mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-30 16:58:03 +08:00
John Davis
67 lines
2.0 KiB
Python
67 lines
2.0 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 (
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create_engine,
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MetaData,
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)
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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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from galaxy.model.tool_shed_install import mapping as tsi_mapping
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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 and tool_shed_install/mapping.py
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metadata = mapping.metadata
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mapping_indexes = load_indexes(metadata)
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tsi_metadata = tsi_mapping.metadata
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tsi_mapping_indexes = load_indexes(tsi_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()
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engine = create_engine(db_url)
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metadata.reflect(bind=engine)
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indexes_in_db = load_indexes(metadata)
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all_indexes = set(mapping_indexes.keys()) | set(tsi_mapping_indexes.keys())
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if missing_indexes := all_indexes - set(indexes_in_db.keys()):
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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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