From 0353d9590ca85c9a36b0d8eeabc03237e2c79d6f Mon Sep 17 00:00:00 2001
From: Eleanor Lewis <elewis@bcgsc.ca>
Date: Mon, 1 Jul 2024 14:16:02 -0700
Subject: [PATCH] get url from env first if possible

---
 pori_python/graphkb/util.py   | 3 ++-
 pori_python/ipr/connection.py | 2 +-
 pori_python/ipr/inputs.py     | 5 +++--
 pori_python/ipr/main.py       | 4 ++--
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/pori_python/graphkb/util.py b/pori_python/graphkb/util.py
index 7c6ef94..def8f0d 100644
--- a/pori_python/graphkb/util.py
+++ b/pori_python/graphkb/util.py
@@ -1,5 +1,6 @@
 import hashlib
 import json
+import os
 import logging
 import re
 import time
@@ -95,7 +96,7 @@ def cache_key(request_body) -> str:
 class GraphKBConnection:
     def __init__(
         self,
-        url: str = DEFAULT_URL,
+        url: str = os.environ.get("GRAPHKB_URL", DEFAULT_URL),
         username: str = "",
         password: str = "",
         use_global_cache: bool = True,
diff --git a/pori_python/ipr/connection.py b/pori_python/ipr/connection.py
index c86a373..d842f0d 100644
--- a/pori_python/ipr/connection.py
+++ b/pori_python/ipr/connection.py
@@ -11,7 +11,7 @@
 
 
 class IprConnection:
-    def __init__(self, username: str, password: str, url: str = DEFAULT_URL):
+    def __init__(self, username: str, password: str, url: str = os.environ.get("IPR_URL", DEFAULT_URL)):
         self.token = None
         self.url = url
         self.username = username
diff --git a/pori_python/ipr/inputs.py b/pori_python/ipr/inputs.py
index c18608e..2d97797 100644
--- a/pori_python/ipr/inputs.py
+++ b/pori_python/ipr/inputs.py
@@ -18,13 +18,14 @@
     IprVariant,
 )
 from .util import hash_key, logger, pandas_falsy
+from .constants import DEFAULT_URL
 
 protein_letters_3to1.setdefault('Ter', '*')
 
 SPECIFICATION = os.path.join(os.path.dirname(__file__), 'content.spec.json')
-# content in the local specification should match the values in IPR_API_SPEC_JSON_URL
-IPR_API_SPEC_JSON_URL = 'https://ipr-api.bcgsc.ca/api/spec.json'
 
+# content in the local specification should match the values in IPR_API_SPEC_JSON_URL
+IPR_API_SPEC_JSON_URL = f'{os.environ.get("IPR_URL", DEFAULT_URL)}/spec.json'
 
 # TODO: GERO-307 - use SPECIFICATION json to derive the variant required and optional details defined below
 
diff --git a/pori_python/ipr/main.py b/pori_python/ipr/main.py
index ea53473..74d15cb 100644
--- a/pori_python/ipr/main.py
+++ b/pori_python/ipr/main.py
@@ -69,8 +69,8 @@ def command_interface() -> None:
     req.add_argument(
         '-c', '--content', required=True, type=file_path, help="Report Content as JSON"
     )
-    parser.add_argument('--ipr_url', default=DEFAULT_URL)
-    parser.add_argument('--graphkb_url', default=None)
+    parser.add_argument('--ipr_url', default=os.environ.get("IPR_URL", DEFAULT_URL))
+    parser.add_argument('--graphkb_url', default=os.environ.get("GRAPHKB_URL", None))
     parser.add_argument('--log_level', default='info', choices=LOG_LEVELS.keys())
     parser.add_argument(
         '--therapeutics', default=False, help='Generate therapeutic options', action='store_true'