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WIP - Refactor #1138

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merged 6 commits into from
Nov 28, 2024
Merged

WIP - Refactor #1138

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d800700
contextmanager
hainm Nov 28, 2024
8dfd35c
group
hainm Nov 28, 2024
ac6fbae
_handle_nglview_custom_msg
hainm Nov 28, 2024
219e49d
_load_data
hainm Nov 28, 2024
2c61e18
_load_data
hainm Nov 28, 2024
1c7c101
_load_data
hainm Nov 28, 2024
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257 changes: 128 additions & 129 deletions nglview/widget.py
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Original file line number Diff line number Diff line change
@@ -1,23 +1,21 @@
import base64
import json
import re
import threading
import time
import uuid
from logging import getLogger
from contextlib import contextmanager

import ipywidgets as widgets
from ipywidgets import embed
import numpy as np
from IPython.display import display
from ipywidgets import (Image, Box, DOMWidget, HBox, VBox, IntSlider, Output,
Play, Widget, jslink)
import ipywidgets as widgets
from ipywidgets import (Image, Box, DOMWidget, HBox, IntSlider, Play, jslink)
from ipywidgets import embed
from ipywidgets import widget as _widget
from traitlets import (Bool, CaselessStrEnum, Dict, Instance, Int, Integer,
List, Unicode, observe, validate)
import traitlets

from . import color, interpolate
from . import color
from .adaptor import Structure, Trajectory
from .component import ComponentViewer
from .config import BACKENDS
Expand All @@ -31,7 +29,6 @@
seq_to_string)
from .viewer_control import ViewerControl
from ._frontend import __frontend_version__
from .base import BaseWidget

logger = getLogger(__name__)

Expand Down Expand Up @@ -86,43 +83,49 @@ def write_html(fp, views, frame_range=None):
>>> nglview.write_html('index.html', [view]) # doctest: +SKIP
>>> nglview.write_html('index.html', [view], frame_range=(0, 5)) # doctest: +SKIP
"""
views = isinstance(views, DOMWidget) and [views] or views
views = [views] if isinstance(views, DOMWidget) else views

for _, v in _INIT_VIEWS.items():
views.insert(0, v)

def _set_serialization(views):
for view in views:
if hasattr(view, '_set_serialization'):
view._set_serialization(frame_range=frame_range)
elif isinstance(view, Box):
_set_serialization(view.children)

def _unset_serialization(views):
for view in views:
if hasattr(view, '_unset_serialization'):
view._unset_serialization()
elif isinstance(view, Box):
_unset_serialization(view.children)

_set_serialization(views)
# FIXME: allow add jquery-ui link?
snippet = '<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.0/jquery-ui.css">\n'
snippet += '<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.15.4/css/all.css">\n'
snippet += embed.embed_snippet(views)
html_code = embed.html_template.format(title='nglview-demo',
snippet=snippet)

# from ipywidgets
# Check if fp is writable:
if hasattr(fp, 'write'):
fp.write(html_code)
else:
# Assume fp is a filename:
with open(fp, "w") as f:
f.write(html_code)

_unset_serialization(views)
@contextmanager
def manage_serialization(views):
def _set_serialization(views):
for view in views:
if hasattr(view, '_set_serialization'):
view._set_serialization(frame_range=frame_range)
elif isinstance(view, Box):
_set_serialization(view.children)

def _unset_serialization(views):
for view in views:
if hasattr(view, '_unset_serialization'):
view._unset_serialization()
elif isinstance(view, Box):
_unset_serialization(view.children)

_set_serialization(views)
try:
yield
finally:
_unset_serialization(views)

with manage_serialization(views):
snippet = (
'<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.0/jquery-ui.css">\n'
'<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.15.4/css/all.css">\n'
+ embed.embed_snippet(views)
)
html_code = embed.html_template.format(title='nglview-embed', snippet=snippet)

# from ipywidgets
# Check if fp is writable:
if hasattr(fp, 'write'):
fp.write(html_code)
else:
# Assume fp is a filename:
with open(fp, "w") as f:
f.write(html_code)


class NGLWidget(DOMWidget):
Expand All @@ -133,31 +136,15 @@ class NGLWidget(DOMWidget):
_model_module = Unicode("nglview-js-widgets").tag(sync=True)
_model_module_version = Unicode(__frontend_version__).tag(sync=True)
_ngl_version = Unicode().tag(sync=True)
# _model_name = Unicode("NGLView").tag(sync=True)
# _model_module = Unicode("nglview-js-widgets").tag(sync=True)

# View and model attributes
_image_data = Unicode().tag(sync=False)
# use Integer here, because mdtraj uses a long datatype here on Python-2.7
frame = Integer().tag(sync=True)
max_frame = Int(0).tag(sync=True)
background = Unicode('white').tag(sync=True)
loaded = Bool(False).tag(sync=False)
picked = Dict().tag(sync=True)
n_components = Int(0).tag(sync=True)
_view_width = Unicode().tag(sync=True) # px
_view_height = Unicode().tag(sync=True) # px
_scene_position = Dict().tag(sync=True)
_scene_rotation = Dict().tag(sync=True)
# hack to always display movie
# TODO: remove _parameters?
_parameters = Dict().tag(sync=False)
_ngl_full_stage_parameters = Dict().tag(sync=True)
_ngl_original_stage_parameters = Dict().tag(sync=True)
_coordinates_dict = Dict().tag(sync=False)
_camera_str = CaselessStrEnum(['perspective', 'orthographic'],
default_value='orthographic').tag(sync=True)
_camera_str = CaselessStrEnum(['perspective', 'orthographic'], default_value='orthographic').tag(sync=True)
_camera_orientation = List().tag(sync=True)
_synced_model_ids = List().tag(sync=True)
_synced_repr_model_ids = List().tag(sync=True)
_ngl_view_id = List().tag(sync=True)
_ngl_repr_dict = Dict().tag(sync=True)
_ngl_component_ids = List().tag(sync=False)
Expand All @@ -166,24 +153,36 @@ class NGLWidget(DOMWidget):
_send_binary = Bool(True).tag(sync=False)
_init_gui = Bool(False).tag(sync=False)
gui_style = CaselessStrEnum(['ngl'], allow_none=True).tag(sync=True)
_gui_theme = CaselessStrEnum(['dark', 'light'],
allow_none=True).tag(sync=True)
_gui_theme = CaselessStrEnum(['dark', 'light'], allow_none=True).tag(sync=True)
_widget_theme = None
_ngl_serialize = Bool(False).tag(sync=True)
_ngl_msg_archive = List().tag(sync=True)
_ngl_coordinate_resource = Dict().tag(sync=True)

# Frame and background attributes
frame = Integer().tag(sync=True)
max_frame = Int(0).tag(sync=True)
background = Unicode('white').tag(sync=True)

# Component and parameter attributes
n_components = Int(0).tag(sync=True)
_parameters = Dict().tag(sync=False)
_ngl_full_stage_parameters = Dict().tag(sync=True)
_ngl_original_stage_parameters = Dict().tag(sync=True)
_coordinates_dict = Dict().tag(sync=False)
_representations = List().tag(sync=False)
_ngl_color_dict = Dict().tag(sync=True)
_player_dict = Dict().tag(sync=True)

# instance
_iplayer = Instance(widgets.Box,
allow_none=True).tag(sync=True, **widget_serialization)
_igui = Instance(widgets.Tab, allow_none=True).tag(sync=True,
**widget_serialization)
_ibtn_fullscreen = Instance(widgets.Button,
allow_none=True).tag(sync=True,
**widget_serialization)
# State and synchronization attributes
loaded = Bool(False).tag(sync=False)
picked = Dict().tag(sync=True)
_synced_model_ids = List().tag(sync=True)
_synced_repr_model_ids = List().tag(sync=True)
_ngl_serialize = Bool(False).tag(sync=True)
_ngl_msg_archive = List().tag(sync=True)
_ngl_coordinate_resource = Dict().tag(sync=True)

_iplayer = Instance(widgets.Box, allow_none=True).tag(sync=True, **widget_serialization)
_igui = Instance(widgets.Tab, allow_none=True).tag(sync=True, **widget_serialization)
_ibtn_fullscreen = Instance(widgets.Button, allow_none=True).tag(sync=True, **widget_serialization)

def __init__(self,
structure=None,
Expand Down Expand Up @@ -972,24 +971,21 @@ def _handle_nglview_custom_msg(self, _, msg, buffers):
self._ngl_msg = msg

msg_type = self._ngl_msg.get('type')
if msg_type == 'request_frame':
self._handle_request_frame()
elif msg_type == 'updateIDs':
self._handle_update_ids()
elif msg_type == 'removeComponent':
self._handle_remove_component()
elif msg_type == 'repr_parameters':
self._handle_repr_parameters()
elif msg_type == 'request_loaded':
self._handle_request_loaded()
elif msg_type == 'request_repr_dict':
self._handle_request_repr_dict()
elif msg_type == 'stage_parameters':
self._handle_stage_parameters()
elif msg_type == 'async_message':
self._handle_async_message()
elif msg_type == 'image_data':
self._handle_image_data()
handlers = {
'request_frame': self._handle_request_frame,
'updateIDs': self._handle_update_ids,
'removeComponent': self._handle_remove_component,
'repr_parameters': self._handle_repr_parameters,
'request_loaded': self._handle_request_loaded,
'request_repr_dict': self._handle_request_repr_dict,
'stage_parameters': self._handle_stage_parameters,
'async_message': self._handle_async_message,
'image_data': self._handle_image_data,
}

handler = handlers.get(msg_type)
if handler:
handler()

def _request_repr_parameters(self, component=0, repr_index=0):
if self.n_components > 0:
Expand Down Expand Up @@ -1112,58 +1108,61 @@ def add_component(self, filename, **kwargs):
return self[-1]

def _load_data(self, obj, **kwargs):
'''
"""
Parameters
----------
obj : nglview.Structure or any object having 'get_structure_string' method or
string buffer (open(fn).read())
'''
kwargs2 = _camelize_dict(kwargs)
"""
kwargs = _camelize_dict(kwargs)

try:
is_url = FileManager(obj).is_url
except NameError:
is_url = False

if 'defaultRepresentation' not in kwargs2:
kwargs2['defaultRepresentation'] = True
if 'defaultRepresentation' not in kwargs:
kwargs['defaultRepresentation'] = True

if not is_url:
if hasattr(obj, 'get_structure_string'):
blob = obj.get_structure_string()
kwargs2['ext'] = obj.ext
passing_buffer = True
binary = False
else:
fh = FileManager(obj,
ext=kwargs.get('ext'),
compressed=kwargs.get('compressed'))
# assume passing string
blob = fh.read(force_buffer=True)
passing_buffer = True

if fh.ext is None and passing_buffer:
raise ValueError('must provide extension')

kwargs2['ext'] = fh.ext
binary = fh.is_binary
use_filename = fh.use_filename

if binary and not use_filename:
# send base64
blob = base64.b64encode(blob).decode('utf8')
blob_type = 'blob' if passing_buffer else 'path'
args = [{'type': blob_type, 'data': blob, 'binary': binary}]
if is_url:
self._load_data_from_url(obj, kwargs)
else:
# is_url
blob_type = 'url'
url = obj
args = [{'type': blob_type, 'data': url, 'binary': False}]
self._load_data_from_object(obj, kwargs)

def _load_data_from_url(self, url, kwargs):
args = [{'type': 'url', 'data': url, 'binary': False}]
self._remote_call("loadFile", target='Stage', args=args, kwargs=kwargs)

def _load_data_from_object(self, obj, kwargs):
if hasattr(obj, 'get_structure_string'):
blob, ext, binary = self._get_structure_string_data(obj)
else:
blob, ext, binary, use_filename = self._get_file_manager_data(obj, kwargs)

if binary and not use_filename:
blob = base64.b64encode(blob).decode('utf8')

name = py_utils.get_name(obj, **kwargs2)
args = [{'type': 'blob', 'data': blob, 'binary': binary}]
kwargs['ext'] = ext
name = py_utils.get_name(obj, **kwargs)
self._ngl_component_names.append(name)
self._remote_call("loadFile", target='Stage', args=args, kwargs=kwargs2)
self._remote_call("loadFile", target='Stage', args=args, kwargs=kwargs)

def _get_structure_string_data(self, obj):
blob = obj.get_structure_string()
ext = obj.ext
binary = False
return blob, ext, binary

def _get_file_manager_data(self, obj, kwargs):
fh = FileManager(obj, ext=kwargs.get('ext'), compressed=kwargs.get('compressed'))
blob = fh.read(force_buffer=True)
if fh.ext is None:
raise ValueError('must provide extension')
ext = fh.ext
binary = fh.is_binary
use_filename = fh.use_filename
return blob, ext, binary, use_filename

def remove_component(self, c):
"""remove component by its uuid.
Expand Down
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