diff --git a/.github/workflows/blast-jobs.yml b/.github/workflows/blast-jobs.yml new file mode 100644 index 0000000..442b6a8 --- /dev/null +++ b/.github/workflows/blast-jobs.yml @@ -0,0 +1,48 @@ +# The blast-jobs jobs that download BLAST+ from NCBI. They live apart from ci.yml so a native path filter +# keeps a slow NCBI from reddening unrelated changes (design 3.12). The fast unit job stays in ci.yml. +name: blast-jobs +on: + push: + branches: [master] + paths: ['blast-jobs/**', '.github/workflows/blast-jobs.yml'] + pull_request: + paths: ['blast-jobs/**', '.github/workflows/blast-jobs.yml'] +permissions: + contents: read +jobs: + blast-jobs-integration: + runs-on: ubuntu-latest + defaults: { run: { working-directory: blast-jobs } } + steps: + - uses: actions/checkout@v4 + - uses: dtolnay/rust-toolchain@stable + - uses: Swatinem/rust-cache@v2 + with: { workspaces: blast-jobs } + # The tarball URL and SHA-256 are pinned once, in the Dockerfile. + - id: pin + run: | + echo "url=$(sed -n 's/^ARG BLAST_URL=//p' Dockerfile)" >> "$GITHUB_OUTPUT" + echo "sha=$(sed -n 's/^ARG BLAST_SHA256=//p' Dockerfile)" >> "$GITHUB_OUTPUT" + - uses: actions/cache@v4 + id: blast-cache + with: + path: ~/ncbi-blast.tar.gz + key: ncbi-blast-${{ steps.pin.outputs.sha }} + - if: steps.blast-cache.outputs.cache-hit != 'true' + env: { BLAST_URL: "${{ steps.pin.outputs.url }}" } + run: curl -fsSL --retry 3 -o ~/ncbi-blast.tar.gz "$BLAST_URL" + - env: { BLAST_SHA256: "${{ steps.pin.outputs.sha }}" } + run: | + test -n "$BLAST_SHA256" + echo "$BLAST_SHA256 $HOME/ncbi-blast.tar.gz" | sha256sum -c - + mkdir -p ~/ncbi-blast && tar -xzf ~/ncbi-blast.tar.gz -C ~/ncbi-blast --strip-components 1 + ~/ncbi-blast/bin/blastn -version | grep -F '2.17.0+' + - run: BLAST_JOBS_REAL_BLAST="$HOME/ncbi-blast/bin" cargo test --test real_blast + blast-jobs-image: + runs-on: ubuntu-latest + defaults: { run: { working-directory: blast-jobs } } + steps: + - uses: actions/checkout@v4 + - run: docker build -t blast-jobs:ci . + - run: docker image ls blast-jobs:ci + - run: tests/image-smoke.sh blast-jobs:ci diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6241437..58a1c28 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,5 +1,7 @@ name: ci on: [push, pull_request] +permissions: + contents: read jobs: lint-and-unit: runs-on: ubuntu-latest @@ -37,3 +39,19 @@ jobs: - run: cd mcp && cargo test --tests env: CHADO_URL: postgres://flybase_mcp:flybase_mcp@127.0.0.1:5499/flybase + blast-jobs-unit: + runs-on: ubuntu-latest + defaults: { run: { working-directory: blast-jobs } } + steps: + - uses: actions/checkout@v4 + - uses: dtolnay/rust-toolchain@stable + with: { components: "clippy, rustfmt" } + - uses: Swatinem/rust-cache@v2 + with: { workspaces: blast-jobs } + - run: cargo fmt --check + - run: cargo clippy --all-targets -- -D warnings + - uses: EmbarkStudios/cargo-deny-action@v2 + with: + manifest-path: blast-jobs/Cargo.toml + command: check advisories licenses + - run: cargo test diff --git a/README.md b/README.md index 128ac89..6c90562 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ Tools for using FlyBase data from AI assistants. - `mcp/`: the hosted FlyBase MCP server (Rust). Endpoint: `https://mcp.flybase.org/mcp`. - `plugins/flybase/`: a Claude Code plugin that registers the MCP server. Skills will live here later. +- `blast-jobs/`: the BLAST job service behind the MCP's BLAST tools (Rust, NCBI BLAST+ 2.17.0). The server's tools and their arguments are listed in [docs/tools.md](docs/tools.md). @@ -19,6 +20,14 @@ features in a range, cytology, release 5 to 6 coordinates), controlled vocabular gene groups, disease models, stocks, interactions), RNA-seq expression, and BLAST. Each is described in [docs/tools.md](docs/tools.md). +## BLAST + +The MCP's BLAST tools are clients of a private job API. `blast-jobs/` implements it. The service is a +small Rust process that runs NCBI BLAST+ 2.17.0 against a directory of BLAST databases described by a +catalogue file, in its own container with the databases mounted read-only. Nothing in it is specific to +FlyBase, so anyone with BLAST databases and a catalogue can run it. Configuration, the image and the run +shape are in [docs/blast-jobs.md](docs/blast-jobs.md). + ## Develop See `docs/deployment.md` for running the server and `mcp/README.md` for the crate. diff --git a/blast-jobs/.dockerignore b/blast-jobs/.dockerignore new file mode 100644 index 0000000..566b50d --- /dev/null +++ b/blast-jobs/.dockerignore @@ -0,0 +1,9 @@ +target +tests +fixture +deploy +bench +rust-toolchain.toml +README.md +Dockerfile +.dockerignore diff --git a/blast-jobs/.gitignore b/blast-jobs/.gitignore new file mode 100644 index 0000000..2f7896d --- /dev/null +++ b/blast-jobs/.gitignore @@ -0,0 +1 @@ +target/ diff --git a/blast-jobs/Cargo.lock b/blast-jobs/Cargo.lock new file mode 100644 index 0000000..fb75b0b --- /dev/null +++ b/blast-jobs/Cargo.lock @@ -0,0 +1,1349 @@ +# This file is automatically @generated by Cargo. +# It is not intended for manual editing. +version = 4 + +[[package]] +name = "aho-corasick" +version = "1.1.5" +source = 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b/blast-jobs/Cargo.toml new file mode 100644 index 0000000..0aa69d3 --- /dev/null +++ b/blast-jobs/Cargo.toml @@ -0,0 +1,33 @@ +[package] +name = "blast-jobs" +version = "0.1.0" +edition = "2024" +license = "MIT" +description = "Minimal BLAST+ job runner behind the FlyBase MCP's internal BLAST API" +repository = "https://github.com/FlyBase/flybase-ai-tools" +publish = false + +[lib] +name = "blast_jobs" +path = "src/lib.rs" + +[[bin]] +name = "blast-jobs" +path = "src/main.rs" + +[dependencies] +axum = "0.8" +tokio = { version = "1.53", features = ["full"] } +serde = { version = "1", features = ["derive"] } +serde_json = "1" +tracing = "0.1" +tracing-subscriber = { version = "0.3", features = ["env-filter", "json"] } +rand = "0.9" +base64 = "0.22" +subtle = "2" +anyhow = "1" +thiserror = "2" + +[dev-dependencies] +reqwest = { version = "0.13", default-features = false, features = ["json"] } +tempfile = "3" diff --git a/blast-jobs/Dockerfile b/blast-jobs/Dockerfile new file mode 100644 index 0000000..5ddb414 --- /dev/null +++ b/blast-jobs/Dockerfile @@ -0,0 +1,44 @@ +# blast-jobs: the service binary plus NCBI BLAST+ 2.17.0 from NCBI's official tarball (design 3.9, ruling 6). +# rust-toolchain.toml is excluded by .dockerignore: the image pins its own toolchain here, and rustup would +# otherwise try to install the file's channel at build time. +FROM rust:1.90-bookworm AS build +WORKDIR /src +COPY Cargo.toml Cargo.lock ./ +COPY src ./src +RUN cargo build --release --locked --bin blast-jobs + +# Versioned path (never LATEST), pinned by SHA-256. NCBI publishes only an MD5 next to the tarball +# (bdec166721de3b55f90a3badc83538e8); the SHA-256 below was computed from a download that matched it. +FROM debian:bookworm-slim AS blast +ARG BLAST_URL=https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.17.0/ncbi-blast-2.17.0+-x64-linux.tar.gz +ARG BLAST_SHA256=3888112d8207831aa47371d93583c601f058f88b5db22dc782438b039a3a411b +RUN apt-get update && apt-get install -y --no-install-recommends ca-certificates curl && rm -rf /var/lib/apt/lists/* +RUN curl -fsSL --retry 3 -o /tmp/blast.tar.gz "$BLAST_URL" \ + && echo "$BLAST_SHA256 /tmp/blast.tar.gz" | sha256sum -c - \ + && mkdir -p /opt/ncbi-blast/bin \ + && tar -xzf /tmp/blast.tar.gz -C /tmp \ + && cd /tmp/ncbi-blast-2.17.0+/bin \ + && cp blastn blastp blastx tblastn tblastx blastdbcmd makeblastdb /opt/ncbi-blast/bin/ \ + && cp /tmp/ncbi-blast-2.17.0+/LICENSE /opt/ncbi-blast/LICENSE \ + && rm -rf /tmp/blast.tar.gz /tmp/ncbi-blast-2.17.0+ + +FROM debian:bookworm-slim +# curl for the HEALTHCHECK; libgomp1 is the one shared library BLAST+ needs beyond the base image. +RUN apt-get update && apt-get install -y --no-install-recommends ca-certificates curl libgomp1 && rm -rf /var/lib/apt/lists/* +COPY --from=blast /opt/ncbi-blast /opt/ncbi-blast +ENV PATH=/opt/ncbi-blast/bin:$PATH NCBI_DONT_USE_NCBIRC=1 NCBI_DONT_USE_LOCAL_CONFIG=1 BLAST_USAGE_REPORT=false +# A missing shared library or a wrong build fails here, not at the first job. +RUN for b in blastn blastp blastx tblastn tblastx blastdbcmd makeblastdb; do \ + "$b" -version | grep -q '2\.17\.0+' || { echo "$b is not BLAST+ 2.17.0" >&2; exit 1; }; \ + done +RUN useradd --system --uid 10002 --no-create-home blastjobs +COPY --from=build /src/target/release/blast-jobs /usr/local/bin/blast-jobs +USER blastjobs +EXPOSE 8800 +ENV RUST_LOG=info +# Liveness only (design 3.8): a full queue answers 503 on the plain health route but must not restart +# the container. The port is the config's `bind`; the sample uses 8800. +HEALTHCHECK --interval=30s --timeout=5s --start-period=10s \ + CMD curl -fsS 'http://127.0.0.1:8800/internal/health?liveness=1' > /dev/null || exit 1 +ENTRYPOINT ["blast-jobs"] +CMD ["serve", "/etc/blast-jobs/config.json"] diff --git a/blast-jobs/README.md b/blast-jobs/README.md new file mode 100644 index 0000000..42060d2 --- /dev/null +++ b/blast-jobs/README.md @@ -0,0 +1,96 @@ +# blast-jobs + +A minimal BLAST+ job runner behind the FlyBase MCP's internal BLAST API (the contract is in +[`docs/handoff-private-side.md`](../docs/handoff-private-side.md) §7; the MCP's client is +`mcp/src/backends/blast.rs`). It runs NCBI BLAST+ against a directory of BLAST databases described by a +catalogue file. Nothing site-specific is compiled in, so it is reusable by anyone with a BLAST database +directory and a catalogue. + +This crate is a sibling of `mcp/`, not a workspace member: it has its own `Cargo.toml` and `Cargo.lock`. + +## Toolchain + +Stable Rust with `clippy` and `rustfmt`. If cargo is not on your `PATH`: + + export PATH="$HOME/.cargo/bin:$PATH" + +Run every command below from `blast-jobs/`. + + cargo test # all targets + cargo fmt && cargo clippy --all-targets -- -D warnings + cargo deny check advisories licenses + +`tests/real_blast.rs` runs only when `BLAST_JOBS_REAL_BLAST` names a BLAST+ bin directory; otherwise each +test prints `skipped: ...` and passes. It builds two tiny databases from `fixture/` (Notch N-RA and N-PA +from the FB2023_04 archive, see `fixture/README.md`) and searches them through the API with all five +programs: + + BLAST_JOBS_REAL_BLAST=/path/to/ncbi-blast-2.17.0+/bin cargo test --test real_blast + +## Running + + blast-jobs check # validate config, catalogue, volumes and binaries; exit 0 or 1 + blast-jobs serve # run the API (needs BLAST_JOBS_TOKEN, or BLAST_JOBS_ALLOW_NO_AUTH=1) + +The image bundles NCBI BLAST+ 2.17.0 (pinned tarball) and runs `serve /etc/blast-jobs/config.json` as +uid 10002: + + docker build -t blast-jobs:dev . + tests/image-smoke.sh blast-jobs:dev # check + one real search inside the image + +`deploy/config.sample.json` and `deploy/run.sample.sh` are the config and `docker run` shape used next to +the MCP. [`docs/blast-jobs.md`](../docs/blast-jobs.md) covers the API, the masking defaults, limits, token +pairing with the MCP and rollback. + +## Configuration + +One JSON file, passed after the subcommand (`blast-jobs serve `). Unknown keys are refused. + +| Key | Default | Meaning | +|---|---|---| +| `bind` | required | listen address, e.g. `0.0.0.0:8800` | +| `blast_bin_dir` | required | directory holding `blastn blastp blastx tblastn tblastx` | +| `database_root` | required | root the catalogue prefixes are relative to | +| `catalogue` | required | catalogue file (below) | +| `database_release` | required | label returned in every `202` and shown to users | +| `state_root` | required | writable directory for job state | +| `concurrency` | 2 | searches run at once (at least 1) | +| `threads_per_job` | 2 | `-num_threads` per search | +| `max_queued` | 20 | queued jobs before `429 queue_full` | +| `wall_seconds` | 600 | wall-clock limit for blastn and blastp | +| `translated_wall_seconds` | 300 | wall-clock limit for blastx, tblastn and tblastx | +| `retention_seconds` | 86400 | how long a job and its results are kept | +| `max_results_bytes` | 16777216 | cap on the served `results.tsv`; at most 16 MiB, the MCP's limit | +| `default_evalue` | 10 | used when a request has no `evalue` | +| `default_max_hits` | 100 | used when a request has no `max_hits` | +| `max_hsps_per_subject` | 50 | `-max_hsps`, and the ceiling for an `advanced` override | +| `max_residues` | blastn 100000, blastp 100000, blastx 30000, tblastn 30000, tblastx 10000 | query residue cap per program; if given, all five programs must be listed | + +## Catalogue + +Any JSON file with a `databases` array whose entries carry `species`, `category`, `protein` and `prefix` +(other fields are ignored): + +```json +{ "databases": [ + { "species": "dmel", "category": "assembly", "protein": false, "prefix": "dmel/dmel-assembly" } +] } +``` + +A request's `database` is the `category`; its `species` are the `species` codes. `prefix` is relative to +`database_root` and names a BLAST volume (`.nsq` for nucleotide, `.psq` for protein). At +startup every prefix must exist, neither it nor `database_root` may contain whitespace or quotes, no `(species, category)` pair may +repeat, and a category must have one molecule type; otherwise the service refuses to start. A search over +several species passes all their prefixes as one `-db` list, so its E-values are computed against the +combined database length. + +## Validation + +Every submit is checked independently of the MCP: program, database and molecule type, species (1 to 20 +lowercase codes, deduplicated), one FASTA record within the program's residue cap and alphabet, `evalue` +in (0, 1000], `max_hits` 1 to 1000, `matrix` (not with blastn), `megablast` (blastn only), `genetic_code` +in the NCBI set (1-6, 9-16, 21-31, 33) for the translated programs (blastn and blastp ignore it). A bad +field answers `invalid_` (`invalid_evalue`, `invalid_max_hits`, ...), which the MCP shows under the +tool argument of that name. The `advanced` string is checked against a typed per-program +allow-list of BLAST+ flags (`src/advanced.rs`, `TABLE`); everything else, including the flags the service +sets itself and anything that could reach the filesystem or network, is refused with `invalid_option`. diff --git a/blast-jobs/bench/README.md b/blast-jobs/bench/README.md new file mode 100644 index 0000000..02d8ac6 --- /dev/null +++ b/blast-jobs/bench/README.md @@ -0,0 +1,143 @@ +# blast-jobs benchmark harness + +`run.sh` loads a running `blast-jobs` service through its internal job API and records how long every +search takes. It sizes `concurrency`, `threads_per_job`, the container's CPU limit and the two wall limits +before a deployment. It is plain bash, `curl` and `jq` (bash 4.3+, curl 7.55+, jq 1.6+). It holds no +hostnames or secrets: the service URL and label are arguments, and the bearer token comes from the +environment. + +## Usage + + export BLAST_JOBS_TOKEN=... # the service's bearer token + bench/run.sh