Revision as of 08:45, 29 September 2019

OsProject
edit
id	gremlin-python-tutorial
state
owner	WolfgangFahl
title	Gremlin-Python mini tutorial
url	https://github.com/WolfgangFahl/gremlin-python-tutorial
version	0.0.1
description
date	2019-09-17
since
until

This tutorial is intended to get you up and running using Gremlin / Apache Tinkerpop with Python. Basic knowledge of Python is assumed.

Do you already now Gremlin / Apache Tinkerpop?

If so you can continue with the preqrequisites part. Otherwise you might want to click on the Gremlin logo below.

There is also an explanation of Gremlin steps based on Java in this wiki.

This mini-tutorial is inspired by this stackoverflow question.

The goal is to get access to an apache tinkerpop/gremlin graph database via Python.

The examples in this tutorial have been tested on Ubuntu 18.04 LTS and MacOS with a MacPorts environment as well as in the travis CI environment see https://github.com/WolfgangFahl/gremlin-python-tutorial.

Prerequisites

Java
Python
Gremlin-Server
Gremlin-Console (for debugging)

To get the preqequisites you can either follow the manual or script based installation below. The script based installation is quicker - the manual installation gives you more insight and control over the installation steps.

Manual Installation

Installing Java

There are many ways to install Java and your mileage may vary.

sudo apt-get install openjdk-8-jre 
java -version
openjdk version "1.8.0_222"
OpenJDK Runtime Environment (build 1.8.0_222-8u222-b10-1ubuntu1~18.04.1-b10)
OpenJDK 64-Bit Server VM (build 25.222-b10, mixed mode)

Installing Python and Pip

We assume you'd like to work with python 3.7

sudo apt install python3.7
python --version
Python 3.7.3
sudo apt install python-pip
pip --version
pip 9.0.1 from /usr/lib/python3/dist-packages (python 3.7)

Installing Gremlin-Python

sudo -H pip install -r requirements.txt

Installing Gremlin Server and Console

http://tinkerpop.apache.org/downloads.html

Download Gremlin Server and optionally Gremlin Console and unzip the downloaded files.

Starting the Gremlin Server

cd apache-tinkerpop-gremlin-server-3.4.3
bin/gremlin-server.sh conf/gremlin-server-modern.yaml

See #Gremlin-Server_start for the expected result.

Starting the Gremlin Console

cd apache-tinkerpop-gremlin-console-3.4.3
bin/gremlin.sh

See #Gremlin-Console_start_.28for_debugging.29 for the expected result.

Script based installation

The "run" installation helper script tries to automate the necessary steps

Installation
Gremlin-Server start
Gremlin-Console start (for debugging)
Python script start

The following command should get you going:

git clone https://github.com/WolfgangFahl/gremlin-python-tutorial
./run -i
./run -s
# in another console
./run -p

Help

usage: ./run  [-c|-h|-i|-n|-p|-s|-t|-v]
  -c|--console: start console
  -h|--help: show this usage
  -i|--install: install prerequisites
  -n|--neo4j: start neo4j server
  -p|--python: start python trial code
  -s|--server: start server
  -t|--test: start pytest
  -v|--version: show version

Version

./run -v
apache-tinkerpop-gremlin version 3.4.3

Installation

 run -i

installs

gremlin server
gremlin console
gremlin python module

checking prerequisites ...
/usr/bin/java
openjdk version "1.8.0_222"
OpenJDK Runtime Environment (build 1.8.0_222-8u222-b10-1ubuntu1~18.04.1-b10)
OpenJDK 64-Bit Server VM (build 25.222-b10, mixed mode)
/usr/bin/python
Python 2.7.15+
/usr/bin/pip
pip 9.0.1 from /usr/lib/python2.7/dist-packages (python 2.7)
downloading apache-tinkerpop-gremlin-server-3.4.3-bin.zip
unzipping apache-tinkerpop-gremlin-server-3.4.3-bin.zip
downloading apache-tinkerpop-gremlin-console-3.4.3-bin.zip
unzipping apache-tinkerpop-gremlin-console-3.4.3-bin.zip
installing needed python modules
Requirement already satisfied: futures in /usr/local/lib/python2.7/dist-packages (from -r requirements.txt (line 2))
Requirement already satisfied: gremlinpython in /usr/local/lib/python2.7/dist-packages (from -r requirements.txt (line 4))
Requirement already satisfied: isodate>=0.6.0 in /usr/local/lib/python2.7/dist-packages (from gremlinpython->-r requirements.txt (line 4))
Requirement already satisfied: six>=1.10.0 in /usr/lib/python2.7/dist-packages (from gremlinpython->-r requirements.txt (line 4))
Requirement already satisfied: aenum>=1.4.5 in /usr/local/lib/python2.7/dist-packages (from gremlinpython->-r requirements.txt (line 4))
Requirement already satisfied: tornado<5.0,>=4.4.1 in /usr/local/lib/python2.7/dist-packages (from gremlinpython->-r requirements.txt (line 4))
Requirement already satisfied: certifi in /usr/local/lib/python2.7/dist-packages (from tornado<5.0,>=4.4.1->gremlinpython->-r requirements.txt (line 4))
Requirement already satisfied: singledispatch in /usr/local/lib/python2.7/dist-packages (from tornado<5.0,>=4.4.1->gremlinpython->-r requirements.txt (line 4))
Requirement already satisfied: backports-abc>=0.4 in /usr/local/lib/python2.7/dist-packages (from tornado<5.0,>=4.4.1->gremlinpython->-r requirements.txt (line 4))

Gremlin-Server start

 ./run -s

starts the gremlin server with a default yaml-file in foreground

starting gremlin-server ...
[INFO] GremlinServer - 3.4.3
         \,,,/
         (o o)
-----oOOo-(3)-oOOo-----

[INFO] GremlinServer - Configuring Gremlin Server from /home/wf/source/python/gremlin-python-tutorial/apache-tinkerpop-gremlin-server-3.4.3/conf/gremlin-server-modern.yaml
[INFO] MetricManager - Configured Metrics Slf4jReporter configured with interval=180000ms and loggerName=org.apache.tinkerpop.gremlin.server.Settings$Slf4jReporterMetrics
[INFO] DefaultGraphManager - Graph [graph] was successfully configured via [conf/tinkergraph-empty.properties].
[INFO] ServerGremlinExecutor - Initialized Gremlin thread pool.  Threads in pool named with pattern gremlin-*
[INFO] ServerGremlinExecutor - Initialized GremlinExecutor and preparing GremlinScriptEngines instances.
[INFO] ServerGremlinExecutor - Initialized gremlin-groovy GremlinScriptEngine and registered metrics
[INFO] ServerGremlinExecutor - A GraphTraversalSource is now bound to [g] with graphtraversalsource[tinkergraph[vertices:0 edges:0], standard]
[INFO] OpLoader - Adding the standard OpProcessor.
[INFO] OpLoader - Adding the session OpProcessor.
[INFO] OpLoader - Adding the traversal OpProcessor.
[INFO] TraversalOpProcessor - Initialized cache for TraversalOpProcessor with size 1000 and expiration time of 600000 ms
[INFO] GremlinServer - Executing start up LifeCycleHook
[INFO] Logger$info - Loading 'modern' graph data.
[INFO] GremlinServer - idleConnectionTimeout was set to 0 which resolves to 0 seconds when configuring this value - this feature will be disabled
[INFO] GremlinServer - keepAliveInterval was set to 0 which resolves to 0 seconds when configuring this value - this feature will be disabled
[WARN] AbstractChannelizer - The org.apache.tinkerpop.gremlin.driver.ser.GryoMessageSerializerV3d0 serialization class is deprecated.
[INFO] AbstractChannelizer - Configured application/vnd.gremlin-v3.0+gryo with org.apache.tinkerpop.gremlin.driver.ser.GryoMessageSerializerV3d0
[WARN] AbstractChannelizer - The org.apache.tinkerpop.gremlin.driver.ser.GryoMessageSerializerV3d0 serialization class is deprecated.
[INFO] AbstractChannelizer - Configured application/vnd.gremlin-v3.0+gryo-stringd with org.apache.tinkerpop.gremlin.driver.ser.GryoMessageSerializerV3d0
[INFO] AbstractChannelizer - Configured application/vnd.gremlin-v3.0+json with org.apache.tinkerpop.gremlin.driver.ser.GraphSONMessageSerializerV3d0
[INFO] AbstractChannelizer - Configured application/json with org.apache.tinkerpop.gremlin.driver.ser.GraphSONMessageSerializerV3d0
[INFO] AbstractChannelizer - Configured application/vnd.graphbinary-v1.0 with org.apache.tinkerpop.gremlin.driver.ser.GraphBinaryMessageSerializerV1
[INFO] AbstractChannelizer - Configured application/vnd.graphbinary-v1.0-stringd with org.apache.tinkerpop.gremlin.driver.ser.GraphBinaryMessageSerializerV1
[INFO] GremlinServer$1 - Gremlin Server configured with worker thread pool of 1, gremlin pool of 4 and boss thread pool of 1.
[INFO] GremlinServer$1 - Channel started at port 8182.

Quick way to stop server

If you ran the server in foreground you can stop it with "CTRL-C" in the console where you started it. Otherwise you can simply kill the corresponding process e.g. with:

pkill -9 -fl gremlin-server

Gremlin-Console start (for debugging)

 ./run -c

starts the gremlin console

starting gremlin-console ...
Sep 17, 2019 4:16:03 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.

         \,,,/
         (o o)
-----oOOo-(3)-oOOo-----
plugin activated: tinkerpop.server
plugin activated: tinkerpop.utilities
plugin activated: tinkerpop.tinkergraph
gremlin>

You can try out https://stackoverflow.com/a/52998299/1497139:

gremlin>  :remote connect tinkerpop.server conf/remote.yaml
==>Configured localhost/127.0.0.1:8182
:> g.V().values('name')
==>marko
==>vadas
==>lop
==>josh
==>ripple
==>peter
gremlin>  :remote console
==>All scripts will now be sent to Gremlin Server - [localhost/127.0.0.1:8182] - type ':remote console' to return to local mode
g.V()
==>v[1]
==>v[2]
==>v[3]
==>v[4]
==>v[5]
==>v[6]
gremlin> :exit

Python script start

./run -p

starts the python test script.

./run -p
starting python test code
g.V().count=6
g.E().count=6

Python unit tests start

./run -t

Starts the pytest unit tests. Please make sure a gremlin-server is running.

./run -t
==================================== test session starts =====================================
platform darwin -- Python 3.7.4, pytest-5.1.2, py-1.8.0, pluggy-0.12.0
rootdir: /Users/wf/source/python/gremlin-python-tutorial
collected 1 item                                                                             

test_001.py .                                                                          [100%]

===================================== 1 passed in 12.92s =====================================

Getting Started

The Apache Tinkerpop Getting Started tutorial assumes you are using the groovy console to try things out. We'll use these steps of the tutorial to show how the same traversals are available via gremlin-python.

The modern graph will be the basis for our first steps.

Gremlin-Python is just a Gremlin Language Variant - this means that the Graph Traversals are not executed in the Python enviroment but instead sent as "bytecode" to a server that will execute the traversal and sent back the result.

The first five minutes

test_tutorial.py is the relevant source code for this section.

g - the graph traversal

In the python environment to get the starting point "g" - the graph traversal you need to create a remote connection to a gremlin server. That's why we have to start the gremlin server e.g. with run -s from our automation script above. The gremlin server is configured to supply travesals for the "modern graph" example depicted above.

from gremlin_python.process.anonymous_traversal import traversal
from gremlin_python.driver.driver_remote_connection import DriverRemoteConnection

g = traversal().withRemote(DriverRemoteConnection('ws://localhost:8182/gremlin','g'))

In https://github.com/WolfgangFahl/gremlin-python-tutorial/blob/master/tutorial/remote.py there is a helper class "RemoteTraversal" which allows to read the server configuration from a yaml file. In the tutorial examples the above code is reduced to

# see https://github.com/WolfgangFahl/gremlin-python-tutorial/blob/master/test_001.py
from tutorial import remote

# initialize a remote traversal
g = remote.RemoteTraversal().g()

Steps 1 to 6

see https://github.com/WolfgangFahl/gremlin-python-tutorial/blob/master/test_002_tutorial.py The source code in github is slightly different since some gremlin-server providers do not work with the set of id's starting from 1. To keep things simple the original source code is shown here:

# http://wiki.bitplan.com/index.php/Gremlin_python#g.V.28.29_-_the_vertices
#gremlin> g.V() //(1)
#    ==>v[1]
#    ==>v[2]
#    ==>v[3]
#    ==>v[4]
#    ==>v[5]
#    ==>v[6]
def test_tutorial1():
  # get the vertices
  gV=g.V()
  # we have a traversal now
  assert isinstance(gV,GraphTraversal)
  # convert it to a list to get the actual vertices
  vList=gV.toList()
  # there should be 6 vertices
  assert len(vList)==6
  # the default string representation of a vertex is showing the id
  # of a vertex
  assert str(vList)=="[v[1], v[2], v[3], v[4], v[5], v[6]]"

#gremlin> g.V(1) //(2)
#    ==>v[1]
def test_tutorial2():
   assert str(g.V(1).toList())=="[v[1]]"

#gremlin> g.V(1).values('name') //3
#  ==>marko
def test_tutorial3():
    assert str( g.V(1).values('name').toList())=="['marko']"

#     gremlin> g.V(1).outE('knows') //4
#    ==>e[7][1-knows->2]
#    ==>e[8][1-knows->4]
def test_tutorial4():
    assert str(g.V(1).outE("knows").toList()) == "[e[7][1-knows->2], e[8][1-knows->4]]"

#    gremlin> g.V(1).outE('knows').inV().values('name') //5\
#    ==>vadas
#    ==>josh
def test_tutorial5():
    assert str(g.V(1).outE("knows").inV().values("name").toList())=="['vadas', 'josh']"

#     gremlin> g.V(1).out('knows').values('name') //6\
#    ==>vadas
#    ==>josh
def test_tutorial6():
    assert str(g.V(1).out("knows").values("name").toList())=="['vadas', 'josh']"

Loading and Saving a graph

Given that gremlin-python is a Gremlin Language Variant (GLV) and doesn't have it's own traversal implementation loading and saving graphs is a bit more tricky than in non-GLV environments.

For this tutorial we assume you only work with small, experimental, non-production graph databases. Be warned! We simply clear the whole graph when loading!

Loading the air-routes example

Kelvin Lawrence has a nice example in his tutorial - the https://github.com/krlawrence/graph/blob/master/sample-data/air-routes-small.graphml is also available for this tutorial

from tutorial import remote
import os

# initialize a remote traversal
g = remote.RemoteTraversal().g()

# test loading a graph
def test_loadGraph():
   graphmlFile="air-routes-small.xml";
   # make the local file accessible to the server
   airRoutesPath=os.path.abspath(graphmlFile)
   # drop the existing content of the graph
   g.V().drop().iterate()
   # read the content from the air routes example
   g.io(airRoutesPath).read().iterate()
   vCount=g.V().count().next()
   print ("%s has %d vertices" % (graphmlFile,vCount))
   assert vCount==47

test_loadGraph()

Saving a graph

Let's create a graph containing a single node for the fish named Wanda and save it.

# test saving a graph
def test_saveGraph():
   graphmlPath="/tmp/A-Fish-Named-Wanda.xml"
   # drop the existing content of the graph
   g.V().drop().iterate()
   g.addV("Fish").property("name","Wanda").iterate()
   g.io(graphmlPath).write().iterate()
   print("wrote graph to %s" % (graphmlPath))
   # check that the graphml file exists
   assert os.path.isfile(graphmlPath)

Creating a graphical representation of a graph

A simple way to visualize your graphs is using graphviz. There is a graphviz python module with documentation.

Example Graphviz Usage

see https://github.com/WolfgangFahl/gremlin-python-tutorial/blob/master/test_005_graphviz.py

# see https://github.com/WolfgangFahl/gremlin-python-tutorial/blob/master/test_005_graphviz.py
from tutorial import remote
from graphviz import Digraph
import os.path
from gremlin_python.process.traversal import T

# initialize a remote traversal
g = remote.RemoteTraversal().g()

# test creating a graphviz graph from the tinkerpop graph
def test_createGraphvizGraph():
    # make sure we re-load the tinkerpop modern example
    remoteTraversal=remote.RemoteTraversal()
    remoteTraversal.load("tinkerpop-modern.xml")
    # start a graphviz
    dot = Digraph(comment='Modern')
    # get vertice properties including id and label as dicts
    for vDict in g.V().valueMap(True).toList():
        # uncomment to debug
        # print vDict
        # get id and label
        vId=vDict[T.id]
        vLabel=vDict[T.label]
        # greate a graphviz node label
        # name property is alway there
        gvLabel=r"%s\n%s\nname=%s" % (vId,vLabel,vDict["name"][0])
        # if there is an age property add it to the label
        if "age" in vDict:
            gvLabel=gvLabel+r"\nage=%s" % (vDict["age"][0])
        # create a graphviz node
        dot.node("node%d" % (vId),gvLabel)
    # loop over all edges
    for e in g.E():
        # get the detail information with a second call per edge (what a pitty to be so inefficient ...)
        eDict=g.E(e.id).valueMap(True).next()
        # uncomment if you'd like to debug
        # print (e,eDict)
        # create a graphviz label
        geLabel=r"%s\n%s\nweight=%s" % (e.id,e.label,eDict["weight"])
        # add a graphviz edge
        dot.edge("node%d" % (e.outV.id),"node%d" % (e.inV.id),label=geLabel)
    # modify the styling see http://www.graphviz.org/doc/info/attrs.html
    dot.edge_attr.update(arrowsize='2',penwidth='2')
    dot.node_attr.update(style='filled',fillcolor="#A8D0E4")
    # print the source code
    print (dot.source)
    # render without viewing - default is creating a pdf file
    dot.render('/tmp/modern.gv', view=False)
    # check that the pdf file exists
    assert os.path.isfile('/tmp/modern.gv.pdf')

# call the test
test_createGraphvizGraph()

Resutling graphviz dot source

// Modern
digraph {
	node [fillcolor="#A8D0E4" style=filled]
	edge [arrowsize=2 penwidth=2]
	node1 [label="1\nperson\nname=marko\nage=29"]
	node2 [label="2\nperson\nname=vadas\nage=27"]
	node3 [label="3\nsoftware\nname=lop"]
	node4 [label="4\nperson\nname=josh\nage=32"]
	node5 [label="5\nsoftware\nname=ripple"]
	node6 [label="6\nperson\nname=peter\nage=35"]
	node1 -> node2 [label="7\nknows\nweight=0.5"]
	node1 -> node4 [label="8\nknows\nweight=1.0"]
	node1 -> node3 [label="9\ncreated\nweight=0.4"]
	node4 -> node5 [label="10\ncreated\nweight=1.0"]
	node4 -> node3 [label="11\ncreated\nweight=0.4"]
	node6 -> node3 [label="12\ncreated\nweight=0.2"]
}

Resulting pdf file

If you set "view=True" the pdf display will be directly initiated from the python script.

Connecting to Gremlin enabled graph databases

According to the Gremlin Wiki page there are few different graph databases out there that support Gremlin/Apache Tinkerpop. We'll try to connect to a few of these using gremlin-python.

❌ means we didn't get it to work even after trying
❓ we didn't test it yet
✅ means we got it working

Amazon Neptune ❓

https://docs.aws.amazon.com/de_de/neptune/latest/userguide/access-graph-gremlin-node-js.html

Blazegraph ❓

Cosmos ❓

https://docs.microsoft.com/de-de/azure/cosmos-db/gremlin-support

DataStax ❌

Trial

# https://hub.docker.com/_/datastax
image=datastax/dse-server:6.7.2
docker pull $image
docker run --name datastax  -e DS_LICENSE=accept -p 8182:8182 $image

JanusGraph ❌

Trial

Downloaded 275 MByte janusgraph-0.4.0-hadoop2.zip - unzipped and started bin/gremlin-server.sh (already given several error messages)
followed getting started procedure above
started bin/gremlin.sh

graph = JanusGraphFactory.open('conf/janusgraph-berkeleyje-es.properties')
17:41:38 WARN  org.janusgraph.diskstorage.es.rest.RestElasticSearchClient  - Unable to determine Elasticsearch server version. Default to FIVE.
java.net.ConnectException: Connection refused

Neo4J ✅

Trial

scripts/runNeo4j -rc
./run -n
ln -f Neo4j.yaml server.yaml 
./run -t

Visualization

https://stackoverflow.com/a/51098550/1497139

MATCH (n) RETURN n

Does unfortunately show no results ...

OrientDB ❌

see https://github.com/WolfgangFahl/gremlin-python-tutorial/blob/master/scripts/runOrientDB

# https://hub.docker.com/_/orientdb
docker pull orientdb:3.0.23-tp3
docker run -d --name odbtp3 -p 2424:2424 -p 2480:2480 -p 8182:8182 -e ORIENTDB_ROOT_PASSWORD=rootpwd orientdb:3.0.23-tp3
ln -f OrientDB.yaml server.yaml
./run -t

Tests fail see:

https://github.com/orientechnologies/orientdb-gremlin/issues/167

Links

@@ Line 36: / Line 36: @@
 === Installing Java ===
 There are many ways to install Java and your mileage may vary.
-<source lang='bash' highlight="1">
+<source lang='bash' highlight="1-2">
 sudo apt-get install openjdk-8-jre
 java -version
@@ Line 56: / Line 56: @@
 === Installing Gremlin-Python ===
-<source lang='bash'>
+<source lang='bash' highlight="1">
 sudo -H pip install -r requirements.txt
 </source>
@@ Line 63: / Line 63: @@
 Download Gremlin Server and optionally Gremlin Console and unzip the downloaded files.
 === Starting the Gremlin Server ===
-<source lang='bash'>
+<source lang='bash' highlight="1-2">
 cd apache-tinkerpop-gremlin-server-3.4.3
 bin/gremlin-server.sh conf/gremlin-server-modern.yaml
@@ Line 70: / Line 70: @@
 === Starting the Gremlin Console ===
-<source lang='bash'>
+<source lang='bash' highlight="1-2">
 cd apache-tinkerpop-gremlin-console-3.4.3
 bin/gremlin.sh

Difference between revisions of "Gremlin python"

Revision as of 08:45, 29 September 2019

Do you already now Gremlin / Apache Tinkerpop?

Prerequisites

Manual Installation

Installing Java

Installing Python and Pip

Installing Gremlin-Python

Installing Gremlin Server and Console

Starting the Gremlin Server

Starting the Gremlin Console

Script based installation

Help

Version

Installation

Gremlin-Server start

Quick way to stop server

Gremlin-Console start (for debugging)

Python script start

Python unit tests start

Getting Started

The first five minutes

g - the graph traversal

Steps 1 to 6

Loading and Saving a graph

Loading the air-routes example

Saving a graph

Creating a graphical representation of a graph

Example Graphviz Usage

Resutling graphviz dot source

Resulting pdf file

Connecting to Gremlin enabled graph databases

Amazon Neptune ❓

Blazegraph ❓

Cosmos ❓

DataStax ❌

Trial

JanusGraph ❌

Trial

Neo4J ✅

Trial

Visualization

OrientDB ❌

Links

Navigation menu

Search