Merge pull request #18892 from jmchilton/axe_drill_down_filters

Remove some unused dynamic drill down options.

lib/galaxy/tool_util/parser/interface.py

@@ -443,19 +443,12 @@ def get_index_file_name(self) -> Optional[str]:
         """If dynamic options are loaded from an index file, return the name."""
 
 
-DrillDownDynamicFilters = Dict[str, Dict[str, dict]]  # {input key: {metadata_key: metadata values}}
-
-
 class DrillDownDynamicOptions(metaclass=ABCMeta):
 
     @abstractmethod
     def from_code_block(self) -> Optional[str]:
         """Get a code block to do an eval on."""
 
-    @abstractmethod
-    def from_filters(self) -> Optional[DrillDownDynamicFilters]:
-        """Get filters to apply to target datasets."""
-
 
 class InputSource(metaclass=ABCMeta):
     default_optional = False

lib/galaxy/tool_util/parser/xml.py

@@ -38,7 +38,6 @@
 from .interface import (
     AssertionList,
     Citation,
-    DrillDownDynamicFilters,
     DrillDownDynamicOptions,
     DrillDownOptionsDict,
     DynamicOptions,
@@ -1374,50 +1373,13 @@ def parse_static_options(self) -> List[Tuple[str, str, bool]]:
     def parse_drill_down_dynamic_options(
         self, tool_data_path: Optional[str] = None
     ) -> Optional[DrillDownDynamicOptions]:
-        from_file = self.input_elem.get("from_file", None)
-        if from_file:
-            if not os.path.isabs(from_file):
-                assert tool_data_path, "This tool cannot be parsed outside of a Galaxy context"
-                from_file = os.path.join(tool_data_path, from_file)
-            elem = XML(f"<root>{open(from_file).read()}</root>")
-        else:
-            elem = self.input_elem
-
+        elem = self.input_elem
         dynamic_options_raw = elem.get("dynamic_options", None)
         dynamic_options: Optional[str] = str(dynamic_options_raw) if dynamic_options_raw else None
-        filters: Optional[DrillDownDynamicFilters] = None
-        if elem.find("filter"):
-            _filters: DrillDownDynamicFilters = {}
-            for filter in elem.findall("filter"):
-                # currently only filtering by metadata key matching input file is allowed
-                filter_type = filter.get("type")
-                if filter_type == "data_meta":
-                    data_ref = filter.get("data_ref")
-                    assert data_ref
-                    if data_ref not in _filters:
-                        _filters[data_ref] = {}
-                    meta_key = filter.get("meta_key")
-                    assert meta_key
-                    if meta_key not in _filters[data_ref]:
-                        _filters[data_ref][meta_key] = {}
-                    meta_value = filter.get("value")
-                    if meta_value not in _filters[data_ref][meta_key]:
-                        _filters[data_ref][meta_key][meta_value] = []
-                    assert meta_value
-                    options_elem = filter.find("options")
-                    assert options_elem
-                    _recurse_drill_down_elems(
-                        _filters[data_ref][meta_key][meta_value],
-                        options_elem.findall("option"),
-                    )
-            filters = _filters
-        if filters is None and dynamic_options is None:
+        if dynamic_options is None:
             return None
         else:
-            return XmlDrillDownDynamicOptions(
-                code_block=dynamic_options,
-                filters=filters,
-            )
+            return XmlDrillDownDynamicOptions(code_block=dynamic_options)
 
     def parse_drill_down_static_options(
         self, tool_data_path: Optional[str] = None
@@ -1575,17 +1537,13 @@ def parse_citation_elem(citation_elem: Element) -> Optional[Citation]:
 
 class XmlDrillDownDynamicOptions(DrillDownDynamicOptions):
 
-    def __init__(self, code_block: Optional[str], filters: Optional[DrillDownDynamicFilters]):
+    def __init__(self, code_block: Optional[str]):
         self._code_block = code_block
-        self._filters = filters
 
     def from_code_block(self) -> Optional[str]:
         """Get a code block to do an eval on."""
         return self._code_block
 
-    def from_filters(self) -> Optional[DrillDownDynamicFilters]:
-        return self._filters
-
 
 def _element_to_dict(elem: Element) -> Dict[str, Any]:
     # every call to this function needs to be replaced with something more type safe and with

lib/galaxy/tools/parameters/basic.py

@@ -1646,13 +1646,11 @@ def __init__(self, tool, input_source, context=None):
         drill_down_dynamic_options = input_source.parse_drill_down_dynamic_options(tool_data_path)
         if drill_down_dynamic_options is not None:
             self.is_dynamic = True
-            self.dynamic_options = drill_down_dynamic_options.code_block
-            self.filtered = drill_down_dynamic_options.filters
+            self.dynamic_options = drill_down_dynamic_options.from_code_block()
             self.options = []
         else:
             self.is_dynamic = False
             self.dynamic_options = None
-            self.filtered = {}
             self.options = input_source.parse_drill_down_static_options(tool_data_path)
 
     def _get_options_from_code(self, trans=None, other_values=None):
@@ -1673,20 +1671,6 @@ def get_options(self, trans=None, other_values=None):
                 options = self._get_options_from_code(trans=trans, other_values=other_values)
             else:
                 options = []
-            for filter_key, filter_value in self.filtered.items():
-                dataset = other_values.get(filter_key)
-                if dataset.__class__.__name__.endswith(
-                    "DatasetFilenameWrapper"
-                ):  # this is a bad way to check for this, but problems importing class (due to circular imports?)
-                    dataset = dataset.dataset
-                if dataset:
-                    for meta_key, meta_dict in filter_value.items():
-                        if hasattr(dataset, "metadata") and hasattr(dataset.metadata, "spec"):
-                            check_meta_val = dataset.metadata.spec[meta_key].param.to_string(
-                                dataset.metadata.get(meta_key)
-                            )
-                            if check_meta_val in meta_dict:
-                                options.extend(meta_dict[check_meta_val])
             return options
         return self.options
 
@@ -1830,10 +1814,7 @@ def get_option_display(value, options):
         return "Nothing selected."
 
     def get_dependencies(self):
-        """
-        Get the *names* of the other params this param depends on.
-        """
-        return list(self.filtered.keys())
+        return []
 
     def to_dict(self, trans, other_values=None):
         other_values = other_values or {}