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Merge pull request #2077 from guerler/revise_workflow_run_004
Run workflow form revision
This commit is contained in:
John Chilton
@@ -1,8 +1,9 @@
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/** This is the run workflow tool form view. */
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define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-data', 'mvc/tool/tool-form-base' ],
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function( Utils, Deferred, Ui, Form, FormData, ToolFormBase ) {
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define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-data', 'mvc/tool/tool-form-base', 'mvc/ui/ui-modal' ],
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function( Utils, Deferred, Ui, Form, FormData, ToolFormBase, Modal ) {
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var View = Backbone.View.extend({
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initialize: function( options ) {
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this.modal = parent.Galaxy.modal || new Modal.View();
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this.model = options && options.model || new Backbone.Model( options );
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this.deferred = new Deferred();
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this.setElement( $( '<div/>' ).addClass( 'ui-form-composite' )
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@@ -330,7 +331,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
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var self = this;
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var job_def = {
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new_history_name : this.history_form.data.create()[ 'new_history|name' ],
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wf_parm : this.wp_form ? this.wp_form.data.create() : {},
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replacement_params : this.wp_form ? this.wp_form.data.create() : {},
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inputs : {}
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};
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var validated = true;
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@@ -371,7 +372,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
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Galaxy.emit.debug( 'tool-form-composite::submit()', 'Validation complete.', job_def );
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Utils.request({
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type : 'POST',
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url : Galaxy.root + 'api/workflows/' + this.workflow_id + '/invocations',
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url : Galaxy.root + 'api/workflows/' + this.model.id + '/run',
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data : job_def,
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success : function( response ) {
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Galaxy.emit.debug( 'tool-form-composite::submit', 'Submission successful.', response );
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@@ -393,13 +394,12 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
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}
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}
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} else {
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var modal = parent.Galaxy.modal;
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modal && modal.show({
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self.modal.show({
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title : 'Job submission failed',
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body : self._templateError( response && response.err_msg || job_def ),
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buttons : {
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'Close' : function() {
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modal.hide();
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self.modal.hide();
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}
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}
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});
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@@ -15,9 +15,12 @@ from galaxy.web import _future_expose_api as expose_api
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from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
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from galaxy.web.base.controller import SharableMixin
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from galaxy.workflow.extract import extract_workflow
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from galaxy.workflow.run import invoke, queue_invoke
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from galaxy.workflow.run import invoke, queue_invoke, WorkflowRunConfig
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from galaxy.workflow.run_request import build_workflow_run_config
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from galaxy.workflow.modules import module_factory
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from galaxy.workflow.modules import module_factory, WorkflowModuleInjector
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from galaxy.tools.parameters.basic import workflow_building_modes
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from galaxy.tools.parameters.meta import expand_workflow_inputs
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log = logging.getLogger(__name__)
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@@ -82,6 +85,68 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
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style = "instance"
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return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style=style )
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@expose_api
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def run( self, trans, workflow_id, payload, **kwd ):
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"""
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POST /api/workflows/{encoded_workflow_id}/run
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Run a workflow with a dictionary of prefixed_name/value pairs e.g.
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payload = { inputs: { step_0: { parameter_0|parameter_1 : value_0, ... }, ... } }
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"""
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workflow = self.__get_stored_accessible_workflow( trans, workflow_id ).latest_workflow
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trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
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module_injector = WorkflowModuleInjector( trans )
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params, param_keys = expand_workflow_inputs( payload.get( 'inputs', [] ) )
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errors = {}
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for workflow_args in params:
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for step in workflow.steps:
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step_args = workflow_args.get( str( step.id ), {} )
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step_errors = module_injector.inject( step, step_args )
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if step_errors:
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errors[ step.id ] = step_errors
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if errors:
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log.exception( errors )
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raise exceptions.MessageException( err_data=errors )
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invocations = []
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for index, workflow_args in enumerate( params ):
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for step in workflow.steps:
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step_args = workflow_args.get( str( step.id ), {} )
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module_injector.inject( step, step_args )
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new_history = None
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if 'new_history_name' in payload:
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if payload[ 'new_history_name' ]:
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nh_name = payload[ 'new_history_name' ]
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else:
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nh_name = 'History from %s workflow' % workflow.name
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if index in param_keys:
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ids = param_keys[ index ]
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nids = len( ids )
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if nids == 1:
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nh_name = '%s on %s' % ( nh_name, ids[ 0 ] )
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elif nids > 1:
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nh_name = '%s on %s and %s' % ( nh_name, ', '.join( ids[ 0:-1 ] ), ids[ -1 ] )
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new_history = trans.app.model.History( user=trans.user, name=nh_name )
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new_history.copy_tags_from( trans.user, trans.history )
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trans.sa_session.add( new_history )
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target_history = new_history
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elif 'history_id' in payload:
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target_history = histories.HistoryManager( trans.app ).get_owned( trans.security.decode_id( payload.get( 'history_id' ), trans.user, current_history=trans.history ) )
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else:
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target_history = trans.history
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run_config = WorkflowRunConfig(
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target_history=target_history,
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replacement_dict=payload.get( 'replacement_params', {} ),
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copy_inputs_to_history=new_history is not None )
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invocation = queue_invoke(
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trans=trans,
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workflow=workflow,
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workflow_run_config=run_config,
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populate_state=False )
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invocations.append({ 'history' : { 'id' : trans.app.security.encode_id( new_history.id ), 'name' : new_history.name } if new_history else None,
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'scheduled' : invocation.state == trans.app.model.WorkflowInvocation.states.SCHEDULED })
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trans.sa_session.flush()
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return invocations
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@expose_api
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def create(self, trans, payload, **kwd):
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"""
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@@ -271,6 +271,7 @@ def populate_api_routes( webapp, app ):
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webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' )
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webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
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webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" )
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webapp.mapper.connect( '/api/workflows/{workflow_id}/run', action='run', controller="workflows", conditions=dict( method=['POST'] ) )
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webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
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webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
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webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" )
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@@ -1336,11 +1336,9 @@ def populate_module_and_state( trans, workflow, param_map, allow_tool_state_corr
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step_errors = module_injector.inject( step, step_args=step_args )
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if step.type == 'tool' or step.type is None:
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if step_errors:
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message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors
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raise exceptions.MessageException( message )
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raise exceptions.MessageException( step_errors )
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if step.upgrade_messages:
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if allow_tool_state_corrections:
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log.debug( 'Workflow step "%i" had upgrade messages: %s', step.id, step.upgrade_messages )
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else:
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message = "Workflow cannot be run because of step upgrade messages: %s" % step.upgrade_messages
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raise exceptions.MessageException( message )
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raise exceptions.MessageException( step.upgrade_messages )
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File diff suppressed because one or more lines are too long
@@ -1 +1 @@
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{"version":3,"file":"tool-template.js","sources":["../../../src/mvc/tool/tool-template.js"],"names":["define","help","options","$tmpl","$","addClass","append","find","attr","success","response","jobs","length","this","error","njobs","njobs_text","tmpl","i","outputs","hid","name","JSON","stringify","undefined","requirements","requirements_message","req","version"],"mappings":"AACAA,UAAW,WAGX,OACIC,KAAM,SAAUC,GACZ,GAAIC,GAAQC,EAAG,UAAWC,SAAU,gBAAiBC,OAAQJ,EAAQD,KAErE,OADAE,GAAMI,KAAM,KAAMC,KAAM,SAAU,UAC3BL,GAGXM,QAAS,SAASC,GAEd,IAAKA,EAASC,OAASD,EAASC,KAAKC,OACjC,MAAOC,MAAKC,MAAMJ,EAItB,IAAIK,GAAQL,EAASC,KAAKC,OAGtBI,EAAa,EAEbA,GADS,GAATD,EACa,YAEAA,EAAQ,YAIzB,IAAIE,GAAQ,oCACYD,EAAa,kFACrC,KAAK,GAAIE,KAAKR,GAASS,QACnBF,GAAY,qCAAuCP,EAASS,QAAQD,GAAGE,IAAM,KAAOV,EAASS,QAAQD,GAAGG,KAAO,UAMnH,OAJAJ,IAAgB,qQAOpBH,MAAO,SAASJ,GACZ,MAAQ,uMAKQY,KAAKC,UAAUb,EAAUc,OAAW,GACxC,qBAIhBC,aAAc,SAASvB,GACnB,GAAIwB,GAAuB,qBAC3B,KAAK,GAAIR,KAAKhB,GAAQuB,aAAc,CAChC,GAAIE,GAAMzB,EAAQuB,aAAaP,EAC/BQ,IAAwBC,EAAIN,KACxBM,EAAIC,UACJF,GAAwB,aAAeC,EAAIC,QAAU,KAErDV,EAAIhB,EAAQuB,aAAab,OAAS,IAClCc,GAAwB,MAExBR,GAAKhB,EAAQuB,aAAab,OAAS,IACnCc,GAAwB,SAGhC,MAAOA,GAAuB"}
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{"version":3,"file":"tool-template.js","sources":["../../../src/mvc/tool/tool-template.js"],"names":["define","error","response","$","append","text","addClass","css","color","height","JSON","stringify","undefined"],"mappings":"AAAAA,UAAW,WACX,OACIC,MAAO,SAAUC,GACb,MAAQC,GAAG,SAAUC,OAAQD,EAAG,QACPE,KAAM,sGACVD,OAAQD,EAAG,eAAgBG,SAAU,eAAgBC,KAAOC,MAAO,QAASC,OAAU,qBAClFJ,KAAMK,KAAKC,UAAWT,EAAUU,OAAW"}
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File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -1,2 +1,2 @@
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define([],function(){return{help:function(a){var b=$("<div/>").addClass("ui-form-help").append(a.help);return b.find("a").attr("target","_blank"),b},success:function(a){if(!a.jobs||!a.jobs.length)return this.error(a);var b=a.jobs.length,c="";c=1==b?"1 job has":b+" jobs have";var d='<div class="donemessagelarge"><p>'+c+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in a.outputs)d+='<p style="padding: 10px 20px;"><b>'+a.outputs[e].hid+": "+a.outputs[e].name+"</b></p>";return d+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>"},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black; height: 300px !important;">'+JSON.stringify(a,void 0,4)+"</textarea></div>"},requirements:function(a){var b="This tool requires ";for(var c in a.requirements){var d=a.requirements[c];b+=d.name,d.version&&(b+=" (Version "+d.version+")"),c<a.requirements.length-2&&(b+=", "),c==a.requirements.length-2&&(b+=" and ")}return b+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}});
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define([],function(){return{error:function(a){return $("<div>").append($("<p/>").text("The server could not complete the request. Please contact the Galaxy Team if this error persists.")).append($("<textarea/>").addClass("ui-textarea").css({color:"black",height:"300px !important"}).text(JSON.stringify(a,void 0,4)))}}});
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//# sourceMappingURL=../../../maps/mvc/tool/tool-template.js.map
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