fix(decoder): resolve issue #7

able to now decode zlib compressed empty binary data fix #7
vmalnathnambiar · Apr 18, 2024 · 6e9dce0 · 6e9dce0
1 parent 332cbff
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diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ authors:
     given-names: 'Shabarinath'
     orcid: 'https://orcid.org/0000-0002-6713-1705'
 title: 'ExfilMS'
-version: 1.2.5
+version: 1.2.6
 abstract: 'ExfilMS is a cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with filtering capabilities.'
 keywords:
   - 'mass spectrometry'

diff --git a/README.md b/README.md
@@ -184,7 +184,7 @@ For more guidance on how to use ExfilMS, please refer to our available guides be
 
 If you use ExfilMS in your work, please cite it using the following:
 
-Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.2.5) [Computer software]. https://doi.org/10.5281/zenodo.10976761
+Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.2.6) [Computer software]. https://doi.org/10.5281/zenodo.10976761
 
 <br>
 

diff --git a/data/mzML/S15_Bruker_ImpactII_QToFMS.mzML b/data/mzML/S15_Bruker_ImpactII_QToFMS.mzML
@@ -209,7 +209,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </spectrum>
-        <spectrum index="3" id="scan=4" defaultArrayLength="231">
+        <spectrum index="3" id="scan=4" defaultArrayLength="0">
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
           <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -248,17 +248,17 @@
             </precursor>
           </precursorList>
           <binaryDataArrayList count="2">
-            <binaryDataArray encodedLength="2464">
+            <binaryDataArray encodedLength="0">
               <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000576" name="zlib compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-              <binary>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</binary>
+              <binary></binary>
             </binaryDataArray>
-            <binaryDataArray encodedLength="1232">
+            <binaryDataArray encodedLength="0">
               <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000576" name="zlib compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
-              <binary>AACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAASEIAAJBBAACAQQAA8EEAAABCAACQQQAAgEEAAEBCAACAQQAAoEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAAChQwAAeEIAABZDAADgQgAAwEEAAIBBAACAQQAAgEEAAIBBAACZQwAAhEIAALBBAAAwQgAAAEIAACxDAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAADQQgAAgEEAABhCAACAQQAAgEEAAKBBAACAQQAAKEIAAFBCAIBcRAAAgEEAAKhCAACAQQAAYEIAAIBBAACAQQAAkEEAAIRCAACAQQAAgEEAAIBBAACAQQAA4EEAAIBBAACAQQAAgEEAAIBBAACAQQAAAEIAAIBBAABYQgAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAkEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACQQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACQQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBBAACAQQAAgEEAAIBB</binary>
+              <binary></binary>
             </binaryDataArray>
           </binaryDataArrayList>
         </spectrum>

diff --git a/data/mzML/S46_SCIEX_QTRAP6500P_TQMS_New.mzML b/data/mzML/S46_SCIEX_QTRAP6500P_TQMS_New.mzML
@@ -56,7 +56,7 @@
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
-    <run id="_x0032_0230608_MR-LIPT-001_RLIP_Stress_Test-20230605_MR-LIPT-001_RLIP_Stress_Test_VLTR_96" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2023-06-09T17:24:53Z" defaultSourceFileRef="WIFF">
+    <run id="S46_SCIEX_QTRAP6500P_TQMS_New" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2023-06-09T17:24:53Z" defaultSourceFileRef="WIFF">
       <chromatogramList count="1" defaultDataProcessingRef="pwiz_Reader_ABI_conversion">
         <chromatogram index="0" id="TIC" defaultArrayLength="6053">
           <cvParam cvRef="MS" accession="MS:1000235" name="total ion current chromatogram" value=""/>

diff --git a/src/__tests__/decoder.test.js b/src/__tests__/decoder.test.js
@@ -141,6 +141,14 @@ describe('decoder', () => {
     ).toStrictEqual(testMZ);
   });
 
+  test('decode encoded data (empty binary): 64-bit', async () => {
+    expect(
+      Array.from(
+        await decoder(encoding.precisionValue, encoding.compressionMethod, ''),
+      ),
+    ).toStrictEqual([]);
+  });
+
   test('decode encoded data: 32-bit', async () => {
     encoding.precisionValue = 32;
 
@@ -177,4 +185,12 @@ describe('decoder', () => {
       ),
     ).toStrictEqual(testIntensity);
   });
+
+  test('decode encoded data (empty binary): 32-bit', async () => {
+    expect(
+      Array.from(
+        await decoder(encoding.precisionValue, encoding.compressionMethod, ''),
+      ),
+    ).toStrictEqual([]);
+  });
 });
diff --git a/src/utils/decoder.js b/src/utils/decoder.js
@@ -25,6 +25,11 @@ export async function decoder(precisionValue, compressionMethod, encodedData) {
 
   let decodedData;
 
+  // Check if encodedData is empty
+  if (encodedData.length === 0) {
+    return precisionValue === 64 ? new Float64Array() : new Float32Array();
+  }
+
   // Check compression method used
   if (compressionMethod === 'none') {
     decodedData = decode(encodedData);