Commit 35162ef0 authored by mvdbeek's avatar mvdbeek
Browse files

Iterate over param_dict only once 

This should fix https://github.com/galaxyproject/galaxy/issues/12179.
Ideally we wouldn't have to do this at all, we should be able to hide
this behind a profile flag. For regular tools this is a fallback for
referencing datasets without prefix.
parent a87405cb

lib/galaxy/tools/evaluation.py

+5 −5
Original line number Diff line number Diff line
@@ -272,17 +272,17 @@ class ToolEvaluator: 
        # - Only necessary when self.check_values is False (==external dataset

        #   tool?: can this be abstracted out as part of being a datasouce tool?)

        # For now we try to not wrap unnecessarily, but this should be untangled at some point.

        matches = None

        for name, data in input_datasets.items():

            param_dict_value = param_dict.get(name, None)

            if data and param_dict_value is None:

                # We may have a nested parameter that is not fully prefixed.

                # We try recovering from param_dict, but tool authors should really use fully-qualified

                # variables

                wrappers = find_instance_nested(param_dict,

                                                instances=(DatasetFilenameWrapper, DatasetListWrapper),

                                                match_key=name)

                if len(wrappers) == 1:

                    wrapper = wrappers[0]

                if matches is None:

                    matches = find_instance_nested(param_dict, instances=(DatasetFilenameWrapper, DatasetListWrapper))

                wrapper = matches.get(name)

                if wrapper:

                    param_dict[name] = wrapper

                    continue

            if not isinstance(param_dict_value, (DatasetFilenameWrapper, DatasetListWrapper)):

lib/galaxy/util/__init__.py

+7 −6
Original line number Diff line number Diff line
@@ -621,20 +621,21 @@ def sanitize_for_filename(text, default=None): 
    return out





def find_instance_nested(item, instances, match_key=None):

def find_instance_nested(item, instances):

    """

    Recursively find instances from lists, dicts, tuples.



    `instances` should be a tuple of valid instances

    If match_key is given the key must match for an instance to be added to the list of found instances.

    `instances` should be a tuple of valid instances.

    Returns a dictionary, where keys are the deepest key at which an instance has been found,

    and the value is the matched instance.

    """



    matches = []

    matches = {}



    def visit(path, key, value):

        if isinstance(value, instances):

            if match_key is None or match_key == key:

                matches.append(value)

            if key not in matches:

                matches[key] = value

        return key, value



    def enter(path, key, value):