Merge pull request #5 from di-hardt/fix-handling-empty-spectra

handling empty spectra

Author: RalfG

src/parse_timsrust.rs

@@ -1,5 +1,7 @@
 use std::collections::HashMap;
 
+use timsrust::readers::SpectrumReaderError;
+
 use crate::ms2_spectrum::MS2Spectrum;
 use crate::precursor::Precursor;
 
@@ -30,18 +32,46 @@ impl From<timsrust::Spectrum> for MS2Spectrum {
     }
 }
 
+/// Handles errors from the spectrum reader by converting each error into std::io::Error except for
+/// the `Decompression`` fails error.
+///
+/// # Arguments
+/// * `err` - The error to handle
+///
+fn handle_spectrum_reader_error(err: SpectrumReaderError) -> Result<(), std::io::Error> {
+    // Unfortunately, the timsrust library does not make all errors publicly available yet,
+    // so we have to convert them to string for comparison. As soon as the development branch of
+    // timsrust is merged into the main branch, we can use the "No binary data"
+    // (TdfBlobReaderError::EmptyData) error to be more specific.
+    if err.to_string() == "Decompression fails" {
+        return Ok(());
+    }
+
+    Err(std::io::Error::other(format!(
+        "SpectrumReaderError: {}",
+        err
+    )))
+}
+
 /// Parse precursor info from spectrum files with timsrust
 pub fn parse_precursor_info(
     spectrum_path: &str,
 ) -> Result<HashMap<String, Precursor>, std::io::Error> {
     let reader = timsrust::readers::SpectrumReader::new(spectrum_path)
-        .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
+        .map_err(|e| std::io::Error::other(e.to_string()))?;
 
-    let spectra = reader
-        .get_all()
+    let spectra = (0..reader.len())
+        .map(|index| match reader.get(index) {
+            Ok(spectrum) => Ok(Some(spectrum)),
+            Err(err) => handle_spectrum_reader_error(err).map(|_| None),
+        })
+        // resolve errors
+        .collect::<Result<Vec<Option<timsrust::Spectrum>>, std::io::Error>>()
+        .map_err(|e| std::io::Error::other(e.to_string()))?
+        // remove None values
         .into_iter()
-        .collect::<Result<Vec<_>, _>>()
-        .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
+        .flatten()
+        .collect::<Vec<_>>();
 
     let precursor_info = spectra
         .into_iter()
@@ -57,13 +87,20 @@ pub fn parse_precursor_info(
 /// Read MS2 spectra from spectrum files with timsrust
 pub fn read_ms2_spectra(spectrum_path: &str) -> Result<Vec<MS2Spectrum>, std::io::Error> {
     let reader = timsrust::readers::SpectrumReader::new(spectrum_path)
-        .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
+        .map_err(|e| std::io::Error::other(e.to_string()))?;
 
-    let spectra = reader
-        .get_all()
+    let spectra = (0..reader.len())
+        .map(|index| match reader.get(index) {
+            Ok(spectrum) => Ok(Some(spectrum)),
+            Err(err) => handle_spectrum_reader_error(err).map(|_| None),
+        })
+        // resolve errors
+        .collect::<Result<Vec<Option<timsrust::Spectrum>>, std::io::Error>>()
+        .map_err(|e| std::io::Error::other(e.to_string()))?
+        // remove None values
         .into_iter()
-        .collect::<Result<Vec<_>, _>>()
-        .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
+        .flatten()
+        .collect::<Vec<_>>();
 
     Ok(spectra.into_iter().map(MS2Spectrum::from).collect())
 }