Merged parser intergtion.

nomad/config.py

@@ -20,6 +20,11 @@ This module is used to store all configuration values. It makes use of
 import os
 import logging
 from collections import namedtuple
+import warnings
+
+warnings.filterwarnings("ignore", message="numpy.dtype size changed")
+warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
+
 
 FilesConfig = namedtuple(
     'FilesConfig', ['uploads_bucket', 'raw_bucket', 'archive_bucket', 'staging_bucket', 'public_bucket'])

nomad/normalizing/repository.py

@@ -18,6 +18,8 @@ from nomad.parsing import BadContextURI
 
 from .normalizer import Normalizer
 
+unavailable_label = 'unavailable'
+
 
 class RepositoryNormalizer(Normalizer):
     """
@@ -31,13 +33,16 @@ class RepositoryNormalizer(Normalizer):
         'hyb': 'hybrid',
         'mgga': 'meta-GGA',
         'vdw': 'vdW',
-        'lda': 'LDA'
+        'lda': 'LDA',
     }
     """ https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-functional """
 
     version_re = re.compile(r'(\d+(\.\d+(\.\d+)?)?)')
 
     def map_functional_name_to_xc_treatment(self, name):
+        if name == unavailable_label:
+            return name
+
         return RepositoryNormalizer.xc_treatments.get(name[:3].lower(), name)
 
     def simplify_version(self, version):
@@ -47,6 +52,12 @@ class RepositoryNormalizer(Normalizer):
         else:
             return match.group(0)
 
+    def get_optional_value(self, key):
+        try:
+            return self._backend.get_value(key, 0)
+        except KeyError:
+            return unavailable_label
+
     def normalize(self, logger=None) -> None:
         super().normalize(logger)
         b = self._backend
@@ -61,22 +72,25 @@ class RepositoryNormalizer(Normalizer):
         b.openNonOverlappingSection('section_repository_parserdata')
 
         b.addValue('repository_checksum', b.get_value('calc_hash', 0))
-        b.addValue('repository_chemical_formula', b.get_value('chemical_composition_bulk_reduced', 0))
-        b.addValue('repository_parser_id', b.get_value('parser_name', 0))
-        atom_labels = b.get_value('atom_labels', 0)
-        b.addValue('repository_atomic_elements', list(set(atom_labels)))
-        b.addValue('repository_atomic_elements_count', len(atom_labels))
-        b.addValue('repository_basis_set_type', b.get_value('program_basis_set_type', 0))
-        b.addValue('repository_crystal_system', b.get_value('crystal_system', 0))
         b.addValue('repository_program_name', b.get_value('program_name', 0))
         b.addValue(
             'repository_code_version',
             self.simplify_version(b.get_value('program_version', 0)))
-        b.addValue('repository_spacegroup_nr', b.get_value('space_group_number', 0))
+        b.addValue('repository_parser_id', b.get_value('parser_name', 0))
+
+        b.addValue('repository_chemical_formula', b.get_value('chemical_composition_bulk_reduced', 0))
+        atom_labels = b.get_value('atom_labels', 0)
+        b.addValue('repository_atomic_elements', list(set(atom_labels)))
+        b.addValue('repository_atomic_elements_count', len(atom_labels))
         b.addValue('repository_system_type', b.get_value('system_type', 0))
+
+        b.addValue('repository_crystal_system', self.get_optional_value('crystal_system'))
+        b.addValue('repository_spacegroup_nr', self.get_optional_value('space_group_number'))
+
+        b.addValue('repository_basis_set_type', self.get_optional_value('program_basis_set_type'))
         b.addValue(
             'repository_xc_treatment',
-            self.map_functional_name_to_xc_treatment(b.get_value('XC_functional_name', 0)))
+            self.map_functional_name_to_xc_treatment(self.get_optional_value(('XC_functional_name'))))
 
         b.closeNonOverlappingSection('section_repository_parserdata')
         if repository_info_context is None:

nomad/parsing/backend.py

@@ -449,6 +449,9 @@ class LocalBackend(LegacyParserBackend):
             if g_index != -1:
                 sections = [section for section in sections if section.gIndex == g_index]
 
+            if len(sections) == 0:
+                raise KeyError
+
             assert len(sections) == 1
             section = sections[0]
 

nomad/patch.py

@@ -12,14 +12,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import systax.analysis.symmetryanalyzer
+
+import matid.symmetry.symmetryanalyzer
+import matid.utils.segfault_protect
 
 
 # A patch for the segfault protection of systax (internally uses protection for spglib calls.)
 # We basically disable the protection. The multiprocessing based original protection.
-# somehow interfers with the celery work infrastructure and leads to a deaklock. Its a TODO.
+# somehow interfers with the celery work infrastructure and leads to a deadlock. Its a TODO.
 def segfault_protect_patch(f, *args, **kwargs):
     return f(*args, **kwargs)
 
 
-systax.analysis.symmetryanalyzer.segfault_protect = segfault_protect_patch
+matid.symmetry.symmetryanalyzer.segfault_protect = segfault_protect_patch
+matid.utils.segfault_protect.segfault_protect = segfault_protect_patch