mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Sergey Golitsynskiy
3cd1c7f1c7
This should fix the `scripts/check_model.py` script and the database indexes github workflow. Accessing index columns has changed: index.columns gives access to a DedupedColumnCollection instead of a ColumnCollection. Columns can be accessed by key; keys are accessed via keys() attr. Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#select-objects-and-derived-from-clauses-allow-for-duplicate-columns-and-column-labels https://docs.sqlalchemy.org/en/14/core/sqlelement.html?highlight=dedupecolumncollection#sqlalchemy.sql.expression.ColumnCollection
58 lines
1.7 KiB
Python
58 lines
1.7 KiB
Python
"""
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Check for db indexes defined in mapping.py but missing in the database.
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Note: pass '-c /path/to/galaxy.yml' to use the database_connection set in galaxy.yml.
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Otherwise the default sqlite database will be used.
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"""
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import json
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import os
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import sys
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from collections import namedtuple
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
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from sqlalchemy import create_engine, MetaData
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from galaxy.model import mapping
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from galaxy.model.orm.scripts import get_config
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IndexTuple = namedtuple('IndexTuple', 'table column_names')
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def tuple_from_index(index):
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columns = tuple([index.columns[key].name for key in index.columns.keys()])
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if len(columns) == 1:
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columns = columns[0]
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return IndexTuple(index.table.name, columns)
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def find_missing_indexes():
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def load_indexes(metadata):
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indexes = {}
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for t in metadata.tables.values():
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for index in t.indexes:
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index_tuple = tuple_from_index(index)
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indexes[index_tuple] = index.name
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return indexes
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# load metadata from mapping.py
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metadata = mapping.metadata
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mapping_indexes = load_indexes(metadata)
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# create EMPTY metadata, then load from database
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db_url = get_config(sys.argv)['db_url']
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metadata = MetaData(bind=create_engine(db_url))
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metadata.reflect()
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indexes_in_db = load_indexes(metadata)
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missing_indexes = set(mapping_indexes.keys()) - set(indexes_in_db.keys())
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if missing_indexes:
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return [(mapping_indexes[index], index.table, index.column_names) for index in missing_indexes]
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if __name__ == '__main__':
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indexes = find_missing_indexes()
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if indexes:
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print(json.dumps(indexes, indent=4, sort_keys=True))
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sys.exit(1)
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