def test_embed_data_two_widgets(self):
feature_track = pileup.Track(
viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
variant_track = pileup.Track(
viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
w1 = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[feature_track])
w2 = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[variant_track])
jslink((w1, 'reference'), (w2, 'reference'))
state = dependency_state([w1, w2], drop_defaults=True)
data = embed_data(views=[w1, w2], drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 2
model_names = [s['model_name'] for s in state.values()]
widget_names = list(
filter(lambda x: x == 'PileupViewerModel', model_names))
assert len(widget_names) == 2
def __init__(self, widget, **kwargs):
from ipywidgets import embed, Widget
super().__init__(**kwargs)
spec = widget.get_view_spec()
state = Widget.get_manager_state(widgets=[])
state["state"] = embed.dependency_state([widget], drop_defaults=True)
self.bundle = dict(spec=spec, state=state)
def to_html(self, path):
"""
This function embed the chart widget into an HTML file dumped at the inputted path location.
To see more details about embeding an ipywidget see: https://ipywidgets.readthedocs.io/en/latest/embedding.html
"""
embed_minimal_html(path, views=[self], state=dependency_state([self]))
def dict_from_widget(self):
"""generate a JSON-ready dict from a widget"""
d = {}
w = self.tracked_widget
if w is not None:
s = E.dependency_state(w)[w.comm.comm_id]["state"]
for k in self.tracked_traits or list(s):
d[k] = s.get(k, None)
return d
def test_minimal_features_html(self):
w = pileup.Features(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
output = StringIO()
state = dependency_state(w, drop_defaults=True)
embed_minimal_html(output, views=w, drop_defaults=True, state=state)
content = output.getvalue()
assert content.splitlines()[0] == '<!DOCTYPE html>'
def to_html(self, imports=True, html_frame=True):
# Bake positions (fixes centering bug in offline rendering)
if len(self.__objects) == 0:
return
ma = np.zeros((len(self.__objects), 3))
mi = np.zeros((len(self.__objects), 3))
for r, obj in enumerate(self.__objects):
ma[r] = self.__objects[obj]["max"]
mi[r] = self.__objects[obj]["min"]
ma = np.max(ma, axis=0)
mi = np.min(mi, axis=0)
diag = np.linalg.norm(ma-mi)
mean = (ma - mi) / 2 + mi
for r, obj in enumerate(self.__objects):
v = self.__objects[obj]["geometry"].attributes["position"].array
v -= mean
scale = self.__s["scale"] * (diag)
self._orbit.target = [0.0, 0.0, 0.0]
self._cam.lookAt([0.0, 0.0, 0.0])
self._cam.position = [0.0, 0.0, scale]
self._light.position = [0.0, 0.0, scale]
state = embed.dependency_state(self._renderer)
# Somehow these entries are missing when the state is exported in python.
# Exporting from the GUI works, so we are inserting the missing entries.
for k in state:
if state[k]["model_name"] == "OrbitControlsModel":
state[k]["state"]["maxAzimuthAngle"] = "inf"
state[k]["state"]["maxDistance"]= "inf"
state[k]["state"]["maxZoom"]= "inf"
state[k]["state"]["minAzimuthAngle"] = "-inf"
tpl = embed.load_requirejs_template
if not imports:
embed.load_requirejs_template = ""
s = embed.embed_snippet(self._renderer, state=state)
#s = embed.embed_snippet(self.__w, state=state)
embed.load_requirejs_template = tpl
if html_frame:
s = "<html>\n<body>\n" + s + "\n</body>\n</html>"
# Revert changes
for r, obj in enumerate(self.__objects):
v = self.__objects[obj]["geometry"].attributes["position"].array
v += mean
self.__update_view()
return s
def ipywidget_state(widgets):
from jinja2 import Markup
from ipywidgets import embed as wembed
drop_defaults = True
state = wembed.dependency_state(widgets, drop_defaults=drop_defaults)
from ipywidgets import Widget
json_data = Widget.get_manager_state(widgets=[])
json_data['state'] = state
json_data_str = json.dumps(json_data, indent=' ')
snippet = wembed.snippet_template.format(load='',
widget_views='',
json_data=json_data_str)
return Markup(snippet)
def test_minimal_pileup_html(self):
track = pileup.Track(viz="pileup",
label="myReads",
source=pileup.sources.GA4GHAlignmentJson('{}'))
w = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
output = StringIO()
state = dependency_state(w, drop_defaults=True)
embed_minimal_html(output, views=w, drop_defaults=True, state=state)
content = output.getvalue()
assert content.splitlines()[0] == '<!DOCTYPE html>'
def test_snippet(self):
class Parser(HTMLParser):
state = 'initial'
states = []
def handle_starttag(self, tag, attrs):
attrs = dict(attrs)
if tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-state+json":
self.state = 'widget-state'
self.states.append(self.state)
elif tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-view+json":
self.state = 'widget-view'
self.states.append(self.state)
def handle_endtag(self, tag):
self.state = 'initial'
def handle_data(self, data):
if self.state == 'widget-state':
manager_state = json.loads(data)['state']
assert len(manager_state) == 2
self.states.append('check-widget-state')
elif self.state == 'widget-view':
view = json.loads(data)
assert isinstance(view, dict)
self.states.append('check-widget-view')
track = pileup.Track(viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
w = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[track])
state = dependency_state(w, drop_defaults=True)
snippet = embed_snippet(views=w, drop_defaults=True, state=state)
parser = Parser()
parser.feed(snippet)
assert parser.states == [
'widget-state', 'check-widget-state', 'widget-view',
'check-widget-view'
]
def test_embed_variants(self):
w = pileup.Variants(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
state = dependency_state(w, drop_defaults=True)
data = embed_data(views=w, drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 1
model_names = [s['model_name'] for s in state.values()]
assert 'VariantModel' in model_names
def test_snippet(self):
class Parser(HTMLParser):
state = 'initial'
states = []
def handle_starttag(self, tag, attrs):
attrs = dict(attrs)
if tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-state+json":
self.state = 'widget-state'
self.states.append(self.state)
elif tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-view+json":
self.state = 'widget-view'
self.states.append(self.state)
def handle_endtag(self, tag):
self.state = 'initial'
def handle_data(self, data):
if self.state == 'widget-state':
manager_state = json.loads(data)['state']
assert len(manager_state) == 2
self.states.append('check-widget-state')
elif self.state == 'widget-view':
view = json.loads(data)
assert isinstance(view, dict)
self.states.append('check-widget-view')
w = pileup.Reads(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
state = dependency_state(w, drop_defaults=True)
snippet = embed_snippet(views=w, drop_defaults=True, state=state)
parser = Parser()
parser.feed(snippet)
assert parser.states == [
'widget-state', 'check-widget-state', 'widget-view',
'check-widget-view'
]
def test_embed_pileup(self):
track = pileup.Track(viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
w = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
state = dependency_state(w, drop_defaults=True)
data = embed_data(views=w, drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 1
model_names = [s['model_name'] for s in state.values()]
assert 'PileupViewerModel' in model_names
def test_embed_data_two_widgets(self):
w1 = pileup.Variants(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
w2 = pileup.Features(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
jslink((w1, 'start'), (w2, 'start'))
state = dependency_state([w1, w2], drop_defaults=True)
data = embed_data(views=[w1, w2], drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 2
model_names = [s['model_name'] for s in state.values()]
assert 'VariantModel' in model_names
assert 'FeatureModel' in model_names
def generate_html(widgets, title, path, makedirs=True, all_states=False,
offline=False,
drop_defaults=False,
template_options=(("extra_script_head", ""), ("body_pre", ""), ("body_post", "")),
devmode=False, offline_cors=False, only_body=False, as_dict=False,):
""" Write a minimal HTML file with widget views embedded.
:type filepath: str
:param filepath: The file to write the HTML output to.
:type widgets: widget or collection of widgets or None
:param widgets:The widgets to include views for. If None, all DOMWidgets are included (not just the displayed ones).
:param makedirs: whether to make directories in the filename path, if they do not already exist
:param title: title for the html page
:param all_states: if True, the state of all widgets know to the widget manager is included, else only those in widgets
:param offline: if True, use local urls for required js/css packages and download all js/css required packages
(if not already available), such that the html can be viewed with no internet connection
:param scripts_path: the directory to save required js/css packages to (relative to the filepath)
:type drop_defaults: bool
:param drop_defaults: Whether to drop default values from the widget states
:param template: template string for the html, must contain at least {title} and {snippet} place holders
:param template_options: list or dict of additional template options
:param devmode: if True, attempt to get index.js from local js/dist directory
:param devmode: if True, attempt to get index.js from local js/dist folder
:param offline_cors: if True, sets crossorigin attribute to anonymous, this allows for the return of error data
from js scripts but can block local loading of the scripts in some browsers
"""
#dir_name_dst = os.path.dirname(os.path.abspath(filepath))
#if not os.path.exists(dir_name_dst) and makedirs: os.makedirs(dir_name_dst)
template_opts = {"extra_script_head": "", "body_pre": "", "body_post": ""}
template_opts.update(dict(template_options))
if all_states: state = None
else:
state = wembed.dependency_state(widgets, drop_defaults=drop_defaults)
# if not offline:
#
# # we have to get the snippet (rather than just call embed_minimal_html), because if the new template includes
# # {} characters (such as in the bokeh example) then an error is raised when trying to format
# snippet = wembed.embed_snippet(widgets, state=state, requirejs=True, drop_defaults=drop_defaults)
# directory = os.path.dirname(filepath)
#else:
if True:
#if not os.path.isabs(scripts_path):
# scripts_path = os.path.join(os.path.dirname(filepath), scripts_path)
# ensure script path is above filepath
# rel_script_path = os.path.relpath(scripts_path, os.path.dirname(filepath))
# if rel_script_path.startswith(".."):
# raise ValueError("The scripts_path must have the same root directory as the filepath")
# elif rel_script_path=='.':
# rel_script_path = ''
# else:
# rel_script_path += '/'
scripts_path = path
rel_script_path = path
if not rel_script_path.endswith("/"): rel_script_path += "/"
fname_pyv = save_ipyvolumejs(scripts_path, devmode=devmode)
fname_require = save_requirejs(os.path.join(scripts_path))
fname_embed = save_embed_js(os.path.join(scripts_path))
fname_fontawe = save_font_awesome(os.path.join(scripts_path))
subsnippet = wembed.embed_snippet(widgets, embed_url=rel_script_path+fname_embed,
requirejs=False, drop_defaults=drop_defaults, state=state)
if not offline_cors:
# TODO DIRTY hack, we need to do this cleaner upstream
subsnippet = subsnippet.replace(' crossorigin="anonymous"', '')
cors_attribute = 'crossorigin="anonymous"' if offline_cors else ' '
snippet = """
<link href="{rel_script_path}{fname_fontawe}/css/font-awesome.min.css" rel="stylesheet">
<script src="{rel_script_path}{fname_require}"{cors} data-main='./{rel_script_path}' ></script>
<script>
require.config({{
map: {{
'*': {{
'ipyvolume': '{fname_pyv}',
}}
}}}})
</script>
{subsnippet}
""".format(rel_script_path=rel_script_path, fname_fontawe=fname_fontawe, fname_require=fname_require,
fname_pyv=os.path.splitext(fname_pyv)[0],
subsnippet=subsnippet, cors=cors_attribute)
# Generate HTML
template_opts['snippet'] = snippet
template_opts['title'] = title
# Give
if as_dict: return template_opts
elif only_body:
html_code = html_body_template.format(**template_opts)
return html_code
else:
html_code = html_template.format(**template_opts)
return html_code
def embed_html(
filepath,
widgets,
makedirs=True,
title=u'IPyVolume Widget',
all_states=False,
offline=False,
scripts_path='js',
drop_defaults=False,
template=html_template,
template_options=(("extra_script_head", ""), ("body_pre", ""), ("body_post", "")),
devmode=False,
offline_cors=False,
):
"""Write a minimal HTML file with widget views embedded.
:param str filepath: The file to write the HTML output to.
:type widgets: widget or collection of widgets or None
:param widgets:The widgets to include views for. If None, all DOMWidgets are included (not just the displayed ones).
:param makedirs: whether to make directories in the filename path, if they do not already exist
:param title: title for the html page
:param all_states: if True, the state of all widgets know to the widget manager is included, else only those in widgets
:param offline: if True, use local urls for required js/css packages and download all js/css required packages
(if not already available), such that the html can be viewed with no internet connection
:param scripts_path: the directory to save required js/css packages to (relative to the filepath)
:param bool drop_defaults: Whether to drop default values from the widget states
:param template: template string for the html, must contain at least {title} and {snippet} place holders
:param template_options: list or dict of additional template options
:param devmode: if True, attempt to get index.js from local js/dist directory
:param devmode: if True, attempt to get index.js from local js/dist folder
:param offline_cors: if True, sets crossorigin attribute to anonymous, this allows for the return of error data
from js scripts but can block local loading of the scripts in some browsers
"""
dir_name_dst = os.path.dirname(os.path.abspath(filepath))
if not os.path.exists(dir_name_dst) and makedirs:
os.makedirs(dir_name_dst)
template_opts = {"extra_script_head": "", "body_pre": "", "body_post": ""}
template_opts.update(dict(template_options))
if all_states:
state = None
else:
state = wembed.dependency_state(widgets, drop_defaults=drop_defaults)
if not offline:
# we have to get the snippet (rather than just call embed_minimal_html), because if the new template includes
# {} characters (such as in the bokeh example) then an error is raised when trying to format
snippet = wembed.embed_snippet(widgets, state=state, requirejs=True, drop_defaults=drop_defaults)
else:
if not os.path.isabs(scripts_path):
scripts_path = os.path.join(os.path.dirname(filepath), scripts_path)
# ensure script path is above filepath
rel_script_path = os.path.relpath(scripts_path, os.path.dirname(filepath))
if rel_script_path.startswith(".."):
raise ValueError("The scripts_path must have the same root directory as the filepath")
elif rel_script_path == '.':
rel_script_path = ''
else:
rel_script_path += '/'
fname_pyv = save_ipyvolumejs(scripts_path, devmode=devmode)
fname_require = save_requirejs(os.path.join(scripts_path))
fname_embed = save_embed_js(os.path.join(scripts_path))
fname_fontawe = save_font_awesome(os.path.join(scripts_path))
subsnippet = wembed.embed_snippet(
widgets, embed_url=rel_script_path + fname_embed, requirejs=False, drop_defaults=drop_defaults, state=state
)
if not offline_cors:
# TODO DIRTY hack, we need to do this cleaner upstream
subsnippet = subsnippet.replace(' crossorigin="anonymous"', '')
cors_attribute = 'crossorigin="anonymous"' if offline_cors else ' '
snippet = """
<link href="{rel_script_path}{fname_fontawe}/css/font-awesome.min.css" rel="stylesheet">
<script src="{rel_script_path}{fname_require}"{cors} data-main='./{rel_script_path}' ></script>
<script>
require.config({{
map: {{
'*': {{
'ipyvolume': '{fname_pyv}',
}}
}}}})
</script>
{subsnippet}
""".format(
rel_script_path=rel_script_path,
fname_fontawe=fname_fontawe,
fname_require=fname_require,
fname_pyv=os.path.splitext(fname_pyv)[0],
subsnippet=subsnippet,
cors=cors_attribute,
)
template_opts['snippet'] = snippet
template_opts['title'] = title
html_code = template.format(**template_opts)
with io.open(filepath, "w", encoding='utf8') as f:
f.write(html_code)
activity_data = activity_data.dropna()
locations = list(
zip(activity_data.latitude_degrees.values,
activity_data.longitude_degrees.values))
# Create Map
from ipyleaflet import Map, Marker, AntPath
center = (34.1137553, -118.2001699)
m = Map(center=center, zoom=12)
marker = Marker(location=center, draggable=False)
m.add_layer(marker)
ant_path = AntPath(locations=locations,
dash_array=[1, 10],
delay=1000,
color='#7590ba',
pulse_color='#3f6fba')
m.add_layer(ant_path)
# Export Map into HTML
from ipywidgets.embed import embed_minimal_html, dependency_state
embed_minimal_html('export.html', views=[m], state=dependency_state([m]))
