refactor: extract business logic from listeners into services

.github/workflows/ci.yml

@@ -0,0 +1,102 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+env:
+  PYTHON_VERSION: "3.13"
+
+jobs:
+  lint:
+    name: Lint & Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install just
+        uses: extractions/setup-just@v2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install ${{ env.PYTHON_VERSION }}
+
+      - name: Install dependencies
+        run: uv sync --frozen
+
+      - name: Check formatting
+        run: uv run ruff format --check .
+
+      - name: Check linting
+        run: uv run ruff check .
+
+  typecheck:
+    name: Type Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install just
+        uses: extractions/setup-just@v2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install ${{ env.PYTHON_VERSION }}
+
+      - name: Install dependencies
+        run: uv sync --frozen
+
+      - name: Run type checker
+        run: uv run ty check osa
+
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install just
+        uses: extractions/setup-just@v2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install ${{ env.PYTHON_VERSION }}
+
+      - name: Install dependencies
+        run: uv sync --frozen
+
+      - name: Run unit tests with coverage
+        run: uv run pytest tests/unit -v --tb=short --cov=osa --cov-report=xml --cov-report=term-missing
+        env:
+          TEST: "1"
+
+      - name: Code Coverage Summary
+        uses: irongut/CodeCoverageSummary@v1.3.0
+        with:
+          filename: coverage.xml
+          badge: true
+          format: markdown
+          output: both
+
+      - name: Add coverage PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        if: github.event_name == 'pull_request'
+        with:
+          path: code-coverage-results.md

.gitignore

@@ -195,9 +195,9 @@ cython_debug/
 .abstra/
 
 # Visual Studio Code
-#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
 #   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
 #   you could uncomment the following to ignore the entire vscode folder
 # .vscode/
 
@@ -213,4 +213,4 @@ marimo/_lsp/
 __marimo__/
 
 # Streamlit
-.streamlit/secrets.toml
+.streamlit/secrets.toml

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+repos:
+  # Basic file hygiene
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  # Ruff - linting and formatting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.10
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  # Local hooks for ty and tests (no official pre-commit hooks yet)
+  - repo: local
+    hooks:
+      - id: ty-check
+        name: ty type check
+        entry: uv run ty check osa
+        language: system
+        types: [python]
+        pass_filenames: false
+
+      - id: unit-tests
+        name: unit tests
+        entry: uv run pytest tests/unit -q --tb=short
+        language: system
+        types: [python]
+        pass_filenames: false
+        stages: [pre-commit]

Justfile

@@ -75,6 +75,9 @@ up: db-up
 down: db-down
 
 # Testing commands
+test kind="unit":
+    @TEST=1 uv run pytest "tests/{{kind}}" -v --tb=short
+
 test-s kind="unit":
     @TEST=1 uv run pytest -s -o log_cli=True -o log_cli_level=DEBUG "tests/{{kind}}"
 
@@ -96,7 +99,7 @@ fix thing="osa":
 
 lint thing="osa":
     uv run ruff check {{thing}}
-    uv run pyright {{thing}}
+    uv run ty check {{thing}}
 
 # Docker commands (standalone)
 docker-build:

LICENSE

@@ -198,4 +198,4 @@
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
-   limitations under the License.
+   limitations under the License.

ingestors/geo_entrez/ingestor.py

@@ -120,9 +120,7 @@ async def _search_uids(self, query: str, limit: int | None) -> list[str]:
         resp.raise_for_status()
 
         tree = ElementTree.fromstring(resp.text)
-        return [
-            id_elem.text for id_elem in tree.findall(".//Id") if id_elem.text
-        ]
+        return [id_elem.text for id_elem in tree.findall(".//Id") if id_elem.text]
 
     async def _fetch_batch(self, uids: list[str]) -> list[UpstreamRecord]:
         """Fetch metadata for a batch of UIDs via ESummary."""

migrations/README

@@ -1 +1 @@
-Generic single-database configuration.
+Generic single-database configuration.

migrations/env.py

@@ -15,7 +15,8 @@
 
 # add your model's MetaData object here
 # for 'autogenerate' support
-from osa.infrastructure.persistence.tables import metadata
+from osa.infrastructure.persistence.tables import metadata  # noqa: E402
+
 target_metadata = metadata
 
 # other values from the config, defined by the needs of env.py,

osa/cli/commands/search.py

@@ -21,9 +21,7 @@ def extract_short_id(srn: str) -> str:
 
     SRN format: urn:osa:{domain}:{type}:{uuid}[@{version}]
     """
-    match = re.search(
-        r"[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}", srn
-    )
+    match = re.search(r"[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}", srn)
     if match:
         return match.group(0)[:6]
     return srn[:6]

osa/cli/commands/server.py

@@ -41,6 +41,7 @@ def _resolve_config(paths: OSAPaths, config: Path | None = None) -> Path:
             )
             sys.exit(1)
 
+    assert config is not None  # Guaranteed by logic above
     if not config.exists():
         console.error(f"Config file not found: {config}")
         sys.exit(1)

osa/cli/commands/show.py

@@ -25,9 +25,10 @@ def show(ref: str, /) -> None:
     if cache is None:
         console.error(
             "No search results cached",
-            hint="Run a search first: osa search vector \"your query\"",
+            hint='Run a search first: osa search vector "your query"',
         )
         sys.exit(1)
+        return  # Unreachable, but helps type checker
 
     # Try to interpret ref as a number first
     result: SearchHit | None = None
@@ -51,9 +52,7 @@ def show(ref: str, /) -> None:
             console.error(f"Ambiguous short ID '{ref}'")
             console.print("[dim]Matches:[/dim]")
             for m in matches:
-                console.print(
-                    f"  [cyan]{m.short_id}[/cyan]  {m.metadata.title[:50]}"
-                )
+                console.print(f"  [cyan]{m.short_id}[/cyan]  {m.metadata.title[:50]}")
             sys.exit(1)
         else:
             console.error(

osa/cli/util/daemon.py

@@ -172,9 +172,7 @@ def start(
         if process.poll() is not None:
             # Process exited immediately - error
             self._paths.remove_server_state()
-            raise RuntimeError(
-                f"Server failed to start. Check logs at {self._paths.server_log}"
-            )
+            raise RuntimeError(f"Server failed to start. Check logs at {self._paths.server_log}")
 
         return ServerInfo(
             status=ServerStatus.RUNNING,

osa/config.py

@@ -77,9 +77,7 @@ def name(self) -> str:
 class YamlConfigSettingsSource(PydanticBaseSettingsSource):
     """Load settings from YAML file specified by OSA_CONFIG_FILE env var."""
 
-    def get_field_value(
-        self, field: Any, field_name: str
-    ) -> tuple[Any, str, bool]:
+    def get_field_value(self, field: Any, field_name: str) -> tuple[Any, str, bool]:
         """Get the value for a field from the YAML config."""
         yaml_data = self._load_yaml_config()
         field_value = yaml_data.get(field_name)

osa/domain/curation/listener/auto_approve_curation_tool.py

@@ -21,17 +21,13 @@ async def handle(self, event: ValidationCompleted) -> None:
         """Emit DepositionApproved if validation passed and no curation required."""
         # Only auto-approve if validation passed
         if event.status != RunStatus.COMPLETED:
-            logger.warning(
-                f"Validation failed for {event.deposition_srn}, skipping auto-approve"
-            )
+            logger.warning(f"Validation failed for {event.deposition_srn}, skipping auto-approve")
             return
 
         # TODO: Load curation config to check if manual curation is required
         curation_required = False  # False for v1
         if curation_required:
-            logger.info(
-                f"Curation required for {event.deposition_srn}, not auto-approving"
-            )
+            logger.info(f"Curation required for {event.deposition_srn}, not auto-approving")
             return
 
         logger.debug(f"Auto-approving deposition: {event.deposition_srn}")

osa/domain/deposition/command/delete_files.py

@@ -13,9 +13,7 @@ class DepositionFilesDeleted(Result):
     pass
 
 
-class DeleteDepositionFilesHandler(
-    CommandHandler[DeleteDepositionFiles, DepositionFilesDeleted]
-):
+class DeleteDepositionFilesHandler(CommandHandler[DeleteDepositionFiles, DepositionFilesDeleted]):
     repository: DepositionRepository
     storage: StoragePort
 

osa/domain/index/listener/__init__.py

@@ -2,4 +2,4 @@
 
 from osa.domain.index.listener.index_projector import ProjectNewRecordToIndexes
 
-__all__ = ["IndexProjector"]
+__all__ = ["ProjectNewRecordToIndexes"]

osa/domain/index/listener/index_projector.py

@@ -1,27 +1,21 @@
 """IndexProjector - indexes published records into storage backends."""
 
-import logging
-
-from osa.domain.index.model.registry import IndexRegistry
+from osa.domain.index.service import IndexService
 from osa.domain.record.event.record_published import RecordPublished
 from osa.domain.shared.event import EventListener
 
-logger = logging.getLogger(__name__)
-
 
 class ProjectNewRecordToIndexes(EventListener[RecordPublished]):
-    """Projects published records into index backends."""
+    """Projects published records into index backends.
 
-    indexes: IndexRegistry
+    This listener delegates to IndexService for all business logic.
+    """
 
-    async def handle(self, event: RecordPublished) -> None:
-        """Index record into all configured backends."""
-        srn_str = str(event.record_srn)
+    service: IndexService
 
-        # Index into all configured backends
-        for name, backend in self.indexes.items():
-            try:
-                await backend.ingest(srn_str, event.metadata)
-                logger.debug(f"Indexed {srn_str} into backend '{name}'")
-            except Exception as e:
-                logger.error(f"Failed to index {srn_str} into '{name}': {e}")
+    async def handle(self, event: RecordPublished) -> None:
+        """Delegate to IndexService to index the record."""
+        await self.service.index_record(
+            record_srn=event.record_srn,
+            metadata=event.metadata,
+        )

osa/domain/index/service/__init__.py

@@ -0,0 +1,5 @@
+"""Index service module."""
+
+from osa.domain.index.service.index import IndexService
+
+__all__ = ["IndexService"]