Raw file connection not closing (#709)

* ini * // * Tests Passing * Cleaning * Deleted redundant files * Directory path fix * Tests Passing * tests passed * clean up * stream.Close() removed * better coverage * ready to go * Lock added to ensure only one thread can access msDataScans * Update ThermoRawFileReader.cs * fixes from comments in PR --------- Co-authored-by: Nic Bollis <nbollis@comcast.net> Co-authored-by: trishorts <mshort@chem.wisc.edu> Co-authored-by: Alexander-Sol <41119316+Alexander-Sol@users.noreply.github.com>
smith-chem-wisc · Sep 22, 2023 · 732c003 · 732c003
1 parent e4c48c6
commit 732c003
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diff --git a/mzLib/MassSpectrometry/MsDataFile.cs b/mzLib/MassSpectrometry/MsDataFile.cs
@@ -16,13 +16,10 @@
 // You should have received a copy of the GNU Lesser General Public
 // License along with MassSpectrometry. If not, see <http://www.gnu.org/licenses/>.
 
-using Chemistry;
-using MzLibUtil;
 using System;
 using System.Collections;
 using System.Collections.Generic;
 using System.Linq;
-using System.Threading.Tasks;
 
 namespace MassSpectrometry
 {

diff --git a/mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs b/mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs
@@ -480,14 +480,17 @@ private bool Peak2satisfiesRatio(double peak1theorIntensity, double peak2theorIn
 
         public static byte[] Get64Bitarray(IEnumerable<double> array)
         {
-            var mem = new MemoryStream();
-            foreach (var okk in array)
+            using (var mem = new MemoryStream())
             {
-                byte[] ok = BitConverter.GetBytes(okk);
-                mem.Write(ok, 0, ok.Length);
+                foreach (var okk in array)
+                {
+                    byte[] ok = BitConverter.GetBytes(okk);
+                    mem.Write(ok, 0, ok.Length);
+                }
+                mem.Position = 0;
+                var memory = mem.ToArray();
+                return memory;
             }
-            mem.Position = 0;
-            return mem.ToArray();
         }
 
         public byte[] Get64BitYarray()
@@ -505,7 +508,9 @@ public override string ToString()
             return string.Format("{0} (Peaks {1})", Range, Size);
         }
 
-        public void XCorrPrePreprocessing(double scanRangeMinMz, double scanRangeMaxMz, double precursorMz, double precursorDiscardRange = 1.5, double discreteMassBin = 1.0005079, double minimumAllowedIntensityRatioToBasePeak = 0.05)
+        public void XCorrPrePreprocessing(double scanRangeMinMz, double scanRangeMaxMz,
+            double precursorMz, double precursorDiscardRange = 1.5,
+            double discreteMassBin = 1.0005079, double minimumAllowedIntensityRatioToBasePeak = 0.05)
         {
             //The discrete bin value 1.0005079 was from J. Proteome Res., 2018, 17 (11), pp 3644–3656
 
@@ -544,9 +549,13 @@ public void XCorrPrePreprocessing(double scanRangeMinMz, double scanRangeMaxMz,
 
             //we've already filtered for when multiple mzs appear in a single nominal mass bin
             int nominalWindowWidthDaltons = (int)(Math.Round((scanRangeMaxMz - scanRangeMinMz) / 10d, 0));
-            FilteringParams secondFilter = new FilteringParams(null, minimumAllowedIntensityRatioToBasePeak, nominalWindowWidthDaltons, null, true, false, false);
 
-            WindowModeHelper.Run(ref genericIntensityArray, ref genericMzArray, secondFilter, genericMzArray.Min(), genericMzArray.Max(), true);
+            FilteringParams secondFilter = new FilteringParams(null,
+                minimumAllowedIntensityRatioToBasePeak, nominalWindowWidthDaltons, null,
+                true, false, false);
+
+            WindowModeHelper.Run(ref genericIntensityArray, ref genericMzArray, secondFilter,
+                genericMzArray.Min(), genericMzArray.Max(), true);
 
             Array.Sort(genericMzArray, genericIntensityArray);
 

diff --git a/mzLib/Readers/Bruker/BrukerFileReader.cs b/mzLib/Readers/Bruker/BrukerFileReader.cs
@@ -81,9 +81,9 @@ public override MsDataFile LoadAllStaticData(FilteringParams? filteringParams =
 			// close the file connection. At this point, you don't need to be connected to the sqlite database anymore. You have all the data 
 			// you need. 
 			CloseFileConnection();
-			Scans = scans.OrderBy(x => x.OneBasedScanNumber).ToArray();
+            Scans = scans.OrderBy(x => x.OneBasedScanNumber).ToArray();
 			SourceFile = GetSourceFile();
-			return this; 
+            return this; 
 		}
 
 		private const string nativeIdFormat = "scan number only nativeID format";
@@ -450,7 +450,7 @@ private void OpenFileConnection(string path)
 			_connection = new SQLiteConnection();
 			_connection.ConnectionString = "DataSource=" + sqlite_fn; 
 			_connection.Open();
-		}
+        }
 		private void CloseFileConnection()
 		{
 			baf2sql_array_close_storage(_handle!.Value);

diff --git a/mzLib/Readers/MsDataFileReader.cs b/mzLib/Readers/MsDataFileReader.cs
@@ -11,6 +11,7 @@ namespace Readers
 {
     public static class MsDataFileReader 
     {
+
         public static MsDataFile GetDataFile(string filePath)
         {
             return filePath.ParseFileType() switch

diff --git a/mzLib/Readers/MzML/Mzml.cs b/mzLib/Readers/MzML/Mzml.cs
@@ -18,17 +18,12 @@
 
 using MassSpectrometry;
 using MzLibUtil;
-using System;
 using System.Collections.Concurrent;
-using System.Collections.Generic;
 using System.Globalization;
-using System.IO;
 using System.IO.Compression;
-using System.Linq;
 using System.Security.Cryptography;
 using System.Text;
 using System.Text.RegularExpressions;
-using System.Threading.Tasks;
 using System.Xml;
 using UsefulProteomicsDatabases;
 
@@ -161,20 +156,20 @@ public override MsDataFile LoadAllStaticData(FilteringParams filterParams = null
             }
 
             Loaders.LoadElements();
-            
-            SourceFile = GetSourceFile(); 
+
+            SourceFile = GetSourceFile();
 
             var numSpecta = _mzMLConnection.run.spectrumList.spectrum.Length;
             MsDataScan[] scans = new MsDataScan[numSpecta];
 
-            Parallel.ForEach(Partitioner.Create(0, numSpecta), new ParallelOptions 
-                { MaxDegreeOfParallelism = maxThreads }, fff =>
+            Parallel.ForEach(Partitioner.Create(0, numSpecta), new ParallelOptions
+            { MaxDegreeOfParallelism = maxThreads }, fff =>
+        {
+            for (int i = fff.Item1; i < fff.Item2; i++)
             {
-                for (int i = fff.Item1; i < fff.Item2; i++)
-                {
-                    scans[i] = GetMsDataOneBasedScanFromConnection(_mzMLConnection, i + 1, filterParams);
-                }
-            });
+                scans[i] = GetMsDataOneBasedScanFromConnection(_mzMLConnection, i + 1, filterParams);
+            }
+        });
 
             scans = scans.Where(s => s.MassSpectrum != null).ToArray();
 
@@ -236,7 +231,9 @@ public override MsDataFile LoadAllStaticData(FilteringParams filterParams = null
         public override SourceFile GetSourceFile()
         {
             SourceFile sourceFile;
-            if (_mzMLConnection.fileDescription.sourceFileList != null && _mzMLConnection.fileDescription.sourceFileList.sourceFile != null && _mzMLConnection.fileDescription.sourceFileList.sourceFile[0] != null && _mzMLConnection.fileDescription.sourceFileList.sourceFile[0].cvParam != null)
+            if (_mzMLConnection.fileDescription.sourceFileList != null && _mzMLConnection.fileDescription.sourceFileList.sourceFile
+                != null && _mzMLConnection.fileDescription.sourceFileList.sourceFile[0] != null
+                && _mzMLConnection.fileDescription.sourceFileList.sourceFile[0].cvParam != null)
             {
                 var simpler = _mzMLConnection.fileDescription.sourceFileList.sourceFile[0];
                 string nativeIdFormat = null;

diff --git a/mzLib/Readers/MzML/ReverseLineReader.cs b/mzLib/Readers/MzML/ReverseLineReader.cs
@@ -1,9 +1,5 @@
-using System;
-using System.Collections;
-using System.Collections.Generic;
-using System.Linq;
+using System.Collections;
 using System.Text;
-using System.Threading.Tasks;
 
 namespace Readers
 {
@@ -266,5 +262,5 @@ IEnumerator IEnumerable.GetEnumerator()
         }
     }
 
-    
+
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ namespace Readers @@
     {
         public static class MsDataFileReader
         {
             public static MsDataFile GetDataFile(string filePath)
             {
                 return filePath.ParseFileType() switch
@@ Expand Down @@