Merge pull request #313 from sneakers-the-rat/sort-classes

Add inheritance ordering, unify element ordering

Author: cmungall

linkml_runtime/exceptions.py

@@ -0,0 +1,2 @@
+class OrderingError(RuntimeError):
+    """Exception raised when there is a problem with SchemaView ordering"""

linkml_runtime/utils/schemaview.py

@@ -6,14 +6,15 @@
 from copy import copy, deepcopy
 from collections import defaultdict, deque
 from pathlib import Path
-from typing import Mapping, Tuple
+from typing import Mapping, Tuple, TypeVar
 import warnings
 
 from linkml_runtime.utils.namespaces import Namespaces
 from deprecated.classic import deprecated
 from linkml_runtime.utils.context_utils import parse_import_map, map_import
 from linkml_runtime.utils.pattern import PatternResolver
 from linkml_runtime.linkml_model.meta import *
+from linkml_runtime.exceptions import OrderingError
 from enum import Enum
 
 logger = logging.getLogger(__name__)
@@ -33,11 +34,23 @@
 TYPE_NAME = Union[TypeDefinitionName, str]
 ENUM_NAME = Union[EnumDefinitionName, str]
 
+ElementType = TypeVar("ElementType", bound=Element)
+ElementNameType = TypeVar("ElementNameType", bound=Union[ElementName,str])
+DefinitionType = TypeVar("DefinitionType", bound=Definition)
+DefinitionNameType = TypeVar("DefinitionNameType", bound=Union[DefinitionName,str])
+ElementDict = Dict[ElementNameType, ElementType]
+DefDict = Dict[DefinitionNameType, DefinitionType]
+
 
 class OrderedBy(Enum):
     RANK = "rank"
     LEXICAL = "lexical"
     PRESERVE = "preserve"
+    INHERITANCE = "inheritance"
+    """
+    Order according to inheritance such that if C is a child of P then C appears after P
+    """
+
 
 
 def _closure(f, x, reflexive=True, depth_first=True, **kwargs):
@@ -305,7 +318,22 @@ def all_class(self, imports=True) -> Dict[ClassDefinitionName, ClassDefinition]:
         """
         return self._get_dict(CLASSES, imports)
 
-    def _order_lexically(self, elements: dict):
+    def ordered(self, elements: ElementDict, ordered_by: Optional[OrderedBy] = None) -> ElementDict:
+        """
+        Order a dictionary of elements with some ordering method in :class:`.OrderedBy`
+        """
+        if ordered_by in (OrderedBy.LEXICAL, OrderedBy.LEXICAL.value):
+            return self._order_lexically(elements)
+        elif ordered_by in (OrderedBy.RANK, OrderedBy.RANK.value):
+            return self._order_rank(elements)
+        elif ordered_by in (OrderedBy.INHERITANCE, OrderedBy.INHERITANCE.value):
+            return self._order_inheritance(elements)
+        elif ordered_by is None or ordered_by in (OrderedBy.PRESERVE, OrderedBy.PRESERVE.value):
+            return elements
+        else:
+            raise ValueError(f"ordered_by must be in OrderedBy or None, got {ordered_by}")
+
+    def _order_lexically(self, elements: ElementDict) -> ElementDict:
         """
         :param element: slots or class type to order
         :param imports
@@ -320,7 +348,7 @@ def _order_lexically(self, elements: dict):
             ordered_elements[self.get_element(name).name] = self.get_element(name)
         return ordered_elements
 
-    def _order_rank(self, elements: dict):
+    def _order_rank(self, elements: ElementDict) -> ElementDict:
         """
         :param elements: slots or classes to order
         :return: all classes or slots sorted by their rank in schema view
@@ -342,6 +370,32 @@ def _order_rank(self, elements: dict):
         rank_ordered_elements.update(unranked_map)
         return rank_ordered_elements
 
+    def _order_inheritance(self, elements: DefDict) -> DefDict:
+        """
+        sort classes such that if C is a child of P then C appears after P in the list
+        """
+        clist = list(elements.values())
+        slist = []  # sorted
+        can_add = False
+        while len(clist) > 0:
+            for i in range(len(clist)):
+                candidate = clist[i]
+                can_add = False
+                if candidate.is_a is None:
+                    can_add = True
+                else:
+                    if candidate.is_a in [p.name for p in slist]:
+                        can_add = True
+                if can_add:
+                    slist = slist + [candidate]
+                    del clist[i]
+                    break
+            if not can_add:
+                raise OrderingError(f"could not find suitable element in {clist} that does not ref {slist}")
+
+        return {s.name: s for s in slist}
+
+
     @lru_cache(None)
     def all_classes(self, ordered_by=OrderedBy.PRESERVE, imports=True) -> Dict[ClassDefinitionName, ClassDefinition]:
         """
@@ -350,15 +404,8 @@ def all_classes(self, ordered_by=OrderedBy.PRESERVE, imports=True) -> Dict[Class
         :return: all classes in schema view
         """
         classes = copy(self._get_dict(CLASSES, imports))
-
-        if ordered_by == OrderedBy.LEXICAL:
-            ordered_classes = self._order_lexically(elements=classes)
-        elif ordered_by == OrderedBy.RANK:
-            ordered_classes = self._order_rank(elements=classes)
-        else:  # else preserve the order in the yaml
-            ordered_classes = classes
-
-        return ordered_classes
+        classes = self.ordered(classes, ordered_by=ordered_by)
+        return classes
 
     @deprecated("Use `all_slots` instead")
     @lru_cache(None)
@@ -386,14 +433,8 @@ def all_slots(self, ordered_by=OrderedBy.PRESERVE, imports=True, attributes=True
                     if aname not in slots:
                         slots[aname] = a
 
-        if ordered_by == OrderedBy.LEXICAL:
-            ordered_slots = self._order_lexically(elements=slots)
-        elif ordered_by == OrderedBy.RANK:
-            ordered_slots = self._order_rank(elements=slots)
-        else:
-            # preserve order in YAML
-            ordered_slots = slots
-        return ordered_slots
+        slots = self.ordered(slots, ordered_by=ordered_by)
+        return slots
 
     @deprecated("Use `all_enums` instead")
     @lru_cache(None)