Implement computing of diffs

1 files changed, 27 insertions, 2 deletions

diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py
index 78fc579..cc5feb7 100644
--- a/gn3/case_attributes.py
+++ b/gn3/case_attributes.py
@@ -1,9 +1,14 @@
 """Implement case-attribute manipulations."""
+import os
+import csv
+import tempfile
 from functools import reduce
 
 from MySQLdb.cursors import DictCursor
 from flask import jsonify, Response, Blueprint, current_app
 
+from gn3.commands import run_cmd
+
 from gn3.db_utils import Connection, database_connection
 
 from gn3.auth.authentication.users import User
@@ -84,9 +89,29 @@ def __process_edit_data__(form_data) -> tuple[dict, ...]:
     """Process data from form and return tuple of dicts."""
     raise NotImplementedError
 
-def __compute_diff__(original_data: tuple[dict, ...], edit_data: tuple[dict, ...]):
+def __write_csv__(fieldnames, data):
+    """Write the given `data` to a csv file and return the path to the file."""
+    fd, filepath = tempfile.mkstemp(".csv")
+    os.close(fd)
+    with open(filepath, "w", encoding="utf-8") as csvfile:
+        writer = csv.DictWriter(filename, fieldnames=fieldnames, dialect="unix")
+        writer.writeheader()
+        writer.writerows(data)
+
+    return filepath
+
+def __compute_diff__(calabels: tuple[str, ...], original_data: tuple[dict, ...], edit_data: tuple[dict, ...]):
     """Return the diff of the data."""
-    raise NotImplementedError
+    fieldnames = ["Strain"] + sorted(calabels) # Make first column the strain.
+    basefilename = __write_csv__(fieldnames, original_data)
+    deltafilename = __write_csv__(fieldnames, edit_data)
+    diff_results = run_cmd(json.dumps(
+        ["csvdiff", basefilename, deltafilename, "--format", "json"]))
+    os.unlink(basefilename)
+    os.unlink(deltafilename)
+    if diff_results["code"] == 0:
+        return json.loads(diff_results["output"])
+    return {}
 
 def __queue_diff__(conn: Connection, user: User, diff) -> str:
     """