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upload error on local galaxy instance. #18380

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realzhang opened this issue Jun 12, 2024 · 4 comments
Open

upload error on local galaxy instance. #18380

realzhang opened this issue Jun 12, 2024 · 4 comments

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@realzhang
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when upload a file:

galaxy-dev/.venv/lib64/python3.9/site-packages/sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) near "FROM": syntax error
[SQL: 
            UPDATE history_dataset_association
            SET
                info = ?,
                update_time = ?
            FROM dataset
            WHERE
                history_dataset_association.dataset_id = dataset.id
                AND dataset.job_id = ?;
        ]
[parameters: (None, datetime.datetime(2024, 6, 12, 6, 4, 58, 808553), 1)]
(Background on this error at: https://sqlalche.me/e/20/e3q8)
@mvdbeek
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mvdbeek commented Jun 12, 2024

@realzhang can you tell us what version of Galaxy you're running and include the entire trace back section?

@jdavcs
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jdavcs commented Jun 12, 2024

@tcollins2011 ran into the same error a few weeks ago on a local dev setup. This seems to be an issue with your local sqlite. Tyler, were you able to run a clean clone without this error?

@tcollins2011
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@jdavcs When I pulled a new clone locally the error persisted. I ended up fully reinstalling python eventually and the issue went away after that.

@mvdbeek
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mvdbeek commented Jun 13, 2024

Right, update from is a feature added to sqlite in 2020 https://www.sqlite.org/lang_update.html:

is supported beginning in SQLite version 3.33.0 (2020-08-14)

Python links to sqlite, so an update should help.

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4 participants
@realzhang @jdavcs @mvdbeek @tcollins2011