def populate_element_name_table(engine, purge=False):
if not setup_table(engine, ElementNameProperty, purge):
return False
with session_scope(engine) as session:
ref = require_reference(session, 'wikipedia2016',
author='Wikipedia',
year=2016)
for z, name_en in enumerate(NAMES_EN, 1):
element = require_element(session, z)
prop = ElementNameProperty(element=element, name=name_en,
language_code='en', reference=ref)
session.add(prop)
for lang, name in _find_wikipedia_names(name_en).items():
prop = ElementNameProperty(element=element, name=name,
language_code=lang, reference=ref)
session.add(prop)
logger.debug('Processed {0}'.format(name_en))
session.commit()
return True
def populate_notation_type_table(engine, purge=False):
if not setup_table(engine, NotationType, purge):
return False
with session_scope(engine) as session:
ref_unattributed = require_reference(session, 'unattributed')
n = NotationType(name='Siegbahn', reference=ref_unattributed)
session.add(n)
n = NotationType(name='Atomic', reference=ref_unattributed)
session.add(n)
ref_iupac = \
require_reference(session, 'jenkins1991',
author='Jenkins, R. and Manne, R. and Robin, R. and Senemaud, C.',
year='1991',
pages='149--155',
journal='X-Ray Spectrometry',
title='{IUPAC} --- nomenclature system for x-ray spectroscopy',
volume='20')
n = NotationType(name='IUPAC', reference=ref_iupac)
session.add(n)
session.commit()
return True
def _query_with_references(self, q, exception, reference=None):
q = q.add_columns(Reference.bibtexkey)
q = q.join(Reference)
q = q.order_by(Reference.id)
with session_scope(self.engine) as session:
q = q.with_session(session)
results = OrderedDict((k, v) for * v, k in q.all())
# No results from query
if not results:
raise exception
# Check result from specified reference
if reference is not None:
if reference in results:
return one_or_list(results[reference]), reference
else:
raise exception
# Check result from preferred references
for reference in self.reference_priority:
if reference in results:
return one_or_list(results[reference]), reference
# Return first result
reference, value = results.popitem(last=False)
return one_or_list(value), reference
def _query_one(self, q, exception):
with session_scope(self.engine) as session:
q = q.with_session(session)
try:
return one_or_list(q.one())
except NoResultFound:
raise exception
def create_mock_database():
engine = create_engine('sqlite:///:memory:')
Base.metadata.create_all(engine) #@UndefinedVariable
elements = {}
data = [(26, 'Fe'), (8, 'O')]
with session_scope(engine) as session:
for z, symbol in data:
e = Element(z=z, symbol=symbol)
elements[z] = e
session.add(e)
session.commit()
ref1 = Reference(bibtexkey='ref1')
ref2 = Reference(bibtexkey='ref2')
data = [(26, 'Iron', 'Eisen', 55.845, 7874.0, ref1),
(26, 'Iron', 'Eisen', 58.0, 9000.0, ref2),
(8, 'Oxygen', 'Sauerstoff', 15.9994, 1.429, ref1)]
with session_scope(engine) as session:
for z, name_en, name_de, aw, rho, ref in data:
e = elements[z]
p = ElementNameProperty(element=e,
language_code='en',
name=name_en,
reference=ref)
session.add(p)
p = ElementNameProperty(element=e,
language_code='de',
name=name_de,
reference=ref)
session.add(p)
p = ElementAtomicWeightProperty(element=e, value=aw, reference=ref)
session.add(p)
p = ElementMassDensityProperty(element=e,
value_kg_per_m3=rho,
reference=ref)
session.add(p)
session.commit()
return engine
def populate_reference_table(engine, purge=False):
if not setup_table(engine, Reference, purge):
return False
with session_scope(engine) as session:
ref = Reference(bibtexkey='unattributed')
session.add(ref)
session.commit()
return True
def create_mock_database():
engine = create_engine('sqlite:///:memory:')
Base.metadata.create_all(engine) #@UndefinedVariable
elements = {}
data = [(26, 'Fe'), (8, 'O')]
with session_scope(engine) as session:
for z, symbol in data:
e = Element(z=z, symbol=symbol)
elements[z] = e
session.add(e)
session.commit()
ref1 = Reference(bibtexkey='ref1')
ref2 = Reference(bibtexkey='ref2')
data = [(26, 'Iron', 'Eisen', 55.845, 7874.0, ref1),
(26, 'Iron', 'Eisen', 58.0, 9000.0, ref2),
(8, 'Oxygen', 'Sauerstoff', 15.9994, 1.429, ref1)]
with session_scope(engine) as session:
for z, name_en, name_de, aw, rho, ref in data:
e = elements[z]
p = ElementNameProperty(element=e, language_code='en',
name=name_en, reference=ref)
session.add(p)
p = ElementNameProperty(element=e, language_code='de',
name=name_de, reference=ref)
session.add(p)
p = ElementAtomicWeightProperty(element=e, value=aw, reference=ref)
session.add(p)
p = ElementMassDensityProperty(element=e, value_kg_per_m3=rho,
reference=ref)
session.add(p)
session.commit()
return engine
def populate_atomic_shell_table(engine, purge=False):
if not setup_table(engine, AtomicShell, purge):
return False
with session_scope(engine) as session:
for n in range(1, 7 + 1):
s = AtomicShell(principal_quantum_number=n)
session.add(s)
session.commit()
return True
def populate_element_table(engine, purge=False):
if not setup_table(engine, Element, purge):
return False
with session_scope(engine) as session:
for z, symbol in enumerate(SYMBOLS, 1):
element = Element(z=z, symbol=symbol)
session.add(element)
session.commit()
return True
def populate_atomic_shell_notation_table(engine, purge=False):
if not setup_table(engine, AtomicShellNotationProperty, purge):
return False
with session_scope(engine) as session:
notation_types = [require_notation(session, 'iupac'),
require_notation(session, 'siegbahn'), ]
for n, notation in enumerate(SHELL_NOTATION, 1):
shell = require_shell(session, n)
for notation_type in notation_types:
p = AtomicShellNotationProperty(atomic_shell=shell,
value=notation,
value_html=notation,
value_latex=notation,
notation_type=notation_type)
session.add(p)
session.commit()
return True
def populate_element_atomic_weight_table(engine, purge=False):
if not setup_table(engine, ElementAtomicWeightProperty, purge):
return False
with session_scope(engine) as session:
r = requests.get('http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=Li&all=all&ascii=ascii2&isotype=some')
rdata = r.text
data = rdata.split('\n')
current_z = "1"
value = 0
for l in data:
z = re.search(r"Atomic\sNumber\s=\s([0-9]*)", l)
relative_mass = re.search(r"Relative\sAtomic\sMass\s=\s([0-9]*.{0,1}[0-9]*)", l)
composition = re.search(r"Isotopic\sComposition\s=\s([0-9]*.{0,1}[0-9]*)", l)
if z!=None:
if current_z != z.group(1):
current_z = z.group(1)
if value = 0:
value = None
atomicweight = ElementAtomicWeightProperty(value = value)
session.add(atomicweight)
value = 0
elif relative_mass!=None:
if relative_mass.group(1) == '':
r_m = 0.0
else:
r_m = float(relative_mass.group(1))
elif composition!=None:
if composition.group(1) == '':
c = 0.0
else:
c = float(composition.group(1))
value = value + r_m*c