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Add parameter expansion caller and test cases as preparation for workflow api extension

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guerler
2016-06-07 16:58:46 -04:00
parent e2f2193355
commit ed919805c8
1 changed files with 58 additions and 1 deletions
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lib/galaxy/tools/parameters/meta.py
+58 -1
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@@ -2,11 +2,68 @@ from galaxy.util import permutations
from galaxy import model
from galaxy import util
from galaxy import exceptions
import itertools
import copy
import logging
log = logging.getLogger( __name__ )
def expand_workflow_inputs( inputs ):
"""
Expands incoming encoded multiple payloads, into the set of all individual payload combinations
>>> params, param_keys = expand_workflow_inputs( {'1': {'input': {'batch': True, 'product': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}} )
>>> print sorted( [ "%s" % ( p[ '1' ][ 'input' ][ 'hid' ] ) for p in params ] )
['1', '2']
>>> params, param_keys = expand_workflow_inputs( {'1': {'input': {'batch': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}} )
>>> print sorted( [ "%s" % ( p[ '1' ][ 'input' ][ 'hid' ] ) for p in params ] )
['1', '2']
>>> params, param_keys = expand_workflow_inputs( {'1': {'input': {'batch': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}, '2': {'input': {'batch': True, 'values': [{'hid': '3'}, {'hid': '4'}] }}} )
>>> print sorted( [ "%s%s" % ( p[ '1' ][ 'input' ][ 'hid' ], p[ '2' ][ 'input' ][ 'hid' ] ) for p in params ] )
['13', '24']
>>> params, param_keys = expand_workflow_inputs( {'1': {'input': {'batch': True, 'product': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}, '2': {'input': {'batch': True, 'values': [{'hid': '3'}, {'hid': '4'}, {'hid': '5'}] }}} )
>>> print sorted( [ "%s%s" % ( p[ '1' ][ 'input' ][ 'hid' ], p[ '2' ][ 'input' ][ 'hid' ] ) for p in params ] )
['13', '14', '15', '23', '24', '25']
>>> params, param_keys = expand_workflow_inputs( {'1': {'input': {'batch': True, 'product': True, 'values': [{'hid': '1'}, {'hid': '2'}] }}, '2': {'input': {'batch': True, 'product': True, 'values': [{'hid': '3'}, {'hid': '4'}, {'hid': '5'}] }}, '3': {'input': {'batch': True, 'product': True, 'values': [{'hid': '6'}, {'hid': '7'}, {'hid': '8'}] }}} )
>>> print sorted( [ "%s%s%s" % ( p[ '1' ][ 'input' ][ 'hid' ], p[ '2' ][ 'input' ][ 'hid' ], p[ '3' ][ 'input' ][ 'hid' ] ) for p in params ] )
['136', '137', '138', '146', '147', '148', '156', '157', '158', '236', '237', '238', '246', '247', '248', '256', '257', '258']
"""
linked_n = None
linked = []
product = []
linked_keys = []
product_keys = []
for step_id, step in inputs.items():
for key, value in step.items():
if isinstance( value, dict ) and 'batch' in value and value[ 'batch' ] is True and 'values' in value and isinstance( value[ 'values' ], list ):
nval = len( value[ 'values' ] )
if 'product' in value and value[ 'product' ] is True:
product.append( value[ 'values' ] )
product_keys.append( ( step_id, key ) )
else:
if linked_n is None:
linked_n = nval
elif linked_n != nval or nval is 0:
raise exceptions.RequestParameterInvalidException( 'Failed to match linked batch selections. Please select equal number of data files.' )
linked.append( value[ 'values' ] )
linked_keys.append( ( step_id, key ) )
params = []
params_keys = []
linked = linked or [ [ None ] ]
product = product or [ [ None ] ]
linked_keys = linked_keys or [ ( None, None ) ]
product_keys = product_keys or [ ( None, None ) ]
for linked_values, product_values in itertools.product( *[ zip( *linked ), itertools.product( *product ) ] ):
new_params = copy.deepcopy( inputs )
new_keys = []
for ( step_id, key ), value in zip( linked_keys, linked_values ) + zip( product_keys, product_values ):
if step_id is not None:
new_params[ step_id ][ key ] = value
new_keys.append( value[ 'hid' ] )
params_keys.append( new_keys )
params.append( new_params )
return params, params_keys
def expand_meta_parameters( trans, tool, incoming ):
"""
Take in a dictionary of raw incoming parameters and expand to a list