From 7f097e78a2ab7d88dda5d03b86477f6c23be78cf Mon Sep 17 00:00:00 2001
From: Alan Cleary <acleary@ncgr.org>
Date: Thu, 14 Jul 2022 13:19:32 -0600
Subject: [PATCH] Updated the chromosome service to use the redis package in
 place of the aioredis and redisearch packages.

---
 chromosome/chromosome/aioredisearch.py   | 58 ------------------------
 chromosome/chromosome/database.py        |  4 +-
 chromosome/chromosome/request_handler.py |  4 +-
 chromosome/setup.cfg                     |  5 +-
 genes/setup.cfg                          |  2 +-
 5 files changed, 6 insertions(+), 67 deletions(-)
 delete mode 100644 chromosome/chromosome/aioredisearch.py

diff --git a/chromosome/chromosome/aioredisearch.py b/chromosome/chromosome/aioredisearch.py
deleted file mode 100644
index 10abb20d..00000000
--- a/chromosome/chromosome/aioredisearch.py
+++ /dev/null
@@ -1,58 +0,0 @@
-# Python
-import time
-# dependencies
-import redisearch
-import six
-
-
-# copy of RediSearch's to_string function that's not exported
-def to_string(s):
-  if isinstance(s, six.string_types):
-    return s
-  elif isinstance(s, six.binary_type):
-    return s.decode('utf-8')
-  else:
-    return s  # Not a string we care about
-
-
-# a class that overrides a subset of the RediSearch Client methods to be
-# asynchronous
-class Client(redisearch.Client):
-
-  async def load_document(self, id):
-    fields = await self.redis.hgetall(id)
-    if six.PY3:
-      f2 = {to_string(k): to_string(v) for k, v in fields.items()}
-      fields = f2
-    try:
-      del fields['id']
-    except KeyError:
-      pass
-    return redisearch.Document(id=id, **fields)
-
-  # unlike RediSearch get, this implementation returns a Document instance for
-  # each id that exists in the database and None for those that don't
-  async def get(self, *ids):
-    flat_fields = await self.redis.execute_command('FT.MGET', self.index_name, *ids)
-    docs = []
-    for id, id_flat_fields in zip(ids, flat_fields):
-      if id_flat_fields is None:
-        docs.append(None)
-      else:
-        id_fields = dict(
-          dict(zip(map(to_string, id_flat_fields[::2]),
-                   map(to_string, id_flat_fields[1::2])))
-        )
-        doc = redisearch.Document(id, payload=None, **id_fields)
-        docs.append(doc)
-    return docs
-
-  async def search(self, query):
-    args, query = self._mk_query_args(query)
-    st = time.time()
-    res = await self.redis.execute_command(self.SEARCH_CMD, *args)
-    return redisearch.Result(res,
-                  not query._no_content,
-                  duration=(time.time() - st) * 1000.0,
-                  has_payload=query._with_payloads,
-                  with_scores=query._with_scores)
diff --git a/chromosome/chromosome/database.py b/chromosome/chromosome/database.py
index 112b76cc..c2bd2fb7 100644
--- a/chromosome/chromosome/database.py
+++ b/chromosome/chromosome/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
diff --git a/chromosome/chromosome/request_handler.py b/chromosome/chromosome/request_handler.py
index a19abd18..29fc8ea4 100644
--- a/chromosome/chromosome/request_handler.py
+++ b/chromosome/chromosome/request_handler.py
@@ -1,5 +1,5 @@
 # module
-from chromosome.aioredisearch import Client
+from redis.commands.search import AsyncSearch
 
 
 class RequestHandler:
@@ -9,7 +9,7 @@ def __init__(self, redis_connection):
 
   async def process(self, name):
     # connect to the index
-    chromosome_index = Client('chromosomeIdx', conn=self.redis_connection)
+    chromosome_index = AsyncSearch(self.redis_connection, index_name='chromosomeIdx')
     # get the chromosome
     chromosome_doc = await chromosome_index.load_document(f'chromosome:{name}')
     if not hasattr(chromosome_doc, 'name'):
diff --git a/chromosome/setup.cfg b/chromosome/setup.cfg
index 067b0590..252c2cd1 100644
--- a/chromosome/setup.cfg
+++ b/chromosome/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]
diff --git a/genes/setup.cfg b/genes/setup.cfg
index 83fedc95..8f0fbcd7 100644
--- a/genes/setup.cfg
+++ b/genes/setup.cfg
@@ -29,11 +29,11 @@ project_urls =
 packages = find:
 python_requires = >=3.5,<4
 install_requires =
-    redis >=4.3.4,<5
     aiohttp >=3.7,<4
     aiohttp-cors
     grpcio >=1.39,<2
     grpcio-tools >=1.39,<2
+    redis >=4.3.4,<5
     uvloop >=0.16,<1
 
 [options.entry_points]