import os import pprint import warnings import tiledb from tiledb.libtiledb import version as libtiledb_version from .main import PyFragmentInfo """ Classes and functions relating to TileDB fragments. """ class FragmentInfoList: """ Class representing an ordered list of FragmentInfo objects. :param array_uri: URI for the TileDB array (any supported TileDB URI) :type array_uri: str :param include_mbrs: (default False) include minimum bounding rectangles in FragmentInfo result :type include_mbrs: bool :param ctx: A TileDB context :type ctx: tiledb.Ctx :ivar uri: URIs of fragments :ivar version: Fragment version of each fragment :ivar nonempty_domain: Non-empty domain of each fragment :ivar cell_num: Number of cells in each fragment :ivar timestamp_range: Timestamp range of when each fragment was written :ivar sparse: For each fragment, True if fragment is sparse, else False :ivar has_consolidated_metadata: For each fragment, True if fragment has consolidated fragment metadata, else False :ivar unconsolidated_metadata_num: Number of unconsolidated metadata fragments in each fragment :ivar to_vacuum: URIs of already consolidated fragments to vacuum :ivar mbrs: (TileDB Embedded 2.5.0+ only) The mimimum bounding rectangle of each fragment; only present when `include_mbrs=True` :ivar array_schema_name: (TileDB Embedded 2.5.0+ only) The array schema's name **Example:** >>> import tiledb, numpy as np, tempfile >>> with tempfile.TemporaryDirectory() as tmp: ... # The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4] and space tiles 2x2 ... dom = tiledb.Domain( ... tiledb.Dim(name="rows", domain=(1, 4), tile=2, dtype=np.int32), ... tiledb.Dim(name="cols", domain=(1, 4), tile=2, dtype=np.int32), ... ) ... # The array will be dense with a single attribute "a" so each (i,j) cell can store an integer. ... schema = tiledb.ArraySchema( ... domain=dom, sparse=False, attrs=[tiledb.Attr(name="a", dtype=np.int32)] ... ) ... # Set URI of the array ... uri = tmp + "/array" ... # Create the (empty) array on disk. ... tiledb.Array.create(uri, schema) ... ... # Write three fragments to the array ... with tiledb.DenseArray(uri, mode="w") as A: ... A[1:3, 1:5] = np.array(([[1, 2, 3, 4], [5, 6, 7, 8]])) ... with tiledb.DenseArray(uri, mode="w") as A: ... A[2:4, 2:4] = np.array(([101, 102], [103, 104])) ... with tiledb.DenseArray(uri, mode="w") as A: ... A[3:4, 4:5] = np.array(([202])) ... ... # tiledb.array_fragments() requires TileDB-Py version > 0.8.5 ... fragments_info = tiledb.array_fragments(uri) ... ... "====== FRAGMENTS INFO ======" ... f"number of fragments: {len(fragments_info)}" ... f"nonempty domains: {fragments_info.nonempty_domain}" ... f"sparse fragments: {fragments_info.sparse}" ... ... for fragment in fragments_info: ... f"===== FRAGMENT NUMBER {fragment.num} =====" ... f"is sparse: {fragment.sparse}" ... f"cell num: {fragment.cell_num}" ... f"has consolidated metadata: {fragment.has_consolidated_metadata}" ... f"nonempty domain: {fragment.nonempty_domain}" '====== FRAGMENTS INFO ======' 'number of fragments: 3' 'nonempty domains: (((1, 2), (1, 4)), ((2, 3), (2, 3)), ((3, 3), (4, 4)))' 'sparse fragments: (False, False, False)' '===== FRAGMENT NUMBER 0 =====' 'is sparse: False' 'cell num: 8' 'has consolidated metadata: False' 'nonempty domain: ((1, 2), (1, 4))' '===== FRAGMENT NUMBER 1 =====' 'is sparse: False' 'cell num: 16' 'has consolidated metadata: False' 'nonempty domain: ((2, 3), (2, 3))' '===== FRAGMENT NUMBER 2 =====' 'is sparse: False' 'cell num: 4' 'has consolidated metadata: False' 'nonempty domain: ((3, 3), (4, 4))' """ def __init__(self, array_uri, include_mbrs=False, ctx=None): if ctx is None: ctx = tiledb.default_ctx() schema = tiledb.ArraySchema.load(array_uri, ctx=ctx) self.array_uri = array_uri fi = PyFragmentInfo(self.array_uri, schema, include_mbrs, ctx) self.__nums = fi.get_num_fragments() self.uri = fi.get_uri() self.version = fi.get_version() self.nonempty_domain = fi.get_nonempty_domain() self.cell_num = fi.get_cell_num() self.timestamp_range = fi.get_timestamp_range() self.sparse = fi.get_sparse() self.unconsolidated_metadata_num = fi.get_unconsolidated_metadata_num() self.has_consolidated_metadata = fi.get_has_consolidated_metadata() self.to_vacuum = fi.get_to_vacuum() if include_mbrs: if libtiledb_version() >= (2, 5, 0): self.mbrs = fi.get_mbrs() else: warnings.warn( "MBRs for fragments not available; " "please install libtiledb 2.5.0+", UserWarning, ) if libtiledb_version() >= (2, 5, 0): self.array_schema_name = fi.get_array_schema_name() def __getattr__(self, name): if name == "mbrs": raise AttributeError( "'FragmentInfoList' object has no attribute 'mbrs'. " "(Hint: retrieving minimum bounding rectangles is disabled " "by default to optimize speed and space. " "Use tiledb.array_fragments(include_mbrs=True) to enable)" ) return self.__getattribute__(name) def __iter__(self): return FragmentsInfoIterator(self) def __getitem__(self, key): if isinstance(key, slice): # Get the start, stop, and step from the slice return [FragmentInfo(self, idx) for idx in range(*key.indices(len(self)))] elif isinstance(key, int): return FragmentInfo(self, key) else: raise TypeError("Invalid argument type.") def __len__(self): return self.__nums def __repr__(self): public_attrs = { key: value for (key, value) in self.__dict__.items() if not key.startswith("_") } return pprint.PrettyPrinter().pformat(public_attrs) def _repr_html_(self) -> str: from io import StringIO output = StringIO() output.write("
\n") output.write(f"

Fragments for {self.array_uri}

\n") for frag in self: output.write("
\n") output.write(f"{frag.uri}\n") output.write(frag._repr_html_()) output.write("
\n") output.write("
\n") return output.getvalue() class FragmentsInfoIterator: """ Iterator class for the FragmentsInfo container. """ def __init__(self, fragments): self._fragments = fragments self._index = 0 def __next__(self): if self._index < len(self._fragments): fi = FragmentInfo(self._fragments, self._index) self._index += 1 return fi raise StopIteration class FragmentInfo: """ Class representing the metadata for a single fragment. See :py:class:`tiledb.FragmentInfoList` for example of usage. :ivar uri: URIs of fragments :ivar version: Fragment version of each fragment :ivar nonempty_domain: Non-empty domain of each fragment :ivar cell_num: Number of cells in each fragment :ivar timestamp_range: Timestamp range of when each fragment was written :ivar sparse: For each fragment, True if fragment is sparse, else False :ivar has_consolidated_metadata: For each fragment, True if fragment has consolidated fragment metadata, else False :ivar unconsolidated_metadata_num: Number of unconsolidated metadata fragments in each fragment :ivar to_vacuum: URIs of already consolidated fragments to vacuum :ivar mbrs: (TileDB Embedded 2.5.0+ only) The mimimum bounding rectangle of each fragment; only present when `include_mbrs=True` :ivar array_schema_name: (TileDB Embedded 2.5.0+ only) The array schema's name """ def __init__(self, fragments: FragmentInfoList, num): self.num = num self.uri = fragments.uri[num] self.version = fragments.version[num] self.nonempty_domain = fragments.nonempty_domain[num] self.cell_num = fragments.cell_num[num] self.timestamp_range = fragments.timestamp_range[num] self.sparse = fragments.sparse[num] self.has_consolidated_metadata = fragments.has_consolidated_metadata[num] self.unconsolidated_metadata_num = fragments.unconsolidated_metadata_num if hasattr(fragments, "mbrs"): self.mbrs = fragments.mbrs[num] if hasattr(fragments, "array_schema_name"): self.array_schema_name = fragments.array_schema_name[num] def __repr__(self): public_attrs = { key: value for (key, value) in self.__dict__.items() if not key.startswith("_") } return pprint.PrettyPrinter().pformat(public_attrs) def _repr_html_(self) -> str: from io import StringIO output = StringIO() output.write("
\n") output.write("\n") for key in self.__dict__: if not key.startswith("_"): output.write("\n") output.write(f"\n") output.write(f"\n") output.write("\n") output.write("
{key}{self.__dict__[key]}
\n") output.write("
\n") return output.getvalue() def __getattr__(self, name): if name == "mbrs": raise AttributeError( "'FragmentInfo' object has no attribute 'mbrs'. " "(Hint: retrieving minimum bounding rectangles is disabled " "by default to optimize speed and space. " "Use tiledb.array_fragments(include_mbrs=True) to enable)" ) return self.__getattribute__(name) def create_array_from_fragments( src_uri, dst_uri, timestamp_range, config=None, ctx=None, verbose=False, dry_run=False, ): """ (POSIX only). Create a new array from an already existing array by selecting fragments that fall withing a given timestamp_range. The original array is located at src_uri and the new array is created at dst_uri. :param str src_uri: URI for the source TileDB array (any supported TileDB URI) :param str dst_uri: URI for the newly created TileDB array (any supported TileDB URI) :param (int, int) timestamp_range: (default None) If not None, vacuum the array using the given range (inclusive) :param config: Override the context configuration. Defaults to ctx.config() :param ctx: (optional) TileDB Ctx :param verbose: (optional) Print fragments being copied (default: False) :param dry_run: (optional) Preview fragments to be copied without running (default: False) """ if tiledb.array_exists(dst_uri): raise tiledb.TileDBError(f"Array URI `{dst_uri}` already exists") if not isinstance(timestamp_range, tuple) and len(timestamp_range) != 2: raise TypeError( "'timestamp_range' argument expects tuple(start: int, end: int)" ) if not ctx: ctx = tiledb.default_ctx() if config is None: config = tiledb.Config(ctx.config()) vfs = tiledb.VFS(config=config, ctx=ctx) fragment_info = tiledb.array_fragments(src_uri) if len(fragment_info) < 1: print("Cannot create new array; no fragments to copy") return if verbose or dry_run: print(f"Creating directory for array at {dst_uri}\n") if not dry_run: vfs.create_dir(dst_uri) src_lock = os.path.join(src_uri, "__lock.tdb") dst_lock = os.path.join(dst_uri, "__lock.tdb") if verbose or dry_run: print(f"Copying lock file {dst_uri}\n") if not dry_run: vfs.copy_file(f"{src_lock}", f"{dst_lock}") list_new_style_schema = [ver >= 10 for ver in fragment_info.version] is_mixed_versions = len(set(list_new_style_schema)) > 1 if is_mixed_versions: raise tiledb.TileDBError( "Cannot copy fragments - this array contains a mix of old and " "new style schemas" ) is_new_style_schema = list_new_style_schema[0] for frag in fragment_info: if not ( timestamp_range[0] <= frag.timestamp_range[0] and frag.timestamp_range[1] <= timestamp_range[1] ): continue schema_name = frag.array_schema_name if is_new_style_schema: schema_name = os.path.join("__schema", schema_name) src_schema = os.path.join(src_uri, schema_name) dst_schema = os.path.join(dst_uri, schema_name) if verbose or dry_run: print(f"Copying schema `{src_schema}` to `{dst_schema}`\n") if not dry_run: if is_new_style_schema: new_style_schema_uri = os.path.join(dst_uri, "__schema") if not vfs.is_dir(new_style_schema_uri): vfs.create_dir(new_style_schema_uri) if not vfs.is_file(dst_schema): vfs.copy_file(src_schema, dst_schema) base_name = os.path.basename(frag.uri) if frag.version < 12: frag_name = base_name else: vfs.create_dir(os.path.join(dst_uri, "__fragments")) frag_name = os.path.join("__fragments", base_name) src_frag = os.path.join(src_uri, frag_name) dst_frag = os.path.join(dst_uri, frag_name) if frag.version < 12: ok_or_wrt_name = f"{base_name}.ok" else: vfs.create_dir(os.path.join(dst_uri, "__commits")) ok_or_wrt_name = os.path.join("__commits", f"{base_name}.wrt") src_ok_or_wrt = os.path.join(src_uri, ok_or_wrt_name) dst_ok_or_wrt = os.path.join(dst_uri, ok_or_wrt_name) if verbose or dry_run: print(f"Copying `{src_frag}` to `{dst_frag}`\n") print(f"Copying `{src_ok_or_wrt}` to `{dst_ok_or_wrt}`\n") if not dry_run: vfs.copy_dir(src_frag, dst_frag) vfs.copy_file(src_ok_or_wrt, dst_ok_or_wrt) def copy_fragments_to_existing_array( src_uri, dst_uri, timestamp_range, config=None, ctx=None, verbose=False, dry_run=False, ): """ (POSIX only). Copy fragments from an array at src_uri to another array at dst_uri by selecting fragments that fall withing a given timestamp_range. :param str src_uri: URI for the source TileDB array (any supported TileDB URI) :param str dst_uri: URI for the destination TileDB array (any supported TileDB URI) :param (int, int) timestamp_range: (default None) If not None, vacuum the array using the given range (inclusive) :param config: Override the context configuration. Defaults to ctx.config() :param ctx: (optional) TileDB Ctx :param verbose: (optional) Print fragments being copied (default: False) :param dry_run: (optional) Preview fragments to be copied without running (default: False) """ if not tiledb.array_exists(dst_uri): raise tiledb.TileDBError(f"Array URI `{dst_uri}` does not exist") if not isinstance(timestamp_range, tuple) and len(timestamp_range) != 2: raise TypeError( "'timestamp_range' argument expects tuple(start: int, end: int)" ) if not ctx: ctx = tiledb.default_ctx() if config is None: config = tiledb.Config(ctx.config()) vfs = tiledb.VFS(config=config, ctx=ctx) dst_schema_file = os.path.join(dst_uri, "__array_schema.tdb") src_schema_file = os.path.join(src_uri, "__array_schema.tdb") dst_schema_dir = os.path.join(dst_uri, "__schema") src_schema_dir = os.path.join(src_uri, "__schema") is_old_style = vfs.is_file(dst_schema_file) and vfs.is_file(src_schema_file) is_new_style = vfs.is_dir(dst_schema_dir) and vfs.is_dir(src_schema_dir) if is_old_style and is_new_style: raise tiledb.TileDBError( "Mix of old and new style schemas detected. There can only be " "one schema version present in both the source and destination " "arrays and both must be identical" ) elif is_new_style: def filtered_schema_dir(uri): return [x for x in vfs.ls(uri) if "__enumerations" not in x] if ( len(filtered_schema_dir(dst_schema_dir)) != 1 or len(filtered_schema_dir(src_schema_dir)) != 1 ): raise tiledb.TileDBError( "Mutltiple evolved schemas detected. There can only be one " "schema version present in both the source and destination " "arrays and both must be identical" ) schema_name = os.path.basename(vfs.ls(src_schema_dir)[0]) src_schema = os.path.join(src_uri, "__schema", schema_name) dst_schema = os.path.join(dst_uri, "__schema", schema_name) if tiledb.ArraySchema.load(src_uri) != tiledb.ArraySchema.load(dst_uri): raise tiledb.TileDBError( "The source and destination array must have matching schemas." ) if is_new_style: if verbose or dry_run: print(f"Copying schema `{src_schema}` to `{dst_schema}`\n") if not dry_run: vfs.copy_file(src_schema, dst_schema) array_fragments = tiledb.array_fragments(src_uri) for frag in array_fragments: if not ( timestamp_range[0] <= frag.timestamp_range[0] and frag.timestamp_range[1] <= timestamp_range[1] ): continue base_name = os.path.basename(frag.uri) if frag.version < 12: frag_name = base_name else: vfs.create_dir(os.path.join(dst_uri, "__fragments")) frag_name = os.path.join("__fragments", base_name) src_frag = os.path.join(src_uri, frag_name) dst_frag = os.path.join(dst_uri, frag_name) if frag.version < 12: ok_or_wrt_name = f"{base_name}.ok" else: ok_or_wrt_name = os.path.join("__commits", f"{base_name}.wrt") src_ok_or_wrt = os.path.join(src_uri, ok_or_wrt_name) dst_ok_or_wrt = os.path.join(dst_uri, ok_or_wrt_name) if src_frag == dst_frag: if verbose or dry_run: print( f"Fragment {src_frag} not copied. Already exists in " "destination array.\n" ) continue if verbose or dry_run: print(f"Copying `{src_frag}` to `{dst_frag}`\n") print(f"Copying `{src_ok_or_wrt}` to `{dst_ok_or_wrt}`\n") if not dry_run: vfs.copy_dir(src_frag, dst_frag) vfs.copy_file(src_ok_or_wrt, dst_ok_or_wrt)