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Type:

Package

Title:

Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)

Version:

2.6.3

Description:

Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena https://aws.amazon.com/athena/. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' https://github.com/paws-r/paws is used as a driver.

Imports:

data.table (≥ 1.12.4), DBI (≥ 0.7), methods, paws (≥ 0.2.0), stats, utils, uuid (≥ 0.1-4)

Suggests:

arrow, bit64, dplyr (≥ 1.0.0), dbplyr (≥ 2.3.3), testthat, tibble, vroom (≥ 1.2.0), covr, knitr, rmarkdown, jsonify, jsonlite

VignetteBuilder:

knitr

Depends:

R (≥ 3.2.0)

License:

MIT + file LICENSE

Encoding:

UTF-8

RoxygenNote:

7.3.3

URL:

https://dyfanjones.github.io/noctua/, https://github.com/DyfanJones/noctua

BugReports:

https://github.com/DyfanJones/noctua/issues

Collate:

'utils.R' 'dplyr_integration.R' 'noctua.R' 'Driver.R' 'Connection.R' 'DataTypes.R' 'File_Parser.R' 'Options.R' 'fetch_utils.R' 'Result.R' 'Table.R' 'View.R' 'athena_low_api.R' 'column_parser.R' 'sql_translate_utils.R' 'sql_translate_env.R' 'zzz.R'

NeedsCompilation:

Packaged:

2025-09-15 19:03:56 UTC; dyfanjones

Author:

Dyfan Jones [aut, cre]

Maintainer:

Dyfan Jones <dyfan.r.jones@gmail.com>

Repository:

CRAN

Date/Publication:

2025-09-15 19:40:02 UTC

noctua: a DBI interface into Athena using paws SDK

Description

noctua provides a seamless DBI interface into Athena using the R package paws.

Goal of Package

The goal of the noctua package is to provide a DBI-compliant interface to Amazon’s Athena using paws software development kit (SDK). This allows for an efficient, easy setup connection to Athena using the paws SDK as a driver.

AWS Command Line Interface

As noctua is using paws as it's backend, AWS Command Line Interface (AWS CLI) can be used to remove user credentials when interacting with Athena.

This allows AWS profile names to be set up so that noctua can connect to different accounts from the same machine, without needing hard code any credentials.

Author(s)

Maintainer: Dyfan Jones dyfan.r.jones@gmail.com

Athena Connection Methods

Description

Implementations of pure virtual functions defined in the DBI package for AthenaConnection objects.

Method to get Athena schema, tables and table types return as a data.frame

This method returns all partitions from Athena table.

Executes a statement to return the data description language (DDL) of the Athena table.

Usage

## S4 method for signature 'AthenaConnection'
show(object)

## S4 method for signature 'AthenaConnection'
dbDisconnect(conn, ...)

## S4 method for signature 'AthenaConnection'
dbIsValid(dbObj, ...)

## S4 method for signature 'AthenaConnection,character'
dbSendQuery(conn, statement, unload = athena_unload(), ...)

## S4 method for signature 'AthenaConnection,character'
dbSendStatement(conn, statement, unload = athena_unload(), ...)

## S4 method for signature 'AthenaConnection,character'
dbExecute(conn, statement, unload = athena_unload(), ...)

## S4 method for signature 'AthenaConnection,ANY'
dbDataType(dbObj, obj, ...)

## S4 method for signature 'AthenaConnection,data.frame'
dbDataType(dbObj, obj, ...)

## S4 method for signature 'AthenaConnection,character'
dbQuoteString(conn, x, ...)

## S4 method for signature 'AthenaConnection,POSIXct'
dbQuoteString(conn, x, ...)

## S4 method for signature 'AthenaConnection,Date'
dbQuoteString(conn, x, ...)

## S4 method for signature 'AthenaConnection,SQL'
dbQuoteIdentifier(conn, x, ...)

dbGetTables(conn, ...)

## S4 method for signature 'AthenaConnection'
dbGetTables(conn, catalog = NULL, schema = NULL, ...)

## S4 method for signature 'AthenaConnection,character'
dbListFields(conn, name, ...)

## S4 method for signature 'AthenaConnection,character'
dbExistsTable(conn, name, ...)

## S4 method for signature 'AthenaConnection,Id'
dbExistsTable(conn, name, ...)

## S4 method for signature 'AthenaConnection,character'
dbRemoveTable(conn, name, delete_data = TRUE, confirm = FALSE, ...)

## S4 method for signature 'AthenaConnection,Id'
dbRemoveTable(conn, name, delete_data = TRUE, confirm = FALSE, ...)

## S4 method for signature 'AthenaConnection,character'
dbGetQuery(conn, statement, statistics = FALSE, unload = athena_unload(), ...)

## S4 method for signature 'AthenaConnection'
dbGetInfo(dbObj, ...)

dbGetPartition(conn, name, ..., .format = FALSE)

## S4 method for signature 'AthenaConnection'
dbGetPartition(conn, name, ..., .format = FALSE)

dbShow(conn, name, ...)

## S4 method for signature 'AthenaConnection'
dbShow(conn, name, ...)

## S4 method for signature 'AthenaConnection'
dbBegin(conn, ...)

## S4 method for signature 'AthenaConnection'
dbCommit(conn, ...)

## S4 method for signature 'AthenaConnection'
dbRollback(conn, ...)

Arguments

object

Any R object

conn

A DBI::DBIConnection object, as returned by dbConnect().

...

Other parameters passed on to methods.

dbObj

An object inheriting from DBIObject, i.e. DBIDriver, DBIConnection, or a DBIResult.

statement

a character string containing SQL.

unload

boolean input to modify statement to align with AWS Athena UNLOAD, default is set to FALSE.

obj

An R object whose SQL type we want to determine.

x

A character vector to quote as string.

catalog

Athena catalog, default set to NULL to return all tables from all Athena catalogs

schema

Athena schema, default set to NULL to return all tables from all Athena schemas. Note: The use of DATABASE and SCHEMA is interchangeable within Athena.

name

The table name, passed on to dbQuoteIdentifier(). Options are:

a character string with the unquoted DBMS table name, e.g. "table_name",
a call to Id() with components to the fully qualified table name, e.g. Id(schema = "my_schema", table = "table_name")
a call to SQL() with the quoted and fully qualified table name given verbatim, e.g. SQL('"my_schema"."table_name"')

delete_data

Deletes S3 files linking to AWS Athena table

confirm

Allows for S3 files to be deleted without the prompt check. It is recommend to leave this set to FALSE to avoid deleting other S3 files when the table's definition points to the root of S3 bucket.

statistics

If set to TRUE will print out AWS Athena statistics of query.

.format

re-formats AWS Athena partitions format. So that each column represents a partition from the AWS Athena table. Default set to FALSE to prevent breaking previous package behaviour.

Value

dbGetTables() returns a data.frame.

data.frame that returns all partitions in table, if no partitions in Athena table then function will return error from Athena.

dbShow() returns SQL characters of the Athena table DDL.

Slots

ptr: a list of connecting objects from the SDK paws package.
info: a list of metadata objects
quote: syntax to quote sql query when creating Athena ddl

Athena Driver Methods

Description

Implementations of pure virtual functions defined in the DBI package for AthenaDriver objects.

Usage

## S4 method for signature 'AthenaDriver'
show(object)

## S4 method for signature 'AthenaDriver,ANY'
dbDataType(dbObj, obj, ...)

## S4 method for signature 'AthenaDriver,list'
dbDataType(dbObj, obj, ...)

Arguments

object

Any R object

dbObj

A object inheriting from DBI::DBIDriver or DBI::DBIConnection.

obj

An R object whose SQL type we want to determine.

...

Other arguments passed on to methods.

List objects in a connection.

Description

Lists all of the objects in the connection, or all the objects which have specific attributes.

Usage

AthenaListObjects(connection, ...)

Arguments

connection

A connection object, as returned by dbConnect().

...

Attributes to filter by.

Details

When used without parameters, this function returns all of the objects known by the connection. Any parameters passed will filter the list to only objects which have the given attributes; for instance, passing schema = "foo" will return only objects matching the schema foo.

Value

A data frame with name and type columns, listing the objects.

Preview the data in an object.

Description

Return the data inside an object as a data frame.

Usage

AthenaPreviewObject(connection, rowLimit, ...)

Arguments

connection

A connection object, as returned by dbConnect().

rowLimit

The maximum number of rows to display.

...

Parameters specifying the object.

Details

The object to previewed must be specified as one of the arguments (e.g. table = "employees"); depending on the driver and underlying data store, additional specification arguments may be required.

Value

A data frame containing the data in the object.

Athena Result Methods

Description

Implementations of pure virtual functions defined in the DBI package for AthenaResult objects.

Returns AWS Athena Statistics from execute queries DBI::dbSendQuery

Usage

## S4 method for signature 'AthenaResult'
dbClearResult(res, ...)

## S4 method for signature 'AthenaResult'
dbFetch(res, n = -1, ...)

## S4 method for signature 'AthenaResult'
dbHasCompleted(res, ...)

## S4 method for signature 'AthenaResult'
dbIsValid(dbObj, ...)

## S4 method for signature 'AthenaResult'
dbGetInfo(dbObj, ...)

## S4 method for signature 'AthenaResult'
dbColumnInfo(res, ...)

dbStatistics(res, ...)

## S4 method for signature 'AthenaResult'
dbStatistics(res, ...)

## S4 method for signature 'AthenaResult'
dbGetStatement(res, ...)

Arguments

res

An object inheriting from DBI::DBIResult.

...

Other arguments passed on to methods.

n

maximum number of records to retrieve per fetch. Use n = -1 or n = Inf to retrieve all pending records. Some implementations may recognize other special values.

dbObj

An object inheriting from DBI::DBIResult, DBI::DBIConnection, or DBI::DBIDriver.

Value

dbStatistics() returns list containing Athena Statistics return from paws.

Note

If a user does not have permission to remove AWS S3 resource from AWS Athena output location, then an AWS warning will be returned. For example AccessDenied (HTTP 403). Access Denied. It is better use query caching or optionally prevent clear AWS S3 resource using noctua_options

Convenience functions for reading/writing DBMS tables

Description

Convenience functions for reading/writing DBMS tables

Usage

## S4 method for signature 'AthenaConnection,character,data.frame'
dbWriteTable(
  conn,
  name,
  value,
  overwrite = FALSE,
  append = FALSE,
  row.names = NA,
  field.types = NULL,
  partition = NULL,
  s3.location = NULL,
  file.type = c("tsv", "csv", "parquet", "json"),
  compress = FALSE,
  max.batch = Inf,
  ...
)

## S4 method for signature 'AthenaConnection,Id,data.frame'
dbWriteTable(
  conn,
  name,
  value,
  overwrite = FALSE,
  append = FALSE,
  row.names = NA,
  field.types = NULL,
  partition = NULL,
  s3.location = NULL,
  file.type = c("tsv", "csv", "parquet", "json"),
  compress = FALSE,
  max.batch = Inf,
  ...
)

## S4 method for signature 'AthenaConnection,SQL,data.frame'
dbWriteTable(
  conn,
  name,
  value,
  overwrite = FALSE,
  append = FALSE,
  row.names = NA,
  field.types = NULL,
  partition = NULL,
  s3.location = NULL,
  file.type = c("tsv", "csv", "parquet", "json"),
  compress = FALSE,
  max.batch = Inf,
  ...
)

Arguments

conn

An AthenaConnection object, produced by DBI::dbConnect()

name

A character string specifying a table name. Names will be automatically quoted so you can use any sequence of characters, not just any valid bare table name.

value

A data.frame to write to the database.

overwrite

Allows overwriting the destination table. Cannot be TRUE if append is also TRUE.

append

Allow appending to the destination table. Cannot be TRUE if overwrite is also TRUE. Existing Athena DDL file type will be retained and used when uploading data to AWS Athena. If parameter file.type doesn't match AWS Athena DDL file type a warning message will be created notifying user and noctua will use the file type for the Athena DDL. When appending to an Athena DDL that has been created outside of noctua. noctua can support the following SerDes and Data Formats.

csv/tsv: LazySimpleSerDe
parquet: Parquet SerDe
json: JSON SerDe Libraries

row.names

Either TRUE, FALSE, NA or a string.

If TRUE, always translate row names to a column called "row_names". If FALSE, never translate row names. If NA, translate rownames only if they're a character vector.

A string is equivalent to TRUE, but allows you to override the default name.

For backward compatibility, NULL is equivalent to FALSE.

field.types

Additional field types used to override derived types.

partition

Partition Athena table (needs to be a named list or vector) for example: c(var1 = "2019-20-13")

s3.location

s3 bucket to store Athena table, must be set as a s3 uri for example ("s3://mybucket/data/"). By default, the s3.location is set to s3 staging directory from AthenaConnection object. Note: When creating a table for the first time s3.location will be formatted from "s3://mybucket/data/" to the following syntax "s3://{mybucket/data}/{schema}/{table}/{parition}/" this is to support tables with the same name but existing in different schemas. If schema isn't specified in name parameter then the schema from dbConnect is used instead.

file.type

What file type to store data.frame on s3, noctua currently supports c("tsv", "csv", "parquet", "json"). Default delimited file type is "tsv", in previous versions of noctua (=< 1.4.0) file type "csv" was used as default. The reason for the change is that columns containing Array/JSON format cannot be written to Athena due to the separating value ",". This would cause issues with AWS Athena. Note: "parquet" format is supported by the arrow package and it will need to be installed to utilise the "parquet" format. "json" format is supported by jsonlite package and it will need to be installed to utilise the "json" format.

compress

FALSE | TRUE To determine if to compress file.type. If file type is c("csv", "tsv") then "gzip" compression is used, for file type "parquet" "snappy" compression is used. Currently noctua doesn't support compression for "json" file type.

max.batch

Split the data frame by max number of rows i.e. 100,000 so that multiple files can be uploaded into AWS S3. By default when compression is set to TRUE and file.type is "csv" or "tsv" max.batch will split data.frame into 20 batches. This is to help the performance of AWS Athena when working with files compressed in "gzip" format. max.batch will not split the data.frame when loading file in parquet format. For more information please go to link

...

Other arguments used by individual methods.

Value

dbWriteTable() returns TRUE, invisibly. If the table exists, and both append and overwrite arguments are unset, or append = TRUE and the data frame with the new data has different column names, an error is raised; the remote table remains unchanged.

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.
# - Different connection methods can be used please see `noctua::dbConnect` documnentation

library(DBI)

# Demo connection to Athena using profile name
con <- dbConnect(noctua::athena())

# List existing tables in Athena
dbListTables(con)

# Write data.frame to Athena table
dbWriteTable(con, "mtcars", mtcars,
  partition = c("TIMESTAMP" = format(Sys.Date(), "%Y%m%d")),
  s3.location = "s3://mybucket/data/"
)

# Read entire table from Athena
dbReadTable(con, "mtcars")

# List all tables in Athena after uploading new table to Athena
dbListTables(con)

# Checking if uploaded table exists in Athena
dbExistsTable(con, "mtcars")

# using default s3.location
dbWriteTable(con, "iris", iris)

# Read entire table from Athena
dbReadTable(con, "iris")

# List all tables in Athena after uploading new table to Athena
dbListTables(con)

# Checking if uploaded table exists in Athena
dbExistsTable(con, "iris")

# Disconnect from Athena
dbDisconnect(con)

## End(Not run)

Assume AWS ARN Role

Description

Returns a set of temporary security credentials that you can use to access AWS resources that you might not normally have access to (link). These temporary credentials consist of an access key ID, a secret access key, and a security token. Typically, you use AssumeRole within your account or for cross-account access.

Usage

assume_role(
  profile_name = NULL,
  region_name = NULL,
  role_arn = NULL,
  role_session_name = sprintf("noctua-session-%s", as.integer(Sys.time())),
  duration_seconds = 3600L,
  set_env = FALSE
)

Arguments

profile_name

The name of a profile to use. If not given, then the default profile is used. To set profile name, the AWS Command Line Interface (AWS CLI) will need to be configured. To configure AWS CLI please refer to: Configuring the AWS CLI.

region_name

Default region when creating new connections. Please refer to link for AWS region codes (region code example: Region = EU (Ireland) region_name = "eu-west-1")

role_arn

The Amazon Resource Name (ARN) of the role to assume (such as arn:aws:sts::123456789012:assumed-role/role_name/role_session_name)

role_session_name

An identifier for the assumed role session. By default noctua creates a session name sprintf("noctua-session-%s", as.integer(Sys.time()))

duration_seconds

The duration, in seconds, of the role session. The value can range from 900 seconds (15 minutes) up to the maximum session duration setting for the role. This setting can have a value from 1 hour to 12 hours. By default duration is set to 3600 seconds (1 hour).

set_env

If set to TRUE environmental variables AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY and AWS_SESSION_TOKEN will be set.

Value

assume_role() returns a list containing: "AccessKeyId", "SecretAccessKey", "SessionToken" and "Expiration"

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.

library(noctua)
library(DBI)

# Assuming demo ARN role
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 ARN Role
con <- dbConnect(noctua::athena())

## End(Not run)

Athena Driver

Description

Driver for an Athena paws connection.

Usage

athena()

Value

athena() returns a s4 class. This class is used active Athena method for DBI::dbConnect

Athena S3 implementation of dbplyr backend functions

Description

These functions are used to build the different types of SQL queries. The AWS Athena implementation give extra parameters to allow access the to standard DBI Athena methods. They also utilise AWS Glue to speed up sql query execution.

Usage

sql_query_explain.AthenaConnection(con, sql, format = "text", type = NULL, ...)

sql_query_fields.AthenaConnection(con, sql, ...)

sql_escape_date.AthenaConnection(con, x)

sql_escape_datetime.AthenaConnection(con, x)

Arguments

con

A dbConnect object, as returned by dbConnect()

sql

SQL code to be sent to AWS Athena

format

returning format for explain queries, default set to "text". Other formats can be found: https://docs.aws.amazon.com/athena/latest/ug/athena-explain-statement.html

type

return plan for explain queries, default set to NULL. Other type can be found: https://docs.aws.amazon.com/athena/latest/ug/athena-explain-statement.html

...

other parameters, currently not implemented

x

R object to be transformed into athena equivalent

Value

sql_query_explain: Returns sql query for AWS Athena explain statement
sql_query_fields: Returns sql query column names
sql_escape_date: Returns sql escaping from dates
sql_escape_datetime: Returns sql escaping from date times

Athena S3 implementation of dbplyr backend functions (api version 1).

Description

Usage

db_explain.AthenaConnection(con, sql, ...)

db_query_fields.AthenaConnection(con, sql, ...)

Arguments

con

A dbConnect object, as returned by dbConnect()

sql

SQL code to be sent to AWS Athena

...

other parameters, currently not implemented

Value

db_explain: Returns AWS Athena explain statement
db_query_fields: Returns sql query column names

Connect to Athena using R's sdk paws

Description

It is never advised to hard-code credentials when making a connection to Athena (even though the option is there). Instead it is advised to use profile_name (set up by AWS Command Line Interface), Amazon Resource Name roles or environmental variables. Here is a list of supported environment variables:

AWS_ACCESS_KEY_ID: is equivalent to the dbConnect parameter - aws_access_key_id
AWS_SECRET_ACCESS_KEY: is equivalent to the dbConnect parameter - aws_secret_access_key
AWS_SESSION_TOKEN: is equivalent to the dbConnect parameter - aws_session_token
AWS_EXPIRATION: is equivalent to the dbConnect parameter - duration_seconds
AWS_ATHENA_S3_STAGING_DIR: is equivalent to the dbConnect parameter - s3_staging_dir
AWS_ATHENA_WORK_GROUP: is equivalent to dbConnect parameter - work_group
AWS_REGION: is equivalent to dbConnect parameter - region_name

NOTE: If you have set any environmental variables in .Renviron please restart your R in order for the changes to take affect.

Usage

## S4 method for signature 'AthenaDriver'
dbConnect(
  drv,
  aws_access_key_id = NULL,
  aws_secret_access_key = NULL,
  aws_session_token = NULL,
  catalog_name = "AwsDataCatalog",
  schema_name = "default",
  work_group = NULL,
  poll_interval = NULL,
  encryption_option = c("NULL", "SSE_S3", "SSE_KMS", "CSE_KMS"),
  kms_key = NULL,
  profile_name = NULL,
  role_arn = NULL,
  role_session_name = sprintf("noctua-session-%s", as.integer(Sys.time())),
  duration_seconds = 3600L,
  s3_staging_dir = NULL,
  region_name = NULL,
  bigint = c("integer64", "integer", "numeric", "character"),
  binary = c("raw", "character"),
  json = c("auto", "character"),
  timezone = "UTC",
  keyboard_interrupt = TRUE,
  rstudio_conn_tab = TRUE,
  endpoint_override = NULL,
  ...
)

Arguments

drv

A object inheriting from DBI::DBIDriver.

aws_access_key_id

AWS access key ID

aws_secret_access_key

AWS secret access key

aws_session_token

AWS temporary session token

catalog_name

The catalog_name to which the connection belongs

schema_name

The schema_name to which the connection belongs

work_group

The name of the work group to run Athena queries , Currently defaulted to NULL.

poll_interval

Amount of time took when checking query execution status. Default set to a random interval between 0.5 - 1 seconds.

encryption_option

Athena encryption at rest link. Supported Amazon S3 Encryption Options c("NULL", "SSE_S3", "SSE_KMS", "CSE_KMS"). Connection will default to NULL, usually changing this option is not required.

kms_key

AWS Key Management Service, please refer to link for more information around the concept.

profile_name

role_arn

The Amazon Resource Name (ARN) of the role to assume (such as arn:aws:sts::123456789012:assumed-role/role_name/role_session_name)

role_session_name

An identifier for the assumed role session. By default noctua creates a session name sprintf("noctua-session-%s", as.integer(Sys.time()))

duration_seconds

s3_staging_dir

The location in Amazon S3 where your query results are stored, such as s3://path/to/query/bucket/

region_name

Default region when creating new connections. Please refer to link for AWS region codes (region code example: Region = EU (Ireland) region_name = "eu-west-1")

bigint

The R type that 64-bit integer types should be mapped to, default is bit64::integer64, which allows the full range of 64 bit integers.

binary

The R type that binary/varbinary types should be mapped to, default is raw. If the mapping fails R will resort to character type. To ignore data type conversion set to "character".

json

Attempt to converts AWS Athena data types arrays, json using jsonlite:parse_json. If the mapping fails R will resort to character type. Custom Json parsers can be provide by using a function with data frame parameter. To ignore data type conversion set to "character".

timezone

Sets the timezone for the connection. The default is UTC. If NULL then no timezone is set, which defaults to the server's time zone. ⁠AWS Athena⁠ accepted time zones: https://docs.aws.amazon.com/athena/latest/ug/athena-supported-time-zones.html.

keyboard_interrupt

Stops AWS Athena process when R gets a keyboard interrupt, currently defaults to TRUE

rstudio_conn_tab

Optional to get AWS Athena Schema from AWS Glue Catalogue and display it in RStudio's Connections Tab. Default set to TRUE. For large ⁠AWS Glue Catalogue⁠ it is recommended to set rstudio_conn_tab=FALSE to ensure a fast connection.

endpoint_override

(character/list) The complete URL to use for the constructed client. Normally, paws will automatically construct the appropriate URL to use when communicating with a service. You can specify a complete URL (including the "http/https" scheme) to override this behaviour. If this value is provided, then disable_ssl is ignored. If endpoint_override is a character then AWS Athena endpoint is overridden. To override AWS S3 or AWS Glue endpoints a named list needs to be provided. The list can only have the following names ⁠c('athena', 's3', glue')⁠ for example list(glue = "https://glue.eu-west-1.amazonaws.com")

...

other parameters for paws session.

disable_ssl: (boolean) Whether or not to use SSL. By default, SSL is used. Note that not all services support non-ssl connections.
timeout: (numeric) The time in seconds till a timeout exception is thrown when attempting to make a connection. The default is 60 seconds.
disable_param_validation: (bool) Whether parameter validation should occur when serializing requests. The default is FALSE You can disable parameter validation for performance reasons. Otherwise, it's recommended to leave parameter validation enabled.
s3_force_path_style: Addressing style is always by path. Endpoints will be addressed as such: s3.amazonaws.com/mybucket
s3_use_accelerate: Refers to whether to use the S3 Accelerate endpoint. The value must be a boolean. If True, the client will use the S3 Accelerate endpoint. If the S3 Accelerate endpoint is being used then the addressing style will always be virtual.
use_dual_stack: Setting to TRUE enables dual stack endpoint resolution.

Value

dbConnect() returns DBI::DBIConnection. This object is used to communicate with AWS Athena.

Examples

# Connect to Athena using your aws access keys
## Not run: 
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 = "us-west-2"
)
dbDisconnect(con)

# Connect to Athena using your profile name
# Profile name can be created by using AWS CLI
con <- dbConnect(noctua::athena(),
  profile_name = "YOUR_PROFILE_NAME",
  s3_staging_dir = "s3://path/to/query/bucket/"
)
dbDisconnect(con)

# Connect to Athena using ARN role
con <- dbConnect(noctua::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/"
)

dbDisconnect(con)

## End(Not run)

dbConvertTable aws s3 backend file types.

Description

Utilises AWS Athena to convert AWS S3 backend file types. It also also to create more efficient file types i.e. "parquet" and "orc" from SQL queries.

Usage

dbConvertTable(conn, obj, name, ...)

## S4 method for signature 'AthenaConnection'
dbConvertTable(
  conn,
  obj,
  name,
  partition = NULL,
  s3.location = NULL,
  file.type = c("NULL", "csv", "tsv", "parquet", "json", "orc"),
  compress = TRUE,
  data = TRUE,
  ...
)

Arguments

conn

A DBI::DBIConnection object,

obj

Athena table or SQL DML query to be converted. For SQL, the query need to be wrapped with DBI::SQL() and follow AWS Athena DML format link

name

Name of destination table

...

Extra parameters, currently not used

partition

Partition Athena table

s3.location

location to store output file, must be in s3 uri format for example ("s3://mybucket/data/").

file.type

File type for name, currently support c("NULL","csv", "tsv", "parquet", "json", "orc"). "NULL" will let Athena set the file type for you.

compress

Compress name, currently can only compress c("parquet", "orc") (AWS Athena CTAS)

data

If name should be created with data or not.

Value

dbConvertTable() returns TRUE but invisible.

List Athena Tables

Description

Returns the unquoted names of Athena tables accessible through this connection.

Usage

## S4 method for signature 'AthenaConnection'
dbListTables(conn, catalog = NULL, schema = NULL, ...)

Arguments

conn

A DBI::DBIConnection object, as returned by dbConnect().

catalog

Athena catalog, default set to NULL to return all tables from all Athena catalogs

schema

Athena schema, default set to NULL to return all tables from all Athena schemas. Note: The use of DATABASE and SCHEMA is interchangeable within Athena.

...

Other parameters passed on to methods.

Value

dbListTables() returns a character vector with all the tables from Athena.

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.
# - Different connection methods can be used please see `noctua::dbConnect` documnentation

library(DBI)

# Demo connection to Athena using profile name
con <- dbConnect(noctua::athena())

# Return list of tables in Athena
dbListTables(con)

# Disconnect conenction
dbDisconnect(con)

## End(Not run)

S3 implementation of `db_compute` for Athena

Description

This is a backend function for dplyr's compute function. Users won't be required to access and run this function.

Usage

db_compute.AthenaConnection(
  con,
  table,
  sql,
  ...,
  overwrite = FALSE,
  temporary = FALSE,
  unique_indexes = list(),
  indexes = list(),
  analyze = TRUE,
  in_transaction = FALSE,
  partition = NULL,
  s3_location = NULL,
  file_type = c("csv", "tsv", "parquet"),
  compress = FALSE
)

sql_query_save.AthenaConnection(
  con,
  sql,
  name,
  temporary = TRUE,
  ...,
  partition = NULL,
  s3_location = NULL,
  file_type = NULL,
  compress = FALSE
)

Arguments

con

A dbConnect object, as returned by dbConnect()

table

Table name, if left default noctua will use the default from dplyr's compute function.

sql

SQL code to be sent to the data

...

passes noctua table creation parameters: file_type,s3_location,partition.

overwrite

Allows overwriting the destination table. Cannot be TRUE if append is also TRUE.

temporary

if TRUE, will create a temporary table that is local to this connection and will be automatically deleted when the connection expires

unique_indexes

a list of character vectors. Each element of the list will create a new unique index over the specified column(s). Duplicate rows will result in failure.

indexes

a list of character vectors. Each element of the list will create a new index.

analyze

if TRUE (the default), will automatically ANALYZE the new table so that the query optimiser has useful information.

in_transaction

Should the table creation be wrapped in a transaction? This typically makes things faster, but you may want to suppress if the database doesn't support transactions, or you're wrapping in a transaction higher up (and your database doesn't support nested transactions.)

partition

Partition Athena table (needs to be a named list or vector) for example: c(var1 = "2019-20-13")

s3_location

s3 bucket to store Athena table, must be set as a s3 uri for example ("s3://mybucket/data/")

file_type

What file type to store data.frame on s3, noctua currently supports c("tsv", "csv", "parquet"). Default delimited file type is "tsv", in previous versions of noctua (=< 1.4.0) file type "csv" was used as default. The reason for the change is that columns containing Array/JSON format cannot be written to Athena due to the separating value ",". This would cause issues with AWS Athena. Note: "parquet" format is supported by the arrow package and it will need to be installed to utilise the "parquet" format.

compress

FALSE | TRUE To determine if to compress file.type. If file type is c("csv", "tsv") then "gzip" compression is used, for file type "parquet" "snappy" compression is used.

file_type: What file type to store data.frame on s3, noctua currently supports c("NULL","csv", "parquet", "json"). "NULL" will let Athena set the file_type for you.
s3_location: s3 bucket to store Athena table, must be set as a s3 uri for example ("s3://mybucket/data/")
partition: Partition Athena table, requires to be a partitioned variable from previous table.

name

Table name, if left default noctua will use the default from dplyr's compute function.

Value

db_compute returns table name

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.
# - Different connection methods can be used please see `noctua::dbConnect` documentation

library(DBI)
library(dplyr)

# Demo connection to Athena using profile name
con <- dbConnect(noctua::athena())

# 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)

## End(Not run)

S3 implementation of `db_connection_describe` for Athena (api version 2).

Description

This is a backend function for dplyr to retrieve meta data about Athena queries. Users won't be required to access and run this function.

Usage

db_connection_describe.AthenaConnection(con)

Arguments

con

A dbConnect object, as returned by dbConnect()

Value

Character variable containing Meta Data about query sent to Athena. The Meta Data is returned in the following format:

"Athena <paws version> [<profile_name>@region/database]"

S3 implementation of `db_copy_to` for Athena

Description

This is an Athena method for dbplyr function db_copy_to to create an Athena table from a data.frame.

Usage

db_copy_to.AthenaConnection(
  con,
  table,
  values,
  ...,
  partition = NULL,
  s3_location = NULL,
  file_type = c("csv", "tsv", "parquet"),
  compress = FALSE,
  max_batch = Inf,
  overwrite = FALSE,
  append = FALSE,
  types = NULL,
  temporary = TRUE,
  unique_indexes = NULL,
  indexes = NULL,
  analyze = TRUE,
  in_transaction = FALSE
)

Arguments

con

A dbConnect object, as returned by dbConnect()

table

A character string specifying a table name. Names will be automatically quoted so you can use any sequence of characters, not just any valid bare table name.

values

A data.frame to write to the database.

...

other parameters currently not supported in noctua

partition

Partition Athena table (needs to be a named list or vector) for example: c(var1 = "2019-20-13")

s3_location

s3 bucket to store Athena table, must be set as a s3 uri for example ("s3://mybucket/data/")

file_type

compress

FALSE | TRUE To determine if to compress file.type. If file type is c("csv", "tsv") then "gzip" compression is used, for file type "parquet" "snappy" compression is used.

max_batch

overwrite

Allows overwriting the destination table. Cannot be TRUE if append is also TRUE.

append

types

Additional field types used to override derived types.

temporary

if TRUE, will create a temporary table that is local to this connection and will be automatically deleted when the connection expires

unique_indexes

a list of character vectors. Each element of the list will create a new unique index over the specified column(s). Duplicate rows will result in failure.

indexes

a list of character vectors. Each element of the list will create a new index.

analyze

if TRUE (the default), will automatically ANALYZE the new table so that the query optimiser has useful information.

in_transaction

Value

db_copy_to returns table name

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.
# - Different connection methods can be used please see `noctua::dbConnect` documnentation

library(DBI)
library(dplyr)

# Demo connection to Athena using profile name
con <- dbConnect(noctua::athena())

# List existing tables in Athena
dbListTables(con)

# Write data.frame to Athena table
copy_to(con, mtcars,
  s3_location = "s3://mybucket/data/"
)

# Checking if uploaded table exists in Athena
dbExistsTable(con, "mtcars")

# Write Athena table from tbl_sql
athena_mtcars <- tbl(con, "mtcars")
mtcars_filter <- athena_mtcars %>% filter(gear >= 4)

copy_to(con, mtcars_filter)

# Checking if uploaded table exists in Athena
dbExistsTable(con, "mtcars_filter")

# Disconnect from Athena
dbDisconnect(con)

## End(Not run)

S3 implementation of `db_desc` for Athena (api version 1).

Description

This is a backend function for dplyr to retrieve meta data about Athena queries. Users won't be required to access and run this function.

Usage

db_desc.AthenaConnection(x)

Arguments

x

A dbConnect object, as returned by dbConnect()

Value

Character variable containing Meta Data about query sent to Athena. The Meta Data is returned in the following format:

"Athena <paws version> [<profile_name>@region/database]"

Declare which version of dbplyr API is being called.

Description

Declare which version of dbplyr API is being called.

Usage

dbplyr_edition.AthenaConnection(con)

Arguments

con

A dbConnect object, as returned by dbConnect()

Value

Integer for which version of dbplyr is going to be used.

A method to configure noctua backend options.

Description

noctua_options() provides a method to change the backend. This includes changing the file parser, whether noctua should cache query ids locally and number of retries on a failed api call.

Usage

noctua_options(
  file_parser,
  bigint,
  binary,
  json,
  cache_size,
  clear_cache,
  retry,
  retry_quiet,
  unload,
  clear_s3_resource,
  verbose
)

Arguments

file_parser

Method to read and write tables to Athena, currently default to "data.table". The file_parser also determines the data format returned for example "data.table" will return data.table and "vroom" will return tibble.

bigint

The R type that 64-bit integer types should be mapped to (default: "integer64"). Inbuilt bigint conversion types c("integer64", "integer", "numeric", "character").

binary

The R type that binary/varbinary types should be mapped to (default "raw"). Inbuilt binary conversion types c("raw", "character").

json

Attempt to converts AWS Athena data types c(arrays, json) using jsonlite:parse_json (default: "auto"). Inbuilt json conversion types c("auto", "character"). Custom Json parsers can be provide by using a function with data frame parameter.

cache_size

Number of queries to be cached. Currently only support caching up to 100 distinct queries (default: 0).

clear_cache

Clears all previous cached query metadata

retry

Maximum number of requests to attempt (default: 5).

retry_quiet

This method is deprecated please use verbose instead.

unload

set AWS Athena unload functionality globally (default: FALSE)

clear_s3_resource

Clear down ⁠AWS Athena⁠ ⁠AWS S3⁠ resource (s3_staging_dir location). This is useful for users that don't have the ⁠AWS IAM role⁠ permissions delete from s3_staging_dir (default: TRUE)

verbose

print package info messages (default: TRUE)

Value

noctua_options() returns the list of athena option environment invisibly.

Examples

library(noctua)

# change file parser from default data.table to vroom
noctua_options("vroom")

# cache queries locally
noctua_options(cache_size = 5)

Get Session Tokens for PAWS Connection

Description

Returns a set of temporary credentials for an AWS account or IAM user (link).

Usage

get_session_token(
  profile_name = NULL,
  region_name = NULL,
  serial_number = NULL,
  token_code = NULL,
  duration_seconds = 3600L,
  set_env = FALSE
)

Arguments

profile_name

region_name

Default region when creating new connections. Please refer to link for AWS region codes (region code example: Region = EU (Ireland) region_name = "eu-west-1")

serial_number

The identification number of the MFA device that is associated with the IAM user who is making the GetSessionToken call. Specify this value if the IAM user has a policy that requires MFA authentication. The value is either the serial number for a hardware device (such as GAHT12345678) or an Amazon Resource Name (ARN) for a virtual device (such as arn:aws:iam::123456789012:mfa/user).

token_code

The value provided by the MFA device, if MFA is required. If any policy requires the IAM user to submit an MFA code, specify this value. If MFA authentication is required, the user must provide a code when requesting a set of temporary security credentials. A user who fails to provide the code receives an "access denied" response when requesting resources that require MFA authentication.

duration_seconds

The duration, in seconds, that the credentials should remain valid. Acceptable duration for IAM user sessions range from 900 seconds (15 minutes) to 129,600 seconds (36 hours), with 3,600 seconds (1 hour) as the default.

set_env

If set to TRUE environmental variables AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY and AWS_SESSION_TOKEN will be set.

Value

get_session_token() returns a list containing: "AccessKeyId", "SecretAccessKey", "SessionToken" and "Expiration"

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.

library(noctua)
library(DBI)

# Create Temporary Credentials duration 1 hour
get_session_token("YOUR_PROFILE_NAME",
  serial_number = "arn:aws:iam::123456789012:mfa/user",
  token_code = "531602",
  set_env = TRUE
)

# Connect to Athena using temporary credentials
con <- dbConnect(athena())

## End(Not run)

Creates query to create a simple Athena table

Description

Creates an interface to compose CREATE EXTERNAL TABLE.

Usage

## S4 method for signature 'AthenaConnection'
sqlCreateTable(
  con,
  table,
  fields,
  field.types = NULL,
  partition = NULL,
  s3.location = NULL,
  file.type = c("tsv", "csv", "parquet", "json"),
  compress = FALSE,
  ...
)

Arguments

con

A database connection.

table

The table name, passed on to dbQuoteIdentifier(). Options are:

a character string with the unquoted DBMS table name, e.g. "table_name",
a call to Id() with components to the fully qualified table name, e.g. Id(schema = "my_schema", table = "table_name")
a call to SQL() with the quoted and fully qualified table name given verbatim, e.g. SQL('"my_schema"."table_name"')

fields

Either a character vector or a data frame.

A named character vector: Names are column names, values are types. Names are escaped with dbQuoteIdentifier(). Field types are unescaped.

A data frame: field types are generated using dbDataType().

field.types

Additional field types used to override derived types.

partition

Partition Athena table (needs to be a named list or vector) for example: c(var1 = "2019-20-13")

s3.location

s3 bucket to store Athena table, must be set as a s3 uri for example ("s3://mybucket/data/"). By default s3.location is set s3 staging directory from AthenaConnection object.

file.type

compress

...

Other arguments used by individual methods.

Value

sqlCreateTable returns data.frame's DDL in the SQL format.

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.
# - Different connection methods can be used please see `noctua::dbConnect` documnentation

library(DBI)

# Demo connection to Athena using profile name
con <- dbConnect(noctua::athena())

# Create DDL for iris data.frame
sqlCreateTable(con, "iris", iris, s3.location = "s3://path/to/athena/table")

# Create DDL for iris data.frame with partition
sqlCreateTable(con, "iris", iris,
  partition = "timestamp",
  s3.location = "s3://path/to/athena/table"
)

# Create DDL for iris data.frame with partition and file.type parquet
sqlCreateTable(con, "iris", iris,
  partition = "timestamp",
  s3.location = "s3://path/to/athena/table",
  file.type = "parquet"
)

# Disconnect from Athena
dbDisconnect(con)

## End(Not run)

Converts data frame into suitable format to be uploaded to Athena

Description

This method converts data.frame columns into the correct format so that it can be uploaded Athena.

Usage

## S4 method for signature 'AthenaConnection'
sqlData(
  con,
  value,
  row.names = NA,
  file.type = c("tsv", "csv", "parquet", "json"),
  ...
)

Arguments

con

A database connection.

value

A data frame

row.names

Either TRUE, FALSE, NA or a string.

If TRUE, always translate row names to a column called "row_names". If FALSE, never translate row names. If NA, translate rownames only if they're a character vector.

A string is equivalent to TRUE, but allows you to override the default name.

For backward compatibility, NULL is equivalent to FALSE.

file.type

What file type to store data.frame on s3, noctua currently supports c("csv", "tsv", "parquet", "json"). Note: This parameter is used for format any special characters that clash with file type separator.

...

Other arguments used by individual methods.

Value

sqlData returns a dataframe formatted for Athena. Currently converts list variable types into character split by '|', similar to how data.table writes out to files.

AWS Athena backend dbplyr version 1 and 2

Description

Create s3 implementation of sql_translate_env for AWS Athena sql translate environment based off Athena Data Types and DML Queries, Functions, and Operators

Usage

sql_translation.AthenaConnection(con)

sql_translate_env.AthenaConnection(con)

Arguments

con

An AthenaConnection object, produced by DBI::dbConnect()

Athena Work Groups

Description

Lower level API access, allows user to create and delete Athena Work Groups.

create_work_group: Creates a workgroup with the specified name (link). The work group utilises parameters from the dbConnect object, to determine the encryption and output location of the work group. The s3_staging_dir, encryption_option and kms_key parameters are gotten from dbConnect
tag_options: Helper function to create tag options for function create_work_group()
delete_work_group: Deletes the workgroup with the specified name (link). The primary workgroup cannot be deleted.
list_work_groups: Lists available workgroups for the account (link).
get_work_group: Returns information about the workgroup with the specified name (link).
update_work_group: Updates the workgroup with the specified name (link). The workgroup's name cannot be changed. The work group utilises parameters from the dbConnect object, to determine the encryption and output location of the work group. The s3_staging_dir, encryption_option and kms_key parameters are gotten from dbConnect

Usage

create_work_group(
  conn,
  work_group = NULL,
  enforce_work_group_config = FALSE,
  publish_cloud_watch_metrics = FALSE,
  bytes_scanned_cut_off = 10000000L,
  description = NULL,
  tags = tag_options(key = NULL, value = NULL)
)

tag_options(key = NULL, value = NULL)

delete_work_group(conn, work_group = NULL, recursive_delete_option = FALSE)

list_work_groups(conn)

get_work_group(conn, work_group = NULL)

update_work_group(
  conn,
  work_group = NULL,
  remove_output_location = FALSE,
  enforce_work_group_config = FALSE,
  publish_cloud_watch_metrics = FALSE,
  bytes_scanned_cut_off = 10000000L,
  description = NULL,
  state = c("ENABLED", "DISABLED"),
  engine_version = list()
)

Arguments

conn

A dbConnect object, as returned by dbConnect()

work_group

The Athena workgroup name.

enforce_work_group_config

If set to TRUE, the settings for the workgroup override client-side settings. If set to FALSE, client-side settings are used. For more information, see Workgroup Settings Override Client-Side Settings.

publish_cloud_watch_metrics

Indicates that the Amazon CloudWatch metrics are enabled for the workgroup.

bytes_scanned_cut_off

The upper data usage limit (cutoff) for the amount of bytes a single query in a workgroup is allowed to scan.

description

The workgroup description.

tags

A tag that you can add to a resource. A tag is a label that you assign to an AWS Athena resource (a workgroup). Each tag consists of a key and an optional value, both of which you define. Tags enable you to categorize workgroups in Athena, for example, by purpose, owner, or environment. Use a consistent set of tag keys to make it easier to search and filter workgroups in your account. The maximum tag key length is 128 Unicode characters in UTF-8. The maximum tag value length is 256 Unicode characters in UTF-8. You can use letters and numbers representable in UTF-8, and the following characters: "+ - = . _ : / @". Tag keys and values are case-sensitive. Tag keys must be unique per resource. Please use the helper function tag_options() to create tags for work group, if no tags are required please put NULL for this parameter.

key

A tag key. The tag key length is from 1 to 128 Unicode characters in UTF-8. You can use letters and numbers representable in UTF-8, and the following characters: "+ - = . _ : / @". Tag keys are case-sensitive and must be unique per resource.

value

A tag value. The tag value length is from 0 to 256 Unicode characters in UTF-8. You can use letters and numbers representable in UTF-8, and the following characters: "+ - = . _ : / @". Tag values are case-sensitive.

recursive_delete_option

The option to delete the workgroup and its contents even if the workgroup contains any named queries

remove_output_location

If set to TRUE, indicates that the previously-specified query results location (also known as a client-side setting) for queries in this workgroup should be ignored and set to null. If set to FALSE the out put location in the workgroup's result configuration will be updated with the new value. For more information, see Workgroup Settings Override Client-Side Settings.

state

The workgroup state that will be updated for the given workgroup.

engine_version

The engine version requested when a workgroup is updated.

SelectedEngineVersion: The engine version requested by the user.
EffectiveEngineVersion: The engine version on which the query runs.

Value

create_work_group: Returns NULL but invisible
tag_options: Returns list but invisible
delete_work_group: Returns NULL but invisible
list_work_groups: Returns list of available work groups
get_work_group: Returns list of work group meta data
update_work_group: Returns NULL but invisible

Examples

## Not run: 
# Note:
# - Require AWS Account to run below example.
# - Different connection methods can be used please see `noctua::dbConnect` documnentation

library(noctua)

# Demo connection to Athena using profile name
con <- dbConnect(noctua::athena())

# List current work group available
list_work_groups(con)

# Create a new work group
wg <- 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 to see new work group
list_work_groups(con)

# get meta data from work group
wg <- get_work_group(con, "demo_work_group")

# Update work group
wg <- update_work_group(con, "demo_work_group",
  description = "This is a demo work group update"
)


# get updated meta data from work group
wg <- get_work_group(con, "demo_work_group")

# Delete work group
delete_work_group(con, "demo_work_group")

# Disconect from Athena
dbDisconnect(con)

## End(Not run)

noctua: a DBI interface into Athena using paws SDK

Description

Goal of Package

AWS Command Line Interface

Author(s)

See Also

Athena Connection Methods

Description

Usage

Arguments

Value

Slots

Athena Driver Methods

Description

Usage

Arguments

List objects in a connection.

Description

Usage

Arguments

Details

Value

Preview the data in an object.

Description

Usage

Arguments

Details

Value

Athena Result Methods

Description

Usage

Arguments

Value

Note

Convenience functions for reading/writing DBMS tables

Description

Usage

Arguments

Value

See Also

Examples

Assume AWS ARN Role

Description

Usage

Arguments

Value

See Also

Examples

Athena Driver

Description

Usage

Value

See Also

Athena S3 implementation of dbplyr backend functions

Description

Usage

Arguments

Value

Athena S3 implementation of dbplyr backend functions (api version 1).

Description

Usage

Arguments

Value

Connect to Athena using R's sdk paws

Description

Usage

Arguments

Value

See Also

Examples

dbConvertTable aws s3 backend file types.

Description

Usage

Arguments

Value

List Athena Tables

Description

Usage

Arguments

Value

S3 implementation of `db_compute` for Athena

S3 implementation of `db_connection_describe` for Athena (api version 2).

S3 implementation of `db_copy_to` for Athena

S3 implementation of `db_desc` for Athena (api version 1).