CI

pynxtools/dataconverter/convert.py

@@ -34,7 +34,7 @@
 from pynxtools.dataconverter.template import Template
 from pynxtools.nexus import nexus
 
-from .logger import logger
+from pynxtools.dataconverter.logger import logger as pynx_logger
 
 
 def get_reader(reader_name) -> BaseReader:
@@ -60,7 +60,7 @@ def get_names_of_all_readers() -> List[str]:
     return all_readers
 
 
-# pylint: disable=too-many-arguments,too-many-locals
+# pylint: disable=too-many-arguments,too-many-locals,W1203
 def convert(input_file: Tuple[str],
             reader: str,
             nxdl: str,
@@ -72,8 +72,9 @@ def convert(input_file: Tuple[str],
             **kwargs):
     """The conversion routine that takes the input parameters and calls the necessary functions."""
     if logger_:
-        global logger
         logger = logger_
+    else:
+        logger = pynx_logger
     # Reading in the NXDL and generating a template
     definitions_path = nexus.get_nexus_definitions_path()
     if nxdl == "NXtest":
@@ -123,7 +124,7 @@ def convert(input_file: Tuple[str],
         if "/@default" in path:
             continue
         logger.info(
-            f"NO DOCUMENTATION: The path, {path}  is being written but has no documentation."
+            f"NO DOCUMENTATION: The path, {path} is being written but has no documentation."
         )
 
     helpers.add_default_root_attributes(data=data, filename=os.path.basename(output))

pynxtools/dataconverter/logger.py

@@ -1,3 +1,4 @@
+"""Logger for pynxtools"""
 #
 # Copyright The NOMAD Authors.
 #

tests/dataconverter/test_helpers.py

@@ -24,6 +24,7 @@
 import numpy as np
 
 from pynxtools.dataconverter import helpers
+from pynxtools.dataconverter.logger import logger as pynx_logger
 from pynxtools.dataconverter.template import Template
 
 
@@ -286,7 +287,7 @@ def fixture_filled_test_data(template, tmp_path):
         id="opt-group-completely-removed"
     ),
 ])
-def test_validate_data_dict(data_dict, error_message, template, nxdl_root, request):
+def test_validate_data_dict(caplog, data_dict, error_message, template, nxdl_root, request):
     """Unit test for the data validation routine"""
     if request.node.callspec.id in ("valid-data-dict",
                                     "lists",
@@ -298,11 +299,16 @@ def test_validate_data_dict(data_dict, error_message, template, nxdl_root, reque
                                     "link-dict-instead-of-bool",
                                     "allow-required-and-empty-group",
                                     "opt-group-completely-removed"):
-        helpers.validate_data_dict(template, data_dict, nxdl_root)
+        helpers.validate_data_dict(template, data_dict, nxdl_root, logger=pynx_logger)
     else:
-        with pytest.raises(Exception) as execinfo:
-            helpers.validate_data_dict(template, data_dict, nxdl_root)
-        assert (error_message) == str(execinfo.value)
+        try:
+            captured_logs = caplog.records
+            helpers.validate_data_dict(template, data_dict, nxdl_root, pynx_logger)
+            assert any(error_message in rec.message for rec in captured_logs)
+        except Exception:
+            with pytest.raises(Exception) as execinfo:
+                helpers.validate_data_dict(template, data_dict, nxdl_root, pynx_logger)
+            assert (error_message) == str(execinfo.value)
 
 
 @pytest.mark.parametrize("nxdl_path,expected", [

tests/dataconverter/test_readers.py

@@ -25,6 +25,7 @@
 import pytest
 from _pytest.mark.structures import ParameterSet
 
+from pynxtools.dataconverter.logger import logger as pynx_logger
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.convert import \
     get_names_of_all_readers, get_reader
@@ -101,7 +102,7 @@ def test_has_correct_read_func(reader):
             read_data = reader().read(template=Template(template), file_paths=tuple(input_files))
 
             assert isinstance(read_data, Template)
-            assert validate_data_dict(template, read_data, root)
+            assert validate_data_dict(template, read_data, root, logger=pynx_logger)
 
 
 @pytest.mark.parametrize("reader_name,nxdl,undocumented_keys", [
@@ -129,5 +130,5 @@ def test_shows_correct_warnings(reader_name, nxdl, undocumented_keys):
         template=Template(template), file_paths=tuple(input_files)
     )
 
-    assert validate_data_dict(template, read_data, root)
+    assert validate_data_dict(template, read_data, root, logger=pynx_logger)
     assert list(read_data.undocumented.keys()) == undocumented_keys