Updated the pairwise_macro_synteny_blocks service to use the redis pa…

…ckage in place of the aioredis and redisearch packages.

pairwise_macro_synteny_blocks/pairwise_macro_synteny_blocks/database.py

@@ -1,10 +1,10 @@
 # dependencies
-import aioredis
+import redis.asyncio as redis
 
 
 async def connectToRedis(host='localhost', port=6379, db=0, password=None):
   # connect to database
-  connection = await aioredis.Redis(host=host, port=port, db=db, password=password, decode_responses=True)
+  connection = await redis.Redis(host=host, port=port, db=db, password=password, decode_responses=True)
   # ping to force connection, preventing errors downstream
   await connection.ping()
   return connection

pairwise_macro_synteny_blocks/pairwise_macro_synteny_blocks/request_handler.py

@@ -1,8 +1,9 @@
 # Python
 from collections import defaultdict
 from itertools import chain
+# dependencies
+from redis.commands.search import AsyncSearch
 # module
-from pairwise_macro_synteny_blocks.aioredisearch import Client
 from pairwise_macro_synteny_blocks.metrics import METRICS
 
 
@@ -146,8 +147,7 @@ def _indexPairsToIndexBlocks(self, pairs, intermediate, matched):
   async def process(self, query_chromosome, target, matched, intermediate, mask, metrics, chromosome_genes, chromosome_length):
 
     # connect to the indexes
-    chromosome_index = Client('chromosomeIdx', conn=self.redis_connection)
-    gene_index = Client('geneIdx', conn=self.redis_connection)
+    chromosome_index = AsyncSearch(self.redis_connection, index_name='chromosomeIdx')
 
     # check if the target chromosome exists
     target_doc_id = f'chromosome:{target}'

pairwise_macro_synteny_blocks/setup.cfg

@@ -17,8 +17,6 @@ classifiers =
     Operating System :: OS Independent
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.5
-    Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
@@ -31,12 +29,11 @@ project_urls =
 packages = find:
 python_requires = >=3.5,<4
 install_requires =
-    aioredis >=2.0,<3
     aiohttp >=3.7,<4
     aiohttp-cors
     grpcio >=1.39,<2
     grpcio-tools >=1.39,<2
-    redisearch >=2,<3
+    redis >=4.3.4,<5
     uvloop >=0.16,<1
 
 [options.entry_points]