def drop_indexes(self, engine: Engine, metadata: MetaData) -> None:
for tablename, tabledict in self._index_requests.items():
index_names = list(tabledict.keys())
tablename_casematch = get_case_insensitive_dict_key(
metadata.tables, tablename)
if not tablename_casematch:
log.warning("add_indexes: Skipping index as table {} "
"absent".format(tablename))
continue
table = metadata.tables[tablename_casematch]
drop_indexes(engine, table, index_names)
def process_table(table: Table, engine: Engine,
configoptions: PcmisConfigOptions) -> None:
"""
Processes a PCMIS table by checking it has appropriate columns, perhaps
adding a CRATE integer PK, and indexing it.
Args:
table: an SQLAlchemy Table to process
engine: an SQLAlchemy Engine
configoptions: an instance of :class:`PcmisConfigOptions`
"""
tablename = table.name
column_names = table.columns.keys()
log.debug(f"TABLE: {tablename}; COLUMNS: {column_names}")
existing_pk_cols = get_pk_colnames(table)
assert len(existing_pk_cols) < 2, (
f"Table {tablename} has >1 PK column; don't know what to do")
if existing_pk_cols and not get_effective_int_pk_col(table):
raise ValueError(f"Table {table!r} has a non-integer PK")
adding_crate_pk = not existing_pk_cols
required_cols = [CRATE_COL_PK] if not configoptions.print_sql_only else []
if configoptions.drop_not_create:
# ---------------------------------------------------------------------
# DROP STUFF! Opposite order to creation (below)
# ---------------------------------------------------------------------
drop_indexes(engine, table, [CRATE_IDX_PK])
drop_columns(engine, table, [CRATE_COL_PK])
else:
# ---------------------------------------------------------------------
# CREATE STUFF!
# ---------------------------------------------------------------------
# SQL Server requires Table-bound columns in order to generate DDL:
if adding_crate_pk:
crate_pk_col = make_bigint_autoincrement_column(
CRATE_COL_PK, engine.dialect)
table.append_column(crate_pk_col)
add_columns(engine, table, [crate_pk_col])
ensure_columns_present(engine,
tablename=table.name,
column_names=required_cols)
add_indexes(engine, table, [{
'index_name': CRATE_IDX_PK,
'column': CRATE_COL_PK,
'unique': True
}])
def drop_indexes(self, engine: Engine, metadata: MetaData) -> None:
"""
Drop indexes from the source database. Reverses the effects of
:func:`create_indexes`.
Args:
engine: SQLAlchemy database Engine
metadata: SQLAlchemy ORM Metadata
"""
for tablename, tabledict in self._index_requests.items():
index_names = list(tabledict.keys())
tablename_casematch = get_case_insensitive_dict_key(
metadata.tables, tablename)
if not tablename_casematch:
log.warning(
f"add_indexes: Skipping index as table {tablename} absent")
continue
table = metadata.tables[tablename_casematch]
drop_indexes(engine, table, index_names)
def process_table(table: Table, engine: Engine, progargs: Any) -> None:
tablename = table.name
column_names = table.columns.keys()
log.debug("TABLE: {}; COLUMNS: {}".format(tablename, column_names))
existing_pk_cols = get_pk_colnames(table)
assert len(existing_pk_cols) < 2, (
"Table {} has >1 PK column; don't know what to do".format(tablename))
if existing_pk_cols and not get_effective_int_pk_col(table):
raise ValueError("Table {} has a non-integer PK".format(repr(table)))
adding_crate_pk = not existing_pk_cols
required_cols = [CRATE_COL_PK] if not progargs.print else []
if progargs.drop_danger_drop:
# ---------------------------------------------------------------------
# DROP STUFF! Opposite order to creation (below)
# ---------------------------------------------------------------------
drop_indexes(engine, table, [CRATE_IDX_PK])
drop_columns(engine, table, [CRATE_COL_PK])
else:
# ---------------------------------------------------------------------
# CREATE STUFF!
# ---------------------------------------------------------------------
# SQL Server requires Table-bound columns in order to generate DDL:
if adding_crate_pk:
crate_pk_col = make_bigint_autoincrement_column(
CRATE_COL_PK, engine.dialect)
table.append_column(crate_pk_col)
add_columns(engine, table, [crate_pk_col])
ensure_columns_present(engine,
tablename=table.name,
column_names=required_cols)
add_indexes(engine, table, [{
'index_name': CRATE_IDX_PK,
'column': CRATE_COL_PK,
'unique': True
}])
def drop_for_clindocs_table(table: Table, engine: Engine) -> None:
drop_indexes(
engine, table,
[CRATE_IDX_RIONUM_SERIALNUM, CRATE_IDX_MAX_DOCVER, CRATE_IDX_LAST_DOC])
drop_columns(engine, table, [CRATE_COL_MAX_DOCVER, CRATE_COL_LAST_DOC])
def drop_for_progress_notes(table: Table, engine: Engine) -> None:
drop_view(engine, VIEW_RCEP_CPFT_PROGRESS_NOTES_CURRENT)
drop_indexes(
engine, table,
[CRATE_IDX_RIONUM_NOTENUM, CRATE_IDX_MAX_SUBNUM, CRATE_IDX_LAST_NOTE])
drop_columns(engine, table, [CRATE_COL_MAX_SUBNUM, CRATE_COL_LAST_NOTE])
def drop_for_nonpatient_table(table: Table, engine: Engine) -> None:
drop_indexes(engine, table, [CRATE_IDX_PK])
drop_columns(engine, table, [CRATE_COL_PK])
def drop_for_patient_table(table: Table, engine: Engine) -> None:
drop_indexes(engine, table, [CRATE_IDX_PK, CRATE_IDX_RIONUM])
drop_columns(engine, table, [CRATE_COL_PK, CRATE_COL_RIO_NUMBER])