Merge pull request #111 from Aratz/fix_checkQC

Update NovaSeqX reagent recognizer
Molmed · Dec 7, 2023 · 639d3e2 · 639d3e2
2 parents 6c7c39d + 11fc43d
commit 639d3e2
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Showing 3 changed files with 30 additions and 3 deletions.
diff --git a/checkQC/__init__.py b/checkQC/__init__.py
@@ -1,2 +1,2 @@
 
-__version__ = "4.0.0-rc1"
+__version__ = "4.0.0-rc2"
diff --git a/checkQC/run_type_recognizer.py b/checkQC/run_type_recognizer.py
@@ -68,10 +68,18 @@ def reagent_version(runtype_recognizer):
         try:
             run_parameters = runtype_recognizer.run_parameters['RunParameters']
             consumables = run_parameters["ConsumableInfo"]["ConsumableInfo"]
-            reagent_version = next(
+            flowcell = next(
                 consumable for consumable in consumables
                 if consumable['Type'] == 'FlowCell'
-            )['Mode']
+            )
+
+            # "Mode" was used to specify the reagent version in the first runfolders that came out
+            # of the NovaSeqX. This is kept for backward compatibility.
+            reagent_version = flowcell.get("Name", flowcell.get("Mode"))
+
+            if not reagent_version:
+                raise KeyError
+
             return reagent_version
         except (KeyError, StopIteration):
             raise ReagentVersionUnknown("Could not identify flowcell mode for NovaSeqXPlus")

diff --git a/tests/test_run_type_recognizer.py b/tests/test_run_type_recognizer.py
@@ -168,6 +168,25 @@ def test_novaseq_reagent_version_raises(self):
             self.novaseq.reagent_version(mock_runtype_recognizer)
 
     def test_novaseqxplus_reagent_version(self):
+        runtype_dict = {
+            "RunParameters": {
+                "ConsumableInfo": {
+                    "ConsumableInfo": [
+                        {"Type": "FlowCell", "Name": "10B"},
+                        {"Type": "Reagent"},
+                        {"Type": "Buffer"},
+                    ]
+                }
+            }
+        }
+        mock_runtype_recognizer = self.MockRunTypeRecognizer(run_parameters=runtype_dict)
+
+        actual = self.novaseqxplus.reagent_version(mock_runtype_recognizer)
+        expected = "10B"
+
+        self.assertEqual(actual, expected)
+
+    def test_novaseqxplus_reagent_version_old(self):
         runtype_dict = {
             "RunParameters": {
                 "ConsumableInfo": {