{"id":4696,"date":"2016-12-05T15:51:47","date_gmt":"2016-12-05T20:51:47","guid":{"rendered":"https:\/\/rud.is\/b\/?p=4696"},"modified":"2018-03-07T17:33:00","modified_gmt":"2018-03-07T22:33:00","slug":"interacting-with-amazon-athena-from-r","status":"publish","type":"post","link":"https:\/\/rud.is\/b\/2016\/12\/05\/interacting-with-amazon-athena-from-r\/","title":{"rendered":"Interacting With Amazon Athena from R"},"content":{"rendered":"

This is a short post for those looking to test out Amazon Athena<\/a> with R.<\/p>\n

Amazon makes Athena available via JDBC, so you can use RJDBC<\/code> to query data. All you need is their JAR file and some setup information. Here’s how to get the JAR file to the current working directory:<\/p>\n

URL <- 'https:\/\/s3.amazonaws.com\/athena-downloads\/drivers\/AthenaJDBC41-1.0.0.jar'\r\nfil <- basename(URL)\r\nif (!file.exists(fil)) download.file(URL, fil)<\/code><\/pre>\n
To avoid putting credentials in code, you can store the AWS key and secret you’re using for the queries in ATHENA_USER<\/code> and ATHENA_PASSWORD<\/code> environment variables via ~\/.Renviron<\/code>. You’ll also need an S3 bucket writable by those credentials for the Athena staging directory. With that info in hand, it’s easy to connect:<\/p>\n
library(RJDBC)\r\nlibrary(dplyr)\r\n\r\ndrv <- JDBC(driverClass="com.amazonaws.athena.jdbc.AthenaDriver", fil, identifier.quote="'")\r\n\r\ncon <- jdbcConnection <- dbConnect(drv, 'jdbc:awsathena:\/\/athena.us-east-1.amazonaws.com:443\/',\r\n                                   s3_staging_dir="s3:\/\/accessible-bucket",\r\n                                   user=Sys.getenv("ATHENA_USER"),\r\n                                   password=Sys.getenv("ATHENA_PASSWORD"))<\/code><\/pre>\n
Even if you have no data configured in Athena, you can check out the test data available to all:<\/p>\n
dbListTables(con)\r\n## [1] "elb_logs"<\/code><\/pre>\n
If that worked, then you should be able to query data (using the fully qualified table name in this case):<\/p>\n
dbGetQuery(con, "SELECT * FROM sampledb.elb_logs LIMIT 10") %>% \r\n  dplyr::glimpse()\r\n## Observations: 10\r\n## Variables: 16\r\n## $ timestamp             <chr> "2014-09-27T00:00:25.424956Z", "2014-09-27T00:00:56.439218Z", "2014-09-27T00:01:27.441734Z", "2014-09-27T00:01:58.366715Z", "2014-09-27T00:02:29.446363Z", "2014-09-2...\r\n## $ elbname               <chr> "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo"\r\n## $ requestip             <chr> "241.230.198.83", "252.26.60.51", "250.244.20.109", "247.59.58.167", "254.64.224.54", "245.195.140.77", "245.195.140.77", "243.71.49.173", "240.139.5.14", "251.192.4...\r\n## $ requestport           <dbl> 27026, 27026, 27026, 27026, 27026, 27026, 27026, 27026, 27026, 27026\r\n## $ backendip             <chr> "251.192.40.76", "249.89.116.3", "251.111.156.171", "251.139.91.156", "251.111.156.171", "254.64.224.54", "254.64.224.54", "250.244.20.109", "247.65.176.249", "250.2...\r\n## $ backendport           <dbl> 443, 8888, 8888, 8888, 8000, 8888, 8888, 8888, 8888, 8888\r\n## $ requestprocessingtime <dbl> 9.1e-05, 9.4e-05, 8.4e-05, 9.7e-05, 9.1e-05, 9.3e-05, 9.4e-05, 8.3e-05, 9.0e-05, 9.0e-05\r\n## $ backendprocessingtime <dbl> 0.046598, 0.038973, 0.047054, 0.039845, 0.061461, 0.037791, 0.047035, 0.048792, 0.045724, 0.029918\r\n## $ clientresponsetime    <dbl> 4.9e-05, 4.7e-05, 4.9e-05, 4.9e-05, 4.0e-05, 7.7e-05, 7.5e-05, 7.3e-05, 4.0e-05, 6.7e-05\r\n## $ elbresponsecode       <chr> "200", "200", "200", "200", "200", "200", "200", "200", "200", "200"\r\n## $ backendresponsecode   <chr> "200", "200", "200", "200", "200", "400", "400", "200", "200", "200"\r\n## $ receivedbytes         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0\r\n## $ sentbytes             <dbl> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2\r\n## $ requestverb           <chr> "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET"\r\n## $ url                   <chr> "http:\/\/www.abcxyz.com:80\/jobbrowser\/?format=json&state=running&user=20g578y", "http:\/\/www.abcxyz.com:80\/jobbrowser\/?format=json&state=running&user=20g578y", "http:\/...\r\n## $ protocol              <chr> "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1", "HTTP\/1.1"<\/code><\/pre>\n
And, you can disconnect when done:<\/p>\n
dbDisconnect(con)<\/code><\/pre>\n
You should probably store the JAR file in a central location and refer to it that way in “production” scripts.<\/p>\n
Now, you can go crazy querying data and racking up AWS charges ?.<\/p>\n","protected":false},"excerpt":{"rendered":"
This is a short post for those looking to test out Amazon Athena with R. Amazon makes Athena available via JDBC, so you can use RJDBC to query data. All you need is their JAR file and some setup information. 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It supports a plethora of kernels\/interpreters and can do a ton of things that this post isn't going to discuss (perhaps future ones will, especially since it's the first \"notebook\" environment I've been able to tolerate for longer than\u2026","rel":"","context":"In "athena"","block_context":{"text":"athena","link":"https:\/\/rud.is\/b\/category\/athena\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2018\/08\/athena-example-1.png?fit=1200%2C704&ssl=1&resize=350%2C200","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2018\/08\/athena-example-1.png?fit=1200%2C704&ssl=1&resize=350%2C200 1x, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2018\/08\/athena-example-1.png?fit=1200%2C704&ssl=1&resize=525%2C300 1.5x, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2018\/08\/athena-example-1.png?fit=1200%2C704&ssl=1&resize=700%2C400 2x, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2018\/08\/athena-example-1.png?fit=1200%2C704&ssl=1&resize=1050%2C600 3x"},"classes":[]},{"id":11070,"url":"https:\/\/rud.is\/b\/2018\/07\/14\/alleviating-aws-athena-aggravation-with-asynchronous-assistance\/","url_meta":{"origin":4696,"position":4},"title":"Alleviating AWS Athena Aggravation with Asynchronous Assistance","author":"hrbrmstr","date":"2018-07-14","format":false,"excerpt":"I've blogged about how to use Amazon Athena with R before and if you are a regular Athena user, you've likely run into a situation where you prepare a dplyr chain, fire off a collect() and then wait. And, wait. And, wait. And, wait. Queries that take significant processing time\u2026","rel":"","context":"In "athena"","block_context":{"text":"athena","link":"https:\/\/rud.is\/b\/category\/athena\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":11077,"url":"https:\/\/rud.is\/b\/2018\/07\/20\/a-new-boto3-amazon-athena-client-wrapper-with-dplyr-async-query-support\/","url_meta":{"origin":4696,"position":5},"title":"A new ‘boto3’ Amazon Athena client wrapper with dplyr async query support","author":"hrbrmstr","date":"2018-07-20","format":false,"excerpt":"A previous post explored how to deal with Amazon Athena queries asynchronously. The function presented is a beast, though it is on purpose (to provide options for folks). In reality, nobody really wants to use rJava wrappers much anymore and dealing with icky Python library calls directly just feels wrong,\u2026","rel":"","context":"In "athena"","block_context":{"text":"athena","link":"https:\/\/rud.is\/b\/category\/athena\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts\/4696","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/comments?post=4696"}],"version-history":[{"count":0,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts\/4696\/revisions"}],"wp:attachment":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/media?parent=4696"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/categories?post=4696"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/tags?post=4696"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}