Record and list reference bundle inputs in job

galaxyproject · Feb 9, 2024 · de6d264 · de6d264
1 parent d53a14e
commit de6d264
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Showing 4 changed files with 18 additions and 14 deletions.
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
@@ -901,23 +901,24 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
 
         for input in input_params.values():
             if input.name in param_values:
+                input_value = param_values[input.name]
                 if input.type == "repeat":
-                    for i in range(len(param_values[input.name])):
-                        rval.extend(inputs_recursive(input.inputs, param_values[input.name][i], depth=depth + 1))
+                    for i in range(len(input_value)):
+                        rval.extend(inputs_recursive(input.inputs, input_value[i], depth=depth + 1))
                 elif input.type == "section":
                     # Get the value of the current Section parameter
                     rval.append(dict(text=input.name, depth=depth))
                     rval.extend(
                         inputs_recursive(
                             input.inputs,
-                            param_values[input.name],
+                            input_value,
                             depth=depth + 1,
                             upgrade_messages=upgrade_messages.get(input.name),
                         )
                     )
                 elif input.type == "conditional":
                     try:
-                        current_case = param_values[input.name]["__current_case__"]
+                        current_case = input_value["__current_case__"]
                         is_valid = True
                     except Exception:
                         current_case = None
@@ -929,7 +930,7 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
                         rval.extend(
                             inputs_recursive(
                                 input.cases[current_case].inputs,
-                                param_values[input.name],
+                                input_value,
                                 depth=depth + 1,
                                 upgrade_messages=upgrade_messages.get(input.name),
                             )
@@ -948,12 +949,16 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
                         dict(
                             text=input.group_title(param_values),
                             depth=depth,
-                            value=f"{len(param_values[input.name])} uploaded datasets",
+                            value=f"{len(input_value)} uploaded datasets",
                         )
                     )
-                elif input.type == "data" or input.type == "data_collection":
+                elif (
+                    input.type == "data"
+                    or input.type == "data_collection"
+                    or isinstance(input_value, model.HistoryDatasetAssociation)
+                ):
                     value = []
-                    for element in listify(param_values[input.name]):
+                    for element in listify(input_value):
                         element_id = element.id
                         if isinstance(element, model.HistoryDatasetAssociation):
                             hda = element
@@ -977,7 +982,7 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
                         dict(
                             text=label,
                             depth=depth,
-                            value=input.value_to_display_text(param_values[input.name]),
+                            value=input.value_to_display_text(input_value),
                             notes=upgrade_messages.get(input.name, ""),
                         )
                     )

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
@@ -32,6 +32,7 @@
     DataCollectionToolParameter,
     DataToolParameter,
     RuntimeValue,
+    SelectToolParameter,
 )
 from galaxy.tools.parameters.wrapped import (
     LegacyUnprefixedDict,
@@ -283,6 +284,8 @@ def process_dataset(data, formats=None):
                         value.child_collection = new_collection
                     else:
                         value.collection = new_collection
+            elif isinstance(input, SelectToolParameter) and isinstance(value, HistoryDatasetAssociation):
+                input_datasets[prefixed_name] = value
 
         tool.visit_inputs(param_values, visitor)
         return input_datasets, all_permissions

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
@@ -406,7 +406,7 @@ def __populate_input_dataset_wrappers(self, param_dict, input_datasets):
                 if wrapper:
                     param_dict[name] = wrapper
                     continue
-            if not isinstance(param_dict_value, (DatasetFilenameWrapper, DatasetListWrapper)):
+            if not isinstance(param_dict_value, ToolParameterValueWrapper):
                 wrapper_kwds = dict(
                     datatypes_registry=self.app.datatypes_registry,
                     tool=self.tool,

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
@@ -1028,10 +1028,6 @@ def from_json(self, value, trans, other_values=None, require_legal_value=True):
             raise ParameterValueError(
                 "requires a value, but no legal values defined", self.name, is_dynamic=self.is_dynamic
             )
-        # TODO: dataset security check ??
-        if dataset := history_item_dict_to_python(value, app=trans.app, name=self.name):
-            if dataset in legal_values:
-                return dataset
         if isinstance(value, list):
             if not self.multiple:
                 raise ParameterValueError(