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[18.01] More tool state performance fixes.

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Fix performance problems that can be encountered when matching collection inputs. It would use the old style matching to find an initial value to plug into the tool state - if there were no collections that matched or there were some big collections toward the top of the history that did not match this could completely undo performance fixes in 5997.

More Pythonic input type conditional logic.
This commit is contained in:
John Chilton
2018-05-02 15:14:42 -04:00
parent b35340c77f
commit 624e9028cc
2 changed files with 18 additions and 15 deletions
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lib/galaxy/tools/__init__.py
+1 -1
View File
@@ -1822,6 +1822,7 @@ class Tool(object, Dictifiable):
if self.input_translator:
self.input_translator.translate(params)
set_dataset_matcher_factory(request_context, self)
# create tool state
state_inputs = {}
state_errors = {}
@@ -1830,7 +1831,6 @@ class Tool(object, Dictifiable):
# create tool model
tool_model = self.to_dict(request_context)
tool_model['inputs'] = []
set_dataset_matcher_factory(request_context, self, state_inputs)
self.populate_model(request_context, self.inputs, state_inputs, tool_model['inputs'])
unset_dataset_matcher_factory(request_context)
lib/galaxy/tools/parameters/dataset_matcher.py
+17 -14
View File
@@ -5,8 +5,8 @@ import galaxy.model
log = getLogger(__name__)
def set_dataset_matcher_factory(trans, tool, param_values):
trans.dataset_matcher_factory = DatasetMatcherFactory(trans, tool, param_values)
def set_dataset_matcher_factory(trans, tool):
trans.dataset_matcher_factory = DatasetMatcherFactory(trans, tool)
def unset_dataset_matcher_factory(trans):
@@ -21,7 +21,7 @@ def get_dataset_matcher_factory(trans):
class DatasetMatcherFactory(object):
""""""
def __init__(self, trans, tool=None, param_values=None):
def __init__(self, trans, tool=None):
self._trans = trans
self._tool = tool
self._data_inputs = []
@@ -32,8 +32,9 @@ class DatasetMatcherFactory(object):
valid_input_states = galaxy.model.Dataset.valid_input_states
self.valid_input_states = valid_input_states
can_process_summary = False
if tool is not None and param_values is not None:
self._collect_data_inputs(tool, param_values)
if tool is not None:
for input in tool.inputs.values():
self._collect_data_inputs(input)
require_public = self._tool and self._tool.tool_type == 'data_destination'
if not require_public and self._data_inputs:
@@ -62,15 +63,17 @@ class DatasetMatcherFactory(object):
return formats[format]
def _collect_data_inputs(self, tool, param_values):
def visitor(input, value, prefix, parent=None, **kwargs):
type_name = type(input).__name__
if "DataToolParameter" in type_name:
self._data_inputs.append(input)
elif "DataCollectionToolParameter" in type_name:
self._data_inputs.append(input)
tool.visit_inputs(param_values, visitor)
def _collect_data_inputs(self, input):
type_name = input.type
if type_name == "repeat" or type_name == "upload_dataset" or type_name == "section":
for child_input in input.inputs.values():
self._collect_data_inputs(child_input)
elif type_name == "conditional":
for case in input.cases:
for child_input in case.inputs.values():
self._collect_data_inputs(child_input)
elif type_name == "data" or type_name == "data_collection":
self._data_inputs.append(input)
def dataset_matcher(self, param, other_values):
return DatasetMatcher(self, self._trans, param, other_values)