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Merge pull request #3593 from guerler/unify_name_label

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Introduce label and annotation attributes to subworkflows, fix annotation display, unify module form update handler
This commit is contained in:
John Chilton
2017-02-21 08:03:54 -05:00
committed by GitHub
parent 430ac221ba 8557c32034
commit cdb15f6392
25 changed files with 273 additions and 284 deletions
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client/galaxy/scripts/mvc/tool/tool-form-base.js
+1 -1
View File
@@ -40,7 +40,7 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
var self = this;
this.model.set( options );
this.model.set({
title : '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Version ' + options.version + ')',
title : options.title || '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Version ' + options.version + ')',
operations : !this.model.get( 'hide_operations' ) && this._operations(),
onchange : function() {
self.deferred.reset();
client/galaxy/scripts/mvc/tool/tool-form-composite.js
+8 -3
View File
@@ -39,12 +39,18 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
_.each( this.model.get( 'steps' ), function( step, i ) {
Galaxy.emit.debug( 'tool-form-composite::initialize()', i + ' : Preparing workflow step.' );
var icon = WorkflowIcons[ step.step_type ];
var title = parseInt( i + 1 ) + ': ' + ( step.step_label || step.step_name );
if ( step.annotation ) {
title += ' - ' + step.annotation;
}
if ( step.step_version ) {
title += ' (Galaxy Version ' + step.step_version + ')';
}
step = Utils.merge( {
index : i,
name : step.name,
title : _.escape( title ),
icon : icon || '',
help : null,
description : step.annotation && ' - ' + step.annotation || step.description,
citations : null,
collapsible : true,
collapsed : i > 0 && !self._isDataStep( step ),
@@ -300,7 +306,6 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
var is_simple_input = ([ 'data_input', 'data_collection_input' ]).indexOf( step.step_type ) != -1;
_.each( step.inputs, function( input ) { input.flavor = 'module'; input.hide_label = is_simple_input; } );
form = new Form( Utils.merge({
title : '<b>' + step.name + '</b>',
onchange : function() { _.each( self.links[ step.index ], function( link ) { self._refreshStep( link ) } ) },
inputs : step.inputs && step.inputs.length > 0 ? step.inputs : [ { type: 'hidden', name: 'No options available.', ignore: null } ]
}, step ) );
client/galaxy/scripts/mvc/tool/tool-form-workflow.js
+3 -2
View File
@@ -38,6 +38,7 @@ define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
var current_state = {
tool_id : options.id,
tool_version : options.version,
type : 'tool',
inputs : $.extend( true, {}, form.data.create() )
}
Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Sending current state.', current_state );
@@ -46,8 +47,8 @@ define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
url : Galaxy.root + 'api/workflows/build_module',
data : current_state,
success : function( data ) {
form.update( data.tool_model );
form.errors( data.tool_model );
form.update( data.config_form );
form.errors( data.config_form );
// This hasn't modified the workflow, just returned
// module information for the tool to update the workflow
// state stored on the client with. User needs to save
client/galaxy/scripts/mvc/workflow/workflow-view.js
+41 -45
View File
@@ -670,54 +670,50 @@ define([
content.datatypes = this.datatypes;
form = new ToolForm.View( content );
} else {
if ( content.inputs && content.inputs.length > 0 ) {
content.inputs.unshift({
type : 'text',
name : '__label',
label : 'Label',
value : node.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;
}
content.inputs.unshift({
type : 'text',
name : '__label',
label : 'Label',
value : node.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' );
}
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',
name : '__annotation',
label : 'Annotation',
value : node.annotation,
area : true,
help : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.'
});
content.onchange = function() {
Utils.request({
type : 'POST',
url : Galaxy.root + 'api/workflows/build_module',
data : {
id : node.id,
type : node.type,
content_id : node.content_id,
inputs : form.data.create()
},
success : function( data ) {
node.update_field_data( data );
}
});
content.inputs.push({
type : 'text',
name : '__annotation',
label : 'Annotation',
value : node.annotation,
area : true,
help : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.'
});
content.onchange = function() {
Utils.request({
type : 'POST',
url : Galaxy.root + 'api/workflows/build_module',
data : {
id : node.id,
type : node.type,
inputs : form.data.create()
},
success : function( data ) {
node.update_field_data( data );
}
});
};
} else {
content.message = 'No inputs available for this module.';
content.message_status = 'info';
}
};
form = new Form( content );
}
$el.append( form.$el );
lib/galaxy/managers/workflows.py
+8 -11
View File
@@ -370,10 +370,6 @@ class WorkflowContentsManager(UsesAnnotations):
step_models = []
for i, step in enumerate( workflow.steps ):
step_model = None
def step_title(step, default_name):
return "%d: %s" % (step.order_index + 1, step.label or default_name)
if step.type == 'tool':
incoming = {}
tool = trans.app.toolbox.get_tool( step.tool_id )
@@ -385,14 +381,15 @@ class WorkflowContentsManager(UsesAnnotations):
'output_name' : pja.output_name,
'action_arguments' : pja.action_arguments
} for pja in step.post_job_actions ]
step_model["name"] = step_title(step, step_model.get("name"))
else:
inputs = step.module.get_runtime_inputs( connections=step.output_connections )
step_model = {
'name' : step_title(step, step.module.name),
'inputs' : [ input.to_dict( trans ) for input in inputs.itervalues() ]
}
step_model[ 'step_type' ] = step.type
step_model[ 'step_label' ] = step.label
step_model[ 'step_name' ] = step.module.get_name()
step_model[ 'step_version' ] = step.module.get_version()
step_model[ 'step_index' ] = step.order_index
step_model[ 'output_connections' ] = [ {
'input_step_index' : step_order_indices.get( oc.input_step_id ),
@@ -452,6 +449,7 @@ class WorkflowContentsManager(UsesAnnotations):
step_dict = {
'id': step.order_index,
'type': module.type,
'label': module.label,
'content_id': module.get_content_id(),
'name': module.get_name(),
'tool_state': module.get_state(),
@@ -463,7 +461,6 @@ class WorkflowContentsManager(UsesAnnotations):
'annotation': annotation_str,
'post_job_actions': {},
'uuid': str(step.uuid) if step.uuid else None,
'label': step.label or None,
'workflow_outputs': []
}
# Connections
@@ -615,7 +612,7 @@ class WorkflowContentsManager(UsesAnnotations):
# Data inputs
input_dicts = []
step_state = module.state.inputs
step_state = module.state.inputs or {}
if "name" in step_state:
name = step_state.get( "name" )
input_dicts.append( { "name": name, "description": annotation_str } )
@@ -711,9 +708,9 @@ class WorkflowContentsManager(UsesAnnotations):
inputs = {}
for step in workflow.input_steps:
step_type = step.type
step_name = step.name
if step_name:
label = step_name
step_label = step.label or step.tool_inputs.get( 'name' )
if step_label:
label = step_label
elif step_type == "data_input":
label = "Input Dataset"
elif step_type == "data_collection_input":
lib/galaxy/model/__init__.py
-9
View File
@@ -34,7 +34,6 @@ from galaxy.util import (directory_hash_id, Params, ready_name_for_url,
from galaxy.util.bunch import Bunch
from galaxy.util.dictifiable import Dictifiable
from galaxy.util.hash_util import new_secure_hash
from galaxy.util.json import safe_loads
from galaxy.util.multi_byte import is_multi_byte
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField,
@@ -3759,14 +3758,6 @@ class WorkflowStep( object ):
content_id = None
return content_id
@property
def name( self ):
state = self.tool_inputs
if state:
state = safe_loads( state )
identifier = state.get( 'name' )
return safe_loads( identifier )
@property
def input_connections_by_name(self):
if self._input_connections_by_name is None:
lib/galaxy/tools/__init__.py
+3 -78
View File
@@ -46,6 +46,7 @@ from galaxy.tools.parameters import (
params_from_strings,
params_to_incoming,
params_to_strings,
populate_state,
visit_input_values
)
from galaxy.tools.parameters import output_collect
@@ -1238,7 +1239,7 @@ class Tool( object, Dictifiable ):
else:
# Update state for all inputs on the current page taking new
# values from `incoming`.
self.populate_state( request_context, self.inputs, expanded_incoming, params, errors )
populate_state( request_context, self.inputs, expanded_incoming, params, errors )
# If the tool provides a `validate_input` hook, call it.
validate_input = self.get_hook( 'validate_input' )
@@ -1834,7 +1835,7 @@ class Tool( object, Dictifiable ):
# create tool state
state_inputs = {}
state_errors = {}
self.populate_state( request_context, self.inputs, params.__dict__, state_inputs, state_errors )
populate_state( request_context, self.inputs, params.__dict__, state_inputs, state_errors )
# create tool model
tool_model = self.to_dict( request_context )
@@ -1877,82 +1878,6 @@ class Tool( object, Dictifiable ):
})
return tool_model
# populates state from incoming parameters
def populate_state( self, request_context, inputs, incoming, state, errors={}, prefix='', context=None ):
context = ExpressionContext( state, context )
for input in inputs.values():
state[ input.name ] = input.get_initial_value( request_context, context )
key = prefix + input.name
group_state = state[ input.name ]
group_prefix = '%s|' % ( key )
if input.type == 'repeat':
rep_index = 0
del group_state[:]
while True:
rep_prefix = '%s_%d' % ( key, rep_index )
if not any( incoming_key.startswith( rep_prefix ) for incoming_key in incoming.keys() ) and rep_index >= input.min:
break
if rep_index < input.max:
new_state = { '__index__' : rep_index }
group_state.append( new_state )
self.populate_state( request_context, input.inputs, incoming, new_state, errors, prefix=rep_prefix + '|', context=context )
rep_index += 1
elif input.type == 'conditional':
if input.value_ref and not input.value_ref_in_group:
test_param_key = prefix + input.test_param.name
else:
test_param_key = group_prefix + input.test_param.name
test_param_value = incoming.get( test_param_key, group_state.get( input.test_param.name ) )
value, error = check_param( request_context, input.test_param, test_param_value, context )
if error:
errors[ test_param_key ] = error
else:
try:
current_case = input.get_current_case( value )
group_state = state[ input.name ] = {}
self.populate_state( request_context, input.cases[ current_case ].inputs, incoming, group_state, errors, prefix=group_prefix, context=context )
group_state[ '__current_case__' ] = current_case
except Exception:
errors[ test_param_key ] = 'The selected case is unavailable/invalid.'
pass
group_state[ input.test_param.name ] = value
elif input.type == 'section':
self.populate_state( request_context, input.inputs, incoming, group_state, errors, prefix=group_prefix, context=context )
elif input.type == 'upload_dataset':
d_type = input.get_datatype( request_context, context=context )
writable_files = d_type.writable_files
while len( group_state ) > len( writable_files ):
del group_state[ -1 ]
while len( writable_files ) > len( group_state ):
new_state = { '__index__' : len( group_state ) }
for upload_item in input.inputs.values():
new_state[ upload_item.name ] = upload_item.get_initial_value( request_context, context )
group_state.append( new_state )
for i, rep_state in enumerate( group_state ):
rep_index = rep_state[ '__index__' ]
rep_prefix = '%s_%d|' % ( key, rep_index )
self.populate_state( request_context, input.inputs, incoming, rep_state, errors, prefix=rep_prefix, context=context )
else:
param_value = self._get_incoming_value( incoming, key, state.get( input.name ) )
value, error = check_param( request_context, input, param_value, context )
if error:
errors[ key ] = error
state[ input.name ] = value
def _get_incoming_value( self, incoming, key, default ):
"""
Fetch value from incoming dict directly or check special nginx upload
created variants of this key.
"""
if '__' + key + '__is_composite' in incoming:
composite_keys = incoming[ '__' + key + '__keys' ].split()
value = dict()
for composite_key in composite_keys:
value[ composite_key ] = incoming[ key + '_' + composite_key ]
return value
else:
return incoming.get( key, default )
def _get_job_remap( self, job):
if job:
if job.state == job.states.ERROR:
lib/galaxy/tools/parameters/__init__.py
+118
View File
@@ -214,3 +214,121 @@ def update_param( prefixed_name, input_values, new_value ):
update_param( match.group( 1 ), input_values[ key ], new_value )
elif prefixed_name == key:
input_values[ key ] = new_value
def populate_state( request_context, inputs, incoming, state, errors={}, prefix='', context=None, check=True ):
"""
Populates nested state dict from incoming parameter values.
>>> from xml.etree.ElementTree import XML
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util.odict import odict
>>> from galaxy.tools.parameters.basic import TextToolParameter, BooleanToolParameter
>>> from galaxy.tools.parameters.grouping import Repeat
>>> trans = Bunch( workflow_building_mode=False )
>>> a = TextToolParameter( None, XML( '<param name="a"/>' ) )
>>> b = Repeat()
>>> b.min = 0
>>> b.max = 1
>>> c = TextToolParameter( None, XML( '<param name="c"/>' ) )
>>> d = Repeat()
>>> d.min = 0
>>> d.max = 1
>>> e = TextToolParameter( None, XML( '<param name="e"/>' ) )
>>> f = Conditional()
>>> g = BooleanToolParameter( None, XML( '<param name="g"/>' ) )
>>> h = TextToolParameter( None, XML( '<param name="h"/>' ) )
>>> i = TextToolParameter( None, XML( '<param name="i"/>' ) )
>>> b.name = 'b'
>>> b.inputs = odict([ ('c', c), ('d', d) ])
>>> d.name = 'd'
>>> d.inputs = odict([ ('e', e), ('f', f) ])
>>> f.test_param = g
>>> f.name = 'f'
>>> f.cases = [ Bunch( value='true', inputs= { 'h': h } ), Bunch( value='false', inputs= { 'i': i } ) ]
>>> inputs = odict([('a',a),('b',b)])
>>> flat = odict([ ('a', 1 ), ( 'b_0|c', 2 ), ( 'b_0|d_0|e', 3 ), ( 'b_0|d_0|f|h', 4 ), ( 'b_0|d_0|f|g', True ) ])
>>> state = odict()
>>> populate_state( trans, inputs, flat, state, check=False )
>>> print state[ 'a' ]
1
>>> print state[ 'b' ][ 0 ][ 'c' ]
2
>>> print state[ 'b' ][ 0 ][ 'd' ][ 0 ][ 'e' ]
3
>>> print state[ 'b' ][ 0 ][ 'd' ][ 0 ][ 'f' ][ 'h' ]
4
"""
context = ExpressionContext( state, context )
for input in inputs.values():
state[ input.name ] = input.get_initial_value( request_context, context )
key = prefix + input.name
group_state = state[ input.name ]
group_prefix = '%s|' % ( key )
if input.type == 'repeat':
rep_index = 0
del group_state[:]
while True:
rep_prefix = '%s_%d' % ( key, rep_index )
if not any( incoming_key.startswith( rep_prefix ) for incoming_key in incoming.keys() ) and rep_index >= input.min:
break
if rep_index < input.max:
new_state = { '__index__' : rep_index }
group_state.append( new_state )
populate_state( request_context, input.inputs, incoming, new_state, errors, prefix=rep_prefix + '|', context=context )
rep_index += 1
elif input.type == 'conditional':
if input.value_ref and not input.value_ref_in_group:
test_param_key = prefix + input.test_param.name
else:
test_param_key = group_prefix + input.test_param.name
test_param_value = incoming.get( test_param_key, group_state.get( input.test_param.name ) )
value, error = check_param( request_context, input.test_param, test_param_value, context ) if check else [ test_param_value, None ]
if error:
errors[ test_param_key ] = error
else:
try:
current_case = input.get_current_case( value )
group_state = state[ input.name ] = {}
populate_state( request_context, input.cases[ current_case ].inputs, incoming, group_state, errors, prefix=group_prefix, context=context )
group_state[ '__current_case__' ] = current_case
except Exception:
errors[ test_param_key ] = 'The selected case is unavailable/invalid.'
pass
group_state[ input.test_param.name ] = value
elif input.type == 'section':
populate_state( request_context, input.inputs, incoming, group_state, errors, prefix=group_prefix, context=context )
elif input.type == 'upload_dataset':
d_type = input.get_datatype( request_context, context=context )
writable_files = d_type.writable_files
while len( group_state ) > len( writable_files ):
del group_state[ -1 ]
while len( writable_files ) > len( group_state ):
new_state = { '__index__' : len( group_state ) }
for upload_item in input.inputs.values():
new_state[ upload_item.name ] = upload_item.get_initial_value( request_context, context )
group_state.append( new_state )
for i, rep_state in enumerate( group_state ):
rep_index = rep_state[ '__index__' ]
rep_prefix = '%s_%d|' % ( key, rep_index )
populate_state( request_context, input.inputs, incoming, rep_state, errors, prefix=rep_prefix, context=context )
else:
param_value = _get_incoming_value( incoming, key, state.get( input.name ) )
value, error = check_param( request_context, input, param_value, context ) if check else [ param_value, None ]
if error:
errors[ key ] = error
state[ input.name ] = value
def _get_incoming_value( incoming, key, default ):
"""
Fetch value from incoming dict directly or check special nginx upload
created variants of this key.
"""
if '__' + key + '__is_composite' in incoming:
composite_keys = incoming[ '__' + key + '__keys' ].split()
value = dict()
for composite_key in composite_keys:
value[ composite_key ] = incoming[ key + '_' + composite_key ]
return value
else:
return incoming.get( key, default )
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+2 -1
View File
@@ -19,6 +19,7 @@ from galaxy import web
from galaxy.exceptions import ObjectNotFound
from galaxy.managers import folders, roles
from galaxy.tools.actions import upload_common
from galaxy.tools.parameters import populate_state
from galaxy.util.streamball import StreamBall
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
@@ -451,7 +452,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
tool_id = 'upload1'
tool = trans.app.toolbox.get_tool( tool_id )
state = tool.new_state( trans )
tool.populate_state( trans, tool.inputs, kwd, state.inputs )
populate_state( trans, tool.inputs, kwd, state.inputs )
tool_params = state.inputs
dataset_upload_inputs = []
for input in tool.inputs.itervalues():
lib/galaxy/webapps/galaxy/api/workflows.py
+15 -40
View File
@@ -18,6 +18,7 @@ from galaxy.managers import (
workflows
)
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.tools.parameters import populate_state
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import (
@@ -358,48 +359,22 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
def build_module( self, trans, payload={} ):
"""
POST /api/workflows/build_module
Builds module details including a tool model for the workflow editor.
Builds module models for the workflow editor.
"""
type = payload.get( 'type' )
tool_id = payload.get( 'tool_id' )
content_id = payload.get( 'content_id' )
inputs = payload.get( 'inputs', {} )
annotation = inputs.get( '__annotation', '' )
label = inputs.get( '__label', '' )
if tool_id:
tool_version = payload.get( 'tool_version' )
tool = self._get_tool( tool_id, tool_version=tool_version, user=trans.user )
module = module_factory.from_dict( trans, {
'type' : 'tool',
'tool_id' : tool.id,
'tool_state' : None
} )
tool_model = module.tool.to_json( trans, inputs, workflow_building_mode=True )
module.recover_state( tool_model[ 'state_inputs' ] )
return {
'tool_model' : tool_model,
'tool_state' : module.get_state(),
'data_inputs' : module.get_data_inputs(),
'data_outputs' : module.get_data_outputs(),
'config_form' : module.get_config_form(),
'annotation' : annotation,
'post_job_actions' : module.get_post_job_actions(inputs)
}
else:
module = module_factory.from_dict( trans, {
'type' : type,
'label' : label,
'content_id' : content_id
} )
module.recover_state( inputs )
return {
'label' : module.label,
'tool_state' : module.get_state(),
'data_inputs' : module.get_data_inputs(),
'data_outputs' : module.get_data_outputs(),
'config_form' : module.get_config_form(),
'annotation' : annotation
}
module = module_factory.from_dict( trans, payload )
module_state = {}
populate_state( trans, module.get_inputs(), inputs, module_state, check=False )
module.recover_state( module_state )
return {
'label' : inputs.get( '__label', '' ),
'annotation' : inputs.get( '__annotation', '' ),
'tool_state' : module.get_state(),
'data_inputs' : module.get_data_inputs(),
'data_outputs' : module.get_data_outputs(),
'config_form' : module.get_config_form(),
'post_job_actions' : module.get_post_job_actions( inputs )
}
#
# -- Helper methods --
lib/galaxy/webapps/galaxy/controllers/library_common.py
+2 -1
View File
@@ -19,6 +19,7 @@ from sqlalchemy.orm import eagerload_all
from galaxy import util, web
from galaxy.security import Action
from galaxy.tools.actions import upload_common
from galaxy.tools.parameters import populate_state
from galaxy.util import inflector, unicodify, FILENAME_VALID_CHARS
from galaxy.util.streamball import StreamBall
from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems
@@ -1044,7 +1045,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
tool_id = 'upload1'
tool = trans.app.toolbox.get_tool( tool_id )
state = tool.new_state( trans )
tool.populate_state( trans, tool.inputs, kwd, state.inputs )
populate_state( trans, tool.inputs, kwd, state.inputs )
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
lib/galaxy/workflow/modules.py
+57 -64
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@@ -81,6 +81,9 @@ class WorkflowModule( object ):
def get_name( self ):
return self.name
def get_version( self ):
return None
def get_content_id( self ):
""" If this component has an identifier external to the step (such
as a tool or another workflow) return the identifier for that content.
@@ -114,7 +117,7 @@ class WorkflowModule( object ):
if inputs:
self.state.decode( state, Bunch( inputs=inputs ), self.trans.app )
else:
self.state.inputs = safe_loads( state )
self.state.inputs = safe_loads( state ) or {}
def get_errors( self ):
""" This returns a step related error message as string or None """
@@ -131,6 +134,9 @@ class WorkflowModule( object ):
def get_data_outputs( self ):
return []
def get_post_job_actions( self, incoming ):
return []
def check_and_update_state( self ):
"""
If the state is not in sync with the current implementation of the
@@ -227,17 +233,18 @@ class SubWorkflowModule( WorkflowModule ):
# - Second pass actually turn RuntimeInputs into inputs if possible.
type = "subworkflow"
name = "Subworkflow"
default_name = "Subworkflow"
@classmethod
def from_dict( Class, trans, d, **kwds ):
module = Class( trans )
if "subworkflow" in d:
module.subworkflow = d["subworkflow"]
module.subworkflow = d[ "subworkflow" ]
elif "content_id" in d:
content_id = d["content_id"]
module.subworkflow = SubWorkflowModule.subworkflow_from_content_id( trans, content_id )
module.label = d.get( "label", None ) or None
from galaxy.managers.workflows import WorkflowsManager
module.subworkflow = WorkflowsManager( trans.app ).get_owned_workflow( trans, d[ "content_id" ] )
else:
raise Exception( "Step associated subworkflow could not be found." )
module.label = d.get( "label" )
return module
@classmethod
@@ -252,7 +259,7 @@ class SubWorkflowModule( WorkflowModule ):
step.subworkflow = self.subworkflow
def get_name( self ):
if hasattr( self, 'subworkflow' ) and hasattr( self.subworkflow, 'name' ):
if hasattr( self.subworkflow, 'name' ):
return self.subworkflow.name
return self.name
@@ -264,43 +271,45 @@ class SubWorkflowModule( WorkflowModule ):
"data_collection_input": "dataset_collection",
}
inputs = []
for step in self.subworkflow.input_steps:
name = step.label
if name is None:
step_module = module_factory.from_workflow_step( self.trans, step )
name = step_module.state.inputs.get( "name" )
if not name:
raise Exception( "Failed to find name for workflow module." )
step_type = step.type
assert step_type in step_to_input_type
input = dict(
input_subworkflow_step_id=step.order_index,
name=name,
label=name,
multiple=False,
extensions="input",
input_type=step_to_input_type[step_type],
)
inputs.append(input)
if hasattr( self.subworkflow, 'input_steps' ):
for step in self.subworkflow.input_steps:
name = step.label
if name is None:
step_module = module_factory.from_workflow_step( self.trans, step )
name = step_module.state.inputs.get( "name" )
if not name:
raise Exception( "Failed to find name for workflow module." )
step_type = step.type
assert step_type in step_to_input_type
input = dict(
input_subworkflow_step_id=step.order_index,
name=name,
label=name,
multiple=False,
extensions="input",
input_type=step_to_input_type[step_type],
)
inputs.append(input)
return inputs
def get_data_outputs( self ):
outputs = []
for workflow_output in self.subworkflow.workflow_outputs:
output_step = workflow_output.workflow_step
label = workflow_output.label
if label is None:
label = "%s:%s" % (output_step.order_index, workflow_output.output_name)
output = dict(
name=label,
label=label,
extensions=['input'], # TODO
)
outputs.append(output)
if hasattr( self.subworkflow, 'workflow_outputs' ):
for workflow_output in self.subworkflow.workflow_outputs:
output_step = workflow_output.workflow_step
label = workflow_output.label
if label is None:
label = "%s:%s" % (output_step.order_index, workflow_output.output_name)
output = dict(
name=label,
label=label,
extensions=['input'], # TODO
)
outputs.append(output)
return outputs
def get_content_id( self ):
return self.trans.security.encode_id(self.subworkflow.id)
return self.trans.security.encode_id( self.subworkflow.id )
def execute( self, trans, progress, invocation, step ):
""" Execute the given workflow step in the given workflow invocation.
@@ -316,7 +325,6 @@ class SubWorkflowModule( WorkflowModule ):
workflow_output_label = workflow_output.label
replacement = subworkflow_progress.get_replacement_workflow_output( workflow_output )
outputs[ workflow_output_label ] = replacement
progress.set_step_outputs( step, outputs )
return None
@@ -325,13 +333,6 @@ class SubWorkflowModule( WorkflowModule ):
state.inputs = dict( )
return state
@classmethod
def subworkflow_from_content_id(clazz, trans, content_id):
from galaxy.managers.workflows import WorkflowsManager
workflow_manager = WorkflowsManager(trans.app)
subworkflow = workflow_manager.get_owned_workflow( trans, content_id )
return subworkflow
class InputModule( WorkflowModule ):
@@ -404,10 +405,10 @@ class InputDataModule( InputModule ):
class InputDataCollectionModule( InputModule ):
default_name = "Input Dataset Collection"
default_collection_type = "list"
type = "data_collection_input"
name = "Input dataset collection"
default_name = "Input Dataset Collection"
default_collection_type = "list"
collection_type = default_collection_type
def get_inputs( self ):
@@ -442,17 +443,15 @@ class InputDataCollectionModule( InputModule ):
class InputParameterModule( WorkflowModule ):
default_name = "input_parameter"
type = "parameter_input"
name = "Input parameter"
default_parameter_type = "text"
default_optional = False
type = "parameter_input"
name = default_name
parameter_type = default_parameter_type
optional = default_optional
def get_inputs( self ):
# TODO: Use an external xml or yaml file to load the parameter definition
name = self.state.inputs.get( "name", self.default_name )
parameter_type = self.state.inputs.get( "parameter_type", self.default_parameter_type )
optional = self.state.inputs.get( "optional", self.default_optional )
input_parameter_type = SelectToolParameter( None, XML(
@@ -465,12 +464,10 @@ class InputParameterModule( WorkflowModule ):
<option value="color">Color</option>
</param>
''' % parameter_type ) )
return odict([( "name", TextToolParameter( None, Element( "param", name="name", label="Name", type="text", value=name ) ) ),
( "parameter_type", input_parameter_type ),
return odict([( "parameter_type", input_parameter_type ),
( "optional", BooleanToolParameter( None, Element( "param", name="optional", label="Optional", type="boolean", value=optional )))])
def get_runtime_inputs( self, **kwds ):
label = self.state.inputs.get( "name", self.default_name )
parameter_type = self.state.inputs.get("parameter_type", self.default_parameter_type)
optional = self.state.inputs.get("optional", self.default_optional)
if parameter_type not in ["text", "boolean", "integer", "float", "color"]:
@@ -481,7 +478,7 @@ class InputParameterModule( WorkflowModule ):
parameter_kwds["value"] = str(0)
# TODO: Use a dict-based description from YAML tool source
element = Element("param", name="input", label=label, type=parameter_type, optional=str(optional), **parameter_kwds )
element = Element("param", name="input", label=self.label, type=parameter_type, optional=str(optional), **parameter_kwds )
input = parameter_class( None, element )
return dict( input=input )
@@ -505,11 +502,6 @@ class PauseModule( WorkflowModule ):
"""
type = "pause"
name = "Pause for dataset review"
default_name = "Pause for Dataset Review"
def get_inputs( self ):
name = self.state.inputs.get( "name", self.default_name )
return dict( name=TextToolParameter( None, Element( "param", name="name", type="text", value=name ) ) )
def get_data_inputs( self ):
input = dict(
@@ -559,6 +551,7 @@ class PauseModule( WorkflowModule ):
class ToolModule( WorkflowModule ):
type = "tool"
name = "Tool"
def __init__( self, trans, tool_id, tool_version=None, exact_tools=False, **kwds ):
super( ToolModule, self ).__init__( trans, content_id=tool_id, **kwds )
@@ -588,8 +581,8 @@ class ToolModule( WorkflowModule ):
message = ""
if tool_id != module.tool_id:
message += "The tool (id '%s') specified in this step is not available. Using the tool with id %s instead." % (tool_id, module.tool_id)
if d.get('tool_version', 'Unspecified') != module.get_tool_version():
message += "%s: using version '%s' instead of version '%s' specified in this workflow." % ( tool_id, module.get_tool_version(), d.get( 'tool_version', 'Unspecified' ) )
if d.get('tool_version', 'Unspecified') != module.get_version():
message += "%s: using version '%s' instead of version '%s' specified in this workflow." % ( tool_id, module.get_version(), d.get( 'tool_version', 'Unspecified' ) )
if message:
log.debug( message )
module.version_changes.append( message )
@@ -629,7 +622,7 @@ class ToolModule( WorkflowModule ):
def save_to_step( self, step ):
super( ToolModule, self ).save_to_step( step )
step.tool_id = self.tool_id
step.tool_version = self.get_tool_version()
step.tool_version = self.get_version()
for k, v in self.post_job_actions.iteritems():
pja = self.__to_pja( k, v, step )
self.trans.sa_session.add( pja )
@@ -642,7 +635,7 @@ class ToolModule( WorkflowModule ):
def get_content_id( self ):
return self.tool_id
def get_tool_version( self ):
def get_version( self ):
return self.tool.version if self.tool else self.tool_version
def get_tooltip( self, static_path='' ):
lib/galaxy/workflow/run_request.py
+2 -16
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@@ -63,10 +63,9 @@ def _normalize_inputs(steps, inputs, inputs_by):
elif inputs_by_el == "step_uuid":
possible_input_keys.append(str( step.uuid ))
elif inputs_by_el == "name":
possible_input_keys.append( step.name )
possible_input_keys.append( step.label or step.tool_inputs.get( 'name' ) )
else:
message = "Workflow cannot be run because unexpected inputs_by value specified."
raise exceptions.MessageException( message )
raise exceptions.MessageException( "Workflow cannot be run because unexpected inputs_by value specified." )
inputs_key = None
for possible_input_key in possible_input_keys:
if possible_input_key in inputs:
@@ -369,13 +368,11 @@ def workflow_run_config_to_request( trans, run_config, workflow ):
def workflow_request_to_run_config( work_request_context, workflow_invocation ):
param_types = model.WorkflowRequestInputParameter.types
history = workflow_invocation.history
replacement_dict = {}
inputs = {}
param_map = {}
copy_inputs_to_history = None
for parameter in workflow_invocation.input_parameters:
parameter_type = parameter.type
@@ -384,25 +381,14 @@ def workflow_request_to_run_config( work_request_context, workflow_invocation ):
elif parameter_type == param_types.META_PARAMETERS:
if parameter.name == "copy_inputs_to_history":
copy_inputs_to_history = (parameter.value == "true")
# for parameter in workflow_invocation.step_parameters:
# step_id = parameter.workflow_step_id
# if step_id not in param_map:
# param_map[ step_id ] = {}
# param_map[ step_id ][ parameter.name ] = parameter.value
for input_association in workflow_invocation.input_datasets:
inputs[ input_association.workflow_step_id ] = input_association.dataset
for input_association in workflow_invocation.input_dataset_collections:
inputs[ input_association.workflow_step_id ] = input_association.dataset_collection
for input_association in workflow_invocation.input_step_parameters:
inputs[ input_association.workflow_step_id ] = input_association.parameter_value
if copy_inputs_to_history is None:
raise exceptions.InconsistentDatabase("Failed to find copy_inputs_to_history parameter loading workflow_invocation from database.")
workflow_run_config = WorkflowRunConfig(
target_history=history,
replacement_dict=replacement_dict,
lib/tool_shed/util/workflow_util.py
+1 -1
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@@ -233,7 +233,7 @@ def get_workflow_data_outputs( step, module, steps ):
found = False
for workflow_step in steps:
for wfsc in workflow_step.input_connections:
if step.name == wfsc.output_step.name:
if step.label == wfsc.output_step.label:
data_outputs_dict[ 'name' ] = wfsc.output_name
found = True
break
static/maps/mvc/tool/tool-form-base.js.map
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static/maps/mvc/workflow/workflow-view.js.map
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static/scripts/bundled/analysis.bundled.js
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static/scripts/mvc/tool/tool-form-base.js
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static/scripts/mvc/tool/tool-form-workflow.js
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static/scripts/mvc/workflow/workflow-view.js
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