Add support for Elasticsearch 6

.travis.yml

@@ -20,6 +20,9 @@ env:
   - ES_VERSION=5.3.0
   - ES_VERSION=5.4.0
   - ES_VERSION=5.5.0
+  - ES_VERSION=6.0.0
+  - ES_VERSION=6.1.0
+  - ES_VERSION=6.2.0
 
 before_install:
   - case "$ES_VERSION" in
@@ -79,18 +82,33 @@ before_install:
       export ES_VERSION=5.5.0 ;
       curl -O https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-$ES_VERSION.deb && sudo dpkg -i --force-confnew elasticsearch-$ES_VERSION.deb && sudo service elasticsearch start
       ;;
+
+    "6.0.0")
+      export ES_VERSION=6.0.0 ;
+      curl -O https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-$ES_VERSION.deb && sudo dpkg -i --force-confnew elasticsearch-$ES_VERSION.deb && sudo service elasticsearch start
+      ;;
+
+    "6.1.0")
+      export ES_VERSION=6.1.0 ;
+      curl -O https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-$ES_VERSION.deb && sudo dpkg -i --force-confnew elasticsearch-$ES_VERSION.deb && sudo service elasticsearch start
+      ;;
+
+    "6.2.0")
+      export ES_VERSION=6.2.0 ;
+      curl -O https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-$ES_VERSION.deb && sudo dpkg -i --force-confnew elasticsearch-$ES_VERSION.deb && sudo service elasticsearch start
+      ;;
    esac
 
   - sleep 20
   - sudo service elasticsearch status
   - wget https://download.elastic.co/demos/kibana/gettingstarted/shakespeare.json -O shakespeare.json
   - mv inst/testdata/shakespeare_mapping.json shakespeare_mapping.json
   - echo $(ls)
-  - curl --silent -X PUT "http://127.0.0.1:9200/shakespeare" -d @shakespeare_mapping.json
+  - curl --silent -X PUT "http://127.0.0.1:9200/shakespeare" -H 'Content-Type:application/json' -d @shakespeare_mapping.json
   - head -10000 shakespeare.json > sample_data.json
   - split -l 1000 sample_data.json data_
-  - for filename in $(ls | grep data_); do curl --silent -X POST "http://127.0.0.1:9200/shakespeare/_bulk" --data-binary "@$filename"; done
-  - curl -X GET "http://127.0.0.1:9200/shakespeare/_search?size=1"
+  - for filename in $(ls | grep data_); do curl --silent -X POST "http://127.0.0.1:9200/shakespeare/_bulk" -H 'Content-Type:application/json' --data-binary "@$filename"; done
+  - curl -X GET "http://127.0.0.1:9200/shakespeare/_search?size=1" -H 'Content-Type:application/json'
 
 after_success:
 - Rscript -e 'install.packages("covr"); covr::codecov()'

NAMESPACE

@@ -21,6 +21,7 @@ importFrom(futile.logger,flog.info)
 importFrom(futile.logger,flog.warn)
 importFrom(httr,GET)
 importFrom(httr,RETRY)
+importFrom(httr,add_headers)
 importFrom(httr,content)
 importFrom(httr,stop_for_status)
 importFrom(jsonlite,fromJSON)

R/elasticsearch_eda_funs.R

@@ -3,7 +3,7 @@
 #' @name get_counts
 #' @description For a given field, return a data.table with its unique values in a time range.
 #' @importFrom data.table := data.table setnames setkeyv
-#' @importFrom httr content RETRY
+#' @importFrom httr add_headers content RETRY
 #' @importFrom purrr transpose
 #' @export
 #' @param field A valid field in whatever Elasticsearch index you are querying
@@ -64,8 +64,13 @@ get_counts <- function(field
                         ]}}}}, "aggs": {"', field, '": {"terms": {"field": "', field, '", "size":', max_terms,'}}}}')
 
     #===== Build search URL =====#
-    searchURL  <- paste0(es_host, "/", es_index, "/_search?size=0")
-    result     <- httr::RETRY(verb = "POST", url = searchURL, body = aggsQuery)
+    searchURL <- paste0(es_host, "/", es_index, "/_search?size=0")
+    result <- httr::RETRY(
+        verb = "POST"
+        , httr::add_headers(c('Content-Type' = 'application/json'))
+        , url = searchURL
+        , body = aggsQuery
+    )
     counts     <- httr::content(result, as = "parsed")[["aggregations"]][[field]][["buckets"]]
 
     #===== Get data =====#
@@ -93,7 +98,12 @@ get_counts <- function(field
         {"missing": {"field": "', field, '"}}]}}}}}')
 
     # Get result
-    result      <- httr::RETRY(verb = "POST", url = searchURL, body = missingQuery)
+    result <- httr::RETRY(
+        verb = "POST"
+        , httr::add_headers(c('Content-Type' = 'application/json'))
+        , url = searchURL
+        , body = missingQuery
+    )
     numMissings <- httr::content(result, as = "parsed")[["hits"]][["total"]]
 
     # Return now if user asked to only see NAs if there are any
@@ -116,7 +126,7 @@ get_counts <- function(field
 #' @name get_fields
 #' @description For a given Elasticsearch index, return the mapping from field name
 #'              to data type for all indexed fields.
-#' @importFrom httr GET content stop_for_status
+#' @importFrom httr add_headers content GET stop_for_status
 #' @importFrom data.table := uniqueN
 #' @param es_indices A character vector that contains the names of indices for
 #'                   which to get mappings. Default is \code{'_all'}, which means
@@ -154,7 +164,10 @@ get_fields <- function(es_host
     ########################## make the query ################################
     log_info(paste('Getting indexed fields for indices:', indices))
 
-    result <- httr::GET(url = url)
+    result <- httr::GET(
+        url = url
+        , httr::add_headers(c('Content-Type' = 'application/json'))
+    )
     httr::stop_for_status(result)
     resultContent <- httr::content(result, as = 'parsed')
 
@@ -211,14 +224,17 @@ get_fields <- function(es_host
 
 # [title] Get a data.table containing names of indices and aliases
 # [es_host] A string identifying an Elasticsearch host.
-#' @importFrom httr content GET stop_for_status
+#' @importFrom httr add_headers content GET stop_for_status
 .get_aliases <- function(es_host) {
 
     # construct the url to the alias endpoint
     url <- paste0(es_host, '/_cat/aliases')
 
     # make the request
-    result <- httr::GET(url = url)
+    result <- httr::GET(
+        url = url
+        , httr::add_headers(c('Content-Type' = 'application/json'))
+    )
     httr::stop_for_status(result)
     resultContent <- httr::content(result, as = 'text')
 

R/elasticsearch_parsers.R

@@ -944,7 +944,7 @@ es_search <- function(es_host
 #          hits_to_pull - Total hits to be pulled (documents matching user's query).
 #                       Or, in the case where max_hits < number of matching docs,
 #                       max_hits.
-#' @importFrom httr content RETRY stop_for_status
+#' @importFrom httr add_headers content RETRY stop_for_status
 #' @importFrom jsonlite fromJSON
 #' @importFrom uuid UUIDgenerate
 .keep_on_pullin <- function(scroll_id
@@ -958,7 +958,12 @@ es_search <- function(es_host
     while (hits_pulled < max_hits){
 
         # Grab a page of hits, break if we got back an error
-        result  <- httr::RETRY(verb = "POST", url = scroll_url, body = scroll_id)
+        result  <- httr::RETRY(
+            verb = "POST"
+            , httr::add_headers(c('Content-Type' = 'application/json'))
+            , url = scroll_url
+            , body = scroll_id
+        )
         httr::stop_for_status(result)
         resultJSON  <- httr::content(result, as = "text")
 
@@ -1081,7 +1086,7 @@ es_search <- function(es_host
 #  write(result, 'results.json')
 # 
 # }
-#' @importFrom httr content RETRY stop_for_status
+#' @importFrom httr add_headers content RETRY stop_for_status
 .search_request <- function(es_host
                           , es_index
                           , trailing_args = NULL
@@ -1098,7 +1103,12 @@ es_search <- function(es_host
     }
 
     # Make request
-    result <- httr::RETRY(verb = "POST", url = reqURL, body = query_body)
+    result <- httr::RETRY(
+        verb = "POST"
+        , httr::add_headers(c('Content-Type' = 'application/json'))
+        , url = reqURL
+        , body = query_body
+    )
     httr::stop_for_status(result)
     result <- httr::content(result, as = "text")
 

inst/testdata/shakespeare_mapping.json

@@ -18,7 +18,7 @@
           "type": "integer"
         },
         "text_entry": {
-          "type": "string"
+          "type": "text"
         }
       }
     }

tests/testthat/test-integration.R

@@ -22,9 +22,11 @@ futile.logger::flog.threshold(0)
     test_that("es_search works as expected for a simple request",
               {testthat::skip_on_cran()
 
-               outDT <- es_search(es_host = "http://127.0.0.1:9200"
-                                  , es_index = "shakespeare"
-                                  , max_hits = 100)
+                outDT <- es_search(
+                    es_host = "http://localhost:9200"
+                    , es_index = "shakespeare"
+                    , max_hits = 100
+                )
 
                expect_true("data.table" %in% class(outDT))
                expect_true(nrow(outDT) == 100)