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Revise label handling and duplicate check, move save controller to ap…
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…i for proper error response
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@guerler
guerler committed Jan 11, 2017
1 parent 20c2707 commit e571fce
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Showing 16 changed files with 96 additions and 160 deletions.
8 changes: 4 additions & 4 deletions client/galaxy/scripts/mvc/tool/tool-form-base.js
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Original file line number Diff line number Diff line change
Expand Up @@ -80,18 +80,18 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
Utils.get({
url : build_url,
data : build_data,
success : function( new_model ) {
if( !new_model.display ) {
success : function( data ) {
if( !data.display ) {
window.location = Galaxy.root;
return;
}
self._buildForm( new_model );
self._buildForm( data );
!hide_message && self.message.update({
status : 'success',
message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + ', id \'' + self.options.id + '\'.',
persistent : false
});
Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model ready.', new_model);
Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model ready.', data);
process.resolve();
},
error : function( response, status ) {
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38 changes: 0 additions & 38 deletions client/galaxy/scripts/mvc/workflow/workflow-manager.js
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Original file line number Diff line number Diff line change
Expand Up @@ -11,47 +11,9 @@ function( Connector, Toastr ) {
this.name = null;
this.has_changes = false;
this.active_form_has_changes = false;
this.nodeLabels = {};
this.workflowOutputLabels = {};
}
$.extend( Workflow.prototype, {
canLabelNodeWith: function( label ) {
if( label ) {
return ! (label in this.nodeLabels);
} else {
// empty labels are non-exclusive, so allow this one.
return true;
}
},
registerNodeLabel: function( label ) {
if( label ) {
this.nodeLabels[label] = true;
}
},
unregisterNodeLabel: function( label ) {
if( label ) {
delete this.nodeLabels[label];
}
},
updateNodeLabel: function( fromLabel, toLabel ) {
if( fromLabel ) {
this.unregisterNodeLabel( fromLabel );
}
if( ! this.canLabelNodeWith( toLabel ) ) {
Toastr.warning("Workflow contains duplicate node labels " + toLabel + ". This must be fixed before it can be saved.");
}
if( toLabel ) {
this.registerNodeLabel( toLabel );
}
},
attemptUpdateNodeLabel: function( node, label ) {
if( this.canLabelNodeWith( label ) ) {
node.setLabel( label );
return true;
} else {
return false;
}
},
canLabelOutputWith: function( label ) {
if( label ) {
return ! (label in this.workflowOutputLabels);
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12 changes: 3 additions & 9 deletions client/galaxy/scripts/mvc/workflow/workflow-node.js
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Original file line number Diff line number Diff line change
Expand Up @@ -148,10 +148,6 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
// Remove active class
$(element).removeClass( "toolForm-active" );
},
setLabel: function(label) {
this.app.workflow.updateNodeLabel(this.label, label);
this.label = label || null;
},
init_field_data : function ( data ) {
if ( data.type ) {
this.type = data.type;
Expand All @@ -163,17 +159,15 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
this.tooltip = data.tooltip ? data.tooltip : "";
this.annotation = data.annotation;
this.post_job_actions = data.post_job_actions ? data.post_job_actions : {};
this.setLabel(data.label);
this.label = data.label;
this.uuid = data.uuid;
this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];

var node = this;
var nodeView = new NodeView({
el: this.element[ 0 ],
node: node,
});
node.nodeView = nodeView;

$.each( data.data_inputs, function( i, input ) {
nodeView.addDataInput( input );
});
Expand All @@ -188,12 +182,12 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
},
update_field_data : function( data ) {
var node = this;
nodeView = node.nodeView;
var nodeView = node.nodeView;
this.tool_state = data.tool_state;
this.config_form = data.config_form;
this.errors = data.errors;
this.annotation = data['annotation'];
this.setLabel(data.label);
this.label = data.label;
if( "post_job_actions" in data ) {
// Won't be present in response for data inputs
var pja_in = data.post_job_actions;
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112 changes: 46 additions & 66 deletions client/galaxy/scripts/mvc/workflow/workflow-view.js
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,6 @@ define([
var self = Globals.app = this;
this.options = options;
this.urls = options && options.urls || {};
this.active_ajax_call = false;
var close_editor = function() {
self.workflow.check_changes_in_active_form();
if ( workflow && self.workflow.has_changes ) {
Expand Down Expand Up @@ -95,56 +94,37 @@ define([
return;
}
self.workflow.rectify_workflow_outputs();
var savefn = function(callback) {
$.ajax( {
url: self.urls.save_workflow,
type: "POST",
data: {
id: self.options.id,
workflow_data: function() { return JSON.stringify( self.workflow.to_simple() ); },
"_": "true"
},
dataType: 'json',
success: function( data ) {
var body = $("<div></div>").text( data.message );
if ( data.errors ) {
body.addClass( "warningmark" );
var errlist = $( "<ul/>" );
$.each( data.errors, function( i, v ) {
$("<li></li>").text( v ).appendTo( errlist );
});
body.append( errlist );
} else {
body.addClass( "donemark" );
}
self.workflow.name = data.name;
self.workflow.has_changes = false;
self.workflow.stored = true;
self.showWorkflowParameters();
if ( data.errors ) {
window.show_modal( "Saving workflow", body, { "Ok" : hide_modal } );
} else {
if (callback) {
callback();
}
hide_modal();
}
Utils.request( {
url: Galaxy.root + 'api/workflows/' + self.options.id + '/save',
type: "POST",
data: self.workflow.to_simple(),
success: function( data ) {
var body = $( "<div/>" ).text( data.message );
if ( data.errors ) {
body.addClass( "warningmark" );
var errlist = $( "<ul/>" );
$.each( data.errors, function( i, v ) {
$( "<li/>" ).text( v ).appendTo( errlist );
});
body.append( errlist );
} else {
body.addClass( "donemark" );
}
});
};

// We bind to ajaxStop because of auto-saving, since the form submission ajax
// call needs to be completed so that the new data is saved
if (self.active_ajax_call) {
$(document).bind('ajaxStop.save_workflow', function() {
$(document).unbind('ajaxStop.save_workflow');
savefn();
$(document).unbind('ajaxStop.save_workflow'); // IE7 needs it here
self.active_ajax_call = false;
});
} else {
savefn(success_callback);
}
self.workflow.name = data.name;
self.workflow.has_changes = false;
self.workflow.stored = true;
self.showWorkflowParameters();
if ( data.errors ) {
window.show_modal( "Saving workflow", body, { "Ok" : hide_modal } );
} else {
success_callback && success_callback();
hide_modal();
}
},
error: function( response ) {
window.show_modal( "Saving workflow failed.", response.err_msg, { "Ok" : hide_modal } );
}
});
};

// Init searching.
Expand Down Expand Up @@ -273,21 +253,6 @@ define([
}
});

// For autosave purposes
$(document).ajaxStart( function() {
self.active_ajax_call = true;
$(document).bind( "ajaxStop.global", function() {
self.active_ajax_call = false;
});
});

$(document).ajaxError( function ( e, x ) {
// console.log( e, x );
var message = x.responseText || x.statusText || "Could not connect to server";
window.show_modal( "Server error", message, { "Ignore error" : hide_modal } );
return false;
});

window.make_popupmenu && make_popupmenu( $("#workflow-options-button"), {
"Save" : save_current_workflow,
"Save As": workflow_save_as,
Expand Down Expand Up @@ -690,6 +655,7 @@ define([
},

showForm: function ( content, node ) {
var self = this;
var cls = 'right-content';
var id = cls + '-' + node.id;
var $container = $( '#' + cls );
Expand All @@ -711,7 +677,21 @@ define([
name : '__label',
label : 'Label',
value : node.label,
help : 'Add a step label.'
help : 'Add a step label.',
onchange: function( new_label ) {
var duplicate = false;
for ( var i in self.workflow.nodes ) {
var n = self.workflow.nodes[ i ];
if ( n.label && n.label == new_label && n.id != node.id ) {
duplicate = true;
break;
}
}
var input_id = form.data.match( '__label' );
var input_element = form.element_list[ input_id ];
input_element.model.set( 'error_text', duplicate && 'Duplicate label. Please fix this before saving the workflow.' );
form.trigger( 'change' );
}
});
content.inputs.push({
type : 'text',
Expand Down
33 changes: 33 additions & 0 deletions lib/galaxy/webapps/galaxy/api/workflows.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,6 +295,39 @@ def import_new_workflow_deprecated(self, trans, payload, **kwd):
"""
return self.__api_import_new_workflow( trans, payload, **kwd )

@expose_api
def save( self, trans, id, payload, **kwd ):
"""
POST /api/workflows/id/save
Save the workflow described by `workflow_data` with id `id`.
"""
print payload
# Get the stored workflow
stored = self.__get_stored_workflow( trans, id )
try:
workflow, errors = self.workflow_contents_manager.update_workflow_from_dict(
trans,
stored,
payload,
)
except workflows.MissingToolsException as e:
return dict(
name=e.workflow.name,
message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.",
errors=e.errors,
)
if workflow.has_errors:
errors.append( "Some steps in this workflow have validation errors." )
if workflow.has_cycles:
errors.append( "This workflow contains cycles." )
if errors:
rval = dict( message="Workflow saved, but will not be runnable due to the following errors.",
errors=errors )
else:
rval = dict( message="Workflow saved." )
rval['name'] = workflow.name
return rval

@expose_api
def update( self, trans, id, payload, **kwds ):
"""
Expand Down
1 change: 1 addition & 0 deletions lib/galaxy/webapps/galaxy/buildapp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -284,6 +284,7 @@ def populate_api_routes( webapp, app ):
webapp.mapper.connect( '/api/genomes/{id}/sequences', controller='genomes', action='sequences' )
webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" )
webapp.mapper.connect( '/api/workflows/{id}/save', action='save', controller="workflows" )
webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" )
Expand Down
34 changes: 0 additions & 34 deletions lib/galaxy/webapps/galaxy/controllers/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -684,40 +684,6 @@ def load_workflow( self, trans, id ):
workflow_contents_manager = workflows.WorkflowContentsManager(trans.app)
return workflow_contents_manager.workflow_to_dict( trans, stored, style="editor" )

@web.json
def save_workflow( self, trans, id, workflow_data ):
"""
Save the workflow described by `workflow_data` with id `id`.
"""
# Get the stored workflow
stored = self.get_stored_workflow( trans, id )
workflow_contents_manager = workflows.WorkflowContentsManager(trans.app)
try:
workflow, errors = workflow_contents_manager.update_workflow_from_dict(
trans,
stored,
workflow_data,
)
except workflows.MissingToolsException as e:
return dict(
name=e.workflow.name,
message="This workflow includes missing or invalid tools. "
"It cannot be saved until the following steps are removed or the missing tools are enabled.",
errors=e.errors,
)

if workflow.has_errors:
errors.append( "Some steps in this workflow have validation errors" )
if workflow.has_cycles:
errors.append( "This workflow contains cycles" )
if errors:
rval = dict( message="Workflow saved, but will not be runnable due to the following errors",
errors=errors )
else:
rval = dict( message="Workflow saved" )
rval['name'] = workflow.name
return rval

@web.expose
@web.require_login( "use workflows" )
def export_to_myexp( self, trans, id, myexp_username, myexp_password ):
Expand Down

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