Develop sw

benches/speed_performance.rs

@@ -34,7 +34,7 @@ fn criterion_benchmark_dda(c: &mut Criterion) {
     group.significance_level(0.001).sample_size(10);
     let d_folder_name: &str = DDA_TEST;
     let frame_reader = FrameReader::new(d_folder_name).unwrap();
-    let spectrum_reader = SpectrumReader::new(d_folder_name);
+    let spectrum_reader = SpectrumReader::new(d_folder_name).unwrap();
     group.bench_function("DDA read_all_frames 6m", |b| {
         b.iter(|| read_all_frames(black_box(&frame_reader)))
     });
@@ -56,7 +56,7 @@ fn criterion_benchmark_dia(c: &mut Criterion) {
     group.significance_level(0.001).sample_size(10);
     let d_folder_name: &str = DIA_TEST;
     let frame_reader = FrameReader::new(d_folder_name).unwrap();
-    let spectrum_reader = SpectrumReader::new(d_folder_name);
+    let spectrum_reader = SpectrumReader::new(d_folder_name).unwrap();
     group.bench_function("DIA read_all_frames 6m", |b| {
         b.iter(|| read_all_frames(black_box(&frame_reader)))
     });
@@ -75,7 +75,7 @@ fn criterion_benchmark_syp(c: &mut Criterion) {
     group.significance_level(0.001).sample_size(10);
     let d_folder_name: &str = SYP_TEST;
     let frame_reader = FrameReader::new(d_folder_name).unwrap();
-    let spectrum_reader = SpectrumReader::new(d_folder_name);
+    let spectrum_reader = SpectrumReader::new(d_folder_name).unwrap();
     group.bench_function("SYP read_all_frames 6m", |b| {
         b.iter(|| read_all_frames(black_box(&frame_reader)))
     });

src/io/readers/file_readers/tdf_blob_reader.rs

@@ -75,7 +75,7 @@ impl IndexedTdfBlobReader {
     pub fn new(
         file_name: impl AsRef<Path>,
         binary_offsets: Vec<usize>,
-    ) -> Result<Self, TdfBlobReaderError> {
+    ) -> Result<Self, IndexedTdfBlobReaderError> {
         let blob_reader = TdfBlobReader::new(file_name)?;
         let reader = Self {
             binary_offsets,

src/io/readers/precursor_reader/tdf.rs

@@ -41,9 +41,11 @@ impl TDFPrecursorReader {
                     Box::new(DIATDFPrecursorReader::new(path)?)
                 },
                 acquisition_type => {
-                    return Err(TDFPrecursorReaderError::UnknownPrecursorType(
-                        format!("{:?}", acquisition_type),
-                    ))
+                    return Err(
+                        TDFPrecursorReaderError::UnsupportedAcquisition(
+                            format!("{:?}", acquisition_type),
+                        ),
+                    )
                 },
             };
         let reader = Self { precursor_reader };
@@ -70,5 +72,5 @@ pub enum TDFPrecursorReaderError {
     #[error("{0}")]
     DIATDFPrecursorReaderError(#[from] DIATDFPrecursorReaderError),
     #[error("Invalid acquistion type for precursor reader: {0}")]
-    UnknownPrecursorType(String),
+    UnsupportedAcquisition(String),
 }

src/io/readers/spectrum_reader.rs

@@ -2,10 +2,10 @@ mod minitdf;
 mod tdf;
 
 use core::fmt;
-use minitdf::MiniTDFSpectrumReader;
+use minitdf::{MiniTDFSpectrumReader, MiniTDFSpectrumReaderError};
 use rayon::iter::{IntoParallelIterator, ParallelIterator};
 use std::path::{Path, PathBuf};
-use tdf::TDFSpectrumReader;
+use tdf::{TDFSpectrumReader, TDFSpectrumReaderError};
 
 use crate::ms_data::Spectrum;
 
@@ -20,14 +20,15 @@ impl fmt::Debug for SpectrumReader {
 }
 
 impl SpectrumReader {
-    pub fn new(path: impl AsRef<Path>) -> Self {
+    pub fn new(path: impl AsRef<Path>) -> Result<Self, SpectrumReaderError> {
         let spectrum_reader: Box<dyn SpectrumReaderTrait> =
             match path.as_ref().extension().and_then(|e| e.to_str()) {
-                Some("ms2") => Box::new(MiniTDFSpectrumReader::new(path)),
-                Some("d") => Box::new(TDFSpectrumReader::new(path)),
+                Some("ms2") => Box::new(MiniTDFSpectrumReader::new(path)?),
+                Some("d") => Box::new(TDFSpectrumReader::new(path)?),
                 _ => panic!(),
             };
-        Self { spectrum_reader }
+        let reader = Self { spectrum_reader };
+        Ok(reader)
     }
 
     pub fn get(&self, index: usize) -> Spectrum {
@@ -62,3 +63,11 @@ trait SpectrumReaderTrait: Sync {
     fn len(&self) -> usize;
     fn calibrate(&mut self);
 }
+
+#[derive(Debug, thiserror::Error)]
+pub enum SpectrumReaderError {
+    #[error("{0}")]
+    MiniTDFSpectrumReaderError(#[from] MiniTDFSpectrumReaderError),
+    #[error("{0}")]
+    TDFSpectrumReaderError(#[from] TDFSpectrumReaderError),
+}

src/io/readers/spectrum_reader/minitdf.rs

@@ -4,11 +4,15 @@ use crate::{
     io::readers::{
         file_readers::{
             parquet_reader::{
-                precursors::ParquetPrecursor, ReadableParquetTable,
+                precursors::ParquetPrecursor, ParquetError,
+                ReadableParquetTable,
+            },
+            sql_reader::SqlError,
+            tdf_blob_reader::{
+                IndexedTdfBlobReader, IndexedTdfBlobReaderError,
             },
-            tdf_blob_reader::IndexedTdfBlobReader,
         },
-        PrecursorReader,
+        PrecursorReader, PrecursorReaderError,
     },
     ms_data::Spectrum,
     utils::find_extension,
@@ -25,31 +29,36 @@ pub struct MiniTDFSpectrumReader {
 }
 
 impl MiniTDFSpectrumReader {
-    pub fn new(path: impl AsRef<Path>) -> Self {
-        let parquet_file_name =
-            find_extension(&path, "ms2spectrum.parquet").unwrap();
-        let precursor_reader =
-            PrecursorReader::new(&parquet_file_name).unwrap();
-        let offsets = ParquetPrecursor::from_parquet_file(&parquet_file_name)
-            .unwrap()
+    pub fn new(
+        path: impl AsRef<Path>,
+    ) -> Result<Self, MiniTDFSpectrumReaderError> {
+        let parquet_file_name = find_extension(&path, "ms2spectrum.parquet")
+            .ok_or(MiniTDFSpectrumReaderError::FileNotFound(
+                "analysis.tdf".to_string(),
+            ))?;
+        let precursor_reader = PrecursorReader::new(&parquet_file_name)?;
+        let offsets = ParquetPrecursor::from_parquet_file(&parquet_file_name)?
             .iter()
             .map(|x| x.offset as usize)
             .collect();
         let collision_energies =
-            ParquetPrecursor::from_parquet_file(&parquet_file_name)
-                .unwrap()
+            ParquetPrecursor::from_parquet_file(&parquet_file_name)?
                 .iter()
                 .map(|x| x.collision_energy)
                 .collect();
-        let bin_file_name = find_extension(&path, "bin").unwrap();
-        let blob_reader =
-            IndexedTdfBlobReader::new(&bin_file_name, offsets).unwrap();
-        Self {
+        let bin_file_name = find_extension(&path, "bin").ok_or(
+            MiniTDFSpectrumReaderError::FileNotFound(
+                "analysis.tdf".to_string(),
+            ),
+        )?;
+        let blob_reader = IndexedTdfBlobReader::new(&bin_file_name, offsets)?;
+        let reader = Self {
             path: path.as_ref().to_path_buf(),
             precursor_reader,
             blob_reader,
             collision_energies,
-        }
+        };
+        Ok(reader)
     }
 }
 
@@ -100,3 +109,17 @@ impl SpectrumReaderTrait for MiniTDFSpectrumReader {
 
     fn calibrate(&mut self) {}
 }
+
+#[derive(Debug, thiserror::Error)]
+pub enum MiniTDFSpectrumReaderError {
+    #[error("{0}")]
+    SqlError(#[from] SqlError),
+    #[error("{0}")]
+    PrecursorReaderError(#[from] PrecursorReaderError),
+    #[error("{0}")]
+    ParquetError(#[from] ParquetError),
+    #[error("{0}")]
+    IndexedTdfBlobReaderError(#[from] IndexedTdfBlobReaderError),
+    #[error("{0}")]
+    FileNotFound(String),
+}

src/io/readers/spectrum_reader/tdf.rs

@@ -2,15 +2,16 @@ mod dda;
 mod dia;
 mod raw_spectra;
 
-use raw_spectra::{RawSpectrum, RawSpectrumReader};
+use raw_spectra::{RawSpectrum, RawSpectrumReader, RawSpectrumReaderError};
 use rayon::iter::{IntoParallelIterator, ParallelIterator};
 use std::path::{Path, PathBuf};
 
 use crate::{
     domain_converters::{ConvertableDomain, Tof2MzConverter},
     io::readers::{
-        file_readers::sql_reader::SqlReader, FrameReader, MetadataReader,
-        PrecursorReader,
+        file_readers::sql_reader::{SqlError, SqlReader},
+        FrameReader, FrameReaderError, MetadataReader, MetadataReaderError,
+        PrecursorReader, PrecursorReaderError,
     },
     ms_data::Spectrum,
     utils::find_extension,
@@ -31,25 +32,30 @@ pub struct TDFSpectrumReader {
 }
 
 impl TDFSpectrumReader {
-    pub fn new(path_name: impl AsRef<Path>) -> Self {
-        let frame_reader: FrameReader = FrameReader::new(&path_name).unwrap();
-        let sql_path = find_extension(&path_name, "analysis.tdf").unwrap();
-        let metadata = MetadataReader::new(&sql_path).unwrap();
+    pub fn new(
+        path_name: impl AsRef<Path>,
+    ) -> Result<Self, TDFSpectrumReaderError> {
+        let frame_reader: FrameReader = FrameReader::new(&path_name)?;
+        let sql_path = find_extension(&path_name, "analysis.tdf").ok_or(
+            TDFSpectrumReaderError::FileNotFound("analysis.tdf".to_string()),
+        )?;
+        let metadata = MetadataReader::new(&sql_path)?;
         let mz_reader: Tof2MzConverter = metadata.mz_converter;
-        let tdf_sql_reader = SqlReader::open(&sql_path).unwrap();
-        let precursor_reader = PrecursorReader::new(&sql_path).unwrap();
+        let tdf_sql_reader = SqlReader::open(&sql_path)?;
+        let precursor_reader = PrecursorReader::new(&sql_path)?;
         let acquisition_type = frame_reader.get_acquisition();
         let raw_spectrum_reader = RawSpectrumReader::new(
             &tdf_sql_reader,
             frame_reader,
             acquisition_type,
-        );
-        Self {
+        )?;
+        let reader = Self {
             path: path_name.as_ref().to_path_buf(),
             precursor_reader,
             mz_reader,
             raw_spectrum_reader,
-        }
+        };
+        Ok(reader)
     }
 
     pub fn read_single_raw_spectrum(&self, index: usize) -> RawSpectrum {
@@ -104,3 +110,19 @@ impl SpectrumReaderTrait for TDFSpectrumReader {
         }
     }
 }
+
+#[derive(Debug, thiserror::Error)]
+pub enum TDFSpectrumReaderError {
+    #[error("{0}")]
+    SqlError(#[from] SqlError),
+    #[error("{0}")]
+    PrecursorReaderError(#[from] PrecursorReaderError),
+    #[error("{0}")]
+    MetadaReaderError(#[from] MetadataReaderError),
+    #[error("{0}")]
+    FrameReaderError(#[from] FrameReaderError),
+    #[error("{0}")]
+    RawSpectrumReaderError(#[from] RawSpectrumReaderError),
+    #[error("{0}")]
+    FileNotFound(String),
+}

src/io/readers/spectrum_reader/tdf/dda.rs

@@ -1,7 +1,8 @@
 use crate::{
     io::readers::{
         file_readers::sql_reader::{
-            pasef_frame_msms::SqlPasefFrameMsMs, ReadableSqlTable, SqlReader,
+            pasef_frame_msms::SqlPasefFrameMsMs, ReadableSqlTable, SqlError,
+            SqlReader,
         },
         FrameReader,
     },
@@ -19,13 +20,15 @@ pub struct DDARawSpectrumReader {
 }
 
 impl DDARawSpectrumReader {
-    pub fn new(tdf_sql_reader: &SqlReader, frame_reader: FrameReader) -> Self {
-        let pasef_frames =
-            SqlPasefFrameMsMs::from_sql_reader(&tdf_sql_reader).unwrap();
+    pub fn new(
+        tdf_sql_reader: &SqlReader,
+        frame_reader: FrameReader,
+    ) -> Result<Self, DDARawSpectrumReaderError> {
+        let pasef_frames = SqlPasefFrameMsMs::from_sql_reader(&tdf_sql_reader)?;
         let pasef_precursors =
             &pasef_frames.iter().map(|x| x.precursor).collect();
         let order: Vec<usize> = argsort(&pasef_precursors);
-        let max_precursor = pasef_precursors.iter().max().unwrap();
+        let max_precursor = pasef_precursors.iter().max().unwrap(); // SqlReader cannot return empty vecs, so always succeeds
         let mut offsets: Vec<usize> = Vec::with_capacity(max_precursor + 1);
         offsets.push(0);
         for (offset, &index) in order.iter().enumerate().take(order.len() - 1) {
@@ -35,12 +38,13 @@ impl DDARawSpectrumReader {
             }
         }
         offsets.push(order.len());
-        Self {
+        let reader = Self {
             order,
             offsets,
             pasef_frames,
             frame_reader,
-        }
+        };
+        Ok(reader)
     }
 
     pub fn iterate_over_pasef_frames(
@@ -97,3 +101,9 @@ impl RawSpectrumReaderTrait for DDARawSpectrumReader {
         raw_spectrum
     }
 }
+
+#[derive(Debug, thiserror::Error)]
+pub enum DDARawSpectrumReaderError {
+    #[error("{0}")]
+    SqlError(#[from] SqlError),
+}

src/io/readers/spectrum_reader/tdf/dia.rs

@@ -1,9 +1,9 @@
 use crate::{
     io::readers::{
         file_readers::sql_reader::{
-            frame_groups::SqlWindowGroup, ReadableSqlTable, SqlReader,
+            frame_groups::SqlWindowGroup, ReadableSqlTable, SqlError, SqlReader,
         },
-        FrameReader, QuadrupoleSettingsReader,
+        FrameReader, QuadrupoleSettingsReader, QuadrupoleSettingsReaderError,
     },
     ms_data::QuadrupoleSettings,
     utils::vec_utils::group_and_sum,
@@ -18,11 +18,13 @@ pub struct DIARawSpectrumReader {
 }
 
 impl DIARawSpectrumReader {
-    pub fn new(tdf_sql_reader: &SqlReader, frame_reader: FrameReader) -> Self {
-        let window_groups =
-            SqlWindowGroup::from_sql_reader(&tdf_sql_reader).unwrap();
+    pub fn new(
+        tdf_sql_reader: &SqlReader,
+        frame_reader: FrameReader,
+    ) -> Result<Self, DIARawSpectrumReaderError> {
+        let window_groups = SqlWindowGroup::from_sql_reader(&tdf_sql_reader)?;
         let quadrupole_settings =
-            QuadrupoleSettingsReader::new(&tdf_sql_reader.get_path()).unwrap();
+            QuadrupoleSettingsReader::new(&tdf_sql_reader.get_path())?;
         let mut expanded_quadrupole_settings: Vec<QuadrupoleSettings> = vec![];
         for window_group in window_groups {
             let window = window_group.window_group;
@@ -40,10 +42,11 @@ impl DIARawSpectrumReader {
                 expanded_quadrupole_settings.push(sub_quad_settings)
             }
         }
-        Self {
+        let reader = Self {
             expanded_quadrupole_settings,
             frame_reader,
-        }
+        };
+        Ok(reader)
     }
 }
 
@@ -76,3 +79,11 @@ impl RawSpectrumReaderTrait for DIARawSpectrumReader {
         raw_spectrum
     }
 }
+
+#[derive(Debug, thiserror::Error)]
+pub enum DIARawSpectrumReaderError {
+    #[error("{0}")]
+    SqlError(#[from] SqlError),
+    #[error("{0}")]
+    QuadrupoleSettingsReaderError(#[from] QuadrupoleSettingsReaderError),
+}