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Merge pull request #2029 from mvdbeek/element_identifier_in_repeat

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Better element_identifier handling in repeat sections
This commit is contained in:
John Chilton
2016-04-01 09:29:57 -04:00
parent ff48ad9b54 78c839cccd
commit 569b87dc00
1 changed files with 8 additions and 5 deletions
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lib/galaxy/tools/evaluation.py
+8 -5
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@@ -131,7 +131,7 @@ class ToolEvaluator( object ):
param_dict.update( incoming )
input_dataset_paths = dataset_path_rewrites( input_paths )
self.__populate_wrappers(param_dict, input_dataset_paths, job_working_directory)
self.__populate_wrappers(param_dict, input_datasets, input_dataset_paths, job_working_directory)
self.__populate_input_dataset_wrappers(param_dict, input_datasets, input_dataset_paths)
self.__populate_output_dataset_wrappers(param_dict, output_datasets, output_paths, job_working_directory)
self.__populate_output_collection_wrappers(param_dict, output_collections, output_paths, job_working_directory)
@@ -167,7 +167,7 @@ class ToolEvaluator( object ):
do_walk( inputs, input_values )
def __populate_wrappers(self, param_dict, input_dataset_paths, job_working_directory):
def __populate_wrappers(self, param_dict, input_datasets, input_dataset_paths, job_working_directory):
def wrap_input( input_values, input ):
if isinstance( input, DataToolParameter ) and input.multiple:
@@ -219,14 +219,16 @@ class ToolEvaluator( object ):
tool=self,
name=input.name
)
identifier_key = "%s|__identifier__" % input.name
if identifier_key in param_dict:
wrapper_kwds["identifier"] = param_dict[identifier_key]
if dataset:
# A None dataset does not have a filename
real_path = dataset.file_name
if real_path in input_dataset_paths:
wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ]
identifier_key = param_dict[ "identifier_key" ].get( dataset, None )
if identifier_key:
element_identifier = param_dict.get(identifier_key, None)
if element_identifier:
wrapper_kwds[ "identifier" ] = element_identifier
input_values[ input.name ] = \
DatasetFilenameWrapper( dataset, **wrapper_kwds )
elif isinstance( input, DataCollectionToolParameter ):
@@ -254,6 +256,7 @@ class ToolEvaluator( object ):
# tools where the inputs don't even get passed through. These
# tools (e.g. UCSC) should really be handled in a special way.
if self.tool.check_values:
param_dict[ "identifier_key" ] = dict((v, "%s|__identifier__" % k) for k, v in input_datasets.iteritems()) # allows lookup of identifier through HDA.
self.__walk_inputs( self.tool.inputs, param_dict, wrap_input )
def __populate_input_dataset_wrappers(self, param_dict, input_datasets, input_dataset_paths):