Source code for higlass.viewer

import json
import logging
import os
import threading
import time

import ipywidgets as widgets
from traitlets import Bool, Dict, Float, Int, List, Unicode, Union

import slugid

from ._version import __version__

[docs]def save_b64_image_to_png(filename, b64str): """Save a base64 encoded image to a file.""" import base64 imgdata = base64.b64decode(b64str.split(",")[1]) with open(filename, "wb") as f: f.write(imgdata)
@widgets.register class HiGlassDisplay(widgets.DOMWidget): _view_name = Unicode("HiGlassDisplayView").tag(sync=True) _model_name = Unicode("HiGlassDisplayModel").tag(sync=True) _view_module = Unicode("higlass-jupyter").tag(sync=True) _model_module = Unicode("higlass-jupyter").tag(sync=True) _view_module_version = Unicode(__version__).tag(sync=True) _model_module_version = Unicode(__version__).tag(sync=True) _model_data = List([]).tag(sync=True) viewconf = Dict({}).tag(sync=True) height = Int().tag(sync=True) dom_element_id = Unicode(read_only=True).tag(sync=True) # Read-only properties that get updated by HiGlass exclusively location = List(Union([Float(), List()]), read_only=True).tag(sync=True) cursor_location = List([], read_only=True).tag(sync=True) selection = List([], read_only=True).tag(sync=True) # Short-hand options auth_token = Unicode().tag(sync=True) bounded = Bool(None, allow_none=True).tag(sync=True) default_track_options = Dict({}).tag(sync=True) dark_mode = Bool(False).tag(sync=True) renderer = Unicode().tag(sync=True) select_mode = Bool(False).tag(sync=True) selection_on_alt = Bool(False).tag(sync=True) # For any kind of options. Note that whatever is defined in options will # be overwritten by the short-hand options options = Dict({}).tag(sync=True) def __init__(self, **kwargs): self.on_msg(self._handle_js_events) self.callbacks = {} super(HiGlassDisplay, self).__init__(**kwargs) def get_base64_img(self, callback): uuid = slugid.nice() self.callbacks[uuid] = callback self.send(json.dumps({"request": "save_as_png", "params": {"uuid": uuid},})) def _handle_js_events(self, widget, content, buffers=None): try: if self.callbacks[content["params"]["uuid"]]: self.callbacks[content["params"]["uuid"]](content["imgData"]) del self.callbacks[content["params"]["uuid"]] except Exception as e: self.log.error(e) self.log.exception("Unhandled exception while handling msg") # def save_as_png(self, filename): # """Save the currently visible plot to a png file""" # from IPython.display import Javascript # js = Javascript( # f""" # let d = document.getElementById('{self.dom_element_id}'); # d.api.exportAsPngBlobPromise().then(blob => {{ # let reader = new FileReader(); # reader.readAsDataURL(blob); # reader.onloadend = function() {{ # let base64data = reader.result; # let kernel = IPython.notebook.kernel; # let command = `from higlass.viewer import save_b64_image_to_png; save_b64_image_to_png('{filename}', '''${{base64data}}''')` # let ex = kernel.execute(command); # }} # }}) # """ # ) # return js
[docs]def display( views, location_syncs=[], value_scale_syncs=[], zoom_syncs=[], host="localhost", server_port=None, dark_mode=False, log_level=logging.ERROR, fuse=True, auth_token=None, ): """ Instantiate a HiGlass display with the given views. Args: views: A list of views to display. If the items in the list are lists themselves, then automatically create views out of them. location_syncs: A list of lists, each containing a list of views which will scroll together. value_scale_syncs: A list containing the value scale syncs. Each sync can be one of: 1. a list of (View, Track) tuples 2. a list of Tracks (assumes that there is only one view) 3. a list of strings of the form "{viewUid}.{trackUid}" zoom_syncs: A list of lists, each containing a list of views that will zoom together. host: The host on which the internal higlass server will be running on. server_port: The port on which the internal higlass server will be running on. dark_mode: Whether to use dark mode or not. log_level: Level of logging to perform. fuse: Whether to mount the fuse filesystem. Set to False if not loading any data over http or https. Returns: (display: HiGlassDisplay, server: higlass.server.Server, higlass.client.viewconf) tuple Display is an object used to create a HiGlass viewer within a Jupyter notebook. The server object encapsulates a Flask instance of a higlass server and the viewconf is a Python object containing the viewconf describing the higlass dashboard. """ from .server import Server from .client import CombinedTrack, DividedTrack, View, ViewConf, ViewportProjection tilesets = [] # views can also be passed in as lists of tracks new_views = [] for view in views: if isinstance(view, (tuple, list)): # view is a list of tracks new_views.append(View(view)) else: new_views.append(view) views = new_views for view in views: for track in view.tracks: if hasattr(track, "tracks"): for track1 in track.tracks: if not isinstance(track1, ViewportProjection) and track1.tileset: tilesets += [track1.tileset] if track.tileset: tilesets += [track.tileset] server = Server( tilesets, host=host, port=server_port, fuse=fuse, log_level=log_level ) server.start() cloned_views = [View.from_dict(view.to_dict()) for view in views] for view in cloned_views: for track in view.tracks: if isinstance(track, CombinedTrack): for track1 in track.tracks: if "fromViewUid" in track1.conf: # this is a viewport projection and doesn't have # a server pass elif "server" not in track1.conf or track1.conf["server"] is None: track1.conf["server"] = server.api_address elif "fromViewUid" in track.conf: pass elif "data" in track.conf: # probably a divided track with a custom # data fetcher pass else: if "server" not in track.conf or track.conf["server"] is None: track.conf["server"] = server.api_address viewconf = ViewConf( cloned_views, location_syncs=location_syncs, value_scale_syncs=value_scale_syncs, zoom_syncs=zoom_syncs, ) extra_args = {} if auth_token: extra_args["auth_token"] = auth_token return ( HiGlassDisplay( viewconf=viewconf.to_dict(), hg_options={"theme": "dark" if dark_mode else "light",}, **extra_args ), server, viewconf, )