import io import numbers import warnings from typing import Sequence, Tuple, Union import numpy as np import tiledb.cc as lt from tiledb.libtiledb import version as libtiledb_version from .attribute import Attr from .ctx import Ctx, CtxMixin, default_ctx from .dimension_label import DimLabel from .domain import Domain from .filter import Filter, FilterList if libtiledb_version()[0] == 2 and libtiledb_version()[1] >= 25: from .current_domain import CurrentDomain _tiledb_order_to_string = { lt.LayoutType.ROW_MAJOR: "row-major", lt.LayoutType.COL_MAJOR: "col-major", lt.LayoutType.GLOBAL_ORDER: "global", lt.LayoutType.UNORDERED: "unordered", lt.LayoutType.HILBERT: "hilbert", } _string_to_tiledb_order = {v: k for k, v in _tiledb_order_to_string.items()} _string_to_tiledb_order.update( { "C": lt.LayoutType.ROW_MAJOR, "R": lt.LayoutType.COL_MAJOR, "H": lt.LayoutType.HILBERT, "U": lt.LayoutType.UNORDERED, None: lt.LayoutType.ROW_MAJOR, # default (fixed in SC-27374) } ) class ArraySchema(CtxMixin, lt.ArraySchema): """ Schema class for TileDB dense / sparse array representations :param domain: Domain of schema :param attrs: tuple of attributes :param cell_order: TileDB label for cell layout :param tile_order: TileDB label for tile layout :param int capacity: tile cell capacity :param offsets_filters: (default None) offsets filter list :param validity_filters: (default None) validity filter list :param bool allows_duplicates: True if duplicates are allowed :param bool sparse: True if schema is sparse, else False \ (set by SparseArray and DenseArray derived classes) :param dim_labels: dict(dim_index, dict(dim_name, tiledb.DimSchema)) :param enums: list of enumeration names :param tiledb.Ctx ctx: A TileDB Context :raises: :py:exc:`tiledb.TileDBError` """ def __init__( self, domain: Domain = None, attrs: Sequence[Attr] = (), cell_order: str = "row-major", tile_order: str = "row-major", capacity: int = 0, coords_filters: Union[FilterList, Sequence[Filter]] = None, offsets_filters: Union[FilterList, Sequence[Filter]] = None, validity_filters: Union[FilterList, Sequence[Filter]] = None, allows_duplicates: bool = False, sparse: bool = False, dim_labels={}, enums=None, ctx: Ctx = None, ): super().__init__(ctx, lt.ArrayType.SPARSE if sparse else lt.ArrayType.DENSE) if enums is not None: for enum_name in enums: self._add_enumeration(self._ctx, enum_name) if attrs is not None: for att in attrs: if not isinstance(att, Attr): raise TypeError( "Cannot create schema with non-Attr value for 'attrs' argument" ) self._add_attr(att) try: self._cell_order = _string_to_tiledb_order.get(cell_order) except (TypeError, ValueError): raise ValueError(f"unknown tiledb layout: {cell_order}") try: self._tile_order = _string_to_tiledb_order.get(tile_order) except (TypeError, ValueError): raise ValueError(f"unknown tiledb layout: {tile_order}") if capacity > 0: self._capacity = capacity if coords_filters is not None: warnings.warn( "coords_filters is deprecated; set the FilterList for each dimension", DeprecationWarning, ) self._coords_filters = FilterList() dims_with_coords_filters = [] for dim in domain: dim._filters = FilterList(coords_filters) dims_with_coords_filters.append(dim) domain = Domain(dims_with_coords_filters) if domain is not None: self._domain = domain if offsets_filters is not None: self._offsets_filters = FilterList(offsets_filters) if validity_filters is not None: self._validity_filters = FilterList(validity_filters) self._allows_dups = allows_duplicates for dim_index, labels_on_dim in dim_labels.items(): for label_name, label_schema in labels_on_dim.items(): self._add_dim_label(self._ctx, label_name, dim_index, label_schema) self._check() @classmethod def load(cls, uri, ctx: Ctx = None, key: str = None): if not ctx: ctx = default_ctx() args = [ctx, uri] if key is not None: args.extend((lt.EncryptionType.AES_256_GCM, key)) return cls.from_pybind11(ctx, lt.ArraySchema(*args)) @classmethod def from_file(cls, uri: str = None, ctx: Ctx = None): """Create an ArraySchema for a Filestore Array from a given file. If a uri is not given, then create a default schema.""" schema = lt.Filestore._schema_create(ctx or default_ctx(), uri) return cls.from_pybind11(ctx, schema) def __eq__(self, other): """Instance is equal to another ArraySchema""" if not isinstance(other, ArraySchema): return False if not ( self.sparse == other.sparse and self.cell_order == other.cell_order and self.tile_order == other.tile_order and self.capacity == other.capacity and self.coords_filters == other.coords_filters and self.offsets_filters == other.offsets_filters and self.validity_filters == other.validity_filters and self.nattr == other.nattr and self.domain == other.domain ): return False if self.sparse and self.allows_duplicates != other.allows_duplicates: return False for i in range(self.nattr): if self.attr(i) != other.attr(i): return False return True def __len__(self): """Returns the number of Attributes in the ArraySchema""" return self._nattr def __iter__(self): """Returns a generator object that iterates over the ArraySchema's Attribute objects""" return (self.attr(i) for i in range(self.nattr)) @property def ctx(self) -> Ctx: """The array schema's context :rtype: tiledb.Ctx """ return self._ctx def check(self) -> bool: """Checks the correctness of the array schema :rtype: None :raises: :py:exc:`tiledb.TileDBError` if invalid """ return self._check() @property def sparse(self) -> bool: """True if the array is a sparse array representation :rtype: bool :raises: :py:exc:`tiledb.TileDBError` """ return self._array_type == lt.ArrayType.SPARSE @property def allows_duplicates(self) -> bool: """Returns True if the (sparse) array allows duplicates.""" if not self.sparse: raise lt.TileDBError( "ArraySchema.allows_duplicates does not apply to dense arrays" ) return self._allows_dups @property def capacity(self) -> int: """The array capacity :rtype: int :raises: :py:exc:`tiledb.TileDBError` """ return self._capacity @property def cell_order(self) -> str: """The cell order layout of the array. :rtype: str """ return _tiledb_order_to_string[self._cell_order] @property def tile_order(self) -> str: """The tile order layout of the array. :rtype: str :raises: :py:exc:`tiledb.TileDBError` """ layout_string = _tiledb_order_to_string[self._tile_order] return layout_string if self.cell_order != "hilbert" else None @property def offsets_filters(self) -> FilterList: """The FilterList for the array's variable-length attribute offsets :rtype: tiledb.FilterList :raises: :py:exc:`tiledb.TileDBError` """ return FilterList.from_pybind11(self._ctx, self._offsets_filters) @property def coords_filters(self) -> FilterList: """The FilterList for the array's coordinates :rtype: tiledb.FilterList :raises: :py:exc:`tiledb.TileDBError` """ return FilterList.from_pybind11(self._ctx, self._coords_filters) @coords_filters.setter def coords_filters(self, value): warnings.warn( "coords_filters is deprecated; set the FilterList for each dimension", DeprecationWarning, ) @property def validity_filters(self) -> FilterList: """The FilterList for the array's validity :rtype: tiledb.FilterList :raises: :py:exc:`tiledb.TileDBError` """ return FilterList.from_pybind11(self._ctx, self._validity_filters) @property def domain(self) -> Domain: """The Domain associated with the array. :rtype: tiledb.Domain :raises: :py:exc:`tiledb.TileDBError` """ return Domain.from_pybind11(self._ctx, self._domain) @property def nattr(self) -> int: """The number of array attributes. :rtype: int :raises: :py:exc:`tiledb.TileDBError` """ return self._nattr @property def ndim(self) -> int: """The number of array domain dimensions. :rtype: int """ return self.domain.ndim @property def shape(self) -> Tuple[np.dtype, np.dtype]: """The array's shape :rtype: tuple(numpy scalar, numpy scalar) :raises TypeError: floating point (inexact) domain """ return self.domain.shape @property def version(self) -> int: """The array's schema (storage) version. :rtype: int :raises: :py:exc:`tiledb.TileDBError` """ return self._version def _needs_var_buffer(self, name: str) -> bool: """ Returns true if the given attribute or dimension is var-sized :param name: :rtype: bool """ if self.has_attr(name): return self.attr(name).isvar elif self.domain.has_dim(name): return self.domain.dim(name).isvar else: raise ValueError( f"Requested name '{name}' is not an attribute or dimension" ) def attr(self, key: Union[str, int]) -> Attr: """Returns an Attr instance given an int index or string label :param key: attribute index (positional or associative) :type key: int or str :rtype: tiledb.Attr :return: The ArraySchema attribute at index or with the given name (label) :raises TypeError: invalid key type """ if isinstance(key, str): return Attr.from_pybind11(self._ctx, self._attr(key)) elif isinstance(key, numbers.Integral): return Attr.from_pybind11(self._ctx, self._attr(int(key))) raise TypeError( "attr indices must be a string name, " "or an integer index, not {0!r}".format(type(key)) ) def dim_label(self, name: str) -> DimLabel: """Returns a TileDB DimensionLabel given the label name :param name: name of the dimensin label :return: The dimension label associated with the given name """ return DimLabel.from_pybind11(self._ctx, self._dim_label(self._ctx, name)) def has_attr(self, name: str) -> bool: """Returns true if the given name is an Attribute of the ArraySchema :param name: attribute name :rtype: boolean """ return self._has_attribute(name) def has_dim_label(self, name: str) -> bool: """Returns true if the given name is a DimensionLabel of the ArraySchema Note: If using an version of libtiledb that does not support dimension labels this will return false. :param name: dimension label name :rtype: boolean """ return self._has_dim_label(self._ctx, name) if libtiledb_version()[0] == 2 and libtiledb_version()[1] >= 25: @property def current_domain(self) -> CurrentDomain: """Get the current domain :rtype: tiledb.CurrentDomain """ curr_dom = CurrentDomain.from_pybind11( self._ctx, self._current_domain(self._ctx) ) curr_dom._set_domain(self.domain) return curr_dom def set_current_domain(self, current_domain): """Set the current domain :param current_domain: The current domain to set :type current_domain: tiledb.CurrentDomain """ self._set_current_domain(self._ctx, current_domain) def attr_or_dim_dtype(self, name: str) -> bool: if self.has_attr(name): dtype = self.attr(name).dtype elif self.domain.has_dim(name): dtype = self.domain.dim(name).dtype else: raise lt.TileDBError(f"Unknown attribute or dimension ('{name}')") if dtype.itemsize == 0: # special handling for flexible numpy dtypes: change itemsize from 0 to 1 dtype = np.dtype((dtype, 1)) return dtype def dump(self): """Dumps a string representation of the array object to standard output (stdout)""" print(self._dump(), "\n") def __repr__(self): # use safe repr if pybind11 constructor failed or the array schema did # not construct properly try: self._check() except lt.TileDBError: return object.__repr__(self) if self._ctx is None: return object.__repr__(self) # TODO support/use __qualname__ output = io.StringIO() output.write("ArraySchema(\n") output.write(" domain=Domain(*[\n") for i in range(self.domain.ndim): output.write(f" {repr(self.domain.dim(i))},\n") output.write(" ]),\n") output.write(" attrs=[\n") for i in range(self.nattr): output.write(f" {repr(self.attr(i))},\n") output.write(" ],\n") output.write( f" cell_order='{self.cell_order}',\n" f" tile_order={repr(self.tile_order)},\n" ) if self.sparse: output.write(f" capacity={self.capacity},\n") output.write(f" sparse={self.sparse},\n") if self.sparse: output.write(f" allows_duplicates={self.allows_duplicates},\n") output.write(")\n") return output.getvalue() def _repr_html_(self): output = io.StringIO() output.write("") output.write("") output.write(f"") output.write("") output.write("") output.write("") output.write("") output.write("") output.write(f"") output.write("") output.write(f"") if self.sparse: output.write("") output.write(f"") output.write("") output.write(f"") if self.sparse: output.write("") output.write(f"") output.write("
Domain
{self.domain._repr_html_()}
Attributes
") output.write("") output.write("") output.write("") output.write("") output.write("") output.write("") output.write("") output.write("") for i in range(self.nattr): output.write(f"{self.attr(i)._repr_html_row_only_()}") output.write("
NameData TypeIs Var-LenIs NullableFilters
") output.write("
Cell Order
{self.cell_order}
Tile Order
{self.tile_order}
Capacity
{self.capacity}
Sparse
{self.sparse}
Allows DuplicatesK/th>
{self.allows_duplicates}
") return output.getvalue()