metis

Helpers for Accessing and Querying Amazon Athena

Including a lightweight RJDBC shim.

In Greek mythology, Metis was Athena’s “helper”.

Description

Still fairly beta-quality level but getting there.

The goal will be to get around enough of the “gotchas” that are preventing raw RJDBC Athena connections from “just working” with dplyr v0.6.0+ and also get around the fetchSize problem without having to not use dbGetQuery().

The AthenaJDBC42_2.0.2.jar JAR file is included out of convenience but that will likely move to a separate package as this gets closer to prime time if this goes on CRAN.

NOTE that the updated driver REQUIRES JDK 1.8+.

See the Usage section for an example.

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 Make a JDBC connection to Athena

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: AthenaJDBC
• dbExistsTable-method: AthenaJDBC
• dbGetQuery-method: AthenaJDBC
• dbListFields-method: AthenaJDBC
• dbListTables-method: AthenaJDBC
• dbReadTable-method: AthenaJDBC
• dbSendQuery-method: AthenaJDBC

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_github("hrbrmstr/metis")

Usage

library(metis)
library(tidyverse)

# current verison
packageVersion("metis")

## [1] '0.3.0'

use_credentials("default")

athena_connect(
  default_schema = "sampledb", 
  s3_staging_dir = "s3://accessible-bucket",
  log_path = "/tmp/athena.log",
  log_level = "DEBUG"
) -> ath

dbListTables(ath, schema="sampledb")

## [1] "elb_logs"

dbExistsTable(ath, "elb_logs", schema="sampledb")

## [1] TRUE

dbListFields(ath, "elb_logs", "sampledb")

##  [1] "timestamp"             "elbname"               "requestip"             "requestport"          
##  [5] "backendip"             "backendport"           "requestprocessingtime" "backendprocessingtime"
##  [9] "clientresponsetime"    "elbresponsecode"       "backendresponsecode"   "receivedbytes"        
## [13] "sentbytes"             "requestverb"           "url"                   "protocol"

dbGetQuery(ath, "SELECT * FROM sampledb.elb_logs LIMIT 10") %>% 
  type_convert() %>% 
  glimpse()

## Observations: 10
## Variables: 16
## $ timestamp             <dttm> 2014-09-30 01:28:17, 2014-09-30 00:01:30, 2014-09-30 00:01:30, 2014-09-30 00:01:30, ...
## $ elbname               <chr> "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo...
## $ requestip             <chr> "246.140.190.136", "240.109.129.138", "242.251.232.153", "253.227.207.81", "253.227.2...
## $ requestport           <dbl> 63777, 22705, 22705, 22705, 23282, 24178, 22916, 23807, 22916, 21443
## $ backendip             <chr> "250.193.168.100", "251.103.130.45", "243.140.114.254", "243.82.95.243", "246.129.102...
## $ backendport           <dbl> 8888, 8888, 8888, 8888, 8899, 8888, 8888, 8888, 8888, 8888
## $ requestprocessingtime <dbl> 7.2e-05, 6.9e-05, 8.7e-05, 9.7e-05, 8.1e-05, 4.6e-05, 4.3e-05, 5.3e-05, 5.5e-05, 4.4e-05
## $ backendprocessingtime <dbl> 0.379241, 0.007541, 0.187126, 0.413337, 0.037030, 0.050222, 0.043706, 0.045953, 0.015...
## $ clientresponsetime    <dbl> 8.0e-05, 4.3e-05, 7.5e-05, 8.7e-05, 4.5e-05, 3.3e-05, 3.3e-05, 6.9e-05, 8.5e-05, 4.9e-05
## $ elbresponsecode       <int> 200, 302, 302, 200, 200, 200, 200, 200, 200, 200
## $ backendresponsecode   <int> 200, 200, 200, 400, 200, 200, 200, 404, 200, 200
## $ receivedbytes         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
## $ sentbytes             <dbl> 58402, 0, 0, 58402, 32370, 20766, 3408, 152213, 84245, 3884
## $ requestverb           <chr> "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET"
## $ url                   <chr> "http://www.abcxyz.com:80/", "http://www.abcxyz.com:80/", "http://www.abcxyz.com:80/a...
## $ protocol              <chr> "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "...

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.