elastic introduction

elastic is an R client for Elasticsearch. This vignette is an introduction to the package, while other vignettes dive into the details of various topics.

Installation

You can install from CRAN (once the package is up there)

install.packages("elastic")

Or the development version from GitHub

install.packages("remotes")
remotes::install_github("ropensci/elastic")

Then load the package

library("elastic")

Elasticsearch info

Install Elasticsearch

Elasticsearch installation help

Unix (linux/osx)

Replace 6.5.3 with the version you are working with.

Download zip or tar file from Elasticsearch see here for download, e.g., curl -L -O https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-6.5.3.tar.gz
Extract: tar -zxvf elasticsearch-6.5.3.tar.gz
Move it: sudo mv elasticsearch-6.5.3 /usr/local
Navigate to /usr/local: cd /usr/local
Delete symlinked elasticsearch directory: rm -rf elasticsearch
Add shortcut: sudo ln -s elasticsearch-6.5.3 elasticsearch (replace version with your version)

On OSX, you can install via Homebrew: brew install elasticsearch

Windows

Windows users can follow the above, but unzip the zip file instead of uncompressing the tar file.

Start Elasticsearch

Navigate to elasticsearch: cd /usr/local/elasticsearch
Start elasticsearch: bin/elasticsearch

I create a little bash shortcut called es that does both of the above commands in one step (cd /usr/local/elasticsearch && bin/elasticsearch).

Note: Windows users should run the elasticsearch.bat file

Initialize connection

The function connect() is used before doing anything else to set the connection details to your remote or local elasticsearch store. The details created by connect() are written to your options for the current session, and are used by elastic functions.

x <- connect()
x

#> <Elasticsearch Connection> 
#>   transport:  http 
#>   host:       127.0.0.1 
#>   port:       9200 
#>   path:       NULL 
#>   username:   NULL 
#>   password:   NULL 
#>   errors:     simple 
#>   headers (names):   
#>   cainfo:  NULL

On package load, your base url and port are set to http://127.0.0.1 and 9200, respectively. You can of course override these settings per session or for all sessions.

Get some data

Elasticsearch has a bulk load API to load data in fast. The format is pretty weird though. It’s sort of JSON, but would pass no JSON linter. I include a few data sets in elastic so it’s easy to get up and running, and so when you run examples in this package they’ll actually run the same way (hopefully).

I have prepared a non-exported function useful for preparing the weird format that Elasticsearch wants for bulk data loads (see below). See elastic:::make_bulk_plos and elastic:::make_bulk_gbif.

Shakespeare data

Elasticsearch provides some data on Shakespeare plays. I’ve provided a subset of this data in this package. Get the path for the file specific to your machine:

shakespeare <- system.file("examples", "shakespeare_data.json", package = "elastic")

Then load the data into Elasticsearch:

docs_bulk(x, shakespeare)

If you need some big data to play with, the shakespeare dataset is a good one to start with. You can get the whole thing and pop it into Elasticsearch (beware, may take up to 10 minutes or so.):

curl -XGET https://www.elastic.co/guide/en/kibana/3.0/snippets/shakespeare.json > shakespeare.json
curl -XPUT localhost:9200/_bulk --data-binary @shakespeare.json

Public Library of Science (PLOS) data

A dataset inluded in the elastic package is metadata for PLOS scholarly articles. Get the file path, then load:

plosdat <- system.file("examples", "plos_data.json", package = "elastic")
docs_bulk(x, plosdat)

Global Biodiversity Information Facility (GBIF) data

A dataset inluded in the elastic package is data for GBIF species occurrence records. Get the file path, then load:

gbifdat <- system.file("examples", "gbif_data.json", package = "elastic")
docs_bulk(x, gbifdat)

GBIF geo data with a coordinates element to allow geo_shape queries

gbifgeo <- system.file("examples", "gbif_geo.json", package = "elastic")
docs_bulk(x, gbifgeo)

More data sets

There are more datasets formatted for bulk loading in the sckott/elastic_data GitHub repository. Find it at https://github.com/sckott/elastic_data

Search

Search the plos index and only return 1 result

Search(x, index="plos", size=1)$hits$hits

#> [[1]]
#> [[1]]$`_index`
#> [1] "plos"
#> 
#> [[1]]$`_type`
#> [1] "article"
#> 
#> [[1]]$`_id`
#> [1] "0"
#> 
#> [[1]]$`_score`
#> [1] 1
#> 
#> [[1]]$`_source`
#> [[1]]$`_source`$id
#> [1] "10.1371/journal.pone.0007737"
#> 
#> [[1]]$`_source`$title
#> [1] "Phospholipase C-β4 Is Essential for the Progression of the Normal Sleep Sequence and Ultradian Body Temperature Rhythms in Mice"

Search the plos index, and the article document type, and query for antibody, limit to 1 result

Search(x, index="plos", type="article", q="antibody", size=1)$hits$hits

#> [[1]]
#> [[1]]$`_index`
#> [1] "plos"
#> 
#> [[1]]$`_type`
#> [1] "article"
#> 
#> [[1]]$`_id`
#> [1] "813"
#> 
#> [[1]]$`_score`
#> [1] 5.18676
#> 
#> [[1]]$`_source`
#> [[1]]$`_source`$id
#> [1] "10.1371/journal.pone.0107638"
#> 
#> [[1]]$`_source`$title
#> [1] "Sortase A Induces Th17-Mediated and Antibody-Independent Immunity to Heterologous Serotypes of Group A Streptococci"

Get documents

Get document with id=1

docs_get(x, index='plos', type='article', id=1)

#> $`_index`
#> [1] "plos"
#> 
#> $`_type`
#> [1] "article"
#> 
#> $`_id`
#> [1] "1"
#> 
#> $`_version`
#> [1] 1
#> 
#> $`_seq_no`
#> [1] 1
#> 
#> $`_primary_term`
#> [1] 1
#> 
#> $found
#> [1] TRUE
#> 
#> $`_source`
#> $`_source`$id
#> [1] "10.1371/journal.pone.0098602"
#> 
#> $`_source`$title
#> [1] "Population Genetic Structure of a Sandstone Specialist and a Generalist Heath Species at Two Levels of Sandstone Patchiness across the Strait of Gibraltar"

Get certain fields

docs_get(x, index='plos', type='article', id=1, fields='id')

#> $`_index`
#> [1] "plos"
#> 
#> $`_type`
#> [1] "article"
#> 
#> $`_id`
#> [1] "1"
#> 
#> $`_version`
#> [1] 1
#> 
#> $`_seq_no`
#> [1] 1
#> 
#> $`_primary_term`
#> [1] 1
#> 
#> $found
#> [1] TRUE

Get multiple documents at once

Same index and type, different document ids

docs_mget(x, index="plos", type="article", id=3:4)

#> $docs
#> $docs[[1]]
#> $docs[[1]]$`_index`
#> [1] "plos"
#> 
#> $docs[[1]]$`_type`
#> [1] "article"
#> 
#> $docs[[1]]$`_id`
#> [1] "3"
#> 
#> $docs[[1]]$`_version`
#> [1] 1
#> 
#> $docs[[1]]$`_seq_no`
#> [1] 3
#> 
#> $docs[[1]]$`_primary_term`
#> [1] 1
#> 
#> $docs[[1]]$found
#> [1] TRUE
#> 
#> $docs[[1]]$`_source`
#> $docs[[1]]$`_source`$id
#> [1] "10.1371/journal.pone.0107756"
#> 
#> $docs[[1]]$`_source`$title
#> [1] "The Effect of S-Adenosylmethionine on Cognitive Performance in Mice: An Animal Model Meta-Analysis"
#> 
#> 
#> 
#> $docs[[2]]
#> $docs[[2]]$`_index`
#> [1] "plos"
#> 
#> $docs[[2]]$`_type`
#> [1] "article"
#> 
#> $docs[[2]]$`_id`
#> [1] "4"
#> 
#> $docs[[2]]$`_version`
#> [1] 1
#> 
#> $docs[[2]]$`_seq_no`
#> [1] 4
#> 
#> $docs[[2]]$`_primary_term`
#> [1] 1
#> 
#> $docs[[2]]$found
#> [1] TRUE
#> 
#> $docs[[2]]$`_source`
#> $docs[[2]]$`_source`$id
#> [1] "10.1371/journal.pone.0107758"
#> 
#> $docs[[2]]$`_source`$title
#> [1] "Lactobacilli Inactivate Chlamydia trachomatis through Lactic Acid but Not H2O2"

Different indeces, types, and ids

docs_mget(x, index_type_id=list(c("plos","article",1), c("gbif","record",1)))$docs[[1]]

#> $`_index`
#> [1] "plos"
#> 
#> $`_type`
#> [1] "article"
#> 
#> $`_id`
#> [1] "1"
#> 
#> $`_version`
#> [1] 1
#> 
#> $`_seq_no`
#> [1] 1
#> 
#> $`_primary_term`
#> [1] 1
#> 
#> $found
#> [1] TRUE
#> 
#> $`_source`
#> $`_source`$id
#> [1] "10.1371/journal.pone.0098602"
#> 
#> $`_source`$title
#> [1] "Population Genetic Structure of a Sandstone Specialist and a Generalist Heath Species at Two Levels of Sandstone Patchiness across the Strait of Gibraltar"

Raw JSON data

You can optionally get back raw json from Search(), docs_get(), and docs_mget() setting parameter raw=TRUE.

For example:

(out <- docs_mget(x, index="plos", type="article", id=5:6, raw=TRUE))

#> [1] "{\"docs\":[{\"_index\":\"plos\",\"_type\":\"article\",\"_id\":\"5\",\"_version\":1,\"_seq_no\":5,\"_primary_term\":1,\"found\":true,\"_source\":{\"id\":\"10.1371/journal.pone.0085123\",\"title\":\"MiR-21 Is under Control of STAT5 but Is Dispensable for Mammary Development and Lactation\"}},{\"_index\":\"plos\",\"_type\":\"article\",\"_id\":\"6\",\"_version\":1,\"_seq_no\":6,\"_primary_term\":1,\"found\":true,\"_source\":{\"id\":\"10.1371/journal.pone.0098600\",\"title\":\"Correction: Designing Mixed Species Tree Plantations for the Tropics: Balancing Ecological Attributes of Species with Landholder Preferences in the Philippines\"}}]}"
#> attr(,"class")
#> [1] "elastic_mget"

Then parse

jsonlite::fromJSON(out)

#> $docs
#>   _index   _type _id _version _seq_no _primary_term found
#> 1   plos article   5        1       5             1  TRUE
#> 2   plos article   6        1       6             1  TRUE
#>                     _source.id
#> 1 10.1371/journal.pone.0085123
#> 2 10.1371/journal.pone.0098600
#>                                                                                                                                                     _source.title
#> 1                                                                       MiR-21 Is under Control of STAT5 but Is Dispensable for Mammary Development and Lactation
#> 2 Correction: Designing Mixed Species Tree Plantations for the Tropics: Balancing Ecological Attributes of Species with Landholder Preferences in the Philippines

Scott Chamberlain

2020-07-27