Patch 4.90.1: fix parsing mme dates (#4961)

* Fix parsing of Matchmaker Exchange's matches dates

* Make it a patch release

* Rename test

* tests depends on other factors, simplify

* typo

* Fix according review

---------

Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>

CHANGELOG.md

@@ -4,6 +4,10 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.90.1]
+### Fixed
+- Parsing Matchmaker Exchange's matches dates
+
 ## [4.90]
 ### Added
 - Link to chanjo2 MANE coverage overview on case page and panel page

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.90"
+__version__ = "4.90.1"

scout/parse/matchmaker.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
-import datetime
 import logging
+from datetime import datetime
+from typing import Union
 
 LOG = logging.getLogger(__name__)
 
@@ -158,6 +159,19 @@ def genomic_features(store, case_obj, sample_name, candidate_vars, genes_only):
     return g_features
 
 
+def parse_datetime(match_date: Union[str, int]) -> datetime:
+    """Converts a date to a datetime. match_date could be either a millisecond timestamp (Patientmatcher < 4.5) or a string (Patientmatcher >= 4.5), including milliseconds or not."""
+    try:
+        date_datetime = datetime.fromtimestamp(match_date / 1000.0)
+    except TypeError:
+        if "." in match_date:
+            date_datetime = datetime.strptime(match_date, "%Y-%m-%dT%H:%M:%S.%fZ")
+        else:
+            date_datetime = datetime.strptime(match_date, "%Y-%m-%dT%H:%M:%SZ")
+
+    return date_datetime
+
+
 def parse_matches(patient_id, match_objs):
     """Parse a list of matchmaker matches objects and returns
        a readable list of matches to display in matchmaker matches view.
@@ -186,11 +200,9 @@ def parse_matches(patient_id, match_objs):
     parsed_matches = []
 
     for match_obj in match_objs:
-        match_date = match_obj["created"]["$date"]
-        try:  # Patientmatcher < 4.5 returns dates in milliseconds
-            mdate = datetime.datetime.fromtimestamp(match_date / 1000.0)
-        except TypeError:  # Patientmatcher >= 4.5 returns dates in isoformat
-            mdate = datetime.datetime.strptime(match_date, "%Y-%m-%dT%H:%M:%S.%fZ")
+
+        mdate = parse_datetime(match_obj["created"]["$date"])
+
         match_type = "external"
         matching_patients = []
 

tests/parse/test_parse_matchmaker.py

@@ -1,6 +1,32 @@
+from datetime import datetime
+
 import pytest
 
-from scout.parse.matchmaker import genomic_features, hpo_terms, omim_terms, parse_matches
+from scout.parse.matchmaker import (
+    genomic_features,
+    hpo_terms,
+    omim_terms,
+    parse_datetime,
+    parse_matches,
+)
+
+
+def test_parse_datetime_timestamp_milliseconds():
+    """Test parsing matching results date in timestamp milliseconds format."""
+    datetime_int = 1729229925000
+    assert isinstance(parse_datetime(datetime_int), datetime)
+
+
+def test_parse_datetime_timestamp():
+    """Test parsing matching results date in timestamp with no fractions of seconds."""
+    datetime_str = "2023-08-16T01:03:53Z"
+    assert parse_datetime(datetime_str) == datetime(2023, 8, 16, 1, 3, 53)
+
+
+def test_parse_datetime_timestamp_fractional_seconds():
+    """Test parsing matching results date in timestamp with fractions of seconds."""
+    datetime_str = "2023-08-16T01:03:53.123456Z"
+    assert parse_datetime(datetime_str) == datetime(2023, 8, 16, 1, 3, 53, 123456)
 
 
 def test_parse_hpo_terms(case_obj, test_hpo_terms):