elastic searching

Load elastic

library("elastic")

The Search function

The main interface to searching documents in your Elasticsearch store is the function Search(). I nearly always develop R software using all lowercase, but R has a function called search(), and I wanted to avoid collision with that function.

Search() is an interface to both the HTTP search API (in which queries are passed in the URI of the request, meaning queries have to be relatively simple), as well as the POST API, or the Query DSL, in which queries are passed in the body of the request (so can be much more complex).

There are a huge amount of ways you can search Elasticsearch documents - this tutorial covers some of them, and highlights the ways in which you interact with the R outputs.

x <- connect()

Search an index

out <- Search(x, index="shakespeare")
out$hits$total

#> [1] 5000

out$hits$hits[[1]]

#> $`_index`
#> [1] "shakespeare"
#> 
#> $`_type`
#> [1] "line"
#> 
#> $`_id`
#> [1] "0"
#> 
#> $`_score`
#> [1] 1
#> 
#> $`_source`
#> $`_source`$line_id
#> [1] 1
#> 
#> $`_source`$play_name
#> [1] "Henry IV"
#> 
#> $`_source`$line_number
#> [1] ""
#> 
#> $`_source`$speaker
#> [1] ""
#> 
#> $`_source`$text_entry
#> [1] "ACT I"

Search an index by type

Search(x, index = "shakespeare", type = "line")$hits$hits[[1]]

#> $`_index`
#> [1] "shakespeare"
#> 
#> $`_type`
#> [1] "line"
#> 
#> $`_id`
#> [1] "0"
#> 
#> $`_score`
#> [1] 1
#> 
#> $`_source`
#> $`_source`$line_id
#> [1] 1
#> 
#> $`_source`$play_name
#> [1] "Henry IV"
#> 
#> $`_source`$line_number
#> [1] ""
#> 
#> $`_source`$speaker
#> [1] ""
#> 
#> $`_source`$text_entry
#> [1] "ACT I"

Return certain fields

Search(x, index = "shakespeare", body = '{
  "_source": ["play_name", "speaker"]
}')$hits$hits[[1]]

#> $`_index`
#> [1] "shakespeare"
#> 
#> $`_type`
#> [1] "line"
#> 
#> $`_id`
#> [1] "0"
#> 
#> $`_score`
#> [1] 1
#> 
#> $`_source`
#> $`_source`$play_name
#> [1] "Henry IV"
#> 
#> $`_source`$speaker
#> [1] ""

Paging

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

#> $total
#> [1] 5000
#> 
#> $max_score
#> [1] 1
#> 
#> $hits
#> $hits[[1]]
#> $hits[[1]]$`_index`
#> [1] "shakespeare"
#> 
#> $hits[[1]]$`_type`
#> [1] "line"
#> 
#> $hits[[1]]$`_id`
#> [1] "14"
#> 
#> $hits[[1]]$`_score`
#> [1] 1
#> 
#> $hits[[1]]$`_source`
#> $hits[[1]]$`_source`$line_id
#> [1] 15
#> 
#> $hits[[1]]$`_source`$play_name
#> [1] "Henry IV"
#> 
#> $hits[[1]]$`_source`$speech_number
#> [1] 1
#> 
#> $hits[[1]]$`_source`$line_number
#> [1] "1.1.12"
#> 
#> $hits[[1]]$`_source`$speaker
#> [1] "KING HENRY IV"
#> 
#> $hits[[1]]$`_source`$text_entry
#> [1] "Did lately meet in the intestine shock"

Queries

Using the q parameter you can pass in a query, which gets passed in the URI of the query. This type of query is less powerful than the below query passed in the body of the request, using the body parameter.

Search(x, index="shakespeare", type="line", q="speaker:KING HENRY IV")$hits$total

#> [1] 5000

More complex queries

Here, query for values from 10 to 20 in the field line_id

Search(x, index="shakespeare", q="line_id:[10 TO 20]")$hits$total

#> [1] 11

Get version number for each document

Version number usually is not returned.

sapply(Search(x, index="shakespeare", version=TRUE, size=2)$hits$hits, "[[", "_version")

#> [1] 3 4

Get raw data

Search(x, index="shakespeare", type="line", raw=TRUE)

#> [1] "{\"took\":0,\"timed_out\":false,\"_shards\":{\"total\":5,\"successful\":5,\"skipped\":0,\"failed\":0},\"hits\":{\"total\":5000,\"max_score\":1.0,\"hits\":[{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"0\",\"_score\":1.0,\"_source\":{\"line_id\":1,\"play_name\":\"Henry IV\",\"line_number\":\"\",\"speaker\":\"\",\"text_entry\":\"ACT I\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"14\",\"_score\":1.0,\"_source\":{\"line_id\":15,\"play_name\":\"Henry IV\",\"speech_number\":1,\"line_number\":\"1.1.12\",\"speaker\":\"KING HENRY IV\",\"text_entry\":\"Did lately meet in the intestine shock\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"19\",\"_score\":1.0,\"_source\":{\"line_id\":20,\"play_name\":\"Henry IV\",\"speech_number\":1,\"line_number\":\"1.1.17\",\"speaker\":\"KING HENRY IV\",\"text_entry\":\"The edge of war, like an ill-sheathed knife,\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"22\",\"_score\":1.0,\"_source\":{\"line_id\":23,\"play_name\":\"Henry IV\",\"speech_number\":1,\"line_number\":\"1.1.20\",\"speaker\":\"KING HENRY IV\",\"text_entry\":\"Whose soldier now, under whose blessed cross\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"24\",\"_score\":1.0,\"_source\":{\"line_id\":25,\"play_name\":\"Henry IV\",\"speech_number\":1,\"line_number\":\"1.1.22\",\"speaker\":\"KING HENRY IV\",\"text_entry\":\"Forthwith a power of English shall we levy;\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"25\",\"_score\":1.0,\"_source\":{\"line_id\":26,\"play_name\":\"Henry IV\",\"speech_number\":1,\"line_number\":\"1.1.23\",\"speaker\":\"KING HENRY IV\",\"text_entry\":\"Whose arms were moulded in their mothers womb\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"26\",\"_score\":1.0,\"_source\":{\"line_id\":27,\"play_name\":\"Henry IV\",\"speech_number\":1,\"line_number\":\"1.1.24\",\"speaker\":\"KING HENRY IV\",\"text_entry\":\"To chase these pagans in those holy fields\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"29\",\"_score\":1.0,\"_source\":{\"line_id\":30,\"play_name\":\"Henry IV\",\"speech_number\":1,\"line_number\":\"1.1.27\",\"speaker\":\"KING HENRY IV\",\"text_entry\":\"For our advantage on the bitter cross.\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"40\",\"_score\":1.0,\"_source\":{\"line_id\":41,\"play_name\":\"Henry IV\",\"speech_number\":2,\"line_number\":\"1.1.38\",\"speaker\":\"WESTMORELAND\",\"text_entry\":\"Whose worst was, that the noble Mortimer,\"}},{\"_index\":\"shakespeare\",\"_type\":\"line\",\"_id\":\"41\",\"_score\":1.0,\"_source\":{\"line_id\":42,\"play_name\":\"Henry IV\",\"speech_number\":2,\"line_number\":\"1.1.39\",\"speaker\":\"WESTMORELAND\",\"text_entry\":\"Leading the men of Herefordshire to fight\"}}]}}"

Curl debugging

Common options are verbose=TRUE, timeout_ms=1, followlocation=TRUE.

out <- Search(x, index="shakespeare", type="line", verbose = TRUE)

Query DSL searches - queries sent in the body of the request

Pass in as an R list

mapping_create(x, "shakespeare", "line", update_all_types = TRUE, body = '{
   "properties": {
     "text_entry": {
       "type":     "text",
       "fielddata": true
    }
  }
}')

#> $acknowledged
#> [1] TRUE

aggs <- list(aggs = list(stats = list(terms = list(field = "text_entry"))))
Search(x, index="shakespeare", body=aggs)$hits$hits[[1]]

#> $`_index`
#> [1] "shakespeare"
#> 
#> $`_type`
#> [1] "line"
#> 
#> $`_id`
#> [1] "0"
#> 
#> $`_score`
#> [1] 1
#> 
#> $`_source`
#> $`_source`$line_id
#> [1] 1
#> 
#> $`_source`$play_name
#> [1] "Henry IV"
#> 
#> $`_source`$line_number
#> [1] ""
#> 
#> $`_source`$speaker
#> [1] ""
#> 
#> $`_source`$text_entry
#> [1] "ACT I"

Or pass in as json query with newlines, easy to read

aggs <- '{
    "aggs": {
        "stats" : {
            "terms" : {
                "field" : "text_entry"
            }
        }
    }
}'
Search(x, index="shakespeare", body=aggs)$hits$hits[[1]]

#> $`_index`
#> [1] "shakespeare"
#> 
#> $`_type`
#> [1] "line"
#> 
#> $`_id`
#> [1] "0"
#> 
#> $`_score`
#> [1] 1
#> 
#> $`_source`
#> $`_source`$line_id
#> [1] 1
#> 
#> $`_source`$play_name
#> [1] "Henry IV"
#> 
#> $`_source`$line_number
#> [1] ""
#> 
#> $`_source`$speaker
#> [1] ""
#> 
#> $`_source`$text_entry
#> [1] "ACT I"

Or pass in collapsed json string

aggs <- '{"aggs":{"stats":{"terms":{"field":"text_entry"}}}}'
Search(x, index="shakespeare", body=aggs)$hits$hits[[1]]

#> $`_index`
#> [1] "shakespeare"
#> 
#> $`_type`
#> [1] "line"
#> 
#> $`_id`
#> [1] "0"
#> 
#> $`_score`
#> [1] 1
#> 
#> $`_source`
#> $`_source`$line_id
#> [1] 1
#> 
#> $`_source`$play_name
#> [1] "Henry IV"
#> 
#> $`_source`$line_number
#> [1] ""
#> 
#> $`_source`$speaker
#> [1] ""
#> 
#> $`_source`$text_entry
#> [1] "ACT I"

Aggregations

Histograms

aggs <- '{
    "aggs": {
        "latbuckets" : {
           "histogram" : {
               "field" : "decimalLatitude",
               "interval" : 5
           }
        }
    }
}'
Search(x, index="gbif", body=aggs, size=0)$aggregations$latbuckets$buckets[1:3]

#> [[1]]
#> [[1]]$key
#> [1] -35
#> 
#> [[1]]$doc_count
#> [1] 1
#> 
#> 
#> [[2]]
#> [[2]]$key
#> [1] -30
#> 
#> [[2]]$doc_count
#> [1] 0
#> 
#> 
#> [[3]]
#> [[3]]$key
#> [1] -25
#> 
#> [[3]]$doc_count
#> [1] 0

A bool query

mmatch <- '{
 "query": {
   "bool" : {
     "must_not" : {
       "range" : {
         "speech_number" : {
           "from" : 1, "to": 5
}}}}}}'
sapply(Search(x, index="shakespeare", body=mmatch)$hits$hits, function(x) x$`_source`$speech_number)

#> [[1]]
#> NULL
#> 
#> [[2]]
#> [1] 6
#> 
#> [[3]]
#> [1] 7
#> 
#> [[4]]
#> [1] 7
#> 
#> [[5]]
#> [1] 7
#> 
#> [[6]]
#> [1] 8
#> 
#> [[7]]
#> [1] 8
#> 
#> [[8]]
#> [1] 9
#> 
#> [[9]]
#> [1] 9
#> 
#> [[10]]
#> [1] 10

Fuzzy query

Fuzzy query on numerics

fuzzy <- list(query = list(fuzzy = list(text_entry = "arms")))
Search(x, index="shakespeare", body = fuzzy)$hits$total

#> [1] 49

fuzzy <- list(query = list(fuzzy = list(text_entry = list(value = "arms", fuzziness = 4))))
Search(x, index="shakespeare", body=fuzzy)$hits$total

#> [1] 617

Range query

With numeric

body <- list(query=list(range=list(decimalLongitude=list(gte=1, lte=3))))
Search(x, 'gbif', body=body)$hits$total

#> [1] 24

body <- list(query=list(range=list(decimalLongitude=list(gte=2.9, lte=10))))
Search(x, 'gbif', body=body)$hits$total

#> [1] 126

With dates

body <- list(query=list(range=list(eventDate=list(gte="2012-01-01", lte="now"))))
Search(x, 'gbif', body=body)$hits$total

#> [1] 301

body <- list(query=list(range=list(eventDate=list(gte="2014-01-01", lte="now"))))
Search(x, 'gbif', body=body)$hits$total

#> [1] 292

More-like-this query (more_like_this can be shortened to mlt)

body <- '{
 "query": {
   "more_like_this": {
     "fields": ["abstract","title"],
     "like": "and then",
     "min_term_freq": 1,
     "max_query_terms": 12
   }
 }
}'
Search(x, 'plos', body=body)$hits$total

#> [1] 488

body <- '{
 "query": {
   "more_like_this": {
     "fields": ["abstract","title"],
     "like": "cell",
     "min_term_freq": 1,
     "max_query_terms": 12
   }
 }
}'
Search(x, 'plos', body=body)$hits$total

#> [1] 58

Highlighting

body <- '{
 "query": {
   "query_string": {
     "query" : "cell"
   }
 },
 "highlight": {
   "fields": {
     "title": {"number_of_fragments": 2}
   }
 }
}'
out <- Search(x, 'plos', 'article', body=body)
out$hits$total

#> [1] 58

sapply(out$hits$hits, function(x) x$highlight$title[[1]])[8:10]

#> [1] "Chronic Hypoxia Promotes Pulmonary Artery Endothelial <em>Cell</em> Proliferation through H2O2-Induced 5-Lipoxygenase"  
#> [2] "Dynamic Visualization of Dendritic <em>Cell</em>-Antigen Interactions in the Skin Following Transcutaneous Immunization"
#> [3] "A New Class of Pluripotent Stem <em>Cell</em> Cytotoxic Small Molecules"

Scrolling search - instead of paging

Search(x, 'shakespeare', q="a*")$hits$total

#> [1] 2747

res <- Search(x, index = 'shakespeare', q="a*", time_scroll = "1m")
length(scroll(x, res$`_scroll_id`, time_scroll = "1m")$hits$hits)

#> [1] 10

res <- Search(x, index = 'shakespeare', q = "a*", time_scroll = "5m")
out <- res$hits$hits
hits <- 1
while (hits != 0) {
  res <- scroll(x, res$`_scroll_id`)
  hits <- length(res$hits$hits)
  if (hits > 0)
    out <- c(out, res$hits$hits)
}
length(out)

#> [1] 2747

res$hits$total

#> [1] 2747

Woohoo! Collected all 2747 documents in very little time.