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schema.rebuild_lineage() fails on PostgreSQL, after emptying ~lineage

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Evaluación

Dificultad
4/5
Tiempo estimado
1-2 días
Aptitud para principiantes
68/100
Tipo de issue
Error
Claridad
Bien especificado
Estado de actividad
Activo
Stack tecnológico
mysql, postgresql, python
Área
backend, databases

Línea de trabajo

Start in lineage.py at rebuild_schema_lineage and compare its information_schema queries with the adapters’ load_primary_keys_sql and load_foreign_keys_sql used by Dependencies.load. Reproduce on PostgreSQL 15 with the supplied schema and check how the function handles ~lineage when rebuilding fails. Done means lineage rebuilding works on PostgreSQL and MySQL, and a failure does not leave ~lineage empty.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

bug

Summary

schema.rebuild_lineage() fails on PostgreSQL. rebuild_schema_lineage (lineage.py) reads keys from information_schema with MySQL-only names:

  • foreign keys from KEY_COLUMN_USAGE.REFERENCED_TABLE_SCHEMA, REFERENCED_TABLE_NAME and REFERENCED_COLUMN_NAME, columns PostgreSQL does not have;
  • primary keys by CONSTRAINT_NAME = 'PRIMARY', while PostgreSQL names a primary-key constraint <table>_pkey.

The foreign-key query raises, so the rebuild stops before writing anything. It has already run DELETE FROM ~lineage by then, so the call leaves the schema with an empty ~lineage table: every join on the schema's tables is then refused, until each table is decorated again and its rows are refilled.

The docs and several messages recommend schema.rebuild_lineage() as the repair for lineage problems, and dj.migrate.rebuild_lineage calls the same function.

Reproduction

DataJoint master, PostgreSQL 15:

import datajoint as dj

schema = dj.Schema("scratch_rebuild_lineage")


@schema
class Image(dj.Manual):
    definition = """
    image_id : int32
    """


schema.rebuild_lineage()
# UnknownAttributeError: column "referenced_table_schema" does not exist
# ~lineage held 1 row before the call and 0 after it

Expected behavior

rebuild_lineage() works on both backends. It could read primary and foreign keys through the adapters' existing load_primary_keys_sql and load_foreign_keys_sql, as Dependencies.load does, and leave ~lineage unchanged if it fails.

Lenguaje dominante
Python
Estrellas
197
Forks
101
Merge medio
3 d 8 h
PR fusionados (30 d)
28

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