elasticsearchr - a Lightweight Elasticsearch Client for R
Posted on Mon 28 November 2016 in r
Elasticsearch is a distributed NoSQL document store search-engine and column-oriented database, whose fast (near real-time) reads and powerful aggregation engine make it an excellent choice as an ‘analytics database’ for R&D, production-use or both. Installation is simple, it ships with default settings that allow it to work effectively out-of-the-box, and all interaction is made via a set of intuitive and extremely well documented RESTful APIs. I’ve been using it for two years now and I am evangelical.
The elasticsearchr package implements a simple Domain-Specific Language (DSL) for indexing, deleting, querying, sorting and aggregating data in Elasticsearch, from within R. The main purpose of this package is to remove the labour involved with assembling HTTP requests to Elasticsearch’s REST APIs and parsing the responses. Instead, users of this package need only send and receive data frames to Elasticsearch resources. Users needing richer functionality are encouraged to investigate the excellent elastic package from the good people at rOpenSci.
This package is available on CRAN or from this GitHub repository. To install the latest (development) version from GitHub, make sure that you have the devtools package installed (this comes bundled with RStudio), and then execute the following on the R command line:
devtools::install_github("alexioannides/elasticsearchr")
Installing Elasticsearch
Elasticsearch can be downloaded here, where the instructions for installing and starting it can also be found. OS X users (such as myself) can also make use of Homebrew to install it with the command,
$ brew install elasticsearch
And then start it by executing $ elasticsearch from within any Terminal window. Successful installation can be checked by navigating any web browser to http://localhost:9200, where the following message should greet you (give or take the cluster name that changes with every restart),
{
"name" : "Kraven the Hunter",
"cluster_name" : "elasticsearch",
"version" : {
"number" : "2.3.5",
"build_hash" : "90f439ff60a3c0f497f91663701e64ccd01edbb4",
"build_timestamp" : "2016-07-27T10:36:52Z",
"build_snapshot" : false,
"lucene_version" : "5.5.0"
},
"tagline" : "You Know, for Search"
}
Elasticsearch 101
If you followed the installation steps above, you have just installed a single Elasticsearch ‘node’. When not testing on your laptop, Elasticsearch usually comes in clusters of nodes (usually there are at least 3). The easiest easy way to get access to a managed Elasticsearch cluster is by using the Elastic Cloud managed service provided by Elastic (Amazon Web Services offer something similar too). For the rest of this brief tutorial I will assuming you’re running a single node on your laptop.
In Elasticsearch a ‘row’ of data is stored as a ‘document’. A document is a JSON object - for example, the first row of R’s iris dataset,
# sepal_length sepal_width petal_length petal_width species
# 1 5.1 3.5 1.4 0.2 setosa
would be represented as follows using JSON,
{
"sepal_length": 5.1,
"sepal_width": 3.5,
"petal_length": 1.4,
"petal_width": 0.2,
"species": "setosa"
}
Documents are classified into ‘types’ and stored in an ‘index’. In a crude analogy with traditional SQL databases that is often used, we would associate an index with a database instance and the document types as tables within that database. In practice this example is not accurate - it is better to think of all documents as residing in a single - possibly sparse - table (defined by the index), where the document types represent sub-sets of columns in the table. This is especially so as fields that occur in multiple document types (within the same index), must have the same data-type - for example, if "name" exists in document type customer as well as in document type address, then "name" will need to be a string in both.
Each document is a ‘resource’ that has a Uniform Resource Locator (URL) associated with it. Elasticsearch URLs all have the following format:
http://your_cluster:9200/your_index/your_doc_type/your_doc_id
For example, the above iris document could be living at
http://localhost:9200/iris/data/1
Although Elasticsearch - like most NoSQL databases - is often referred to as being ‘schema free’, as we have already see this is not entirely correct. What is true, however, is that the schema - or ‘mapping’ as it’s called in Elasticsearch - does not need to be declared up-front (although you certainly can do this). Elasticsearch is more than capable of guessing the types of fields based on new data indexed for the first time. For more information on any of these basic concepts take a look here
elasticsearchr: a Quick Start
elasticsearchr is a lightweight client - by this I mean that it only aims to do ‘just enough’ work to make using Elasticsearch with R easy and intuitive. You will still need to read the Elasticsearch documentation to understand how to compose queries and aggregations. What follows is a quick summary of what is possible.
Resources
Elasticsearch resources, as defined by the URLs described above, are defined as elastic objects in elasticsearchr. For example,
es <- elastic("http://localhost:9200", "iris", "data")
Refers to documents of types ‘data’ in the ‘iris’ index located on an Elasticsearch node on my laptop. Note that:
- it is possible to leave the document type empty if you need to refer to all documents in an index; and,
- elastic objects can be defined even if the underling resources have yet to be brought into existence.
Indexing New Data
To index (insert) data from a data frame, use the %index% operator as follows:
elastic("http://localhost:9200", "iris", "data") %index% iris
In this example, the iris dataset is indexed into the ‘iris’ index and given a document type called ‘data’. Note that I have not provided any document ids here. To explicitly specify document ids there must be a column in the data frame that is labelled id, from which the document ids will be taken.
Deleting Data
Documents can be deleted in three different ways using the %delete% operator. Firstly, an entire index (including the mapping information) can be erased by referencing just the index in the resource - e.g.,
elastic("http://localhost:9200", "iris") %delete% TRUE
Alternatively, documents can be deleted on a type-by-type basis leaving the index and it’s mappings untouched, by referencing both the index and the document type as the resource - e.g.,
elastic("http://localhost:9200", "iris", "data") %delete% TRUE
Finally, specific documents can be deleted by referencing their ids directly - e.g.,
elastic("http://localhost:9200", "iris", "data") %delete% c("1", "2", "3", "4", "5")
Queries
Any type of query that Elasticsearch makes available can be defined in a query object using the native Elasticsearch JSON syntax - e.g. to match every document we could use the match_all query,
for_everything <- query('{
"match_all": {}
}')
To execute this query we use the %search% operator on the appropriate resource - e.g.,
elastic("http://localhost:9200", "iris", "data") %search% for_everything
# sepal_length sepal_width petal_length petal_width species
# 1 4.9 3.0 1.4 0.2 setosa
# 2 4.9 3.1 1.5 0.1 setosa
# 3 5.8 4.0 1.2 0.2 setosa
# 4 5.4 3.9 1.3 0.4 setosa
# 5 5.1 3.5 1.4 0.3 setosa
# 6 5.4 3.4 1.7 0.2 setosa
# ...
Sorting Query Results
Query results can be sorted on multiple fields by defining a sort object using the same Elasticsearch JSON syntax - e.g. to sort by sepal_width in ascending order the required sort object would be defined as,
by_sepal_width <- sort('{"sepal_width": {"order": "asc"}}')
This is then added to a query object whose results we want sorted and executed using the %search% operator as before - e.g.,
elastic("http://localhost:9200", "iris", "data") %search% (for_everything + by_sepal_width)
# sepal_length sepal_width petal_length petal_width species
# 1 5.0 2.0 3.5 1.0 versicolor
# 2 6.0 2.2 5.0 1.5 virginica
# 3 6.0 2.2 4.0 1.0 versicolor
# 4 6.2 2.2 4.5 1.5 versicolor
# 5 4.5 2.3 1.3 0.3 setosa
# 6 6.3 2.3 4.4 1.3 versicolor
# ...
Aggregations
Similarly, any type of aggregation that Elasticsearch makes available can be defined in an aggs object - e.g. to compute the average sepal_width per-species of flower we would specify the following aggregation,
avg_sepal_width <- aggs('{
"avg_sepal_width_per_species": {
"terms": {
"field": "species",
"size": 3
},
"aggs": {
"avg_sepal_width": {
"avg": {
"field": "sepal_width"
}
}
}
}
}')
(Elasticsearch 5.x users please note that when using the out-of-the-box mappings the above aggregation requires that "field": "species" be changed to "field": "species.keyword" - see here for more information as to why)
This aggregation is also executed via the %search% operator on the appropriate resource - e.g.,
elastic("http://localhost:9200", "iris", "data") %search% avg_sepal_width
# key doc_count avg_sepal_width.value
# 1 setosa 50 3.428
# 2 versicolor 50 2.770
# 3 virginica 50 2.974
Queries and aggregations can be combined such that the aggregations are computed on the results of the query. For example, to execute the combination of the above query and aggregation, we would execute,
elastic("http://localhost:9200", "iris", "data") %search% (for_everything + avg_sepal_width)
# key doc_count avg_sepal_width.value
# 1 setosa 50 3.428
# 2 versicolor 50 2.770
# 3 virginica 50 2.974
where the combination yields,
print(for_everything + avg_sepal_width)
# {
# "size": 0,
# "query": {
# "match_all": {
#
# }
# },
# "aggs": {
# "avg_sepal_width_per_species": {
# "terms": {
# "field": "species",
# "size": 0
# },
# "aggs": {
# "avg_sepal_width": {
# "avg": {
# "field": "sepal_width"
# }
# }
# }
# }
# }
# }
For comprehensive coverage of all query and aggregations types please refer to the rather excellent official documentation (newcomers to Elasticsearch are advised to start with the ‘Query String’ query).
Mappings
Finally, I have included the ability to create an empty index with a custom mapping, using the %create% operator - e.g.,
elastic("http://localhost:9200", "iris") %create% mapping_default_simple()
Where in this instance mapping_default_simple() is a default mapping that I have shipped with elasticsearchr. It switches-off the text analyser for all fields of type ‘string’ (i.e. switches off free text search), allows all text search to work with case-insensitive lower-case terms, and maps any field with the name ‘timestamp’ to type ‘date’, so long as it has the appropriate string or long format.
Forthcoming Attractions
I do not have a grand vision for elasticsearchr - I want to keep it a lightweight client that requires knowledge of Elasticsearch - but I would like to add the ability to compose major query and aggregation types, without having to type-out lots of JSON, and to be able to retrieve simple information like the names of all indices in a cluster, and all the document types within an index, etc. Future development will likely be focused in these areas.
Acknowledgements
A big thank you to Hadley Wickham and Jeroen Ooms, the authors of the httr and jsonlite packages that elasticsearchr leans upon heavily.