Merge pull request #209 from umccr/docker

Docker release support

.github/workflows/benchmarking.yml

@@ -12,7 +12,7 @@ permissions:
   contents: write
 
 jobs:
-  test:
+  benchmark:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

.github/workflows/build.yml

@@ -7,13 +7,20 @@ on:
   pull_request:
 
 jobs:
-  test:
+  build:
     runs-on: ${{ matrix.os }}
+    env:
+      CARGO_TERM_COLOR: always
+      CARGO_INCREMENTAL: 0
+      SCCACHE_GHA_ENABLED: "true"
+      RUSTC_WRAPPER: "sccache"
     strategy:
       matrix:
         rust: [stable]
         os: [ubuntu-latest]
     steps:
+      - name: Cache
+        uses: mozilla-actions/sccache-action@v0.0.3
       - name: Check out
         uses: actions/checkout@v3
       - name: Install Rust
@@ -22,11 +29,6 @@ jobs:
         with:
           toolchain: ${{ matrix.rust }}
       - run: rustup override set ${{ steps.toolchain.outputs.name }}
-      - name: Cache
-        uses: Swatinem/rust-cache@v2
-        with:
-          shared-key: build-cache
-          save-if: ${{ github.ref == 'refs/heads/main' }}
       - name: Build all features
         uses: actions-rs/cargo@v1
         with:
@@ -47,3 +49,15 @@ jobs:
         with:
           command: build
           args: --all-targets --features url-storage
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Test Docker build
+        id: docker_build
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          file: deploy/Dockerfile
+          push: false
+          tags: |
+            ghcr.io/umccr/htsget-rs:dev-latest
+            ghcr.io/umccr/htsget-rs:dev-${{ github.run_number }}

.github/workflows/release.yml

@@ -21,3 +21,21 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           CARGO_REGISTRY_TOKEN: ${{ secrets.HTSGET_RS_CRATES_IO_TOKEN }}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Login to GHCR.io (GH's Container Registry)
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Docker GitHub release 
+        id: docker_build
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          file: deploy/Dockerfile
+          push: true
+          tags: |
+            ghcr.io/umccr/htsget-rs:dev-latest
+            ghcr.io/umccr/htsget-rs:dev-${{ github.run_number }}

.github/workflows/tests.yml

@@ -9,11 +9,18 @@ on:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
+    env:
+      CARGO_TERM_COLOR: always
+      CARGO_INCREMENTAL: 0
+      SCCACHE_GHA_ENABLED: "true"
+      RUSTC_WRAPPER: "sccache"
     strategy:
       matrix:
         rust: [stable]
         os: [ubuntu-latest]
     steps:
+      - name: Cache
+        uses: mozilla-actions/sccache-action@v0.0.3
       - name: Check out
         uses: actions/checkout@v3
       - name: Install Rust
@@ -23,11 +30,6 @@ jobs:
           toolchain: ${{ matrix.rust }}
           components: rustfmt, clippy
       - run: rustup override set ${{ steps.toolchain.outputs.name }}
-      - name: Cache
-        uses: Swatinem/rust-cache@v2
-        with:
-          shared-key: build-cache
-          save-if: false
       - name: Cargo fmt
         uses: actions-rs/cargo@v1
         with:

deploy/Dockerfile

@@ -1,25 +1,22 @@
-# syntax=docker/dockerfile:1.4
-FROM rust:1.61.0 AS builder
+FROM rust:1.73.0 AS builder
 
-ARG TARGETPLATFORM
+WORKDIR /build
 
-WORKDIR /root
-
-RUN --mount=type=cache,target=/usr/local/cargo/registry,id=${TARGETPLATFORM} \
-    cargo install cargo-strip
+RUN cargo install cargo-strip
 
 COPY . .
 
-RUN --mount=type=cache,target=/usr/local/cargo/registry,id=${TARGETPLATFORM} --mount=type=cache,target=/root/target,id=${TARGETPLATFORM} \
-    cargo build --release && \
-    cargo strip && \
-    mv /root/target/release/htsget-actix /root
+RUN cargo build --features url-storage --release && \
+    cargo strip
 
+FROM debian:sid-slim
 
-FROM gcr.io/distroless/cc-debian11
+RUN apt update && apt install -y libc6-dev && rm -rf /var/lib/apt/lists/*
 
-COPY --from=builder /root/htsget-actix /
+COPY --from=builder /etc/ssl/certs/ /etc/ssl/certs/
+COPY --from=builder /build/target/release/htsget-actix /usr/local/bin/htsget-actix
 
-ENTRYPOINT ["./htsget-actix"]
+EXPOSE 8080
+EXPOSE 8081
 
-EXPOSE 3000
+CMD [ "htsget-actix" ]

deploy/README.md

@@ -159,6 +159,27 @@ cargo lambda invoke htsget-lambda --data-file data/events/event_get.json
 
 Examples of different Lambda events are located in the [`data/events`][data-events] directory.
 
+## Docker
+
+There are multiple options to use docker containers with htsget-rs:
+
+### Local
+
+```
+$ docker build . -f deploy/Dockerfile -t htsget-rs-actix
+$ docker run htsget-rs-actix
+% docker run htsget-rs-actix
+2023-10-25T01:01:38.412471Z  INFO bind_addr{addr=127.0.0.1:8081 cors=CorsConfig { allow_credentials: false, allow_origins: List([HeaderValue("http://localhost:8080")]), allow_headers: Tagged(All), allow_methods: Tagged(All), max_age: 86400, expose_headers: List([]) }}: htsget_search::storage::data_server: data server address bound to address=127.0.0.1:8081
+2023-10-25T01:01:38.412710Z  INFO run_server: htsget_actix: using non-TLS ticket server
+2023-10-25T01:01:38.412805Z  INFO run_server: htsget_actix: htsget query server addresses bound addresses=[127.0.0.1:8080]
+2023-10-25T01:01:38.412837Z  INFO run_server: actix_server::builder: starting 8 workers
+2023-10-25T01:01:38.412892Z  INFO actix_server::server: Actix runtime found; starting in Actix runtime
+```
+
+### Local with MinIO (S3) backend
+
+TBD
+
 [htsget-lambda]: ../htsget-lambda
 [cargo-lambda]: https://github.com/cargo-lambda/cargo-lambda
 [data-events]: ../data/events

htsget-search/src/storage/mod.rs

@@ -269,10 +269,7 @@ impl Display for BytesRange {
       .start
       .map(|start| start.to_string())
       .unwrap_or_else(|| "0".to_string());
-    let end = self
-      .end
-      .map(|end| end.to_string())
-      .unwrap_or_else(|| "".to_string());
+    let end = self.end.map(|end| end.to_string()).unwrap_or_default();
     write!(f, "bytes={start}-{end}")
   }
 }