Source code for dataCAT.database

"""A module which holds the :class:`.Database` class.

.. currentmodule:: dataCAT
.. autosummary::

.. autoclass:: Database


import reprlib
import textwrap
import warnings
from os import getcwd, PathLike
from os.path import abspath
from types import MappingProxyType
from functools import partial
from typing import (
    Optional, Sequence, List, Union, Any, Dict, TypeVar, Mapping,
    overload, Tuple, Type, Iterable, TYPE_CHECKING

import h5py
import numpy as np
import pandas as pd
from pymongo import MongoClient
from pymongo.errors import PyMongoError, DuplicateKeyError

from rdkit.Chem import Mol
from scm.plams import Settings, Molecule, from_rdmol
from nanoutils import TypedDict
from CAT.workflows import HDF5_INDEX, OPT, MOL

from .create_database import create_csv, create_hdf5, create_mongodb, QD, Ligand, IDX_DTYPE
from .context_managers import OpenLig, OpenQD
from .functions import df_to_mongo_dict, even_index, hdf5_availability
from .pdb_array import PDBContainer
from .hdf5_log import update_hdf5_log
from .property_dset import create_prop_dset, update_prop_dset
from ._parse_settings import _update_hdf5_settings

    from .df_proxy import DFProxy
    from numpy.typing import DTypeLike
    DFProxy = 'dataCAT.DFProxy'
    DTypeLike = 'numpy.typing.DTypeLike'

__all__ = ['Database']

KT = TypeVar('KT')
ST = TypeVar('ST', bound='Database')
MIT = TypeVar('MIT', bound=pd.MultiIndex)

class JobRecipe(TypedDict):
    """A :class:`~typing.TypedDict` representing the input of :class:`.Database.update_yaml`."""

    key: Union[str, type]
    value: Union[str, Settings]

def _to_int64_array(ar: np.ndarray) -> np.ndarray:
    ret = ar.astype(np.int64)
    if ar.dtype.kind in "SU":
        return ret

    is_eq = (ret == ar)
    if not isinstance(is_eq, (np.ndarray, np.bool_)) or not is_eq.all():
        raise TypeError(f"Cannot safelly cast {ar.dtype} to {ret.dtype}")
    return ret

[docs]class Database: """The Database class.""" __slots__ = ('__weakref__', '_dirname', '_csv_lig', '_csv_qd', '_hdf5', '_mongodb', '_hash') @property def dirname(self) -> str: """Get the path+filename of the directory containing all database components.""" return self._dirname @property def csv_lig(self) -> 'partial[OpenLig]': """:data:`Callable[..., dataCAT.OpenLig]<typing.Callable>`: Get a function for constructing an :class:`dataCAT.OpenLig` context manager.""" # noqa: E501 return self._csv_lig @property def csv_qd(self) -> 'partial[OpenQD]': """:data:`Callable[..., dataCAT.OpenQD]<typing.Callable>`: Get a function for constructing an :class:`dataCAT.OpenQD` context manager.""" # noqa: E501 return self._csv_qd @property def hdf5(self) -> 'partial[h5py.File]': """:data:`Callable[..., h5py.File]<typing.Callable>`: Get a function for constructing a :class:`h5py.File` context manager.""" # noqa: E501 return self._hdf5 @property def mongodb(self) -> Optional[Mapping[str, Any]]: """:class:`Mapping[str, Any]<typing.Mapping>`, optional: Get a mapping with keyword arguments for :class:`pymongo.MongoClient<pymongo.mongo_client.MongoClient>`.""" # noqa: E501 return self._mongodb def __init__(self, path: Union[str, 'PathLike[str]', None] = None, host: str = 'localhost', port: int = 27017, **kwargs) -> None: """Initialize :class:`Database`. Parameters ---------- path : str The path+directory name of the directory which is to contain all database components (see :attr:`Database.dirname`). host : str Hostname or IP address or Unix domain socket path of a single mongod or mongos instance to connect to, or a mongodb URI, or a list of hostnames mongodb URIs. If **host** is an IPv6 literal it must be enclosed in ``"["`` and ``"]"`` characters following the RFC2732 URL syntax (e.g. ``"[::1]"`` for localhost). Multihomed and round robin DNS addresses are not supported. See :attr:`Database.mongodb`. port : str port number on which to connect. See :attr:`Database.mongodb`. **kwargs Optional keyword argument for :class:`pymongo.MongoClient<pymongo.mongo_client.MongoClient>`. See :attr:`Database.mongodb`. """ # noqa: E501 self._dirname: str = abspath(path) if path is not None else getcwd() # Create the database components and return the filename lig_path = create_csv(self.dirname, database='ligand') qd_path = create_csv(self.dirname, database='qd') hdf5_path = create_hdf5(self.dirname) # Populate attributes with MetaManager instances self._csv_lig = partial(OpenLig, filename=lig_path) self._csv_qd = partial(OpenQD, filename=qd_path) self._hdf5 = partial(h5py.File, hdf5_path, libver='latest') # Try to create or access the mongodb database try: self._mongodb: Optional[Mapping[str, Any]] = MappingProxyType( create_mongodb(host, port, **kwargs) ) except PyMongoError: self._mongodb = None def __repr__(self) -> str: """Implement :class:`str(self)<str>` and :func:`repr(self)<repr>`.""" attr_tup = ('dirname', 'csv_lig', 'csv_qd', 'hdf5', 'mongodb') attr_max = max(len(i) for i in attr_tup) iterator = ((name, getattr(self, name)) for name in attr_tup[:-1]) args = ',\n'.join(f'{name:{attr_max}} = {attr!r}' for name, attr in iterator) args += f',\n{attr_tup[-1]:{attr_max}} = {reprlib.repr(self.mongodb)}' indent = 4 * ' ' return f'{self.__class__.__name__}(\n{textwrap.indent(args, indent)}\n)' def __eq__(self, value: Any) -> bool: """Implement :meth:`self == value<object.__eq__>`.""" if type(self) is not type(value): return False ret: bool = self.dirname == value.dirname and self.mongodb == value.mongodb if not ret: return False partial_names = ('csv_lig', 'csv_qd', 'hdf5') iterator = ((getattr(self, name), getattr(value, name)) for name in partial_names) return all(func1.args == func2.args and func1.keywords == func2.keywords and func1.func is func2.func for func1, func2 in iterator) def __hash__(self) -> int: """Implement :func:`hash(self)<hash>`.""" try: return self._hash except AttributeError: cls, args, state = self.__reduce__() if state is not None: state = frozenset(state.items()) # type: ignore self._hash: int = hash((cls, args, state)) return self._hash def __reduce__(self: ST) -> Tuple[Type[ST], Tuple[str], Optional[Dict[str, Any]]]: """Helper for :mod:`pickle`.""" cls = type(self) mongodb = self.mongodb if self.mongodb is None else dict(self.mongodb) return cls, (self.dirname,), mongodb def __setstate__(self, state: Optional[Dict[str, Any]]) -> None: """Helper for :mod:`pickle` and :meth:`~Database.__reduce__`.""" if state is None: self._mongodb = None return try: self._mongodb = MappingProxyType(create_mongodb(**state)) except PyMongoError: self._mongodb = None def __copy__(self: ST) -> ST: """Implement :func:`copy.copy(self)<copy.copy>`.""" return self def __deepcopy__(self: ST, memo: Optional[Dict[int, Any]] = None) -> ST: """Implement :func:`copy.deepcopy(self, memo=memo)<copy.deepcopy>`.""" return self """ ################################# Updating the database ############################## """ @overload def _parse_database(self, database: Ligand) -> 'partial[OpenLig]': ... @overload # noqa: E301 def _parse_database(self, database: QD) -> 'partial[OpenQD]': ... def _parse_database(self, database): # noqa: E301 """Operate on either the ligand or quantum dot database.""" if database in {'ligand', 'ligand_no_opt'}: return self.csv_lig elif database in {'qd', 'qd_no_opt'}: return self.csv_qd raise ValueError(f"database={database!r}; accepted values for are 'ligand' and 'qd'")
[docs] def update_mongodb(self, database: Union[str, Mapping[str, pd.DataFrame]] = 'ligand', overwrite: bool = False) -> None: """Export ligand or qd results to the MongoDB database. Examples -------- .. code:: python >>> from dataCAT import Database >>> kwargs = dict(...) # doctest: +SKIP >>> db = Database(**kwargs) # doctest: +SKIP # Update from db.csv_lig >>> db.update_mongodb('ligand') # doctest: +SKIP # Update from a lig_df, a user-provided DataFrame >>> db.update_mongodb({'ligand': lig_df}) # doctest: +SKIP >>> print(type(lig_df)) # doctest: +SKIP <class 'pandas.core.frame.DataFrame'> Parameters ---------- database : :class:`str` or :class:`Mapping[str, pandas.DataFrame]<typing.Mapping>` The type of database. Accepted values are ``"ligand"`` and ``"qd"``, opening :attr:`Database.csv_lig` and :attr:`Database.csv_qd`, respectivelly. Alternativelly, a dictionary with the database name and a matching DataFrame can be passed directly. overwrite : :class:`bool` Whether or not previous entries can be overwritten or not. :rtype: :data:`None` """ if self.mongodb is None: raise ValueError('Database.Mongodb is None') # Open the MongoDB database client = MongoClient(**self.mongodb) mongo_db = client.cat_database if callable(getattr(database, 'items', None)): database, db = next(iter(database.items())) # type: ignore dict_gen = df_to_mongo_dict(db) idx_keys = db.index.names collection = mongo_db.ligand_database if database == 'ligand' else mongo_db.qd_database else: # Operate on either the ligand or quantum dot database if database == 'ligand': idx_keys = ('smiles', 'anchor') collection = mongo_db.ligand_database manager = self.csv_lig elif database == 'qd': idx_keys = ('core', 'core anchor', 'ligand smiles', 'ligand anchor') collection = mongo_db.qd_database manager = self.csv_lig # Parse the ligand or qd dataframe with manager(write=False) as db: dict_gen = df_to_mongo_dict(db) # Update the collection # Try to insert al keys at once try: collection.insert_many(dict_gen) except DuplicateKeyError: pass else: return # Simultaneous insertion failed, resort to plan B for item in dict_gen: try: collection.insert_one(item) except DuplicateKeyError: # An item is already present in the collection if overwrite: filter_ = {i: item[i] for i in idx_keys} collection.replace_one(filter_, item)
[docs] def update_csv(self, df: pd.DataFrame, index: Union[None, slice, pd.Series] = None, database: Union[Ligand, QD] = 'ligand', columns: Optional[Sequence] = None, overwrite: bool = False, job_recipe: None = None, status: Optional[str] = None) -> None: """Update :attr:`Database.csv_lig` or :attr:`Database.csv_qd` with new settings. Parameters ---------- df : :class:`pandas.DataFrame` A dataframe of new (potential) database entries. database : :class:`str` The type of database; accepted values are ``"ligand"`` (:attr:`Database.csv_lig`) and ``"qd"`` (:attr:`Database.csv_qd`). columns : :class:``, optional Optional: A sequence of column keys in **df** which (potentially) are to be added to this instance. If :data:`None` Add all columns. overwrite : :class:`bool` Whether or not previous entries can be overwritten or not. status : :class:`str`, optional A descriptor of the status of the moleculair structures. Set to ``"optimized"`` to treat them as optimized geometries. :rtype: :data:`None` """ # Operate on either the ligand or quantum dot database manager = self._parse_database(database) if job_recipe is not None: warnings.warn("job_recipe .yaml storage has been discontinued", DeprecationWarning) df_index = slice(None) if index is None else index with manager(write=True) as db: # Update **db.index** db.ndframe = even_index(db.ndframe, df.loc[df_index]) df.sort_values(by=[HDF5_INDEX], inplace=True) # Filter columns export_mol = False if columns is None: df_columns = df.columns else: df_columns = pd.Index(columns) if MOL in df_columns: df_columns = df_columns.drop(MOL) export_mol = True # Remove columns with the (now deprecated) `settings` key if isinstance(df_columns, pd.MultiIndex): df_columns = pd.Index([(i, j) for i, j in df_columns if i != 'settings']) # Update **db.columns** bool_ar = df_columns.isin(db.columns) df_columns = self._even_df_columns(df, db, df_columns, ~bool_ar) # Update **self.hdf5**; returns a new series of indices if export_mol: hdf5_series = self.update_hdf5( df, df_index, database=database, overwrite=overwrite, status=status ) # Update **db.values** db.update(df.loc[df_index, df_columns], overwrite=overwrite) if export_mol: db.update(hdf5_series, overwrite=True) df.update(hdf5_series, overwrite=True) if status == 'optimized': db.update(df.loc[df_index, OPT], overwrite=True) # Update the hdf5 file with self.hdf5('r+') as f: # Get the appropiate group name = 'ligand' if manager == self.csv_lig else 'qd' group = f[f'{name}/properties'] # Define the indices hdf5_index = df[HDF5_INDEX].values # "Fix" for rare bug wherein the index dtype is incorrect if hdf5_index.dtype.kind != "i": warnings.warn(f"Invalid {HDF5_INDEX!r} dtype: {hdf5_index.dtype}") hdf5_index = df[HDF5_INDEX] = _to_int64_array(hdf5_index) # Define the properties lvl0_ignore = {OPT[0], HDF5_INDEX[0], MOL[0]} lvl0_ignore.update(i for i in df_columns.levels[0] if i.startswith("job_settings")) lvl0 = set(df_columns.levels[0]).difference(lvl0_ignore) dct = {k: df_columns.get_loc_level(k)[1] for k in lvl0} for n, name_seq in dct.items(): data = df[n].values if data.dtype == object: dtype = h5py.string_dtype(encoding='utf-8') else: dtype = data.dtype # Get the dataset try: dset = group[n] except KeyError: if not name_seq.any(): name_seq = None dset = create_prop_dset(group, n, dtype, name_seq) # Update the dataset update_prop_dset(dset, data, hdf5_index) # Add an entry to the logger names = [group[k].name for k in dct] message = f'datasets={names!r}; overwrite={overwrite!r}' update_hdf5_log(f[f'{name}/logger'], hdf5_index, message=message)
def _even_df_columns(self, df: pd.DataFrame, db: DFProxy, columns: MIT, subset: np.ndarray) -> MIT: """Even the columns of **df** and **db**.""" drop_idx = [] for i in columns[subset]: # Check for job settings if 'job_settings' in i[0]: self._update_hdf5_settings(df, i[0]) del df[i] drop_idx.append(i) continue # Ensure that **db** has the same keys as **df** try: db[i] = np.array((None), dtype=df[i].dtype) except TypeError: # e.g. if csv[i] consists of the datatype np.int64 db[i] = -1 return columns.drop(drop_idx) # type: ignore
[docs] def update_hdf5(self, df: pd.DataFrame, index: Union[slice, pd.Series], database: Union[Ligand, QD] = 'ligand', overwrite: bool = False, status: Optional[str] = None) -> pd.Series: """Export molecules (see the ``"mol"`` column in **df**) to the structure database. Returns a series with the :attr:`Database.hdf5` indices of all new entries. Parameters ---------- df : :class:`pandas.DataFrame` A dataframe of new (potential) database entries. database : :class:`str` The type of database; accepted values are ``"ligand"`` and ``"qd"``. overwrite : :class:`bool` Whether or not previous entries can be overwritten or not. status : :class:`str`, optional A descriptor of the status of the moleculair structures. Set to ``"optimized"`` to treat them as optimized geometries. Returns ------- :class:`pandas.Series` A series with the indices of all new molecules in :attr:`Database.hdf5`. """ # Identify new and preexisting entries sub_df = df.loc[index, :] if status == 'optimized': new = sub_df.loc[(sub_df[OPT] == False) & ~sub_df[MOL].isnull(), HDF5_INDEX] # noqa old = sub_df.loc[sub_df[OPT] == True, HDF5_INDEX] # noqa opt = True else: new = sub_df.loc[(sub_df[HDF5_INDEX] == -1) & ~sub_df[MOL].isnull(), HDF5_INDEX] old = sub_df.loc[sub_df[HDF5_INDEX] >= 0, HDF5_INDEX] opt = False # Add new entries to the database self.hdf5_availability() with self.hdf5('r+') as f: group = f[database] dtype = IDX_DTYPE[database] if new.any(): ret = self._write_hdf5(group, df, new.index, dtype, database, opt=opt) else: ret = pd.Series(name=HDF5_INDEX, dtype=int) # If **overwrite** is *True* if overwrite and old.any(): self._overwrite_hdf5(group, old, df, dtype, opt=opt) return ret
@classmethod def _write_hdf5(cls, group: h5py.Group, df: pd.DataFrame, new_index: pd.Index, dtype: DTypeLike, database: Union[Ligand, QD] = 'ligand', opt: bool = False) -> pd.Index: """Helper method for :meth:`update_hdf5` when :code:`overwrite = False`.""" mol_series = df.loc[new_index, MOL] i = len(group['atoms']) j = i + len(mol_series) ret = pd.Series(np.arange(i, j), index=new_index, name=HDF5_INDEX) scale = cls._sanitize_multi_idx(new_index, dtype, database) pdb_new = PDBContainer.from_molecules(mol_series, scale=scale) pdb_new.to_hdf5(group, index=np.s_[i:j], update_scale=not opt) names = ('atoms', 'bonds', 'atom_count', 'bond_count') message = f"datasets={[group[n].name for n in names]!r}; overwrite=False" update_hdf5_log(group['logger'], index=ret.values, message=message) df.update(ret, overwrite=True) if opt: df.loc[new_index, OPT] = True return ret @staticmethod def _overwrite_hdf5(group: h5py.Group, old: pd.Series, df: pd.DataFrame, dtype: DTypeLike, opt: bool = False) -> None: """Helper method for :meth:`update_hdf5` when :code:`overwrite = True`.""" mol_series = df.loc[old.index, MOL] scale = mol_series.index.values.astype(dtype) pdb_old = PDBContainer.from_molecules(mol_series, scale=scale) pdb_old.to_hdf5(group, index=old.values) names = ('atoms', 'bonds', 'atom_count', 'bond_count') message = f"datasets={[group[n].name for n in names]!r}; overwrite=True" update_hdf5_log(group['logger'], index=old.values, message=message) if opt: df.loc[old.index, OPT] = True @staticmethod def _sanitize_multi_idx(index: MIT, dtype: DTypeLike, database: Union[Ligand, QD]) -> MIT: """Parse and sanitize the passed MultiIndex.""" return index.values.astype(dtype) # type: ignore def _update_hdf5_settings(self, df: pd.DataFrame, column: str) -> None: """Export all files in **df[column]** to hdf5 dataset **column**.""" self.hdf5_availability() with self.hdf5('r+') as f: _update_hdf5_settings(f, df, column) """ ######################## Pulling results from the database ########################### """
[docs] def from_csv(self, df: pd.DataFrame, database: Union[Ligand, QD] = 'ligand', get_mol: bool = True, inplace: bool = True) -> Optional[pd.Series]: """Pull results from :attr:`Database.csv_lig` or :attr:`Database.csv_qd`. Performs in inplace update of **df** if **inplace** = :data:`True`, thus returing :data:`None`. Parameters ---------- df : :class:`pandas.DataFrame` A dataframe of new (potential) database entries. database : :class:`str` The type of database; accepted values are ``"ligand"`` and ``"qd"``. get_mol : :class:`bool` Attempt to pull preexisting molecules from the database. See the **inplace** argument for more details. inplace : :class:`bool` If :data:`True` perform an inplace update of the ``"mol"`` column in **df**. Otherwise return a new series of PLAMS molecules. Returns ------- :class:`pandas.Series`, optional Optional: A Series of PLAMS molecules if **get_mol** = :data:`True` and **inplace** = :data:`False`. """ # Operate on either the ligand or quantum dot database manager = self._parse_database(database) # Update the *hdf5 index* column in **df** with manager(write=False) as db: df.update(db.ndframe, overwrite=True) df[HDF5_INDEX] = df[HDF5_INDEX].astype(int, copy=False) # **df** has been updated and **get_mol** = *False* if not get_mol: return None return self._get_csv_mol(df, database, inplace)
def _get_csv_mol(self, df: pd.DataFrame, database: Union[Ligand, QD] = 'ligand', inplace: bool = True) -> Optional[pd.Series]: """A method which handles the retrieval and subsequent formatting of molecules. Called internally by :meth:`Database.from_csv`. Parameters ---------- df : :class:`pandas.DataFrame` A dataframe of new (potential) database entries. database : :class:`str` The type of database; accepted values are ``"ligand"`` and ``"qd"``. inplace : :class:`bool` If :data:`True` perform an inplace update of the ``("mol", "")`` column in **df**. Otherwise return a new series of PLAMS molecules. Returns ------- :class:`pandas.Series`, optional Optional: A Series of PLAMS molecules if **inplace** is :data:`False`. """ # Sort and find all valid HDF5 indices df.sort_values(by=[HDF5_INDEX], inplace=True) if 'no_opt' in database: df_slice = df[HDF5_INDEX] >= 0 else: df_slice = df[OPT] == True # noqa idx = df[HDF5_INDEX][df_slice].values # If no HDF5 indices are availble in **df** then abort the function if not df_slice.any(): if inplace: return None return pd.Series(None, name=MOL, dtype=object) # Update **df** with preexisting molecules from **self**, returning *None* if inplace: self.from_hdf5(idx, database=database, mol_list=df.loc[df_slice, MOL], rdmol=False) return None # Create and return a new series of PLAMS molecules else: mol_list = self.from_hdf5(idx, database=database, rdmol=False) return pd.Series(mol_list, index=df[df_slice].index, name=MOL)
[docs] def from_hdf5(self, index: Union[slice, Sequence[int]], database: Union[Ligand, QD] = 'ligand', rdmol: bool = True, mol_list: Optional[Iterable[Molecule]] = None) -> List[Union[Molecule, Mol]]: """Import structures from the hdf5 database as RDKit or PLAMS molecules. Parameters ---------- index : :class:`Sequence[int]<typing.Sequence>` or :class:`slice` The indices of the to be retrieved structures. database : :class:`str` The type of database; accepted values are ``"ligand"`` and ``"qd"``. rdmol : :class:`bool` If :data:`True`, return an RDKit molecule instead of a PLAMS molecule. Returns ------- :class:`List[plams.Molecule]<typing.List>` or :class:`List[rdkit.Mol]<typing.List>` A list of PLAMS or RDKit molecules. """ # Open the database and pull entries self.hdf5_availability() with self.hdf5('r') as f: pdb = PDBContainer.from_hdf5(f[database], index) mol_list_ = pdb.to_molecules(mol=mol_list) is_opt = not ('no_opt' in database) for mol in mol_list_: = is_opt if rdmol: return [from_rdmol(mol) for mol in mol_list_] return mol_list_
[docs] def hdf5_availability(self, timeout: float = 5.0, max_attempts: Optional[int] = 10) -> None: """Check if a .hdf5 file is opened by another process; return once it is not. If two processes attempt to simultaneously open a single hdf5 file then h5py will raise an :exc:`OSError`. The purpose of this method is ensure that a .hdf5 file is actually closed, thus allowing the :meth:`Database.from_hdf5` method to safely access **filename** without the risk of raising an :exc:`OSError`. Parameters ---------- timeout : :class:`float` Time timeout, in seconds, between subsequent attempts of opening **filename**. max_attempts : :class:`int`, optional Optional: The maximum number attempts for opening **filename**. If the maximum number of attempts is exceeded, raise an :exc:`OSError`. Setting this value to :data:`None` will set the number of attempts to unlimited. Raises ------ :exc:`OSError` Raised if **max_attempts** is exceded. See Also -------- :func:`dataCAT.functions.hdf5_availability` This method as a function. """ filename = self.hdf5.args[0] hdf5_availability(filename, timeout, max_attempts, libver='latest')