IntegrityError: (psycopg2.errors.ForeignKeyViolation) Insert Or Update On Table "workflow_invocation_message" Vio...

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IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey"

Understanding the Error

When dealing with database operations, it's not uncommon to encounter errors that can be frustrating to resolve. In this article, we'll delve into the details of a specific error that occurs when trying to insert or update data in the workflow_invocation_message table. The error message indicates a foreign key constraint violation, which can be caused by a variety of factors.

The Error Message

The error message provided is as follows:

IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey"

DETAIL: Key (hda_id)=(20179) is not present in table "history_dataset_association".

This message indicates that the foreign key constraint workflow_invocation_message_hda_id_fkey is being violated. The constraint is checking if the hda_id value being inserted or updated exists in the history_dataset_association table. In this case, the hda_id value 20179 is not present in the history_dataset_association table.

Additional Information

The additional information provided suggests that this error may be related to a High-Performance Computing (HPC) environment, specifically a High-Throughput Computing (HTC) environment created by materializing a dataset. The fact that an id for a HDA (History Dataset Association) is present in the database but not yet in the history_dataset_association table is surprising and may indicate a commit issue.

Sentry Issue

The Sentry issue linked to this error is GALAXY-TEST-2RZ, which can be accessed at https://sentry.galaxyproject.org/organizations/galaxy/issues/214638/?referrer=github_integration.

Code Snippet

The code snippet provided is as follows:

ForeignKeyViolation: insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey"
DETAIL:  Key (hda_id)=(20179) is not present in table "history_dataset_association".

  File "sqlalchemy/engine/base.py", line 1964, in _exec_single_context
    self.dialect.do_execute(
  File "sqlalchemy/engine/default.py", line 945, in do_execute
    cursor.execute(statement, parameters)

IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey"
DETAIL:  Key (hda_id)=(20179) is not present in table "history_dataset_association".

[SQL: INSERT INTO workflow_invocation_message (workflow_invocation_id, reason, details, output_name, workflow_step_id, dependent_workflow_step_id, job_id, hda_id, hdca_id) VALUES (%(workflow_invocation_id)s, %(reason)s, %(details)s, %(output_name)s, %(workflow_step_id)s, %(dependent_workflow_step_id)s, %(job_id)s %(hda_id)s, %(hdca_id)s) RETURNING workflow_invocation_message.id]
[parameters: {'workflow_invocation_id': 4028, 'reason': <FailureReason.dataset_failed: 'dataset_failed'>, 'details': None, 'output_name': None, 'workflow_step_id': 46780, 'dependent_workflow_step_id': 46779, 'job_id': None, 'hda_id': 20179, 'hdca_id': None}]
(Background on this error at: https://sqlalche.me/e/20/gkpj)
(23 additional frame(s) were not displayed)
...
  File "galaxy/workflow/schedulers/core.py", line 41, in schedule
    run.schedule(
  File "galaxy/workflow/run.py", line 75, in schedule
    return __invoke(trans, workflow, workflow_run_config, workflow_invocation)
  File "galaxy/workflow/run.py", line 126, in __invoke
    trans.sa_session.commit()
  File "<string>", line 2, in commit
    # Copyright (C) 2005-2025 the SQLAlchemy authors and contributors
  File "<string>", line 2, in _prepare_impl
    # Copyright (C) 2005-2025 the SQLAlchemy authors and contributors

Exception raised while attempting to schedule workflow request.

Possible Solutions

Based on the error message and additional information, here are some possible solutions:

  1. Commit before adding invocation messages: As suggested in the additional information, committing the transaction before adding invocation messages may resolve the issue.
  2. Check the history_dataset_association table: Verify that the hda_id value 20179 is present in the history_dataset_association table.
  3. Update the foreign key constraint: If the hda_id value is not present in the history_dataset_association table, update the foreign key constraint to allow null values or modify the constraint to use a different column.
  4. Check the database schema: Review the database schema to ensure that the foreign key constraint is correctly defined and that the history_dataset_association table is properly linked to the workflow_invocation_message table.

Conclusion

In conclusion, the IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey" error is caused by a foreign key constraint violation. To resolve this issue, commit the transaction before adding invocation messages, check the history_dataset_association table, update the foreign key constraint, or review the database schema.
Q&A: IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey"

Q: What is the cause of the IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey" error?

A: The error is caused by a foreign key constraint violation. The foreign key constraint workflow_invocation_message_hda_id_fkey is checking if the hda_id value being inserted or updated exists in the history_dataset_association table. In this case, the hda_id value 20179 is not present in the history_dataset_association table.

Q: What is the relationship between the workflow_invocation_message table and the history_dataset_association table?

A: The workflow_invocation_message table has a foreign key constraint workflow_invocation_message_hda_id_fkey that references the hda_id column in the history_dataset_association table. This means that the workflow_invocation_message table is linked to the history_dataset_association table through the hda_id column.

Q: How can I resolve the IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey" error?

A: To resolve the error, you can try the following:

  1. Commit before adding invocation messages: Commit the transaction before adding invocation messages to ensure that the data is properly saved in the database.
  2. Check the history_dataset_association table: Verify that the hda_id value 20179 is present in the history_dataset_association table.
  3. Update the foreign key constraint: If the hda_id value is not present in the history_dataset_association table, update the foreign key constraint to allow null values or modify the constraint to use a different column.
  4. Check the database schema: Review the database schema to ensure that the foreign key constraint is correctly defined and that the history_dataset_association table is properly linked to the workflow_invocation_message table.

Q: What is the significance of the hda_id column in the history_dataset_association table?

A: The hda_id column in the history_dataset_association table is a foreign key that references the id column in the history_dataset table. This means that the history_dataset_association table is linking the history_dataset table to the workflow_invocation_message table through the hda_id column.

Q: How can I troubleshoot the IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey" error?

A: To troubleshoot the error, you can try the following:

  1. Check the database logs: Review the database logs to see if there are any errors or warnings related to the foreign key constraint.
  2. Use a database client: Use a database such as pgAdmin or psql to inspect the database schema and data.
  3. Run a query: Run a query to verify that the hda_id value 20179 is present in the history_dataset_association table.
  4. Consult the database documentation: Consult the database documentation to ensure that the foreign key constraint is correctly defined and that the history_dataset_association table is properly linked to the workflow_invocation_message table.

Q: What are some best practices for avoiding the IntegrityError: (psycopg2.errors.ForeignKeyViolation) insert or update on table "workflow_invocation_message" violates foreign key constraint "workflow_invocation_message_hda_id_fkey" error?

A: To avoid the error, follow these best practices:

  1. Verify data integrity: Verify that the data is properly saved in the database before attempting to insert or update data.
  2. Check foreign key constraints: Check the foreign key constraints to ensure that they are correctly defined and that the referenced tables exist.
  3. Use transactions: Use transactions to ensure that data is properly committed to the database.
  4. Consult the database documentation: Consult the database documentation to ensure that the database schema is correctly defined and that the foreign key constraints are properly set up.