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Create metadata table for stored properties (#156)
* add metadata table * fix typos * fix typos * add metadata table with initial contents * add ParrPearson on hardness * update metadata schema and data * add documentation for PropertyMetadata class * update docstring * add propertymetadata to fetch tables * correct format * update units * render updated data docs * update isotope metadata * add isotope metadata to PropertyMetadata * docs * add PropertyMetadata to models.__all__
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‎README.md

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@@ -286,7 +286,7 @@ the `Element` object:
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>>> from mendeleev import element
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The `element` method accepts unique identifiers: atomic number, atomic
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symbol or element\'s name in english. To retrieve the entries on Silicon
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symbol or element\'s name in English. To retrieve the entries on Silicon
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by symbol type
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``` {.sourceCode .python}
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The columns represent the attributes `atomic_number`, `mass`,
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`abundance` and `mass_number` respectively.
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### Accesing data tables and the database
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### Accessing data tables and the database
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[mendeleev](http://mendeleev.readthedocs.org) offers also methods for
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accessing whole tables of data, e.g. table with the data on all isotopes

‎alembic/versions/7d745d77a7c1_add_propertymetadata_table.py

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"""add PropertyMetadata table
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Revision ID: 7d745d77a7c1
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Revises: 703682715347
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Create Date: 2024-05-21 13:11:24.427405
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"""
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# revision identifiers, used by Alembic.
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revision = '7d745d77a7c1'
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down_revision = '703682715347'
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branch_labels = None
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depends_on = None
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from alembic import op
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import sqlalchemy as sa
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value_origin_enum = sa.Enum('STORED', 'COMPUTED', name='valueorigin')
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def upgrade():
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op.create_table(
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'propertymetadata',
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sa.Column('id', sa.Integer, primary_key=True, autoincrement=True),
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sa.Column('table_name', sa.String, nullable=True),
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sa.Column('column_name', sa.String, nullable=True),
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sa.Column('class_name', sa.String, nullable=False),
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sa.Column('attribute_name', sa.String, nullable=False),
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sa.Column('category', sa.String, nullable=False),
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sa.Column('value_origin', value_origin_enum, nullable=False),
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sa.Column('description', sa.Text, nullable=False),
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sa.Column('unit', sa.String, nullable=True),
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sa.Column('annotations', sa.Text, nullable=True),
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sa.Column('citation_keys', sa.String, nullable=True)
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)
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def downgrade():
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op.drop_table('propertymetadata')
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value_origin_enum.drop(op.get_bind())

‎docs/source/api/mendeleev.cli.rst

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mendeleev.cli
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=============
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.. automodule:: mendeleev.cli
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.. rubric:: Functions
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.. autosummary::
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clielement
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.. currentmodule:: mendeleev
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.. autodata:: cli

‎docs/source/api/mendeleev.ion.rst

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mendeleev.ion
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=============
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.. automodule:: mendeleev.ion
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.. rubric:: Classes
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.. autosummary::
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Ion
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.. currentmodule:: mendeleev
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.. autodata:: ion

‎docs/source/api/mendeleev.models.rst

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IsotopeDecayMode
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OxidationState
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PhaseTransition
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PropertyMetadata
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ScreeningConstant
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Series
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ValueOrigin
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‎docs/source/api/models.rst

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.. autoclass:: mendeleev.models.OxidationState
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:members:
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.. _propertymetadata-class:
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PropertyMetadata
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----------------
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.. currentmodule:: mendeleev.models
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.. autoclass:: mendeleev.models.PropertyMetadata
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:members:
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.. _econf-class:
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‎docs/source/data.rst

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‎docs/source/data_access.rst

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- :ref:`oxidationstates <oxidationstate-class>`
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- :ref:`screeningconstants <screeningconstant-class>`
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- :ref:`series <series-class>`
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- :ref:`propertymetadata <propertymetadata-class>`
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.. autofunction:: fetch_table
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‎docs/source/references.bib

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edition = {97th},
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pages = {2704}
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}
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@article{ParrPearson1983,
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author = {Parr, Robert G. and Pearson, Ralph G.},
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title = {Absolute hardness: companion parameter to absolute electronegativity},
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journal = {Journal of the American Chemical Society},
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volume = {105},
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number = {26},
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pages = {7512-7516},
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year = {1983},
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doi = {10.1021/ja00364a005},
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url = {https://doi.org/10.1021/ja00364a005},
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eprint = {https://doi.org/10.1021/ja00364a005}
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}

‎mendeleev/elements.db

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‎mendeleev/fetch.py

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@@ -54,6 +54,7 @@ def fetch_table(table: str, **kwargs) -> pd.DataFrame:
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"isotopes",
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"oxidationstates",
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"phasetransitions",
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"propertymetadata",
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"screeningconstants",
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"series",
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}

‎mendeleev/models.py

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# -*- coding: utf-8 -*-
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"""module specifying the database models"""
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"""module defining the database models"""
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from typing import Any, Callable, Dict, List, Tuple, Union
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from operator import attrgetter
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import enum
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import math
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import urllib.parse
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import numpy as np
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from sqlalchemy import Column, Boolean, Integer, String, Float, ForeignKey
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from sqlalchemy import Column, Boolean, Integer, String, Float, ForeignKey, Text, Enum
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from sqlalchemy.orm import declarative_base, relationship, reconstructor
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from sqlalchemy.ext.associationproxy import association_proxy
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from sqlalchemy.ext.hybrid import hybrid_property, hybrid_method
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"IonicRadius",
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"OxidationState",
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"Isotope",
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"PropertyMetadata",
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"Series",
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"ScreeningConstant",
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]
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)
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class ValueOrigin(enum.Enum):
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"Options for the origin of the property value."
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STORED = "stored"
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COMPUTED = "computed"
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class PropertyMetadata(Base):
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"""Metadata for properties of elements and isotopes.
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Args:
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annotations (str): Additional information about the property.
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attribute_name (str): Name of the attribute of the ORM class.
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category (str): Category of the property.
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citation_keys (str): Comma separated list of citation keys. See references.bib for full bibliography.
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class_name (str): Name of the ORM class.
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column_name (str): Name of the column in the database.
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description (str): Description of the property.
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table_name (str): Name of the table in the database.
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unit (str): Unit of the property.
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value_origin (ValueOrigin): Origin of the value, either stored or computed.
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"""
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__tablename__ = "propertymetadata"
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id = Column(Integer, primary_key=True)
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annotations = Column(Text)
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attribute_name = Column(String, nullable=False)
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category = Column(String)
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citation_keys = Column(String)
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class_name = Column(String, nullable=False)
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column_name = Column(String, nullable=True)
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description = Column(Text, nullable=False)
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table_name = Column(String, nullable=True)
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unit = Column(String)
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value_origin = Column(Enum(ValueOrigin), nullable=False)
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def __repr__(self) -> str:
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return "%s(\n%s)" % (
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self.__class__.__name__,
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" ".join(
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"\t%s=%r,\n" % (key, getattr(self, key))
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for key in sorted(self.__dict__.keys())
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if not key.startswith("_")
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),
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)
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def fetch_attrs_for_group(attrs: List[str], group: int = 18) -> Tuple[List[Any]]:
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"""
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A convenience function for getting a specified attribute for all

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