From 75bf98004684e707eb1349866da15e1083b215ad Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 24 Apr 2026 17:14:33 +0200
Subject: [PATCH] (deps) Add regex crate and improve MIME type detection

- Added `regex` dependency to obiread crate
- Replaced manual byte checks with regex-based detection for FASTA/FASTQ formats in mimetype.rs
- Switched from `once_cell::sync::Lazy` to standard library's `std:: sync :: LazyLock`
- Added generic text/plain fallback detection for ASCII-compatible content
- Updated `MimeTypeGuesser::new` constructor call syntax and simplified API usage of PeekReader's header method
- Implemented `Read trait for MimeTypeGuesser to allow transparent passthrough reading
---
 src/Cargo.lock              | 13 ++++++++++++
 src/obiread/Cargo.toml      |  1 +
 src/obiread/src/lib.rs      |  1 +
 src/obiread/src/mimetype.rs | 40 ++++++++++++++++++++++++-------------
 4 files changed, 41 insertions(+), 14 deletions(-)

diff --git a/src/Cargo.lock b/src/Cargo.lock
index 2d0becb..5b41240 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -706,6 +706,7 @@ dependencies = [
  "infer",
  "niffler",
  "obikrope",
+ "regex",
  "tracing",
  "tracing-subscriber",
  "ureq",
@@ -815,6 +816,18 @@ dependencies = [
  "crossbeam-utils",
 ]
 
+[[package]]
+name = "regex"
+version = "1.12.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e10754a14b9137dd7b1e3e5b0493cc9171fdd105e0ab477f51b72e7f3ac0e276"
+dependencies = [
+ "aho-corasick",
+ "memchr",
+ "regex-automata",
+ "regex-syntax",
+]
+
 [[package]]
 name = "regex-automata"
 version = "0.4.14"
diff --git a/src/obiread/Cargo.toml b/src/obiread/Cargo.toml
index b982392..9d4d0b1 100644
--- a/src/obiread/Cargo.toml
+++ b/src/obiread/Cargo.toml
@@ -10,3 +10,4 @@ ureq   = "2"
 tracing = "0.1.44"
 tracing-subscriber = { version = "0.3.23", features = ["fmt", "env-filter"] }
 infer = "0.19.0"
+regex = "1"
diff --git a/src/obiread/src/lib.rs b/src/obiread/src/lib.rs
index c758579..047d0b8 100644
--- a/src/obiread/src/lib.rs
+++ b/src/obiread/src/lib.rs
@@ -8,6 +8,7 @@
 pub mod chunk;
 mod fasta;
 mod fastq;
+pub mod mimetype;
 pub mod normalize;
 mod path_iterator;
 pub mod peakreader;
diff --git a/src/obiread/src/mimetype.rs b/src/obiread/src/mimetype.rs
index fda9f28..78a66c7 100644
--- a/src/obiread/src/mimetype.rs
+++ b/src/obiread/src/mimetype.rs
@@ -1,25 +1,37 @@
+use std::io;
+use std::sync::LazyLock;
+
 use infer::Infer;
-use once_cell::sync::Lazy;
 use regex::Regex;
 
+use crate::peakreader::PeekReader;
+
 const BUF_SIZE: usize = 4096;
 
-static RE_FASTA: Lazy<Regex> = Lazy::new(|| Regex::new(r"^>[^ ]").unwrap());
+static RE_FASTA: LazyLock<Regex> = LazyLock::new(|| Regex::new(r"^>[^ ]").unwrap());
 fn is_fasta(buf: &[u8]) -> bool {
-    RE_FASTA.is_match(buf)
+    std::str::from_utf8(buf).map_or(false, |s| RE_FASTA.is_match(s))
 }
 
-static RE_FASTQ: Lazy<Regex> = Lazy::new(|| Regex::new(r"^@[^ ].*\n[A-Za-z.-]+").unwrap());
+static RE_FASTQ: LazyLock<Regex> = LazyLock::new(|| Regex::new(r"^@[^ ].*\n[A-Za-z.-]+").unwrap());
 fn is_fastq(buf: &[u8]) -> bool {
-    RE_FASTQ.is_match(buf)
+    std::str::from_utf8(buf).map_or(false, |s| RE_FASTQ.is_match(s))
 }
 
-static INFER: Lazy<Infer> = Lazy::new(|| {
+fn is_text(buf: &[u8]) -> bool {
+    !buf.is_empty()
+        && buf
+            .iter()
+            .all(|&b| b.is_ascii() && (b >= 0x20 || matches!(b, b'\t' | b'\n' | b'\r')))
+}
+
+// Custom matchers are checked in insertion order (first added = first checked).
+// Most specific formats (fastq, fasta) come before the generic text/plain fallback.
+static INFER: LazyLock<Infer> = LazyLock::new(|| {
     let mut infer = Infer::new();
-    infer.add("text/fasta", "fasta", |buf| buf.starts_with(b">"));
-    infer.add("text/fastq", "fastq", |buf| {
-        buf.starts_with(b"@") && !buf.starts_with(b"@param,")
-    });
+    infer.add("text/fastq", "fastq", is_fastq);
+    infer.add("text/fasta", "fasta", is_fasta);
+    infer.add("text/plain", "txt", is_text);
     infer
 });
 
@@ -27,16 +39,16 @@ pub struct MimeTypeGuesser<R: std::io::Read>(PeekReader<R>);
 
 impl<R: std::io::Read> MimeTypeGuesser<R> {
     pub fn new(reader: R) -> Self {
-        Self { PeekReader::new(reader, BUF_SIZE) }
+        Self(PeekReader::new(reader, BUF_SIZE))
     }
 
     pub fn mime_type(&mut self) -> Option<&'static str> {
-        let buf = self.0.header(BUF_SIZE)?;
-        INFER.get_mime_type_for_bytes(buf).map(|kind| kind.mime_type())
+        let buf = self.0.header();
+        INFER.get(buf).map(|kind| kind.mime_type())
     }
 }
 
-impl<R: std::io::Read>  for MimeTypeGuesser<R> {
+impl<R: std::io::Read> io::Read for MimeTypeGuesser<R> {
     fn read(&mut self, out: &mut [u8]) -> io::Result<usize> {
         self.0.read(out)
     }