refactor: move rust tools out of role

.github/workflows/srsilo-ci.yml

@@ -12,7 +12,7 @@ env:
 
 jobs:
   rust-checks:
-    name: srSILO Rust Tools - Quality Checks
+    name: srSILO Updater - Quality Checks
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -26,35 +26,35 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.cargo/registry
-          key: ${{ runner.os }}-cargo-registry-${{ hashFiles('roles/srsilo/files/tools/**/Cargo.lock') }}
+          key: ${{ runner.os }}-cargo-registry-${{ hashFiles('srsilo-updater/**/Cargo.lock') }}
 
       - name: Cache cargo index
         uses: actions/cache@v4
         with:
           path: ~/.cargo/git
-          key: ${{ runner.os }}-cargo-index-${{ hashFiles('roles/srsilo/files/tools/**/Cargo.lock') }}
+          key: ${{ runner.os }}-cargo-index-${{ hashFiles('srsilo-updater/**/Cargo.lock') }}
 
       - name: Cache cargo build
         uses: actions/cache@v4
         with:
-          path: roles/srsilo/files/tools/target
-          key: ${{ runner.os }}-cargo-build-target-${{ hashFiles('roles/srsilo/files/tools/**/Cargo.lock') }}
+          path: srsilo-updater/target
+          key: ${{ runner.os }}-cargo-build-target-${{ hashFiles('srsilo-updater/**/Cargo.lock') }}
 
       - name: Check formatting
         run: cargo fmt --all -- --check
-        working-directory: roles/srsilo/files/tools
+        working-directory: srsilo-updater
 
       - name: Run clippy
         run: cargo clippy --workspace --all-targets -- -D warnings
-        working-directory: roles/srsilo/files/tools
+        working-directory: srsilo-updater
 
       - name: Build
         run: cargo build --release --workspace
-        working-directory: roles/srsilo/files/tools
+        working-directory: srsilo-updater
 
       - name: Test
         run: cargo test --workspace
-        working-directory: roles/srsilo/files/tools
+        working-directory: srsilo-updater
 
   # srsilo-integration:
   #   name: srSILO Pipeline - Integration Test

docs/architecture/srsilo-pipeline.md

@@ -13,6 +13,7 @@ Automated multi-virus genomic data processing: monitors LAPIS API for new sequen
 
 ## Directory Structure
 
+**Deployment:**
 ```
 /opt/srsilo/
 ├── covid/                    # SARS-CoV-2 instance
@@ -24,10 +25,26 @@ Automated multi-virus genomic data processing: monitors LAPIS API for new sequen
 │   ├── .last_update         # Timestamp checkpoint
 │   └── sorted.ndjson.zst    # Merged data
 ├── rsva/                     # RSV-A instance (same structure)
-└── tools/                    # Shared Rust binaries
+└── tools/                    # Deployed Rust binaries (from srsilo-updater)
     └── target/release/
 ```
 
+**Repository:**
+```
+WisePulse/
+├── srsilo-updater/          # Rust workspace - data pipeline tools
+│   ├── src/
+│   │   ├── add_offset/
+│   │   ├── check_new_data/
+│   │   ├── fetch_silo_data/
+│   │   ├── merge_sorted_chunks/
+│   │   └── split_into_sorted_chunks/
+│   ├── Cargo.toml
+│   └── Cargo.lock
+├── roles/srsilo/            # Ansible role
+└── playbooks/srsilo/        # Ansible playbooks
+```
+
 ## Components
 
 **Playbooks:**
@@ -37,7 +54,7 @@ Automated multi-virus genomic data processing: monitors LAPIS API for new sequen
 - `setup.yml` - Initial setup
 - `setup-timer.yml` - Configure systemd timer
 
-**Rust Tools:** `check_new_data`, `fetch_silo_data`, `split_into_sorted_chunks`, `merge_sorted_chunks`, `add_offset`
+**Rust Tools (srsilo-updater):** `check_new_data`, `fetch_silo_data`, `split_into_sorted_chunks`, `merge_sorted_chunks`, `add_offset`
 
 **Docker:** SILO (genspectrum/lapis-silo), LAPIS API (genspectrum/lapis)
 

roles/srsilo/tasks/prerequisites.yml

@@ -68,9 +68,9 @@
     mode: '0750'
   become: yes
 
-- name: Copy tools directory from repository to base path
+- name: Copy srsilo-updater from repository to deployment path
   copy:
-    src: "{{ wisepulse_repo_path }}/roles/srsilo/files/tools/"
+    src: "{{ wisepulse_repo_path }}/srsilo-updater/"
     dest: "{{ srsilo_tools_path }}/"
     remote_src: yes
   become: yes

srsilo-updater/README.md

@@ -0,0 +1,47 @@
+# srSILO Updater
+
+Rust-based data pipeline tools for the srSILO multi-virus genomic database.
+
+## Overview
+
+This workspace contains 5 binaries that power the srSILO data pipeline:
+
+- `check_new_data` - Queries LAPIS API to detect new sequence data
+- `fetch_silo_data` - Downloads NDJSON data from LAPIS API
+- `split_into_sorted_chunks` - Splits large datasets for parallel processing
+- `merge_sorted_chunks` - Merges sorted chunks into final dataset
+- `add_offset` - Adjusts timestamps for incremental updates
+
+## Building
+
+```bash
+# Development build
+cargo build
+
+# Release build (used in deployment)
+cargo build --release
+```
+
+## Testing
+
+```bash
+cargo test --workspace
+```
+
+## Code Quality
+
+```bash
+# Format check
+cargo fmt --all -- --check
+
+# Linting
+cargo clippy --workspace --all-targets -- -D warnings
+```
+
+## Deployment
+
+These tools are deployed to `/opt/srsilo/tools/` on srSILO hosts via Ansible. See the main WisePulse documentation for deployment instructions.
+
+## CI/CD
+
+Quality checks run automatically on all PRs via GitHub Actions (`.github/workflows/srsilo-ci.yml`).