#!/usr/bin/env python
# coding: utf-8

# # Neo4j Graph
# This notebook demonstrates the visualization of subgraphs from the [Neo4j](https://neo4j.com/) Graph Database. It uses the [py2neo](https://py2neo.org/) library to access a Neo4j database instance.
# 
# The examples in this notebook access the [COVID-19-Net](https://github.com/covid-19-net/covid-19-community) Knowledge Graph.
# 
# **NOTE, this notebook does not run on MyBinder.org due to a blocked port.**
# 
# **However, you can run this and other example notebooks on Pangeo Binder [here](https://github.com/sbl-sdsc/neo4j-ipycytoscape).**
# 
# Author: Peter W. Rose (pwrose@ucsd.edu)

# In[1]:


import random
import ipycytoscape
from py2neo import Graph


# #### Node and edge styles

# In[2]:


node_centered = {'selector': 'node',
                 'style': {'font-size': '10',
                           'label': 'data(name)',
                           'height': '60',
                           'width': '80',
                           'text-max-width': '80',
                           'text-wrap': 'wrap',
                           'text-valign': 'center',
                           'background-color': 'blue',
                           'background-opacity': 0.6}
             }


# In[3]:


edge_directed = {'selector': 'edge',
                 'style':  {'line-color': '#9dbaea',
                            'target-arrow-shape': 'triangle',
                            'target-arrow-color': '#9dbaea',
                            'curve-style': 'bezier'}
                }


# In[4]:


edge_directed_named = {'selector': 'edge',
                       'style':  {'font-size': '8',
                                  'label': 'data(name)',
                                  'line-color': '#9dbaea',
                                  'text-rotation': 'autorotate',
                                  'target-arrow-shape': 'triangle',
                                  'target-arrow-color': '#9dbaea',
                                  'curve-style': 'bezier'}
                }


# In[5]:


edge_undirected = {'selector': 'edge',
                   'style':  {'line-color': '#9dbaea'}
                  }


# #### Node colors
# Change seed to select a different color palette.

# In[6]:


def random_color_palette(n_colors, seed=3):
    """ 
    Creates a random color palette of n_colors.
    
    Parameters
    ----------
    n_colors : int
        number of colors in the color palette
    seed : int
        random number seed

    See https://stackoverflow.com/questions/28999287/generate-random-colors-rgb)
    """
    random.seed(seed)
    return ['#'+''.join([random.choice('0123456789ABCDEF') for j in range(6)]) for i in range(n_colors)]


# ### Connect to a Neo4j Database
# Here we use the [COVID-19-Net](https://github.com/covid-19-net/covid-19-community) Knowledge Graph to demonstrate how to run a Neo4j Cypher query and pass the resulting subgraph into Cytoscape.

# In[7]:


graph = Graph("bolt://132.249.238.185:7687", user="reader", password="demo")


# ### Example 1: Find all cities with the name "San Francisco"
# This query demonstrates the geographic hierachy in COVID-19-Net.

# In[8]:


query1 = """
MATCH p=(:City{name:'San Francisco'})-[:IN*]->(:World) RETURN p
"""
subgraph1 = graph.run(query1).to_subgraph()


# #### Add Neo4j subgraph to Cytoscape Widget
# We create a `tooltip` named 'tooltip' and use this attribute later to create a tool tip.

# In[9]:


widget1 = ipycytoscape.CytoscapeWidget()
widget1.graph.add_graph_from_neo4j(subgraph1)


# #### Set node and edge styles

# In[10]:


style1 = [node_centered, edge_directed]


# #### Set node specific colors based on node labels

# In[11]:


labels1 = list(subgraph1.labels())
labels1.sort()
print('Node labels:', labels1)


# In[12]:


colors1 = random_color_palette(len(labels1))


# In[13]:


for label, color in zip(labels1, colors1):
    style1.append({'selector': 'node[label = "' + label + '"]', 'style': {'background-color': color}})


# In[14]:


widget1.set_style(style1)


# In[15]:


widget1.set_layout(name='dagre', padding=0)


# When a Neo4j subgraph is added to a Cytoscape graph, a ```tooltip``` attribute is generated that contains all Neo4j node properties.

# In[16]:


widget1.set_tooltip_source('tooltip')


# Click on a node to show the tooltip

# In[17]:


widget1


# ### Example 2: Find all proteins that interact with the SARS-CoV-2 Spike protein
# Here we run an undirected query (no "->" arrow) since the direction of interaction is arbitrary.

# In[18]:


query2 = """
MATCH p=(:Protein{name: 'Spike glycoprotein', taxonomyId: 'taxonomy:2697049'})-[:INTERACTS_WITH]-(:Protein) RETURN p
"""
subgraph2 = graph.run(query2).to_subgraph()


# In[19]:


query2 = """
MATCH p=(:Protein{name: 'Angiotensin-converting enzyme 2', taxonomyId: 'taxonomy:9606'})-[:INTERACTS_WITH]-(:Protein) RETURN p
"""
subgraph2 = graph.run(query2).to_subgraph()


# In[20]:


widget2 = ipycytoscape.CytoscapeWidget()
widget2.graph.add_graph_from_neo4j(subgraph2)


# In[21]:


style2 = [node_centered, edge_undirected]


# In[22]:


labels2 = list(subgraph2.labels())
labels2.sort()
print('Node labels:', labels2)


# In[23]:


colors2 = random_color_palette(len(labels2))


# In[24]:


for label, color in zip(labels2, colors2):
    style2.append({'selector': 'node[label = "' + label + '"]', 'style': {'background-color': color}})


# In[25]:


widget2.set_style(style2)


# In[26]:


widget2.set_layout(name='concentric', padding=0)


# In[27]:


widget2.set_tooltip_source('tooltip')


# Click on a node to show the tooltip

# TODO: The rendering of this concentric network has a rendering error. This must be a cytoscape issue.

# In[28]:


widget2


# ### Example 3: Explore the Data Sources used to create the COVID-19-Net Knowledge Graph

# In[29]:


query3 = """
MATCH p=(:MetaNode)-[:ETL_FROM]->(:DataSource) RETURN p  // ETL_FROM: Extracted, transformed, and loaded FROM
"""
subgraph3 = graph.run(query3).to_subgraph()


# In[30]:


widget3 = ipycytoscape.CytoscapeWidget()
widget3.graph.add_graph_from_neo4j(subgraph3)


# In[31]:


style3 = [node_centered, edge_directed]


# In[32]:


labels3 = list(subgraph3.labels())
labels3.sort()
print('Node labels:', labels3)


# In[33]:


colors3 = random_color_palette(len(labels3))


# In[34]:


for label, color in zip(labels3, colors3):
    style3.append({'selector': 'node[label = "' + label + '"]', 'style': {'background-color': color}})


# In[35]:


widget3.set_style(style3)


# In[36]:


widget3.set_layout(name='klay', padding=0)


# In[37]:


widget3.set_tooltip_source('tooltip')


# Click on a node to show the tooltip

# In[38]:


widget3


# ### Example 4: Create a Metagraph that shows the Nodes and their Relationships in the COVID-19-Net Knowledge Graph

# In[39]:


query4 = """
MATCH p=(a:MetaNode)-[:META_RELATIONSHIP]->(b:MetaNode) 
WHERE a.name <> 'Location' AND b.name <> 'Location' // exclude Location nodes since they make the graph too crowded
RETURN p
"""
subgraph4 = graph.run(query4).to_subgraph()


# In[40]:


widget4 = ipycytoscape.CytoscapeWidget()
widget4.graph.add_graph_from_neo4j(subgraph4)


# In[41]:


style4 = [node_centered, edge_directed_named]


# In[42]:


labels4 = list(subgraph4.labels())
labels4.sort()
print('Node labels:', labels4)


# In[43]:


colors4 = random_color_palette(len(labels4))


# In[44]:


for label, color in zip(labels4, colors4):
    style4.append({'selector': 'node[label = "' + label + '"]', 'style': {'background-color': color}})


# In[45]:


widget4.set_style(style4)


# Cola layout [options](https://github.com/cytoscape/cytoscape.js-cola#api)

# In[46]:


widget4.set_layout(name='cola', padding=0, nodeSpacing=65, nodeDimensionsIncludeLabels=True, unconstrIter=5000)


# In[47]:


widget4.set_tooltip_source('tooltip')


# Click on a node to show the tooltip

# In[48]:


widget4


# In[ ]: