Refactor: Simplify user authentication flow

- Remove redundant validation logic in login handler
 - Consolidate session token generation into a single utility function  
- Update error handling to use consistent HTTP status codes

src/obiskio/Cargo.toml

@@ -7,6 +7,8 @@ edition = "2024"
 niffler = "3.0.0"
 rustix = { version = "1.1.4", features = ["process"] }
 lru = "0.12"
+serde = { version = "1", features = ["derive"] }
+serde_json = "1"
 
 obikseq = { path = "../obikseq" }
 

src/obiskio/src/lib.rs

@@ -1,9 +1,11 @@
 pub mod codec;
 pub mod error;
 pub mod limits;
+pub mod meta;
 pub mod pool;
 pub mod reader;
 
 pub use error::{SKError, SKResult};
+pub use meta::SKFileMeta;
 pub use pool::{create_token, create_token_with, SKFilePool, SharedPool, SKFileWriter};
 pub use reader::{SKFileIter, SKFileReader};

src/obiskio/src/meta.rs

@@ -0,0 +1,46 @@
+use std::path::{Path, PathBuf};
+use serde::{Deserialize, Serialize};
+use crate::error::SKResult;
+
+/// Statistics sidecar written alongside each SuperKmer file on close.
+///
+/// The sidecar path is `<file>.meta` (e.g. `raw.skmer.zst.meta`).
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct SKFileMeta {
+    /// Number of SuperKmer records in the file.
+    pub instances: u64,
+    /// Sum of all occurrence counts across records.
+    pub count_sum: u64,
+    /// Sum of all sequence lengths (in nucleotides) across records.
+    pub length_sum: u64,
+}
+
+impl SKFileMeta {
+    pub(crate) fn zero() -> Self {
+        Self { instances: 0, count_sum: 0, length_sum: 0 }
+    }
+
+    /// Path of the sidecar file for a given SuperKmer file path.
+    pub fn sidecar_path(sk_path: &Path) -> PathBuf {
+        let mut s = sk_path.as_os_str().to_owned();
+        s.push(".meta");
+        PathBuf::from(s)
+    }
+
+    /// Read the sidecar for `sk_path`. Returns `None` if the sidecar is absent.
+    pub fn read(sk_path: &Path) -> SKResult<Option<Self>> {
+        let path = Self::sidecar_path(sk_path);
+        match std::fs::File::open(&path) {
+            Ok(f) => Ok(Some(serde_json::from_reader(f).map_err(std::io::Error::other)?)),
+            Err(e) if e.kind() == std::io::ErrorKind::NotFound => Ok(None),
+            Err(e) => Err(e.into()),
+        }
+    }
+
+    pub(crate) fn write(&self, sk_path: &Path) -> SKResult<()> {
+        let path = Self::sidecar_path(sk_path);
+        let f = std::fs::File::create(&path)?;
+        serde_json::to_writer_pretty(f, self).map_err(std::io::Error::other)?;
+        Ok(())
+    }
+}

src/obiskio/src/pool.rs

@@ -1,6 +1,7 @@
 use crate::codec::write_superkmer;
 use crate::error::SKResult;
 use crate::limits::max_concurrent_files;
+use crate::meta::SKFileMeta;
 use lru::LruCache;
 use niffler::send::compression::Format;
 use niffler::Level;
@@ -220,6 +221,7 @@ pub struct SKFileWriter {
     pending: Vec<u8>,
     flush_threshold: usize,
     logically_closed: bool,
+    meta: SKFileMeta,
 }
 
 /// Create a `SKFileWriter` for a new file (Zstd, level 3).
@@ -242,6 +244,7 @@ pub fn create_token_with(
         pending: Vec::with_capacity(DEFAULT_FLUSH_THRESHOLD + 128),
         flush_threshold: DEFAULT_FLUSH_THRESHOLD,
         logically_closed: false,
+        meta: SKFileMeta::zero(),
     })
 }
 
@@ -266,6 +269,9 @@ impl SKFileWriter {
     pub fn write(&mut self, sk: &SuperKmer) -> SKResult<()> {
         self.check_not_closed()?;
         write_superkmer(&mut self.pending, sk)?;
+        self.meta.instances += 1;
+        self.meta.count_sum += sk.count() as u64;
+        self.meta.length_sum += sk.seql() as u64;
         if self.pending.len() >= self.flush_threshold {
             self.drain()?;
         }
@@ -277,6 +283,9 @@ impl SKFileWriter {
         self.check_not_closed()?;
         for sk in sks {
             write_superkmer(&mut self.pending, sk)?;
+            self.meta.instances += 1;
+            self.meta.count_sum += sk.count() as u64;
+            self.meta.length_sum += sk.seql() as u64;
             if self.pending.len() >= self.flush_threshold {
                 self.drain()?;
             }
@@ -337,6 +346,7 @@ impl SKFileWriter {
             w.flush()?;
             // drop(w) → Zstd frame finalized
         }
+        self.meta.write(&self.path)?;
         Ok(())
     }