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FAIRmat-NFDI · Apr 26, 2024 · 485ffd9 · 485ffd9
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Showing 6 changed files with 53 additions and 42 deletions.
diff --git a/pynxtools/dataconverter/convert.py b/pynxtools/dataconverter/convert.py
@@ -37,7 +37,7 @@
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.template import Template
 from pynxtools.dataconverter.writer import Writer
-from pynxtools.nexus import nexus
+from pynxtools.definitions.dev_tools.utils.nxdl_utils import get_nexus_definitions_path
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -120,7 +120,7 @@ def get_nxdl_root_and_path(nxdl: str):
         Error if no file with the given nxdl name is found.
     """
     # Reading in the NXDL and generating a template
-    definitions_path = nexus.get_nexus_definitions_path()
+    definitions_path = get_nexus_definitions_path()
     if nxdl == "NXtest":
         nxdl_f_path = os.path.join(
             f"{os.path.abspath(os.path.dirname(__file__))}/../../",

diff --git a/pynxtools/dataconverter/helpers.py b/pynxtools/dataconverter/helpers.py
@@ -31,6 +31,7 @@
 from ase.data import chemical_symbols
 from pint import UndefinedUnitError
 
+import pynxtools.definitions.dev_tools.utils.nxdl_utils as nexus
 from pynxtools import get_nexus_version, get_nexus_version_hash
 from pynxtools.dataconverter.template import Template
 from pynxtools.dataconverter.units import ureg
@@ -40,6 +41,9 @@
     get_inherited_nodes,
     get_node_at_nxdl_path,
 )
+from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
+    get_required_string as nexus_get_required_string,
+)
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -212,7 +216,7 @@ def get_all_defined_required_children(nxdl_path, nxdl_name):
     if nxdl_name == "NXtest":
         return []
 
-    elist = nexus.get_inherited_nodes(nxdl_path, nx_name=nxdl_name)[2]
+    elist = get_inherited_nodes(nxdl_path, nx_name=nxdl_name)[2]
     list_of_children_to_add = set()
     for elem in elist:
         list_of_children_to_add.update(get_all_defined_required_children_for_elem(elem))
@@ -315,7 +319,7 @@ def generate_template_from_nxdl(
 
 def get_required_string(elem):
     """Helper function to return nicely formatted names for optionality."""
-    return nexus.get_required_string(elem)[2:-2].lower()
+    return nexus_get_required_string(elem)[2:-2].lower()
 
 
 def convert_nexus_to_caps(nexus_name):

diff --git a/pynxtools/dataconverter/verify.py b/pynxtools/dataconverter/verify.py
@@ -29,7 +29,7 @@
 
 from pynxtools.dataconverter import helpers
 from pynxtools.dataconverter.template import Template
-from pynxtools.nexus import nexus
+from pynxtools.definitions.dev_tools.utils.nxdl_utils import get_nexus_definitions_path
 
 logger = logging.getLogger(__name__)
 
@@ -68,7 +68,7 @@ def _get_def_map(file: str) -> Dict[str, str]:
 
 
 def _get_nxdl_root(nxdl: str) -> ET.Element:
-    definitions_path = nexus.get_nexus_definitions_path()
+    definitions_path = get_nexus_definitions_path()
     nxdl_path = os.path.join(
         definitions_path, "contributed_definitions", f"{nxdl}.nxdl.xml"
     )

diff --git a/pynxtools/dataconverter/writer.py b/pynxtools/dataconverter/writer.py
@@ -29,6 +29,10 @@
 
 from pynxtools.dataconverter import helpers
 from pynxtools.dataconverter.exceptions import InvalidDictProvided
+from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
+    NxdlAttributeNotFoundError,
+    get_node_at_nxdl_path,
+)
 from pynxtools.nexus import nexus
 
 logger = logging.getLogger(__name__)  # pylint: disable=C0103
@@ -219,10 +223,8 @@ def __nxdl_to_attrs(self, path: str = "/") -> dict:
         nxdl_path = helpers.convert_data_converter_dict_to_nxdl_path(path)
 
         try:
-            elem = nexus.get_node_at_nxdl_path(
-                nxdl_path, elem=copy.deepcopy(self.nxdl_data)
-            )
-        except nexus.NxdlAttributeNotFoundError:
+            elem = get_node_at_nxdl_path(nxdl_path, elem=copy.deepcopy(self.nxdl_data))
+        except NxdlAttributeNotFoundError:
             return None
 
         # Remove the name attribute as we only use it to name the HDF5 entry

diff --git a/tests/data/dataconverter/readers/json_map/data.mapping.json b/tests/data/dataconverter/readers/json_map/data.mapping.json
@@ -1,14 +1,14 @@
 {
-    "/ENTRY[entry]/NXODD_name[odd_name]/bool_value": "/a_level_down/bool_value",
-    "/ENTRY[entry]/NXODD_name[odd_name]/char_value": "/a_level_down/char_value",
-    "/ENTRY[entry]/NXODD_name[odd_name]/date_value": "/date_value",
-    "/ENTRY[entry]/NXODD_name[odd_name]/float_value": "/a_level_down/float_value",
-    "/ENTRY[entry]/NXODD_name[odd_name]/float_value/@units": "/a_level_down/float_value_units",
-    "/ENTRY[entry]/NXODD_name[odd_name]/int_value": "/a_level_down/int_value",
-    "/ENTRY[entry]/NXODD_name[odd_name]/int_value/@units": "/a_level_down/another_level_down/int_value_units",
-    "/ENTRY[entry]/NXODD_name[odd_name]/posint_value": "/a_level_down/another_level_down/posint_value",
-    "/ENTRY[entry]/NXODD_name[odd_name]/posint_value/@units": "/posint_value_units",
-    "/ENTRY[entry]/NXODD_name[odd_name]/type": "/type",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/bool_value": "/a_level_down/bool_value",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/char_value": "/a_level_down/char_value",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/date_value": "/date_value",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/float_value": "/a_level_down/float_value",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/float_value/@units": "/a_level_down/float_value_units",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/int_value": "/a_level_down/int_value",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/int_value/@units": "/a_level_down/another_level_down/int_value_units",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/posint_value": "/a_level_down/another_level_down/posint_value",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/posint_value/@units": "/posint_value_units",
+    "/ENTRY[entry]/NXODD_name[nxodd_name]/type": "/type",
     "/ENTRY[entry]/definition": "/definition",
     "/ENTRY[entry]/definition/@version": "/definition_version",
     "/ENTRY[entry]/optional_parent/optional_child": {

diff --git a/tests/nexus/test_nexus.py b/tests/nexus/test_nexus.py
@@ -22,6 +22,13 @@
 
 import lxml.etree as ET
 
+from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
+    get_inherited_nodes,
+    get_node_at_nxdl_path,
+    get_nx_attribute_type,
+    get_nx_classes,
+    get_nx_units,
+)
 from pynxtools.nexus import nexus
 
 logger = logging.getLogger(__name__)
@@ -35,16 +42,16 @@ def test_get_nexus_classes_units_attributes():
     the tested functions can be found in nexus.py file"""
 
     # Test 1
-    nexus_classes_list = nexus.get_nx_classes()
+    nexus_classes_list = get_nx_classes()
 
     assert "NXbeam" in nexus_classes_list
 
     # Test 2
-    nexus_units_list = nexus.get_nx_units()
+    nexus_units_list = get_nx_units()
     assert "NX_TEMPERATURE" in nexus_units_list
 
     # Test 3
-    nexus_attribute_list = nexus.get_nx_attribute_type()
+    nexus_attribute_list = get_nx_attribute_type()
     assert "NX_FLOAT" in nexus_attribute_list
 
 
@@ -86,59 +93,57 @@ def test_get_node_at_nxdl_path():
     local_dir = os.path.abspath(os.path.dirname(__file__))
     nxdl_file_path = os.path.join(local_dir, "../data/dataconverter/NXtest.nxdl.xml")
     elem = ET.parse(nxdl_file_path).getroot()
-    node = nexus.get_node_at_nxdl_path("/ENTRY/NXODD_name", elem=elem)
+    node = get_node_at_nxdl_path("/ENTRY/NXODD_name", elem=elem)
     assert node.attrib["type"] == "NXdata"
     assert node.attrib["name"] == "NXODD_name"
 
-    node = nexus.get_node_at_nxdl_path("/ENTRY/NXODD_name/float_value", elem=elem)
+    node = get_node_at_nxdl_path("/ENTRY/NXODD_name/float_value", elem=elem)
     assert node.attrib["type"] == "NX_FLOAT"
     assert node.attrib["name"] == "float_value"
 
-    node = nexus.get_node_at_nxdl_path(
-        "/ENTRY/NXODD_name/AXISNAME/long_name", elem=elem
-    )
+    node = get_node_at_nxdl_path("/ENTRY/NXODD_name/AXISNAME/long_name", elem=elem)
     assert node.attrib["name"] == "long_name"
 
     nxdl_file_path = os.path.join(local_dir, "../data/nexus/NXtest2.nxdl.xml")
     elem = ET.parse(nxdl_file_path).getroot()
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/measurement/EVENT_DATA_EM/USER/affiliation", elem=elem
     )
     assert node.attrib["name"] == "affiliation"
 
-    node = nexus.get_node_at_nxdl_path("/ENTRY/measurement", elem=elem)
+    node = get_node_at_nxdl_path("/ENTRY/measurement", elem=elem)
     assert node.attrib["type"] == "NXevent_data_em_set"
 
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/measurement/EVENT_DATA_EM/SPECTRUM_SET/collection", elem=elem
     )
     assert node.attrib["type"] == "NXdata"
 
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/measurement/EVENT_DATA_EM/SPECTRUM_SET/collection/DATA", elem=elem
     )
     assert node.attrib["type"] == "NX_NUMBER"
 
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/measurement/EVENT_DATA_EM/SPECTRUM_SET/collection/AXISNAME_indices",
         elem=elem,
     )
     assert node.attrib["name"] == "AXISNAME_indices"
 
-    node = nexus.get_node_at_nxdl_path("/ENTRY/COORDINATE_SYSTEM_SET", elem=elem)
+    node = get_node_at_nxdl_path("/ENTRY/COORDINATE_SYSTEM_SET", elem=elem)
     assert node.attrib["type"] == "NXcoordinate_system_set"
 
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/COORDINATE_SYSTEM_SET/TRANSFORMATIONS", elem=elem
     )
     assert node.attrib["type"] == "NXtransformations"
 
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/COORDINATE_SYSTEM_SET/TRANSFORMATIONS/AXISNAME", elem=elem
     )
     assert node.attrib["type"] == "NX_NUMBER"
 
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/COORDINATE_SYSTEM_SET/TRANSFORMATIONS/AXISNAME/transformation_type",
         elem=elem,
     )
@@ -149,12 +154,12 @@ def test_get_node_at_nxdl_path():
         "../../pynxtools/definitions/contributed_definitions/NXiv_temp.nxdl.xml",
     )
     elem = ET.parse(nxdl_file_path).getroot()
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/INSTRUMENT/ENVIRONMENT/voltage_controller", elem=elem
     )
     assert node.attrib["name"] == "voltage_controller"
 
-    node = nexus.get_node_at_nxdl_path(
+    node = get_node_at_nxdl_path(
         "/ENTRY/INSTRUMENT/ENVIRONMENT/voltage_controller/calibration_time", elem=elem
     )
     assert node.attrib["name"] == "calibration_time"
@@ -168,17 +173,17 @@ def test_get_inherited_nodes():
         "../../pynxtools/definitions/contributed_definitions/NXiv_temp.nxdl.xml",
     )
     elem = ET.parse(nxdl_file_path).getroot()
-    (_, _, elist) = nexus.get_inherited_nodes(
+    (_, _, elist) = get_inherited_nodes(
         nxdl_path="/ENTRY/INSTRUMENT/ENVIRONMENT", elem=elem
     )
     assert len(elist) == 3
 
-    (_, _, elist) = nexus.get_inherited_nodes(
+    (_, _, elist) = get_inherited_nodes(
         nxdl_path="/ENTRY/INSTRUMENT/ENVIRONMENT/voltage_controller", elem=elem
     )
     assert len(elist) == 4
 
-    (_, _, elist) = nexus.get_inherited_nodes(
+    (_, _, elist) = get_inherited_nodes(
         nxdl_path="/ENTRY/INSTRUMENT/ENVIRONMENT/voltage_controller",
         nx_name="NXiv_temp",
     )