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GrapheekDB Tutorial part 1 : Adding and removing nodes and edges

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Let’s learn by example

Throughout this tutorial, we’ll walk you through the creation of a :

Basic collaborative filtering recommandation engine for an online book shop

We’ll assume you have GrapheekDB installed already. You can tell GrapheekDB is installed and which version by running the following command in a shell:

python -c "import grapheekdb; print(grapheekdb.__version__)"

If GrapheekDB is installed, you should see the version of your installation. If it isn’t, you’ll get an error telling “No module named grapheekdb”.

See How to install GrapheekDB if it is not installed

Things you should do before starting this tutorial

(but don't absolutely need)

  • You should create a virtual environment dedicated to this tutorial
  • (Strongly recommended) install a recent IPython in this virtual environment, this will allow you to run IPython Notebooks and visualize your graphs
  • Start a new notebook, type in a shell:
ipython notebook
  • This will open a browser with a listing of notebooks
  • Create a new notebook
  • In the first cell, type:
%install_ext https://raw.github.com/cjdrake/ipython-magic/master/gvmagic.py
  • This will install Chris Drake Graphviz Magics Ipython Extension
  • This needs to be done once
  • After that, enable the extension by typing in a new cell:
%load_ext gvmagic

This will allow you to vizualise graphs

Let's add some books

But first, create a new graph

from grapheekdb.backends.data.localmem import LocalMemoryGraph
g = LocalMemoryGraph()

Add books

book1 = g.add_node(kind='book', name='python tutorial', author='tim aaaa', thema='programming')
book2 = g.add_node(kind='book', name='cooking for dummies', author='tom bbbb', thema='cooking')
book3 = g.add_node(kind='book', name='grapheekdb', author='raf cccc', thema='programming')
book4 = g.add_node(kind='book', name='python secrets', author='tim aaaa', thema='programming')
book5 = g.add_node(kind='book', name='cooking a python', author='tom bbbb', thema='cooking')
book6 = g.add_node(kind='book', name='rst the hard way', author='raf cccc', thema='documentation')

Let's explain what we did so far :

  • We add nodes using the graph .add_node method
  • Each node has some properties (kind/name/author/thema)
  • For your information, some books could have more properties, or less, or even none : GrapheekDB is schemaless.

If, as recommended, you use IPython and GraphViz Magics extension, you can see the result by typing in a cell :

%dotobj g.V().dot('name')

It should look like :

/docs/img/graph1.png

Let's explain the code line :

  • %dotobj is an IPython magic clause (which was "imported" when we loaded gvmagic extension)
  • g is the graph
  • g.V() represents all the vertices (other name for "nodes")
  • (advanced : g.V() is a python iterator, I will call it 'entity iterator' in the next parts)
  • g.V().dot() returns an object than can be used by %dotobj to draw the graph
  • g.V().dot('name') means that we want to use the 'name' property as a label for nodes
  • you can try using something else than 'name' such as nothing or 'author' or 'thema'
  • when no arguments is provided to the .dot method, you will see the node internal ids - those ids are automatically created for you and are used internally by GrapheekDB

Now let's add persons

person1 = g.add_node(kind='person', name='sam xxxx')
person2 = g.add_node(kind='person', name='sam xxxx')
person3 = g.add_node(kind='person', name='sam xxxx')
person4 = g.add_node(kind='person', name='sam xxxx')

Now the graph looks like :

/docs/img/graph2.png

Note for readers : I know this is bit small, but it will be more readable when we'll start to filter nodes or create edges

First edges : buyers

It appeared that some persons bought some books, let's save this information in the database :

g.add_edge(person1, book1, action='bought')
g.add_edge(person1, book3, action='bought')
g.add_edge(person1, book4, action='bought')
g.add_edge(person2, book2, action='bought')
g.add_edge(person2, book5, action='bought')
g.add_edge(person3, book1, action='bought')
g.add_edge(person3, book3, action='bought')
g.add_edge(person3, book5, action='bought')
g.add_edge(person3, book6, action='bought')

Now the graph looks like :

/docs/img/graph3.png

So far, person4 didn't buy any books but it appears he saw the 1st book, let's add this information :

g.add_edge(person4, book1, action='saw')

Hmmm, I'd like to see which actions persons did

%dotobj g.V().dot('name', 'action')

This gives :

/docs/img/graph4.png

That's cool, isn't it ? :)

Let's explain what g.V().dot('name', 'action') did :

  • The .dot method can take up to 3 arguments
  • The first argument defines the node property that must be used for nodes label
  • The second argument defines the edge property that must be used for edges label
  • There's a 3rd argument : limit, it defines how much entities should be displayed. The default is 100.

And now for something completely different

So far, we see how to add nodes and edges, but sometimes we need to remove them

This is easy :

# Just adding a node to remove it immediately :
you_dont_know_it_but_you_re_already_dead_node = g.add_node(foo=1)
# Remove it :
you_dont_know_it_but_you_re_already_dead_node.remove()

Part 1 summary :

  • We created a graph
  • We learned how to add nodes
  • We learned how to add edges
  • We learned how to see graph
  • We learned how to choose label for nodes and edges vizualisation.
  • we learned how to remove a node

But hey ! the goal is to recommend a book to new user !

  • Well, now we have a person (person4) who saw a book, we will see in next tutorial parts how we can achieve this <-> recommend him a book

Let's go to next part : Part 2 : Lookup nodes and edges