nuclides.py
ArthurPSmith (Arthur Smith)
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	ArthurPSmith
	Oct 9 2015, 5:08 PM

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nuclides.py
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	import json
	import operator
	from units import time_quantity_in_seconds
	from urllib import urlencode
	from urllib2 import urlopen
	from collections import defaultdict

	try:
	from functools import ttl_cache
	except ImportError:
	from cachetools import ttl_cache


	# cachetools does not support maxsize=None
	@ttl_cache(maxsize=20, ttl=21600)
	def get_json_cached(url, data):
	"""The information is cached for 6 hours."""
	return json.load(urlopen(url, data))


	def get_json(url, data):
	return get_json_cached(url, urlencode(data))


	class NuclideProvider(object):
	"""Base class for nuclide providers."""

	WD_API = 'http://www.wikidata.org/w/api.php'
	API_LIMIT = 50
	WDQ_API = 'http://wdq.wmflabs.org/api'

	def __init__(self, language):
	self.language = language

	@classmethod
	def get_available_languages(cls):
	query = dict(action='query', format='json', meta='siteinfo', siprop='languages')
	result = get_json(cls.WD_API, query).get('query', {}).get('languages', [])
	return [lang['code'] for lang in result]

	@classmethod
	def get_entities(cls, ids, **kwargs):
	entities = {}
	query = dict(action='wbgetentities', format='json', **kwargs)
	for index in range(0, len(ids), cls.API_LIMIT):
	query['ids'] = '\|'.join(ids[index:index + cls.API_LIMIT])
	new_entities = get_json(cls.WD_API, query).get('entities', {})
	entities.update(new_entities)
	return entities

	def iter_good(self):
	iterator = iter(self)
	while True:
	try:
	yield next(iterator)
	except StopIteration:
	raise

	def get_table(self):
	table = {}
	nuclides = []
	incomplete = []
	lastanum = -1
	lastnnum = -1
	for nuclide in self.iter_good():
	if nuclide.atomic_number is not None and nuclide.neutron_number is not None:
	if nuclide.atomic_number > lastanum:
	lastanum = nuclide.atomic_number
	if nuclide.neutron_number > lastnnum:
	lastnnum = nuclide.neutron_number
	if nuclide.atomic_number not in table:
	table[nuclide.atomic_number] = {}
	table[nuclide.atomic_number][nuclide.neutron_number] = nuclide
	nuclides.append(nuclide)
	else:
	incomplete.append(nuclide)
	nuclides.sort(key=operator.attrgetter('atomic_number', 'neutron_number'))
	for anum in range(0, lastanum+1):
	if anum not in table:
	table[anum] = {}
	for nnum in range(0,lastnnum+1):
	if nnum in table[anum]:
	table[anum][nnum].__class__ = NuclideCell
	else:
	table[anum][nnum] = EmptyCell()

	return nuclides, table, incomplete


	class WdqNuclideProvider(NuclideProvider):
	"""Load nuclides from Wikidata Query."""
	def __iter__(self):
	wdq = self.get_wdq()
	ids = ['Q%d' % item_id for item_id in wdq['items']]
	entities = self.get_entities(ids, props='labels\|claims',
	languages=self.language, languagefallback=1)
	nuclides = defaultdict(Nuclide)
	wdq['props'] = defaultdict(list, wdq.get('props', {}))
	for item_id, datatype, value in wdq['props'][str(Nuclide.atomic_number_pid)]:
	if datatype != 'quantity':
	continue
	value = value.split('\|')
	if len(value) == 4:
	value = map(float, value)
	if len(set(value[:3])) == 1 and value[3] == 1 and value[0] == int(value[0]):
	nuclides[item_id].atomic_number = int(value[0])
	for item_id, datatype, value in wdq['props'][str(Nuclide.neutron_number_pid)]:
	if datatype != 'quantity':
	continue
	value = value.split('\|')
	if len(value) == 4:
	value = map(float, value)
	if len(set(value[:3])) == 1 and value[3] == 1 and value[0] == int(value[0]):
	nuclides[item_id].neutron_number = int(value[0])
	for item_id, datatype, value in wdq['props'][str(Nuclide.decay_mode_pid)]:
	if datatype != 'item':
	continue
	nuclides[item_id].decay_modes.append(value)
	for item_id, nuclide in nuclides.items():
	nuclide.item_id = 'Q%d' % item_id
	for prop in ('atomic_number', 'neutron_number'):
	if not hasattr(nuclide, prop):
	setattr(nuclide, prop, None)
	# ?? nuclide.load_data_from_superclasses(subclass_of[item_id])
	label = None
	entity = entities.get(nuclide.item_id)
	if entity and 'labels' in entity and len(entity['labels']) == 1:
	label = entity['labels'].values()[0]['value']
	nuclide.label = label

	half_life = "unknown";
	if entity:
	claims = entity['claims']
	hlprop = 'P%d' % Nuclide.half_life_pid
	if hlprop in claims:
	hl_claims = claims[hlprop]
	for hl_claim in hl_claims:
	half_life = time_quantity_in_seconds(hl_claim)
	nuclide.half_life = half_life

	yield nuclide

	@classmethod
	def get_wdq(cls):
	pids = [str(getattr(Nuclide, name))
	for name in ('atomic_number_pid', 'neutron_number_pid', 'decay_mode_pid')]
	query = {
	'q': 'claim[%d:(tree[%d][][%d])]' % (Nuclide.instance_pid, Nuclide.isotope_qid, Nuclide.subclass_pid),
	'props': ','.join(pids)
	}
	return get_json(cls.WDQ_API, query)


	class PropertyAlreadySetException(Exception):
	"""Property already set."""


	class Nuclide(object):

	props = ('atomic_number', 'neutron_number', 'item_id', 'label', 'half_life', 'decay_modes')
	atomic_number_pid = 1086
	neutron_number_pid = 1148
	half_life_pid = 2114
	decay_mode_pid = 817
	instance_pid = 31
	subclass_pid = 279
	isotope_qid = 25276 # top-level class under which all isotopes to be found
	# isotope_qid = 471790

	def __init__(self, **kwargs):
	self.decay_modes = []
	for key, val in kwargs.items():
	if key in self.props:
	setattr(self, key, val)
	self.classes = []

	def __setattr__(self, key, value):
	if (key in self.props and hasattr(self, key) and
	getattr(self, key) is not None and getattr(self, key) != value):
	raise PropertyAlreadySetException
	super(Nuclide, self).__setattr__(key, value)

	def __iter__(self):
	for key in self.props:
	yield (key, getattr(self, key))


	class TableCell(object):
	"""A table cell."""

	class NuclideCell(Nuclide, TableCell):
	"""A nuclide cell."""

	class EmptyCell(TableCell):
	"""An empty cell."""

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