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("| Domain |
")
output.write(f"| {self.domain._repr_html_()} |
")
output.write("| Attributes |
")
output.write("")
output.write("")
output.write("")
output.write("")
output.write("| Name | ")
output.write("Data Type | ")
output.write("Is Var-Len | ")
output.write("Is Nullable | ")
output.write("Filters | ")
output.write(" ")
for i in range(self.nattr):
output.write(f"{self.attr(i)._repr_html_row_only_()}")
output.write(" ")
output.write(" | ")
output.write("
")
output.write("| Cell Order |
")
output.write(f"| {self.cell_order} |
")
output.write("| Tile Order |
")
output.write(f"| {self.tile_order} |
")
if self.sparse:
output.write("| Capacity |
")
output.write(f"| {self.capacity} |
")
output.write("| Sparse |
")
output.write(f"| {self.sparse} |
")
if self.sparse:
output.write("| Allows DuplicatesK/th> |
")
output.write(f"| {self.allows_duplicates} |
")
output.write("
")
return output.getvalue()