diff --git a/dependencies/nomad-meta-info b/dependencies/nomad-meta-info
index c3bb8b69771a3cc87ca500f80a182380175e09cf..6cc658ff3117dfccad9aace953d225385e59c5cf 160000
--- a/dependencies/nomad-meta-info
+++ b/dependencies/nomad-meta-info
@@ -1 +1 @@
-Subproject commit c3bb8b69771a3cc87ca500f80a182380175e09cf
+Subproject commit 6cc658ff3117dfccad9aace953d225385e59c5cf
diff --git a/nomad/config.py b/nomad/config.py
index 6ab76ca2c953d0f8ec37f577ce0f11f644d17369..b25ed02b14ea15e6edda2567fc89f87af5dbea53 100644
--- a/nomad/config.py
+++ b/nomad/config.py
@@ -206,6 +206,7 @@ max_upload_size = 32 * (1024 ** 3)
springer_db_relative_path = 'normalizing/data/SM_all08.db'
springer_db_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), springer_db_relative_path)
+
def normalize_loglevel(value, default_level=logging.INFO):
plain_value = value
if plain_value is None:
diff --git a/nomad/normalizing/system.py b/nomad/normalizing/system.py
index 90df65c1b7b697e4062dfdbeff297d2ed1651263..aef180f44f2655b7b8d1dc1548bc74e5b89b156a 100644
--- a/nomad/normalizing/system.py
+++ b/nomad/normalizing/system.py
@@ -42,9 +42,10 @@ atom_label_re = re.compile('|'.join(
springer_db_connection = None
+
def open_springer_database():
"""
- Create a global connection to the Springer database in a way that
+ Create a global connection to the Springer database in a way that
each worker opens the database just once.
"""
global springer_db_connection
@@ -54,10 +55,11 @@ def open_springer_database():
if not os.path.exists(db_file):
utils.get_logger(__name__).error('Springer database not found')
return None
- springer_db_connection = sqlite3.connect(db_file)
+ springer_db_connection = sqlite3.connect(db_file)
return springer_db_connection
+
def normalized_atom_labels(atom_labels):
"""
Normalizes the given atom labels: they either are labels right away, or contain
@@ -68,26 +70,26 @@ def normalized_atom_labels(atom_labels):
ase.data.chemical_symbols[0] if match is None else match.group(0)
for match in [re.search(atom_label_re, atom_label) for atom_label in atom_labels]]
+
def formula_normalizer(atoms):
"""
Reads the chemical symbols in ase.atoms and returns a normalized formula.
Formula normalization is on the basis of atom counting,
- e.g., Tc -> Tc100, SZn -> S50Zn50, Co2Nb -> Co67Nb33
+ e.g., Tc -> Tc100, SZn -> S50Zn50, Co2Nb -> Co67Nb33
"""
- #
+ #
chem_symb = atoms.get_chemical_symbols()
-
- atoms_counter = Counter(chem_symb) # dictionary
+ atoms_counter = Counter(chem_symb) # dictionary
atoms_total = sum(atoms_counter.values())
atoms_normed = []
for key in atoms_counter.keys():
- norm = str(round(100 * atoms_counter[key] / atoms_total))
- atoms_normed.append( key + norm)
+ norm = str(round(100 * atoms_counter[key] / atoms_total))
+ atoms_normed.append(key + norm)
#
atoms_normed.sort()
return ''.join(atoms_normed)
-
+
class SystemNormalizer(SystemBasedNormalizer):
@@ -170,7 +172,7 @@ class SystemNormalizer(SystemBasedNormalizer):
if atom_species is None:
atom_species = atoms.get_atomic_numbers().tolist()
self._backend.addArrayValues('atom_species', atom_species)
- else:
+ else:
if not isinstance(atom_species, list):
atom_species = [atom_species]
if atom_species != atoms.get_atomic_numbers().tolist():
@@ -385,31 +387,31 @@ class SystemNormalizer(SystemBasedNormalizer):
self._backend.addArrayValues('equivalent_atoms_original', orig_equivalent_atoms)
self._backend.closeSection('section_original_system', orig_gid)
self._backend.closeSection('section_symmetry', symmetry_gid)
-
- self.springer_classification(atoms, space_group_number) # Springer Normalizer
+
+ self.springer_classification(atoms, space_group_number) # Springer Normalizer
self.prototypes(prim_num, prim_wyckoff, space_group_number)
self._backend.closeSection('section_symmetry', symmetry_gid)
-
+
def springer_classification(self, atoms, space_group_number):
# SPRINGER NORMALIZER
- normalized_formula = formula_normalizer(atoms)
- #
+ normalized_formula = formula_normalizer(atoms)
+ #
springer_db_connection = open_springer_database()
- if springer_db_connection is None:
+ if springer_db_connection is None:
return
- cur = springer_db_connection.cursor()
+ cur = springer_db_connection.cursor()
- # SQL QUERY
+ # SQL QUERY
# (this replaces the four queries done in the old 'classify4me_SM_normalizer.py')
- cur.execute("""
+ cur.execute("""
SELECT
entry.entry_id,
entry.alphabetic_formula,
GROUP_CONCAT(DISTINCT compound_classes.compound_class_name),
- GROUP_CONCAT(DISTINCT classification.classification_name)
+ GROUP_CONCAT(DISTINCT classification.classification_name)
FROM entry
LEFT JOIN entry_compound_class as ecc ON ecc.entry_nr = entry.entry_nr
LEFT JOIN compound_classes ON ecc.compound_class_nr = compound_classes.compound_class_nr
@@ -422,57 +424,57 @@ class SystemNormalizer(SystemBasedNormalizer):
""" % (normalized_formula, space_group_number))
results = cur.fetchall()
# All SQL queries done
-
-
+
dbdict = {}
- for ituple in results:
+ for ituple in results:
for item in ituple:
# 'spr' means 'springer'
spr_id = ituple[0]
- spr_aformula = ituple[1] # alphabetical formula
+ spr_aformula = ituple[1] # alphabetical formula
spr_url = 'http://materials.springer.com/isp/crystallographic/docs/' + spr_id
spr_compound = ituple[2].split(',') # convert string to list
spr_classification = ituple[3].split(',')
- #
-
+ #
+
spr_compound.sort()
spr_classification.sort()
- dbdict[spr_id] = {'spr_id': spr_id,
- 'spr_aformula': spr_aformula,
- 'spr_url': spr_url,
- 'spr_compound': spr_compound,
- 'spr_classification': spr_classification }
-
+ dbdict[spr_id] = {'spr_id': spr_id,
+ 'spr_aformula': spr_aformula,
+ 'spr_url': spr_url,
+ 'spr_compound': spr_compound,
+ 'spr_classification': spr_classification}
- # SPRINGER's METAINFO UPDATE
- # LAYOUT: Five sections under 'section_springer_material' for each material ID:
+ # SPRINGER's METAINFO UPDATE
+ # LAYOUT: Five sections under 'section_springer_material' for each material ID:
# id, alphabetical formula, url, compound_class, clasification.
# As per Markus/Luca's emails, we don't expose Springer bib references (Springer's paywall)
- for material in dbdict.values():
- self._backend.openNonOverlappingSection('section_springer_material')
+ for material in dbdict.values():
+ self._backend.openNonOverlappingSection('section_springer_material')
self._backend.addValue('springer_id', material['spr_id'])
- self._backend.addValue('springer_alphabetical_formula', material['spr_aformula'])
+ self._backend.addValue('springer_alphabetical_formula', material['spr_aformula'])
self._backend.addValue('springer_url', material['spr_url'])
self._backend.addArrayValues('springer_compound_class', material['spr_compound'])
self._backend.addArrayValues('springer_classification', material['spr_classification'])
-
- self._backend.closeNonOverlappingSection('section_springer_material')
+ self._backend.closeNonOverlappingSection('section_springer_material')
- # CHECK if the springer_classification and springer_compound_class found for each springer_id match
+ # Check the 'springer_classification' and 'springer_compound_class' information
+ # found is the same for all springer_id's
dkeys = list(dbdict.keys())
- class_0 = dbdict[dkeys[0]]['spr_classification']
- comp_0 = dbdict[spr_id]['spr_compound']
-
- for ii in range(1, len(dkeys)):
- class_test = class_0 == dbdict[dkeys[ii]]['spr_classification']
- comp_test = comp_0 == dbdict[dkeys[ii]]['spr_compound']
-
- if (class_test or comp_test) is False:
- self.logger.warning('Mismatch in Springer classification or compounds')
-
+ if len(dkeys) != 0:
+ class_0 = dbdict[dkeys[0]]['spr_classification']
+ comp_0 = dbdict[spr_id]['spr_compound']
+
+ # compare 'class_0' and 'comp_0' against the rest
+ for ii in range(1, len(dkeys)):
+ class_test = (class_0 == dbdict[dkeys[ii]]['spr_classification'])
+ comp_test = (comp_0 == dbdict[dkeys[ii]]['spr_compound'])
+
+ if (class_test or comp_test) is False:
+ self.logger.warning('Mismatch in Springer classification or compounds')
+
def prototypes(self, atomSpecies, wyckoffs, spg_nr):
try:
norm_wyckoff = SystemNormalizer.get_normalized_wyckoff(atomSpecies, wyckoffs)
diff --git a/tests/test_normalizing.py b/tests/test_normalizing.py
index fb4aae49fd33f1fbaeb1530363b676c17021ff17..f9cf12c5a974ff6aa1449f698c8e4d2681506eb5 100644
--- a/tests/test_normalizing.py
+++ b/tests/test_normalizing.py
@@ -205,31 +205,31 @@ def test_vasp_incar_system():
"""
backend = parse_file(vasp_parser)
backend = run_normalize(backend)
- expected_value = 'SrTiO3' # material's formula in vasp.xml
+ expected_value = 'SrTiO3' # material's formula in vasp.xml
+
+ # backend_value = backend.get_value('x_vasp_unknown_incars') # OK
+ # backend_value = backend.get_value('x_vasp_atom_kind_refs') # OK
+ backend_value = backend.get_value('x_vasp_incar_SYSTEM') # OK
- #backend_value = backend.get_value('x_vasp_unknown_incars') # OK
- #backend_value = backend.get_value('x_vasp_atom_kind_refs') # OK
- backend_value = backend.get_value('x_vasp_incar_SYSTEM') # OK
-
print("backend_value: ", backend_value)
assert expected_value == backend_value
def test_springer_normalizer():
"""
- Ensure the Springer normalizer works well with the VASP example.
+ Ensure the Springer normalizer works well with the VASP example.
"""
backend = parse_file(vasp_parser)
backend = run_normalize(backend)
- backend_value = backend.get_value('springer_url', 89)
- # with get_value('springer_id') fails.
- expected_value = 'http://materials.springer.com/isp/crystallographic/docs/sd_1932539'
- print("backend_value: ", backend_value)
- assert expected_value == backend_value
+ backend_value = backend.get_value('springer_id', 89)
+ expected_value = 'sd_1932539'
+ assert expected_value == backend_value
- # FIXME: search for ID,
- # also check NON empty for the others
- # avois storing single use variables
+ backend_value = backend.get_value('springer_alphabetical_formula', 89)
+ expected_value = 'O3SrTi'
+ assert expected_value == backend_value
- # TODO: add test fo rptototypes
\ No newline at end of file
+ backend_value = backend.get_value('springer_url', 89)
+ expected_value = 'http://materials.springer.com/isp/crystallographic/docs/sd_1932539'
+ assert expected_value == backend_value