From bc0cf7321dcd68027d4997facf21e9d2c9015b34 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Fri, 7 Apr 2023 11:00:39 -0700
Subject: [PATCH] refactor: rename SEQREPO_DATA_PATH --> SEQREPO_ROOT_DIR
 (#186)

---
 README.md                    | 2 ++
 docs/source/full_install.rst | 2 ++
 gene/__init__.py             | 4 ++--
 gene/etl/base.py             | 4 ++--
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 91fc990d..fe329d89 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,8 @@ You will want to do the following:\
 sudo mv /usr/local/share/seqrepo/2021-01-29._fkuefgd /usr/local/share/seqrepo/2021-01-29
 ```
 
+Use the `SEQREPO_ROOT_DIR` environment variable to set the path of an already existing SeqRepo directory. The default is `/usr/local/share/seqrepo/latest`.
+
 ### Database Initialization
 
 The Normalizer supports two data storage options:
diff --git a/docs/source/full_install.rst b/docs/source/full_install.rst
index 980b95e8..188c5dc5 100644
--- a/docs/source/full_install.rst
+++ b/docs/source/full_install.rst
@@ -38,6 +38,8 @@ You may need to manually finish moving sequence files (replace the `XXXXXX` char
 
     sudo mv /usr/local/share/seqrepo/2021-01-29.XXXXXXX /usr/local/share/seqrepo/2021-01-29
 
+Use the ``SEQREPO_ROOT_DIR`` environment variable to set the path of an already existing SeqRepo directory. The default is ``/usr/local/share/seqrepo/latest``.
+
 
 Database setup
 --------------
diff --git a/gene/__init__.py b/gene/__init__.py
index 96ac81d7..55f744cb 100644
--- a/gene/__init__.py
+++ b/gene/__init__.py
@@ -22,8 +22,8 @@
 logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO)  # noqa: E501
 
 
-SEQREPO_DATA_PATH = Path(
-    environ.get("SEQREPO_DATA_PATH", "/usr/local/share/seqrepo/latest")
+SEQREPO_ROOT_DIR = Path(
+    environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
 )
 
 
diff --git a/gene/etl/base.py b/gene/etl/base.py
index 2396e2ce..946f9482 100644
--- a/gene/etl/base.py
+++ b/gene/etl/base.py
@@ -2,7 +2,7 @@
 from abc import ABC, abstractmethod
 from typing import Dict, Optional, List
 from gene.database import AbstractDatabase
-from gene import ITEM_TYPES, SEQREPO_DATA_PATH
+from gene import ITEM_TYPES, SEQREPO_ROOT_DIR
 from biocommons.seqrepo import SeqRepo
 from pathlib import Path
 from ftplib import FTP
@@ -23,7 +23,7 @@ class Base(ABC):
     """The ETL base class."""
 
     def __init__(self, database: AbstractDatabase, host: str, data_dir: str,
-                 src_data_dir: Path, seqrepo_dir: Path = SEQREPO_DATA_PATH,
+                 src_data_dir: Path, seqrepo_dir: Path = SEQREPO_ROOT_DIR,
                  *args, **kwargs) -> None:
         """Instantiate Base class.