From 3285ec6e2e85f2cc5faa49c2f48ebb4131e4ee46 Mon Sep 17 00:00:00 2001
From: Sander Willems <sander.willems@bruker.com>
Date: Thu, 3 Oct 2024 10:03:45 +0200
Subject: [PATCH] CHORE: added todos and changed unwraps to expects when known
 to not panic

---
 README.md                                      |  3 +++
 .../file_readers/tdf_blob_reader/tdf_blobs.rs  |  4 +++-
 src/io/readers/metadata_reader.rs              |  5 ++++-
 src/io/readers/quad_settings_reader.rs         | 18 ++++++++++++++----
 src/io/readers/spectrum_reader/tdf/dda.rs      |  5 ++++-
 5 files changed, 28 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 5b0ffac..be2aef5 100644
--- a/README.md
+++ b/README.md
@@ -53,6 +53,9 @@ TODO
 * Improve docs
 * Improve tests
 * Pase CompressionType1
+* Tarred file reader
+* Clean up src (FrameReader, ...)
+* Cleaner try_from conversions/readers
 * Make Path of TimsTOF data into special type
 * Single access point for all readers?
 * Few unchecked unwraps left
diff --git a/src/io/readers/file_readers/tdf_blob_reader/tdf_blobs.rs b/src/io/readers/file_readers/tdf_blob_reader/tdf_blobs.rs
index 12024c6..78c0c36 100644
--- a/src/io/readers/file_readers/tdf_blob_reader/tdf_blobs.rs
+++ b/src/io/readers/file_readers/tdf_blob_reader/tdf_blobs.rs
@@ -16,7 +16,9 @@ impl TdfBlob {
 
     pub fn get_all(&self) -> Vec<u32> {
         (0..self.len())
-            .map(|index| self.get(index).unwrap())
+            .map(|index| self.get(index).expect(
+                "When iterating over the length of a tdf blob, you cannot go out of bounds"
+            ))
             .collect()
     }
 
diff --git a/src/io/readers/metadata_reader.rs b/src/io/readers/metadata_reader.rs
index 8944001..cf29a9a 100644
--- a/src/io/readers/metadata_reader.rs
+++ b/src/io/readers/metadata_reader.rs
@@ -97,7 +97,10 @@ fn get_im_converter(
 ) -> Result<Scan2ImConverter, MetadataReaderError> {
     let scan_counts: Vec<u32> =
         tdf_sql_reader.read_column_from_table("NumScans", "Frames")?;
-    let scan_max_index = *scan_counts.iter().max().unwrap(); // SqlReader cannot return empty vecs, so always succeeds
+    let scan_max_index = *scan_counts
+        .iter()
+        .max()
+        .expect("SqlReader cannot return empty vecs, so there is always a max scan index");
     let (im_min, im_max) = get_im_bounds(sql_metadata)?;
     Ok(Scan2ImConverter::from_boundaries(
         im_min,
diff --git a/src/io/readers/quad_settings_reader.rs b/src/io/readers/quad_settings_reader.rs
index eb67dfc..90aa4d3 100644
--- a/src/io/readers/quad_settings_reader.rs
+++ b/src/io/readers/quad_settings_reader.rs
@@ -37,7 +37,8 @@ impl QuadrupoleSettingsReader {
             .iter()
             .map(|x| x.window_group)
             .max()
-            .unwrap() as usize; // SqlReader cannot return empty vecs, so always succeeds
+            .expect("SqlReader cannot return empty vecs, so there is always a max window_group")
+            as usize;
         let quadrupole_settings = (0..window_group_count)
             .map(|window_group| {
                 let mut quad = QuadrupoleSettings::default();
@@ -306,9 +307,18 @@ fn expand_window_settings(
         let window = window_group.window_group;
         let frame = window_group.frame;
         let group = &quadrupole_settings[window as usize - 1];
-        let window_group_start =
-            group.scan_starts.iter().min().unwrap().clone(); // SqlReader cannot return empty vecs, so always succeeds
-        let window_group_end = group.scan_ends.iter().max().unwrap().clone(); // SqlReader cannot return empty vecs, so always succeeds
+        let window_group_start = group
+            .scan_starts
+            .iter()
+            .min()
+            .expect("SqlReader cannot return empty vecs, so there is always min window_group index")
+            .clone();
+        let window_group_end = group
+            .scan_ends
+            .iter()
+            .max()
+            .expect("SqlReader cannot return empty vecs, so there is always max window_group index")
+            .clone();
         for (sws, swe) in
             scan_range_subsplit(window_group_start, window_group_end, &strategy)
         {
diff --git a/src/io/readers/spectrum_reader/tdf/dda.rs b/src/io/readers/spectrum_reader/tdf/dda.rs
index 2434192..2e1e9c5 100644
--- a/src/io/readers/spectrum_reader/tdf/dda.rs
+++ b/src/io/readers/spectrum_reader/tdf/dda.rs
@@ -30,7 +30,10 @@ impl DDARawSpectrumReader {
         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(); // SqlReader cannot return empty vecs, so always succeeds
+        let max_precursor = pasef_precursors
+            .iter()
+            .max()
+            .expect("SqlReader cannot return empty vecs, so there is always a max precursor index");
         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) {