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Fix SQLAlchemy 2.0 compatibility issues for Invenio upgrade #911

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Fix SQLAlchemy 2.0 compatibility issues for Invenio upgrade #911

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Copilot Sep 17, 2025
89d54b5
Fix SQLAlchemy 2.0 compatibility issues in core modules
Copilot Sep 17, 2025
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3 changes: 2 additions & 1 deletion hepdata/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -269,7 +269,8 @@ def execute(query):
"""Execute a SQL query via SQLAlchemy Engine."""
print("Executing query: {}".format(query))
if query:
result = db.session.execute(query)
from sqlalchemy import text
result = db.session.execute(text(query))
if result.returns_rows:
for i, row in enumerate(result):
print('Row {}:'.format(i + 1), row)
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2 changes: 1 addition & 1 deletion hepdata/ext/opensearch/query_builder.py
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Expand Up @@ -79,7 +79,7 @@ def parse_query(query_string):
def _quote_phrase(phrase):
# Match phrases containing a reaction (including "-->") or a doi (word
# chars with / in the middle) and quote them
pattern = re.compile("(.*-->.*|[\w\.]+\/[\w\.]+)")
pattern = re.compile(r"(.*-->.*|[\w\.]+\/[\w\.]+)")

if '"' not in phrase and pattern.fullmatch(phrase):
return f'"{phrase}"'
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5 changes: 3 additions & 2 deletions hepdata/modules/records/utils/data_files.py
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Expand Up @@ -29,6 +29,7 @@
from celery import shared_task
from flask import current_app
from invenio_db import db
from sqlalchemy import text

from hepdata.modules.email.utils import create_send_email_task
from hepdata.modules.records.utils.common import allowed_file
Expand Down Expand Up @@ -254,7 +255,7 @@ def _delete_all_orphan_file_resources(): # pragma: no cover
# ~196k rows in datafile_identifier - explain analyse on QA takes 92ms
# Produces ~300k orphans on QA.
result = db.session.execute(
"""
text("""
CREATE TEMP TABLE valid_resource_ids(id INT);
LOCK TABLE data_resource_link IN EXCLUSIVE MODE;
INSERT INTO valid_resource_ids
Expand All @@ -270,7 +271,7 @@ def _delete_all_orphan_file_resources(): # pragma: no cover
SELECT id from valid_resource_ids
WHERE valid_resource_ids.id = dataresource.id
);
"""
""")
)

ids_to_delete = [x[0] for x in result]
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