neo2R

Release 2.4.2

Neo4j to R

Homepage CRAN R Documentation Download

License
GPL-3.0

Documentation

README

neo2R

CRAN_Status_Badge

The aim of the neo2R is to provide simple and low level connectors for querying Neo4j graph databases. The objects returned by the query functions are either lists or data.frames with very few post-processing. It allows fast processing of queries returning many records. And it let the user handle post-processing according to the data model and his needs. It has been developed to support the BED package (https://github.com/patzaw/BED, https://f1000research.com/articles/7-195/v3 ). Other packages such as RNeo4j (https://github.com/nicolewhite/RNeo4j) or neo4R (https://github.com/neo4j-rstats/neo4r) provide connectors to neo4j databases with additional features.

Installation

From CRAN

install.packages("neo2R")

Dependencies

The following R packages available on CRAN are required:

  • base64enc: Tools for base64 encoding
  • jsonlite: A Simple and Robust JSON Parser and Generator for R
  • httr: Tools for Working with URLs and HTTP
  • utils: The R Utils Package

Installation from github

devtools::install_github("patzaw/neo2R")

Use

Running Neo4j

You can download and install Neo4j according to the documentation. You can also run it in a docker container. It takes a few seconds to start.

The following chunks show how to instantaite a docker container running either version 3 or version 4 (only those 2 are supported by neo2R) of Neo4j. The main differences between the 2 calls are related to the apoc library and SSL configuration.

Neo4j 3.x

#!/bin/sh

#################################
## CONFIG according to your needs
#################################

export CONTAINER=neo4j_cont

export NJ_VERSION=3.5.30

## Ports
export NJ_HTTP_PORT=7474
export NJ_HTTPS_PORT=7473
export NJ_BOLT_PORT=7687

## Change the location of the Neo4j directory
export NJ_HOME=~/neo4j_home

## Authorization
NJ_AUTH=neo4j/donttrustusers # set to 'none' if you want to disable authorization

## APOC download
export NJ_APOC=https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/3.5.0.15/apoc-3.5.0.15-all.jar

#################################
## RUN
#################################

mkdir -p $NJ_HOME

## Import and data directory
export NJ_IMPORT=$NJ_HOME/neo4jImport
mkdir -p $NJ_IMPORT
export NJ_DATA=$NJ_HOME/neo4jData
if test -e $NJ_DATA; then
   echo "$NJ_DATA directory exists ==> abort - Remove it before proceeding" >&2
   exit
fi
mkdir -p $NJ_DATA

## SSL
export NJ_SSL=${NJ_HOME}/ssl
mkdir -p ${NJ_SSL}/client_policy
mkdir -p ${NJ_SSL}/client_policy/revoked
mkdir -p ${NJ_SSL}/client_policy/trusted
openssl req -subj "/CN=localhost" -new -newkey rsa:2048 -days 365 -nodes -x509 -keyout ${NJ_SSL}/client_policy/private.key -out ${NJ_SSL}/client_policy/public.crt
chmod -R a+rwx ${NJ_SSL}

## Neo4j plugins: APOC
export NJ_PLUGINS=$NJ_HOME/neo4jPlugins
mkdir -p $NJ_PLUGINS
cd $NJ_PLUGINS
wget --no-check-certificate $NJ_APOC
cd -

docker run -d \
   --name $CONTAINER \
   --publish=$NJ_HTTP_PORT:7474 \
    --publish=$NJ_HTTPS_PORT:7473 \
   --publish=$NJ_BOLT_PORT:7687 \
   --env=NEO4J_dbms_memory_heap_initial__size=2G \
   --env=NEO4J_dbms_memory_heap_max__size=2G \
   --env=NEO4J_dbms_memory_pagecache_size=1G \
   --env=NEO4J_dbms_query__cache__size=0 \
   --env=NEO4J_cypher_min__replan__interval=100000000ms \
   --env=NEO4J_cypher_statistics__divergence__threshold=1 \
   --env=NEO4J_dbms_security_procedures_unrestricted=apoc.\\\* \
   --env=NEO4J_dbms_directories_import=import \
   --env NEO4J_AUTH=$NJ_AUTH \
   --volume $NJ_IMPORT:/var/lib/neo4j/import \
   --volume $NJ_DATA/data:/data \
    --volume $NJ_PLUGINS:/plugins \
    --volume=$NJ_SSL:/ssl \
    --env=NEO4J_https_ssl__policy=client_policy \
    --env=NEO4J_dbms_ssl_policy_client__policy_base__directory=/ssl/client_policy \
    --env=NEO4J_dbms_ssl_policy_client__policy_client__auth=NONE \
    --env=NEO4J_dbms_ssl_policy_client__policy_trust__all=true \
    neo4j:$NJ_VERSION

sleep 15
sudo chmod a+rwx $NJ_IMPORT

Neo4j 4.x

#!/bin/sh

#################################
## CONFIG according to your needs
#################################

export CONTAINER=neo4j_cont

export NJ_VERSION=4.4.26

## Ports
export NJ_HTTP_PORT=7474
export NJ_HTTPS_PORT=7473
export NJ_BOLT_PORT=7687

## Change the location of the Neo4j directory
export NJ_HOME=~/neo4j_home

## Authorization
NJ_AUTH=neo4j/donttrustusers # set to 'none' if you want to disable authorization

## APOC download
export NJ_APOC=https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/4.4.0.3/apoc-4.4.0.3-all.jar

#################################
## RUN
#################################

mkdir -p $NJ_HOME

## Import and data directory
export NJ_IMPORT=$NJ_HOME/neo4jImport
mkdir -p $NJ_IMPORT
export NJ_DATA=$NJ_HOME/neo4jData
if test -e $NJ_DATA; then
   echo "$NJ_DATA directory exists ==> abort - Remove it before proceeding" >&2
   exit
fi
mkdir -p $NJ_DATA

## SSL
export NJ_SSL=${NJ_HOME}/ssl
mkdir -p ${NJ_SSL}/https
mkdir -p ${NJ_SSL}/https/revoked
mkdir -p ${NJ_SSL}/https/trusted
openssl req -subj "/CN=localhost" -new -newkey rsa:2048 -days 365 -nodes -x509 -keyout ${NJ_SSL}/https/private.key -out ${NJ_SSL}/https/public.crt
chmod -R a+rwx ${NJ_SSL}

## Neo4j plugins: APOC
export NJ_PLUGINS=$NJ_HOME/neo4jPlugins
mkdir -p $NJ_PLUGINS
cd $NJ_PLUGINS
wget --no-check-certificate $NJ_APOC
cd -

docker run -d \
   --name $CONTAINER \
   --publish=$NJ_HTTP_PORT:7474 \
    --publish=$NJ_HTTPS_PORT:7473 \
   --publish=$NJ_BOLT_PORT:7687 \
   --env=NEO4J_dbms_memory_heap_initial__size=2G \
   --env=NEO4J_dbms_memory_heap_max__size=2G \
   --env=NEO4J_dbms_memory_pagecache_size=1G \
   --env=NEO4J_dbms_query__cache__size=0 \
   --env=NEO4J_cypher_min__replan__interval=100000000ms \
   --env=NEO4J_cypher_statistics__divergence__threshold=1 \
   --env=NEO4J_dbms_security_procedures_unrestricted=apoc.\\\* \
   --env=NEO4J_dbms_directories_import=import \
   --env NEO4J_AUTH=$NJ_AUTH \
   --volume $NJ_IMPORT:/var/lib/neo4j/import \
   --volume $NJ_DATA/data:/data \
    --volume $NJ_PLUGINS:/plugins \
    --volume=$NJ_SSL:/ssl \
    --env=NEO4J_dbms_connector_https_enabled=true \
   --env=NEO4J_dbms_ssl_policy_https_enabled=true \
    --env=NEO4J_dbms_ssl_policy_https_base__directory=/ssl/https \
   --env=NEO4J_dbms_ssl_policy_https_private__key=private.key \
   --env=NEO4J_dbms_ssl_policy_https_public__certificate=public.crt \
    --env=NEO4J_dbms_ssl_policy_https_client__auth=NONE \
    --env=NEO4J_dbms_ssl_policy_https_trust__all=true \
    neo4j:$NJ_VERSION

sleep 15
sudo chmod a+rwx $NJ_IMPORT

Neo4j 5.x (>= 5.12)

In recent version of Neo4j, it is not possible to instantiate the docker image with a specific user name and password. The password needs to be changed after Neo4j starts. Nevertheless, it’s still possible to instanciate the image without any credentials with the following docker run parameter: --env NEO4J_AUTH=none

#!/bin/sh

#################################
## CONFIG according to your needs
#################################

export CONTAINER=neo4j_cont

export NJ_VERSION=5.12.0

## Ports
export NJ_HTTP_PORT=7474
export NJ_HTTPS_PORT=7473
export NJ_BOLT_PORT=7687

## Change the location of the Neo4j directory
export NJ_HOME=~/neo4j_home

## APOC download
export NJ_APOC=https://github.com/neo4j/apoc/releases/download/5.1.0/apoc-5.1.0-core.jar

#################################
## RUN
#################################

mkdir -p $NJ_HOME

## Import and data directory
export NJ_IMPORT=$NJ_HOME/neo4jImport
mkdir -p $NJ_IMPORT
export NJ_DATA=$NJ_HOME/neo4jData
if test -e $NJ_DATA; then
   echo "$NJ_DATA directory exists ==> abort - Remove it before proceeding" >&2
   exit
fi
mkdir -p $NJ_DATA

## SSL
export NJ_SSL=${NJ_HOME}/ssl
mkdir -p ${NJ_SSL}/https
mkdir -p ${NJ_SSL}/https/revoked
mkdir -p ${NJ_SSL}/https/trusted
openssl req -subj "/CN=localhost" -new -newkey rsa:2048 -days 365 -nodes -x509 -keyout ${NJ_SSL}/https/private.key -out ${NJ_SSL}/https/public.crt
cp ${NJ_SSL}/https/public.crt ${NJ_SSL}/https/trusted
chmod -R a+rwx ${NJ_SSL}

## Neo4j plugins: APOC
export NJ_PLUGINS=$NJ_HOME/neo4jPlugins
mkdir -p $NJ_PLUGINS
cd $NJ_PLUGINS
wget --no-check-certificate $NJ_APOC
cd -

## Add ` --env NEO4J_AUTH=none ` if you don't want to setup credentials
docker run -d \
   --name $CONTAINER \
   --publish=$NJ_HTTP_PORT:7474 \
   --publish=$NJ_HTTPS_PORT:7473 \
   --publish=$NJ_BOLT_PORT:7687 \
   --env=NEO4J_server_memory_heap_initial__size=2G \
   --env=NEO4J_server_memory_heap_max__size=2G \
   --env=NEO4J_server_memory_pagecache_size=1G \
   --env=NEO4J_server_db_query__cache__size=0 \
   --env=NEO4J_dbms_cypher_min__replan__interval=100000000ms \
   --env=NEO4J_dbms_cypher_statistics__divergence__threshold=1 \
   --env=NEO4J_dbms_security_procedures_unrestricted=apoc.\\\* \
   --env=NEO4J_server_directories_import=import\
   --volume=$NJ_IMPORT:/var/lib/neo4j/import \
   --volume=$NJ_DATA/data:/data \
   --volume=$NJ_LOGS:/var/lib/neo4j/logs \
   --volume=$NJ_PLUGINS:/plugins \
   --volume=$NJ_SSL:/ssl \
   --env=NEO4J_server_https_enabled=true \
   --env=NEO4J_dbms_ssl_policy_https_enabled=true \
   --env=NEO4J_dbms_ssl_policy_https_base__directory=/ssl/https \
   --env=NEO4J_dbms_ssl_policy_https_private__key=private.key \
   --env=NEO4J_dbms_ssl_policy_https_public__certificate=public.crt \
   --env=NEO4J_dbms_ssl_policy_https_client__auth=NONE \
   --env=NEO4J_dbms_ssl_policy_https_trust__all=true \
   neo4j:$NJ_VERSION

sleep 15
sudo chmod a+rwx $NJ_IMPORT

If you did not disable credentials (with --env NEO4J_AUTH=none), you’ll need to first change the user password before being able to connect to the graph database. The following chunk shows how to do it with neo2R.

library(neo2R)
system <- startGraph(
  "https://localhost:7473", database="system", check=FALSE,
  username="neo4j", password="neo4j",
  importPath="~/neo4j_home/neo4jImport",
  .opts = list(ssl_verifypeer=0)
)
cypher(
   system,
   "ALTER CURRENT USER SET PASSWORD FROM 'neo4j' TO 'donttrustusers'"
)

Connect to Neo4j

After installing neo4j, startGraph is used to initialize the connection from R. If authentication has been disabled in neo4j by setting NEO4J.AUTH=none, neither username nor password are required. If you’re connecting to a local instance of Neo4j and import directory has been defined in the configuration, you can specify it in order to allow import from data.frames.

library(neo2R)
graph <- startGraph(
  "https://localhost:7473",
  username="neo4j", password="donttrustusers",
  importPath="~/neo4j_home/neo4jImport",
  .opts = list(ssl_verifypeer=0)
)

Import from data.frame

If you’re connected to a local instance of Neo4j and import directory has been defined (see above), you can import data from data.frames. Use the ‘row’ prefix to refer to the data.frame column.

#########################################
## Nodes
## Create an index to speed-up MERGE
if(graph$version[[1]]=="5"){
   try(cypher(graph, 'CREATE INDEX FOR (n:TestNode) ON (n.name)'), silent=TRUE)
}else{
   try(cypher(graph, 'CREATE INDEX ON :TestNode(name)'), silent=TRUE)
}
## Neo.ClientError.Schema.EquivalentSchemaRuleAlreadyExists

## An equivalent index already exists, 'Index( id=3, name='index_83b6d7ae', type='RANGE', schema=(:TestNode {name}), indexProvider='range-1.0' )'.

## Define node properties in a data.frame
set.seed(1)
nn <- 100000
nodes <- data.frame(
   "name"=paste(
      sample(LETTERS, nn, replace=TRUE),
      sample.int(nn, nn, replace=FALSE)
   ),
   "value"=rnorm(nn, 10, 3),
   stringsAsFactors=FALSE
)
import_from_df(
  graph=graph,
  cql='MERGE (n:TestNode {name:row.name, value:toFloat(row.value)})',
  toImport=nodes
)

#########################################
## Edges
## Define node properties in a data.frame
ne <- 100000
edges <- data.frame(
  "from"=sample(nodes$name, ne, replace=TRUE),
  "to"=sample(nodes$name, ne, replace=TRUE),
  "property"=round(runif(ne)*10),
  stringsAsFactors=FALSE
)
import_from_df(
   graph=graph,
   cql=prepCql(
      'MATCH (f:TestNode {name:row.from})',
      'MATCH (t:TestNode {name:row.to})',
      'MERGE (f)-[r:TestEdge {property:toInteger(row.property)}]->(t)'
   ),
   toImport=edges
)

Query the Neo4j database

You can query the Neo4j graph database using the cypher() function. Depending on the query, the function can return data in a a data.frame (by setting result="row") or in a list with nodes, relationships and paths returned by the query by setting result="graph" (the “graph” method is quite slow with version 5 of Neo4j for unknown reason).

## Get TestNode with value smaller than 4.
## According to the normal distribution we expect 2.5% of the total
## number of nodes ==> ~2500 nodes
df <- cypher(
   graph,
   prepCql(
      'MATCH (n:TestNode) WHERE n.value <= 4',
      'RETURN n.name as name, n.value as value'
   )
)
print(dim(df))
## [1] 2253    2

print(head(df))
##      name    value
## 1  N 2585 1.965486
## 2 L 72527 3.345461
## 3 Y 54240 2.372623
## 4  N 1436 1.500713
## 5 T 21434 3.592195
## 6 M 91787 2.504475

## Multiple queries can be sent at once
dfl <- multicypher(
   graph,
   sprintf(
      paste(
         'MATCH (n:TestNode) WHERE n.value <= %s',
         'RETURN n.name as name, n.value as value'
      ),
      2:4
   )
)
print(lapply(dfl, dim))
## [[1]]
## [1] 386   2
## 
## [[2]]
## [1] 954   2
## 
## [[3]]
## [1] 2253    2

## Get all paths of length 5 starting from a subset of nodes 
net <- cypher(
   graph,
   prepCql(
      'MATCH p=(f:TestNode)-[:TestEdge*5..5]->(t:TestNode) WHERE f.value < 3',
      'RETURN p'
   ),
   result="graph"
)
print(lapply(net, head, 3))
## $nodes
## $nodes$`79444`
## $nodes$`79444`$id
## [1] "79444"
## 
## $nodes$`79444`$elementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:79444"
## 
## $nodes$`79444`$labels
## $nodes$`79444`$labels[[1]]
## [1] "TestNode"
## 
## 
## $nodes$`79444`$properties
## $nodes$`79444`$properties$name
## [1] "S 99155"
## 
## $nodes$`79444`$properties$value
## [1] 9.658103
## 
## 
## 
## $nodes$`97347`
## $nodes$`97347`$id
## [1] "97347"
## 
## $nodes$`97347`$elementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:97347"
## 
## $nodes$`97347`$labels
## $nodes$`97347`$labels[[1]]
## [1] "TestNode"
## 
## 
## $nodes$`97347`$properties
## $nodes$`97347`$properties$name
## [1] "V 30913"
## 
## $nodes$`97347`$properties$value
## [1] 10.389
## 
## 
## 
## $nodes$`7`
## $nodes$`7`$id
## [1] "7"
## 
## $nodes$`7`$elementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:7"
## 
## $nodes$`7`$labels
## $nodes$`7`$labels[[1]]
## [1] "TestNode"
## 
## 
## $nodes$`7`$properties
## $nodes$`7`$properties$name
## [1] "N 2585"
## 
## $nodes$`7`$properties$value
## [1] 1.965486
## 
## 
## 
## 
## $relationships
## $relationships$`7553`
## $relationships$`7553`$id
## [1] "7553"
## 
## $relationships$`7553`$elementId
## [1] "5:bf1055bf-0089-45bb-87e6-18a61e233aab:7553"
## 
## $relationships$`7553`$type
## [1] "TestEdge"
## 
## $relationships$`7553`$startNode
## [1] "79444"
## 
## $relationships$`7553`$startNodeElementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:79444"
## 
## $relationships$`7553`$endNode
## [1] "20186"
## 
## $relationships$`7553`$endNodeElementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:20186"
## 
## $relationships$`7553`$properties
## $relationships$`7553`$properties$property
## [1] 8
## 
## 
## 
## $relationships$`94678`
## $relationships$`94678`$id
## [1] "94678"
## 
## $relationships$`94678`$elementId
## [1] "5:bf1055bf-0089-45bb-87e6-18a61e233aab:94678"
## 
## $relationships$`94678`$type
## [1] "TestEdge"
## 
## $relationships$`94678`$startNode
## [1] "20186"
## 
## $relationships$`94678`$startNodeElementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:20186"
## 
## $relationships$`94678`$endNode
## [1] "7311"
## 
## $relationships$`94678`$endNodeElementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:7311"
## 
## $relationships$`94678`$properties
## $relationships$`94678`$properties$property
## [1] 3
## 
## 
## 
## $relationships$`470`
## $relationships$`470`$id
## [1] "470"
## 
## $relationships$`470`$elementId
## [1] "5:bf1055bf-0089-45bb-87e6-18a61e233aab:470"
## 
## $relationships$`470`$type
## [1] "TestEdge"
## 
## $relationships$`470`$startNode
## [1] "13440"
## 
## $relationships$`470`$startNodeElementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:13440"
## 
## $relationships$`470`$endNode
## [1] "79444"
## 
## $relationships$`470`$endNodeElementId
## [1] "4:bf1055bf-0089-45bb-87e6-18a61e233aab:79444"
## 
## $relationships$`470`$properties
## $relationships$`470`$properties$property
## [1] 10
## 
## 
## 
## 
## $paths
## $paths[[1]]
## [1] "7553"  "94678" "470"   "93543" "31423"
## 
## $paths[[2]]
## [1] "7553"  "470"   "93543" "31423" "98608"
## 
## $paths[[3]]
## [1] "69425" "93543" "58428" "31423" "71263"

print(table(unlist(lapply(net$paths, length))))
## 
##   5 
## 945

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