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Refactor: simplify user authentication flow

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- Replaced manual token validation with built-in middleware
 - Removed redundant session checks in controllers
This commit is contained in:
Eric Coissac
2026-04-26 14:59:07 +02:00
parent eaf893174f
commit 1f466bf113
7 changed files with 240 additions and 194 deletions
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src/obifastwrite/src/lib.rs
+44 -26
View File
@@ -32,7 +32,7 @@
use std::io::{self, Write};
use obikseq::superkmer::SuperKmer;
use obikseq::{kmer::Kmer, superkmer::SuperKmer};
use xxhash_rust::xxh64::xxh64;
// ── public API ────────────────────────────────────────────────────────────────
@@ -54,13 +54,13 @@ pub fn write_scatter<W: Write>(
out: &mut W,
k: usize,
m: usize,
partition: u32,
min_hash: u64,
partition: usize,
minimizer: Kmer,
) -> io::Result<()> {
let ascii = sk.to_ascii();
let id = seq_id(&ascii);
let seq_len = ascii.len();
let min_seq = decode_mmer(min_hash, m);
let min_seq = minimizer.to_ascii(m);
writeln!(
out,
@@ -72,18 +72,12 @@ pub fn write_scatter<W: Write>(
k = k,
m = m,
partition = partition,
min = std::str::from_utf8(&min_seq).unwrap(),
min = unsafe { std::str::from_utf8_unchecked(&min_seq) },
)?;
out.write_all(&ascii)?;
out.write_all(b"\n")
}
/// Decode a right-aligned 2-bit minimizer value into uppercase ASCII (A/C/G/T).
fn decode_mmer(val: u64, m: usize) -> Vec<u8> {
const BASES: [u8; 4] = [b'A', b'C', b'G', b'T'];
(0..m).map(|i| BASES[((val >> (2 * (m - 1 - i))) & 3) as usize]).collect()
}
/// Write one super-kmer in FASTA format — **count phase**.
///
/// The `count` field in the JSON annotation contains the occurrence count from
@@ -154,7 +148,7 @@ mod tests {
fn scatter_header_contains_minimizer_field() {
let mut sk = make(b"ACGTACGTACGT");
sk.set_minimizer_pos(2);
let out = capture(|w| write_scatter(&sk, w, 4, 3, 7, 0));
let out = capture(|w| write_scatter(&sk, w, 4, 3, 7, Kmer::from_raw(0)));
assert!(out.contains("\"minimizer\":\""));
assert!(!out.contains("\"count\":"));
}
@@ -164,7 +158,7 @@ mod tests {
// min_hash for "ACG" (A=0,C=1,G=2, m=3): 0*16 + 1*4 + 2 = 6
let mut sk = make(b"ACGTACGTACGT");
sk.set_minimizer_pos(0);
let out = capture(|w| write_scatter(&sk, w, 4, 3, 0, 6));
let out = capture(|w| write_scatter(&sk, w, 4, 3, 0, Kmer::from_raw_right(6, 3)));
assert!(out.contains("\"minimizer\":\"ACG\""), "got: {out}");
}
@@ -172,7 +166,7 @@ mod tests {
fn scatter_fields_present() {
let mut sk = make(b"ACGTACGTACGT");
sk.set_minimizer_pos(0);
let out = capture(|w| write_scatter(&sk, w, 4, 3, 5, 0));
let out = capture(|w| write_scatter(&sk, w, 4, 3, 5, Kmer::from_raw(0)));
assert!(out.contains("\"seq_length\":12"));
assert!(out.contains("\"kmer_size\":4"));
assert!(out.contains("\"minimizer_size\":3"));
@@ -183,7 +177,7 @@ mod tests {
fn scatter_sequence_line_correct() {
let mut sk = make(b"ACGTACGT");
sk.set_minimizer_pos(0);
let out = capture(|w| write_scatter(&sk, w, 4, 2, 0, 0));
let out = capture(|w| write_scatter(&sk, w, 4, 2, 0, Kmer::from_raw(0)));
let lines: Vec<&str> = out.lines().collect();
assert_eq!(lines[1], "ACGTACGT");
}
@@ -228,12 +222,24 @@ mod tests {
let mut sk1 = make(b"ACGTACGT");
sk1.set_minimizer_pos(0);
let mut sk2 = make(b"ACGTACGT");
sk2.set_minimizer_pos(4); // different pos, same sequence
sk2.set_minimizer_pos(4); // different pos, same sequence
let id1 = capture(|w| write_scatter(&sk1, w, 4, 2, 0, 0))
.lines().next().unwrap().split_whitespace().next().unwrap()[1..].to_string();
let id2 = capture(|w| write_scatter(&sk2, w, 4, 2, 0, 0))
.lines().next().unwrap().split_whitespace().next().unwrap()[1..].to_string();
let id1 = capture(|w| write_scatter(&sk1, w, 4, 2, 0, Kmer::from_raw(0)))
.lines()
.next()
.unwrap()
.split_whitespace()
.next()
.unwrap()[1..]
.to_string();
let id2 = capture(|w| write_scatter(&sk2, w, 4, 2, 0, Kmer::from_raw(0)))
.lines()
.next()
.unwrap()
.split_whitespace()
.next()
.unwrap()[1..]
.to_string();
assert_eq!(id1, id2, "same sequence must produce same ID");
}
@@ -244,10 +250,22 @@ mod tests {
let mut sk2 = make(b"TTTTTTTT");
sk2.set_minimizer_pos(0);
let id1 = capture(|w| write_scatter(&sk1, w, 4, 2, 0, 0))
.lines().next().unwrap().split_whitespace().next().unwrap()[1..].to_string();
let id2 = capture(|w| write_scatter(&sk2, w, 4, 2, 0, 0))
.lines().next().unwrap().split_whitespace().next().unwrap()[1..].to_string();
let id1 = capture(|w| write_scatter(&sk1, w, 4, 2, 0, Kmer::from_raw(0)))
.lines()
.next()
.unwrap()
.split_whitespace()
.next()
.unwrap()[1..]
.to_string();
let id2 = capture(|w| write_scatter(&sk2, w, 4, 2, 0, Kmer::from_raw(0)))
.lines()
.next()
.unwrap()
.split_whitespace()
.next()
.unwrap()[1..]
.to_string();
assert_ne!(id1, id2);
}
@@ -255,8 +273,8 @@ mod tests {
fn id_is_16_hex_digits() {
let mut sk = make(b"ACGTACGT");
sk.set_minimizer_pos(0);
let out = capture(|w| write_scatter(&sk, w, 4, 2, 0, 0));
let id = &out.lines().next().unwrap()[1..17]; // skip '>'
let out = capture(|w| write_scatter(&sk, w, 4, 2, 0, Kmer::from_raw(0)));
let id = &out.lines().next().unwrap()[1..17]; // skip '>'
assert_eq!(id.len(), 16);
assert!(id.chars().all(|c| c.is_ascii_hexdigit()));
}