class CopyDocs(object):
def __init__(self, src_server, dest_server, src_index, src_type, dst_index,
dst_type):
self.src_data_loader_utils = DataLoaderUtils(src_server, src_index,
src_type)
self.dest_data_loader_utils = DataLoaderUtils(dest_server, dst_index,
dst_type)
self.processed_doc_count = 0
self.total_doc_count = 0
self.data_utils = DataUtils()
def get_total_doc_count(self):
return self.data_utils.get_total_doc_count(
base_url=self.src_data_loader_utils.server,
index=self.src_data_loader_utils.index,
type=self.src_data_loader_utils.type)
def docs_fetched(self, docs, index, type):
docs_to_copy = {}
# print 'Docs fetched', len(docs)
for doc in docs:
_id = doc['_id']
if '_source' in doc:
existing_doc = doc['_source']
docs_to_copy[_id] = existing_doc
self.index_docs(docs_to_copy)
self.processed_doc_count += len(docs)
progress = ((self.processed_doc_count / float(self.total_doc_count)) *
100)
print '---------------------------------------------------------------------------------------------'
print 'Progress', self.processed_doc_count, '/', self.total_doc_count, progress, '%'
print '---------------------------------------------------------------------------------------------'
def export_doc_ids(self, server, src_index, src_type):
print 'Fetching doc ids for', src_index, src_type
query = {"match_all": {}}
self.data_utils.batch_fetch_ids_for_query(base_url=server,
index=src_index,
type=src_type,
query=query,
ids_fetched=self.ids_fetched)
# print 'Done, fetched', len(documents_ids), 'doc ids'
def ids_fetched(self, ids, index, type):
self.copy_docs_batch(ids)
def create_destination_index(self, mapping=None):
if mapping is None:
# Get mapping from src index
mapping = self.src_data_loader_utils.get_mapping_from_server()
if not self.dest_data_loader_utils.index_exists():
print 'Creating index'
self.dest_data_loader_utils.put_mapping(mapping)
# migrate_index(self.dest_data_loader_utils.index)
else:
print self.dest_data_loader_utils.index, 'exists'
def copy_docs(self):
self.processed_doc_count = 0
self.total_doc_count = self.get_total_doc_count()
print 'Total doc count', self.total_doc_count
self.create_destination_index(mapping=None)
self.export_doc_ids(server=self.src_data_loader_utils.server,
src_index=self.src_data_loader_utils.index,
src_type=self.src_data_loader_utils.type)
def copy_docs_for_ids(self, doc_ids, mapping=None):
self.processed_doc_count = 0
self.total_doc_count = len(doc_ids)
print 'Total doc count', self.total_doc_count
self.create_destination_index(mapping)
print 'Fetching docs from source index'
batch_doc_processor = BatchDocProcessor(doc_ids, self.copy_docs_batch,
3000, 16, 0.33)
batch_doc_processor.run()
def copy_docs_batch(self, doc_ids):
self.data_utils.batch_fetch_docs_for_ids(
base_url=self.src_data_loader_utils.server,
ids=doc_ids,
index=self.src_data_loader_utils.index,
type=self.src_data_loader_utils.type,
docs_fetched=self.docs_fetched)
def index_docs(self, docs_to_copy):
bulk_data = ''
count = 0
for es_id in docs_to_copy:
count += 1
doc = docs_to_copy[es_id]
bulk_data += self.dest_data_loader_utils.bulk_index_header(es_id)
bulk_data += '\n'
bulk_data += json.dumps(doc)
bulk_data += '\n'
# if count % 1000 == 0:
# print 'Processed', 1000, 'docs'
if len(bulk_data) >= 150000:
self.load_bulk_data(bulk_data)
# print 'Copied', count, 'docs'
bulk_data = ''
if len(bulk_data) > 0:
self.load_bulk_data(bulk_data)
# print 'Copied', count, 'docs'
def load_bulk_data(self, bulk_data):
# print 'Bulk data size', len(bulk_data), 'loading...'
response = self.dest_data_loader_utils.load_bulk_data(bulk_data)
if response:
pass
# print 'Done loading bulk data, saving response'
else:
print 'Bulk data load failed'
# src_server = 'http://localhost:9200'
# src_index = 'irdb_v3'
# src_type = 'grant'
# dest_server = 'http://localhost:9200'
# dest_index = 'irdb_v4'
# dest_type = 'grant'
# copy_docs = CopyDocs(src_server=src_server,
# dest_server=dest_server,
# src_index=src_index,
# src_type=src_type,
# dst_index=dest_index,
# dst_type=dest_type)
# copy_docs.copy_docs()
# copy_relations.relations_to_exclude.append({
# "source": "",
# "index_id": ID_PUBMED
# })
# copy_relations.run()
class CopyRelationships(object):
def __init__(self, src_server, dest_server, src_index, src_type, dst_index,
dst_type, username, password):
self.src_data_loader_utils = DataLoaderUtils(src_server, src_index,
src_type)
self.dest_data_loader_utils = DataLoaderUtils(dest_server, dst_index,
dst_type)
self.processed_doc_count = 0
self.total_doc_count = 0
self.data_utils = DataUtils()
self.relations_to_exclude = []
self.missing_destination_ids = []
self.username = username
self.password = password
self.last_time_stamp = 0
self.diff_average = 0
def run(self):
self.processed_doc_count = 0
self.total_doc_count = self.get_total_doc_count()
print 'Total doc count', self.total_doc_count
# self.create_destination_index(mapping=None)
self.export_doc_ids(server=self.src_data_loader_utils.server,
src_index=self.src_data_loader_utils.index,
src_type=self.src_data_loader_utils.type)
print 'saving missing docs'
file_utils.save_file('/data/data_loading/pubmed_2019',
'missing_docs_pubmed2019.json',
self.missing_destination_ids)
def run_for_ids(self, doc_ids, mapping=None):
self.processed_doc_count = 0
self.total_doc_count = len(doc_ids)
print 'Total doc count', self.total_doc_count
print 'Fetching docs from source index'
batch_doc_processor = BatchDocProcessor(doc_ids, self.copy_docs_batch,
1000, 1, 0)
batch_doc_processor.run()
file_utils.save_file('/data/data_loading/pubmed_2019',
'missing_docs_pubmed2019.json',
self.missing_destination_ids)
def export_doc_ids(self, server, src_index, src_type):
print 'Fetching doc ids for', src_index, src_type
query = {"match_all": {}}
self.data_utils.batch_fetch_ids_for_query(base_url=server,
index=src_index,
type=src_type,
query=query,
ids_fetched=self.ids_fetched,
batch_size=10000)
# print 'Done, fetched', len(documents_ids), 'doc ids'
def ids_fetched(self, ids, index, type):
print 'Ids fetched', len(ids)
self.copy_docs_batch(ids)
def copy_docs_batch(self, doc_ids):
print 'Fetching docs'
self.data_utils.batch_fetch_docs_for_ids(
base_url=self.src_data_loader_utils.server,
ids=doc_ids,
index=self.src_data_loader_utils.index,
type=self.src_data_loader_utils.type,
docs_fetched=self.docs_fetched,
batch_size=500)
def docs_fetched(self, docs, index, type):
print 'Docs fetched', len(docs)
docs_to_copy = {}
# print 'Docs fetched', len(docs)
for doc in docs:
_id = doc['_id']
if '_source' in doc:
existing_doc = doc['_source']
docs_to_copy[_id] = existing_doc
self.copy_relations(docs_to_copy)
# Update progress
self.processed_doc_count += len(docs)
progress = ((self.processed_doc_count / float(self.total_doc_count)) *
100)
current_time_stamp = time.time()
diff = current_time_stamp - self.last_time_stamp
self.diff_average = float(diff + self.diff_average) / 2
time_remaining = diff * (float(self.total_doc_count) / len(docs))
self.last_time_stamp = current_time_stamp
print '---------------------------------------------------------------------------------------------'
print 'Progress', self.processed_doc_count, '/', self.total_doc_count, progress, '%', time_remaining, 'secs'
print '---------------------------------------------------------------------------------------------'
def get_src_relations(self, src_doc, relationship_type):
src_relations = []
if relationship_type in src_doc:
relations = src_doc[relationship_type]
for relation_item in relations:
exclude_relation_item = False
for relation_to_exclude in self.relations_to_exclude:
if relation_to_exclude['source'] == relation_item[
'source'] and relation_to_exclude[
'index_id'] == relation_item['index_id']:
exclude_relation_item = True
break
if not exclude_relation_item:
src_relations.append(relation_item)
return src_relations
def get_dest_relations(self, dest_doc, relationship_type):
dest_relations = []
if relationship_type in dest_doc:
dest_relations = dest_doc[relationship_type]
return dest_relations
def add_relations(self, append_ids, relation, relations_list):
relation_found = False
for existing_relation in relations_list:
# print existing_relation['source'], relation['source'], existing_relation['index_id'], relation['index_id']
if existing_relation['source'] == relation[
'source'] and existing_relation['index_id'] == relation[
'index_id']:
existing_relation_ids = existing_relation['ids']
if append_ids:
relation_ids = relation['ids']
for _id in relation_ids:
if _id not in existing_relation_ids:
existing_relation_ids.append(_id)
existing_relation['ids'] = existing_relation_ids
relation_found = True
break
if not relation_found:
relations_list.append(relation)
return relations_list
def merge_relations(self, src_doc, dest_doc, relationship_type):
dest_relations = self.get_dest_relations(dest_doc, relationship_type)
src_relations = self.get_src_relations(src_doc, relationship_type)
# print 'src_relations', len(src_relations)
# print 'dest_relations', len(dest_relations)
combined_relations = []
for relation in dest_relations:
combined_relations = self.add_relations(True, relation,
combined_relations)
for relation in src_relations:
combined_relations = self.add_relations(True, relation,
combined_relations)
return combined_relations
def copy_relations(self, src_docs):
bulk_data = ''
count = 0
# Fetch destination docs
destination_ids = src_docs.keys()
destination_docs_array = self.data_utils.fetch_docs_for_ids(
base_url=self.dest_data_loader_utils.server,
ids=destination_ids,
index=self.dest_data_loader_utils.index,
type=self.dest_data_loader_utils.type,
username=self.username,
password=self.password)
# Create destination doc dict
destination_docs = {}
for doc in destination_docs_array:
_id = doc['_id']
if '_source' in doc:
destination_docs[_id] = doc['_source']
# Find missing destination docs
for _id in destination_ids:
if _id not in destination_docs:
self.missing_destination_ids.append(_id)
print 'Missing ids', len(self.missing_destination_ids)
# print 'dest ids', len()
# Copy relations
for _id in destination_docs:
dest_doc = destination_docs[_id]
src_doc = src_docs[_id]
dest_relations = {}
dest_relations[RELATIONSHIP_TYPE_CITATIONS] = self.merge_relations(
src_doc, dest_doc, RELATIONSHIP_TYPE_CITATIONS)
dest_relations[RELATIONSHIP_TYPE_CITED_BYS] = self.merge_relations(
src_doc, dest_doc, RELATIONSHIP_TYPE_CITED_BYS)
dest_relations[RELATIONSHIP_TYPE_RELATIONS] = self.merge_relations(
src_doc, dest_doc, RELATIONSHIP_TYPE_RELATIONS)
doc = {}
if len(dest_relations[RELATIONSHIP_TYPE_CITATIONS]) > 0:
doc[RELATIONSHIP_TYPE_CITATIONS] = dest_relations[
RELATIONSHIP_TYPE_CITATIONS]
if len(dest_relations[RELATIONSHIP_TYPE_CITED_BYS]) > 0:
doc[RELATIONSHIP_TYPE_CITED_BYS] = dest_relations[
RELATIONSHIP_TYPE_CITED_BYS]
if len(dest_relations[RELATIONSHIP_TYPE_RELATIONS]) > 0:
doc[RELATIONSHIP_TYPE_RELATIONS] = dest_relations[
RELATIONSHIP_TYPE_RELATIONS]
# if len(dest_relations[RELATIONSHIP_TYPE_CITATIONS]) >= 2:
# print _id
count += 1
# doc = docs_to_copy[es_id]
bulk_data += self.dest_data_loader_utils.bulk_update_header(_id)
bulk_data += '\n'
doc = {'doc': doc}
bulk_data += json.dumps(doc)
bulk_data += '\n'
# if count % 1000 == 0:
# print 'Processed', 1000, 'docs'
if len(bulk_data) >= 150000:
print _id
self.load_bulk_data(bulk_data)
# print 'Copied', count, 'docs'
bulk_data = ''
if len(bulk_data) > 0:
self.load_bulk_data(bulk_data)
pass
# print 'Copied', count, 'docs'
# def create_destination_index(self, mapping=None):
# if mapping is None:
# # Get mapping from src index
# mapping = self.src_data_loader_utils.get_mapping_from_server()
# if not self.dest_data_loader_utils.index_exists():
# print 'Creating index'
# self.dest_data_loader_utils.put_mapping(mapping)
# # migrate_index(self.dest_data_loader_utils.index)
# else:
# print self.dest_data_loader_utils.index, 'exists'
def load_bulk_data(self, bulk_data):
print 'Bulk data size', len(bulk_data), 'loading...'
response = self.dest_data_loader_utils.load_bulk_data(bulk_data)
if response:
pass
# print 'Done loading bulk data, saving response'
else:
print 'Bulk data load failed'
def get_total_doc_count(self):
return self.data_utils.get_total_doc_count(
base_url=self.src_data_loader_utils.server,
index=self.src_data_loader_utils.index,
type=self.src_data_loader_utils.type)
# src_server = 'http://localhost:9200'
# src_index = 'pubmed2018_v5'
# src_type = 'article'
# dest_server = 'http://localhost:9200'
# dest_index = 'pubmed2019'
# dest_type = 'article'
# copy_relations = CopyRelationships(src_server=src_server,
# dest_server=dest_server,
# src_index=src_index,
# src_type=src_type,
# dst_index=dest_index,
# dst_type=dest_type,
# username='',
# password='')
# copy_relations.relations_to_exclude.append({
# "source": "",
# "index_id": ID_PUBMED
# })
# copy_relations.run()
# copy_relations.run_for_ids([12620793])