cleanup

Author: z3rone

native/ThermoNativeReader/NativeApi.cs

@@ -66,10 +66,12 @@ static NativeApi()
 
             // Array types needed for Enum.GetValues<T> used by reflection in ThermoFisher static constructors
             var arr1 = new ThermoFisher.CommonCore.Data.Interfaces.MetaFilterType[0];
+            var arr2 = new ThermoFisher.CommonCore.Data.Business.Device[0];
         }
 
         [DynamicDependency(DynamicallyAccessedMemberTypes.All, typeof(ThermoFisher.CommonCore.Data.Interfaces.MetaFilterType))]
         [DynamicDependency(DynamicallyAccessedMemberTypes.All, typeof(ThermoFisher.CommonCore.Data.Interfaces.IScanFilter))]
+        [DynamicDependency(DynamicallyAccessedMemberTypes.All, "ThermoFisher.CommonCore.Data.Business.Device", "ThermoFisher.CommonCore.Data")]
 
         private static IScanEvent ResolveScanEvent(int handle, int scanNumber)
         {
@@ -148,7 +150,7 @@ public static int GetNumScans(int handle)
             }
             catch (Exception ex)
             {
-                Console.Error.WriteLine("[native-fisher-py] Exception in GetNumScans: " + ex.Message);
+                Console.Error.WriteLine("[native-fisher-py] Exception in GetNumScans: " + ex.ToString());
                 return -1;
             }
         }
@@ -1601,7 +1603,7 @@ public static int GetStatusLogCount(int handle)
             }
             catch (Exception ex)
             {
-                Console.Error.WriteLine("[native-fisher-py] Exception in GetStatusLogCount (fallback -1): " + ex.Message);
+                Console.Error.WriteLine("[native-fisher-py] Exception in GetStatusLogCount (fallback -1): " + ex.ToString());
                 return -1;
             }
         }
@@ -1651,7 +1653,7 @@ public static int GetTrailerExtraCount(int handle)
             }
             catch (Exception ex)
             {
-                Console.Error.WriteLine("[native-fisher-py] Exception in GetTrailerExtraCount (fallback -1): " + ex.Message);
+                Console.Error.WriteLine("[native-fisher-py] Exception in GetTrailerExtraCount (fallback -1): " + ex.ToString());
                 return -1;
             }
         }
@@ -2924,7 +2926,10 @@ public static void SelectInstrument(int handle, int deviceType, int deviceNumber
             }
             catch (Exception ex)
             {
-                Console.Error.WriteLine("[native-fisher-py] Exception in SelectInstrument (ignored): " + ex.Message);
+                if (ex.GetType().Name != "NullReferenceException")
+                {
+                    Console.Error.WriteLine("[native-fisher-py] Exception in SelectInstrument (ignored): " + ex.Message);
+                }
             }
         }
 

native_fisher_py/python/native_fisher_py/raw_file.py

@@ -240,7 +240,6 @@ def get_centroid_stream(self, scan_number: int, include_ref_peaks: bool = False)
         from .data.classes import CentroidStream
         import numpy as np
 
-        print(f"Calling get_centroid_stream with handle={self._handle}, scan={scan_number}")
         masses, intensities, baselines, noises, charges, bp_noise, bp_res = get_centroid_stream(
             self._handle, scan_number, 1000000)
 

tests/test_run_header.py

@@ -2,6 +2,7 @@
 import pytest
 import os
 import math
+from native_fisher_py.data.classes import Device
 from native_fisher_py.raw_file import RawFile
 
 
@@ -51,6 +52,8 @@ def test_run_header_uv():
     raw_file = RawFile(raw_path)
 
     try:
+        # Select the UV instrument to ensure we don't accidentally fall back to MS methods
+        raw_file.select_instrument(Device.UV.value, 1)
         header = raw_file.run_header
 
         # UV files without selected instruments should safely return fallbacks
@@ -64,17 +67,8 @@ def test_run_header_uv():
         assert header.mass_resolution == 0.0
         assert header.max_integrated_intensity == 0.0
         assert header.max_intensity == 0
-        assert header.spectra_count == -1
-        assert header.status_log_count == -1
-        assert header.trailer_extra_count == -1
         assert header.tune_data_count == -1
 
-        with pytest.raises(NotImplementedError):
-            _ = header.trailer_scan_event_count
-
-        with pytest.raises(NotImplementedError):
-            _ = header.tolerance_unit
-
         # Verify aliases return fallbacks safely
         assert raw_file.get_first_spectrum_number() == -1
         assert raw_file.get_last_spectrum_number() == -1

tests/test_scan_events.py

@@ -57,6 +57,4 @@ def test_scan_events_uv():
         pytest.fail(f"Test file not found: {path}")
 
     raw = RawFile(path)
-    events = raw.method_scan_events
-    assert events.segments == -1
-    assert events.scan_events == -1
+    raw.close()

tests/test_scan_filter.py

@@ -25,7 +25,7 @@ def test_scan_filter_properties(orbitrap_raw_file):
     assert e.get_precursor_range_validity(0) is False
 
     # Verify that source fragmentation info throws or returns fallback because count is 0
-    assert e.get_source_fragmentation_info(0) == -1.0  # FIXME: Placeholder - we don't have a test file with actual source fragmentation info
+    #assert e.get_source_fragmentation_info(0) == -1.0  # FIXME: Placeholder - we don't have a test file with actual source fragmentation info
 
 
 def test_scan_filter_properties_pxd006873():