style: use Ruff and Black (#259)

.github/workflows/backend_checks.yml

@@ -0,0 +1,31 @@
+name: backend_checks
+on: [push, pull_request]
+jobs:
+  build:
+    name: build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: pip install server/
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: black
+        uses: psf/black@stable
+        with:
+          src: "./server"
+
+      - name: ruff
+        uses: chartboost/ruff-action@v1
+        with:
+          src: "./server"

.gitignore

@@ -160,7 +160,6 @@ dynamodb_local_latest/*
 
 # Build files
 Pipfile.lock
-pyproject.toml
 
 # client-side things
 curation/client/node_modules

.pre-commit-config.yaml

@@ -2,17 +2,21 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.4.0
     hooks:
-      - id: flake8
-        additional_dependencies: [flake8-docstrings]
-        args: ["--config=server/.flake8"]
       - id: check-added-large-files
         args: ["--maxkb=2000"]
       - id: detect-private-key
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
   - repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 23.7.0
     hooks:
       - id: black
-        args: [--diff, --check]
+        language_version: python3.11
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.286
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/pre-commit/mirrors-eslint
     rev: "v8.20.0"
     hooks:

server/curfu/__init__.py

@@ -1,11 +1,10 @@
 """Fusion curation interface."""
-from pathlib import Path
-from os import environ
 import logging
+from os import environ
+from pathlib import Path
 
 from .version import __version__
 
-
 # provide consistent paths
 APP_ROOT = Path(__file__).resolve().parents[0]
 
@@ -51,13 +50,9 @@
     SEQREPO_DATA_PATH = environ["SEQREPO_DATA_PATH"]
 
 
-class ServiceWarning(Exception):
+class LookupServiceError(Exception):
     """Custom Exception to use when lookups fail in curation services."""
 
-    def __init__(self, *args, **kwargs):
-        """Initialize exception."""
-        super().__init__(*args, **kwargs)
-
 
 # define max acceptable matches for autocomplete suggestions
 MAX_SUGGESTIONS = 50

server/curfu/cli.py

@@ -1,15 +1,15 @@
 """Provide command-line interface to application and associated utilities."""
 import os
-from typing import Optional
 from pathlib import Path
+from typing import Optional
 
 import click
-from curfu import APP_ROOT
 
+from curfu import APP_ROOT
 from curfu.devtools import DEFAULT_INTERPRO_TYPES
 from curfu.devtools.build_client_types import build_client_types
-from curfu.devtools.interpro import build_gene_domain_maps
 from curfu.devtools.gene import GeneSuggestionBuilder
+from curfu.devtools.interpro import build_gene_domain_maps
 
 
 @click.command()
@@ -27,9 +27,8 @@ def serve(port: int) -> None:
 
 
 @click.group()
-def devtools():
+def devtools() -> None:
     """Provide setup utilities for constructing data for Fusion Curation app."""
-    pass
 
 
 types_help = """

server/curfu/devtools/__init__.py

@@ -1,10 +1,11 @@
 """Utility functions for application setup."""
 import ftplib
+from typing import Callable
 
 from curfu import logger
 
 
-def ftp_download(domain: str, path: str, fname: str, callback) -> None:
+def ftp_download(domain: str, path: str, fname: str, callback: Callable) -> None:
     """Acquire file via FTP.
     :param str domain: domain name for remote file host
     :param str path: path within host to desired file

server/curfu/devtools/build_client_types.py

@@ -1,9 +1,10 @@
 """Provide client type generation tooling."""
 from pathlib import Path
+
 from pydantic2ts.cli.script import generate_typescript_defs
 
 
-def build_client_types():
+def build_client_types() -> None:
     """Construct type definitions for front-end client."""
     client_dir = Path(__file__).resolve().parents[3] / "client"
     generate_typescript_defs(

server/curfu/devtools/gene.py

@@ -1,15 +1,14 @@
 """Provide tools to build backend data relating to gene identification."""
-from typing import Dict, Tuple
-from pathlib import Path
 from datetime import datetime as dt
+from pathlib import Path
 from timeit import default_timer as timer
+from typing import Dict, Tuple
 
-from gene.query import QueryHandler
 import click
+from gene.query import QueryHandler
 
 from curfu import APP_ROOT, logger
 
-
 # type stub
 Map = Dict[str, Tuple[str, str, str]]
 
@@ -27,7 +26,7 @@ class GeneSuggestionBuilder:
     alias_map = {}
     assoc_with_map = {}
 
-    def __init__(self):
+    def __init__(self) -> None:
         """Initialize class.
 
         TODO: think about how best to force prod environment
@@ -108,7 +107,7 @@ def build_gene_suggest_maps(self, output_dir: Path = APP_ROOT / "data") -> None:
                 break
 
         today = dt.strftime(dt.today(), "%Y%m%d")
-        for (map, name) in (
+        for map, name in (
             (self.xrefs_map, "xrefs"),
             (self.symbol_map, "symbols"),
             (self.label_map, "labels"),

server/curfu/devtools/interpro.py

@@ -1,16 +1,16 @@
 """Provide utilities relating to data fetched from InterPro service."""
-import gzip
-from typing import Tuple, Dict, Optional, Set
-from pathlib import Path
 import csv
-from datetime import datetime
-from timeit import default_timer as timer
+import gzip
 import os
 import shutil
-import xml.etree.ElementTree as ET
+import xml.etree.ElementTree as ET  # noqa: N817
+from datetime import datetime
+from pathlib import Path
+from timeit import default_timer as timer
+from typing import Dict, Optional, Set, Tuple
 
-from gene.query import QueryHandler
 import click
+from gene.query import QueryHandler
 
 from curfu import APP_ROOT, logger
 from curfu.devtools import ftp_download
@@ -34,7 +34,7 @@ def download_protein2ipr(output_dir: Path) -> None:
     gz_file_path = output_dir / "protein2ipr.dat.gz"
     with open(gz_file_path, "w") as fp:
 
-        def writefile(data):
+        def writefile(data):  # noqa
             fp.write(data)
 
         ftp_download(
@@ -283,7 +283,7 @@ def build_gene_domain_maps(
     # get relevant Interpro IDs
     interpro_data_bin = []
 
-    def get_interpro_data(data):
+    def get_interpro_data(data):  # noqa
         interpro_data_bin.append(data)
 
     ftp_download(

server/curfu/domain_services.py

@@ -1,13 +1,15 @@
 """Provide lookup services for functional domains.
 
-TODO
+Todo:
+----
  * domains file should be a JSON and pre-pruned to unique pairs
  * get_possible_domains shouldn't have to force uniqueness
+
 """
-from typing import List, Dict
 import csv
+from typing import Dict, List
 
-from curfu import logger, ServiceWarning
+from curfu import LookupServiceError, logger
 from curfu.utils import get_data_file
 
 
@@ -56,5 +58,5 @@ def get_possible_domains(self, gene_id: str) -> List[Dict]:
             domains = self.domains[gene_id.lower()]
         except KeyError:
             logger.warning(f"Unable to retrieve associated domains for {gene_id}")
-            raise ServiceWarning
+            raise LookupServiceError
         return domains

server/curfu/gene_services.py

@@ -1,15 +1,14 @@
 """Wrapper for required Gene Normalization services."""
-from typing import List, Tuple, Dict, Union
 import csv
+from typing import Dict, List, Tuple, Union
 
+from ga4gh.vrsatile.pydantic.vrsatile_models import CURIE
 from gene.query import QueryHandler
 from gene.schemas import MatchType
-from ga4gh.vrsatile.pydantic.vrsatile_models import CURIE
 
-from curfu import logger, ServiceWarning, MAX_SUGGESTIONS
+from curfu import MAX_SUGGESTIONS, LookupServiceError, logger
 from curfu.utils import get_data_file
 
-
 # term -> (normalized ID, normalized label)
 Map = Dict[str, Tuple[str, str, str]]
 
@@ -51,13 +50,13 @@ def get_normalized_gene(
             if not gd or not gd.gene_id:
                 msg = f"Unexpected null property in normalized response for `{term}`"
                 logger.error(msg)
-                raise ServiceWarning(msg)
+                raise LookupServiceError(msg)
             concept_id = gd.gene_id
             symbol = gd.label
             if not symbol:
                 msg = f"Unable to retrieve symbol for gene {concept_id}"
                 logger.error(msg)
-                raise ServiceWarning(msg)
+                raise LookupServiceError(msg)
             term_lower = term.lower()
             term_cased = None
             if response.match_type == 100:
@@ -100,7 +99,7 @@ def get_normalized_gene(
         else:
             warn = f"Lookup of gene term {term} failed."
             logger.warning(warn)
-            raise ServiceWarning(warn)
+            raise LookupServiceError(warn)
 
     def suggest_genes(self, query: str) -> Dict[str, List[Tuple[str, str, str]]]:
         """Provide autocomplete suggestions based on submitted term.
@@ -153,6 +152,6 @@ def suggest_genes(self, query: str) -> Dict[str, List[Tuple[str, str, str]]]:
         if n > MAX_SUGGESTIONS:
             warn = f"Exceeds max matches: Got {n} possible matches for {query} (limit: {MAX_SUGGESTIONS})"  # noqa: E501
             logger.warning(warn)
-            raise ServiceWarning(warn)
+            raise LookupServiceError(warn)
         else:
             return suggestions

server/curfu/main.py

@@ -3,24 +3,23 @@
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.staticfiles import StaticFiles
 from fastapi.templating import Jinja2Templates
-from starlette.templating import _TemplateResponse as TemplateResponse
 from fusor import FUSOR
+from starlette.templating import _TemplateResponse as TemplateResponse
 
 from curfu import APP_ROOT
-from curfu.version import __version__ as curfu_version
-from curfu.gene_services import GeneService
 from curfu.domain_services import DomainService
+from curfu.gene_services import GeneService
 from curfu.routers import (
-    nomenclature,
-    utilities,
-    constructors,
-    lookup,
     complete,
-    validate,
+    constructors,
     demo,
+    lookup,
     meta,
+    nomenclature,
+    utilities,
+    validate,
 )
-
+from curfu.version import __version__ as curfu_version
 
 fastapi_app = FastAPI(
     version=curfu_version,
@@ -52,8 +51,7 @@
 
 
 def serve_react_app(app: FastAPI) -> FastAPI:
-    """
-    Wrap application initialization in Starlette route param converter.
+    """Wrap application initialization in Starlette route param converter.
 
     :param app: FastAPI application instance
     :return: application with React frontend mounted
@@ -67,8 +65,7 @@ def serve_react_app(app: FastAPI) -> FastAPI:
 
     @app.get("/{full_path:path}")
     async def serve_react_app(request: Request, full_path: str) -> TemplateResponse:
-        """
-        Add arbitrary path support to FastAPI service.
+        """Add arbitrary path support to FastAPI service.
 
         React-router provides something akin to client-side routing based out
         of the Javascript embedded in index.html. However, FastAPI will intercede
@@ -118,14 +115,14 @@ def get_domain_services() -> DomainService:
 
 
 @app.on_event("startup")
-async def startup():
+async def startup() -> None:
     """Get FUSOR reference"""
     app.state.fusor = await start_fusor()
     app.state.genes = get_gene_services()
     app.state.domains = get_domain_services()
 
 
 @app.on_event("shutdown")
-async def shutdown():
+async def shutdown() -> None:
     """Clean up thread pool."""
     await app.state.fusor.cool_seq_tool.uta_db._connection_pool.close()