fix redis

src/pathfinder/get_cooccurrence.py

@@ -1,16 +1,23 @@
 """Get more than pairwise literature cooccurence for a given list of curies."""
 import json
 import gzip
+import os
 import redis
 import time
 from typing import List
 
+REDIS_HOST = os.environ.get("REDIS_HOST", "localhost")
+REDIS_PORT = os.environ.get("REDIS_PORT", 6379)
+PMIDS_DB = os.environ.get("PMIDS_DB", 1)
+CURIES_DB = os.environ.get("CURIES_DB", 2)
+REDIS_PASSWORD = os.environ.get("REDIS_PASSWORD")
 
 def get_the_pmids(curies: List[str]):
     r = redis.Redis(
-        host="localhost",
-        port=6379,
-        db=0
+        host=REDIS_HOST,
+        port=REDIS_PORT,
+        db=PMIDS_DB,
+        password=REDIS_PASSWORD
     )
     curie_pmids = []
     for curie in curies:
@@ -25,9 +32,10 @@ def get_the_pmids(curies: List[str]):
 
 def get_the_curies(pmid: str):
     r = redis.Redis(
-        host="localhost",
-        port=6379,
-        db=1
+        host=REDIS_HOST,
+        port=REDIS_PORT,
+        db=CURIES_DB,
+        password=REDIS_PASSWORD
     )
     curies = r.get(pmid)
     if curies is None: