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Merge pull request #5449 from jmchilton/collection_mapping_fixes

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[18.01] Collection mapping fixes for regression in 18.01.
This commit is contained in:
Dannon Baker
2018-02-04 11:52:33 -05:00
committed by GitHub
parent b2e8d891b7 51e030f4f3
commit 207f5faba0
3 changed files with 74 additions and 20 deletions
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lib/galaxy/dataset_collections/structure.py
+25 -12
View File
@@ -23,11 +23,8 @@ class Leaf(object):
def clone(self):
return self
def multiply(self, other_structure, uninitialized=False):
if not uninitialized:
return other_structure.clone()
else:
return UnitializedTree(other_structure.collection_type_description)
def multiply(self, other_structure):
return other_structure.clone()
def sliced_collection_type(self, collection):
return input
@@ -59,7 +56,7 @@ class UnitializedTree(BaseTree):
def __len__(self):
raise Exception("Unknown length")
def multiply(self, other_structure, uninitialized=False):
def multiply(self, other_structure):
if other_structure.is_leaf:
return self.clone()
@@ -154,14 +151,14 @@ class Tree(BaseTree):
element_identifiers=element_identifiers,
)
def multiply(self, other_structure, uninitialized=False):
def multiply(self, other_structure):
if other_structure.is_leaf:
return self.clone()
new_collection_type = self.collection_type_description.multiply(other_structure.collection_type_description)
new_children = []
for (identifier, structure) in self.children:
new_children.append((identifier, structure.multiply(other_structure, uninitialized=uninitialized)))
new_children.append((identifier, structure.multiply(other_structure)))
return Tree(new_children, new_collection_type)
@@ -173,19 +170,35 @@ class Tree(BaseTree):
return "Tree[collection_type=%s,children=%s]" % (self.collection_type_description, ",".join(map(lambda identifier_and_element: "%s=%s" % (identifier_and_element[0], identifier_and_element[1]), self.children)))
def tool_output_to_structure(get_sliced_input_collection_type, tool_output, collections_manager):
def tool_output_to_structure(get_sliced_input_collection_structure, tool_output, collections_manager):
if not tool_output.collection:
tree = leaf
else:
collection_type_descriptions = collections_manager.collection_type_descriptions
# Okay this is ToolCollectionOutputStructure not a Structure - different
# concepts of structure.
structured_like = tool_output.structure.structured_like
collection_type = tool_output.structure.collection_type
if structured_like:
collection_type = get_sliced_input_collection_type(structured_like)
tree = get_sliced_input_collection_structure(structured_like)
if collection_type and tree.collection_type_description.collection_type != collection_type:
# See tool paired_collection_map_over_structured_like - type should
# override structured_like if they disagree.
tree = UnitializedTree(collection_type_descriptions.for_collection_type(collection_type))
else:
collection_type = tool_output.structure.collection_type
tree = UnitializedTree(collection_type)
# Can't pre-compute the structure in this case, see if we can find a collection type.
if collection_type is None and tool_output.structure.collection_type_source:
collection_type = get_sliced_input_collection_structure(tool_output.structure.collection_type_source).collection_type_description.collection_type
if not collection_type:
raise Exception("Failed to determine collection type for mapping over output %s" % tool_output.name)
tree = UnitializedTree(collection_type_descriptions.for_collection_type(collection_type))
if not tree.children_known and tree.collection_type_description.collection_type == "paired":
# TODO: We don't need to return unitializedtree for pairs I think, we should build
# a paired tree for the known structure here.
pass
return tree
lib/galaxy/tools/execute.py
+11 -8
View File
@@ -12,7 +12,7 @@ import six
from six.moves.queue import Queue
from galaxy import model
from galaxy.dataset_collections.structure import tool_output_to_structure
from galaxy.dataset_collections.structure import get_structure, tool_output_to_structure
from galaxy.tools.actions import filter_output, on_text_for_names, ToolExecutionCache
from galaxy.tools.parser import ToolOutputCollectionPart
from galaxy.util import ExecutionTimer
@@ -210,13 +210,14 @@ class ExecutionTracker(object):
return output_collection_name
def sliced_input_collection_type(self, input_name):
def sliced_input_collection_structure(self, input_name):
input_collection = self.example_params[input_name]
collection_type_description = self.trans.app.dataset_collections_service.collection_type_descriptions.for_collection_type(input_collection.collection.collection_type)
subcollection_mapping_type = None
if self.is_implicit_input(input_name):
subcollection_mapping_type = self.collection_info.subcollection_mapping_type(input_name)
return subcollection_mapping_type
# return self.collection_info.structure.sliced_input_collection_type(self.implicit_inputs[input_name])
else:
return self.mapping_params.param_template[input_name].collection.collection_type
return get_structure(input_collection, collection_type_description, leaf_subcollection_type=subcollection_mapping_type)
def _structure_for_output(self, trans, tool_output):
structure = self.collection_info.structure
@@ -240,12 +241,14 @@ class ExecutionTracker(object):
def _mapped_output_structure(self, trans, tool_output):
collections_manager = trans.app.dataset_collections_service
output_structure = tool_output_to_structure(self.sliced_input_collection_type, tool_output, collections_manager)
output_structure = tool_output_to_structure(self.sliced_input_collection_structure, tool_output, collections_manager)
# self.collection_info.structure - the mapping structure with default_identifier_source
# used to determine the identifiers to use.
mapping_structure = self._structure_for_output(trans, tool_output)
# Output structure may not be known, but input structure must be,
# otherwise this step of the workflow shouldn't have been scheduled
# or the tool should not have been executable on this input.
mapped_output_structure = mapping_structure.multiply(output_structure, uninitialized=True)
mapped_output_structure = mapping_structure.multiply(output_structure)
return mapped_output_structure
def ensure_implicit_collections_populated(self, history, params):