def build_index(config, use_parallel=True, noconfirm=False):
bdr = DataBuilder(backend='mongodb')
bdr.load_build_config(config)
target_collection = bdr.pick_target_collection()
target_es_index = 'genedoc_' + bdr._build_config['name']
if target_collection:
es_idxer = ESIndexer(mapping=bdr.get_mapping())
es_idxer.ES_INDEX_NAME = target_es_index
es_idxer.step = 10000
es_idxer.use_parallel = use_parallel
es_server = es_idxer.conn.servers[0].geturl()
print("ES target: {}/{}/{}".format(es_server, es_idxer.ES_INDEX_NAME,
es_idxer.ES_INDEX_TYPE))
if noconfirm or ask("Continue?") == 'Y':
#es_idxer.s = 609000
#es_idxer.conn.indices.delete_index(es_idxer.ES_INDEX_NAME)
es_idxer.create_index()
es_idxer.delete_index_type(es_idxer.ES_INDEX_TYPE,
noconfirm=noconfirm)
es_idxer.build_index(target_collection, verbose=False)
es_idxer.optimize()
else:
print("Aborted.")
else:
print("Error: target collection is not ready yet or failed to build.")
def build_index(config, use_parallel=True, noconfirm=False):
bdr = DataBuilder(backend='mongodb')
bdr.load_build_config(config)
target_collection = bdr.pick_target_collection()
target_es_index = 'genedoc_' + bdr._build_config['name']
if target_collection:
es_idxer = ESIndexer(mapping=bdr.get_mapping())
es_idxer.ES_INDEX_NAME = target_es_index
es_idxer.step = 10000
es_idxer.use_parallel = use_parallel
es_server = es_idxer.conn.servers[0].geturl()
print "ES target: {}/{}/{}".format(es_server,
es_idxer.ES_INDEX_NAME,
es_idxer.ES_INDEX_TYPE)
if ask("Continue?") == 'Y':
#es_idxer.s = 609000
#es_idxer.conn.indices.delete_index(es_idxer.ES_INDEX_NAME)
es_idxer.create_index()
es_idxer.delete_index_type(es_idxer.ES_INDEX_TYPE, noconfirm=noconfirm)
es_idxer.build_index(target_collection, verbose=False)
es_idxer.optimize()
else:
print "Aborted."
else:
print "Error: target collection is not ready yet or failed to build."
def build_index(self, use_parallel=True):
target_collection = self.get_target_collection()
if target_collection:
es_idxer = ESIndexer(mapping=self.get_mapping())
es_idxer.ES_INDEX_NAME = 'genedoc_' + self._build_config['name']
es_idxer.step = 10000
es_idxer.use_parallel = use_parallel
#es_idxer.s = 609000
#es_idxer.conn.indices.delete_index(es_idxer.ES_INDEX_NAME)
es_idxer.create_index()
es_idxer.delete_index_type(es_idxer.ES_INDEX_TYPE, noconfirm=True)
es_idxer.build_index(target_collection, verbose=False)
es_idxer.optimize()
else:
logging.info("Error: target collection is not ready yet or failed to build.")
def build_index(self, use_parallel=True):
target_collection = self.get_target_collection()
if target_collection:
es_idxer = ESIndexer(mapping=self.get_mapping())
es_idxer.ES_INDEX_NAME = 'genedoc_' + self._build_config['name']
es_idxer.step = 10000
es_idxer.use_parallel = use_parallel
#es_idxer.s = 609000
#es_idxer.conn.indices.delete_index(es_idxer.ES_INDEX_NAME)
es_idxer.create_index()
es_idxer.delete_index_type(es_idxer.ES_INDEX_TYPE, noconfirm=True)
es_idxer.build_index(target_collection, verbose=False)
es_idxer.optimize()
else:
logging.info(
"Error: target collection is not ready yet or failed to build."
)
def make_test_index():
def get_sample_gene(gene):
qbdr = ESQueryBuilder(fields=['_source'], size=1000)
_query = qbdr.dis_max_query(gene)
_query = qbdr.add_species_custom_filters_score(_query)
_q = {'query': _query}
if qbdr.options:
_q.update(qbdr.options)
esq = ESQuery()
res = esq._search(_q)
return [h['_source'] for h in res['hits']['hits']]
gli = get_sample_gene('CDK2') + \
get_sample_gene('BTK') + \
get_sample_gene('insulin')
from utils.es import ESIndexer
index_name = 'genedoc_2'
index_type = 'gene_sample'
esidxer = ESIndexer(None, None)
conn = esidxer.conn
try:
esidxer.delete_index_type(index_type)
except:
pass
mapping = dict(conn.get_mapping('gene', index_name)['gene'])
print conn.put_mapping(index_type, mapping, [index_name])
print "Building index..."
cnt = 0
for doc in gli:
conn.index(doc, index_name, index_type, doc['_id'])
cnt += 1
print cnt, ':', doc['_id']
print conn.flush()
print conn.refresh()
print 'Done! - {} docs indexed.'.format(cnt)
