def update_widgets(self):
self.display_system = DisplaySystem(self)
self.display_system.create_system_widget()
self.figures = DisplayFigures(self)
self.figures.create_figures_widget()
self.tables = DisplayTables(self)
self.tables.create_tables_widget()
class InteractiveInput(object):
def __init__(self, name='', version='', equations=None, parameters=None,
get_parameters=None, auxiliary_variables=[], constraints=[],
symbols={}, resolve_cycles=False, resolve_codominance=False,
centered_axes=False, xaxis=None, yaxis=None, recast=True,
x_range=[1e-3, 1e3], y_range=[1e-3, 1e3],
zlim=None, by_signature=False, kinetic_orders=None,
included_cases=None, biological_constraints=[], resolution=100,
**kwargs):
'''
'''
setattr(self, 'ds', None)
setattr(self, 'equations', [])
setattr(self, 'name', name)
setattr(self, 'version', version)
setattr(self, 'pvals', None)
setattr(self, 'cyclical', resolve_cycles)
setattr(self, 'codominance', resolve_codominance)
setattr(self, 'recast', recast)
setattr(self, 'auxiliary', [])
setattr(self, 'constraints', [])
setattr(self, 'kinetic_orders', [])
setattr(self, 'symbols', symbols)
setattr(self, 'widget', Tab())
setattr(self, 'figures', None)
setattr(self, 'figure_data', [])
setattr(self, 'tables', None)
setattr(self, 'table_data', [])
setattr(self, 'display_system', None)
setattr(self, 'options', dict(kwargs))
self.options.update(center_axes=centered_axes,
xaxis=xaxis, yaxis=yaxis,
range_x=x_range, range_y=y_range, zlim=zlim,
by_signature=by_signature,
kinetic_orders=kinetic_orders,
get_parameters=get_parameters,
included_cases=included_cases,
biological_constraints=biological_constraints,
resolution=resolution)
if equations is not None:
self.equations = equations
if isinstance(equations, list) is False:
self.equations = [equations]
if auxiliary_variables is not None:
self.auxiliary = auxiliary_variables
if isinstance(auxiliary_variables, list) is False:
self.auxiliary = [auxiliary_variables]
if constraints is not None:
self.constraints = constraints
if isinstance(constraints, list) is False:
self.constraints = [constraints]
if parameters is not None:
self.pvals = dspace.VariablePool(names = parameters.keys())
self.pvals.update(parameters)
self.root = VBox(children=[self.widget])
display(self.root)
self.update_child('About', self.help_widget())
self.update_child('Main Menu', self.edit_equations_widget())
def set_defaults(self, key, value):
self.options[key] = value
def defaults(self, key):
if key in self.options:
return self.options[key]
else:
return None
def reload_widgets(self):
self.widget = Tab()
display(self.root)
self.update_child('Main Menu', self.edit_equations_widget())
if self.ds is None:
return
self.update_widgets()
self.figures.load_widgets()
def child_with_name(self, name):
children = self.widget.children
for i in xrange(len(children)):
if children[i].description == name:
return self.widget.children[i]
return None
def update_child(self, name, child, index=None):
previous_children = self.widget.children
children = [i for i in self.widget.children]
added = False
for i in xrange(len(children)):
if children[i].description == name:
self.widget._titles = {}
old = children.pop(i)
break
if added is False:
if child is not None:
child.description = name
children.append(child)
index = len(children)-1
else:
index = 0
self.widget.children = children
for (i, child) in enumerate(children):
self.widget.set_title(i, child.description)
self.widget.selected_index = index
def enumerate_phenotypes_menu(self, b):
cases_table = CasesTable(self)
return cases_table.cases_table_widget()
def case_report_menu(self, b):
case_report = CaseReport(self,
self.defaults('by_signature'))
return case_report.create_case_widget()
def co_localize_menu(self, b):
case_report = CaseColocalization(self,
self.defaults('by_signature'))
return case_report.colocalization_widget()
def case_intersect_menu(self, b):
case_report = CaseIntersection(self,
self.defaults('by_signature'))
return case_report.case_intersection_widget()
def create_plot_menu(self, b):
plot = MakePlot(self)
return plot.create_plot_widget()
def load_widget(self, b):
self.name = str(b.name.value)
self.version = str(self.version_field.value)
saved = WidgetSavedData.load_widget_data(self)
b.wi.visible = True
if self.ds is None:
return
self.make_options_menu(b.button)
self.update_widgets()
self.figures.load_widgets()
self.tables.load_widgets()
## b.version.value = self.version
self.widget.selected_index = 0
def save_widget_data(self, b):
save_widget = SavePopupWidget(self)
widget_container = save_widget.save_popup_widget()
self.root.children = [self.widget, widget_container]
self.widget.visible = False
def modify_equations_widget(self, b):
self.ds = None
self.figure_data = []
self.table_data = []
self.widget.close()
self.widget = Tab()
display(self.root)
self.update_child('Main Menu', self.edit_equations_widget(editing=True))
def make_options_menu(self, b):
wi = b.wi
b.visible = False
b.name.visible = False
b.load.visible = False
actions = [('Enumerate Phenotypes', self.enumerate_phenotypes_menu),
('Analyze Case', self.case_report_menu),
('Intersect Phenotypes', self.case_intersect_menu),
('Co-localize Phenotypes', self.co_localize_menu),
('Create Plot', self.create_plot_menu)]
actions_h = HTML(value='<b>Actions</b>')
options_h = HTML(value='<b>Options</b>')
options = [('Edit Symbols', self.create_edit_symbols),
('Edit Parameters', self.create_edit_parameters),
('Save Data', self.save_widget_data)]
actions_w = Tab()
options_w = []
for name, method in options:
button = Button(description=name)
button.on_click(method)
## button.version = b.version
if method is None:
button.disabled = True
options_w.append(button)
edit = Button(description='Modify System')
edit.on_click(self.modify_equations_widget)
warning = HTML()
warning.value = '<font color="red"><b>Warning! Modifying system erases saved figures and tables.</b></font>'
wi.children = [actions_h, actions_w] + [options_h] + options_w + [edit, warning]
for title, method in actions:
title, widget = method(self)
children = [i for i in actions_w.children] + [widget]
actions_w.children = children
actions_w.set_title(len(children)-1, title)
self.widget.selected_index = 1
def update_widgets(self):
self.display_system = DisplaySystem(self)
self.display_system.create_system_widget()
self.figures = DisplayFigures(self)
self.figures.create_figures_widget()
self.tables = DisplayTables(self)
self.tables.create_tables_widget()
def help_widget(self):
about_str = ['<p style="text-align:justify;"><font color="darkblue">',
'You are using the Design Space Toolbox V2 Jupyter',
'Notebook-based widget, a graphical interface for',
'the Design Space Toolbox V2 created by Jason',
'Lomnitz in the laboratory of Michael A. Savageau.',
'<br><br>',
'This software has been created for the analysis',
'of mathematical models of biochemical systems.',
'This library deconstructs a model into a series of',
'sub-models that can be analyzed by applying a series',
'of numerical and symbolic methods.',
'<br><br>',
'To begin, please enter the information in the required',
'fields (marked by an "*") and optional fields.',
'The Name field is used to save and load a model',
'workspace,which includes the system equations, tables'
' and figures. The primary input into the widget are the',
'system equations, represented by a list of strings.',
'<br><br></font>',
'The equations must satisfy the following rules:<br>',
'1. Each equation has to be explicitly stated as:<br>',
'1.1 A differential equation, where the "." operator',
'denotes the derivative with respect to time.<br>',
'1.2 An algebraic constraint, where the left hand side',
'is either a variable or a mathematical expression.',
'Auxiliary variables associated with the constraint must',
'be explicitly defined (unless the left-hand side is the',
'auxiliary variable).',
'<br>',
'2. Multiplication is represented by the "*" operator.',
'<br>',
'3. Powers are represented by the "^" operator.',
'<br>',
'4. Architectural constraints are defined as inequalities,',
'where both sides of the inequality are products of',
'power-laws.<br><br>',
'</p>']
report_str = ['<p style="text-align:center;">',
'This software is a still under active development and may',
'contain a number of bugs and issues. A complete list of',
'known open issues can be found online here: ',
'<a target="_blank"',
'href="https://bitbucket.org/jglomnitz/design-space-toolbox/issues?status=new&status=open">',
'Project Issue Tracker</a>.<br>',
'<font color="red"><b>If you found a new bug in the stable',
'or release version of the design space toolbox; or would',
'like to request an enhancement that has not yet',
'been reported, please report it here:</b></font>',
'<a target="_blank"',
'href="https://bitbucket.org/jglomnitz/design-space-toolbox/issues/new?title=Issue%20name">',
'REPORT BUG</a>',
'</p>']
html = HTML(value=' '.join(report_str)+' '.join(about_str))
return VBox(children=[html])
def edit_equations_widget(self, editing=False):
kinetic_orders = self.options['kinetic_orders']
if kinetic_orders is None:
kinetic_orders = []
name = Text(description='* Name', value=self.name)
version = Text(description='Version', value=self.version)
self.version_field = version
equations=Textarea(description='* Equations',
value='\n'.join(self.equations))
aux=Textarea(description='Auxiliary Variables',
value=', '.join(self.auxiliary))
html = HTML(value='<b>Architectural Constraints</b>')
constraints=Textarea(description='Parameters',
value=', '.join(self.constraints)
)
options_html = HTML(value='<b>Additional Options</b>')
cyclical = Checkbox(description='Check for Cycles',
value = self.cyclical)
codominance = Checkbox(description='Check for Co-dominance',
value = self.codominance)
recast = Checkbox(description='Recast Equations',
value = self.recast)
replacements=Textarea(description='Kinetic Orders',
value=', '.join(
[i for i in kinetic_orders]))
wi = VBox(children=[equations,
aux, html,
constraints, replacements,
options_html, cyclical,
codominance,recast,
])
button = Button(value=False,
description='Create Design Space')
button.on_click(self.make_design_space)
button.equations = equations
button.aux = aux
button.constraints = constraints
button.cyclical = cyclical
button.codominance = codominance
button.recast = recast
button.replacements = replacements
button.wi = wi
button.name = name
## button.version = version
load = Button(value=False,
description='Load Data')
load.on_click(self.load_widget)
load.equations = equations
## load.version = version
load.aux = aux
load.constraints = constraints
load.cyclical = cyclical
load.codominance = codominance
load.replacements = replacements
load.wi = wi
load.name = name
load.button = button
button.load = load
edit_symbols = Button(value=False, description='Edit Symbols')
edit_symbols.on_click(self.create_edit_symbols)
edit_parameters = Button(value=False, description='Edit Parameters')
edit_parameters.on_click(self.create_edit_parameters)
button.edit_symbols = edit_symbols
button.edit_parameters = edit_parameters
edit_equations = VBox(description='Edit Equations',
children=[name, version, wi,
edit_symbols,
edit_parameters,
button,
load])
wi.visible = False
edit_symbols.visible = False
edit_parameters.visible = False
if self.ds is not None:
wi.visible = True
## self.update_widgets()
self.make_options_menu(button)
if editing is True:
self.make_design_space(button)
return edit_equations
def make_design_space(self, b):
if b.wi.visible == False:
b.wi.visible = True
b.description = 'Done'
return
self.version_field.visible = False
self.equations = [i.strip() for i in str(b.equations.value).split('\n') if len(i.strip()) > 0]
self.auxiliary = [i.strip() for i in str(b.aux.value).split(',') if len(i.strip()) > 0]
self.constraints = [i.strip() for i in str(b.constraints.value).split(',') if len(i.strip()) > 0]
self.cyclical = b.cyclical.value
self.codominance = b.codominance.value
self.recast = b.recast.value
eq = dspace.Equations(self.equations,
auxiliary_variables=self.auxiliary,
latex_symbols=self.symbols)
if self.recast:
eq = eq.recast()
self.name = b.name.value
constraints = self.constraints
replacements = str(b.replacements.value).strip()
self.options.update(kinetic_orders=str(b.replacements.value).split(','))
if len(replacements) > 0:
replacements = str(b.replacements.value).split(',')
replacements = [[j.strip() for j in i.split('=')] for i in replacements]
parameter_dict = {i:j for i,j in replacements}
else:
parameter_dict = {}
if len(constraints) == 0:
constraints = None
self.ds = dspace.DesignSpace(eq, name=b.name.value,
constraints=constraints,
resolve_cycles=self.cyclical,
resolve_codominance=self.codominance,
parameter_dict=parameter_dict)
if self.pvals == None:
self.pvals = dspace.VariablePool(
names=self.ds.independent_variables
)
else:
pvals = dspace.VariablePool(
names=self.ds.independent_variables
)
for i in pvals:
if i in self.pvals:
pvals[i] = self.pvals[i]
self.pvals = pvals
get_parameters = self.defaults('get_parameters')
if get_parameters is not None:
case = self.ds(get_parameters)
self.pvals = case.valid_interior_parameter_set()
self.symbols.update({i:i for i in self.ds.dependent_variables + self.ds.independent_variables if i not in self.symbols})
self.ds.update_latex_symbols(self.symbols)
self.update_widgets()
self.make_options_menu(b)
def create_edit_symbols(self, b):
Edit = EditSymbols(self)
Edit.edit_symbols_widget()
def create_edit_parameters(self, b):
Edit = EditParameters(self)
Edit.edit_parameters_widget()
