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code improvement for safely attaching database #27

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Merged
hyi merged 1 commit into from
Nov 7, 2025
Merged

code improvement for safely attaching database #27

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23 changes: 12 additions & 11 deletions biasanalyzer/database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,16 @@ def __new__(cls, *args, **kwargs):
cls._instance._initialize(*args, **kwargs) # Initialize only once
return cls._instance

def _safe_attach(self, alias: str, url: str, type_clause: str = ""):
try:
self.conn.execute(f"DETACH DATABASE {alias}")
except (duckdb.BinderException, duckdb.CatalogException):
pass
if type_clause:
self.conn.execute(f"ATTACH '{url}' AS {alias} {type_clause}")
else:
self.conn.execute(f"ATTACH '{url}' AS {alias}")

def _initialize(self, db_url, omop_db_url=None):
# by default, duckdb uses in memory database
self.conn = duckdb.connect(db_url)
Expand All @@ -52,18 +62,9 @@ def _initialize(self, db_url, omop_db_url=None):
if omop_db_url.startswith("postgresql://"):
# omop db is postgreSQL
self.load_postgres_extension()
self.conn.execute(f"""
ATTACH '{self.omop_cdm_db_url}' as {self.omop_alias} (TYPE postgres)
""")
self._safe_attach(self.omop_alias, self.omop_cdm_db_url, "(TYPE postgres)")
elif omop_db_url.endswith(".duckdb"):
try:
self.conn.execute(f"DETACH DATABASE {self.omop_alias}")
except (duckdb.BinderException, duckdb.CatalogException):
# ignore if not attached yet
pass
self.conn.execute(f"""
ATTACH '{self.omop_cdm_db_url}' as {self.omop_alias}
""")
self._safe_attach(self.omop_alias, self.omop_cdm_db_url)
else:
raise ValueError("Unsupported OMOP database backend")

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