Eric Coissac
036d044291
Refactor `Kmer`, `SuperKmer`, and chunk reader into optimized, generic representations with compile-time length parameters and bitwise operations. Update the pipeline and scheduler to support batch processing, 1→N flat transformations, and multi-source merging. Introduce an approximate evidence mode using b-bit fingerprints and `.idx` files, alongside existing exact mode. Update CLI documentation, minimizer selection, and query output schema accordingly.
180 lines
7.8 KiB
Markdown
180 lines
7.8 KiB
Markdown
# obipipeline — parallel pipeline library
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`obipipeline` is a generic, multi-threaded data pipeline crate. It connects a **source**, a chain of **stages**, and a **sink** via crossbeam channels, running each stage with a shared worker pool and a biased scheduler.
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## Core types
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| Type alias | Rust type | Role |
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|---|---|---|
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| `SourceFn<D>` | `Box<dyn FnMut() -> Result<D, PipelineError> + Send>` | Called repeatedly; `FnMut` because it holds iterator state |
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| `SharedFn<D>` | `Arc<dyn Fn(D) -> Result<D, PipelineError> + Send + Sync>` | 1→1 transform shared across workers via `Arc::clone` |
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| `SharedFlatFn<D>` | `Arc<dyn Fn(D, &Sender<Result<D, _>>, &Sender<isize>) + Send + Sync>` | 1→N transform; pushes items into channel, sends delta |
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| `SinkFn<D>` | `Box<dyn Fn(D) -> Result<(), PipelineError> + Send>` | Final consumer; returns `Result` so errors propagate back |
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Stages come in two variants:
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```rust
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pub enum Stage<D> {
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Transform(SharedFn<D>), // 1→1
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Flat(SharedFlatFn<D>), // 1→N
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}
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```
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`Pipeline<D>` holds one `SourceFn`, a `Vec<Stage>`, and one `SinkFn`.
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`WorkerPool<D>` wraps a `Pipeline` with `n_workers` and channel `capacity`.
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## WorkerPool
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```rust
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WorkerPool::new(pipeline: Pipeline<D>, n_workers: usize, capacity: usize) -> Self
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WorkerPool::run(self)
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```
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| Parameter | Role |
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|---|---|
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| `n_workers` | Number of parallel worker threads. Each worker is generic — it executes whichever transform the scheduler assigns it. |
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| `capacity` | Bound on every crossbeam channel in the pipeline. Controls memory and back-pressure: a full channel blocks the sender until a slot frees. |
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`run` consumes `self` (all fields are moved into threads). It blocks the calling thread until the pipeline has fully drained — source exhausted and every in-flight item processed by the sink — then joins all threads before returning.
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## Data enum
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All pipeline stages communicate through a single user-defined enum:
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```rust
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enum MyData {
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Unsigned(u64),
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Number(f64),
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Text(String),
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}
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```
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Each variant carries the concrete type for one stage's output. The macros pattern-match on this enum to route values between stages.
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## Macros
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Eight low-level macros build individual stages; one high-level macro (`make_pipeline!`) composes them.
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### Low-level
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```rust
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make_source!(Enum, iterator, OutputVariant) // iterator yields T
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make_source_fallible!(Enum, iterator, OutputVariant) // iterator yields Result<T, E>
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make_transform!(Enum, func, InputVariant, OutputVariant) // func: T -> U
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make_transform_fallible!(Enum, func, InputVariant, OutputVariant) // func: T -> Result<U, E>
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make_flat_transform!(Enum, func, InputVariant, OutputVariant) // func: T -> impl IntoIterator<Item=U>
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make_flat_transform_fallible!(Enum, func, InputVariant, OutputVariant) // func: T -> Result<impl IntoIterator<Item=U>, E>
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make_sink!(Enum, func, InputVariant) // func: T -> ()
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make_sink_fallible!(Enum, func, InputVariant) // func: T -> Result<(), E>
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```
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Each macro wraps the closure in the correct smart pointer (`Box` for source/sink, `Arc` for transforms).
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### make_pipeline! DSL
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```
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make_pipeline! {
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DataEnum,
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source iterator => OutputVariant, // or source? for fallible
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| func: In => Out, // 1→1 non-fallible transform
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|? func: In => Out, // 1→1 fallible transform
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|| func: In => Out, // 1→N non-fallible flat transform
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||? func: In => Out, // 1→N fallible flat transform
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sink func @ InputVariant, // or sink? for fallible
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}
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```
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`?` marks fallibility on source, individual transforms, or sink independently.
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Implemented as a **TT muncher**: the internal rule `@build` recurses over transform tokens one at a time, accumulating them into a `vec![]`, then terminates on `sink`/`sink?`.
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### make_pipe! DSL
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`make_pipe!` builds a sourceless/sinkless `Pipe<D, In, Out>` — a reusable, composable stage sequence:
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```
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make_pipe! {
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DataEnum : InType => OutType,
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| func: InVariant => OutVariant,
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|? func: InVariant => OutVariant,
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|| func: InVariant => OutVariant,
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||? func: InVariant => OutVariant,
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}
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```
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Two pipes compose with `.then(other)`. Apply to an iterator with `.apply(iter, n_workers, capacity)` to get a `PipeIter<Out>` — an iterator over the pipeline output, backed by a background `WorkerPool`. The scatter step in `obikmer` uses `make_pipe!` and `.apply()` rather than the full `make_pipeline!` / `WorkerPool` pattern.
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## Scheduler architecture
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```
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Source thread ──► [source_rx] ──► Scheduler ──► [worker_tx] ──► Workers (×N)
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▲ │
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[stage_rxs] ────────┘◄──────────────────────────────┘
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[flat_delta_rx] ──► Scheduler (in_flight adjustment)
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│
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[sink_err_rx] ← errors from sink (highest priority)
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│
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Sink thread
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```
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The scheduler is a single thread running a biased `Select` over all input channels. Priority order (highest first):
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```
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index 0 sink_err_rx abort on sink error
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index 1 flat_delta_rx adjust in_flight before dispatching
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index 2..=n+1 stage_rxs[n-1..0] drain last stage first
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index n+2 source_rx pull new data last
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```
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This back-pressure-friendly ordering ensures downstream stages are drained before new items enter the pipeline.
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**Workers** are generic: each receives a `WorkerTask` — either `Transform(data, stage_idx)` or `Flat(data, stage_idx)`. For `Transform`, the worker calls `f(data)` and sends the result to `stage_txs[stage_idx]`. For `Flat`, the worker calls `f(data, &push_tx, &delta_tx)`: the closure pushes N items into `push_tx` then sends `N-1` to `delta_tx`. The scheduler uses the delta to adjust `in_flight` without knowing N in advance.
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**Termination** uses an `in_flight: isize` counter and a `flat_workers_active: usize` counter:
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- `in_flight` incremented when an item is dispatched from source to workers
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- `in_flight` decremented when the item exits the last stage to the sink
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- `flat_workers_active` incremented when a `Flat` task is dispatched, decremented when the delta arrives
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- the loop exits only when `source_done && in_flight == 0 && flat_workers_active == 0`
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This guarantees all in-flight items complete (including all N outputs of a flat stage) before `join()`.
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## Error handling
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`PipelineError` has four variants:
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| Variant | Meaning |
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|---|---|
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| `EndOfStream` | Source exhausted (normal termination, not sent downstream) |
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| `TypeMismatch` | Wrong enum variant arrived at a stage |
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| `StepKindMismatch` | Internal routing error |
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| `StepError(Box<dyn Error + Send + Sync>)` | Error from user code (wrapped by `make_*_fallible!`) |
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Sink errors flow back to the scheduler via a dedicated `Receiver<PipelineError>` registered at index 0 of the Select — the pipeline stops immediately on the first sink error.
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## Example
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```rust
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enum PipelineData { Unsigned(u64), Number(f64), Text(String) }
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fn to_f64(x: u64) -> f64 { x as f64 }
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fn format_num(n: f64) -> String { format!("{}", n) }
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fn reverse(s: String) -> String { s.chars().rev().collect() }
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fn hash(s: String) -> u64 { /* djb2 */ }
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fn print_hash(h: u64) -> Result<(), std::io::Error> { println!("{}", h); Ok(()) }
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let pipeline = make_pipeline! {
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PipelineData,
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source 1u64..=10 => Unsigned,
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| to_f64: Unsigned => Number,
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| format_num: Number => Text,
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| reverse: Text => Text,
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| hash: Text => Unsigned,
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sink? print_hash @ Unsigned,
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};
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WorkerPool::new(pipeline, 4, 64).run();
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```
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