From 3bad598d2192de039a5b6a12ca2735db3d4bbc4f Mon Sep 17 00:00:00 2001
From: m-goggins <53578688+m-goggins@users.noreply.github.com>
Date: Tue, 13 Jun 2023 08:14:44 -0700
Subject: [PATCH] fix test to close invalid json file (#657)

---
 phdi/linkage/link.py           | 15 +++++++++------
 tests/not_valid_json_test.json |  1 -
 2 files changed, 9 insertions(+), 7 deletions(-)
 delete mode 100644 tests/not_valid_json_test.json

diff --git a/phdi/linkage/link.py b/phdi/linkage/link.py
index c966cb88d0..e77f5b009a 100644
--- a/phdi/linkage/link.py
+++ b/phdi/linkage/link.py
@@ -949,12 +949,15 @@ def read_linkage_config(config_file: pathlib.Path) -> List[dict]:
       various parts of linkage pass function.
     """
     try:
-        algo_config = json.load(open(config_file))
-        # Need to convert function keys back to column indices, since
-        # JSON serializes dict keys as strings
-        for rl_pass in algo_config.get("algorithm"):
-            rl_pass["funcs"] = {int(col): f for (col, f) in rl_pass["funcs"].items()}
-        return algo_config.get("algorithm", [])
+        with open(config_file) as f:
+            algo_config = json.load(f)
+            # Need to convert function keys back to column indices, since
+            # JSON serializes dict keys as strings
+            for rl_pass in algo_config.get("algorithm"):
+                rl_pass["funcs"] = {
+                    int(col): f for (col, f) in rl_pass["funcs"].items()
+                }
+            return algo_config.get("algorithm", [])
     except FileNotFoundError:
         raise FileNotFoundError(f"No file exists at path {config_file}.")
     except json.decoder.JSONDecodeError as e:
diff --git a/tests/not_valid_json_test.json b/tests/not_valid_json_test.json
deleted file mode 100644
index bb73d201e6..0000000000
--- a/tests/not_valid_json_test.json
+++ /dev/null
@@ -1 +0,0 @@
-this is a random string that is not in json format