def metrics_doc(doc: Document) -> None:
settings = Settings()
logdir = settings.log_path / doc.session_context.request.arguments['model'][0].decode('utf-8')
plots = get_plots()
doc.add_root(row(plots.loss.plot, plots.score.plot))
doc.theme = Theme(filename="visualization/theme.yaml")
threading.Thread(target=load_data_for_model, args=(doc, plots, logdir)).start()
def test_setting_built_in_theme_str(self) -> None:
obj = SomeModel()
doc = Document()
doc.add_root(obj)
doc.theme = DARK_MINIMAL
assert "#20262B" == doc.theme._json['attrs']['Figure'][
'background_fill_color']
def test_setting_built_in_theme_obj(self) -> None:
obj = SomeModel()
doc = Document()
doc.add_root(obj)
doc.theme = built_in_themes[LIGHT_MINIMAL]
assert "#5B5B5B" == doc.theme._json['attrs']['ColorBar'][
'title_text_color']
def sea_surface_handler(doc: Document) -> None:
df = sea_surface_temperature.copy()
source = ColumnDataSource(data=df)
plot = figure(x_axis_type="datetime",
y_range=(0, 25),
y_axis_label="Temperature (Celsius)",
title="Sea Surface Temperature at 43.18, -70.43")
plot.line("time", "temperature", source=source)
def callback(attr: str, old: Any, new: Any) -> None:
if new == 0:
data = df
else:
data = df.rolling("{0}D".format(new)).mean()
source.data = dict(ColumnDataSource(data=data).data)
slider = Slider(start=0,
end=30,
value=0,
step=1,
title="Smoothing by N Days")
slider.on_change("value", callback)
doc.theme = theme
doc.add_root(column(slider, plot))
def profiler_doc(doc: Document) -> None:
settings = Settings()
model_name = doc.session_context.request.arguments['model'][0].decode('utf-8')
logdir = settings.log_path / model_name
plots = get_profiler_plots()
doc.add_root(row(plots.full_epoch.plot))
doc.theme = Theme(filename="visualization/theme.yaml")
threading.Thread(target=load_profiling_data, args=(doc, plots, logdir, model_name)).start()
def test_setting_document_theme_to_none(self) -> None:
theme = Theme(json={'attrs': {'ThemedModel': {'string': 'w00t'}}})
obj = ThemedModel()
doc = Document()
doc.add_root(obj)
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.theme = theme
assert 'w00t' == obj.string
# setting to None reverts to default theme
doc.theme = None
assert doc.theme is not None
assert 'hello' == obj.string
assert [('string', 'hello', 'w00t'),
('string', 'w00t', 'hello')] == changes['calls']
def test_setting_document_theme_to_none(self):
theme = Theme(json={'attrs': {'ThemedModel': {'string': 'w00t'}}})
obj = ThemedModel()
doc = Document()
doc.add_root(obj)
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.theme = theme
self.assertEqual('w00t', obj.string)
# setting to None reverts to default theme
doc.theme = None
self.assertIsNot(doc.theme, None)
self.assertEqual('hello', obj.string)
self.assertEqual([('string', 'hello', 'w00t'),
('string', 'w00t', 'hello')], changes['calls'])
def get_plot(self_or_cls, obj, doc=None, renderer=None):
"""
Given a HoloViews Viewable return a corresponding plot instance.
Allows supplying a document attach the plot to, useful when
combining the bokeh model with another plot.
"""
if doc is None:
doc = Document() if self_or_cls.notebook_context else curdoc()
doc.theme = self_or_cls.theme
plot = super(BokehRenderer, self_or_cls).get_plot(obj, renderer)
plot.document = doc
return plot
def test_setting_document_theme_to_none(self):
theme = Theme(json={
'attrs' : {
'ThemedModel' : {
'string' : 'w00t'
}
}
})
obj = ThemedModel()
doc = Document()
doc.add_root(obj)
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.theme = theme
assert 'w00t' == obj.string
# setting to None reverts to default theme
doc.theme = None
assert doc.theme is not None
assert 'hello' == obj.string
assert [('string', 'hello', 'w00t'), ('string', 'w00t', 'hello')] == changes['calls']
def test_setting_document_theme_to_none(self):
theme = Theme(json={
'attrs' : {
'ThemedModel' : {
'string' : 'w00t'
}
}
})
obj = ThemedModel()
doc = Document()
doc.add_root(obj)
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.theme = theme
self.assertEqual('w00t', obj.string)
# setting to None reverts to default theme
doc.theme = None
self.assertIsNot(doc.theme, None)
self.assertEqual('hello', obj.string)
self.assertEqual([('string', 'hello', 'w00t'),
('string', 'w00t', 'hello')], changes['calls'])
def get_plot(self_or_cls, obj, doc=None, renderer=None, **kwargs):
"""
Given a HoloViews Viewable return a corresponding plot instance.
Allows supplying a document attach the plot to, useful when
combining the bokeh model with another plot.
"""
if doc is None:
doc = Document() if self_or_cls.notebook_context else curdoc()
if self_or_cls.notebook_context:
curdoc().theme = self_or_cls.theme
doc.theme = self_or_cls.theme
plot = super(BokehRenderer, self_or_cls).get_plot(obj, renderer, **kwargs)
plot.document = doc
return plot
def test_directory_has_theme_file(self) -> None:
doc = Document()
def load(filename: str):
handler = bahd.DirectoryHandler(filename=filename)
handler.modify_document(doc)
if handler.failed:
raise RuntimeError(handler.error)
custom_theme = """
attrs:
AnotherModelInTestDirectoryTheme:
bar: 42
SomeModelInTestDirectoryTheme:
foo: 14
"""
with_directory_contents(
{
'main.py':
script_adds_two_roots('SomeModelInTestDirectoryTheme',
'AnotherModelInTestDirectoryTheme') + """
# we're testing that the script can override the theme
some = next(m for m in curdoc().roots if isinstance(m, SomeModelInTestDirectoryTheme))
some.foo = 57
""",
'theme.yaml':
custom_theme
}, load)
assert len(doc.roots) == 2
some_model = next(
m for m in doc.roots
if m.__class__.__name__ == 'SomeModelInTestDirectoryTheme')
another_model = next(
m for m in doc.roots
if m.__class__.__name__ == 'AnotherModelInTestDirectoryTheme')
assert another_model.bar == 42
assert some_model.foo == 57
# test that we use the theme if we delete our explicit-set value
del some_model.foo
assert some_model.foo == 14
# test that removing the theme gets us back to the base
doc.theme = None
assert some_model.foo == 2
assert another_model.bar == 1
def test_theming_a_document_before_adding_root(self) -> None:
theme = Theme(json={'attrs': {'ThemedModel': {'string': 'w00t'}}})
obj = ThemedModel()
doc = Document()
assert 'hello' == obj.string
doc.theme = theme
assert doc.theme is theme
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.add_root(obj)
assert 'w00t' == obj.string
doc.remove_root(obj)
assert 'hello' == obj.string
assert [('string', 'hello', 'w00t'),
('string', 'w00t', 'hello')] == changes['calls']
def test_theming_a_document_before_adding_root(self):
theme = Theme(json={'attrs': {'ThemedModel': {'string': 'w00t'}}})
obj = ThemedModel()
doc = Document()
self.assertEqual('hello', obj.string)
doc.theme = theme
self.assertIs(doc.theme, theme)
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.add_root(obj)
self.assertEqual('w00t', obj.string)
doc.remove_root(obj)
self.assertEqual('hello', obj.string)
self.assertEqual([('string', 'hello', 'w00t'),
('string', 'w00t', 'hello')], changes['calls'])
def test_theming_a_document_before_adding_root(self):
theme = Theme(json={
'attrs' : {
'ThemedModel' : {
'string' : 'w00t'
}
}
})
obj = ThemedModel()
doc = Document()
assert 'hello' == obj.string
doc.theme = theme
assert doc.theme is theme
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.add_root(obj)
assert 'w00t' == obj.string
doc.remove_root(obj)
assert 'hello' == obj.string
assert [('string', 'hello', 'w00t'), ('string', 'w00t', 'hello')] == changes['calls']
def test_directory_has_theme_file(self):
doc = Document()
def load(filename):
handler = DirectoryHandler(filename=filename)
handler.modify_document(doc)
if handler.failed:
raise RuntimeError(handler.error)
custom_theme = """
attrs:
AnotherModelInTestDirectoryTheme:
bar: 42
SomeModelInTestDirectoryTheme:
foo: 14
"""
_with_directory_contents({
'main.py' : script_adds_two_roots('SomeModelInTestDirectoryTheme',
'AnotherModelInTestDirectoryTheme') +
"""
# we're testing that the script can override the theme
some = next(m for m in curdoc().roots if isinstance(m, SomeModelInTestDirectoryTheme))
some.foo = 57
""",
'theme.yaml' : custom_theme
}, load)
self.assertEqual(2, len(doc.roots))
some_model = next(m for m in doc.roots if m.__class__.__name__ == 'SomeModelInTestDirectoryTheme')
another_model = next(m for m in doc.roots if m.__class__.__name__ == 'AnotherModelInTestDirectoryTheme')
self.assertEqual(42, another_model.bar)
self.assertEqual(57, some_model.foo)
# test that we use the theme if we delete our explicit-set value
del some_model.foo
self.assertEqual(14, some_model.foo)
# test that removing the theme gets us back to the base
doc.theme = None
self.assertEqual(2, some_model.foo)
self.assertEqual(1, another_model.bar)
def test_theming_a_document_before_adding_root(self):
theme = Theme(json={
'attrs' : {
'ThemedModel' : {
'string' : 'w00t'
}
}
})
obj = ThemedModel()
doc = Document()
self.assertEqual('hello', obj.string)
doc.theme = theme
self.assertIs(doc.theme, theme)
changes = dict(calls=[])
def record_trigger(attr, old, new_):
changes['calls'].append((attr, old, new_))
obj.on_change('string', record_trigger)
doc.add_root(obj)
self.assertEqual('w00t', obj.string)
doc.remove_root(obj)
self.assertEqual('hello', obj.string)
self.assertEqual([('string', 'hello', 'w00t'),
('string', 'w00t', 'hello')], changes['calls'])
def test_setting_built_in_theme_error(self):
obj = Model()
doc = Document()
doc.add_root(obj)
with pytest.raises(ValueError):
doc.theme = 1337
def test_setting_built_in_theme_missing(self):
obj = Model()
doc = Document()
doc.add_root(obj)
with pytest.raises(ValueError):
doc.theme = 'some_theme_i_guess'
def test_setting_built_in_theme_obj(self):
obj = Model()
doc = Document()
doc.add_root(obj)
doc.theme = built_in_themes[LIGHT_MINIMAL]
assert "#5B5B5B" == doc.theme._json['attrs']['ColorBar']['title_text_color']
def test_setting_built_in_theme_str(self):
obj = Model()
doc = Document()
doc.add_root(obj)
doc.theme = DARK_MINIMAL
assert "#20262B" == doc.theme._json['attrs']['Figure']['background_fill_color']
def distanceApp(doc: Document) -> None:
distances = lipid_residue_distances[0]
time = lipid_residue_distances[1]['time']
proteins = lipid_residue_distances[1]['protein']
lipids = list(distances.keys())
residues = list(distances[lipids[0]].keys())
protein_id = list(distances[lipids[0]][residues[0]].keys())
residues = [str(x) for x in residues]
protein_id = [str(x) for x in protein_id]
source = ColumnDataSource(data=dict(x=[], y=[]))
protein_name = Select(title="Protein",
value=proteins[0],
options=proteins,
width=100)
pc = Select(title="Protein Copy",
value=protein_id[0],
options=protein_id,
width=100)
res = Select(title="Residue Selection",
value=residues[0],
options=residues,
width=100)
lip = Select(title="Lipid Selection",
value=lipids[0],
options=lipids,
width=100)
p = figure(plot_width=1500,
plot_height=400,
tools='pan, box_zoom, ywheel_zoom, save, reset, help')
color = '#%02x%02x%02x' % tuple(np.random.choice(range(256), size=3))
p.line(x='x', y='y', line_color=color, source=source, line_width=4)
p.y_range = Range1d(0, 4)
p.x_range = Range1d(time[0], time[-1])
p.toolbar.autohide = True
p.axis.axis_label_text_font_size = "12pt"
p.axis.axis_label_text_font_style = "bold"
p.title.align = 'center'
p.xaxis.axis_label = "Trajectory Time"
p.yaxis.axis_label = "Distance (nm)"
def update():
protein_selected = protein_name.value
copy_selected = pc.value
residue_selected = res.value
lipid_selected = lip.value
residues = list(distances[lipid_selected].keys())
if int(residue_selected) not in residues:
residue_selected = residues[0]
res.options = [str(x) for x in residues]
y = distances[lipid_selected][int(residue_selected)][int(
copy_selected)]
source.data = dict(x=time, y=y)
controls = [protein_name, pc, res, lip]
for control in controls:
control.on_change('value', lambda attr, old, new: update())
inputs2 = row([*controls])
layout1 = layout([[inputs2]])
layout2 = layout([p])
update()
doc.add_root(layout1)
doc.add_root(layout2)
doc.title = "Distance Calculations"
doc.theme = Theme(json=yaml.load("""
attrs:
Figure:
toolbar_location: above
height: 500
width: 1000
Grid:
grid_line_dash: [6, 4]
grid_line_color: black
""",
Loader=yaml.FullLoader))
def test_setting_built_in_theme_missing(self):
obj = Model()
doc = Document()
doc.add_root(obj)
with pytest.raises(ValueError):
doc.theme = 'some_theme_i_guess'
def line_handler(doc: Document) -> None:
task_id = doc.session_context.request.arguments.get('task_id')
username = doc.session_context.request.arguments.get('username')
user_dir = os.path.join(settings.USER_DATA, username)
path_to_db = os.path.join(user_dir, task_id)
conn = os.path.join(path_to_db, 'distances.p')
with open(conn, 'rb') as fp:
lipid_residue_distances = pickle.load(fp)
# variables
distances = lipid_residue_distances[0]
time = lipid_residue_distances[1]['time']
proteins = lipid_residue_distances[1]['protein']
lipids = list(distances.keys())
residues = list(distances[lipids[0]].keys())
protein_id = list(distances[lipids[0]][residues[0]].keys())
residues = [str(x) for x in residues]
protein_id = [str(x) for x in protein_id]
# columndatasource
source = ColumnDataSource(data=dict(x=[], y=[]))
#widgets
protein_name = Select(title="Protein",
value=proteins[0],
options=proteins,
width=100)
pc = Select(title="Protein Copy",
value=protein_id[0],
options=protein_id,
width=100)
res = Select(title="Residue Selection",
value=residues[0],
options=residues,
width=100)
lip = Select(title="Lipid Selection",
value=lipids[0],
options=lipids,
width=100)
p = figure(plot_width=1500,
plot_height=400,
tools='pan, box_zoom, ywheel_zoom, save, reset, help')
# line with random color
color = '#%02x%02x%02x' % tuple(np.random.choice(range(256), size=3))
p.line(x='x', y='y', line_color=color, source=source, line_width=2)
# make pretty
p.y_range = Range1d(0, 4)
p.x_range = Range1d(time[0], time[-1])
p.toolbar.autohide = True
p.axis.axis_label_text_font_size = "12pt"
p.axis.axis_label_text_font_style = "bold"
p.title.align = 'center'
p.xaxis.axis_label = "Trajectory Time"
p.yaxis.axis_label = "Distance (nm)"
def update():
protein_selected = protein_name.value
copy_selected = pc.value
residue_selected = res.value
lipid_selected = lip.value
residues = list(distances[lipid_selected].keys())
if int(residue_selected) not in residues:
residue_selected = residues[0]
res.options = [str(x) for x in residues]
y = distances[lipid_selected][int(residue_selected)][int(
copy_selected)]
source.data = dict(x=time, y=y)
# add controls
controls = [protein_name, pc, res, lip]
for control in controls:
control.on_change('value', lambda attr, old, new: update())
# align plot elements
inputs2 = row([*controls])
layout1 = layout([[inputs2]])
layout2 = layout([p])
# render
update()
doc.add_root(layout1)
doc.add_root(layout2)
doc.title = "Distance Calculations"
doc.theme = Theme(json=yaml.load("""
attrs:
Figure:
toolbar_location: above
height: 500
width: 1000
Grid:
grid_line_dash: [6, 4]
grid_line_color: black
""",
Loader=yaml.FullLoader))
def test_setting_built_in_theme_error(self):
obj = Model()
doc = Document()
doc.add_root(obj)
with pytest.raises(ValueError):
doc.theme = 1337
