From 97263b107767f8907b69cc5dcaa94804704c83ac Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Fri, 1 Nov 2024 04:54:37 -0700
Subject: [PATCH] (refactor) moved format reader dispatch

---
 crates/sage-cli/src/runner.rs     | 29 +++-----------
 crates/sage-cloudpath/src/util.rs | 65 +++++++++++++++++++++++++++++++
 2 files changed, 71 insertions(+), 23 deletions(-)

diff --git a/crates/sage-cli/src/runner.rs b/crates/sage-cli/src/runner.rs
index 4903ff9..7e16150 100644
--- a/crates/sage-cli/src/runner.rs
+++ b/crates/sage-cli/src/runner.rs
@@ -161,34 +161,17 @@ impl Runner {
             min_deisotope_mz.unwrap_or(0.0),
         );
 
-        let bruker_extensions = [".d", ".tdf", ".tdf_bin", "ms2", "raw"];
         let spectra = chunk
             .par_iter()
             .enumerate()
             .flat_map(|(idx, path)| {
                 let file_id = chunk_idx * batch_size + idx;
-
-                let path_lower = path.to_lowercase();
-                let res = if path_lower.ends_with(".mgf.gz") || path_lower.ends_with(".mgf") {
-                    sage_cloudpath::util::read_mgf(path, file_id)
-                } else if bruker_extensions.iter().any(|ext| {
-                    if path_lower.ends_with(std::path::MAIN_SEPARATOR) {
-                        path_lower
-                            .strip_suffix(std::path::MAIN_SEPARATOR)
-                            .unwrap()
-                            .ends_with(ext)
-                    } else {
-                        path_lower.ends_with(ext)
-                    }
-                }) {
-                    sage_cloudpath::util::read_tdf(
-                        path,
-                        file_id,
-                        self.parameters.bruker_spectrum_processor,
-                    )
-                } else {
-                    sage_cloudpath::util::read_mzml(path, file_id, sn)
-                };
+                let res = sage_cloudpath::util::read_spectra(
+                    path,
+                    file_id,
+                    sn,
+                    self.parameters.bruker_spectrum_processor,
+                );
 
                 match res {
                     Ok(s) => {
diff --git a/crates/sage-cloudpath/src/util.rs b/crates/sage-cloudpath/src/util.rs
index c3f18b8..3bbc500 100644
--- a/crates/sage-cloudpath/src/util.rs
+++ b/crates/sage-cloudpath/src/util.rs
@@ -3,6 +3,55 @@ use sage_core::spectrum::RawSpectrum;
 use serde::Serialize;
 use tokio::io::AsyncReadExt;
 
+#[derive(Debug, PartialEq, Eq)]
+enum FileFormat {
+    MzML,
+    MGF,
+    TDF,
+    Unidentified,
+}
+
+const BRUKER_EXTENSIONS: [&str; 5] = [".d", ".tdf", ".tdf_bin", "ms2", "raw"];
+
+fn is_bruker(path: &str) -> bool {
+    BRUKER_EXTENSIONS.iter().any(|ext| {
+        if path.ends_with(std::path::MAIN_SEPARATOR) {
+            path.strip_suffix(std::path::MAIN_SEPARATOR)
+                .unwrap()
+                .ends_with(ext)
+        } else {
+            path.ends_with(ext)
+        }
+    })
+}
+
+fn identify_format(s: &str) -> FileFormat {
+    let path_lower = s.to_lowercase();
+    if path_lower.ends_with(".mgf.gz") || path_lower.ends_with(".mgf") {
+        FileFormat::MGF
+    } else if is_bruker(&path_lower) {
+        FileFormat::TDF
+    } else if path_lower.ends_with(".mzml.gz") || path_lower.ends_with(".mzml") {
+        FileFormat::MzML
+    } else {
+        FileFormat::Unidentified
+    }
+}
+
+pub fn read_spectra<S: AsRef<str>>(
+    path: S,
+    file_id: usize,
+    sn: Option<u8>,
+    bruker_processor: BrukerSpectrumProcessor,
+) -> Result<Vec<RawSpectrum>, Error> {
+    match identify_format(path.as_ref()) {
+        FileFormat::MzML => read_mzml(path, file_id, sn),
+        FileFormat::MGF => read_mgf(path, file_id),
+        FileFormat::TDF => read_tdf(path, file_id, bruker_processor),
+        FileFormat::Unidentified => panic!("Unable to get type for '{}'", path.as_ref()), // read_mzml(path, file_id, sn),
+    }
+}
+
 pub fn read_mzml<S: AsRef<str>>(
     s: S,
     file_id: usize,
@@ -91,3 +140,19 @@ where
         Ok(())
     })
 }
+
+#[cfg(test)]
+mod test {
+    use super::*;
+
+    #[test]
+    fn test_identify_format() {
+        assert_eq!(identify_format("foo.mzml"), FileFormat::MzML);
+        assert_eq!(identify_format("foo.mzML"), FileFormat::MzML);
+        assert_eq!(identify_format("foo.mgf"), FileFormat::MGF);
+        assert_eq!(identify_format("foo.mgf.gz"), FileFormat::MGF);
+        assert_eq!(identify_format("foo.tdf"), FileFormat::TDF);
+        assert_eq!(identify_format("./tomato/foo.d"), FileFormat::TDF);
+        assert_eq!(identify_format("./tomato/foo.d/"), FileFormat::TDF);
+    }
+}