lsst-felis 27.2024.2400__py3-none-any.whl → 27.2024.2600__py3-none-any.whl

felis/tap.py

@@ -1,3 +1,5 @@
+"""Translate a Felis schema into a TAP_SCHEMA representation."""
+
 # This file is part of felis.
 #
 # Developed for the LSST Data Management System.
@@ -21,8 +23,6 @@
 
 from __future__ import annotations
 
-__all__ = ["Tap11Base", "TapLoadingVisitor", "init_tables"]
-
 import logging
 from collections.abc import Iterable, MutableMapping
 from typing import Any
@@ -39,9 +39,12 @@ from felis import datamodel
 from .datamodel import Constraint, Index, Schema, Table
 from .types import FelisType
 
-Tap11Base: Any = declarative_base()  # Any to avoid mypy mess with SA 2
+__all__ = ["TapLoadingVisitor", "init_tables"]
+
 logger = logging.getLogger(__name__)
 
+Tap11Base: Any = declarative_base()  # Any to avoid mypy mess with SA 2
+
 IDENTIFIER_LENGTH = 128
 SMALL_FIELD_LENGTH = 32
 SIMPLE_FIELD_LENGTH = 128
@@ -60,7 +63,30 @@ def init_tables(
     tap_keys_table: str | None = None,
     tap_key_columns_table: str | None = None,
 ) -> MutableMapping[str, Any]:
-    """Generate definitions for TAP tables."""
+    """Generate definitions for TAP tables.
+
+    Parameters
+    ----------
+    tap_schema_name
+        Name of the TAP schema.
+    tap_tables_postfix
+        Postfix for table names.
+    tap_schemas_table
+        Name of the schemas table.
+    tap_tables_table
+        Name of the tables table.
+    tap_columns_table
+        Name of the columns table.
+    tap_keys_table
+        Name of the keys table.
+    tap_key_columns_table
+        Name of the key columns table.
+
+    Returns
+    -------
+    `dict` [ `str`, `Any`]
+        A dictionary of table definitions.
+    """
     postfix = tap_tables_postfix or ""
 
     # Dirty hack to enable this method to be called more than once, replaces
@@ -133,18 +159,21 @@ def init_tables(
 
 
 class TapLoadingVisitor:
-    """Felis schema visitor for generating TAP schema.
+    """Generate TAP_SCHEMA data and insert it into a database using the
+    SQLAlchemy ORM.
 
     Parameters
     ----------
-    engine : `sqlalchemy.engine.Engine` or `None`
+    engine
         SQLAlchemy engine instance.
-    catalog_name : `str` or `None`
+    catalog_name
         Name of the database catalog.
-    schema_name : `str` or `None`
-        Name of the database schema.
-    tap_tables : `~collections.abc.Mapping`
-        Optional mapping of table name to its declarative base class.
+    schema_name
+        Name of the schema.
+    tap_tables
+        Mapping of TAP_SCHEMA table name to its SQLAlchemy table object.
+    tap_schema_index
+        The index of the schema for this TAP environment.
     """
 
     def __init__(
@@ -154,7 +183,8 @@ class TapLoadingVisitor:
         schema_name: str | None = None,
         tap_tables: MutableMapping[str, Any] | None = None,
         tap_schema_index: int | None = None,
-    ):
+    ) -> None:
+        """Create a TAP loading visitor."""
         self.graph_index: MutableMapping[str, Any] = {}
         self.catalog_name = catalog_name
         self.schema_name = schema_name
@@ -172,12 +202,39 @@ class TapLoadingVisitor:
         tap_tables: MutableMapping[str, Any] | None = None,
         tap_schema_index: int | None = None,
     ) -> TapLoadingVisitor:
+        """Create a TAP visitor from a mock connection.
+
+        Parameters
+        ----------
+        mock_connection
+            Mock connection object.
+        catalog_name
+            Name of the database catalog.
+        schema_name
+            Name of the database schema.
+        tap_tables
+            Optional mapping of table name to its SQLAlchemy table object.
+        tap_schema_index
+            The index of the schema for this TAP environment.
+
+        Returns
+        -------
+        `TapLoadingVisitor`
+            The TAP loading visitor.
+        """
         visitor = cls(engine=None, catalog_name=catalog_name, schema_name=schema_name, tap_tables=tap_tables)
         visitor._mock_connection = mock_connection
         visitor.tap_schema_index = tap_schema_index
         return visitor
 
     def visit_schema(self, schema_obj: Schema) -> None:
+        """Visit a schema object and insert it into the TAP_SCHEMA database.
+
+        Parameters
+        ----------
+        schema_obj
+            The schema object to visit.
+        """
         schema = self.tables["schemas"]()
         # Override with default
         self.schema_name = self.schema_name or schema_obj.name
@@ -226,6 +283,18 @@ class TapLoadingVisitor:
                 conn.execute(_insert(self.tables["key_columns"], key_column))
 
     def visit_constraints(self, schema_obj: Schema) -> tuple:
+        """Visit all constraints in a schema.
+
+        Parameters
+        ----------
+        schema_obj
+            The schema object to visit.
+
+        Returns
+        -------
+        `tuple`
+            A tuple of all TAP_SCHEMA keys and key columns that were created.
+        """
         all_keys = []
         all_key_columns = []
         for table_obj in schema_obj.tables:
@@ -238,6 +307,20 @@ class TapLoadingVisitor:
         return all_keys, all_key_columns
 
     def visit_table(self, table_obj: Table, schema_obj: Schema) -> tuple:
+        """Visit a table object and build its TAP_SCHEMA representation.
+
+        Parameters
+        ----------
+        table_obj
+            The table object to visit.
+        schema_obj
+            The schema object which the table belongs to.
+
+        Returns
+        -------
+        `tuple`
+            A tuple of the SQLAlchemy ORM objects for the tables and columns.
+        """
         table_id = table_obj.id
         table = self.tables["tables"]()
         table.schema_name = self._schema_name()
@@ -257,6 +340,20 @@ class TapLoadingVisitor:
         return table, columns
 
     def check_column(self, column_obj: datamodel.Column) -> None:
+        """Check consistency of VOTable attributes for a column.
+
+        Parameters
+        ----------
+        column_obj
+            The column object to check.
+
+        Notes
+        -----
+        This method checks that a column with a sized datatype has either a
+        ``votable:arraysize`` or a ``length`` attribute and issues a warning
+        message if not. It also checks if a column with a timestamp datatype
+        has a ``arraysize`` attribute and issues a warning if not.
+        """
         _id = column_obj.id
         datatype_name = column_obj.datatype
         felis_type = FelisType.felis_type(datatype_name.value)
@@ -283,6 +380,20 @@ class TapLoadingVisitor:
                 )
 
     def visit_column(self, column_obj: datamodel.Column, table_obj: Table) -> Tap11Base:
+        """Visit a column object and build its TAP_SCHEMA representation.
+
+        Parameters
+        ----------
+        column_obj
+            The column object to visit.
+        table_obj
+            The table object which the column belongs to.
+
+        Returns
+        -------
+        ``Tap11Base``
+            The SQLAlchemy ORM object for the column.
+        """
         self.check_column(column_obj)
         column_id = column_obj.id
         table_name = self._table_name(table_obj.name)
@@ -321,6 +432,15 @@ class TapLoadingVisitor:
         return column
 
     def visit_primary_key(self, primary_key_obj: str | Iterable[str] | None, table_obj: Table) -> None:
+        """Visit a primary key object and update the TAP_SCHEMA representation.
+
+        Parameters
+        ----------
+        primary_key_obj
+            The primary key object to visit.
+        table_obj
+            The table object which the primary key belongs to.
+        """
         if primary_key_obj:
             if isinstance(primary_key_obj, str):
                 primary_key_obj = [primary_key_obj]
@@ -328,9 +448,21 @@ class TapLoadingVisitor:
             # if just one column and it's indexed, update the object
             if len(columns) == 1:
                 columns[0].indexed = 1
-        return None
 
     def visit_constraint(self, constraint_obj: Constraint) -> tuple:
+        """Visit a constraint object and build its TAP_SCHEMA representation.
+
+        Parameters
+        ----------
+        constraint_obj
+            The constraint object to visit.
+
+        Returns
+        -------
+        `tuple`
+            A tuple of the SQLAlchemy ORM objects for the TAP_SCHEMA ``key``
+            and ``key_columns`` data.
+        """
         constraint_type = constraint_obj.type
         key = None
         key_columns = []
@@ -375,13 +507,36 @@ class TapLoadingVisitor:
         return key, key_columns
 
     def visit_index(self, index_obj: Index, table_obj: Table) -> None:
+        """Visit an index object and update the TAP_SCHEMA representation.
+
+        Parameters
+        ----------
+        index_obj
+            The index object to visit.
+        table_obj
+            The table object which the index belongs to.
+        """
         columns = [self.graph_index[col_id] for col_id in getattr(index_obj, "columns", [])]
         # if just one column and it's indexed, update the object
         if len(columns) == 1:
             columns[0].indexed = 1
         return None
 
-    def _schema_name(self, schema_name: str | None = None) -> str | None:
+    def _schema_name(
+        self, schema_name: str | None = None
+    ) -> str | None:  # DM-44870: Usage of this method needs to be better understood and possibly removed
+        """Return the schema name.
+
+        Parameters
+        ----------
+        schema_name
+            Name of the schema.
+
+        Returns
+        -------
+        schema_name
+            The schema name.
+        """
         # If _schema_name is None, SQLAlchemy will catch it
         _schema_name = schema_name or self.schema_name
         if self.catalog_name and _schema_name:
@@ -389,6 +544,13 @@ class TapLoadingVisitor:
         return _schema_name
 
     def _table_name(self, table_name: str) -> str:
+        """Return the table name.
+
+        Parameters
+        ----------
+        table_name
+            Name of the table.
+        """
         schema_name = self._schema_name()
         if schema_name:
             return ".".join([schema_name, table_name])
@@ -400,15 +562,15 @@ def _insert(table: Tap11Base, value: Any) -> Insert:
 
     Parameters
     ----------
-    table : `Tap11Base`
+    table
         The table we are inserting into.
-    value : `Any`
+    value
         An object representing the object we are inserting to the table.
 
     Returns
     -------
-    statement
-        A SQLAlchemy insert statement
+    `Insert`
+        SQLAlchemy insert statement.
     """
     values_dict = {}
     for i in table.__table__.columns:

felis/types.py

@@ -1,3 +1,5 @@
+"""Define the supported Felis datatypes."""
+
 # This file is part of felis.
 #
 # Developed for the LSST Data Management System.
@@ -23,10 +25,29 @@ from __future__ import annotations
 
 from typing import Any
 
+__all__ = [
+    "FelisType",
+    "Boolean",
+    "Byte",
+    "Short",
+    "Int",
+    "Long",
+    "Float",
+    "Double",
+    "Char",
+    "String",
+    "Unicode",
+    "Text",
+    "Binary",
+    "Timestamp",
+]
+
 
 class FelisType:
-    """Base class for types that represent Felis column types.
+    """Base class for a representation of Felis column types.
 
+    Notes
+    -----
     This class plays a role of a metaclass without being an actual metaclass.
     It provides a method to retrieve a class (type) given Felis type name.
     There should be no instances of this class (or sub-classes), the utility
@@ -34,12 +55,22 @@ class FelisType:
     """
 
     felis_name: str
+    """Name of the type as defined in the Felis schema."""
+
     votable_name: str
+    """Name of the type as defined in VOTable."""
+
     is_numeric: bool
+    """Flag indicating if the type is numeric."""
+
     is_sized: bool
+    """Flag indicating if the type is sized, meaning it requires a length."""
+
     is_timestamp: bool
+    """Flag indicating if the type is a timestamp."""
 
     _types: dict[str, type[FelisType]] = {}
+    """Dictionary of all known Felis types."""
 
     @classmethod
     def __init_subclass__(
@@ -52,6 +83,23 @@ class FelisType:
         is_timestamp: bool = False,
         **kwargs: Any,
     ):
+        """Register a new Felis type.
+
+        Parameters
+        ----------
+        felis_name
+            Name of the type.
+        votable_name
+            Name of the type as defined in VOTable.
+        is_numeric
+            Flag indicating if the type is numeric.
+        is_sized
+            Flag indicating if the type is sized.
+        is_timestamp
+            Flag indicating if the type is a timestamp.
+        kwargs
+            Additional keyword arguments.
+        """
         super().__init_subclass__(**kwargs)
         cls.felis_name = felis_name
         cls.votable_name = votable_name
@@ -62,17 +110,17 @@ class FelisType:
 
     @classmethod
     def felis_type(cls, felis_name: str) -> type[FelisType]:
-        """Return specific Felis type for a given type name.
+        """Return specific Felis type for a given name.
 
         Parameters
         ----------
-        felis_name : `str`
-            name of the felis type as defined in felis schema.
+        felis_name
+            Name of the felis type as defined in felis schema.
 
         Returns
         -------
-        felis_type : `type`
-            One of subclasses of `FelisType`.
+        `type` [ `FelisType` ]
+            A specific Felis type class.
 
         Raises
         ------
@@ -106,11 +154,11 @@ class Long(FelisType, felis_name="long", votable_name="long", is_numeric=True):
 
 
 class Float(FelisType, felis_name="float", votable_name="float", is_numeric=True):
-    """Felis definition of single precision floating type."""
+    """Felis definition of single precision floating point type."""
 
 
 class Double(FelisType, felis_name="double", votable_name="double", is_numeric=True):
-    """Felis definition of double precision floating type."""
+    """Felis definition of double precision floating point type."""
 
 
 class Char(FelisType, felis_name="char", votable_name="char", is_sized=True):

felis/version.py

@@ -1,2 +1,2 @@
 __all__ = ["__version__"]
-__version__ = "27.2024.2400"
+__version__ = "27.2024.2600"

{lsst_felis-27.2024.2400.dist-info → lsst_felis-27.2024.2600.dist-info}/COPYRIGHT

@@ -1 +1 @@
-Copyright 2020-2022 The Board of Trustees of the Leland Stanford Junior University, through SLAC National Accelerator Laboratory
+Copyright 2018-2024 The Board of Trustees of the Leland Stanford Junior University, through SLAC National Accelerator Laboratory

{lsst_felis-27.2024.2400.dist-info → lsst_felis-27.2024.2600.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lsst-felis
-Version: 27.2024.2400
+Version: 27.2024.2600
 Summary: A vocabulary for describing catalogs and acting on those descriptions
 Author-email: Rubin Observatory Data Management <dm-admin@lists.lsst.org>
 License: GNU General Public License v3 or later (GPLv3+)
@@ -25,7 +25,9 @@ Requires-Dist: pyyaml >=6
 Requires-Dist: pydantic <3,>=2
 Requires-Dist: lsst-utils
 Provides-Extra: dev
-Requires-Dist: documenteer[guide] ; extra == 'dev'
+Requires-Dist: documenteer[guide] <2 ; extra == 'dev'
+Requires-Dist: autodoc-pydantic ; extra == 'dev'
+Requires-Dist: sphinx-click ; extra == 'dev'
 Provides-Extra: test
 Requires-Dist: pytest >=3.2 ; extra == 'test'
 

lsst_felis-27.2024.2600.dist-info/RECORD

@@ -0,0 +1,21 @@
+felis/__init__.py,sha256=THmRg3ylB4E73XhFjJX7YlnV_CM3lr_gZO_HqQFzIQ4,937
+felis/cli.py,sha256=i5FlA9OBecqHP4SISngaveQ7YbWH8pxRGHeOzMOOMyg,14086
+felis/datamodel.py,sha256=k0wAZpIhwOWVvAlHLLpzCOYYxY5iD8jpjlOu_lpzv-4,25902
+felis/metadata.py,sha256=W1Y4s7izAEiH3MLJkKQpvxHsGE5Dbu4lhhNCzWlfl0o,12290
+felis/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+felis/tap.py,sha256=YBWl1CicdN4jW_KhPJQ7-TuhOfFFTIYIH4tTJ8P_o1c,21035
+felis/types.py,sha256=m80GSGfNHQ3-NzRuTzKOyRXLJboPxdk9kzpp1SO8XdY,5510
+felis/version.py,sha256=aahBy2OK7EjIKUv__rAtLwgu_sqkTymTjJ8WETh6OXg,55
+felis/db/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+felis/db/dialects.py,sha256=IsjdD_2n7tucUdR7TMyRd2gWtnD-2kXPAJUUQdbUe_Q,3526
+felis/db/sqltypes.py,sha256=sDzkqemYwILp8hk0yfg3H0ZK7bGnIJR9x6ntd2coASc,11248
+felis/db/utils.py,sha256=TgNJTBv2Jt4Qq_RtOO_jWj_02tb-fEA2QeOOHYS1GyU,10177
+felis/db/variants.py,sha256=o5m101upQQbWZD_l8qlB8gt-ZQ9-VqsWZrmxQO1eEQA,5246
+lsst_felis-27.2024.2600.dist-info/COPYRIGHT,sha256=vJAFLFTSF1mhy9eIuA3P6R-3yxTWKQgpig88P-1IzRw,129
+lsst_felis-27.2024.2600.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
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+lsst_felis-27.2024.2600.dist-info/entry_points.txt,sha256=Gk2XFujA_Gp52VBk45g5kim8TDoMDJFPctsMqiq72EM,40
+lsst_felis-27.2024.2600.dist-info/top_level.txt,sha256=F4SvPip3iZRVyISi50CHhwTIAokAhSxjWiVcn4IVWRI,6
+lsst_felis-27.2024.2600.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
+lsst_felis-27.2024.2600.dist-info/RECORD,,

{lsst_felis-27.2024.2400.dist-info → lsst_felis-27.2024.2600.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.1.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

felis/validation.py

@@ -1,103 +0,0 @@
-# This file is part of felis.
-#
-# Developed for the LSST Data Management System.
-# This product includes software developed by the LSST Project
-# (https://www.lsst.org).
-# See the COPYRIGHT file at the top-level directory of this distribution
-# for details of code ownership.
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-from __future__ import annotations
-
-import logging
-from collections.abc import Sequence
-from typing import Any
-
-from pydantic import Field, model_validator
-
-from .datamodel import Column, DescriptionStr, Schema, Table
-
-logger = logging.getLogger(__name__)
-
-__all__ = ["RspColumn", "RspSchema", "RspTable", "get_schema"]
-
-
-class RspColumn(Column):
-    """Column for RSP data validation."""
-
-    description: DescriptionStr
-    """Redefine description to make it required."""
-
-
-class RspTable(Table):
-    """Table for RSP data validation.
-
-    The list of columns is overridden to use RspColumn instead of Column.
-
-    Tables for the RSP must have a TAP table index and a valid description.
-    """
-
-    description: DescriptionStr
-    """Redefine description to make it required."""
-
-    tap_table_index: int = Field(..., alias="tap:table_index")
-    """Redefine the TAP_SCHEMA table index so that it is required."""
-
-    columns: Sequence[RspColumn]
-    """Redefine columns to include RSP validation."""
-
-    @model_validator(mode="after")  # type: ignore[arg-type]
-    @classmethod
-    def check_tap_principal(cls: Any, tbl: RspTable) -> RspTable:
-        """Check that at least one column is flagged as 'principal' for
-        TAP purposes.
-        """
-        for col in tbl.columns:
-            if col.tap_principal == 1:
-                return tbl
-        raise ValueError(f"Table '{tbl.name}' is missing at least one column designated as 'tap:principal'")
-
-
-class RspSchema(Schema):
-    """Schema for RSP data validation.
-
-    TAP table indexes must be unique across all tables.
-    """
-
-    tables: Sequence[RspTable]
-    """Redefine tables to include RSP validation."""
-
-    @model_validator(mode="after")  # type: ignore[arg-type]
-    @classmethod
-    def check_tap_table_indexes(cls: Any, sch: RspSchema) -> RspSchema:
-        """Check that the TAP table indexes are unique."""
-        table_indicies = set()
-        for table in sch.tables:
-            table_index = table.tap_table_index
-            if table_index is not None:
-                if table_index in table_indicies:
-                    raise ValueError(f"Duplicate 'tap:table_index' value {table_index} found in schema")
-                table_indicies.add(table_index)
-        return sch
-
-
-def get_schema(schema_name: str) -> type[Schema]:
-    """Get the schema class for the given name."""
-    if schema_name == "default":
-        return Schema
-    elif schema_name == "RSP":
-        return RspSchema
-    else:
-        raise ValueError(f"Unknown schema name '{schema_name}'")

lsst_felis-27.2024.2400.dist-info/RECORD

@@ -1,22 +0,0 @@
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-felis/datamodel.py,sha256=ECXmd78fufrYDBK4S0n3-wSQytWmz-vGLkNRjtrHPCE,19627
-felis/metadata.py,sha256=lSgKy9CksmyJp9zUkzkwOAzjk2Hzivb9VVbYfTPNmvY,12140
-felis/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-felis/tap.py,sha256=fVYvvIFk_vccXqbcFYdgK2yOfp4P5E4guvsSGktsNxs,16795
-felis/types.py,sha256=z_ECfSxpqiFSGppjxKwCO4fPP7TLBaIN3Qo1AGF16Go,4418
-felis/validation.py,sha256=Zq0gyCvPCwRlhfQ-w_p6ccDTkjcyhxSA1-Gr5plXiZI,3465
-felis/version.py,sha256=SKE5LZn31z5ONJXoQypgUH-1aa2Ar0owtNYSiqyaKog,55
-felis/db/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-felis/db/dialects.py,sha256=mSYgS8gqUJQGgZw3IA-zBfKlrJ2r4nEUR94wKZNRKZg,2267
-felis/db/sqltypes.py,sha256=yFlautQ1hv21MHF4AIfBp7_2m1-exKBfc76xYsMHBgk,5735
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