Merge pull request #170 from FAIRmat-NFDI/163-write-nxroot-attributes

Write NXroot attributes

pynxtools/dataconverter/convert.py

@@ -131,6 +131,8 @@ def convert(input_file: Tuple[str],
             path
         )
 
+    helpers.add_default_root_attributes(data=data, filename=os.path.basename(output))
+
     Writer(data=data, nxdl_path=nxdl_path, output_path=output).write()
 
     logger.info("The output file generated: %s", output)

pynxtools/dataconverter/helpers.py

@@ -21,9 +21,11 @@
 from typing import Tuple, Callable, Union
 import re
 import xml.etree.ElementTree as ET
+from datetime import datetime, timezone
 
 import numpy as np
 from ase.data import chemical_symbols
+import h5py
 
 from pynxtools.nexus import nexus
 from pynxtools.nexus.nexus import NxdlAttributeError
@@ -583,12 +585,22 @@ def convert_to_hill(atoms_typ):
     return atom_list + list(atoms_typ)
 
 
+def add_default_root_attributes(data, filename):
+    """Takes a dict/Template and adds NXroot fields/attributes that are inherently available"""
+    data["/@NX_class"] = "NXroot"
+    data["/@file_name"] = filename
+    data["/@file_time"] = str(datetime.now(timezone.utc).astimezone())
+    data["/@file_update_time"] = data["/@file_time"]
+    data["/@NeXus_version"] = "NOT_IMPLEMENTED"
+    data["/@HDF5_version"] = '.'.join(map(str, h5py.h5.get_libversion()))  # pylint: disable=c-extension-no-member
+    data["/@h5py_version"] = h5py.__version__
+
+
 def extract_atom_types(formula, mode='hill'):
     """Extract atom types form chemical formula."""
-
     atom_types: set = set()
     element: str = ""
-    # tested with "(C38H54S4)n(NaO2)5(CH4)NH3B"
+
     for char in formula:
         if char.isalpha():
             if char.isupper() and element == "":

pynxtools/nexus/nxdl_utils.py

@@ -701,6 +701,9 @@ def get_node_at_nxdl_path(nxdl_path: str = None,
     we are looking for or the root elem from a previously loaded NXDL file
     and finds the corresponding XML element with the needed attributes."""
     try:
+        if nxdl_path.count("/") == 1 and nxdl_path not in ("/ENTRY", "/entry"):
+            elem = None
+            nx_name = "NXroot"
         (class_path, nxdlpath, elist) = get_inherited_nodes(nxdl_path, nx_name, elem)
     except ValueError as value_error:
         if exc:

tests/dataconverter/test_helpers.py

@@ -162,6 +162,7 @@ def fixture_filled_test_data(template, tmp_path):
 TEMPLATE["lone_groups"] = ['/ENTRY[entry]/required_group',
                            '/ENTRY[entry]/required_group2',
                            '/ENTRY[entry]/optional_parent/req_group_in_opt_group']
+TEMPLATE["optional"]["/@default"] = "Some NXroot attribute"
 
 
 @pytest.mark.parametrize("data_dict,error_message", [

tests/dataconverter/test_readers.py

@@ -105,7 +105,7 @@ def test_has_correct_read_func(reader):
 
 
 @pytest.mark.parametrize("reader_name,nxdl,undocumented_keys", [
-    ('mpes', 'NXmpes', ['/@default'])
+    ('mpes', 'NXmpes', [])
 ])
 def test_shows_correct_warnings(reader_name, nxdl, undocumented_keys):
     """