Coverage for python/lsst/dax/apdb/apdbSqlSchema.py: 13%
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1# This file is part of dax_apdb.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
22"""Module responsible for APDB schema operations.
23"""
25from __future__ import annotations
27__all__ = ["ApdbSqlSchema"]
29import logging
30from typing import Any, Dict, List, Mapping, Optional, Type
32import sqlalchemy
33from sqlalchemy import (Column, Index, MetaData, PrimaryKeyConstraint,
34 UniqueConstraint, Table)
36from .apdbSchema import ApdbSchema, ApdbTables, ColumnDef, IndexDef, IndexType
39_LOG = logging.getLogger(__name__)
42class ApdbSqlSchema(ApdbSchema):
43 """Class for management of APDB schema.
45 Attributes
46 ----------
47 objects : `sqlalchemy.Table`
48 DiaObject table instance
49 objects_last : `sqlalchemy.Table`
50 DiaObjectLast table instance, may be None
51 sources : `sqlalchemy.Table`
52 DiaSource table instance
53 forcedSources : `sqlalchemy.Table`
54 DiaForcedSource table instance
56 Parameters
57 ----------
58 engine : `sqlalchemy.engine.Engine`
59 SQLAlchemy engine instance
60 dia_object_index : `str`
61 Indexing mode for DiaObject table, see `ApdbSqlConfig.dia_object_index`
62 for details.
63 htm_index_column : `str`
64 Name of a HTM index column for DiaObject and DiaSource tables.
65 schema_file : `str`
66 Name of the YAML schema file.
67 extra_schema_file : `str`, optional
68 Name of the YAML schema file with extra column definitions.
69 prefix : `str`, optional
70 Prefix to add to all scheam elements.
71 """
72 def __init__(self, engine: sqlalchemy.engine.Engine, dia_object_index: str, htm_index_column: str,
73 schema_file: str, extra_schema_file: Optional[str] = None, prefix: str = ""):
75 super().__init__(schema_file, extra_schema_file)
77 self._engine = engine
78 self._dia_object_index = dia_object_index
79 self._prefix = prefix
81 self._metadata = MetaData(self._engine)
83 # map YAML column types to SQLAlchemy
84 self._type_map = dict(DOUBLE=self._getDoubleType(engine),
85 FLOAT=sqlalchemy.types.Float,
86 DATETIME=sqlalchemy.types.TIMESTAMP,
87 BIGINT=sqlalchemy.types.BigInteger,
88 INTEGER=sqlalchemy.types.Integer,
89 INT=sqlalchemy.types.Integer,
90 TINYINT=sqlalchemy.types.Integer,
91 BLOB=sqlalchemy.types.LargeBinary,
92 CHAR=sqlalchemy.types.CHAR,
93 BOOL=sqlalchemy.types.Boolean)
95 # Adjust index if needed
96 if self._dia_object_index == 'pix_id_iov':
97 objects = self.tableSchemas[ApdbTables.DiaObject]
98 objects.primary_key.columns.insert(0, htm_index_column)
100 # Add pixelId column and index to tables that need it
101 for table in (ApdbTables.DiaObject, ApdbTables.DiaObjectLast, ApdbTables.DiaSource):
102 tableDef = self.tableSchemas.get(table)
103 if not tableDef:
104 continue
105 column = ColumnDef(name=htm_index_column,
106 type="BIGINT",
107 nullable=False,
108 default=None,
109 description="",
110 unit="",
111 ucd="")
112 tableDef.columns.append(column)
114 if table is ApdbTables.DiaObjectLast:
115 # use it as a leading PK column
116 tableDef.primary_key.columns.insert(0, htm_index_column)
117 else:
118 # make a regular index
119 index = IndexDef(name=f"IDX_{tableDef.name}_{htm_index_column}",
120 type=IndexType.INDEX, columns=[htm_index_column])
121 tableDef.indices.append(index)
123 # generate schema for all tables, must be called last
124 self._tables = self._makeTables()
126 self.objects = self._tables[ApdbTables.DiaObject]
127 self.objects_last = self._tables.get(ApdbTables.DiaObjectLast)
128 self.sources = self._tables[ApdbTables.DiaSource]
129 self.forcedSources = self._tables[ApdbTables.DiaForcedSource]
130 self.ssObjects = self._tables[ApdbTables.SSObject]
132 def _makeTables(self, mysql_engine: str = 'InnoDB') -> Mapping[ApdbTables, Table]:
133 """Generate schema for all tables.
135 Parameters
136 ----------
137 mysql_engine : `str`, optional
138 MySQL engine type to use for new tables.
139 """
141 info: Dict[str, Any] = {}
143 tables = {}
144 for table_enum in ApdbTables:
146 if table_enum is ApdbTables.DiaObjectLast and self._dia_object_index != "last_object_table":
147 continue
149 columns = self._tableColumns(table_enum)
150 constraints = self._tableIndices(table_enum, info)
151 table = Table(table_enum.table_name(self._prefix),
152 self._metadata,
153 *columns,
154 *constraints,
155 mysql_engine=mysql_engine,
156 info=info)
157 tables[table_enum] = table
159 return tables
161 def makeSchema(self, drop: bool = False, mysql_engine: str = 'InnoDB') -> None:
162 """Create or re-create all tables.
164 Parameters
165 ----------
166 drop : `bool`, optional
167 If True then drop tables before creating new ones.
168 mysql_engine : `str`, optional
169 MySQL engine type to use for new tables.
170 """
172 # re-make table schema for all needed tables with possibly different options
173 _LOG.debug("clear metadata")
174 self._metadata.clear()
175 _LOG.debug("re-do schema mysql_engine=%r", mysql_engine)
176 self._makeTables(mysql_engine=mysql_engine)
178 # create all tables (optionally drop first)
179 if drop:
180 _LOG.info('dropping all tables')
181 self._metadata.drop_all()
182 _LOG.info('creating all tables')
183 self._metadata.create_all()
185 def _tableColumns(self, table_name: ApdbTables) -> List[Column]:
186 """Return set of columns in a table
188 Parameters
189 ----------
190 table_name : `ApdbTables`
191 Name of the table.
193 Returns
194 -------
195 column_defs : `list`
196 List of `Column` objects.
197 """
199 # get the list of columns in primary key, they are treated somewhat
200 # specially below
201 table_schema = self.tableSchemas[table_name]
202 pkey_columns = set()
203 for index in table_schema.indices:
204 if index.type is IndexType.PRIMARY:
205 pkey_columns = set(index.columns)
206 break
208 # convert all column dicts into alchemy Columns
209 column_defs = []
210 for column in table_schema.columns:
211 kwargs: Dict[str, Any] = dict(nullable=column.nullable)
212 if column.default is not None:
213 kwargs.update(server_default=str(column.default))
214 if column.name in pkey_columns:
215 kwargs.update(autoincrement=False)
216 ctype = self._type_map[column.type]
217 column_defs.append(Column(column.name, ctype, **kwargs))
219 return column_defs
221 def _tableIndices(self, table_name: ApdbTables, info: Dict) -> List[sqlalchemy.schema.Constraint]:
222 """Return set of constraints/indices in a table
224 Parameters
225 ----------
226 table_name : `ApdbTables`
227 Name of the table.
228 info : `dict`
229 Additional options passed to SQLAlchemy index constructor.
231 Returns
232 -------
233 index_defs : `list`
234 List of SQLAlchemy index/constraint objects.
235 """
237 table_schema = self.tableSchemas[table_name]
239 # convert all index dicts into alchemy Columns
240 index_defs: List[sqlalchemy.schema.Constraint] = []
241 for index in table_schema.indices:
242 if index.type is IndexType.INDEX:
243 index_defs.append(Index(self._prefix + index.name, *index.columns, info=info))
244 else:
245 kwargs = {}
246 if index.name:
247 kwargs['name'] = self._prefix + index.name
248 if index.type is IndexType.PRIMARY:
249 index_defs.append(PrimaryKeyConstraint(*index.columns, **kwargs))
250 elif index.type is IndexType.UNIQUE:
251 index_defs.append(UniqueConstraint(*index.columns, **kwargs))
253 return index_defs
255 @classmethod
256 def _getDoubleType(cls, engine: sqlalchemy.engine.Engine) -> Type:
257 """DOUBLE type is database-specific, select one based on dialect.
259 Parameters
260 ----------
261 engine : `sqlalchemy.engine.Engine`
262 Database engine.
264 Returns
265 -------
266 type_object : `object`
267 Database-specific type definition.
268 """
269 if engine.name == 'mysql':
270 from sqlalchemy.dialects.mysql import DOUBLE
271 return DOUBLE(asdecimal=False)
272 elif engine.name == 'postgresql':
273 from sqlalchemy.dialects.postgresql import DOUBLE_PRECISION
274 return DOUBLE_PRECISION
275 elif engine.name == 'oracle':
276 from sqlalchemy.dialects.oracle import DOUBLE_PRECISION
277 return DOUBLE_PRECISION
278 elif engine.name == 'sqlite':
279 # all floats in sqlite are 8-byte
280 from sqlalchemy.dialects.sqlite import REAL
281 return REAL
282 else:
283 raise TypeError('cannot determine DOUBLE type, unexpected dialect: ' + engine.name)