Coverage for python/lsst/dax/apdb/apdbSqlSchema.py : 12%

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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="pixelId",
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, "pixelId")
117 else:
118 # make a regular index
119 index = IndexDef(name=f"IDX_{tableDef.name}_pixelId",
120 type=IndexType.INDEX, columns=["pixelId"])
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]
131 def _makeTables(self, mysql_engine: str = 'InnoDB') -> Mapping[ApdbTables, Table]:
132 """Generate schema for all tables.
134 Parameters
135 ----------
136 mysql_engine : `str`, optional
137 MySQL engine type to use for new tables.
138 """
140 info: Dict[str, Any] = {}
142 tables = {}
143 for table_enum in ApdbTables:
145 if table_enum is ApdbTables.DiaObjectLast and self._dia_object_index != "last_object_table":
146 continue
148 columns = self._tableColumns(table_enum)
149 constraints = self._tableIndices(table_enum, info)
150 table = Table(table_enum.table_name(self._prefix),
151 self._metadata,
152 *columns,
153 *constraints,
154 mysql_engine=mysql_engine,
155 info=info)
156 tables[table_enum] = table
158 return tables
160 def makeSchema(self, drop: bool = False, mysql_engine: str = 'InnoDB') -> None:
161 """Create or re-create all tables.
163 Parameters
164 ----------
165 drop : `bool`, optional
166 If True then drop tables before creating new ones.
167 mysql_engine : `str`, optional
168 MySQL engine type to use for new tables.
169 """
171 # re-make table schema for all needed tables with possibly different options
172 _LOG.debug("clear metadata")
173 self._metadata.clear()
174 _LOG.debug("re-do schema mysql_engine=%r", mysql_engine)
175 self._makeTables(mysql_engine=mysql_engine)
177 # create all tables (optionally drop first)
178 if drop:
179 _LOG.info('dropping all tables')
180 self._metadata.drop_all()
181 _LOG.info('creating all tables')
182 self._metadata.create_all()
184 def _tableColumns(self, table_name: ApdbTables) -> List[Column]:
185 """Return set of columns in a table
187 Parameters
188 ----------
189 table_name : `ApdbTables`
190 Name of the table.
192 Returns
193 -------
194 column_defs : `list`
195 List of `Column` objects.
196 """
198 # get the list of columns in primary key, they are treated somewhat
199 # specially below
200 table_schema = self.tableSchemas[table_name]
201 pkey_columns = set()
202 for index in table_schema.indices:
203 if index.type is IndexType.PRIMARY:
204 pkey_columns = set(index.columns)
205 break
207 # convert all column dicts into alchemy Columns
208 column_defs = []
209 for column in table_schema.columns:
210 kwargs: Dict[str, Any] = dict(nullable=column.nullable)
211 if column.default is not None:
212 kwargs.update(server_default=str(column.default))
213 if column.name in pkey_columns:
214 kwargs.update(autoincrement=False)
215 ctype = self._type_map[column.type]
216 column_defs.append(Column(column.name, ctype, **kwargs))
218 return column_defs
220 def _tableIndices(self, table_name: ApdbTables, info: Dict) -> List[sqlalchemy.schema.Constraint]:
221 """Return set of constraints/indices in a table
223 Parameters
224 ----------
225 table_name : `ApdbTables`
226 Name of the table.
227 info : `dict`
228 Additional options passed to SQLAlchemy index constructor.
230 Returns
231 -------
232 index_defs : `list`
233 List of SQLAlchemy index/constraint objects.
234 """
236 table_schema = self.tableSchemas[table_name]
238 # convert all index dicts into alchemy Columns
239 index_defs: List[sqlalchemy.schema.Constraint] = []
240 for index in table_schema.indices:
241 if index.type is IndexType.INDEX:
242 index_defs.append(Index(self._prefix + index.name, *index.columns, info=info))
243 else:
244 kwargs = {}
245 if index.name:
246 kwargs['name'] = self._prefix + index.name
247 if index.type is IndexType.PRIMARY:
248 index_defs.append(PrimaryKeyConstraint(*index.columns, **kwargs))
249 elif index.type is IndexType.UNIQUE:
250 index_defs.append(UniqueConstraint(*index.columns, **kwargs))
252 return index_defs
254 @classmethod
255 def _getDoubleType(cls, engine: sqlalchemy.engine.Engine) -> Type:
256 """DOUBLE type is database-specific, select one based on dialect.
258 Parameters
259 ----------
260 engine : `sqlalchemy.engine.Engine`
261 Database engine.
263 Returns
264 -------
265 type_object : `object`
266 Database-specific type definition.
267 """
268 if engine.name == 'mysql':
269 from sqlalchemy.dialects.mysql import DOUBLE
270 return DOUBLE(asdecimal=False)
271 elif engine.name == 'postgresql':
272 from sqlalchemy.dialects.postgresql import DOUBLE_PRECISION
273 return DOUBLE_PRECISION
274 elif engine.name == 'oracle':
275 from sqlalchemy.dialects.oracle import DOUBLE_PRECISION
276 return DOUBLE_PRECISION
277 elif engine.name == 'sqlite':
278 # all floats in sqlite are 8-byte
279 from sqlalchemy.dialects.sqlite import REAL
280 return REAL
281 else:
282 raise TypeError('cannot determine DOUBLE type, unexpected dialect: ' + engine.name)