Improved get_children_names function

Author: domna

pynxtools/dataconverter/nexus_tree.py

@@ -204,16 +204,32 @@ def search_child_with_name(
             direct_child = next((x for x in self.children if x.name == name), None)
             if direct_child is not None:
                 return direct_child
-            if name in self.get_all_children_names():
+            if name in self.get_all_direct_children_names():
                 return self.add_inherited_node(name)
         return None
 
-    def get_all_children_names(self, depth: Optional[int] = None) -> Set[str]:
+    def get_all_direct_children_names(
+        self,
+        node_type: Optional[str] = None,
+        nx_class: Optional[str] = None,
+        depth: Optional[int] = None,
+    ) -> Set[str]:
         """
         Get all children names of the current node up to a certain depth.
         Only `field`, `group` `choice` or `attribute` are considered as children.
 
         Args:
+            node_type (Optional[str], optional):
+                The tags of the children to consider.
+                This should either be "field", "group", "choice" or "attribute".
+                If None all tags are considered.
+                Defaults to None.
+            nx_class (Optional[str], optional):
+                The NeXus class of the group to consider.
+                This is only used if `node_type` is "group".
+                It should contain the preceding `NX` and the class name in lowercase,
+                e.g., "NXentry".
+                Defaults to None.
             depth (Optional[int], optional):
                 The inheritance depth up to which get children names.
                 `depth=1` will return only the children of the current node.
@@ -229,15 +245,21 @@ def get_all_children_names(self, depth: Optional[int] = None) -> Set[str]:
         if depth is not None and (not isinstance(depth, int) or depth < 0):
             raise ValueError("Depth must be a positive integer or None")
 
+        tag_type = ""
+        if node_type == "group" and nx_class is not None:
+            tag_type = f"[@type='{nx_class}']"
+
+        if node_type is not None:
+            search_tags = f"*[self::nx:{node_type}{tag_type}]"
+        else:
+            search_tags = (
+                r"*[self::nx:field or self::nx:group "
+                r"or self::nx:attribute or self::nx:choice]"
+            )
+
         names = set()
         for elem in self.inheritance[:depth]:
-            for subelems in elem.xpath(
-                (
-                    r"*[self::nx:field or self::nx:group "
-                    r"or self::nx:attribute or self::nx:choice]"
-                ),
-                namespaces=namespaces,
-            ):
+            for subelems in elem.xpath(search_tags, namespaces=namespaces):
                 if "name" in subelems.attrib:
                     names.add(subelems.attrib["name"])
                 elif "type" in subelems.attrib:

pynxtools/dataconverter/validation.py

@@ -44,12 +44,20 @@
 from pynxtools.definitions.dev_tools.utils.nxdl_utils import get_nx_namefit
 
 
-def best_namefit_of_(
-    name: str, concepts: Set[str], nx_class: Optional[str] = None
-) -> str:
-    # TODO: Find the best namefit of name in concepts
-    # Consider nx_class if it is not None
-    ...
+def best_namefit_of_(name: str, concepts: Set[str]) -> str:
+    if not concepts:
+        return None
+
+    if name in concepts:
+        return name
+
+    best_match, score = max(
+        map(lambda x: (x, get_nx_namefit(name, x)), concepts), key=lambda x: x[1]
+    )
+    if score < 0:
+        return None
+
+    return best_match
 
 
 def validate_hdf_group_against(appdef: str, data: h5py.Group):
@@ -64,9 +72,11 @@ def validate_hdf_group_against(appdef: str, data: h5py.Group):
     # Allow for 10000 cache entries. This should be enough for most cases
     @cached(
         cache=LRUCache(maxsize=10000),
-        key=lambda path, _: hashkey(path),
+        key=lambda path, *_: hashkey(path),
     )
-    def find_node_for(path: str, nx_class: Optional[str] = None) -> Optional[NexusNode]:
+    def find_node_for(
+        path: str, node_type: Optional[str] = None, nx_class: Optional[str] = None
+    ) -> Optional[NexusNode]:
         if path == "":
             return tree
 
@@ -75,10 +85,7 @@ def find_node_for(path: str, nx_class: Optional[str] = None) -> Optional[NexusNo
 
         best_child = best_namefit_of_(
             last_elem,
-            # TODO: Consider renaming `get_all_children_names` to
-            # `get_all_direct_children_names`. Because that's what it is.
-            node.get_all_children_names(),
-            nx_class,
+            node.get_all_direct_children_names(nx_class=nx_class, node_type=node_type),
         )
         if best_child is None:
             return None
@@ -92,15 +99,19 @@ def remove_from_req_fields(path: str):
     def handle_group(path: str, data: h5py.Group):
         node = find_node_for(path, data.attrs.get("NX_class"))
         if node is None:
-            # TODO: Log undocumented
+            collector.collect_and_log(
+                path, ValidationProblem.MissingDocumentation, None
+            )
             return
 
         # TODO: Do actual group checks
 
     def handle_field(path: str, data: h5py.Dataset):
         node = find_node_for(path)
         if node is None:
-            # TODO: Log undocumented
+            collector.collect_and_log(
+                path, ValidationProblem.MissingDocumentation, None
+            )
             return
         remove_from_req_fields(f"{path}")
 
@@ -110,7 +121,9 @@ def handle_attributes(path: str, attribute_names: h5py.AttributeManager):
         for attr_name in attribute_names:
             node = find_node_for(f"{path}/{attr_name}")
             if node is None:
-                # TODO: Log undocumented
+                collector.collect_and_log(
+                    path, ValidationProblem.MissingDocumentation, None
+                )
                 continue
             remove_from_req_fields(f"{path}/@{attr_name}")
 
@@ -282,7 +295,7 @@ def get_variations_of(node: NexusNode, keys: Mapping[str, Any]) -> List[str]:
                 continue
             if (
                 get_nx_namefit(name2fit, node.name) >= 0
-                and key not in node.parent.get_all_children_names()
+                and key not in node.parent.get_all_direct_children_names()
             ):
                 variations.append(key)
             if nx_name is not None and not variations:
@@ -315,7 +328,7 @@ def check_nxdata():
                 data_node = node.search_child_with_name((signal, "DATA"))
                 data_bc_node = node.search_child_with_name("DATA")
                 data_node.inheritance.append(data_bc_node.inheritance[0])
-                for child in data_node.get_all_children_names():
+                for child in data_node.get_all_direct_children_names():
                     data_node.search_child_with_name(child)
 
                 handle_field(
@@ -347,7 +360,7 @@ def check_nxdata():
                     axis_node = node.search_child_with_name((axis, "AXISNAME"))
                     axis_bc_node = node.search_child_with_name("AXISNAME")
                     axis_node.inheritance.append(axis_bc_node.inheritance[0])
-                    for child in axis_node.get_all_children_names():
+                    for child in axis_node.get_all_direct_children_names():
                         axis_node.search_child_with_name(child)
 
                     handle_field(
@@ -575,7 +588,7 @@ def is_documented(key: str, node: NexusNode) -> bool:
             return True
 
         for name in key[1:].replace("@", "").split("/"):
-            children = node.get_all_children_names()
+            children = node.get_all_direct_children_names()
             best_name = best_namefit_of(name, children)
             if best_name is None:
                 return False
@@ -688,7 +701,7 @@ def populate_full_tree(node: NexusNode, max_depth: Optional[int] = 5, depth: int
         # but it does while recursing the tree and it should
         # be fixed.
         return
-    for child in node.get_all_children_names():
+    for child in node.get_all_direct_children_names():
         print(child)
         child_node = node.search_child_with_name(child)
         populate_full_tree(child_node, max_depth=max_depth, depth=depth + 1)