diff options
| -rwxr-xr-x | fatcat_scholar/grobid2json.py | 2 | ||||
| -rw-r--r-- | fatcat_scholar/issue_db.py | 2 | ||||
| -rw-r--r-- | fatcat_scholar/search.py | 2 | ||||
| -rw-r--r-- | fatcat_scholar/web.py | 8 | ||||
| -rw-r--r-- | tests/test_djvu_parse.py | 2 | ||||
| -rw-r--r-- | tests/test_grobid2json.py | 2 | ||||
| -rw-r--r-- | tests/test_issue_db.py | 4 | ||||
| -rw-r--r-- | tests/test_refs_transform.py | 2 | ||||
| -rw-r--r-- | tests/test_transform.py | 10 | ||||
| -rw-r--r-- | tests/test_work_pipeline.py | 2 |
10 files changed, 18 insertions, 18 deletions
diff --git a/fatcat_scholar/grobid2json.py b/fatcat_scholar/grobid2json.py index 2c85047..5c44953 100755 --- a/fatcat_scholar/grobid2json.py +++ b/fatcat_scholar/grobid2json.py @@ -223,7 +223,7 @@ def main() -> None: # pragma no cover args = parser.parse_args() for filename in args.teifiles: - content = open(filename).read() + content = open(filename, "r").read() print( json.dumps( teixml2json(content, encumbered=(not args.no_encumbered)), diff --git a/fatcat_scholar/issue_db.py b/fatcat_scholar/issue_db.py index 057869b..3c55b51 100644 --- a/fatcat_scholar/issue_db.py +++ b/fatcat_scholar/issue_db.py @@ -167,7 +167,7 @@ class IssueDB: PRAGMA main.synchronous = OFF; """ ) - with open("schema/issue_db.sql") as fschema: + with open("schema/issue_db.sql", "r") as fschema: self.db.executescript(fschema.read()) def insert_sim_pub(self, pub: SimPubRow, cur: Any = None) -> None: diff --git a/fatcat_scholar/search.py b/fatcat_scholar/search.py index 5b45ba9..be362b7 100644 --- a/fatcat_scholar/search.py +++ b/fatcat_scholar/search.py @@ -387,7 +387,7 @@ def do_fulltext_search( except elasticsearch.exceptions.TransportError as e: # all other errors logging.warn(f"elasticsearch non-200 status code: {e.info}") - raise OSError(str(e.info)) from e + raise IOError(str(e.info)) from e query_delta = datetime.datetime.now() - query_start # convert from API objects to dicts diff --git a/fatcat_scholar/web.py b/fatcat_scholar/web.py index 43a733a..dce732b 100644 --- a/fatcat_scholar/web.py +++ b/fatcat_scholar/web.py @@ -106,7 +106,7 @@ async def search(query: FulltextQuery = Depends(FulltextQuery)) -> FulltextHits: sentry_sdk.set_level("warning") sentry_sdk.capture_exception(e) raise HTTPException(status_code=400, detail=f"Query Error: {e}") - except OSError as e: + except IOError as e: sentry_sdk.capture_exception(e) raise HTTPException(status_code=500, detail=f"Backend Error: {e}") @@ -224,7 +224,7 @@ async def web_search( sentry_sdk.capture_exception(e) search_error = dict(type="query", message=str(e)) status_code = 400 - except OSError as e: + except IOError as e: sentry_sdk.capture_exception(e) search_error = dict(type="backend", message=str(e)) status_code = 500 @@ -282,8 +282,8 @@ async def favicon() -> Any: ) -ROBOTS_ALLOW = open("fatcat_scholar/static/robots.allow.txt").read() -ROBOTS_DISALLOW = open("fatcat_scholar/static/robots.disallow.txt").read() +ROBOTS_ALLOW = open("fatcat_scholar/static/robots.allow.txt", "r").read() +ROBOTS_DISALLOW = open("fatcat_scholar/static/robots.disallow.txt", "r").read() @app.get("/robots.txt", include_in_schema=False) diff --git a/tests/test_djvu_parse.py b/tests/test_djvu_parse.py index f661f33..777f8bf 100644 --- a/tests/test_djvu_parse.py +++ b/tests/test_djvu_parse.py @@ -5,7 +5,7 @@ from fatcat_scholar.djvu import djvu_extract_leaf_texts def test_djvu_extract_leaf_texts() -> None: # https://archive.org/details/ERIC_ED441501 - with open("tests/files/ERIC_ED441501_djvu.xml") as f: + with open("tests/files/ERIC_ED441501_djvu.xml", "r") as f: blob = f.read() leaves = djvu_extract_leaf_texts(io.StringIO(blob), [3, 6]) diff --git a/tests/test_grobid2json.py b/tests/test_grobid2json.py index bd5c0e4..345fd91 100644 --- a/tests/test_grobid2json.py +++ b/tests/test_grobid2json.py @@ -3,7 +3,7 @@ from fatcat_scholar.grobid2json import teixml2json def test_grobid_teixml2json() -> None: - with open("tests/files/example_grobid.tei.xml") as f: + with open("tests/files/example_grobid.tei.xml", "r") as f: blob = f.read() obj = teixml2json(blob, True) diff --git a/tests/test_issue_db.py b/tests/test_issue_db.py index d164ef6..9fdab94 100644 --- a/tests/test_issue_db.py +++ b/tests/test_issue_db.py @@ -16,8 +16,8 @@ def test_issue_db_basics() -> None: issue_db = IssueDB(settings.SCHOLAR_ISSUEDB_PATH) issue_db.init_db() - with open("tests/files/sim_collections.json") as f: + with open("tests/files/sim_collections.json", "r") as f: issue_db.load_pubs(f.readlines(), api) - with open("tests/files/sim_items.json") as f: + with open("tests/files/sim_items.json", "r") as f: issue_db.load_issues(f.readlines(), es_client) diff --git a/tests/test_refs_transform.py b/tests/test_refs_transform.py index 3b18557..c26ee1e 100644 --- a/tests/test_refs_transform.py +++ b/tests/test_refs_transform.py @@ -6,7 +6,7 @@ from fatcat_scholar.transform import refs_from_grobid def test_transform_refs_grobid() -> None: - with open("tests/files/example_grobid.tei.xml") as f: + with open("tests/files/example_grobid.tei.xml", "r") as f: blob = f.read() dummy_release = ReleaseEntity( diff --git a/tests/test_transform.py b/tests/test_transform.py index c5e189b..927c13b 100644 --- a/tests/test_transform.py +++ b/tests/test_transform.py @@ -7,7 +7,7 @@ from fatcat_scholar.transform import * def test_es_release_from_release() -> None: - with open("tests/files/release_hsmo6p4smrganpb3fndaj2lon4.json") as f: + with open("tests/files/release_hsmo6p4smrganpb3fndaj2lon4.json", "r") as f: release = entity_from_json(f.read(), ReleaseEntity) obj = es_release_from_release(release) @@ -20,7 +20,7 @@ def test_es_release_from_release() -> None: def test_es_biblio_from_release() -> None: - with open("tests/files/release_hsmo6p4smrganpb3fndaj2lon4.json") as f: + with open("tests/files/release_hsmo6p4smrganpb3fndaj2lon4.json", "r") as f: release = entity_from_json(f.read(), ReleaseEntity) obj = es_biblio_from_release(release) @@ -36,16 +36,16 @@ def test_es_biblio_from_release() -> None: def test_run_refs() -> None: - with open("tests/files/work_iarm6swodra2bcrzhxrfaah7py_bundle.json") as f: + with open("tests/files/work_iarm6swodra2bcrzhxrfaah7py_bundle.json", "r") as f: run_refs(f.readlines()) def test_run_transform() -> None: - with open("tests/files/work_iarm6swodra2bcrzhxrfaah7py_bundle.json") as f: + with open("tests/files/work_iarm6swodra2bcrzhxrfaah7py_bundle.json", "r") as f: run_transform(f.readlines()) - with open("tests/files/sim_page_bundle.json") as f: + with open("tests/files/sim_page_bundle.json", "r") as f: run_transform(f.readlines()) diff --git a/tests/test_work_pipeline.py b/tests/test_work_pipeline.py index 39b09dc..e0e4a82 100644 --- a/tests/test_work_pipeline.py +++ b/tests/test_work_pipeline.py @@ -84,5 +84,5 @@ def test_run_transform(mocker: Any) -> None: ), ) - with open("tests/files/release_hsmo6p4smrganpb3fndaj2lon4_sans.json") as f: + with open("tests/files/release_hsmo6p4smrganpb3fndaj2lon4_sans.json", "r") as f: wp.run_releases(f.readlines()) |