def score_producer(data, scorer, loader, r_server, lookup_data,
datasources_to_datatypes, dry_run):
target, disease, evidence, is_direct = data
logger = logging.getLogger(__name__)
if evidence:
score = scorer.score(target, disease, evidence, is_direct,
datasources_to_datatypes)
# skip associations only with data with score 0
if score:
gene_data = Gene()
try:
gene_data.load_json(
lookup_data.available_genes.get_gene(target, r_server))
except KeyError as e:
logger.debug('Cannot find gene code "%s" '
'in lookup table' % target)
raise e
score.set_target_data(gene_data)
# create a hpa expression empty jsonserializable class
# to fill from Redis cache lookup_data
hpa_data = HPAExpression()
try:
hpa_data.update(
lookup_data.available_hpa.get_hpa(target, r_server))
except KeyError:
pass
except Exception as e:
raise e
try:
score.set_hpa_data(hpa_data)
except KeyError:
pass
except Exception as e:
raise e
disease_data = EFO()
try:
disease_data.load_json(
lookup_data.available_efos.get_efo(disease, r_server))
except KeyError as e:
logger.debug('Cannot find EFO code "%s" '
'in lookup table' % disease)
logger.exception(e)
score.set_disease_data(disease_data)
element_id = '%s-%s' % (target, disease)
if not dry_run:
loader.put(Const.ELASTICSEARCH_DATA_ASSOCIATION_INDEX_NAME,
Const.ELASTICSEARCH_DATA_ASSOCIATION_DOC_NAME,
element_id, score)
else:
logger.warning('Skipped association with score 0: %s-%s' %
(target, disease))
def score_producer(data,
scorer, lookup_data, datasources_to_datatypes, dry_run):
target, disease, evidence, is_direct = data
if evidence:
score = scorer.score(target, disease, evidence, is_direct,
datasources_to_datatypes)
# skip associations only with data with score 0
if score:
gene_data = Gene()
gene_data_index = lookup_data.available_genes.get_gene(target)
if gene_data_index != None:
gene_data.load_json(gene_data_index)
score.set_target_data(gene_data)
# create a hpa expression empty jsonserializable class
hpa_data = HPAExpression()
try:
hpa_index = lookup_data.available_hpa.get_hpa(target)
if hpa_index is not None:
hpa_data.update(hpa_index)
except KeyError:
pass
except Exception as e:
raise e
try:
score.set_hpa_data(hpa_data)
except KeyError:
pass
except Exception as e:
raise e
disease_data = EFO()
disease_data.load_json(
lookup_data.available_efos.get_efo(disease))
score.set_disease_data(disease_data)
element_id = '%s-%s' % (target, disease)
#convert the score into a JSON-compatible object
#otherwise Python serialization consumes too much memory
return (element_id, score.to_json())
return None
def _get_gene_obj(self, geneid):
gene = Gene(geneid)
gene.load_json(self.available_genes.get_gene(geneid))
return gene