Fix numerous issues with tool input format "21.01"

lib/galaxy/tools/__init__.py

@@ -1836,7 +1836,9 @@ def expand_incoming(
         # Expand these out to individual parameters for given jobs (tool executions).
         expanded_incomings: List[ToolStateJobInstanceT]
         collection_info: Optional[MatchingCollections]
-        expanded_incomings, collection_info = expand_meta_parameters(request_context, self, incoming)
+        expanded_incomings, collection_info = expand_meta_parameters(
+            request_context, self, incoming, input_format=input_format
+        )
 
         self._ensure_expansion_is_valid(expanded_incomings, rerun_remap_job_id)
 

lib/galaxy/tools/parameters/__init__.py

@@ -62,6 +62,8 @@ def visit_input_values(
     context=None,
     no_replacement_value=REPLACE_ON_TRUTHY,
     replace_optional_connections=False,
+    allow_case_inference=False,
+    unset_value=None,
 ):
     """
     Given a tools parameter definition (`inputs`) and a specific set of
@@ -158,7 +160,7 @@ def visit_input_values(
     """
 
     def callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix, context=None, error=None):
-        value = input_values.get(input.name)
+        value = input_values.get(input.name, unset_value)
         args = {
             "input": input,
             "parent": input_values,
@@ -182,13 +184,23 @@ def callback_helper(input, input_values, name_prefix, label_prefix, parent_prefi
             input_values[input.name] = input.value
 
     def get_current_case(input, input_values):
+        test_parameter = input.test_param
+        test_parameter_name = test_parameter.name
         try:
-            return input.get_current_case(input_values[input.test_param.name])
+            if test_parameter_name not in input_values and allow_case_inference:
+                return input.get_current_case(test_parameter.get_initial_value(None, input_values))
+            else:
+                return input.get_current_case(input_values[test_parameter_name])
         except (KeyError, ValueError):
             return -1
 
     context = ExpressionContext(input_values, context)
-    payload = {"context": context, "no_replacement_value": no_replacement_value}
+    payload = {
+        "context": context,
+        "no_replacement_value": no_replacement_value,
+        "allow_case_inference": allow_case_inference,
+        "unset_value": unset_value,
+    }
     for input in inputs.values():
         if isinstance(input, Repeat) or isinstance(input, UploadDataset):
             values = input_values[input.name] = input_values.get(input.name, [])
@@ -411,16 +423,15 @@ def populate_state(
             group_state = state[input.name]
             if input.type == "repeat":
                 repeat_input = cast(Repeat, input)
-                if (
-                    len(incoming[repeat_input.name]) > repeat_input.max
-                    or len(incoming[repeat_input.name]) < repeat_input.min
+                repeat_name = repeat_input.name
+                repeat_incoming = incoming.get(repeat_name) or []
+                if repeat_incoming and (
+                    len(repeat_incoming) > repeat_input.max or len(repeat_incoming) < repeat_input.min
                 ):
-                    errors[repeat_input.name] = (
-                        "The number of repeat elements is outside the range specified by the tool."
-                    )
+                    errors[repeat_name] = "The number of repeat elements is outside the range specified by the tool."
                 else:
                     del group_state[:]
-                    for rep in incoming[repeat_input.name]:
+                    for rep in repeat_incoming:
                         new_state: ToolStateJobInstancePopulatedT = {}
                         group_state.append(new_state)
                         repeat_errors: ParameterValidationErrorsT = {}
@@ -454,10 +465,13 @@ def populate_state(
                         current_case = conditional_input.get_current_case(value)
                         group_state = state[conditional_input.name] = {}
                         cast_errors: ParameterValidationErrorsT = {}
+                        incoming_for_conditional = cast(
+                            ToolStateJobInstanceT, incoming.get(conditional_input.name) or {}
+                        )
                         populate_state(
                             request_context,
                             conditional_input.cases[current_case].inputs,
-                            cast(ToolStateJobInstanceT, incoming.get(conditional_input.name)),
+                            incoming_for_conditional,
                             group_state,
                             cast_errors,
                             context=context,
@@ -475,10 +489,11 @@ def populate_state(
             elif input.type == "section":
                 section_input = cast(Section, input)
                 section_errors: ParameterValidationErrorsT = {}
+                incoming_for_state = cast(ToolStateJobInstanceT, incoming.get(section_input.name) or {})
                 populate_state(
                     request_context,
                     section_input.inputs,
-                    cast(ToolStateJobInstanceT, incoming.get(section_input.name)),
+                    incoming_for_state,
                     group_state,
                     section_errors,
                     context=context,

lib/galaxy/tools/parameters/meta.py

@@ -19,10 +19,19 @@
     matching,
     subcollections,
 )
-from galaxy.util import permutations
+from galaxy.util.permutations import (
+    build_combos,
+    input_classification,
+    is_in_state,
+    state_copy,
+    state_get_value,
+    state_remove_value,
+    state_set_value,
+)
 from . import visit_input_values
 from .wrapped import process_key
 from .._types import (
+    InputFormatT,
     ToolRequestT,
     ToolStateJobInstanceT,
 )
@@ -161,7 +170,15 @@ def is_batch(value):
 ExpandedT = Tuple[List[ToolStateJobInstanceT], Optional[matching.MatchingCollections]]
 
 
-def expand_meta_parameters(trans, tool, incoming: ToolRequestT) -> ExpandedT:
+def expand_flat_parameters_to_nested(incoming_copy: ToolRequestT) -> Dict[str, Any]:
+    nested_dict: Dict[str, Any] = {}
+    for incoming_key, incoming_value in incoming_copy.items():
+        if not incoming_key.startswith("__"):
+            process_key(incoming_key, incoming_value=incoming_value, d=nested_dict)
+    return nested_dict
+
+
+def expand_meta_parameters(trans, tool, incoming: ToolRequestT, input_format: InputFormatT) -> ExpandedT:
     """
     Take in a dictionary of raw incoming parameters and expand to a list
     of expanded incoming parameters (one set of parameters per tool
@@ -176,33 +193,24 @@ def expand_meta_parameters(trans, tool, incoming: ToolRequestT) -> ExpandedT:
     # order matters, so the following reorders incoming
     # according to tool.inputs (which is ordered).
     incoming_copy = incoming.copy()
-    nested_dict: Dict[str, Any] = {}
-    for incoming_key, incoming_value in incoming_copy.items():
-        if not incoming_key.startswith("__"):
-            process_key(incoming_key, incoming_value=incoming_value, d=nested_dict)
-
-    reordered_incoming = {}
-
-    def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs):
-        if prefixed_name in incoming_copy:
-            reordered_incoming[prefixed_name] = incoming_copy[prefixed_name]
-            del incoming_copy[prefixed_name]
+    if input_format == "legacy":
+        nested_dict = expand_flat_parameters_to_nested(incoming_copy)
+    else:
+        nested_dict = incoming_copy
 
-    visit_input_values(inputs=tool.inputs, input_values=nested_dict, callback=visitor)
-    reordered_incoming.update(incoming_copy)
+    collections_to_match = matching.CollectionsToMatch()
 
-    def classifier(input_key):
-        value = incoming[input_key]
+    def classifier_from_value(value, input_key):
         if isinstance(value, dict) and "values" in value:
             # Explicit meta wrapper for inputs...
             is_batch = value.get("batch", False)
             is_linked = value.get("linked", True)
             if is_batch and is_linked:
-                classification = permutations.input_classification.MATCHED
+                classification = input_classification.MATCHED
             elif is_batch:
-                classification = permutations.input_classification.MULTIPLIED
+                classification = input_classification.MULTIPLIED
             else:
-                classification = permutations.input_classification.SINGLE
+                classification = input_classification.SINGLE
             if __collection_multirun_parameter(value):
                 collection_value = value["values"][0]
                 values = __expand_collection_parameter(
@@ -211,24 +219,114 @@ def classifier(input_key):
             else:
                 values = value["values"]
         else:
-            classification = permutations.input_classification.SINGLE
+            classification = input_classification.SINGLE
             values = value
         return classification, values
 
-    collections_to_match = matching.CollectionsToMatch()
+    nested = input_format != "legacy"
+    if not nested:
+        reordered_incoming = reorder_parameters(tool, incoming_copy, nested_dict, nested)
+        incoming_template = reordered_incoming
+
+        def classifier_flat(input_key):
+            return classifier_from_value(incoming[input_key], input_key)
 
-    # Stick an unexpanded version of multirun keys so they can be replaced,
-    # by expand_mult_inputs.
-    incoming_template = reordered_incoming
+        single_inputs, matched_multi_inputs, multiplied_multi_inputs = split_inputs_flat(
+            incoming_template, classifier_flat
+        )
+    else:
+        reordered_incoming = reorder_parameters(tool, incoming_copy, nested_dict, nested)
+        incoming_template = reordered_incoming
+        single_inputs, matched_multi_inputs, multiplied_multi_inputs = split_inputs_nested(
+            tool.inputs, incoming_template, classifier_from_value
+        )
 
-    expanded_incomings = permutations.expand_multi_inputs(incoming_template, classifier)
+    expanded_incomings = build_combos(single_inputs, matched_multi_inputs, multiplied_multi_inputs, nested=nested)
     if collections_to_match.has_collections():
         collection_info = trans.app.dataset_collection_manager.match_collections(collections_to_match)
     else:
         collection_info = None
     return expanded_incomings, collection_info
 
 
+def reorder_parameters(tool, incoming, nested_dict, nested):
+    # If we're going to multiply input dataset combinations
+    # order matters, so the following reorders incoming
+    # according to tool.inputs (which is ordered).
+    incoming_copy = state_copy(incoming, nested)
+
+    reordered_incoming = {}
+
+    def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs):
+        if is_in_state(incoming_copy, prefixed_name, nested):
+            value_to_copy_over = state_get_value(incoming_copy, prefixed_name, nested)
+            state_set_value(reordered_incoming, prefixed_name, value_to_copy_over, nested)
+            state_remove_value(incoming_copy, prefixed_name, nested)
+
+    visit_input_values(inputs=tool.inputs, input_values=nested_dict, callback=visitor)
+
+    def merge_into(from_object, into_object):
+        if isinstance(from_object, dict):
+            for key, value in from_object.items():
+                if key not in into_object:
+                    into_object[key] = value
+                else:
+                    into_target = into_object[key]
+                    merge_into(value, into_target)
+        elif isinstance(from_object, list):
+            for index in from_object:
+                if len(into_object) <= index:
+                    into_object.append(from_object[index])
+                else:
+                    merge_into(from_object[index], into_object[index])
+
+    merge_into(incoming_copy, reordered_incoming)
+    return reordered_incoming
+
+
+def split_inputs_flat(inputs: Dict[str, Any], classifier):
+    single_inputs: Dict[str, Any] = {}
+    matched_multi_inputs: Dict[str, Any] = {}
+    multiplied_multi_inputs: Dict[str, Any] = {}
+
+    for input_key in inputs:
+        input_type, expanded_val = classifier(input_key)
+        if input_type == input_classification.SINGLE:
+            single_inputs[input_key] = expanded_val
+        elif input_type == input_classification.MATCHED:
+            matched_multi_inputs[input_key] = expanded_val
+        elif input_type == input_classification.MULTIPLIED:
+            multiplied_multi_inputs[input_key] = expanded_val
+
+    return (single_inputs, matched_multi_inputs, multiplied_multi_inputs)
+
+
+def split_inputs_nested(inputs, nested_dict, classifier):
+    single_inputs: Dict[str, Any] = {}
+    matched_multi_inputs: Dict[str, Any] = {}
+    multiplied_multi_inputs: Dict[str, Any] = {}
+    unset_value = object()
+
+    def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs):
+        if value is unset_value:
+            # don't want to inject extra nulls into state
+            return
+
+        input_type, expanded_val = classifier(value, prefixed_name)
+        if input_type == input_classification.SINGLE:
+            single_inputs[prefixed_name] = expanded_val
+        elif input_type == input_classification.MATCHED:
+            matched_multi_inputs[prefixed_name] = expanded_val
+        elif input_type == input_classification.MULTIPLIED:
+            multiplied_multi_inputs[prefixed_name] = expanded_val
+
+    visit_input_values(
+        inputs=inputs, input_values=nested_dict, callback=visitor, allow_case_inference=True, unset_value=unset_value
+    )
+    single_inputs_nested = expand_flat_parameters_to_nested(single_inputs)
+    return (single_inputs_nested, matched_multi_inputs, multiplied_multi_inputs)
+
+
 def __expand_collection_parameter(trans, input_key, incoming_val, collections_to_match, linked=False):
     # If subcollectin multirun of data_collection param - value will
     # be "hdca_id|subcollection_type" else it will just be hdca_id

lib/galaxy/tools/parameters/wrapped.py

@@ -25,6 +25,10 @@
     InputValueWrapper,
     SelectToolParameterWrapper,
 )
+from galaxy.util.permutations import (
+    looks_like_flattened_repeat_key,
+    split_flattened_repeat_key,
+)
 
 PARAMS_UNWRAPPED = object()
 
@@ -172,10 +176,9 @@ def process_key(incoming_key: str, incoming_value: Any, d: Dict[str, Any]):
             # In case we get an empty repeat after we already filled in a repeat element
             return
         d[incoming_key] = incoming_value
-    elif key_parts[0].rsplit("_", 1)[-1].isdigit():
+    elif looks_like_flattened_repeat_key(key_parts[0]):
         # Repeat
-        input_name, _index = key_parts[0].rsplit("_", 1)
-        index = int(_index)
+        input_name, index = split_flattened_repeat_key(key_parts[0])
         d.setdefault(input_name, [])
         newlist: List[Dict[Any, Any]] = [{} for _ in range(index + 1)]
         d[input_name].extend(newlist[len(d[input_name]) :])

lib/galaxy/tools/wrappers.py

@@ -802,6 +802,8 @@ def __init__(self, input_datasets: Optional[Dict[str, Any]] = None) -> None:
             self.identifier_key_dict = {}
 
     def identifier(self, dataset_value: str, input_values: Dict[str, str]) -> Optional[str]:
+        if isinstance(dataset_value, list):
+            raise TypeError(f"Expected {dataset_value} to be hashable")
         element_identifier = None
         if identifier_key := self.identifier_key_dict.get(dataset_value, None):
             element_identifier = input_values.get(identifier_key, None)