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Merge pull request #6046 from jmchilton/tool_state_part_2

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[18.01] More tool state performance fixes.
This commit is contained in:
Nicola Soranzo
2018-05-04 11:11:47 +01:00
committed by GitHub
parent b35340c77f 624e9028cc
commit 545b7a4fe2
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)