typing fixes for from_json in basic.py

lib/galaxy/tools/parameters/basic.py

@@ -464,7 +464,7 @@ def __init__(self, tool, input_source):
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
 
-    def from_json(self, value, trans, other_values=None):
+    def from_json(self, value, trans=None, other_values=None):
         other_values = other_values or {}
         try:
             return int(value)
@@ -536,7 +536,7 @@ def __init__(self, tool, input_source):
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
 
-    def from_json(self, value, trans, other_values=None):
+    def from_json(self, value, trans=None, other_values=None):
         other_values = other_values or {}
         try:
             return float(value)
@@ -992,7 +992,10 @@ def get_legal_names(self, trans, other_values):
         """
         return {n: v for n, v, _ in self.get_options(trans, other_values)}
 
-    def from_json(self, value, trans, other_values=None, require_legal_value=True):
+    def from_json(self, value, trans=None, other_values=None):
+        return self._select_from_json(value, trans, other_values=other_values, require_legal_value=True)
+
+    def _select_from_json(self, value, trans, other_values=None, require_legal_value=True):
         other_values = other_values or {}
         try:
             legal_values = self.get_legal_values(trans, other_values, value)
@@ -1268,7 +1271,7 @@ def __init__(self, tool, input_source):
             self.default_value = input_source.get("value", None)
         self.is_dynamic = True
 
-    def from_json(self, value, trans, other_values=None):
+    def from_json(self, value, trans=None, other_values=None):
         other_values = other_values or {}
         if self.multiple:
             tag_list = []
@@ -1290,7 +1293,7 @@ def from_json(self, value, trans, other_values=None):
                 value = None
         # We skip requiring legal values -- this is similar to optional, but allows only subset of datasets to be positive
         # TODO: May not actually be required for (nested) collection input ?
-        return super().from_json(value, trans, other_values, require_legal_value=False)
+        return super()._select_from_json(value, trans, other_values, require_legal_value=False)
 
     def get_tag_list(self, other_values):
         """
@@ -1395,7 +1398,7 @@ def to_json(self, value, app, use_security):
             return value.strip()
         return value
 
-    def from_json(self, value, trans, other_values=None):
+    def from_json(self, value, trans=None, other_values=None):
         """
         Label convention prepends column number with a 'c', but tool uses the integer. This
         removes the 'c' when entered into a workflow.
@@ -1710,7 +1713,7 @@ def recurse_options(legal_values, options):
         recurse_options(legal_values, self.get_options(trans=trans, other_values=other_values))
         return legal_values
 
-    def from_json(self, value, trans, other_values=None):
+    def from_json(self, value, trans=None, other_values=None):
         other_values = other_values or {}
         legal_values = self.get_legal_values(trans, other_values, value)
         if not legal_values and trans.workflow_building_mode:
@@ -2111,7 +2114,7 @@ def __init__(self, tool, input_source, trans=None):
                     )
                 self.conversions.append((name, conv_extension, [conv_type]))
 
-    def from_json(self, value, trans, other_values=None):
+    def from_json(self, value, trans=None, other_values=None):
         session = trans.sa_session
 
         other_values = other_values or {}
@@ -2468,7 +2471,7 @@ def match_multirun_collections(self, trans, history, dataset_collection_matcher)
             if match:
                 yield history_dataset_collection, match.implicit_conversion
 
-    def from_json(self, value, trans, other_values=None):
+    def from_json(self, value, trans=None, other_values=None):
         session = trans.sa_session
 
         other_values = other_values or {}