Fixes #121. Raises exception when wrong dict found. (#122)

pynxtools/dataconverter/exceptions.py

@@ -0,0 +1,22 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""Exceptions defined for use with the Dataconverter"""
+
+
+class InvalidDictProvided(Exception):
+    """An exception for a situation when an unexpected Python dict is provided"""

pynxtools/dataconverter/writer.py

@@ -29,6 +29,7 @@
 
 from pynxtools.dataconverter import helpers
 from pynxtools.nexus import nexus
+from pynxtools.dataconverter.exceptions import InvalidDictProvided
 
 logger = logging.getLogger(__name__)  # pylint: disable=C0103
 logger.setLevel(logging.INFO)
@@ -158,6 +159,11 @@ def handle_dicts_entries(data, grp, entry_name, output_path, path):
                                compression_opts=strength)
         else:
             grp.create_dataset(entry_name, data=data["compress"])
+    else:
+        print("comes here!!")
+        raise InvalidDictProvided("A dictionary was provided to the template but it didn't"
+                                  " fall into any of the know cases of handling"
+                                  " dictionaries. This occured for: " + entry_name)
     return grp[entry_name]
 
 
@@ -260,6 +266,8 @@ def add_units_key(dataset, path):
                                                          self.output_path, path])
                     else:
                         dataset = grp.create_dataset(entry_name, data=data)
+            except InvalidDictProvided as exc:
+                print(str(exc))
             except Exception as exc:
                 raise IOError(f"Unknown error occured writing the path: {path} "
                               f"with the following message: {str(exc)}") from exc

tests/dataconverter/test_convert.py

@@ -18,8 +18,8 @@
 """Test cases for the convert script used to access the DataConverter."""
 
 import os
-from distutils import file_util
 import logging
+from setuptools import distutils
 from click.testing import CliRunner
 import pytest
 import h5py
@@ -32,17 +32,17 @@ def move_xarray_file_to_tmp(tmp_path):
     """Moves the xarray file, which is used to test linking into the tmp_path directory."""
     test_file_path = os.path.join(os.path.dirname(__file__),
                                   "../data/dataconverter/readers/mpes")
-    file_util.copy_file(os.path.join(test_file_path, "xarray_saved_small_calibration.h5"),
-                        os.path.join(tmp_path, "xarray_saved_small_calibration.h5"))
+    distutils.file_util.copy_file(os.path.join(test_file_path, "xarray_saved_small_calibration.h5"),
+                                  os.path.join(tmp_path, "xarray_saved_small_calibration.h5"))
 
 
 def restore_xarray_file_from_tmp(tmp_path):
     """Restores the xarray file from the tmp_path directory."""
     test_file_path = os.path.join(os.path.dirname(__file__),
                                   "../data/dataconverter/readers/mpes")
     os.remove(os.path.join(test_file_path, "xarray_saved_small_calibration.h5"))
-    file_util.move_file(os.path.join(tmp_path, "xarray_saved_small_calibration.h5"),
-                        os.path.join(test_file_path, "xarray_saved_small_calibration.h5"))
+    distutils.file_util.move_file(os.path.join(tmp_path, "xarray_saved_small_calibration.h5"),
+                                  os.path.join(test_file_path, "xarray_saved_small_calibration.h5"))
 
 
 @pytest.mark.parametrize("cli_inputs", [

tests/dataconverter/test_helpers.py

@@ -19,7 +19,7 @@
 
 import xml.etree.ElementTree as ET
 import os
-from distutils import file_util
+from setuptools import distutils
 import pytest
 import numpy as np
 
@@ -93,12 +93,12 @@ def fixture_filled_test_data(template, tmp_path):
     # Copy original measurement file to tmp dir,
     # because h5py.ExternalLink is modifying it while
     # linking the nxs file.
-    file_util.copy_file(f"{os.path.dirname(__file__)}"
-                        f"/../"
-                        f"data/dataconverter/"
-                        f"readers/mpes/"
-                        f"xarray_saved_small_cali"
-                        "bration.h5", tmp_path)
+    distutils.file_util.copy_file(f"{os.path.dirname(__file__)}"
+                                  f"/../"
+                                  f"data/dataconverter/"
+                                  f"readers/mpes/"
+                                  f"xarray_saved_small_cali"
+                                  "bration.h5", tmp_path)
 
     template.clear()
     template["optional"]["/ENTRY[my_entry]/NXODD_name/float_value"] = 2.0

tests/dataconverter/test_writer.py

@@ -21,9 +21,11 @@
 
 import pytest
 import h5py
+from pynxtools.dataconverter.exceptions import InvalidDictProvided
+
 
 from pynxtools.dataconverter.writer import Writer
-from .test_helpers import fixture_filled_test_data, fixture_template  # pylint: disable=unused-import
+from .test_helpers import fixture_filled_test_data, fixture_template, alter_dict  # pylint: disable=unused-import
 
 
 @pytest.mark.usefixtures("filled_test_data")
@@ -59,7 +61,23 @@ def test_write_link(writer):
 Checks whether entries given above get written out when a dictionary containing a link is
 given in the template dictionary."""
     writer.write()
-    print(writer)
-    print(type(writer))
     test_nxs = h5py.File(writer.output_path, "r")
     assert isinstance(test_nxs["/my_entry/links/ext_link"], h5py.Dataset)
+
+
+@pytest.mark.usefixtures("filled_test_data")
+def test_wrong_dict_provided_in_template(filled_test_data, tmp_path):
+    """Tests if the writer correctly fails when a wrong dictionary is provided"""
+    writer = Writer(
+        alter_dict(filled_test_data,
+                   "/ENTRY[my_entry]/links/ext_link",
+                   {"not a link or anything": 2.0}),
+        os.path.join("tests", "data", "dataconverter", "NXtest.nxdl.xml"),
+        os.path.join(tmp_path, "test.nxs")
+    )
+    with pytest.raises(InvalidDictProvided) as execinfo:
+        writer.write()
+        assert str(execinfo.value) == ("pynxtools.dataconverter.exceptions.InvalidDictProvided: "
+                                       "A dictionary was provided to the template but it didn't "
+                                       "fall into any of the know cases of handling dictionaries"
+                                       ". This occured for: ext_link")