def _generate_code_concepts(self):
try:
self.code_cui=shelve.open(self._concepts_file + ".by_code", flag='r')
except:
self.code_cui=shelve.open(self._concepts_file + ".by_code")
for c in self.concepts:
self.code_cui[self.concepts[c].RxCUI]=c
self.code_cui.close()
self.code_cui=shelve.open(self._concepts_file + ".by_code", flag='r')
return
def __init__(self, concepts_file, relations_file, ingredients_file):
self._concepts_file = concepts_file
self._relations_file = relations_file
self._ingredients_file = ingredients_file
# 'concepts' is a dictionary of Drug objects indexed by CUI
self.concepts = shelve.open(self._concepts_file)
# 'relations' is a list of Relation objects
self._relations = shelve.open(self._relations_file)
# 'formulas' is a dictionary of sets of Drug objects indexed
# by the CUI of the drug of which they are a formulation
self.formulas = shelve.open(self._ingredients_file)
self._tradename_relations = None
self._generate_code_concepts()
def __setstate__(self, state):
global type_kinds
global reverse_type_kinds
curdir=os.path.dirname(__file__)
self._concepts_file=state['c']
self._relations_file=state['r']
self._ingredients_file=state['f']
try:
self.concepts = shelve.open(self._concepts_file, flag='r')
except:
# If the file wasn't found, try the current directory (necessary for the WSGI version).
self._concepts_file=os.path.join(curdir, self._concepts_file)
self.concepts = shelve.open(self._concepts_file, flag='r')
try:
self._relations = shelve.open(self._relations_file, flag='r')
except:
self._relations_file = os.path.join(curdir, self._relations_file)
self._relations = shelve.open(self._relations_file, flag='r')
try:
self.formulas = shelve.open(self._ingredients_file, flag='r')
except:
self._ingredients_file=os.path.join(curdir, self._ingredients_file)
self.formulas=shelve.open(self._ingredients_file, flag='r')
type_kinds = state['t']
reverse_type_kinds = state['rt']
self._tradename_relations = None
self._generate_code_concepts()
def __init__(self, rxnorm, treatment, drug_problem=None, concept_name_index=None):
self._rxnorm = rxnorm
self._treatment = treatment
self._drug_problem = drug_problem
concept_names = {}
if concept_name_index is not None:
self._concept_names = shelve.open(concept_name_index, flag='r')
return
for c in rxnorm.concepts:
cn = rxnorm.concepts[c]._name.lower()
cn = cn.split('@')[0].strip() # Just use stuff to the left of a @ for a concept name
if cn in concept_names:
concept_names[cn].add(c)
else:
concept_names[cn] = set([c])
# Use a shelf for
self._concept_names = concept_names
def __init__(self,
rxnorm,
treatment,
drug_problem=None,
concept_name_index=None):
self._rxnorm = rxnorm
self._treatment = treatment
self._drug_problem = drug_problem
concept_names = {}
if concept_name_index is not None:
self._concept_names = shelve.open(concept_name_index, flag='r')
return
for c in rxnorm.concepts:
cn = rxnorm.concepts[c]._name.lower()
cn = cn.split('@')[0].strip(
) # Just use stuff to the left of a @ for a concept name
if cn in concept_names:
concept_names[cn].add(c)
else:
concept_names[cn] = set([c])
# Use a shelf for
self._concept_names = concept_names
print >> sys.stderr, "Ingredients for 10 random drugs:"
for x in [random.choice(ingredients.keys()) for x in xrange(10)]:
print >> sys.stderr, "Ingredients for", concepts[x]._name, ":", [y for y in ingredients[x]]
print >> sys.stderr, "Ingredients that are Pharmacologic Substances for", concepts[x]._name, ":", ', '.join(
y._name for y in ingredients[x] if 'Pharmacologic Substance' in y.semtypes)
print
zoloft = concept_names['zoloft']
for z in zoloft:
print >> sys.stderr, "Ingredients for", concepts[z]._name, ":", [y for y in ingredients[z]]
conc_file = "concepts." + save_file
print >> sys.stderr, "Shelving concepts to", conc_file
#conc_shelf = dbmaccess.open(conc_file, protocol=pickle.HIGHEST_PROTOCOL)
conc_shelf = shelve.open(conc_file, protocol=pickle.HIGHEST_PROTOCOL)
count = 0
for c in concepts:
conc_shelf[c] = concepts[c]
count += 1
display_count(count)
conc_shelf.close()
print >> sys.stderr
ing_file = "ingredients." + save_file
print >> sys.stderr, "Shelving ingredients to", ing_file
ing_shelf = shelve.open(ing_file, protocol=pickle.HIGHEST_PROTOCOL)
count = 0
for i in ingredients:
ing_shelf[i] = ingredients[i]