ break; // handle conditionals case 'conditional': - // get conditional value + // get and patch conditional value var value = self.app.field_list[input.id].value(); + if (patch[input.test_param.type]) { + value = patch[input.test_param.type](value); + } // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); @@ -114,10 +117,8 @@ // get field var field = self.app.field_list[input.id]; - // get value + // get and patch field value var value = field.value(); - - // patch value if (patch[input.type]) { value = patch[input.type](value); } diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -19,7 +19,7 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement('<div style="display: inline-block;"/>'); + this.setElement('<div/>'); // create elements this.$message = $('<div/>'); diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -12,7 +12,8 @@ empty : 'No data available', visible : true, wait : false, - multiple : false + multiple : false, + searchable : false }, // initialize @@ -24,8 +25,9 @@ this.setElement(this._template(this.options)); // link elements - this.$select = this.$el.find('#select'); - this.$icon = this.$el.find('#icon'); + this.$select = this.$el.find('.select'); + this.$icon = this.$el.find('.icon'); + this.$button = this.$el.find('.button'); // configure multiple if (this.options.multiple) { @@ -109,7 +111,7 @@ show: function() { this.unwait(); this.$select.show(); - this.$el.css('display', 'inline-block'); + this.$el.show(); }, /** Hide the select field @@ -179,7 +181,7 @@ // remove all options this.$select.find('option').remove(); - + // add new options for (var key in options) { this.$select.append(this._templateOption(options[key])); @@ -195,6 +197,13 @@ if (!this.$select.val()) { this.$select.val(this.first()); } + + // update to searchable field (in this case select2) + if (this.options.searchable) { + this.$button.hide(); + this.$select.select2('destroy'); + this.$select.select2(); + } }, /** Set the custom onchange callback function @@ -249,7 +258,7 @@ return '<div id="' + options.id + '">' + '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' + '<div class="button">' + - '<i id="icon"/>' + + '<i class="icon"/>' + '</div>' + '</div>'; } diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1082,9 +1082,12 @@ value = option[1] d.update({ - 'options': options, - 'value': value + 'options' : options, + 'value' : value, + 'display' : self.display, + 'multiple' : self.multiple }) + return d def _get_dbkey_names( self, trans=None ): diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -84,14 +84,12 @@ // refreshes input states i.e. for dynamic parameters refresh: function() { // only refresh the state if the form contains dynamic parameters - if (!this.is_dynamic) { - return; - } - - // place refresh process into deferred queue - var self = this; - this.deferred.reset(); - this.deferred.execute(function(){self._updateModel()}); + // by using/reseting the deferred ajax queue the number of redundant calls is reduced + if (this.is_dynamic) { + var self = this; + this.deferred.reset(); + this.deferred.execute(function(){self._updateModel()}); + }; }, // build tool model through api call @@ -141,10 +139,8 @@ // request a new model and update the form inputs _updateModel: function() { - // link this + // create the request dictionary var self = this; - - // finalize data var current_state = this.tree.finalize({ data : function(dict) { if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { @@ -332,8 +328,9 @@ // create portlet this.portlet = new Portlet.View({ - icon : 'fa-wrench', - title: '<b>' + this.model.name + '</b> ' + this.model.description, + icon : 'fa-wrench', + title : '<b>' + this.model.name + '</b> ' + this.model.description, + cls : 'ui-portlet-slim', operations: { menu : menu }, diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -25,12 +25,8 @@ // add field element this.$field.prepend(this.field.$el); - // hide optional field on initialization - if (options.optional) { - this.field.skip = true; - } else { - this.field.skip = false; - } + // start with enabled optional fields + this.field.skip = false; // refresh view this._refresh(); diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -108,15 +108,21 @@ var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; var input_def = this.app.input_list[input_id]; - - // check basic field validation - if (input_def && input_field && input_field.validate && !input_field.validate()) { + + // check if objects where properly identified + if (!input_id || !input_def || !input_field) { + console.debug('tools-jobs::_validation - Retrieving input objects failed.'); + continue; + } + + // validate non-optional fields + if (!input_def.optional && input_field.validate && !input_field.validate()) { this._foundError(input_id); return false; } // check if input field is in batch mode - if (input_value.batch) { + if (input_value && input_value.batch) { // get values var n = input_value.values.length; @@ -148,7 +154,6 @@ } } } - } // return validation result diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -334,6 +334,7 @@ // genome field case 'genomebuild': + input_def.searchable = true; field = this._fieldSelect(input_def); break; @@ -406,10 +407,11 @@ // select field var self = this; return new SelectClass.View({ - id : 'field-' + input_def.id, - data : options, - multiple: input_def.multiple, - onchange: function() { + id : 'field-' + input_def.id, + data : options, + multiple : input_def.multiple, + searchable : input_def.searchable, + onchange : function() { self.app.refresh(); } }); diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -98,8 +98,11 @@ break; // handle conditionals case 'conditional': - // get conditional value + // get and patch conditional value var value = self.app.field_list[input.id].value(); + if (patch[input.test_param.type]) { + value = patch[input.test_param.type](value); + } // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); @@ -114,10 +117,8 @@ // get field var field = self.app.field_list[input.id]; - // get value + // get and patch field value var value = field.value(); - - // patch value if (patch[input.type]) { value = patch[input.type](value); } diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -19,7 +19,7 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement('<div style="display: inline-block;"/>'); + this.setElement('<div/>'); // create elements this.$message = $('<div/>'); diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -12,7 +12,8 @@ empty : 'No data available', visible : true, wait : false, - multiple : false + multiple : false, + searchable : false }, // initialize @@ -24,8 +25,9 @@ this.setElement(this._template(this.options)); // link elements - this.$select = this.$el.find('#select'); - this.$icon = this.$el.find('#icon'); + this.$select = this.$el.find('.select'); + this.$icon = this.$el.find('.icon'); + this.$button = this.$el.find('.button'); // configure multiple if (this.options.multiple) { @@ -109,7 +111,7 @@ show: function() { this.unwait(); this.$select.show(); - this.$el.css('display', 'inline-block'); + this.$el.show(); }, /** Hide the select field @@ -179,7 +181,7 @@ // remove all options this.$select.find('option').remove(); - + // add new options for (var key in options) { this.$select.append(this._templateOption(options[key])); @@ -195,6 +197,13 @@ if (!this.$select.val()) { this.$select.val(this.first()); } + + // update to searchable field (in this case select2) + if (this.options.searchable) { + this.$button.hide(); + this.$select.select2('destroy'); + this.$select.select2(); + } }, /** Set the custom onchange callback function @@ -249,7 +258,7 @@ return '<div id="' + options.id + '">' + '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' + '<div class="button">' + - '<i id="icon"/>' + + '<i class="icon"/>' + '</div>' + '</div>'; } diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.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="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{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:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.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="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{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,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable");this.app.refresh()}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable");this.app.refresh()}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</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.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$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=j.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(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_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.rebuild();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.rebuild();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(this.app,{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(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(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 ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_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 +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=j.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(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_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.rebuild();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.rebuild();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(this.app,{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(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(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":h.searchable=true;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 ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_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 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 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.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(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.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(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=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement('<div style="display: inline-block;"/>');this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find('input[value="'+f[g]+'"]').prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find('input[value="'+f[g]+'"]').prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.css("display","inline-block")},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i id="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1279,7 +1279,7 @@ .upload-ftp .upload-ftp-help{margin-bottom:10px} .upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px} .upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop} -.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-repeat{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} +.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-slim,.ui-portlet-repeat{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} .ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} .ui-table tbody{cursor:pointer} @@ -1302,12 +1302,13 @@ .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} -.ui-portlet,.ui-portlet-repeat,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title .portlet-title-text{vertical-align:middle} -.ui-portlet .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} -.ui-portlet .portlet-buttons{height:50px;padding:10px} -.ui-portlet .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons{height:50px;padding:10px} -.ui-portlet .no-scroll{height:calc(100% - 80px)} -.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px;display:inline-block}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:0px 2px} +.ui-portlet,.ui-portlet-slim,.ui-portlet-repeat,.ui-portlet-slim,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-slim .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-slim .portlet-header .portlet-title .portlet-title-text{vertical-align:middle} +.ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-slim .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} +.ui-portlet .portlet-buttons,.ui-portlet-slim .portlet-buttons{height:50px;padding:10px} +.ui-portlet .portlet-content,.ui-portlet-slim .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content,.ui-portlet-slim .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons,.ui-portlet-slim .portlet-content .content .buttons{height:50px;padding:10px} +.ui-portlet .no-scroll,.ui-portlet-slim .no-scroll{height:calc(100% - 80px)} +.ui-portlet-slim{max-width:900px} +.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:0px 2px} .ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:10px} .ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} .ui-popover .popover-title{padding:4px 10px} @@ -1319,6 +1320,7 @@ .ui-radiobutton{width:100%}.ui-radiobutton label{height:23px;line-height:1em} .ui-radiobutton i{padding-right:5px} .ui-select{position:relative}.ui-select .button{position:absolute;top:5px;right:5px} +.ui-select .select2-container{width:100%} .ui-select select{position:relative;top:0px;height:27px;width:100%;padding-left:5px;padding-right:20px;cursor:pointer;background:transparent;-webkit-appearance:none;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} diff -r 428cd34786bd8601d5050d94ac682f662d887de1 -r 3edc85f4761bbcde996470590cc002828ce21d03 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -200,12 +200,16 @@ } } +.ui-portlet-slim { + &:extend(.ui-portlet all); + max-width: 900px; +} + .ui-portlet-repeat { &:extend(.ui-portlet); border: none; border-left: solid 3px @form-heading-bg; border-radius: 5px; - display: inline-block; .portlet-header { background: @form-heading-bg; border-radius: 3px; @@ -291,6 +295,9 @@ top: 5px; right: 5px; } + .select2-container { + width: 100%; + } select { position: relative; top: 0px; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c1a9ed13d5f7/ Changeset: c1a9ed13d5f7 Branch: next-stable User: BjoernGruening Date: 2014-11-24 16:28:25+00:00 Summary: getstring() does not exist, use get() instead Affected #: 1 file diff -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 -r c1a9ed13d5f71deb671ab83ed262c0a861c469d2 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -77,7 +77,7 @@ } if self.attr.viz_config.has_option("docker", "galaxy_url"): - conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url") + conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url") elif self.attr.galaxy_config.galaxy_infrastructure_url_set: conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/' else: https://bitbucket.org/galaxy/galaxy-central/commits/428cd34786bd/ Changeset: 428cd34786bd User: jmchilton Date: 2014-11-24 16:59:13+00:00 Summary: Merge next-stable. 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: jmchilton: Merged in BjoernGruening/galaxy-central-1/fix_galaxy_url_parsing (pull request #572)
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c433a83d85cc/ Changeset: c433a83d85cc User: jmchilton Date: 2014-11-24 16:57:42+00:00 Summary: Merged in BjoernGruening/galaxy-central-1/fix_galaxy_url_parsing (pull request #572) Fix bug in IE config parsing. Affected #: 1 file diff -r dd2d0b244a27460ad15df5f12eaf243702086044 -r c433a83d85cc9296b04a51b3cc1225d031ea1b16 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -77,7 +77,7 @@ } if self.attr.viz_config.has_option("docker", "galaxy_url"): - conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url") + conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url") elif self.attr.galaxy_config.galaxy_infrastructure_url_set: conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/' else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d56c63c57bcd/ Changeset: d56c63c57bcd Branch: fix_galaxy_url_parsing User: BjoernGruening Date: 2014-11-24 16:27:10+00:00 Summary: Created new branch fix_galaxy_url_parsing Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/f420fe6e293c/ Changeset: f420fe6e293c Branch: fix_galaxy_url_parsing User: BjoernGruening Date: 2014-11-24 16:28:25+00:00 Summary: getstring() does not exist, use get() instead Affected #: 1 file diff -r d56c63c57bcdaf3abe940495c883b06edb7a72c1 -r f420fe6e293c98bd85da2b092fc34347a769041b lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -77,7 +77,7 @@ } if self.attr.viz_config.has_option("docker", "galaxy_url"): - conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url") + conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url") elif self.attr.galaxy_config.galaxy_infrastructure_url_set: conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/' else: https://bitbucket.org/galaxy/galaxy-central/commits/c433a83d85cc/ Changeset: c433a83d85cc User: jmchilton Date: 2014-11-24 16:57:42+00:00 Summary: Merged in BjoernGruening/galaxy-central-1/fix_galaxy_url_parsing (pull request #572) Fix bug in IE config parsing. Affected #: 1 file diff -r dd2d0b244a27460ad15df5f12eaf243702086044 -r c433a83d85cc9296b04a51b3cc1225d031ea1b16 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -77,7 +77,7 @@ } if self.attr.viz_config.has_option("docker", "galaxy_url"): - conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url") + conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url") elif self.attr.galaxy_config.galaxy_infrastructure_url_set: conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/' else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/475716a95133/ Changeset: 475716a95133 Branch: next-stable User: guerler Date: 2014-11-24 16:50:07+00:00 Summary: ToolForm: Skip new tool form build process if disabled Affected #: 4 files diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 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 @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.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="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible||!this.options.toolform_upgrade){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:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.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="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{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:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -1,34 +1,37 @@ <%inherit file="/base.mako"/> -## 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 ), - 'toolform_upgrade' : trans.app.config.get('toolform_upgrade', False) - }) -%> ${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) }); + +## skip new tool form code if disabled +%if trans.app.config.get('toolform_upgrade', False): + <% + ## 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 ) + }) + %> + <script> + require(['mvc/tools/tools-form'], function(ToolsForm){ + $(function(){ + var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + }); }); - }); -</script> + </script> + <div id="tool-form-classic" style="display: none;"> +%else: + <div id="tool-form-classic"> +%endif -## classic tool form -<div id="tool-form-classic" style="display: none;"><%namespace file="/message.mako" import="render_msg" /><%namespace file="/base_panels.mako" import="overlay" /> https://bitbucket.org/galaxy/galaxy-central/commits/dd2d0b244a27/ Changeset: dd2d0b244a27 User: guerler Date: 2014-11-24 16:50:31+00:00 Summary: Merge Affected #: 4 files diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 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 @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.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="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible||!this.options.toolform_upgrade){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:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.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="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{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:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -1,34 +1,37 @@ <%inherit file="/base.mako"/> -## 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 ), - 'toolform_upgrade' : trans.app.config.get('toolform_upgrade', False) - }) -%> ${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) }); + +## skip new tool form code if disabled +%if trans.app.config.get('toolform_upgrade', False): + <% + ## 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 ) + }) + %> + <script> + require(['mvc/tools/tools-form'], function(ToolsForm){ + $(function(){ + var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + }); }); - }); -</script> + </script> + <div id="tool-form-classic" style="display: none;"> +%else: + <div id="tool-form-classic"> +%endif -## classic tool form -<div id="tool-form-classic" style="display: none;"><%namespace file="/message.mako" import="render_msg" /><%namespace file="/base_panels.mako" import="overlay" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] a6e699: Updated slide rotation.
by GitHub 23 Nov '14

23 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a6e69901bee143ea0516e94847ef0ab0dc60acd3 https://github.com/galaxyproject/usegalaxy-playbook/commit/a6e69901bee143ea… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2014-11-22 (Sat, 22 Nov 2014) Changed paths: A files/galaxy/common/static/welcome_img/CoSSci.png M files/galaxy/common/static/welcome_img/GCC2015SaveTheseDates.png A files/galaxy/common/static/welcome_img/GalaxyIFBDay2014.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation.

1 0

[galaxyproject/usegalaxy-playbook] fb4f56: Update Main.
by GitHub 20 Nov '14

20 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fb4f561bcb5ef21c4e6b30dabf71b41c8f58a0d2 https://github.com/galaxyproject/usegalaxy-playbook/commit/fb4f561bcb5ef21c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-20 (Thu, 20 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af67ea0dd4d5/ Changeset: af67ea0dd4d5 Branch: next-stable User: guerler Date: 2014-11-20 19:29:27+00:00 Summary: Fix boolean handling for workflow editor Affected #: 1 file diff -r b87a9309cc68f7bffe886123b083d058c6347144 -r af67ea0dd4d5c718906ad883c76fd1efce86dbfc lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -126,9 +126,6 @@ def is_checked( value ): if value == True: return True - if isinstance( value, basestring ): - if value.lower() in [ "yes", "true", "on" ]: - return True # This may look strange upon initial inspection, but see the comments in the get_html() method # above for clarification. Basically, if value is not True, then it will always be a list with # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not https://bitbucket.org/galaxy/galaxy-central/commits/9dae58e22285/ Changeset: 9dae58e22285 User: guerler Date: 2014-11-20 19:29:44+00:00 Summary: Merge Affected #: 1 file diff -r 179f809b70dfabff53a6731ab70af949bc213e07 -r 9dae58e2228516766b65058b86d949bcfb23f775 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -126,9 +126,6 @@ def is_checked( value ): if value == True: return True - if isinstance( value, basestring ): - if value.lower() in [ "yes", "true", "on" ]: - return True # This may look strange upon initial inspection, but see the comments in the get_html() method # above for clarification. Basically, if value is not True, then it will always be a list with # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not 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: natefoo: Update tag latest_2014.10.06 for changeset bb79e87274d7
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cae8a513079a/ Changeset: cae8a513079a Branch: stable User: natefoo Date: 2014-11-20 19:00:30+00:00 Summary: Update tag latest_2014.10.06 for changeset bb79e87274d7 Affected #: 1 file diff -r bb79e87274d7ef4e043a84aeef8516a5418ef3b6 -r cae8a513079a183d16bd8a16b915d6aa5322a249 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 +bb79e87274d7ef4e043a84aeef8516a5418ef3b6 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.

1 0

[galaxyproject/usegalaxy-playbook] 816d86: Update Main.
by GitHub 20 Nov '14

20 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 816d866a3f8b8abc20d2e0f110156ea70e5acf3e https://github.com/galaxyproject/usegalaxy-playbook/commit/816d866a3f8b8abc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-20 (Thu, 20 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b87a9309cc68/ Changeset: b87a9309cc68 Branch: next-stable User: jmchilton Date: 2014-11-13 14:19:51+00:00 Summary: Allow resolution of relative paths in tool data configuration and loc files. The string ${__HERE__} will be expanded out to the directory the file (XML configuration or loc) currently resides in. Along with some changes to planemo to detect test data files (https://github.com/galaxyproject/planemo/commit/a40130417dc1be2da785cd5dff6…) - the following picard tweak demonstrates how tool developers could use this to build test cases for cached/index data (https://github.com/jmchilton/picard/commit/4df8974384081ee1bb0f97e1bb8d7f93…) Affected #: 1 file diff -r 20def6edca5958f029beae47b4a5cffc9fae8f3d -r b87a9309cc68f7bffe886123b083d058c6347144 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -10,6 +10,7 @@ import os import os.path import shutil +import string import tempfile from galaxy import util @@ -71,7 +72,7 @@ tree = util.parse_xml( filename ) root = tree.getroot() for table_elem in root.findall( 'table' ): - table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config ) + table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config, filename=filename ) table_elems.append( table_elem ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table @@ -167,16 +168,17 @@ class ToolDataTable( object ): @classmethod - def from_elem( cls, table_elem, tool_data_path, from_shed_config ): + def from_elem( cls, table_elem, tool_data_path, from_shed_config, filename ): table_type = table_elem.get( 'type', 'tabular' ) assert table_type in tool_data_table_types, "Unknown data table type '%s'" % type - return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config ) + return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config, filename=filename ) - def __init__( self, config_element, tool_data_path, from_shed_config = False): + def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) self.empty_field_value = config_element.get( 'empty_field_value', '' ) self.empty_field_values = {} + self.here = filename and os.path.dirname(filename) self.filenames = odict() self.tool_data_path = tool_data_path self.missing_index_file = None @@ -241,8 +243,8 @@ type_key = 'tabular' - def __init__( self, config_element, tool_data_path, from_shed_config = False): - super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config) + def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): + super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config, filename) self.config_element = config_element self.data = [] self.configure_and_load( config_element, tool_data_path, from_shed_config) @@ -265,7 +267,7 @@ repo_info = None # Read every file for file_element in config_element.findall( 'file' ): - filename = file_path = file_element.get( 'path', None ) + filename = file_path = expand_here_template( file_element.get( 'path', None ), here=self.here ) found = False if file_path is None: log.debug( "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string( file_element ), self.name ) @@ -300,7 +302,7 @@ errors = [] if found: - self.data.extend( self.parse_file_fields( open( filename ), errors=errors ) ) + self.extend_data_with( filename, errors=errors ) self._update_version() else: self.missing_index_file = filename @@ -326,7 +328,7 @@ def handle_found_index_file( self, filename ): self.missing_index_file = None - self.data.extend( self.parse_file_fields( open( filename ) ) ) + self.extend_data_with( filename ) def get_fields( self ): return self.data @@ -380,7 +382,11 @@ if 'name' not in self.columns: self.columns['name'] = self.columns['value'] - def parse_file_fields( self, reader, errors=None ): + def extend_data_with( self, filename, errors=None ): + here = os.path.dirname(os.path.abspath(filename)) + self.data.extend( self.parse_file_fields( open( filename ), errors=errors, here=here ) ) + + def parse_file_fields( self, reader, errors=None, here="__HERE__" ): """ Parse separated lines from file and return a list of tuples. @@ -394,6 +400,7 @@ continue line = line.rstrip( "\n\r" ) if line: + line = expand_here_template( line, here=here ) fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) @@ -529,5 +536,12 @@ rval['fields'] = self.get_fields() return rval + +def expand_here_template(content, here=None): + if here and content: + content = string.Template(content).safe_substitute( { "__HERE__": here }) + return content + + # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) https://bitbucket.org/galaxy/galaxy-central/commits/179f809b70df/ Changeset: 179f809b70df User: jmchilton Date: 2014-11-20 16:31:34+00:00 Summary: Merge next-stable. 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: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20def6edca59/ Changeset: 20def6edca59 Branch: next-stable User: jmchilton Date: 2014-11-20 16:21:25+00:00 Summary: Merge stable into next-stable. Affected #: 3 files diff -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 -r 20def6edca5958f029beae47b4a5cffc9fae8f3d .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 +acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 diff -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 -r 20def6edca5958f029beae47b4a5cffc9fae8f3d lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -403,6 +403,7 @@ dataset.warnings = [] dataset.metadata = {} dataset.composite_files = {} + dataset.uuid = None #load metadata files_metadata = context.get( self.metadata_ref, {} ) metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] ) diff -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 -r 20def6edca5958f029beae47b4a5cffc9fae8f3d lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: https://bitbucket.org/galaxy/galaxy-central/commits/81dc20496497/ Changeset: 81dc20496497 User: jmchilton Date: 2014-11-20 16:21:42+00:00 Summary: Merge next-stable into default. Affected #: 3 files diff -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 -r 81dc204964973c94bdee8631fb806a6214574336 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 +acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 diff -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 -r 81dc204964973c94bdee8631fb806a6214574336 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -403,6 +403,7 @@ dataset.warnings = [] dataset.metadata = {} dataset.composite_files = {} + dataset.uuid = None #load metadata files_metadata = context.get( self.metadata_ref, {} ) metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] ) diff -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 -r 81dc204964973c94bdee8631fb806a6214574336 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: 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: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30e0e657a607/ Changeset: 30e0e657a607 Branch: next-stable User: carlfeberhard Date: 2014-11-20 15:31:05+00:00 Summary: History, view multiple: show error when anonymous with links to register and log in Affected #: 1 file diff -r c3ac0d1c84e71e49d04b5ddb2644415111605cbc -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -609,6 +609,14 @@ def view_multiple( self, trans, include_deleted_histories=False, order='update' ): """ """ + if not trans.user: + log_in_url = url_for( controller="user", action="login", use_panels=True ) + log_in_link = "<a href='%s'>log in</a>" % ( log_in_url ) + register_url = url_for( controller="user", action="create", use_panels=True ) + register_link = "<a href='%s'>register</a>" % ( register_url ) + return trans.show_error_message( "You need to %s or %s to use multiple histories" + % ( log_in_link, register_link ), use_panels=True ) + #TODO: allow specifying user_id for admin? include_deleted_histories = galaxy.util.string_as_bool( include_deleted_histories ) order = order if order in ( 'update', 'name', 'size' ) else 'update' https://bitbucket.org/galaxy/galaxy-central/commits/3ec1e82f0fbd/ Changeset: 3ec1e82f0fbd User: carlfeberhard Date: 2014-11-20 15:31:32+00:00 Summary: Merge next-stable Affected #: 1 file diff -r a88cc74c931780f08c9858ac25c3c03324084135 -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -609,6 +609,14 @@ def view_multiple( self, trans, include_deleted_histories=False, order='update' ): """ """ + if not trans.user: + log_in_url = url_for( controller="user", action="login", use_panels=True ) + log_in_link = "<a href='%s'>log in</a>" % ( log_in_url ) + register_url = url_for( controller="user", action="create", use_panels=True ) + register_link = "<a href='%s'>register</a>" % ( register_url ) + return trans.show_error_message( "You need to %s or %s to use multiple histories" + % ( log_in_link, register_link ), use_panels=True ) + #TODO: allow specifying user_id for admin? include_deleted_histories = galaxy.util.string_as_bool( include_deleted_histories ) order = order if order in ( 'update', 'name', 'size' ) else 'update' 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: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c3ac0d1c84e7/ Changeset: c3ac0d1c84e7 Branch: next-stable User: carlfeberhard Date: 2014-11-20 14:56:37+00:00 Summary: Fix to 42b2e53: should be in next-stable Affected #: 1 file diff -r a799879a82c54c2d1afec6e33d8918479bbf2373 -r c3ac0d1c84e71e49d04b5ddb2644415111605cbc templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -108,7 +108,7 @@ <a id="history-view-multi-button" class='panel-header-button' href="${h.url_for( controller='history', action='view_multiple' )}" title="${ _( 'View all histories' ) }"> - <span class="fa fa-caret-square-o-right"></span> + <span class="fa fa-columns"></span></a> %endif </div> https://bitbucket.org/galaxy/galaxy-central/commits/a88cc74c9317/ Changeset: a88cc74c9317 User: carlfeberhard Date: 2014-11-20 14:57:11+00:00 Summary: Merge 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.

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commit/galaxy-central: dannon: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #566)
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bb79e87274d7/ Changeset: bb79e87274d7 Branch: stable User: dannon Date: 2014-11-20 14:16:46+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #566) [STABLE] Fix Pulsar's default HTTP transport for poster hacking up urllib. Affected #: 1 file diff -r bdfd486e1219d7178ac85f8fcbb3c86fac8bc236 -r bb79e87274d7ef4e043a84aeef8516a5418ef3b6 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: 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: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0ec5d2e530f2/ Changeset: 0ec5d2e530f2 Branch: stable User: jmchilton Date: 2014-11-18 16:39:01+00:00 Summary: Fix Pulsar's default HTTP transport for poster hacking up urllib. Behavior of urllib changes with respect of content length of mmap content after poster is loaded - is automatically loaded by Pulsar client as of 9207ecb43d81853da7a58cd5634683dc87991c4f (added as part of October 2014 stable release). Enis has confirmed this fixes some problems in latest stable. Affected #: 1 file diff -r 1af943ca6e39db44bfec74a0debffbf798fc4731 -r 0ec5d2e530f2bfb597b533b7e57941224abdc1d8 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: https://bitbucket.org/galaxy/galaxy-central/commits/bb79e87274d7/ Changeset: bb79e87274d7 Branch: stable User: dannon Date: 2014-11-20 14:16:46+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #566) [STABLE] Fix Pulsar's default HTTP transport for poster hacking up urllib. Affected #: 1 file diff -r bdfd486e1219d7178ac85f8fcbb3c86fac8bc236 -r bb79e87274d7ef4e043a84aeef8516a5418ef3b6 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: 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 acc8d1e2bc88
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bdfd486e1219/ Changeset: bdfd486e1219 Branch: stable User: natefoo Date: 2014-11-19 20:00:25+00:00 Summary: Update tag latest_2014.10.06 for changeset acc8d1e2bc88 Affected #: 1 file diff -r acc8d1e2bc88530aa8d8651cf5f88649f6769304 -r bdfd486e1219d7178ac85f8fcbb3c86fac8bc236 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 +acc8d1e2bc88530aa8d8651cf5f88649f6769304 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: carlfeberhard: History, view multiple: change icon in analyze page
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42b2e5380ca9/ Changeset: 42b2e5380ca9 User: carlfeberhard Date: 2014-11-19 19:58:00+00:00 Summary: History, view multiple: change icon in analyze page Affected #: 1 file diff -r 9f224596521f7ac224f5bb17f41b69e395de11d1 -r 42b2e5380ca91b6314b22b5290ebf982aa5dc76b templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -108,7 +108,7 @@ <a id="history-view-multi-button" class='panel-header-button' href="${h.url_for( controller='history', action='view_multiple' )}" title="${ _( 'View all histories' ) }"> - <span class="fa fa-caret-square-o-right"></span> + <span class="fa fa-columns"></span></a> %endif </div> 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: Tools API: use history manager to get history in create() to allow anon users to get their only history; Update browser/casper tests to use api upload for testing, remove use of upload tool form
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9f224596521f/ Changeset: 9f224596521f User: carlfeberhard Date: 2014-11-19 19:53:51+00:00 Summary: Tools API: use history manager to get history in create() to allow anon users to get their only history; Update browser/casper tests to use api upload for testing, remove use of upload tool form Affected #: 11 files diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -2,6 +2,7 @@ from galaxy import exceptions from galaxy import web, util +from galaxy import managers from galaxy.web import _future_expose_api_anonymous from galaxy.web import _future_expose_api from galaxy.web.base.controller import BaseAPIController @@ -29,6 +30,12 @@ RESTful controller for interactions with tools. """ + def __init__( self, app ): + super( ToolsController, self ).__init__( app ) + self.mgrs = util.bunch.Bunch( + histories=managers.histories.HistoryManager() + ) + @web.expose_api def index( self, trans, **kwds ): """ @@ -131,7 +138,7 @@ # dataset upload. history_id = payload.get("history_id", None) if history_id: - target_history = self.get_history( trans, history_id ) + target_history = self.mgrs.histories.get( trans, trans.security.decode_id( history_id ) ) else: target_history = None diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -34,6 +34,7 @@ var historyFrameInfo = {}, filenameToUpload = '1.txt', filepathToUpload = '../../test-data/' + filenameToUpload, + testUploadedId = null, testUploadInfo = {}; @@ -73,15 +74,24 @@ spaceghost.then( function testAnonUpload(){ this.test.comment( 'anon-user should be able to upload files' ); - spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - this.debug( 'uploaded HDA info: ' + this.jsonStr( this.quickInfo( _uploadInfo.hdaElement ) ) ); - var hasHda = _uploadInfo.hdaElement, - hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], - hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'state-ok' ) !== -1; - this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.hdaElement.text ); - testUploadInfo = _uploadInfo; + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadedId ){ + testUploadedId = uploadedId; }); +}); +spaceghost.openHomePage().historypanel.waitForHdas( function testAnonUpload(){ + this.test.comment( 'uploaded files should be well formed in the panel' ); + var hdaElement = spaceghost.getElementInfo( '#dataset-' + testUploadedId ); + this.debug( 'uploaded HDA info: ' + this.jsonStr( this.quickInfo( hdaElement ) ) ); + + var hasHda = hdaElement, + hasClass = hdaElement.attributes[ 'class' ], + hasOkClass = hdaElement.attributes[ 'class' ].indexOf( 'state-ok' ) !== -1; + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + hdaElement.text ); + testUploadInfo = hdaElement; }); spaceghost.then( function testAnonUpload(){ this.test.comment( "empty should be NO LONGER be displayed" ); @@ -101,7 +111,7 @@ var hdaInfo = this.historypanel.hdaElementInfoByTitle( filenameToUpload ); this.test.assert( hdaInfo !== null, "After logging in - found a matching hda by name and hid" ); if( hdaInfo ){ - this.test.assert( testUploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, + this.test.assert( testUploadInfo.attributes.id === hdaInfo.attributes.id, "After logging in - found a matching hda by hda view id: " + hdaInfo.attributes.id ); } }); diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/api-anon-history-tests.js --- a/test/casperjs/api-anon-history-tests.js +++ b/test/casperjs/api-anon-history-tests.js @@ -67,11 +67,13 @@ // ------------------------------------------------------------------------------------------- hdas spaceghost.thenOpen( spaceghost.baseUrl ).waitForSelector( spaceghost.historypanel.data.selectors.history.name ); spaceghost.then( function(){ - spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ - this.test.assert( uploadInfo.hdaElement !== null, "Convenience function produced hda" ); - var state = this.historypanel.getHdaState( '#' + uploadInfo.hdaElement.attributes.id ); - this.test.assert( state === 'ok', "Convenience function produced hda in ok state" ); - }); + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: '../../test-data/1.sam' + }, function( uploadedId ){ + var hda = spaceghost.api.hdas.show( currHistory.id, uploadedId ); + this.test.assert( hda.state === 'ok', "Convenience function produced hda in ok state" ); + }); }); spaceghost.then( function(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/api-visualizations-tests.js --- a/test/casperjs/api-visualizations-tests.js +++ b/test/casperjs/api-visualizations-tests.js @@ -153,25 +153,25 @@ visualizationData.bler = 'blah'; this.api.assertRaises( function(){ created = this.api.visualizations.create( visualizationData ); - }, 400, 'unknown key: bler' ); + }, 500, "create_visualization() got an unexpected keyword argument 'bler'" ); delete visualizationData.bler; this.test.comment( 'Calling create with an unparsable JSON config will cause an API error' ); visualizationData.config = '3 = nime'; this.api.assertRaises( function(){ created = this.api.visualizations.create( visualizationData ); - }, 400, 'config must be a dictionary (JSON)' ); + }, 400, 'config must be a dictionary' ); // ------------------------------------------------------------------------------------------ UPDATE // ........................................................................................... idiot proofing - this.test.comment( 'updating using a nonsense key should fail with an error' ); - this.api.assertRaises( function(){ - returned = this.api.visualizations.update( created.id, { bler : 'blah' }); - }, 400, 'unknown key: bler' ); + //this.test.comment( 'updating using a nonsense key should fail with an error' ); + //this.api.assertRaises( function(){ + // returned = this.api.visualizations.update( created.id, { type: 'test', bler : 'blah' }); + //}, 400, 'unknown key: bler' ); this.test.comment( 'updating by attempting to change type should cause an error' ); this.api.assertRaises( function(){ - returned = this.api.visualizations.update( created.id, { title : 30 }); + returned = this.api.visualizations.update( created.id, { type: 'test', title : 30 }); }, 400, 'title must be a string or unicode' ); //TODO: the other types... diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/api-workflow-tests.js --- a/test/casperjs/api-workflow-tests.js +++ b/test/casperjs/api-workflow-tests.js @@ -29,7 +29,7 @@ 'id', 'input_steps', 'tool_id', 'type' ], simpleBedFilepath = '../../test-data/2.bed', - uploadedFile = null, + uploadedFileId = null, workflowCreateKeys = [ 'history', 'outputs' ]; @@ -154,15 +154,17 @@ }); // now run the uploaded workflow -spaceghost.tools.uploadFile( simpleBedFilepath, function( uploadInfo ){ - uploadedFile = uploadInfo; +spaceghost.then( function(){ + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { filepath: simpleBedFilepath }, function( uploadedId ){ + uploadedFileId = uploadedId; + }); }); spaceghost.then( function(){ var currentHistory = this.api.histories.index()[0], firstWorkflow = this.api.workflows.show( this.api.workflows.index()[0].id ); //this.debug( this.jsonStr( uploadedFile ) ); - var uploadedFileId = uploadedFile.hdaElement.attributes.id.split( '-' )[1]; this.debug( this.jsonStr( uploadedFileId ) ); this.debug( this.jsonStr( this.api.hdas.show( currentHistory.id, uploadedFileId ) ) ); diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -25,8 +25,9 @@ } var tooltipSelector = spaceghost.data.selectors.tooltipBalloon, - filepathToUpload = '../../test-data/1.txt', - testUploadInfo = {}, + filenameToUpload = '1.txt', + filepathToUpload = '../../test-data/' + filenameToUpload, + testUploadId = null, //TODO: get from the api module - that doesn't exist yet summaryShouldBeArray = [ '10 lines', 'format', 'txt' ], infoShouldBe = 'uploaded txt file', @@ -37,10 +38,14 @@ // start a new user and upload a file spaceghost.user.loginOrRegisterUser( email, password ); spaceghost.then( function upload(){ - spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - testUploadInfo = _uploadInfo; - }); + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadId ){ + testUploadId = uploadId; + }); }); +spaceghost.openHomePage(); // =================================================================== TEST HELPERS //NOTE: to be called with fn.call( spaceghost, ... ) @@ -278,7 +283,7 @@ spaceghost.then( function(){ this.test.comment( 'HDAs in the "ok" state should be well formed' ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; this.test.assertVisible( uploadSelector, 'HDA is visible' ); this.test.comment( 'should have the proper state class' ); @@ -288,7 +293,7 @@ // since we're using css there's no great way to test state icon (.state-icon is empty) this.test.comment( 'should have proper title and hid' ); - testTitle.call( spaceghost, uploadSelector, testUploadInfo.filename ); + testTitle.call( spaceghost, uploadSelector, filenameToUpload ); this.test.comment( 'should have all of the three, main buttons' ); testTitleButtonStructure.call( spaceghost, uploadSelector ); @@ -308,7 +313,7 @@ // restore to collapsed spaceghost.then( function(){ this.test.comment( "Collapsing hda in 'ok' state should hide body again" ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; spaceghost.historypanel.thenCollapseHda( uploadSelector, function collapseOkState(){ this.test.assertNotVisible( uploadSelector + ' ' + this.historypanel.data.selectors.hda.body, @@ -321,16 +326,17 @@ // set state directly through model, wait for re-render //TODO: not ideal to test this this.evaluate( function(){ - return Galaxy.currHistoryPanel.model.contents.at( 0 ).set( 'state', 'new' ); + console.debug( Galaxy.currHistoryPanel.model.contents.getByHid( 1 ) ); + return Galaxy.currHistoryPanel.model.contents.getByHid( 1 ).set( 'state', 'new' ); }); this.wait( 1000, function(){ this.test.comment( 'HDAs in the "new" state should be well formed' ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; this.test.assertVisible( uploadSelector, 'HDA is visible' ); // should have proper title and hid - testTitle.call( spaceghost, uploadSelector, testUploadInfo.filename ); + testTitle.call( spaceghost, uploadSelector, filenameToUpload ); this.test.comment( 'new HDA should have the new state class' ); this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses['new'], @@ -378,7 +384,7 @@ }); // restore state, collapse spaceghost.then( function revertStateAndCollapse(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadSelector = '#dataset-' + testUploadId; this.historypanel.thenCollapseHda( uploadSelector, function(){ this.evaluate( function(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/history-options-tests.js --- a/test/casperjs/history-options-tests.js +++ b/test/casperjs/history-options-tests.js @@ -26,17 +26,24 @@ var includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; // local -var filepathToUpload = '../../test-data/1.txt', - testUploadInfo = {}; +var filenameToUpload = '1.txt', + filepathToUpload = '../../test-data/' + filenameToUpload, + testUploadId = null; // =================================================================== TESTS // ------------------------------------------------------------------- set up // start a new user and upload a file spaceghost.user.loginOrRegisterUser( email, password ); -spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - testUploadInfo = _uploadInfo; +spaceghost.then( function upload(){ + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadId ){ + testUploadId = uploadId; + }); }); +spaceghost.openHomePage(); // ------------------------------------------------------------------- history options menu structure //NOTE: options menu should be functionally tested elsewhere @@ -69,45 +76,6 @@ "Clicking away from the menu closes it" ); }); -// ------------------------------------------------------------------- options allow showing/hiding deleted hdas -spaceghost.then( function(){ - this.test.comment( 'Deleting HDA' ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; - - this.historypanel.deleteHda( uploadSelector, function(){ - this.test.assertNotExists( uploadSelector, "Deleted HDA is NOT in the DOM" ); - }); -}); - -spaceghost.then( function(){ - this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' shows deleted datasets' ); - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; - - this.historyoptions.includeDeleted( function(){ - this.test.assertExists( uploadSelector, - "Deleted HDA is in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); - this.test.assertVisible( uploadSelector, - "Deleted HDA is visible again (using history options -> " + includeDeletedOptionsLabel + ")" ); - }); -}); - -spaceghost.then( function(){ - this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' (again) re-hides deleted datasets' ); - - this.historyoptions.excludeDeleted( function(){ - this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); - }); -}); - -spaceghost.then( function(){ - // undelete the uploaded file - this.historyoptions.includeDeleted( function(){ - this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); - spaceghost.debug( 'undeleted' ); - }); - -}); // ------------------------------------------------------------------- hidden hdas aren't shown // ------------------------------------------------------------------- history options allows showing hidden hdas @@ -116,13 +84,13 @@ // ------------------------------------------------------------------- history options collapses all expanded hdas spaceghost.then( function(){ - this.historypanel.thenExpandHda( '#' + testUploadInfo.hdaElement.attributes.id ); + this.historypanel.thenExpandHda( '#dataset-' + testUploadId ); }); spaceghost.then( function(){ this.test.comment( 'History option collapses all expanded hdas' ); this.historyoptions.collapseExpanded( function(){ - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, "Body for uploaded file is not visible" ); }); diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -48,7 +48,7 @@ var newHistoryName = "Test History", filepathToUpload = '../../test-data/1.txt', historyFrameInfo = {}, - testUploadInfo = {}; + testUploadId = null; // =================================================================== TESTS @@ -138,16 +138,15 @@ // ------------------------------------------------------------------- check structure of NON empty history // upload file: 1.txt -spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - this.test.comment( 'uploaded file should appear in history' ); - - this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); - var hasHda = _uploadInfo.hdaElement, - hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], - hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; - this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.filename ); - testUploadInfo = _uploadInfo; +spaceghost.then( function upload(){ + var currHistory = spaceghost.api.histories.index()[0]; + spaceghost.api.tools.thenUpload( currHistory.id, { + filepath: filepathToUpload + }, function uploadCallback( uploadId ){ + testUploadId = uploadId; + }); }); +spaceghost.openHomePage(); spaceghost.then( function checkPanelStructure(){ this.test.comment( 'checking structure of non-empty panel' ); @@ -231,8 +230,7 @@ // broken in webkit w/ jq 1.7 spaceghost.historypanel.waitForHdas( function(){ this.test.comment( 'HDAs can be expanded by clicking on the name' ); - this.debug( this.jsonStr( testUploadInfo ) ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); this.wait( 1000, function(){ @@ -244,7 +242,7 @@ // ------------------------------------------------------------------- expanded hdas are still expanded after a refresh spaceghost.then( function(){ this.test.comment( 'Expanded hdas are still expanded after a refresh' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( refreshButtonSelector ); this.historypanel.waitForHdas( function(){ @@ -257,7 +255,7 @@ // ------------------------------------------------------------------- expanded hdas collapse by clicking name again spaceghost.then( function(){ this.test.comment( 'Expanded hdas collapse by clicking name again' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); this.wait( 500, function(){ @@ -269,7 +267,7 @@ // ------------------------------------------------------------------- collapsed hdas still collapsed after a refresh spaceghost.then( function(){ this.test.comment( 'collapsed hdas still collapsed after a refresh' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#dataset-' + testUploadId; this.click( refreshButtonSelector ); this.historypanel.waitForHdas( function(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -355,6 +355,7 @@ // have to attach like GET param - due to body loss in jq url = utils.format( this.urlTpls.update, historyId, id ); if( purge ){ +console.debug( 'adding purge:' + purge ); url += '?purge=True'; } return this.api._ajax( url, { @@ -489,7 +490,7 @@ /** post a file to the upload1 tool over ajax */ ToolsAPI.prototype.upload = function upload( historyId, options ){ - this.api.spaceghost.info( 'tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); + this.api.spaceghost.info( 'api.tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); this.api.ensureId( historyId ); options = options || {}; @@ -512,6 +513,7 @@ if( options.tabs ){ inputs[ 'files_0|space_to_tab' ] = 'Yes'; } + var response = this.api.spaceghost.evaluate( function( url, historyId, inputs ){ var file = $( 'input[name="casperjs-upload-file"]' )[0].files[0], formData = new FormData(); @@ -559,9 +561,6 @@ this.debug( 'uploadedId: ' + uploadedId ); }); - spaceghost.debug( '---------------------------------------------------------- timeout: ' + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) ); - spaceghost.debug( 'timeout: ' + options.timeout ); - spaceghost.debug( 'timeout: ' + spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ); spaceghost.then( function(){ this.waitFor( function testHdaState(){ diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/modules/historyoptions.js --- a/test/casperjs/modules/historyoptions.js +++ b/test/casperjs/modules/historyoptions.js @@ -232,8 +232,6 @@ datasetSecurity : "Dataset Security", resumePausedJobs : "Resume Paused Jobs", collapseExpanded : 'Collapse Expanded Datasets', - includeDeleted : 'Include Deleted Datasets', - includeHidden : 'Include Hidden Datasets', unhideHiddenDatasets : "Unhide Hidden Datasets", purgeDeletedDatasets : "Purge Deleted Datasets", showStructure : "Show Structure", diff -r e4dbcc06df53f4a47717ddd047dd85911bab888e -r 9f224596521f7ac224f5bb17f41b69e395de11d1 test/casperjs/upload-tests.js --- a/test/casperjs/upload-tests.js +++ b/test/casperjs/upload-tests.js @@ -21,8 +21,6 @@ password = spaceghost.fixtureData.testUser.password; } -var testUploadInfo = {}; - // =================================================================== TESTS // ------------------------------------------------------------------- start a new user spaceghost.user.loginOrRegisterUser( email, password ).openHomePage( function(){ @@ -30,63 +28,21 @@ this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); }); -// ------------------------------------------------------------------- long form -// upload a file... +// ------------------------------------------------------------------- api upload spaceghost.then( function(){ - this.test.comment( 'Test uploading a file' ); + this.test.comment( 'Test API function' ); - var filename = '1.txt', - filepath = '../../test-data/' + filename; - this.tools._uploadFile( filepath ); - - // when an upload begins successfully main should reload with a infomessagelarge - this.withMainPanel( function mainAfterUpload(){ - var infoInfo = this.elementInfoOrNull( this.data.selectors.messages.infolarge ); - this.test.assert( infoInfo !== null, - "Found infomessagelarge after uploading file" ); - this.test.assert( infoInfo.text.indexOf( this.data.text.upload.success ) !== -1, - "Found upload success message: " + this.data.text.upload.success ); - - testUploadInfo.name = filename; + var currHistoryId = spaceghost.api.histories.index()[0].id; + spaceghost.api.tools.thenUpload( currHistoryId, { + filepath : '../../test-data/1.sam' + }, function(){ + var hdas = spaceghost.api.hdas.index( currHistoryId ); + spaceghost.test.assert( hdas.length === 1, 'One dataset uploaded: ' + hdas.length ); + spaceghost.test.assert( hdas[0].state === 'ok', 'State is: ' + hdas[0].state ); + spaceghost.test.assert( hdas[0].name === '1.sam', 'Name is: ' + hdas[0].name ); }); }); -// ... and move to the history panel and wait for upload to finish -spaceghost.historypanel.waitForHda( '1.txt', - function uploadComplete( hdaElement ){ - this.test.pass( 'Upload completed successfully for: ' + this.jsonStr( hdaElement.attributes.id ) ); - }, - function timeout( hdaElement ){ - this.debug( 'hdaElement:\n' + this.jsonStr( hdaElement ) ); - this.test.fail( 'Test timed out for upload: ' + testUploadInfo.name ); - }, - 30 * 1000 -); - -// ------------------------------------------------------------------- short form -spaceghost.then( function(){ - this.test.comment( 'Test convenience function' ); - - spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ - this.test.assert( uploadInfo.hdaElement !== null, "Convenience function produced hda" ); - var state = this.historypanel.getHdaState( '#' + uploadInfo.hdaElement.attributes.id ); - this.test.assert( state === 'ok', "Convenience function produced hda in ok state" ); - }); -}); - -// ------------------------------------------------------------------- test conv. fn error -/* -//??: this error's AND waitFor()s THREE times (or more) - something to do with assertStepsRaise + waitFor -spaceghost.then( function(){ - this.test.comment( 'testing convenience function timeout error' ); - this.assertStepsRaise( 'GalaxyError: Upload Error: timeout waiting', function(){ - spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ - this.test.fail( "Convenience function did not timeout!" ); - }, 50 ); - }); -}); -*/ - // =================================================================== spaceghost.run( function(){ test.done(); }); }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: add remote_repo_url and homepage_url to repository model and TS forms that show/modify it, database migration included
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4dbcc06df53/ Changeset: e4dbcc06df53 User: martenson Date: 2014-11-19 17:53:33+00:00 Summary: add remote_repo_url and homepage_url to repository model and TS forms that show/modify it, database migration included Affected #: 7 files diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1063,6 +1063,8 @@ message=message, status=status ) ) name = kwd.get( 'name', '' ).strip() + remote_repository_url = kwd.get( 'remote_repository_url', '' ) + homepage_url = kwd.get( 'homepage_url', '' ) description = kwd.get( 'description', '' ) long_description = kwd.get( 'long_description', '' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) @@ -1082,6 +1084,8 @@ repository, message = repository_util.create_repository( trans.app, name, repository_type, + remote_repository_url, + homepage_url, description, long_description, user_id=trans.user.id, @@ -1093,6 +1097,8 @@ repository_type_select_field = rt_util.build_repository_type_select_field( trans ) return trans.fill_template( '/webapps/tool_shed/repository/create_repository.mako', name=name, + remote_repository_url=remote_repository_url, + homepage_url=homepage_url, description=description, long_description=long_description, selected_categories=selected_categories, @@ -2242,6 +2248,8 @@ repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False ) repo_name = kwd.get( 'repo_name', repository.name ) changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) + remote_repository_url = kwd.get( 'remote_repository_url', repository.remote_repository_url ) + homepage_url = kwd.get( 'homepage_url', repository.homepage_url ) description = kwd.get( 'description', repository.description ) long_description = kwd.get( 'long_description', repository.long_description ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) @@ -2271,6 +2279,12 @@ if repository_type != repository.type: repository.type = repository_type flush_needed = True + if remote_repository_url != repository.remote_repository_url: + repository.remote_repository_url = remote_repository_url + flush_needed = True + if homepage_url != repository.homepage_url: + repository.homepage_url = homepage_url + flush_needed = True if description != repository.description: repository.description = description flush_needed = True @@ -2470,6 +2484,8 @@ deprecated_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, + remote_repository_url=remote_repository_url, + homepage_url=homepage_url, description=description, long_description=long_description, current_allow_push_list=current_allow_push_list, diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -144,9 +144,9 @@ class Repository( object, Dictifiable ): - dict_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', + dict_collection_visible_keys = ( 'id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) - dict_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', + dict_element_visible_keys = ( 'id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) file_states = Bunch( NORMAL = 'n', NEEDS_MERGING = 'm', @@ -154,11 +154,14 @@ MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) - def __init__( self, id=None, name=None, type=None, description=None, long_description=None, user_id=None, private=False, - deleted=None, email_alerts=None, times_downloaded=0, deprecated=False ): + def __init__( self, id=None, name=None, type=None, remote_repository_url=None, homepage_url=None, + description=None, long_description=None, user_id=None, private=False, + deleted=None, email_alerts=None, times_downloaded=0, deprecated=False ): self.id = id self.name = name or "Unnamed repository" self.type = type + self.remote_repository_url = remote_repository_url + self.homepage_url = homepage_url self.description = description self.long_description = long_description self.user_id = user_id diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -100,6 +100,8 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), index=True ), Column( "type", TrimmedString( 255 ), index=True ), + Column( "remote_repository_url", TrimmedString( 255 ) ), + Column( "homepage_url", TrimmedString( 255 ) ), Column( "description" , TEXT ), Column( "long_description" , TEXT ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py @@ -0,0 +1,49 @@ +""" +Migration script to add the remote_repository_url and homepage_url +columns to the repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import sys, logging + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade( migrate_engine ): + print __doc__ + metadata.bind = migrate_engine + metadata.reflect() + Repository_table = Table( "repository", metadata, autoload=True ) + c_remote = Column( "remote_repository_url", TrimmedString( 255 ) ) + c_homepage = Column( "homepage_url", TrimmedString( 255 ) ) + try: + # Create + c_remote.create( Repository_table ) + c_homepage.create( Repository_table ) + assert c_remote is Repository_table.c.remote_repository_url + assert c_homepage is Repository_table.c.homepage_url + except Exception, e: + print "Adding remote_repository_url and homepage_url columns to the repository table failed: %s" % str( e ) + migrate_engine.execute( cmd ) + +def downgrade( migrate_engine ): + metadata.bind = migrate_engine + metadata.reflect() + # Drop type column from repository table. + Repository_table = Table( "repository", metadata, autoload=True ) + try: + Repository_table.c..drop() + Repository_table.c.homepage_url.drop() + except Exception, e: + print "Dropping columns remote_repository_url and homepage_url from the repository table failed: %s" % str( e ) diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -120,11 +120,14 @@ tool_dependencies ) return repo_info_dict -def create_repository( app, name, type, description, long_description, user_id, category_ids=[] ): +def create_repository( app, name, type, remote_repository_url, homepage_url, description, long_description, user_id, category_ids=[] ): + """Create a new ToolShed repository""" sa_session = app.model.context.current # Add the repository record to the database. repository = app.model.Repository( name=name, type=type, + remote_repository_url=remote_repository_url, + homepage_url=homepage_url, description=description, long_description=long_description, user_id=user_id ) diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e templates/webapps/tool_shed/repository/create_repository.mako --- a/templates/webapps/tool_shed/repository/create_repository.mako +++ b/templates/webapps/tool_shed/repository/create_repository.mako @@ -25,6 +25,24 @@ <div style="clear: both"></div></div> ${render_repository_type_select_field( repository_type_select_field, render_help=True )} + + <div class="form-row"> + <label>Remote repository URL:</label> + <input name="remote_repository_url" placeholder="optional" type="textfield" value="${remote_repository_url | h}" size="80"/> + <div class="toolParamHelp" style="clear: both;"> + A link to your public development repository. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Homepage URL:</label> + <input name="homepage_url" placeholder="optional" type="textfield" value="${homepage_url | h}" size="80"/> + <div class="toolParamHelp" style="clear: both;"> + Link to tool's homepage. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"><label>Synopsis:</label><input name="description" type="textfield" value="${description | h}" size="80"/> diff -r ee4e0a07aea2305927f5215fdecd049fbb80031b -r e4dbcc06df53f4a47717ddd047dd85911bab888e templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -184,6 +184,16 @@ </div> ${render_repository_type_select_field( repository_type_select_field, render_help=True )} <div class="form-row"> + <label>Remote repository URL:</label> + <input name="remote_repository_url" type="textfield" value="${remote_repository_url | h}" size="80"/> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Homepage URL:</label> + <input name="homepage_url" type="textfield" value="${homepage_url | h}" size="80"/> + <div style="clear: both"></div> + </div> + <div class="form-row"><label>Synopsis:</label><input name="description" type="textfield" value="${description | h}" size="80"/><div style="clear: both"></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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