[WIP] Interactive paper graphs

.gitignore

@@ -126,3 +126,6 @@ propnet/core/alternate_graph_algorithms/graph_parallel_recursive.py
 propnet/core/alternate_graph_algorithms/graph_two_threads.py
 propnet/core/alternate_graph_algorithms/old_graph.py
 mpds-api/
+
+# custom dash-cytoscape
+src/

propnet/web/graph_layout_config.yaml

@@ -5,8 +5,8 @@ fit: true
 ungrabifyWhileSimulating: true
 maxIterations: 100000
 maxSimulationTime: 3000
-springCoeff: 0.04
-springLength: 140
+springCoeff: 0.2
+springLength: 100
 gravity: -3000
 pull: 0.25
 theta: 0.9

propnet/web/graph_settings.yaml

@@ -4,7 +4,7 @@ full_view:
   maxZoom: 2
   style:
     width: "100%"
-    height: "800px"
+    height: "1200px"
     border: "1px #BDBDBD solid"
 model_symbol_view:
   boxSelectionEnabled: true

propnet/web/layouts_explore.py

@@ -1,5 +1,6 @@
 import dash_core_components as dcc
 import dash_html_components as html
+from dash.exceptions import PreventUpdate
 
 from dash.dependencies import Input, Output, State
 
@@ -10,10 +11,68 @@
 
 from propnet.web.layouts_models import models_index
 from propnet.web.layouts_symbols import symbols_index
+from propnet.core.registry import Registry
 
+models_to_show = [
+        'cost',
+        'hhi',
+        'magnetization_normalized_volume',
+        'molar_mass_from_formula',
+        'gbml',
+        'density_relations',
+        'pymatgen_structure_properties',
+        'clarke_thermal_conductivity',
+        'voigt_bulk_modulus',
+        'hill_bulk_modulus',
+        'reuss_bulk_modulus',
+        'compliance_from_elasticity',
+        'piezoelectric_tensor',
+        'electromechanical_coupling',
+        'homogeneous_elasticity_relations',
+        'debye_temperature',
+        'sound_velocity_elastic_longitudinal',
+        'sound_velocity_elastic_transverse',
+        'sound_velocity_elastic_mean'
+    ]
+symbols_to_show = [
+        'hhi_production',
+        'hhi_reserve',
+        'cost_per_kg',
+        'cost_per_mol',
+        'total_magnetization_per_volume',
+        'total_magnetization',
+        'molar_mass',
+        'volume_unit_cell',
+        'volume_per_atom',
+        'lattice',
+        'composition',
+        'nsites',
+        'mass_per_atom',
+        'density',
+        'computed_entry',
+        'formula',
+        'youngs_modulus',
+        'bulk_modulus',
+        'compliance_tensor_voigt',
+        'elastic_tensor_voigt',
+        'piezoelectric_tensor',
+        'piezoelectric_tensor_converse',
+        'electromechanical_coupling',
+        'thermal_conductivity',
+        'debye_temperature',
+        'sound_velocity_longitudinal',
+        'sound_velocity_transverse',
+        'sound_velocity_mean',
+    ]
+labels = [Registry("models")[v] for v in models_to_show] + [Registry("symbols")[v] for v in symbols_to_show]
 
 def explore_layout(app):
-    graph_data = graph_conversion(propnet_nx_graph, hide_unconnected_nodes=False)
+    # graph_data = graph_conversion(propnet_nx_graph, hide_unconnected_nodes=False)
+
+    graph_data = graph_conversion(propnet_nx_graph, hide_unconnected_nodes=True,
+                                  labels_to_show=labels,
+                                  show_symbol_labels=False,
+                                  show_model_labels=False)
     graph_component = html.Div(
         id='graph_component',
         children=[Cytoscape(id='pn-graph', elements=graph_data,
@@ -25,13 +84,19 @@ def explore_layout(app):
     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([
+                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'},
+                              style={'display': 'inline-block'}),
+                html.Button('Download PNG', id='download-png',
+                            style={'display': 'inline-block',
+                                   'margin-left': '10px'})
+            ]),
             html.Div(id='graph_explorer',
                      children=[graph_component])])
 
@@ -42,12 +107,30 @@ 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)
+        # update_labels(elements, show_models=show_models, show_symbols=show_properties)
+        update_labels(elements, show_models=show_models, show_symbols=show_properties,
+                      models_to_show=models_to_show, symbols_to_show=symbols_to_show)
 
         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')])
+    @app.callback(Output('pn-graph', 'generateImage'),
+                  [Input('download-png', 'n_clicks')])
+    def download_image(n_clicks):
+        if n_clicks is None:
+            raise PreventUpdate
+        return {
+            'type': 'png',
+            'action': 'download',
+            'filename': 'pngraph'
+        }
+
+    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'),
+        html.Div(id='emptydiv')
+    ])
 
     return layout

propnet/web/utils.py

@@ -3,6 +3,7 @@
 from os import path
 import re
 from urllib.parse import parse_qs, urlsplit
+from pydash import get
 
 from propnet.core.symbols import Symbol
 from propnet.core.models import Model
@@ -34,7 +35,8 @@ def graph_conversion(graph: nx.DiGraph,
                      derivation_pathway=None,
                      hide_unconnected_nodes=True,
                      show_symbol_labels=True,
-                     show_model_labels=False):
+                     show_model_labels=False,
+                     labels_to_show=None):
     """Utility function to render a networkx graph
     from Graph.graph for use in GraphComponent
 
@@ -54,12 +56,12 @@ def graph_conversion(graph: nx.DiGraph,
         # TODO: more dumb crap related to graph
         if isinstance(n, Symbol):
             # property
-            name = n.name
+            name = 'symbol_' + n.name
             label = n.display_names[0]
             node_type = 'symbol'
         elif isinstance(n, Model):
             # model
-            name = n.title
+            name = 'model_' + n.name
             label = n.title
             node_type = 'model'
         else:
@@ -78,7 +80,8 @@ def graph_conversion(graph: nx.DiGraph,
             }
 
             if (node_type == 'model' and show_model_labels) or \
-                    (node_type == 'symbol' and show_symbol_labels):
+                    (node_type == 'symbol' and show_symbol_labels) or \
+                    (labels_to_show and n in labels_to_show):
                 node['classes'].append('label-on')
             else:
                 node['classes'].append('label-off')
@@ -89,7 +92,7 @@ def graph_conversion(graph: nx.DiGraph,
 
     # TODO: need to clean up after model refactor
     def get_node_id(node_):
-        return node_.title if isinstance(node_, Model) else node_.name
+        return 'model_' + node_.name if isinstance(node_, Model) else 'symbol_' + node_.name
 
     for n1, n2 in graph.edges():
         id_n1 = get_node_id(n1)
@@ -105,7 +108,7 @@ def get_node_id(node_):
                     'data': {'source': id_n1, 'target': id_n2},
                     'classes': ['is-input']}
 
-    if not hide_unconnected_nodes or not derivation_pathway:
+    if not hide_unconnected_nodes and not derivation_pathway:
         unconnected_edges = {
             (node['data']['id'], 'unattached_symbols'):
                 {'data': {'source': node['data']['id'],
@@ -233,7 +236,8 @@ def parse_path(pathname, search=None):
     }
 
 
-def update_labels(elements, show_models=True, show_symbols=True):
+def update_labels(elements, show_models=True, show_symbols=True,
+                  models_to_show=None, symbols_to_show=None):
     for elem in elements:
         group = elem['group']
         if group == 'edge':
@@ -252,8 +256,12 @@ def update_labels(elements, show_models=True, show_symbols=True):
             continue
 
         class_to_add = 'label-off'
-        if (is_model and show_models) or (is_symbol and show_symbols):
-            class_to_add = 'label-on'
+        if is_model and show_models:
+            if not models_to_show or (get(elem, 'data.id', '').split('model_', 1)[1] in models_to_show):
+                class_to_add = 'label-on'
+        elif is_symbol and show_symbols:
+            if not symbols_to_show or (get(elem, 'data.id', '').split('symbol_', 1)[1] in symbols_to_show):
+                class_to_add = 'label-on'
 
         for val in ('label-on', 'label-off'):
             try:

requirements.txt

@@ -1,3 +1,5 @@
+-e git+https://github.com/clegaspi/dash-cytoscape.git#egg=dash-cytoscape
+
 # core, utilities
 numpy>=1.15.1
 scipy>=1.0.1
@@ -17,7 +19,7 @@ pandas>=0.23.4
 dash==1.0.1
 gunicorn>=19.7.1
 Flask-Caching>=1.3.3
-dash-cytoscape==0.1.1
+# dash-cytoscape==0.1.1    # Sub for custom package
 
 # references
 habanero>=0.6.0
@@ -41,4 +43,4 @@ minepy>=1.2.3
 # specific models
 gbml>=1.1.0
 
--e .
+-e .