Clean up dataset passing

lib/galaxy/tools/parameters/basic.py

@@ -8,6 +8,7 @@
 import os
 import os.path
 import re
+import typing
 import urllib.parse
 from collections.abc import MutableMapping
 from typing import (
@@ -1101,6 +1102,9 @@ def to_json(self, value, app, use_security):
             return history_item_to_json(value, app, use_security=use_security)
         return value
 
+    def to_python(self, value, app):
+        return history_item_dict_to_python(value, app, self.name) or super().to_python(value, app)
+
     def get_initial_value(self, trans, other_values):
         try:
             options = list(self.get_options(trans, other_values))
@@ -2011,7 +2015,9 @@ def do_validate(v):
                 raise ValueError("At most %d datasets are required for %s" % (self.max, self.name))
 
 
-def src_id_to_item(sa_session: "Session", value: MutableMapping[str, Any], security: "IdEncodingHelper") -> Union[
+def src_id_to_item(
+    sa_session: "Session", value: typing.MutableMapping[str, Any], security: "IdEncodingHelper"
+) -> Union[
     DatasetCollectionElement,
     HistoryDatasetAssociation,
     HistoryDatasetCollectionAssociation,

lib/galaxy/tools/wrappers.py

@@ -3,7 +3,6 @@
 import os
 import shlex
 import tempfile
-from collections.abc import MutableMapping
 from functools import total_ordering
 from typing import (
     Any,
@@ -31,10 +30,7 @@
 from galaxy.model.metadata import FileParameter
 from galaxy.model.none_like import NoneDataset
 from galaxy.security.object_wrapper import wrap_with_safe_string
-from galaxy.tools.parameters.basic import (
-    BooleanToolParameter,
-    history_item_dict_to_python,
-)
+from galaxy.tools.parameters.basic import BooleanToolParameter
 from galaxy.tools.parameters.wrapped_json import (
     data_collection_input_to_staging_path_and_source_path,
     data_input_to_staging_path_and_source_path,
@@ -218,26 +214,17 @@ def __init__(
             self._input = input
             self._value = value
             self._other_values = other_values
-            self._fields: Dict[str, str] = {}
+            self._fields: Dict[str, List[str]] = {}
             self._compute_environment = compute_environment
 
         def __getattr__(self, name: str) -> Any:
             if name not in self._fields:
-                if isinstance(self._value, MutableMapping):
-                    dataset = history_item_dict_to_python(
-                        self._value, app=self._compute_environment.job_io.user_context.trans.app, name=self._input.name
-                    )
-                    self._fields[name] = [self._input.options.get_option_from_dataset(dataset)[name]]
+                if isinstance(self._value, DatasetInstance):
+                    self._fields[name] = [self._input.options.get_option_from_dataset(self._value)[name]]
                 else:
                     self._fields[name] = self._input.options.get_field_by_name_for_value(
-                        # TODO: Replace trans here ...
-                        name,
-                        self._value,
-                        self._compute_environment.job_io.user_context.trans,
-                        self._other_values,
+                        name, self._value, None, self._other_values
                     )
-                # if name == "path":
-                #    dataset = self._input.options.get_field_by_name_for_value("dataset" ... ) ?
             values = map(str, self._fields[name])
             if name in PATH_ATTRIBUTES and self._compute_environment:
                 # If we infer this is a path, rewrite it if needed.

test/unit/app/tools/test_select_parameters.py

@@ -103,5 +103,5 @@ def __init__(self):
         )
         self.missing_index_file = None
 
-    def get_fields(self, user, history):
+    def get_fields(self):
         return [["testname1", "testpath1"], ["testname2", "testpath2"]]