Add test for processing empty section

nomad/normalizing/metainfo.py

@@ -47,16 +47,11 @@ class MetainfoNormalizer(Normalizer):
         logger = logger.bind(normalizer=self.__class__.__name__)
         self.logger = logger
 
-        if self.entry_archive.data:
-            sections = list(self.entry_archive.data.m_traverse())
-            if sections:
+        for sub_section in self.entry_archive.m_contents():
+            if isinstance(sub_section, EntryData):
+                sections = list(sub_section.m_traverse())
                 for section, _, _ in sections:
                     self.normalize_section(section, logger)
-            else:
-                self.normalize_section(self.entry_archive.data, logger)
-
-        for sub_section in self.entry_archive.m_contents():
-            if not isinstance(sub_section, EntryData):
-                self.normalize_section(sub_section, logger)
+            self.normalize_section(sub_section, logger)
 
         self.normalize_section(self.entry_archive, logger)

tests/data/datamodel/metainfo/eln/material_library/chemical-empty.archive.json

+{
+    "data": {
+        "m_def": "nomad.datamodel.metainfo.eln.material_library.Chemical"
+    }
+}
\ No newline at end of file

tests/datamodel/metainfo/eln/test_material_libary.py

@@ -16,33 +16,25 @@
 # limitations under the License.
 #
 
-from nomad.datamodel.context import ServerContext
-from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
-from nomad.parsing.parser import ArchiveParser
-from nomad.processing.data import Upload
-
-from tests.normalizing.conftest import run_normalize
-from tests.test_files import create_test_upload_files
+from tests.normalizing.conftest import run_processing
 
 
 def test_processing(raw_files, no_warn):
     directory = 'tests/data/datamodel/metainfo/eln/material_library'
     mainfile = 'example.archive.json'
-
-    # create upload with example files
-    upload_files = create_test_upload_files('test_upload_id', published=False, raw_files=directory)
-    upload = Upload(upload_id='test_upload_id')
-
-    # parse
-    parser = ArchiveParser()
-    context = ServerContext(upload=upload)
-    test_archive = EntryArchive(m_context=context, metadata=EntryMetadata())
-    parser.parse(
-        upload_files.raw_file_object(mainfile).os_path,
-        test_archive)
-    run_normalize(test_archive)
+    test_archive = run_processing(directory, mainfile)
 
     # assert archive
+    assert test_archive.metadata.entry_type == 'Sample'
     assert len(test_archive.data.processes.pvd_evaporation.substrate_temperature) > 0
     assert len(test_archive.data.measurements.xray_diffraction[0].two_theta) > 0
     assert len(test_archive.data.layers) == 1
+
+
+def test_processing_empty_chemical(raw_files, no_warn):
+    directory = 'tests/data/datamodel/metainfo/eln/material_library'
+    mainfile = 'chemical-empty.archive.json'
+    test_archive = run_processing(directory, mainfile)
+
+    # assert archive
+    assert test_archive.metadata.entry_type == 'Chemical'

tests/normalizing/conftest.py

@@ -47,6 +47,11 @@ from tests.parsing.test_parsing import parsed_vasp_example  # pylint: disable=un
 from tests.parsing.test_parsing import parsed_template_example  # pylint: disable=unused-import
 from tests.parsing.test_parsing import parsed_example  # pylint: disable=unused-import
 from tests.parsing.test_parsing import parse_file
+from nomad.datamodel.context import ServerContext
+from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
+from nomad.parsing.parser import ArchiveParser
+from nomad.processing.data import Upload
+from tests.test_files import create_test_upload_files
 
 
 def run_normalize(entry_archive: EntryArchive) -> EntryArchive:
@@ -56,6 +61,22 @@ def run_normalize(entry_archive: EntryArchive) -> EntryArchive:
     return entry_archive
 
 
+def run_processing(directory, mainfile):
+    # create upload with example files
+    upload_files = create_test_upload_files('test_upload_id', published=False, raw_files=directory)
+    upload = Upload(upload_id='test_upload_id')
+
+    # parse
+    parser = ArchiveParser()
+    context = ServerContext(upload=upload)
+    test_archive = EntryArchive(m_context=context, metadata=EntryMetadata())
+    parser.parse(
+        upload_files.raw_file_object(mainfile).os_path,
+        test_archive)
+    run_normalize(test_archive)
+    return test_archive
+
+
 @pytest.fixture
 def normalized_vasp_example(parsed_vasp_example: EntryArchive) -> EntryArchive:
     return run_normalize(parsed_vasp_example)