The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
The goal of the noctua package is to provide a
DBI-compliant interface to Amazon’s Athena (https://aws.amazon.com/athena/) using paws SDK. This
allows for an efficient, easy setup connection to Athena using the
paws SDK as a driver.
NOTE: Before using noctua you must
have an aws account or have access to aws account with permissions
allowing you to use Athena.
Athena/Minerva is
the Greek/Roman god of wisdom, handicraft, and warfare. One of the main
symbols for Athena is the Owl. Noctua is the latin word for
Owl.
To install noctua you can get it from CRAN with:
install.packages("noctua")Or to get the development version from Github with:
remotes::install_github("dyfanjones/noctua")The most basic way to connect to AWS Athena is to hard-code your access key and secret access key. However this method is not recommended as your credentials are hard-coded.
library(DBI)
con <- dbConnect(noctua::athena(),
aws_access_key_id='YOUR_ACCESS_KEY_ID',
aws_secret_access_key='YOUR_SECRET_ACCESS_KEY',
s3_staging_dir='s3://path/to/query/bucket/',
region_name='eu-west-1')The next method is to use profile names set up by AWS CLI or created
manually in the ~/.aws directory. To create the profile
names manually please refer to:
https://boto3.amazonaws.com/v1/documentation/api/latest/guide/configuration.html.
noctua is compatible with AWS CLI. This allows your aws
credentials to be stored and not be hard coded in your connection.
To install AWS CLI please refer to: https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-install.html, to configure AWS CLI please refer to: https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-configure.html
Once AWS CLI has been set up you will be able to connect to Athena by
only putting the s3_staging_dir.
Using default profile name:
library(DBI)
con <- dbConnect(noctua::athena(),
s3_staging_dir = 's3://path/to/query/bucket/')Connecting to Athena using profile name other than
default.
library(DBI)
con <- dbConnect(noctua::athena(),
profile_name = "your_profile",
s3_staging_dir = 's3://path/to/query/bucket/')Another method in connecting to Athena is to use Amazon Resource Name (ARN) role.
Setting credentials in environmental variables:
library(noctua)
assume_role(profile_name = "YOUR_PROFILE_NAME",
role_arn = "arn:aws:sts::123456789012:assumed-role/role_name/role_session_name",
set_env = TRUE)
# Connect to Athena using temporary credentials
con <- dbConnect(athena(),
s3_staging_dir = 's3://path/to/query/bucket/')Connecting to Athena directly using ARN role:
library(DBI)
con <- dbConnect(athena(),
profile_name = "YOUR_PROFILE_NAME",
role_arn = "arn:aws:sts::123456789012:assumed-role/role_name/role_session_name",
s3_staging_dir = 's3://path/to/query/bucket/')To change the duration of ARN role session please change the
parameter duration_seconds. By default
duration_seconds is set to 3600 seconds (1 hour).
Connect to athena, and send a query and return results back to R.
library(DBI)
# using default profile to connect
con <- dbConnect(noctua::athena(),
s3_staging_dir = 's3://path/to/query/bucket/')
res <- dbExecute(con, "SELECT * FROM one_row")
dbFetch(res)
dbClearResult(res)To retrieve query in 1 step.
dbGetQuery(con, "SELECT * FROM one_row")To create a tables in athena, dbExecute will send the
query to athena and wait until query has been executed. This makes it
and idea method to create tables within athena.
query <-
"CREATE EXTERNAL TABLE impressions (
requestBeginTime string,
adId string,
impressionId string,
referrer string,
userAgent string,
userCookie string,
ip string,
number string,
processId string,
browserCookie string,
requestEndTime string,
timers struct<modelLookup:string, requestTime:string>,
threadId string,
hostname string,
sessionId string)
PARTITIONED BY (dt string)
ROW FORMAT serde 'org.apache.hive.hcatalog.data.JsonSerDe'
with serdeproperties ( 'paths'='requestBeginTime, adId, impressionId, referrer, userAgent, userCookie, ip' )
LOCATION 's3://elasticmapreduce/samples/hive-ads/tables/impressions/' ;"
dbExecute(con, query)noctua has 2 extra function to return extra information around Athena
tables: dbGetParitiions and dbShow
dbGetPartitions will return all the partitions (returns
data.frame):
noctua::dbGetPartition(con, "impressions")dbShow will return the table’s ddl, so you will able to
see how the table was constructed in Athena (returns SQL character):
noctua::dbShow(con, "impressions")library(DBI)
con <- dbConnect(noctua::athena(),
s3_staging_dir = 's3://path/to/query/bucket/')noctua has created a method to send data.frame from R to Athena.
# Check existing tables
dbListTables(con)
# Upload iris to Athena
dbWriteTable(con, "iris", iris,
partition=c("TIMESTAMP" = format(Sys.Date(), "%Y%m%d")))
# Read in iris from Athena
dbReadTable(con, "iris")
# Check new existing tables in Athena
dbListTables(con)
# Check if iris exists in Athena
dbExistsTable(con, "iris")Please check out noctua method for dbWriteTable
for more information in how to upload data to AWS Athena and AWS S3.
For more information around how to get the most out of AWS Athena when uploading data please check out: Top 10 Performance Tuning Tips for Amazon Athena
Creating a connection to Athena and query and already existing table
iris that was created in previous example.
library(DBI)
library(dplyr)
con <- dbConnect(noctua::athena(),
aws_access_key_id='YOUR_ACCESS_KEY_ID',
aws_secret_access_key='YOUR_SECRET_ACCESS_KEY',
s3_staging_dir='s3://path/to/query/bucket/',
region_name='eu-west-1')
tbl(con, sql("SELECT * FROM iris"))# Source: SQL [?? x 5]
# Database: Athena 0.1.4 [eu-west-1/default]
sepal_length sepal_width petal_length petal_width species
<dbl> <dbl> <dbl> <dbl> <chr>
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
7 4.6 3.4 1.4 0.3 setosa
8 5 3.4 1.5 0.2 setosa
9 4.4 2.9 1.4 0.2 setosa
10 4.9 3.1 1.5 0.1 setosa
# … with more rowsdplyr provides lazy querying with allows to short hand
tbl(con, sql("SELECT * FROM iris")) to
tbl(con, "iris"). For more information please look at https://solutions.posit.co/connections/db/r-packages/dplyr/
tbl(con, "iris")# Source: table<iris> [?? x 5]
# Database: Athena 0.1.4 [eu-west-1/default]
sepal_length sepal_width petal_length petal_width species
<dbl> <dbl> <dbl> <dbl> <chr>
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
7 4.6 3.4 1.4 0.3 setosa
8 5 3.4 1.5 0.2 setosa
9 4.4 2.9 1.4 0.2 setosa
10 4.9 3.1 1.5 0.1 setosa
# … with more rowsQuerying Athena with profile_name instead of hard coding
aws_access_key_id and aws_secret_access_key.
By using profile_name extra Meta Data is returned in the
query to give users extra information.
con <- dbConnect(noctua::athena(),
profile_name = "your_profile",
s3_staging_dir='s3://path/to/query/bucket/')
tbl(con, "iris")) %>%
filter(petal_length < 1.3)# Source: lazy query [?? x 5]
# Database: Athena 0.1.4 [your_profile@eu-west-1/default]
sepal_length sepal_width petal_length petal_width species
<dbl> <dbl> <dbl> <dbl> <chr>
1 4.7 3.2 1.3 0.2 setosa
2 4.3 3 1.1 0.1 setosa
3 5.8 4 1.2 0.2 setosa
4 5.4 3.9 1.3 0.4 setosa
5 4.6 3.6 1 0.2 setosa
6 5 3.2 1.2 0.2 setosa
7 5.5 3.5 1.3 0.2 setosa
8 4.4 3 1.3 0.2 setosa
9 5 3.5 1.3 0.3 setosa
10 4.5 2.3 1.3 0.3 setosa
# … with more rowstbl(con, "iris") %>%
select(contains("sepal"), contains("petal"))# Source: lazy query [?? x 4]
# Database: Athena 0.1.4 [your_profile@eu-west-1/default]
sepal_length sepal_width petal_length petal_width
<dbl> <dbl> <dbl> <dbl>
1 5.1 3.5 1.4 0.2
2 4.9 3 1.4 0.2
3 4.7 3.2 1.3 0.2
4 4.6 3.1 1.5 0.2
5 5 3.6 1.4 0.2
6 5.4 3.9 1.7 0.4
7 4.6 3.4 1.4 0.3
8 5 3.4 1.5 0.2
9 4.4 2.9 1.4 0.2
10 4.9 3.1 1.5 0.1
# … with more rowsUpload data using dplyr function copy_to
and compute.
library(DBI)
library(dplyr)
con <- dbConnect(noctua::athena(),
profile_name = "your_profile",
s3_staging_dir='s3://path/to/query/bucket/')Write data.frame to Athena table
copy_to(con, mtcars,
s3_location = "s3://mybucket/data/")Write Athena table from tbl_sql
athena_mtcars <- tbl(con, "mtcars")
mtcars_filter <- athena_mtcars %>% filter(gear >=4)Create athena with unique table name
mtcars_filer %>% compute()Create athena with specified name and s3 location
mtcars_filer %>%
compute("mtcars_filer",
s3_location = "s3://mybucket/mtcars_filer/")
# Disconnect from Athena
dbDisconnect(con)Creating work group:
library(noctua)
library(DBI)
con <- dbConnect(noctua::athena(),
profile_name = "your_profile",
encryption_option = "SSE_S3",
s3_staging_dir='s3://path/to/query/bucket/')
create_work_group(con, "demo_work_group", description = "This is a demo work group",
tags = tag_options(key= "demo_work_group", value = "demo_01"))List work groups:
list_work_groups(con)[[1]]
[[1]]$Name
[1] "demo_work_group"
[[1]]$State
[1] "ENABLED"
[[1]]$Description
[1] "This is a demo work group"
[[1]]$CreationTime
2019-09-06 18:51:28.902000+01:00
[[2]]
[[2]]$Name
[1] "primary"
[[2]]$State
[1] "ENABLED"
[[2]]$Description
[1] ""
[[2]]$CreationTime
2019-08-22 16:14:47.902000+01:00Update work group:
update_work_group(con, "demo_work_group", description = "This is a demo work group update")Return work group meta data:
get_work_group(con, "demo_work_group")$Name
[1] "demo_work_group"
$State
[1] "ENABLED"
$Configuration
$Configuration$ResultConfiguration
$Configuration$ResultConfiguration$OutputLocation
[1] "s3://path/to/query/bucket/"
$Configuration$ResultConfiguration$EncryptionConfiguration
$Configuration$ResultConfiguration$EncryptionConfiguration$EncryptionOption
[1] "SSE_S3"
$Configuration$EnforceWorkGroupConfiguration
[1] FALSE
$Configuration$PublishCloudWatchMetricsEnabled
[1] FALSE
$Configuration$BytesScannedCutoffPerQuery
[1] 10000000
$Configuration$RequesterPaysEnabled
[1] FALSE
$Description
[1] "This is a demo work group update"
$CreationTime
2019-09-06 18:51:28.902000+01:00Connect to Athena using work group:
con <- dbConnect(noctua::athena(),
work_group = "demo_work_group")Delete work group:
delete_work_group(con, "demo_work_group")pyAthena - A python wrapper of the python package
Boto3 using the sqlAlchemy framework: https://github.com/laughingman7743/PyAthenaAWR.Athena - A R wrapper of RJDBC for the AWS Athena’s
JDBC drivers: https://github.com/nfultz/AWR.AthenaRAthena - A R wrapper of the python package
Boto3 using DBI as the framework: https://github.com/DyfanJones/RAthenaawsathena - rJava Interface to AWS Athena SDK https://github.com/hrbrmstr/awsathenametis - Helpers for Accessing and Querying Amazon
Athena using R, Including a lightweight RJDBC shim https://github.com/hrbrmstr/metismetisjars - JARs for metis https://github.com/hrbrmstr/metis-jarsmetis.tidy - Access and Query Amazon Athena via the
Tidyverse https://github.com/hrbrmstr/metis-tidynoctua is basically the same as RAthena
however it utilises the R AWS SDK paws to achieve the same
goal.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.