def clone_index(createidx=False, test=True):
if test:
return
from utils.es import ESIndexer
from utils.common import iter_n
new_idx = 'myvariant_current_3'
step = 10000
if createidx:
from mapping import get_mapping
m = get_mapping()
body = {'settings': {'number_of_shards': 10}} # ###
es.indices.create(new_idx, body=body)
es.indices.put_mapping(index=new_idx, doc_type='variant', body=m)
# helpers.reindex(es, source_index='myvariant_all',
# target_index= new_idx, chunk_size=10000)
esi = ESIndexer()
doc_iter = esi.doc_feeder(index='myvariant_all_1',
doc_type='variant',
step=step)
for doc_batch in iter_n(doc_iter, step):
do_index(doc_batch,
index_name=new_idx,
doc_type='variant',
step=step,
verbose=False,
update=True)
def test():
target = get_target_db()
sync_src = backend.GeneDocMongoDBBackend(
target['genedoc_mygene_allspecies_20130402_uiu7bkyi'])
idxer = ESIndexer()
sync_target = backend.GeneDocESBackend(idxer)
return sync_src, sync_target
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 __init__(self, build_config=None, backend='mongodb'):
self.src = get_src_db()
self.step = 10000
self.use_parallel = False
self.merge_logging = True # save output into a logging file when merge is called.
self.max_build_status = 10 # max no. of records kept in "build" field of src_build collection.
self.using_ipython_cluster = False
self.shutdown_ipengines_after_done = False
self.log_folder = LOG_FOLDER
self._build_config = build_config
self._entrez_geneid_d = None
self._idmapping_d_cache = {}
self.get_src_master()
if backend == 'mongodb':
self.target = databuild.backend.GeneDocMongoDBBackend()
elif backend == 'es':
self.target = databuild.backend.GeneDocESBackend(ESIndexer())
elif backend == 'couchdb':
from config import COUCHDB_URL
import couchdb
self.target = databuild.backend.GeneDocCouchDBBackend(
couchdb.Server(COUCHDB_URL))
elif backend == 'memory':
self.target = databuild.backend.GeneDocMemeoryBackend()
else:
raise ValueError('Invalid backend "%s".' % backend)
def __init__(self, index=None, doc_type=None, es_host=None, step=5000):
self._es = get_es(es_host)
self._index = index or config.ES_INDEX_NAME
self._doc_type = doc_type or config.ES_DOC_TYPE
self._esi = ESIndexer(es_host=es_host)
self._esi._index = self._index
self._src = get_src_db()
self.step = step
def get_backend(target_name, bk_type, **kwargs):
'''Return a backend instance for given target_name and backend type.
currently support MongoDB and ES backend.
'''
if bk_type == 'mongodb':
return GeneDocMongoDBBackend(target_name)
elif bk_type == 'es':
esi = ESIndexer(target_name, **kwargs)
return GeneDocESBackend(esi)
def diff2src(use_parallel=True, noconfirm=False):
src_li = []
target_db = get_target_db()
src_li.extend([(name, target_db[name].count(), 'mongodb')
for name in sorted(target_db.collection_names())
if name.startswith('genedoc')])
es_idxer = ESIndexer()
es_idxer.conn.default_indices = []
for es_idx in es_idxer.conn.indices.get_indices():
if es_idx.startswith('genedoc'):
es_idxer.ES_INDEX_NAME = es_idx
src_li.append((es_idx, es_idxer.count()['count'], 'es'))
print("Found {} sources:".format(len(src_li)))
src_1 = _pick_one(src_li, "Pick first source above: ")
src_li.remove(src_1)
print
src_2 = _pick_one(src_li, "Pick second source above: ")
sync_li = []
for src in (src_1, src_2):
if src[2] == 'mongodb':
b = backend.GeneDocMongoDBBackend(target_db[src[0]])
elif src[2] == 'es':
es_idxer = ESIndexer()
es_idxer.ES_INDEX_NAME = src[0]
es_idxer.step = 10000
b = backend.GeneDocESBackend(es_idxer)
sync_li.append(b)
sync_src, sync_target = sync_li
print('\tsync_src:\t{:<45}{}\t{}'.format(*src_1))
print('\tsync_target\t{:<45}{}\t{}'.format(*src_2))
if noconfirm or ask("Continue?") == "Y":
changes = diff.diff_collections(sync_src,
sync_target,
use_parallel=use_parallel)
return changes
def sync_index(self, use_parallel=True):
from utils import diff
sync_src = self.get_target_collection()
es_idxer = ESIndexer(self.get_mapping())
es_idxer.ES_INDEX_NAME = sync_src.target_collection.name
es_idxer.step = 10000
es_idxer.use_parallel = use_parallel
sync_target = databuild.backend.GeneDocESBackend(es_idxer)
changes = diff.diff_collections(sync_src, sync_target)
return changes
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 validate(build_config=None):
from pprint import pprint
from utils.diff import diff_collections
from databuild.backend import GeneDocMongoDBBackend, GeneDocESBackend
from biothings.utils.mongo import get_src_build, get_target_db
from utils.es import ESIndexer
src_build = get_src_build()
_cfg = src_build.find_one({'_id': build_config})
last_build = _cfg['build'][-1]
print("Last build record:")
pprint(last_build)
target_name = last_build['target']
mongo_target = get_target_db()
b1 = GeneDocMongoDBBackend(mongo_target[target_name])
b2 = GeneDocESBackend(
ESIndexer(es_index_name=target_name,
es_host='127.0.0.1:' + str(es_local_tunnel_port)))
changes = diff_collections(b1, b2, use_parallel=True, step=10000)
return changes
def sync_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']
sync_src = backend.GeneDocMongoDBBackend(target_collection)
es_idxer = ESIndexer(bdr.get_mapping())
es_idxer.ES_INDEX_NAME = target_es_index
es_idxer.step = 10000
es_idxer.use_parallel = use_parallel
sync_target = backend.GeneDocESBackend(es_idxer)
print('\tsync_src:\t{:<40}{}\t{}'.format(target_collection.name,
sync_src.name, sync_src.count()))
print('\tsync_target\t{:<40}{}\t{}'.format(target_es_index,
sync_target.name,
sync_target.count()))
if noconfirm or ask("Continue?") == "Y":
changes = diff.diff_collections(sync_src, sync_target)
return changes
def build_index2(self,
build_config='mygene_allspecies',
last_build_idx=-1,
use_parallel=False,
es_host=None,
es_index_name=None,
noconfirm=False):
"""Build ES index from last successfully-merged mongodb collection.
optional "es_host" argument can be used to specified another ES host, otherwise default ES_HOST.
optional "es_index_name" argument can be used to pass an alternative index name, otherwise same as mongodb collection name
"""
self.load_build_config(build_config)
assert "build" in self._build_config, "Abort. No such build records for config %s" % build_config
last_build = self._build_config['build'][last_build_idx]
logging.info("Last build record:")
logging.info(pformat(last_build))
assert last_build['status'] == 'success', \
"Abort. Last build did not success."
assert last_build['target_backend'] == "mongodb", \
'Abort. Last build need to be built using "mongodb" backend.'
assert last_build.get('stats', None), \
'Abort. Last build stats are not available.'
self._stats = last_build['stats']
assert last_build.get('target', None), \
'Abort. Last build target_collection is not available.'
# Get the source collection to build the ES index
# IMPORTANT: the collection in last_build['target'] does not contain _timestamp field,
# only the "genedoc_*_current" collection does. When "timestamp" is enabled
# in mappings, last_build['target'] collection won't be indexed by ES correctly,
# therefore, we use "genedoc_*_current" collection as the source here:
#target_collection = last_build['target']
target_collection = "genedoc_{}_current".format(build_config)
_db = get_target_db()
target_collection = _db[target_collection]
logging.info("")
logging.info('Source: %s' % target_collection.name)
_mapping = self.get_mapping()
_meta = {}
src_version = self.get_src_version()
if src_version:
_meta['src_version'] = src_version
if getattr(self, '_stats', None):
_meta['stats'] = self._stats
if 'timestamp' in last_build:
_meta['timestamp'] = last_build['timestamp']
if _meta:
_mapping['_meta'] = _meta
es_index_name = es_index_name or target_collection.name
es_idxer = ESIndexer(mapping=_mapping,
es_index_name=es_index_name,
es_host=es_host,
step=5000)
if build_config == 'mygene_allspecies':
es_idxer.number_of_shards = 10 # default 5
es_idxer.check()
if noconfirm or ask("Continue to build ES index?") == 'Y':
es_idxer.use_parallel = use_parallel
#es_idxer.s = 609000
if es_idxer.exists_index(es_idxer.ES_INDEX_NAME):
if noconfirm or ask('Index "{}" exists. Delete?'.format(
es_idxer.ES_INDEX_NAME)) == 'Y':
es_idxer.conn.indices.delete(es_idxer.ES_INDEX_NAME)
else:
logging.info("Abort.")
return
es_idxer.create_index()
#es_idxer.delete_index_type(es_idxer.ES_INDEX_TYPE, noconfirm=True)
es_idxer.build_index(target_collection, verbose=False)
