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https://github.com/DyfanJones/noctua
Connect R to Athena using paws SDK (DBI Interface)
https://github.com/DyfanJones/noctua
athena aws database r
Last synced: 3 months ago
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Connect R to Athena using paws SDK (DBI Interface)
- Host: GitHub
- URL: https://github.com/DyfanJones/noctua
- Owner: DyfanJones
- License: other
- Created: 2019-09-29T13:54:09.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2024-05-28T09:51:04.000Z (5 months ago)
- Last Synced: 2024-07-08T02:05:38.208Z (4 months ago)
- Topics: athena, aws, database, r
- Language: R
- Homepage: https://dyfanjones.github.io/noctua/
- Size: 1.9 MB
- Stars: 45
- Watchers: 3
- Forks: 5
- Open Issues: 12
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# noctua
[](https://www.repostatus.org/#active)
[](https://CRAN.R-project.org/package=noctua)
[](https://app.codecov.io/gh/DyfanJones/noctua?branch=master)
[](https://github.com/dyfanjones/noctua/actions)
[](https://dyfanjones.r-universe.dev)
The goal of the `noctua` package is to provide a DBI-compliant interface
to Amazon’s Athena () using [`paws`](https://github.com/paws-r/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.*
## Why is the package called noctua
[Athena/Minerva](https://en.wikipedia.org/wiki/Athena) 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.
## Installation:
To install `noctua` you can get it from CRAN with:
``` r
install.packages("noctua")
```
Or to get the development version from Github with:
```r
remotes::install_github("dyfanjones/noctua")
```
## Connection Methods
### Hard Coding
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.
```r
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')
```
### AWS Profile Name
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.
##### Setting up AWS CLI
`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:
,
to configure AWS CLI please refer to:
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:
``` r
library(DBI)
con <- dbConnect(noctua::athena(),
s3_staging_dir = 's3://path/to/query/bucket/')
```
Connecting to Athena using profile name other than `default`.
``` r
library(DBI)
con <- dbConnect(noctua::athena(),
profile_name = "your_profile",
s3_staging_dir = 's3://path/to/query/bucket/')
```
## Assuming ARN Role for connection
Another method in connecting to Athena is to use Amazon Resource Name (ARN) role.
Setting credentials in environmental variables:
```r
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:
```r
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).
## Usage
### Basic Usage
Connect to athena, and send a query and return results back to R.
``` 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.
``` r
dbGetQuery(con, "SELECT * FROM one_row")
```
### Intermediate Usage
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.
``` r
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,
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):
``` r
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):
``` r
noctua::dbShow(con, "impressions")
```
### Advanced Usage
``` r
library(DBI)
con <- dbConnect(noctua::athena(),
s3_staging_dir = 's3://path/to/query/bucket/')
```
#### Sending data to Athena
noctua has created a method to send data.frame from R to Athena.
``` r
# 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`](https://dyfanjones.github.io/noctua/reference/AthenaWriteTables.html) 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](https://aws.amazon.com/blogs/big-data/top-10-performance-tuning-tips-for-amazon-athena/)
### Tidyverse Usage
Creating a connection to Athena and query and already existing table
`iris` that was created in previous example.
``` r
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
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 rows
dplyr provides lazy querying with allows to short hand `tbl(con,
sql("SELECT * FROM iris"))` to `tbl(con, "iris")`. For more information
please look at
``` r
tbl(con, "iris")
```
# Source: table [?? x 5]
# Database: Athena 0.1.4 [eu-west-1/default]
sepal_length sepal_width petal_length petal_width species
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 rows
Querying 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.
``` r
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
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 rows
``` r
tbl(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
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 rows
Upload data using `dplyr` function `copy_to` and `compute`.
``` r
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
```r
copy_to(con, mtcars,
s3_location = "s3://mybucket/data/")
```
Write Athena table from tbl_sql
```r
athena_mtcars <- tbl(con, "mtcars")
mtcars_filter <- athena_mtcars %>% filter(gear >=4)
```
Create athena with unique table name
```r
mtcars_filer %>% compute()
```
Create athena with specified name and s3 location
```r
mtcars_filer %>%
compute("mtcars_filer",
s3_location = "s3://mybucket/mtcars_filer/")
# Disconnect from Athena
dbDisconnect(con)
```
## Work Groups
Creating work group:
``` r
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:
``` r
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+01:00
Update work group:
``` r
update_work_group(con, "demo_work_group", description = "This is a demo work group update")
```
Return work group meta data:
``` r
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+01:00
Connect to Athena using work group:
``` r
con <- dbConnect(noctua::athena(),
work_group = "demo_work_group")
```
Delete work group:
``` r
delete_work_group(con, "demo_work_group")
```
# Similar Projects
## Python:
- `pyAthena` - A python wrapper of the python package `Boto3` using
the sqlAlchemy framework:
## R:
- `AWR.Athena` - A R wrapper of RJDBC for the AWS Athena’s JDBC
drivers:
- `RAthena` - A R wrapper of the python package `Boto3` using DBI as the framework:
- `awsathena` - rJava Interface to AWS Athena SDK
- `metis` - Helpers for Accessing and Querying Amazon Athena using R, Including a lightweight RJDBC shim
- `metisjars` - JARs for `metis`
- `metis.tidy` - Access and Query Amazon Athena via the Tidyverse
## Comparison:
`noctua` is basically the same as `RAthena` however it utilises the R AWS SDK `paws` to achieve the same goal.