Fix ruff lint errors and add README badges

Rename ambiguous variable `l` to `line` (E741), remove unused
BASE_IRI import (F401), apply ruff formatting, and add CI + license
badges to README.

Author: marvinm2

README.md

@@ -1,5 +1,8 @@
 # WikiPathways IRI Resolver
 
+[![CI](https://github.com/wikipathways/wikipathways-iri-resolver/actions/workflows/ci.yml/badge.svg)](https://github.com/wikipathways/wikipathways-iri-resolver/actions/workflows/ci.yml)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+
 A lightweight Flask app that makes `http://rdf.wikipathways.org/` IRIs resolvable by proxying requests as SPARQL `DESCRIBE` queries against the WikiPathways Virtuoso endpoint.
 
 ## Features

app.py

@@ -90,6 +90,7 @@
     storage_uri="memory://",
 )
 
+
 # ---------------------------------------------------------------------------
 # CORS & caching headers
 # ---------------------------------------------------------------------------
@@ -163,7 +164,9 @@ def is_empty_turtle(text):
     Virtuoso returns ``# Empty TURTLE`` instead of an empty body.
     """
     stripped = "\n".join(
-        l for l in text.splitlines() if l.strip() and not l.strip().startswith("#")
+        line
+        for line in text.splitlines()
+        if line.strip() and not line.strip().startswith("#")
     )
     return not stripped
 
@@ -176,11 +179,12 @@ def linkify_iris(html):
     Only IRIs starting with the BASE_IRI are made into relative links
     so they resolve within this service; others link externally.
     """
+
     def _replace(match):
         url = match.group(0)
         if url.startswith(BASE_IRI + "/"):
             # Relative link within this service
-            relative = "/" + url[len(BASE_IRI) + 1:]
+            relative = "/" + url[len(BASE_IRI) + 1 :]
             return f'<a href="{relative}">{url}</a>'
         return f'<a href="{url}" rel="noopener">{url}</a>'
 

test_app.py

@@ -3,7 +3,7 @@
 import pytest
 import responses
 
-from app import app, _cache, BASE_IRI, SPARQL_ENDPOINT
+from app import app, _cache, SPARQL_ENDPOINT
 
 
 SAMPLE_TURTLE = """\
@@ -100,9 +100,7 @@ def test_html_contains_clickable_links(client):
 @responses.activate
 def test_resolve_turtle_accept(client):
     responses.get(SPARQL_ENDPOINT, body=SAMPLE_TURTLE, status=200)
-    resp = client.get(
-        "/Pathway/WP4846_r140186", headers={"Accept": "text/turtle"}
-    )
+    resp = client.get("/Pathway/WP4846_r140186", headers={"Accept": "text/turtle"})
     assert resp.status_code == 200
     assert "text/turtle" in resp.content_type
     assert b"wp:Pathway" in resp.data
@@ -130,7 +128,9 @@ def test_resolve_jsonld_extension(client):
 
 @responses.activate
 def test_resolve_rdf_extension(client):
-    rdfxml_body = '<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"></rdf:RDF>'
+    rdfxml_body = (
+        '<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"></rdf:RDF>'
+    )
     responses.get(SPARQL_ENDPOINT, body=rdfxml_body, status=200)
     resp = client.get("/Pathway/WP4846_r140186.rdf")
     assert resp.status_code == 200
@@ -139,7 +139,7 @@ def test_resolve_rdf_extension(client):
 
 @responses.activate
 def test_resolve_nt_extension(client):
-    nt_body = '<http://example.org/s> <http://example.org/p> <http://example.org/o> .\n'
+    nt_body = "<http://example.org/s> <http://example.org/p> <http://example.org/o> .\n"
     responses.get(SPARQL_ENDPOINT, body=nt_body, status=200)
     resp = client.get("/Pathway/WP4846_r140186.nt")
     assert resp.status_code == 200
@@ -178,6 +178,7 @@ def test_empty_result_404_turtle(client):
 @responses.activate
 def test_sparql_connection_error_502(client):
     from requests.exceptions import ConnectionError as RequestsConnectionError
+
     responses.get(SPARQL_ENDPOINT, body=RequestsConnectionError("refused"))
     resp = client.get("/Pathway/WP4846_r140186")
     assert resp.status_code == 502
@@ -186,6 +187,7 @@ def test_sparql_connection_error_502(client):
 @responses.activate
 def test_sparql_timeout_504(client):
     from requests.exceptions import ReadTimeout
+
     responses.get(SPARQL_ENDPOINT, body=ReadTimeout("timed out"))
     resp = client.get("/Pathway/WP4846_r140186")
     assert resp.status_code == 504
@@ -234,9 +236,7 @@ def test_if_none_match_304(client):
     resp1 = client.get("/Pathway/WP4846_r140186")
     etag = resp1.headers["ETag"]
     # Second request with If-None-Match
-    resp2 = client.get(
-        "/Pathway/WP4846_r140186", headers={"If-None-Match": etag}
-    )
+    resp2 = client.get("/Pathway/WP4846_r140186", headers={"If-None-Match": etag})
     assert resp2.status_code == 304
 
 
@@ -271,6 +271,7 @@ def test_rate_limit_handler(client):
     """The 429 error handler returns a proper response."""
     with app.test_request_context():
         from app import handle_429
+
         resp = handle_429(None)
         assert resp.status_code == 429
         assert b"Rate limit" in resp.data