Fix tests, and issues caught by tests

Fix some issues caught by tests due to changes introducing the hand-off of the
partial correlations computations to an external process

Fix some issues due to the changes that introduce context managers for
database connections

Update some tests to take the above two changes into consideration

3 files changed, 5 insertions, 4 deletions

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index f2ac4d7..67897e8 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -112,7 +112,7 @@ def partial_correlation():
 
         return reduce(__field_errors__(request_data), fields, errors)
 
-    args = json.loads(request.get_json())
+    args = request.get_json()
     request_errors = __errors__(
         args, ("primary_trait", "control_traits", "target_db", "method"))
     if request_errors:
diff --git a/gn3/commands.py b/gn3/commands.py
index 29e3df2..0e0b53c 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -84,11 +84,12 @@ Returns the name of the specific redis hash for the specific task.
                  f"{str(uuid4())}")
     conn.rpush(job_queue, unique_id)
     for key, value in {
-            "cmd": json.dumps(cmd), "result": "", "status": "queued",
-            "env": json.dumps(env)}.items():
+            "cmd": json.dumps(cmd), "result": "", "status": "queued"}.items():
         conn.hset(name=unique_id, key=key, value=value)
     if email:
         conn.hset(name=unique_id, key="email", value=email)
+    if env:
+        conn.hset(name=unique_id, key="env", value=json.dumps(env))
     return unique_id
 
 
diff --git a/gn3/computations/diff.py b/gn3/computations/diff.py
index af02f7f..0b6edd6 100644
--- a/gn3/computations/diff.py
+++ b/gn3/computations/diff.py
@@ -6,7 +6,7 @@ from gn3.commands import run_cmd
 
 def generate_diff(data: str, edited_data: str) -> Optional[str]:
     """Generate the diff between 2 files"""
-    results = run_cmd(f"diff {data} {edited_data}", success_codes=(1, 2))
+    results = run_cmd(f'"diff {data} {edited_data}"', success_codes=(1, 2))
     if results.get("code", -1) > 0:
         return results.get("output")
     return None