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Merge pull request #3864 from jmchilton/fix_identifiers_in_conditionals

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[17.01] Fix certain aspects of collection reductions in conditionals/repeats.
This commit is contained in:
Martin Cech
2017-04-03 14:17:20 -04:00
committed by GitHub
parent 268aac2952 5b46c431b4
commit 3c080cae96
5 changed files with 138 additions and 10 deletions
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lib/galaxy/tools/actions/__init__.py
+24 -10
View File
@@ -148,14 +148,14 @@ class DefaultToolAction( object ):
input_dataset_collections = dict()
def visitor( input, value, prefix, parent=None, **kwargs ):
def visitor( input, value, prefix, parent=None, prefixed_name=None, **kwargs ):
if isinstance( input, DataToolParameter ):
values = value
if not isinstance( values, list ):
values = [ value ]
for i, value in enumerate(values):
if isinstance( value, model.HistoryDatasetCollectionAssociation ):
append_to_key( input_dataset_collections, prefix + input.name, ( value, True ) )
append_to_key( input_dataset_collections, prefixed_name, ( value, True ) )
target_dict = parent
if not target_dict:
target_dict = param_values
@@ -541,19 +541,33 @@ class DefaultToolAction( object ):
# FIXME: Don't need all of incoming here, just the defined parameters
# from the tool. We need to deal with tools that pass all post
# parameters to the command as a special case.
reductions = {}
for name, dataset_collection_info_pairs in inp_dataset_collections.items():
first_reduction = True
for ( dataset_collection, reduced ) in dataset_collection_info_pairs:
# TODO: update incoming for list...
if reduced and first_reduction:
first_reduction = False
incoming[ name ] = []
if reduced:
incoming[ name ].append( { 'id': dataset_collection.id, 'src': 'hdca' } )
# Should verify security? We check security of individual
# datasets below?
if name not in reductions:
reductions[name] = []
reductions[name].append(dataset_collection)
# TODO: verify can have multiple with same name, don't want to loose tracability
job.add_input_dataset_collection( name, dataset_collection )
# If this an input collection is a reduction, we expanded it for dataset security, type
# checking, and such, but the persisted input must be the original collection
# so we can recover things like element identifier during tool command evaluation.
def restore_reduction_visitor( input, value, prefix, parent=None, prefixed_name=None, **kwargs ):
if prefixed_name in reductions and isinstance( input, DataToolParameter ):
target_dict = parent
if not target_dict:
target_dict = incoming
target_dict[ input.name ] = []
for reduced_collection in reductions[prefixed_name]:
target_dict[ input.name ].append( { 'id': reduced_collection.id, 'src': 'hdca' } )
if reductions:
tool.visit_inputs( incoming, restore_reduction_visitor )
for name, value in tool.params_to_strings( incoming, trans.app ).items():
job.add_parameter( name, value )
self._check_input_data_access( trans, job, inp_data, current_user_roles )
test/api/test_tools.py
+60
View File
@@ -788,6 +788,66 @@ class ToolsTestCase( api.ApiTestCase ):
output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
self.assertEquals( output1_content.strip(), "forward\nreverse" )
@skip_without_tool( "identifier_multiple_in_conditional" )
def test_identifier_multiple_reduce_in_conditional( self ):
history_id = self.dataset_populator.new_history()
hdca_id = self.__build_pair( history_id, [ "123", "456" ] )
inputs = {
"outer_cond|inner_cond|input1": { 'src': 'hdca', 'id': hdca_id },
}
create_response = self._run( "identifier_multiple_in_conditional", history_id, inputs )
self._assert_status_code_is( create_response, 200 )
create = create_response.json()
outputs = create[ 'outputs' ]
jobs = create[ 'jobs' ]
implicit_collections = create[ 'implicit_collections' ]
self.assertEquals( len( jobs ), 1 )
self.assertEquals( len( outputs ), 1 )
self.assertEquals( len( implicit_collections ), 0 )
output1 = outputs[ 0 ]
output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
self.assertEquals( output1_content.strip(), "forward\nreverse" )
@skip_without_tool( "identifier_multiple_in_repeat" )
def test_identifier_multiple_reduce_in_repeat( self ):
history_id = self.dataset_populator.new_history()
hdca_id = self.__build_pair( history_id, [ "123", "456" ] )
inputs = {
"the_repeat_0|the_data|input1": { 'src': 'hdca', 'id': hdca_id },
}
create_response = self._run( "identifier_multiple_in_repeat", history_id, inputs )
self._assert_status_code_is( create_response, 200 )
create = create_response.json()
outputs = create[ 'outputs' ]
jobs = create[ 'jobs' ]
implicit_collections = create[ 'implicit_collections' ]
self.assertEquals( len( jobs ), 1 )
self.assertEquals( len( outputs ), 1 )
self.assertEquals( len( implicit_collections ), 0 )
output1 = outputs[ 0 ]
output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
self.assertEquals( output1_content.strip(), "forward\nreverse" )
@skip_without_tool( "identifier_multiple_in_conditional" )
def test_identifier_multiple_in_conditional( self ):
history_id = self.dataset_populator.new_history()
new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123', name="Normal HDA1" )
inputs = {
"outer_cond|inner_cond|input1": { 'src': 'hda', 'id': new_dataset1["id"] },
}
create_response = self._run( "identifier_multiple_in_conditional", history_id, inputs )
self._assert_status_code_is( create_response, 200 )
create = create_response.json()
outputs = create[ 'outputs' ]
jobs = create[ 'jobs' ]
implicit_collections = create[ 'implicit_collections' ]
self.assertEquals( len( jobs ), 1 )
self.assertEquals( len( outputs ), 1 )
self.assertEquals( len( implicit_collections ), 0 )
output1 = outputs[ 0 ]
output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
self.assertEquals( output1_content.strip(), "Normal HDA1" )
@skip_without_tool( "identifier_multiple" )
def test_identifier_with_multiple_normal_datasets( self ):
history_id = self.dataset_populator.new_history()
test/functional/tools/identifier_multiple_in_conditional.xml
+25
View File
@@ -0,0 +1,25 @@
<tool id="identifier_multiple_in_conditional" name="identifier_multiple_in_conditional">
<command><![CDATA[
#for $input in $outer_cond.inner_cond.input1#
echo '$input.element_identifier' >> 'output1';
#end for#
]]></command>
<inputs>
<conditional name="outer_cond">
<param name="cond_param_outer" type="boolean" checked="true" />
<when value="true">
<conditional name="inner_cond">
<param name="cond_param_inner" type="boolean" checked="true" />
<when value="true">
<param type="data" name="input1" label="True Input" multiple="true" />
</when>
</conditional>
</when>
</conditional>
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
</tool>
test/functional/tools/identifier_multiple_in_repeat.xml
+27
View File
@@ -0,0 +1,27 @@
<tool id="identifier_multiple_in_repeat" name="identifier_multiple_in_repeat">
<command><![CDATA[
#for $repeat_instance in $the_repeat#
#for $input in $repeat_instance.the_data.input1#
echo '$input.element_identifier' >> 'output1';
#end for#
#end for#
]]></command>
<inputs>
<repeat name="the_repeat" title="Repeat Inputs">
<conditional name="the_data">
<param name="cond_param" type="boolean" />
<when value="true">
<param type="data" name="input1" label="True Input" multiple="true" />
</when>
<when value="false">
<param type="data" name="input1" label="False Input" multiple="true" />
</when>
</conditional>
</repeat>
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
</tool>
test/functional/tools/samples_tool_conf.xml
+2
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@@ -77,6 +77,8 @@
<tool file="explicit_conversion.xml" />
<tool file="identifier_single.xml" />
<tool file="identifier_multiple.xml" />
<tool file="identifier_multiple_in_conditional.xml" />
<tool file="identifier_multiple_in_repeat.xml" />
<tool file="identifier_collection.xml" />
<tool file="tool_directory.xml" />
<tool file="output_action_change_format.xml" />