FAIRmat-NFDI · lukaspie · Apr 3, 2025 · Mar 31, 2025 · Mar 31, 2025 · Mar 31, 2025
diff --git a/src/pynxtools/dataconverter/nexus_tree.py b/src/pynxtools/dataconverter/nexus_tree.py
@@ -29,11 +29,12 @@
 """
 
 from functools import lru_cache, reduce
-from typing import Any, List, Literal, Optional, Set, Tuple, Union
+from typing import Any, List, Dict, Literal, Optional, Set, Tuple, Union
 
 import lxml.etree as ET
 from anytree.node.nodemixin import NodeMixin
 
+from pynxtools import get_definitions_url
 from pynxtools.dataconverter.helpers import (
     get_all_parents_for,
     get_nxdl_root_and_path,
@@ -45,6 +46,7 @@
     get_nx_namefit,
     is_name_type,
 )
+from pynxtools import NX_DOC_BASES
 
 NexusType = Literal[
     "NX_BINARY",
@@ -148,6 +150,8 @@ class NexusNode(NodeMixin):
         parent_of: List["NexusNode"]:
             The inverse of the above `is_a`. In the example case
             `DATA` `parent_of` `my_data`.
+        nxdl_base: str
+            Base of the NXDL file where the XML element for this node is  defined
     """
 
     name: str
@@ -158,6 +162,7 @@ class NexusNode(NodeMixin):
     inheritance: List[ET._Element]
     is_a: List["NexusNode"]
     parent_of: List["NexusNode"]
+    nxdl_base: str
 
     def _set_optionality(self):
         """
@@ -190,12 +195,14 @@ def __init__(
         variadic: Optional[bool] = None,
         parent: Optional["NexusNode"] = None,
         inheritance: Optional[List[Any]] = None,
+        nxdl_base: Optional[str] = None,
     ) -> None:
         super().__init__()
         self.name = name
         self.type = type
         self.name_type = name_type
         self.optionality = optionality
+        self.nxdl_base = nxdl_base
         self.variadic = is_variadic(self.name, self.name_type)
         if variadic is not None:
             self.variadic = variadic
@@ -430,7 +437,7 @@ def required_fields_and_attrs_names(
 
         return req_children
 
-    def get_docstring(self, depth: Optional[int] = None) -> List[str]:
+    def get_docstring(self, depth: Optional[int] = None) -> Dict[str, str]:
         """
         Gets the docstrings of the current node and its parents up to a certain depth.
 
@@ -449,14 +456,48 @@ def get_docstring(self, depth: Optional[int] = None) -> List[str]:
         if depth is not None and depth < 0:
             raise ValueError("Depth must be a positive integer or None")
 
-        docstrings = []
+        docstrings = {}
         for elem in self.inheritance[:depth][::-1]:
             doc = elem.find("nx:doc", namespaces=namespaces)
+
             if doc is not None:
-                docstrings.append(doc.text)
+                name = elem.attrib.get("name")
+                if not name:
+                    name = elem.attrib["type"][2:].upper()
+                docstrings[name] = doc.text
 
         return docstrings
 
+    def get_link(self) -> str:
+        """
+        Get documentation url
+        """
+
+        anchor_segments = [self.type]
+        current_node = self
+
+        while True:
+            if not current_node:
+                break
+
+            segment = current_node.name
+            anchor_segments.append(current_node.name.replace("_", "-"))  # type: ignore[arg-t
10000
ype]
+            current_node = current_node.parent
+
+        definitions_url = get_definitions_url()
+        doc_base = NX_DOC_BASES.get(
+            definitions_url, "https://manual.nexusformat.org/classes"
+        )
+        nx_file = self.nxdl_base.split("/definitions/")[-1].split(".nxdl.xml")[0]
+
+        # add the name of the base file at the end, drop the appdef name
+        anchor_segments = anchor_segments[:-1]
+        anchor_segments += [self.nxdl_base.split("/")[-1].split(".nxdl.xml")[0].lower()]  # type: ignore[list-item]
+
+        anchor = "-".join([name.lower() for name in reversed(anchor_segments)])
+
+        return f"{doc_base}/{nx_file}.html#{anchor}"
+
     def _build_inheritance_chain(self, xml_elem: ET._Element) -> List[ET._Element]:
         """
         Builds the inheritance chain based on the given xml node and the inheritance
@@ -559,6 +600,7 @@ def add_node_from(self, xml_elem: ET._Element) -> Optional["NexusNode"]:
                 name_type=name_type,
                 type=tag,
                 optionality=default_optionality,
+                nxdl_base=xml_elem.base,
             )
         elif tag == "group":
             name = xml_elem.attrib.get("name")
@@ -575,13 +617,15 @@ def add_node_from(self, xml_elem: ET._Element) -> Optional["NexusNode"]:
                 nx_class=xml_elem.attrib["type"],
                 inheritance=inheritance_chain,
                 optionality=default_optionality,
+                nxdl_base=xml_elem.base,
             )
         elif tag == "choice":
             current_elem = NexusChoice(
                 parent=self,
                 name=xml_elem.attrib["name"],
                 name_type=name_type,
                 optionality=default_optionality,
+                nxdl_base=xml_elem.base,
             )
         else:
             # TODO: Tags: link
@@ -932,14 +976,15 @@ def populate_tree_from_parents(node: NexusNode):
         populate_tree_from_parents(child_node)
 
 
-def generate_tree_from(appdef: str) -> NexusNode:
+def generate_tree_from(appdef: str, set_root_attr: bool = True) -> NexusNode:
     """
     Generates a NexusNode tree from an application definition.
     NexusNode is based on anytree nodes and anytree's functions can be used
     for displaying and traversal of the tree.
 
     Args:
         appdef (str): The application definition name to generate the NexusNode tree from.
+        set_root_attr (bool): Whether or not to set the root attributes.
 
     Returns:
         NexusNode: The tree representing the application definition.
@@ -968,6 +1013,7 @@ def add_children_to(parent: NexusNode, xml_elem: ET._Element) -> None:
             add_children_to(current_elem, child)
 
     appdef_xml_root, _ = get_nxdl_root_and_path(appdef)
+
     global namespaces
     namespaces = {"nx": appdef_xml_root.nsmap[None]}
 
@@ -983,18 +1029,19 @@ def add_children_to(parent: NexusNode, xml_elem: ET._Element) -> None:
         variadic=False,
         parent=None,
         inheritance=appdef_inheritance_chain,
+        nxdl_base=appdef_xml_root.base,
     )
     # Set root attributes
-    nx_root, _ = get_nxdl_root_and_path("NXroot")
-    for root_attrib in nx_root.findall("nx:attribute", namespaces=namespaces):
-        child = tree.add_node_from(root_attrib)
-        child.optionality = "optional"
+    if set_root_attr:
+        nx_root, _ = get_nxdl_root_and_path("NXroot")
+        for root_attrib in nx_root.findall("nx:attribute", namespaces=namespaces):
+            child = tree.add_node_from(root_attrib)
+            child.optionality = "optional"
 
     entry = appdef_xml_root.find("nx:group[@type='NXentry']", namespaces=namespaces)
     add_children_to(tree, entry)
 
     # Add all fields and attributes from the parent appdefs
     if len(appdef_inheritance_chain) > 1:
         populate_tree_from_parents(tree)
-
     return tree
diff --git a/src/pynxtools/eln_mapper/README.md b/src/pynxtools/eln_mapper/README.md
@@ -1,8 +1,12 @@
 # ELN generator
+
 This is a helper tool for generating ELN files that can be used to add metadata to the dataconverter routine.
+
 Two types of ELN are supported (by passing the flag `eln-type`):
-- **eln**: The simple ELN generator that can be used in a console or jupyter-notebook.
-- **scheme_eln**: Scheme based ELN generator that can be used in NOMAD and the ELN can be used as a custom scheme in NOMAD.
+
+- **`reader`**: The simple ELN generator that can be used in a console or jupyter-notebook, e.g. by the `pynxtools` dataconverter.
+- **`schema`**: Scheme based ELN generator that can be used in NOMAD and the ELN can be used as a custom scheme in NOMAD.
 
  Here you can find more information about the tool:
+
  - [API documentation](https://fairmat-nfdi.github.io/pynxtools/reference/cli-api.html#generate_eln)