Coverage for python/felis/datamodel.py: 52%
301 statements
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1# This file is part of felis.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://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 <https://www.gnu.org/licenses/>.
22from __future__ import annotations
24import logging
25import re
26from collections.abc import Mapping, Sequence
27from enum import StrEnum, auto
28from typing import Annotated, Any, Literal, TypeAlias
30from astropy import units as units # type: ignore
31from astropy.io.votable import ucd # type: ignore
32from pydantic import BaseModel, ConfigDict, Field, ValidationInfo, field_validator, model_validator
33from sqlalchemy import dialects
34from sqlalchemy import types as sqa_types
35from sqlalchemy.engine import create_mock_engine
36from sqlalchemy.engine.interfaces import Dialect
37from sqlalchemy.types import TypeEngine
39from .db.sqltypes import get_type_func
40from .types import FelisType
42logger = logging.getLogger(__name__)
44__all__ = (
45 "BaseObject",
46 "Column",
47 "CheckConstraint",
48 "Constraint",
49 "DescriptionStr",
50 "ForeignKeyConstraint",
51 "Index",
52 "Schema",
53 "SchemaVersion",
54 "Table",
55 "UniqueConstraint",
56)
58CONFIG = ConfigDict(
59 populate_by_name=True, # Populate attributes by name.
60 extra="forbid", # Do not allow extra fields.
61 str_strip_whitespace=True, # Strip whitespace from string fields.
62)
63"""Pydantic model configuration as described in:
64https://docs.pydantic.dev/2.0/api/config/#pydantic.config.ConfigDict
65"""
67DESCR_MIN_LENGTH = 3
68"""Minimum length for a description field."""
70DescriptionStr: TypeAlias = Annotated[str, Field(min_length=DESCR_MIN_LENGTH)]
71"""Define a type for a description string, which must be three or more
72characters long. Stripping of whitespace is done globally on all str fields."""
75class BaseObject(BaseModel):
76 """Base class for all Felis objects."""
78 model_config = CONFIG
79 """Pydantic model configuration."""
81 name: str
82 """The name of the database object.
84 All Felis database objects must have a name.
85 """
87 id: str = Field(alias="@id")
88 """The unique identifier of the database object.
90 All Felis database objects must have a unique identifier.
91 """
93 description: DescriptionStr | None = None
94 """A description of the database object."""
96 votable_utype: str | None = Field(None, alias="votable:utype")
97 """The VOTable utype (usage-specific or unique type) of the object."""
99 @model_validator(mode="after")
100 def check_description(self, info: ValidationInfo) -> BaseObject:
101 """Check that the description is present if required."""
102 context = info.context
103 if not context or not context.get("require_description", False):
104 return self
105 if self.description is None or self.description == "":
106 raise ValueError("Description is required and must be non-empty")
107 if len(self.description) < DESCR_MIN_LENGTH:
108 raise ValueError(f"Description must be at least {DESCR_MIN_LENGTH} characters long")
109 return self
112class DataType(StrEnum):
113 """`Enum` representing the data types supported by Felis."""
115 boolean = auto()
116 byte = auto()
117 short = auto()
118 int = auto()
119 long = auto()
120 float = auto()
121 double = auto()
122 char = auto()
123 string = auto()
124 unicode = auto()
125 text = auto()
126 binary = auto()
127 timestamp = auto()
130_DIALECTS = {
131 "mysql": create_mock_engine("mysql://", executor=None).dialect,
132 "postgresql": create_mock_engine("postgresql://", executor=None).dialect,
133}
134"""Dictionary of dialect names to SQLAlchemy dialects."""
136_DIALECT_MODULES = {"mysql": getattr(dialects, "mysql"), "postgresql": getattr(dialects, "postgresql")}
137"""Dictionary of dialect names to SQLAlchemy dialect modules."""
139_DATATYPE_REGEXP = re.compile(r"(\w+)(\((.*)\))?")
140"""Regular expression to match data types in the form "type(length)"""
143def string_to_typeengine(
144 type_string: str, dialect: Dialect | None = None, length: int | None = None
145) -> TypeEngine:
146 match = _DATATYPE_REGEXP.search(type_string)
147 if not match:
148 raise ValueError(f"Invalid type string: {type_string}")
150 type_name, _, params = match.groups()
151 if dialect is None:
152 type_class = getattr(sqa_types, type_name.upper(), None)
153 else:
154 try:
155 dialect_module = _DIALECT_MODULES[dialect.name]
156 except KeyError:
157 raise ValueError(f"Unsupported dialect: {dialect}")
158 type_class = getattr(dialect_module, type_name.upper(), None)
160 if not type_class:
161 raise ValueError(f"Unsupported type: {type_class}")
163 if params:
164 params = [int(param) if param.isdigit() else param for param in params.split(",")]
165 type_obj = type_class(*params)
166 else:
167 type_obj = type_class()
169 if hasattr(type_obj, "length") and getattr(type_obj, "length") is None and length is not None:
170 type_obj.length = length
172 return type_obj
175class Column(BaseObject):
176 """A column in a table."""
178 datatype: DataType
179 """The datatype of the column."""
181 length: int | None = None
182 """The length of the column."""
184 nullable: bool | None = None
185 """Whether the column can be ``NULL``.
187 If `None`, this value was not set explicitly in the YAML data. In this
188 case, it will be set to `False` for columns with numeric types and `True`
189 otherwise.
190 """
192 value: Any = None
193 """The default value of the column."""
195 autoincrement: bool | None = None
196 """Whether the column is autoincremented."""
198 mysql_datatype: str | None = Field(None, alias="mysql:datatype")
199 """The MySQL datatype of the column."""
201 postgresql_datatype: str | None = Field(None, alias="postgresql:datatype")
202 """The PostgreSQL datatype of the column."""
204 ivoa_ucd: str | None = Field(None, alias="ivoa:ucd")
205 """The IVOA UCD of the column."""
207 fits_tunit: str | None = Field(None, alias="fits:tunit")
208 """The FITS TUNIT of the column."""
210 ivoa_unit: str | None = Field(None, alias="ivoa:unit")
211 """The IVOA unit of the column."""
213 tap_column_index: int | None = Field(None, alias="tap:column_index")
214 """The TAP_SCHEMA column index of the column."""
216 tap_principal: int | None = Field(0, alias="tap:principal", ge=0, le=1)
217 """Whether this is a TAP_SCHEMA principal column; can be either 0 or 1.
218 """
220 votable_arraysize: int | Literal["*"] | None = Field(None, alias="votable:arraysize")
221 """The VOTable arraysize of the column."""
223 tap_std: int | None = Field(0, alias="tap:std", ge=0, le=1)
224 """TAP_SCHEMA indication that this column is defined by an IVOA standard.
225 """
227 votable_xtype: str | None = Field(None, alias="votable:xtype")
228 """The VOTable xtype (extended type) of the column."""
230 votable_datatype: str | None = Field(None, alias="votable:datatype")
231 """The VOTable datatype of the column."""
233 @field_validator("ivoa_ucd")
234 @classmethod
235 def check_ivoa_ucd(cls, ivoa_ucd: str) -> str:
236 """Check that IVOA UCD values are valid."""
237 if ivoa_ucd is not None:
238 try:
239 ucd.parse_ucd(ivoa_ucd, check_controlled_vocabulary=True, has_colon=";" in ivoa_ucd)
240 except ValueError as e:
241 raise ValueError(f"Invalid IVOA UCD: {e}")
242 return ivoa_ucd
244 @model_validator(mode="before")
245 @classmethod
246 def check_units(cls, values: dict[str, Any]) -> dict[str, Any]:
247 """Check that units are valid."""
248 fits_unit = values.get("fits:tunit")
249 ivoa_unit = values.get("ivoa:unit")
251 if fits_unit and ivoa_unit:
252 raise ValueError("Column cannot have both FITS and IVOA units")
253 unit = fits_unit or ivoa_unit
255 if unit is not None:
256 try:
257 units.Unit(unit)
258 except ValueError as e:
259 raise ValueError(f"Invalid unit: {e}")
261 return values
263 @model_validator(mode="after") # type: ignore[arg-type]
264 @classmethod
265 def validate_datatypes(cls, col: Column, info: ValidationInfo) -> Column:
266 """Check for redundant datatypes on columns."""
267 context = info.context
268 if not context or not context.get("check_redundant_datatypes", False):
269 return col
270 if all(getattr(col, f"{dialect}:datatype", None) is not None for dialect in _DIALECTS.keys()):
271 return col
273 datatype = col.datatype
274 length: int | None = col.length or None
276 datatype_func = get_type_func(datatype)
277 felis_type = FelisType.felis_type(datatype)
278 if felis_type.is_sized:
279 if length is not None:
280 datatype_obj = datatype_func(length)
281 else:
282 raise ValueError(f"Length must be provided for sized type '{datatype}' in column '{col.id}'")
283 else:
284 datatype_obj = datatype_func()
286 for dialect_name, dialect in _DIALECTS.items():
287 db_annotation = f"{dialect_name}_datatype"
288 if datatype_string := col.model_dump().get(db_annotation):
289 db_datatype_obj = string_to_typeengine(datatype_string, dialect, length)
290 if datatype_obj.compile(dialect) == db_datatype_obj.compile(dialect):
291 raise ValueError(
292 "'{}: {}' is a redundant override of 'datatype: {}' in column '{}'{}".format(
293 db_annotation,
294 datatype_string,
295 col.datatype,
296 col.id,
297 "" if length is None else f" with length {length}",
298 )
299 )
300 else:
301 logger.debug(
302 "Type override of 'datatype: {}' with '{}: {}' in column '{}' "
303 "compiled to '{}' and '{}'".format(
304 col.datatype,
305 db_annotation,
306 datatype_string,
307 col.id,
308 datatype_obj.compile(dialect),
309 db_datatype_obj.compile(dialect),
310 )
311 )
312 return col
315class Constraint(BaseObject):
316 """A database table constraint."""
318 deferrable: bool = False
319 """If `True` then this constraint will be declared as deferrable."""
321 initially: str | None = None
322 """Value for ``INITIALLY`` clause, only used if ``deferrable`` is True."""
324 annotations: Mapping[str, Any] = Field(default_factory=dict)
325 """Additional annotations for this constraint."""
327 type: str | None = Field(None, alias="@type")
328 """The type of the constraint."""
331class CheckConstraint(Constraint):
332 """A check constraint on a table."""
334 expression: str
335 """The expression for the check constraint."""
338class UniqueConstraint(Constraint):
339 """A unique constraint on a table."""
341 columns: list[str]
342 """The columns in the unique constraint."""
345class Index(BaseObject):
346 """A database table index.
348 An index can be defined on either columns or expressions, but not both.
349 """
351 columns: list[str] | None = None
352 """The columns in the index."""
354 expressions: list[str] | None = None
355 """The expressions in the index."""
357 @model_validator(mode="before")
358 @classmethod
359 def check_columns_or_expressions(cls, values: dict[str, Any]) -> dict[str, Any]:
360 """Check that columns or expressions are specified, but not both."""
361 if "columns" in values and "expressions" in values:
362 raise ValueError("Defining columns and expressions is not valid")
363 elif "columns" not in values and "expressions" not in values:
364 raise ValueError("Must define columns or expressions")
365 return values
368class ForeignKeyConstraint(Constraint):
369 """A foreign key constraint on a table.
371 These will be reflected in the TAP_SCHEMA keys and key_columns data.
372 """
374 columns: list[str]
375 """The columns comprising the foreign key."""
377 referenced_columns: list[str] = Field(alias="referencedColumns")
378 """The columns referenced by the foreign key."""
381class Table(BaseObject):
382 """A database table."""
384 columns: Sequence[Column]
385 """The columns in the table."""
387 constraints: list[Constraint] = Field(default_factory=list)
388 """The constraints on the table."""
390 indexes: list[Index] = Field(default_factory=list)
391 """The indexes on the table."""
393 primary_key: str | list[str] | None = Field(None, alias="primaryKey")
394 """The primary key of the table."""
396 tap_table_index: int | None = Field(None, alias="tap:table_index")
397 """The IVOA TAP_SCHEMA table index of the table."""
399 mysql_engine: str | None = Field(None, alias="mysql:engine")
400 """The mysql engine to use for the table.
402 For now this is a freeform string but it could be constrained to a list of
403 known engines in the future.
404 """
406 mysql_charset: str | None = Field(None, alias="mysql:charset")
407 """The mysql charset to use for the table.
409 For now this is a freeform string but it could be constrained to a list of
410 known charsets in the future.
411 """
413 @model_validator(mode="before")
414 @classmethod
415 def create_constraints(cls, values: dict[str, Any]) -> dict[str, Any]:
416 """Create constraints from the ``constraints`` field."""
417 if "constraints" in values:
418 new_constraints: list[Constraint] = []
419 for item in values["constraints"]:
420 if item["@type"] == "ForeignKey":
421 new_constraints.append(ForeignKeyConstraint(**item))
422 elif item["@type"] == "Unique":
423 new_constraints.append(UniqueConstraint(**item))
424 elif item["@type"] == "Check":
425 new_constraints.append(CheckConstraint(**item))
426 else:
427 raise ValueError(f"Unknown constraint type: {item['@type']}")
428 values["constraints"] = new_constraints
429 return values
431 @field_validator("columns", mode="after")
432 @classmethod
433 def check_unique_column_names(cls, columns: list[Column]) -> list[Column]:
434 """Check that column names are unique."""
435 if len(columns) != len(set(column.name for column in columns)):
436 raise ValueError("Column names must be unique")
437 return columns
440class SchemaVersion(BaseModel):
441 """The version of the schema."""
443 current: str
444 """The current version of the schema."""
446 compatible: list[str] = Field(default_factory=list)
447 """The compatible versions of the schema."""
449 read_compatible: list[str] = Field(default_factory=list)
450 """The read compatible versions of the schema."""
453class SchemaIdVisitor:
454 """Visitor to build a Schema object's map of IDs to objects.
456 Duplicates are added to a set when they are encountered, which can be
457 accessed via the `duplicates` attribute. The presence of duplicates will
458 not throw an error. Only the first object with a given ID will be added to
459 the map, but this should not matter, since a ValidationError will be thrown
460 by the `model_validator` method if any duplicates are found in the schema.
462 This class is intended for internal use only.
463 """
465 def __init__(self) -> None:
466 """Create a new SchemaVisitor."""
467 self.schema: "Schema" | None = None
468 self.duplicates: set[str] = set()
470 def add(self, obj: BaseObject) -> None:
471 """Add an object to the ID map."""
472 if hasattr(obj, "id"):
473 obj_id = getattr(obj, "id")
474 if self.schema is not None:
475 if obj_id in self.schema.id_map:
476 self.duplicates.add(obj_id)
477 else:
478 self.schema.id_map[obj_id] = obj
480 def visit_schema(self, schema: "Schema") -> None:
481 """Visit the schema object that was added during initialization.
483 This will set an internal variable pointing to the schema object.
484 """
485 self.schema = schema
486 self.duplicates.clear()
487 self.add(self.schema)
488 for table in self.schema.tables:
489 self.visit_table(table)
491 def visit_table(self, table: Table) -> None:
492 """Visit a table object."""
493 self.add(table)
494 for column in table.columns:
495 self.visit_column(column)
496 for constraint in table.constraints:
497 self.visit_constraint(constraint)
499 def visit_column(self, column: Column) -> None:
500 """Visit a column object."""
501 self.add(column)
503 def visit_constraint(self, constraint: Constraint) -> None:
504 """Visit a constraint object."""
505 self.add(constraint)
508class Schema(BaseObject):
509 """The database schema containing the tables."""
511 version: SchemaVersion | str | None = None
512 """The version of the schema."""
514 tables: Sequence[Table]
515 """The tables in the schema."""
517 id_map: dict[str, Any] = Field(default_factory=dict, exclude=True)
518 """Map of IDs to objects."""
520 @field_validator("tables", mode="after")
521 @classmethod
522 def check_unique_table_names(cls, tables: list[Table]) -> list[Table]:
523 """Check that table names are unique."""
524 if len(tables) != len(set(table.name for table in tables)):
525 raise ValueError("Table names must be unique")
526 return tables
528 def _create_id_map(self: Schema) -> Schema:
529 """Create a map of IDs to objects.
531 This method should not be called by users. It is called automatically
532 by the ``model_post_init()`` method. If the ID map is already
533 populated, this method will return immediately.
534 """
535 if len(self.id_map):
536 logger.debug("Ignoring call to create_id_map() - ID map was already populated")
537 return self
538 visitor: SchemaIdVisitor = SchemaIdVisitor()
539 visitor.visit_schema(self)
540 logger.debug(f"Created schema ID map with {len(self.id_map.keys())} objects")
541 if len(visitor.duplicates):
542 raise ValueError(
543 "Duplicate IDs found in schema:\n " + "\n ".join(visitor.duplicates) + "\n"
544 )
545 return self
547 def model_post_init(self, ctx: Any) -> None:
548 """Post-initialization hook for the model."""
549 self._create_id_map()
551 def __getitem__(self, id: str) -> BaseObject:
552 """Get an object by its ID."""
553 if id not in self:
554 raise KeyError(f"Object with ID '{id}' not found in schema")
555 return self.id_map[id]
557 def __contains__(self, id: str) -> bool:
558 """Check if an object with the given ID is in the schema."""
559 return id in self.id_map