Access and Query Amazon Athena via DBI/JDBC
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metis

Access and Query Amazon Athena via DBI/JDBC

Description

In Greek mythology, Metis was Athena’s “helper” so methods are provided to help you accessing and querying Amazon Athena via DBI/JDBC and/or dplyr. #’ Methods are provides to connect to ‘Amazon’ ‘Athena’, lookup schemas/tables,

IMPORTANT

Since R 3.5 (I don’t remember this happening in R 3.4.x) signals sent from interrupting Athena JDBC calls crash the R interpreter. You need to set the -Xrs option to avoid signals being passed on to the JVM owner. That has to be done before rJava is loaded so you either need to remember to put it at the top of all scripts or stick this in your local ~/.Rprofile and/or sitewide Rprofile:

if (!grepl("-Xrs", getOption("java.parameters", ""))) {
  options(
    "java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs")
  )
}

What’s Inside The Tin?

The following functions are implemented:

Easy-interface connection helper:

  • athena_connect Simplified Athena JDBC connection helper

Custom JDBC Classes:

  • Athena: AthenaJDBC (make a new Athena con obj)
  • AthenaConnection-class: AthenaJDBC
  • AthenaDriver-class: AthenaJDBC
  • AthenaResult-class: AthenaJDBC

Custom JDBC Class Methods:

  • dbConnect-method
  • dbExistsTable-method
  • dbGetQuery-method
  • dbListFields-method
  • dbListTables-method
  • dbReadTable-method
  • dbSendQuery-method

Pulled in from other cloudyr pkgs:

  • read_credentials: Use Credentials from .aws/credentials File
  • use_credentials: Use Credentials from .aws/credentials File

Installation

devtools::install_git("https://git.sr.ht/~hrbrmstr/metis-lite")
# OR
devtools::install_gitlab("hrbrmstr/metis-lite")
# OR
devtools::install_github("hrbrmstr/metis-lite")

Usage

library(metis.lite)

# current verison
packageVersion("metis.lite")
## [1] '0.3.0'
library(rJava)
library(RJDBC)
library(metis.lite)
library(magrittr)
library(dbplyr)
library(dplyr)

dbConnect(
  drv = metis.lite::Athena(),
  schema_name = "sampledb",
  provider = "com.simba.athena.amazonaws.auth.PropertiesFileCredentialsProvider",
  AwsCredentialsProviderArguments = path.expand("~/.aws/athenaCredentials.props"),
  s3_staging_dir = "s3://aws-athena-query-results-569593279821-us-east-1",
) -> con

dbListTables(con, schema="sampledb")
## [1] "elb_logs"
dbExistsTable(con, "elb_logs", schema="sampledb")
## [1] TRUE
dbListFields(con, "elb_logs", "sampledb")
##  [1] "timestamp"             "elbname"               "requestip"             "requestport"          
##  [5] "backendip"             "backendport"           "requestprocessingtime" "backendprocessingtime"
##  [9] "clientresponsetime"    "elbresponsecode"       "backendresponsecode"   "receivedbytes"        
## [13] "sentbytes"             "requestverb"           "url"                   "protocol"
dbGetQuery(con, "SELECT * FROM sampledb.elb_logs LIMIT 10") %>% 
  glimpse()
## Observations: 10
## Variables: 16
## $ timestamp             <chr> "2014-09-29T18:18:51.826955Z", "2014-09-29T18:18:51.920462Z", "2014-09-29T18:18:52.2725…
## $ elbname               <chr> "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo",…
## $ requestip             <chr> "255.48.150.122", "249.213.227.93", "245.108.120.229", "241.112.203.216", "241.43.107.2…
## $ requestport           <int> 62096, 62096, 62096, 62096, 56454, 33254, 18918, 64352, 1651, 56454
## $ backendip             <chr> "244.238.214.120", "248.99.214.228", "243.3.190.175", "246.235.181.255", "241.112.203.2…
## $ backendport           <int> 8888, 8888, 8888, 8888, 8888, 8888, 8888, 8888, 8888, 8888
## $ requestprocessingtime <dbl> 9.0e-05, 9.7e-05, 8.7e-05, 9.4e-05, 7.6e-05, 8.3e-05, 6.3e-05, 5.4e-05, 8.2e-05, 8.7e-05
## $ backendprocessingtime <dbl> 0.007410, 0.256533, 0.442659, 0.016772, 0.035036, 0.029892, 0.034148, 0.014858, 0.01518…
## $ clientresponsetime    <dbl> 0.000055, 0.000075, 0.000131, 0.000078, 0.000057, 0.000043, 0.000033, 0.000043, 0.00007…
## $ elbresponsecode       <chr> "302", "302", "200", "200", "200", "200", "200", "200", "200", "200"
## $ backendresponsecode   <chr> "200", "200", "200", "200", "200", "200", "200", "200", "200", "200"
## $ receivedbytes         <S3: integer64> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
## $ sentbytes             <S3: integer64> 0, 0, 58402, 152213, 20766, 32370, 3408, 3884, 84245, 3831
## $ requestverb           <chr> "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET"
## $ url                   <chr> "http://www.abcxyz.com:80/", "http://www.abcxyz.com:80/accounts/login/?next=/", "http:/…
## $ protocol              <chr> "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HT…

Check types

dbGetQuery(con, "
SELECT
  CAST('chr' AS CHAR(4)) achar,
  CAST('varchr' AS VARCHAR) avarchr,
  CAST(SUBSTR(timestamp, 1, 10) AS DATE) AS tsday,
  CAST(100.1 AS DOUBLE) AS justadbl,
  CAST(127 AS TINYINT) AS asmallint,
  CAST(100 AS INTEGER) AS justanint,
  CAST(100000000000000000 AS BIGINT) AS abigint,
  CAST(('GET' = 'GET') AS BOOLEAN) AS is_get,
  ARRAY[1, 2, 3] AS arr1,
  ARRAY['1', '2, 3', '4'] AS arr2,
  MAP(ARRAY['foo', 'bar'], ARRAY[1, 2]) AS mp,
  CAST(ROW(1, 2.0) AS ROW(x BIGINT, y DOUBLE)) AS rw,
  CAST('{\"a\":1}' AS JSON) js
FROM elb_logs
LIMIT 1
") %>% 
  glimpse()
## Observations: 1
## Variables: 13
## $ achar     <chr> "chr "
## $ avarchr   <chr> "varchr"
## $ tsday     <date> 2014-09-26
## $ justadbl  <dbl> 100.1
## $ asmallint <int> 127
## $ justanint <int> 100
## $ abigint   <S3: integer64> 100000000000000000
## $ is_get    <lgl> TRUE
## $ arr1      <chr> "1, 2, 3"
## $ arr2      <chr> "1, 2, 3, 4"
## $ mp        <chr> "{bar=2, foo=1}"
## $ rw        <chr> "{x=1, y=2.0}"
## $ js        <chr> "\"{\\\"a\\\":1}\""

dplyr

tbl(con, sql("
SELECT
  CAST('chr' AS CHAR(4)) achar,
  CAST('varchr' AS VARCHAR) avarchr,
  CAST(SUBSTR(timestamp, 1, 10) AS DATE) AS tsday,
  CAST(100.1 AS DOUBLE) AS justadbl,
  CAST(127 AS TINYINT) AS asmallint,
  CAST(100 AS INTEGER) AS justanint,
  CAST(100000000000000000 AS BIGINT) AS abigint,
  CAST(('GET' = 'GET') AS BOOLEAN) AS is_get,
  ARRAY[1, 2, 3] AS arr,
  ARRAY['1', '2, 3', '4'] AS arr,
  MAP(ARRAY['foo', 'bar'], ARRAY[1, 2]) AS mp,
  CAST(ROW(1, 2.0) AS ROW(x BIGINT, y DOUBLE)) AS rw,
  CAST('{\"a\":1}' AS JSON) js
FROM elb_logs
LIMIT 1
")) %>% 
  glimpse()
## Observations: ??
## Variables: 13
## Database: AthenaConnection
## $ achar     <chr> "chr "
## $ avarchr   <chr> "varchr"
## $ tsday     <date> 2014-09-27
## $ justadbl  <dbl> 100.1
## $ asmallint <int> 127
## $ justanint <int> 100
## $ abigint   <S3: integer64> 100000000000000000
## $ is_get    <lgl> TRUE
## $ arr       <chr> "1, 2, 3"
## $ arr       <chr> "1, 2, 3, 4"
## $ mp        <chr> "{bar=2, foo=1}"
## $ rw        <chr> "{x=1, y=2.0}"
## $ js        <chr> "\"{\\\"a\\\":1}\""

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.