From bff6880121a1e15788ffdb3760361a31667e81c8 Mon Sep 17 00:00:00 2001 From: Trevor Manz Date: Wed, 12 Feb 2025 13:48:43 -0500 Subject: [PATCH] Add `higlass.tilesets.register` decorator (#172) * Add `higlass.tilesets.register` decorator Refactors tileset implementations by introducing the `higlass.tilesets.register` decorator. When applied to a class implementing `TilesetProtocol`, this decorator adds a `track()` method, enabling track creation while automatically registering the tileset instance in the global `TilesetRegistry`. --- src/higlass/__init__.py | 12 +- src/higlass/_tileset_registry.py | 79 +-- src/higlass/_widget.py | 5 + src/higlass/tilesets.py | 316 +++++----- test/test_scale.py | 3 +- test/test_tileset_registery.py | 65 ++- uv.lock | 975 +------------------------------ 7 files changed, 253 insertions(+), 1202 deletions(-) diff --git a/src/higlass/__init__.py b/src/higlass/__init__.py index 59f1e15..d99942f 100644 --- a/src/higlass/__init__.py +++ b/src/higlass/__init__.py @@ -10,15 +10,7 @@ from higlass_schema import * -import higlass.tilesets -from higlass._tileset_registry import create_jupyter_track_helper +import higlass.tilesets as tilesets from higlass.api import * from higlass.fuse import fuse -from higlass.tilesets import remote - -bigwig = create_jupyter_track_helper(higlass.tilesets.bigwig) -multivec = create_jupyter_track_helper(higlass.tilesets.multivec) -cooler = create_jupyter_track_helper(higlass.tilesets.cooler) -hitile = create_jupyter_track_helper(higlass.tilesets.hitile) -bed2ddb = create_jupyter_track_helper(higlass.tilesets.bed2ddb) -beddb = create_jupyter_track_helper(higlass.tilesets.beddb) +from higlass.tilesets import bed2ddb, beddb, bigwig, cooler, hitile, multivec, remote diff --git a/src/higlass/_tileset_registry.py b/src/higlass/_tileset_registry.py index bf0cbbc..0b8567f 100644 --- a/src/higlass/_tileset_registry.py +++ b/src/higlass/_tileset_registry.py @@ -1,38 +1,44 @@ from __future__ import annotations -import functools import typing import weakref -from dataclasses import dataclass -from typing_extensions import ParamSpec +__all__ = ["TilesetInfo", "TilesetProtocol", "TilesetRegistry"] -import higlass.api -from higlass._utils import datatype_default_track -if typing.TYPE_CHECKING: - from higlass.tilesets import LocalTileset, TrackType +class Transform(typing.TypedDict): + name: str + value: str -__all__ = [ - "JupyterTrackHelper", - "TilesetRegistry", - "create_jupyter_track_helper", -] +class TilesetInfo(typing.TypedDict): + resolutions: tuple[int, ...] + transforms: list[Transform] + max_pos: list[int] + min_pos: list[int] + chromsizes: list[tuple[str, int]] + + +class TilesetProtocol(typing.Protocol): + def tiles(self, tile_ids: typing.Sequence[str], /) -> list[dict]: ... + + def info(self) -> TilesetInfo: ... class TilesetRegistry: - _registry: weakref.WeakValueDictionary[str, LocalTileset] = ( + _registry: weakref.WeakValueDictionary[str, TilesetProtocol] = ( weakref.WeakValueDictionary() ) @classmethod - def add(cls, tileset: LocalTileset) -> None: + def add(cls, tileset: TilesetProtocol) -> str: """Register a tileset with a given ID.""" - cls._registry[tileset.uid] = tileset + uid = f"hg_{id(tileset):x}" + cls._registry[uid] = tileset + return uid @classmethod - def get(cls, tileset_id: str) -> LocalTileset: + def get(cls, tileset_id: str) -> TilesetProtocol: """Retrieve a tileset by its ID, or None if it no longer exists.""" tileset = cls._registry.get(tileset_id) if tileset is None: @@ -42,44 +48,3 @@ def get(cls, tileset_id: str) -> LocalTileset: @classmethod def clear(cls) -> None: cls._registry.clear() - - -@dataclass(frozen=True) -class JupyterTrackHelper: - tileset: LocalTileset - - def track(self, type_: TrackType | None = None, **kwargs): - # use default track based on datatype if available - if type_ is None: - if getattr(self.tileset, "datatype", None) is None: - raise ValueError("No default track for tileset") - else: - type_ = typing.cast( - TrackType, datatype_default_track[self.tileset.datatype] - ) - track = higlass.api.track( - type_=type_, - server="jupyter", - tilesetUid=self.tileset.uid, - **kwargs, - ) - if self.tileset.name: - track.opts(name=self.tileset.name, inplace=True) - return track - - -_P = ParamSpec("_P") - - -def create_jupyter_track_helper( - tileset_fn: typing.Callable[_P, LocalTileset], -) -> typing.Callable[_P, JupyterTrackHelper]: - """Create a top-level helper function that adds the tileset to the factory.""" - - @functools.wraps(tileset_fn) - def wrapper(*args: typing.Any, **kwargs: typing.Any) -> JupyterTrackHelper: - tileset = tileset_fn(*args, **kwargs) - TilesetRegistry.add(tileset) - return JupyterTrackHelper(tileset) - - return wrapper # type: ignore diff --git a/src/higlass/_widget.py b/src/higlass/_widget.py index a800515..722a366 100644 --- a/src/higlass/_widget.py +++ b/src/higlass/_widget.py @@ -4,6 +4,7 @@ import functools import itertools import json +import logging import os import pathlib import typing @@ -17,6 +18,8 @@ __all__ = ["HiGlassWidget"] +logger = logging.getLogger("higlass.widget") + class TilesetInfo(pydantic.BaseModel): """A tileset_info request payload.""" @@ -59,8 +62,10 @@ def get_instance(cls): def _handle_custom_message(self, widget, msg, buffers): message = CustomMessage(**msg) + logger.debug("handle_custom_message: %s", message) def respond_with(payload: object): + logger.debug("handle_custom_message::respond_with: %s", message.id) self.send({"id": message.id, "payload": payload}) def process_message(): diff --git a/src/higlass/tilesets.py b/src/higlass/tilesets.py index 5631477..14cfd63 100644 --- a/src/higlass/tilesets.py +++ b/src/higlass/tilesets.py @@ -1,53 +1,118 @@ from __future__ import annotations import functools -import hashlib import pathlib import typing from dataclasses import dataclass -from typing import IO -from ._utils import TrackType -from .api import track +import higlass.api +from higlass._tileset_registry import TilesetInfo, TilesetProtocol, TilesetRegistry +from higlass._utils import TrackType, datatype_default_track __all__ = [ - "LocalTileset", - "RemoteTileset", - "remote", + "bed2ddb", "bigwig", - "multivec", "cooler", "hitile", - "bed2ddb", + "multivec", + "register", + "remote", ] -DataType = typing.Literal["vector", "multivec", "matrix"] - +DataType = typing.Literal[ + "2d-rectangle-domains", + "bedlike", + "chromsizes", + "gene-annotations", + "matrix", + "multivec", + "vector", +] -class LocalTileset: - def __init__( - self, - datatype: DataType, - tiles: typing.Callable[[typing.Sequence[str]], list[typing.Any]], - info: typing.Callable[[], typing.Any], - uid: str, - name: str | None = None, - ): - self.datatype = datatype - self._tiles = tiles - self._info = info - self._uid = uid - self.name = name +T = typing.TypeVar("T", bound=TilesetProtocol) + + +def register(klass: type[T]) -> type[T]: + """Decorator that adds a `track` method to a class implementing `TilesetProtocol`. + + The `track` method automatically registers the tileset with the `TilesetRegistry` + and returns a HiGlass track object, which can be used for visualization. + + Parameters + ---------- + klass : type[T] + A class that implements `TilesetProtocol`. + + Returns + ------- + type[T] + The input class, now with an added `track` method. + + Examples + -------- + >>> from dataclasses import dataclass + >>> from clodius.tiles.cooler import tiles, tileset_info + >>> + >>> @register + >>> @dataclass + >>> class MyCoolerTileset: + >>> filepath: str + >>> datatype = "matrix" + >>> + >>> def info(self): + >>> return tileset_info(self.filepath) + >>> + >>> def tiles(self, tile_ids): + >>> return tiles(self.filepath, tile_ids) + >>> + >>> tileset = MyCoolerTileset("test.mcool") + >>> track = tileset.track("heatmap") + """ + + def track( + self: TilesetProtocol, type_: TrackType | None = None, /, **kwargs + ) -> higlass.api.Track: + """ + Create a HiGlass track for the tileset. + + Registers the tileset with the `TilesetRegistry` and returns a track + of the given `type_`. Defaults to a type based on the tileset's `datatype` + if not specified. + + Parameters + ---------- + type_ : TrackType, optional + Track type. If `None`, a default is inferred. + + Returns + ------- + higlass.api.Track + The configured HiGlass track. + """ + # use default track based on datatype if available + if type_ is None: + datatype = getattr(self, "datatype", None) + if datatype is None: + raise ValueError("No default track for tileset") + else: + type_ = typing.cast(TrackType, datatype_default_track[datatype]) - @property - def uid(self) -> str: - return self._uid + # add tileset registry and get an identifier + uid = TilesetRegistry.add(self) + track = higlass.api.track( + type_=type_, + server="jupyter", + tilesetUid=uid, + **kwargs, + ) + name = getattr(self, "name", None) + if name is not None: + track.opts(name=name, inplace=True) - def tiles(self, tile_ids: typing.Sequence[str]) -> list[typing.Any]: - return self._tiles(tile_ids) + return track - def info(self) -> typing.Any: - return self._info() + setattr(klass, "track", track) + return klass @dataclass @@ -57,135 +122,76 @@ class RemoteTileset: name: str | None = None def track(self, type_: TrackType, **kwargs): - t = track( + track = higlass.api.track( type_=type_, server=self.server, tilesetUid=self.uid, **kwargs, ) - if self.name: - t.opts(name=self.name, inplace=True) - return t - - -def remote(uid: str, server: str = "https://higlass.io/api/v1", **kwargs): - return RemoteTileset(uid, server, **kwargs) - - -def hash_file_as_default_uid(fn: typing.Callable[[str | IO[bytes], str], LocalTileset]): - def wrapper(file: str | IO[bytes], uid: None | str = None): - if uid is None: - if isinstance(file, str): - abspath = pathlib.Path(file).absolute() - uid = hashlib.md5(str(abspath).encode()).hexdigest() - else: - # File-like object likely provided - uid = hashlib.md5(str(hash(file)).encode()).hexdigest() - return fn(file, uid) - - return wrapper - - -@hash_file_as_default_uid -def bigwig(filepath: str, uid: str): - try: - from clodius.tiles.bigwig import tiles, tileset_info - except ImportError: - raise ImportError( - 'You must have `clodius` installed to use "vector" data-server.' - ) - - return LocalTileset( - datatype="vector", - tiles=functools.partial(tiles, filepath), - info=functools.partial(tileset_info, filepath), - uid=uid, - ) - - -@hash_file_as_default_uid -def beddb(filepath: str, uid: str): - try: - from clodius.tiles.beddb import tiles, tileset_info - except ImportError: - raise ImportError( - 'You must have `clodius` installed to use "vector" data-server.' - ) - - return LocalTileset( - datatype="vector", - tiles=functools.partial(tiles, filepath), - info=functools.partial(tileset_info, filepath), - uid=uid, - ) - - -@hash_file_as_default_uid -def multivec(filepath: str, uid: str): - try: - from clodius.tiles.multivec import tiles, tileset_info - except ImportError: - raise ImportError( - 'You must have `clodius` installed to use "multivec" data-server.' - ) - - return LocalTileset( - datatype="multivec", - tiles=functools.partial(tiles, filepath), - info=functools.partial(tileset_info, filepath), - uid=uid, - ) - - -@hash_file_as_default_uid -def cooler(filepath: str, uid: str): - try: - from clodius.tiles.cooler import tiles, tileset_info - except ImportError: - raise ImportError( - 'You must have `clodius` installed to use "matrix" data-server.' - ) - - return LocalTileset( - datatype="matrix", - tiles=functools.partial(tiles, filepath), - info=functools.partial(tileset_info, filepath), - uid=uid, - ) - - -@hash_file_as_default_uid -def hitile(filepath: str, uid: str): - try: - from clodius.tiles.hitile import tiles, tileset_info - except ImportError: - raise ImportError( - 'You must have `clodius` installed to use "vector" data-server.' - ) - - return LocalTileset( - datatype="vector", - tiles=functools.partial(tiles, filepath), - info=functools.partial(tileset_info, filepath), - uid=uid, - ) - - -@hash_file_as_default_uid -def bed2ddb(filepath: str, uid: str): - try: - from clodius.tiles.bed2ddb import tiles, tileset_info - except ImportError: - raise ImportError( - 'You must have `clodius` installed to use "vector" data-server.' + if self.name is not None: + track.opts(name=self.name, inplace=True) + return track + + +def remote( + uid: str, server: str = "https://higlass.io/api/v1", name: str | None = None +): + """Create a remote tileset reference. + + Parameters + ---------- + uid : str + The unique identifier for the remote tileset. + server : str, optional + The HiGlass server URL (default is "https://higlass.io/api/v1"). + name : str, optional + An optional name for the tileset. + + Returns + ------- + RemoteTileset + A RemoteTileset instance that can be used to create HiGlass tracks. + """ + return RemoteTileset(uid, server, name) + + +@register +@dataclass +class ClodiusTileset(TilesetProtocol): + datatype: DataType + tiles_impl: typing.Callable[[typing.Sequence[str]], list[typing.Any]] + info_impl: typing.Callable[[], TilesetInfo] + + def tiles(self, tile_ids: typing.Sequence[str], /) -> list[dict]: + return self.tiles_impl(tile_ids) + + def info(self) -> TilesetInfo: + return self.info_impl() + + +def create_lazy_clodius_loader( + kind: str, datatype: DataType +) -> typing.Callable[[str | pathlib.Path], ClodiusTileset]: + def load(filepath: str | pathlib.Path) -> ClodiusTileset: + try: + module = __import__( + f"clodius.tiles.{kind}", fromlist=["tiles", "tileset_info"] + ) + except (ImportError, AttributeError): + raise ImportError(f"You must have `clodius` installed to use `hg.{kind}`.") + + return ClodiusTileset( + datatype=datatype, + tiles_impl=functools.partial(module.tiles, filepath), + info_impl=functools.partial(module.tileset_info, filepath), ) - return LocalTileset( - datatype="2d-rectangle-domains", - tiles=functools.partial(tiles, filepath), - info=functools.partial(tileset_info, filepath), - uid=uid, - ) + return load -by_filetype = {"cooler": cooler, "bigwig": bigwig} +bed2ddb = create_lazy_clodius_loader("bed2ddb", datatype="2d-rectangle-domains") +beddb = create_lazy_clodius_loader("beddb", datatype="vector") +bigwig = create_lazy_clodius_loader("bigwig", datatype="vector") +cooler = create_lazy_clodius_loader("cooler", datatype="matrix") +hitile = create_lazy_clodius_loader("hitile", datatype="vector") +multivec = create_lazy_clodius_loader("multivec", datatype="multivec") diff --git a/test/test_scale.py b/test/test_scale.py index ebe1454..d2437f9 100644 --- a/test/test_scale.py +++ b/test/test_scale.py @@ -28,8 +28,7 @@ def test_len(scale): def test_repr(scale): assert repr(scale) == ( - "Scale(chromsizes={'chr1': 10000, 'chr2': 20000, 'chr3': 30000}, " - "binsize=1000)" + "Scale(chromsizes={'chr1': 10000, 'chr2': 20000, 'chr3': 30000}, binsize=1000)" ) diff --git a/test/test_tileset_registery.py b/test/test_tileset_registery.py index 7189fe0..6d4a00a 100644 --- a/test/test_tileset_registery.py +++ b/test/test_tileset_registery.py @@ -5,30 +5,61 @@ import pytest from higlass._tileset_registry import TilesetRegistry -from higlass.tilesets import LocalTileset +from higlass.tilesets import ClodiusTileset, register -def mock_tileset(uid: str) -> LocalTileset: - return LocalTileset( - uid=uid or "mock_id", - tiles=lambda tile_ids: [], - info=lambda: {"min_pos": [0, 0], "max_pos": [100, 100]}, +def mock_tileset() -> ClodiusTileset: + return ClodiusTileset( + tiles_impl=lambda tile_ids: [], + info_impl=lambda: {"min_pos": [0, 0], "max_pos": [100, 100]}, datatype="multivec", ) -@pytest.fixture(scope="module") -def registry() -> typing.Generator[type[TilesetRegistry]]: +@pytest.fixture +def Registry() -> typing.Generator[type[TilesetRegistry]]: yield TilesetRegistry TilesetRegistry.clear() -def tileset_registry(registry: type[TilesetRegistry]) -> None: - ts1 = mock_tileset(uid="mock_id_1") - TilesetRegistry.add(ts1) - ts2 = mock_tileset(uid="mock_id_2") - TilesetRegistry.add(ts2) - ts3 = mock_tileset(uid="mock_id_2") - TilesetRegistry.add(ts3) - assert ts1 == TilesetRegistry.get("mock_id_1") - assert ts3 == TilesetRegistry.get("mock_id_2") +def test_tileset_registry(Registry: type[TilesetRegistry]) -> None: + ts1 = mock_tileset() + ts1_id = Registry.add(ts1) + ts2 = mock_tileset() + ts2_id = Registry.add(ts2) + ts3 = mock_tileset() + ts3_id = Registry.add(ts3) + assert ts1 == Registry.get(ts1_id) + assert ts2_id == Registry.add(ts2) + assert ts3 == Registry.get(ts3_id) + + +def test_tilesets_are_weakly_referenced(Registry: type[TilesetRegistry]) -> None: + uid = Registry.add(mock_tileset()) + with pytest.raises(KeyError): + # need hard reference to tileset for it to stay in registry + Registry.get(uid) + + +def test_custom_tileset_without_uid(Registry: type[TilesetRegistry]) -> None: + @register + class MyTileset: + def tiles(self, tile_ids: typing.Sequence[str]) -> list[typing.Any]: + return [] + + def info(self) -> typing.Any: + return {} + + ts = MyTileset() + # doesn't create a tileset + assert len(Registry._registry) == 0 + + ts.track("heatmap") + assert len(Registry._registry) == 1 + + ts.track("heatmap") + assert len(Registry._registry) == 1 + + ts2 = MyTileset() + ts2.track("heatmap") + assert len(Registry._registry) == 2 diff --git a/uv.lock b/uv.lock index cc056cc..9035b0a 100644 --- a/uv.lock +++ b/uv.lock @@ -1,10 +1,5 @@ version = 1 -requires-python = ">=3.9" -resolution-markers = [ - 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