def evaluate(input_rows, data, aggregate):
quantities = [
QuantityFactory.create_quantity(
symbol_type=ROW_IDX_TO_SYMBOL_NAME[idx],
value=ureg.parse_expression(row['Editable Value']))
for idx, row in enumerate(input_rows) if row['Editable Value']
]
if data and len(data) > 0:
quantities += json.loads(data, cls=MontyDecoder).values()
if not quantities:
raise PreventUpdate
material = Material()
for quantity in quantities:
material.add_quantity(quantity)
graph = Graph()
output_material = graph.evaluate(material)
if aggregate:
output_quantities = output_material.get_aggregated_quantities(
).values()
else:
output_quantities = output_material.get_quantities()
output_rows = [{
'Property': quantity.symbol.display_names[0],
'Value': quantity.pretty_string(sigfigs=3)
} for quantity in output_quantities]
output_table = dt.DataTable(id='output-table',
rows=output_rows,
editable=False)
# TODO: clean up
input_quantity_names = [q.symbol.name for q in quantities]
derived_quantity_names = set(
[q.symbol.name for q in output_quantities]) - \
set(input_quantity_names)
material_graph_data = graph_conversion(
graph.get_networkx_graph(),
nodes_to_highlight_green=input_quantity_names,
nodes_to_highlight_yellow=list(derived_quantity_names))
options = AESTHETICS['global_options']
options['edges']['color'] = '#000000'
output_graph = html.Div(GraphComponent(id='material-graph',
graph=material_graph_data,
options=options),
style={
'width': '100%',
'height': '400px'
})
return [output_graph, html.Br(), output_table]
def test_graph_conversion(self):
graph = Graph()
converted = graph_conversion(graph.get_networkx_graph())
serialized = json.dumps(converted)
self.assertIsNotNone(serialized)
# Ensure that there are both nodes and proper edges
self.assertIn('Band gap', [n['label'] for n in converted['nodes']])
self.assertIn({'from': 'band_gap', "to": "Is Metallic"},
converted['edges'])
def test_graph_conversion(self):
graph = Graph()
converted = graph_conversion(graph.get_networkx_graph())
serialized = json.dumps(converted)
self.assertIsNotNone(serialized)
# Ensure that there are both nodes and proper edges
self.assertIn('Band gap', [n['data']['label']
for n in converted if n['group'] == 'nodes'])
self.assertIn({'source': 'band_gap', "target": "Is Metallic"},
[n['data'] for n in converted if n['group'] == 'edges'])
def explore_layout(app):
graph_data = graph_conversion(propnet_nx_graph,
hide_unconnected_nodes=False)
graph_component = html.Div(
id='graph_component',
children=[
Cytoscape(id='pn-graph',
elements=graph_data,
stylesheet=GRAPH_STYLESHEET,
layout=GRAPH_LAYOUT_CONFIG,
**GRAPH_SETTINGS['full_view'])
],
)
graph_layout = html.Div(id='graph_top_level',
children=[
dcc.Checklist(
id='graph_options',
options=[{
'label': 'Show models',
'value': 'show_models'
}, {
'label': 'Show properties',
'value': 'show_properties'
}],
value=['show_properties'],
labelStyle={'display': 'inline-block'}),
html.Div(id='graph_explorer',
children=[graph_component])
])
@app.callback(Output('pn-graph',
'elements'), [Input('graph_options', 'value')],
[State('pn-graph', 'elements')])
def change_propnet_graph_label_selection(props, elements):
show_properties = 'show_properties' in props
show_models = 'show_models' in props
update_labels(elements,
show_models=show_models,
show_symbols=show_properties)
return elements
layout = html.Div([
html.Div([graph_layout], className='row'),
html.Div([
html.Div([models_index], className='six columns'),
html.Div([symbols_index()], className='six columns'),
],
className='row')
])
return layout
def get_graph_component(props):
aesthetics = AESTHETICS.copy()
show_properties = 'show_properties' in props
show_models = 'show_models' in props
set_(aesthetics, "node_aesthetics.Symbol.show_labels", show_properties)
set_(aesthetics, "node_aesthetics.Model.show_labels", show_models)
graph_data = graph_conversion(g, aesthetics=aesthetics)
graph_component = html.Div(
id=str(uuid4()),
children=[
GraphComponent(id=str(uuid4()),
graph=graph_data,
options=AESTHETICS['global_options'])
],
style={
'width': '100%',
'height': '800px'
})
return [graph_component]
def symbol_layout(symbol_name):
"""Create a Dash layout for a provided symbol.
Args:
symbol_name (str): a symbol name
aesthetics (dict): an aesthetics configuration dictionary
Returns:
Dash layout
"""
# list to hold layouts for each section
layouts = []
symbol = Registry("symbols")[symbol_name]
main_name = symbol.display_names[0]
layouts.append(html.H6('Graph'))
# TODO: costly, should just construct subgraph directly?
subgraph = nx.ego_graph(propnet_nx_graph,
symbol,
undirected=True,
radius=2)
subgraph_data = graph_conversion(subgraph,
show_model_labels=True,
show_symbol_labels=True)
if len(subgraph_data) < 50:
graph_config = GRAPH_LAYOUT_CONFIG.copy()
graph_config['maxSimulationTime'] = 1500
else:
graph_config = GRAPH_LAYOUT_CONFIG
layouts.append(
html.Div(
Cytoscape(id="model_graph",
elements=subgraph_data,
stylesheet=GRAPH_STYLESHEET,
layout=graph_config,
**GRAPH_SETTINGS['model_symbol_view'])))
if len(symbol.display_names) > 1:
display_names = ", ".join(symbol.display_names[1:])
other_names = dcc.Markdown("Also known as: {}".format(display_names))
layouts.append(other_names)
if len(symbol.display_symbols) > 1:
symbols = " ".join(symbol.display_symbols)
symbols = dcc.Markdown("Common symbols: {}".format(symbols))
layouts.append(symbols)
if symbol.category in ('property', 'condition'):
units = dcc.Markdown("Canonical units: **{}**".format(
symbol.unit_as_string))
dimension = dcc.Markdown("**{}**".format(symbol.dimension_as_string))
layouts.append(units)
layouts.append(dimension)
if symbol.comment:
layouts.append(dcc.Markdown(symbol.comment))
return html.Div([
main_name,
html.Br(),
html.Div(layouts),
html.Br(),
#dcc.Link('< Back to Properties', href='/property'),
#html.Br(),
dcc.Link('< Back', href='/explore')
])
def symbol_layout(symbol_name, aesthetics=None):
"""Create a Dash layout for a provided symbol.
Args:
model: a symbol name
Returns:
Dash layout
"""
aesthetics = aesthetics or AESTHETICS.copy()
# list to hold layouts for each section
layouts = []
symbol = DEFAULT_SYMBOLS[symbol_name]
main_name = symbol.display_names[0]
layouts.append(html.H6('Graph'))
# TODO: costly, should just construct subgraph directly?
g = Graph()
subgraph = nx.ego_graph(g.graph, symbol, undirected=True, radius=2)
options = AESTHETICS['global_options']
if "arrows" in options["edges"]:
options["edges"]["arrows"] = "to"
set_(aesthetics, "node_options.show_model_labels", True)
layouts.append(
html.Div(GraphComponent(id="model_graph",
graph=graph_conversion(subgraph,
aesthetics=AESTHETICS),
options=AESTHETICS['global_options']),
style={
'width': '100%',
'height': '300px'
}))
if len(symbol.display_names) > 1:
display_names = ", ".join(symbol.display_names[1:])
other_names = dcc.Markdown("Also known as: {}".format(display_names))
layouts.append(other_names)
if len(symbol.display_symbols) > 1:
symbols = " ".join(symbol.display_symbols)
symbols = dcc.Markdown("Common symbols: {}".format(symbols))
layouts.append(symbols)
if symbol.category in ('property', 'condition'):
units = dcc.Markdown("Canonical units: **{}**".format(
symbol.unit_as_string))
dimension = dcc.Markdown("**{}**".format(symbol.dimension_as_string))
layouts.append(units)
layouts.append(dimension)
if symbol.comment:
layouts.append(dcc.Markdown(symbol.comment))
return html.Div([
main_name,
html.Br(),
html.Div(layouts),
html.Br(),
dcc.Link('< Back to Properties', href='/property'),
html.Br(),
dcc.Link('<< Back to Home', href='/')
])
def model_layout(model_name):
"""Create a Dash layout for a provided model.
Args:
model: an instance of an AbstractModel subclass
Returns:
Dash layout
"""
# dict to hold layouts for each section
layouts = OrderedDict()
# instantiate model from name
model = DEFAULT_MODEL_DICT[model_name]
model_title = html.Div(className='row', children=[
html.H3(model.title),
])
# TODO: costly, should just construct subgraph directly?
g = Graph()
subgraph = nx.ego_graph(g.graph, model, undirected=True)
options = AESTHETICS['global_options']
if "arrows" in options["edges"]:
options["edges"]["arrows"] = "to"
layouts['Graph'] = html.Div(GraphComponent(
id="model_graph",
graph=graph_conversion(subgraph),
options=AESTHETICS['global_options']),
style={
'width': '100%',
'height': '300px'
})
if model.categories:
tags = html.Ul(className="tags",
children=[
html.Li(tag, className="tag")
for tag in model.categories
])
layouts['Tags'] = tags
if model.references:
references = html.Div([
dcc.Markdown(references_to_markdown(ref))
for ref in model.references
])
layouts['References'] = references
symbols = html.Div(children=[
html.Div(className='row',
children=[
html.Div(className='two columns', children=[str(symbol)]),
html.Div(
className='ten columns',
children=[
dcc.Link(
DEFAULT_SYMBOLS[prop_name].display_names[0],
href='/property/{}'.format(prop_name))
])
]) for symbol, prop_name in model.symbol_property_map.items()
])
layouts['Symbols'] = symbols
layouts['Description'] = dcc.Markdown(model.description)
if model.validate_from_preset_test():
sample_data_header = html.Div(
className='row',
children=[
html.Div(className='five columns',
style={'text-align': 'center'},
children=[html.H4('Input(s)')]),
html.Div(className='two columns',
style={'text-align': 'center'},
children=[html.H4('->')]),
html.Div(className='five columns',
style={'text-align': 'center'},
children=[html.H4('Output(s)')])
])
layouts['Sample Code'] = dcc.Markdown('```\n{}```'.format(
model.example_code))
sublayouts = []
for title, layout in layouts.items():
sublayouts.append(html.H6(title))
sublayouts.append(layout)
return html.Div([
model_title,
html.Br(), *sublayouts,
html.Br(),
dcc.Link('< Back to Models', href='/model'),
html.Br(),
dcc.Link('<< Back to Home', href='/')
])
app = dash.Dash()
server = app.server
app.config.supress_callback_exceptions = True # TODO: remove this?
app.scripts.config.serve_locally = True
app.title = "The Hitchhikers Guide to Materials Science"
route = dcc.Location(id='url', refresh=False)
cache = Cache(app.server, config={
'CACHE_TYPE': 'filesystem', 'CACHE_DIR': '.tmp'
})
mpr = MPRester()
g = Propnet().graph
graph_data = graph_conversion(g)
graph_component = html.Div(id='graph', children=[
ForceGraphComponent(
id='propnet-graph',
graphData=graph_data,
width=800,
height=350
)], className='box')
# highlight node for corresponding content
@app.callback(
Output('propnet-graph', 'selectedNode'),
[Input('url', 'pathname')]
)
def hightlight_node_for_content(pathname):
def retrieve_material(n_clicks, query, derive_properties):
"""
Gets the material view from options
Args:
n_clicks (int): load material click
formula (string): formula to find
derive_properties ([str]): list of derivation options
Returns:
Div of graph component with fulfilled options
"""
if n_clicks is None:
return ""
log.info("Fetching data from MP for query {}".format(query))
if query.startswith("mp-") or query.startswith("mvc-"):
mpid = query
else:
mpid = mpr.get_mpid_from_formula(query)
material = mpr.get_material_for_mpid(mpid)
if not material:
return "Material not found."
log.info("Retrieved material {} for formula {}".format(
mpid, material['pretty_formula']))
log.debug("Adding material to graph.")
p = Graph()
material_quantity_names = [
q.symbol.name for q in material.get_quantities()
]
g = p.graph
if 'derive' in derive_properties:
log.info("Deriving quantities for {}".format(mpid))
material = p.evaluate(material)
if 'aggregate' in derive_properties:
log.debug("Aggregating quantities for material {}".format(mpid))
# TODO: get aggregated quantities should return a list
quantities = material.get_aggregated_quantities().items()
else:
quantities = [(q.symbol, q) for q in material.get_quantities()]
else:
quantities = [(q.symbol, q) for q in material.get_quantities()]
rows = []
for symbol, quantity in quantities:
rows.append({
'Symbol': symbol.display_names[0],
'Value': quantity.pretty_string(3),
# TODO: node.node_value.value? this has to make sense
# 'Units': str(node.node_value.symbol.unit_as_string)
})
table = dt.DataTable(rows=rows,
row_selectable=True,
filterable=True,
sortable=True,
editable=False,
selected_row_indices=[],
id='datatable')
derived_quantity_names = set([symbol.name for symbol, quantity in quantities]) -\
set(material_quantity_names)
material_graph_data = graph_conversion(
g,
nodes_to_highlight_green=material_quantity_names,
nodes_to_highlight_yellow=list(derived_quantity_names))
options = AESTHETICS['global_options']
options['edges']['color'] = '#000000'
material_graph_component = html.Div(GraphComponent(
id='material-graph', graph=material_graph_data, options=options),
style={
'width': '100%',
'height': '400px'
})
return html.Div(
[html.H3('Graph'), material_graph_component,
html.H3('Table'), table])
def evaluate(input_rows, data, aggregate):
quantities = []
for idx, row in enumerate(input_rows):
if row['Editable Value']:
try:
value = ureg.parse_expression(row['Editable Value'])
units = Registry("units").get(ROW_IDX_TO_SYMBOL_NAME[idx])
value.ito(units)
except Exception:
# Someone put an invalid value in the table
# TODO: Make error known to the user
raise PreventUpdate
q = QuantityFactory.create_quantity(
symbol_type=ROW_IDX_TO_SYMBOL_NAME[idx], value=value)
quantities.append(q)
if data and len(data) > 0:
quantities += json.loads(data, cls=MontyDecoder).values()
if not quantities:
raise PreventUpdate
material = Material()
for quantity in quantities:
material.add_quantity(quantity)
output_material = graph_evaluator.evaluate(material, timeout=5)
if aggregate:
aggregated_quantities = output_material.get_aggregated_quantities()
non_aggregatable_quantities = [
v for v in output_material.get_quantities()
if v.symbol not in aggregated_quantities
]
output_quantities = list(
aggregated_quantities.values()) + non_aggregatable_quantities
else:
output_quantities = output_material.get_quantities()
output_rows = [{
'Property': quantity.symbol.display_names[0],
'Value': quantity.pretty_string(sigfigs=3)
} for quantity in output_quantities]
output_table = dt.DataTable(id='output-table',
data=output_rows,
columns=[{
'id': val,
'name': val
} for val in ('Property', 'Value')],
editable=False,
**DATA_TABLE_STYLE)
# TODO: clean up
input_quantity_names = [q.symbol for q in quantities]
derived_quantity_names = \
set([q.symbol for q in output_quantities]) - \
set(input_quantity_names)
models_evaluated = set(
output_q.provenance.model
for output_q in output_material.get_quantities())
models_evaluated = [
Registry("models").get(m) for m in models_evaluated
if Registry("models").get(m) is not None
]
material_graph_data = graph_conversion(
propnet_nx_graph,
derivation_pathway={
'inputs': input_quantity_names,
'outputs': list(derived_quantity_names),
'models': models_evaluated
})
output_graph = html.Div(children=[
dcc.Checklist(id='material-graph-options',
options=[{
'label': 'Show models',
'value': 'show_models'
}, {
'label': 'Show properties',
'value': 'show_properties'
}],
value=['show_properties'],
labelStyle={'display': 'inline-block'}),
Cytoscape(id='material-graph',
elements=material_graph_data,
stylesheet=GRAPH_STYLESHEET,
layout=GRAPH_LAYOUT_CONFIG,
**GRAPH_SETTINGS['full_view'])
])
return [output_graph, html.Br(), output_table]
def explore_layout(app):
g = Graph().get_networkx_graph()
graph_data = graph_conversion(g)
graph_component = html.Div(id='graph_component',
children=[
GraphComponent(
id='propnet-graph',
graph=graph_data,
options=AESTHETICS['global_options'])
],
style={
'width': '100%',
'height': '800px'
})
graph_layout = html.Div(id='graph_top_level',
children=[
dcc.Checklist(
id='graph_options',
options=[{
'label': 'Show models',
'value': 'show_models'
}, {
'label': 'Show properties',
'value': 'show_properties'
}],
values=['show_properties'],
labelStyle={'display': 'inline-block'}),
html.Div(id='graph_explorer',
children=[graph_component])
])
# Define default graph component
# TODO: this looks bad, re-evaluate
@app.callback(Output('graph_explorer', 'children'),
[Input('graph_options', 'values')])
def get_graph_component(props):
aesthetics = AESTHETICS.copy()
show_properties = 'show_properties' in props
show_models = 'show_models' in props
set_(aesthetics, "node_aesthetics.Symbol.show_labels", show_properties)
set_(aesthetics, "node_aesthetics.Model.show_labels", show_models)
graph_data = graph_conversion(g, aesthetics=aesthetics)
graph_component = html.Div(
id=str(uuid4()),
children=[
GraphComponent(id=str(uuid4()),
graph=graph_data,
options=AESTHETICS['global_options'])
],
style={
'width': '100%',
'height': '800px'
})
return [graph_component]
layout = html.Div([
html.Div([graph_layout], className='row'),
html.Div([
html.Div([models_index], className='six columns'),
html.Div([symbols_index()], className='six columns'),
],
className='row')
])
return layout