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  1. 3
      .Rbuildignore
  2. 26
      DESCRIPTION
  3. 2
      LICENSE
  4. 215
      LICENSE.md
  5. 31
      NAMESPACE
  6. 19
      NEWS.md
  7. 16
      R/a-utils.R
  8. 223
      R/jdbc.r
  9. 32
      R/metis-jars-package.R
  10. 48
      R/metis-lite-package.R
  11. 68
      R/metis.r
  12. 15
      R/metis_jar_path.R
  13. 124
      R/sql_translate_env.R
  14. 15
      R/types.R
  15. 8
      R/version.R
  16. 121
      R/z-dbGetQuery.R
  17. 27
      R/zzz.R
  18. 135
      README.Rmd
  19. 212
      README.md
  20. 69
      inst/COPYRIGHTS
  21. 18
      man/Athena.Rd
  22. 9
      man/AthenaConnection-class.Rd
  23. 9
      man/AthenaDriver-class.Rd
  24. 9
      man/AthenaResult-class.Rd
  25. 57
      man/athena_connect.Rd
  26. 14
      man/athena_supported_types.Rd
  27. 48
      man/dbConnect-AthenaDriver-method.Rd
  28. 22
      man/dbExistsTable-AthenaConnection-character-method.Rd
  29. 19
      man/dbGetQuery-AthenaConnection-character-method.Rd
  30. 22
      man/dbListFields-AthenaConnection-character-method.Rd
  31. 22
      man/dbListTables-AthenaConnection-method.Rd
  32. 21
      man/dbReadTable-AthenaConnection-character-method.Rd
  33. 19
      man/dbSendQuery-AthenaConnection-character-method.Rd
  34. 24
      man/fetch-AthenaResult-numeric-method.Rd
  35. 35
      man/metis.jars.Rd
  36. 35
      man/metis.lite.Rd
  37. 14
      man/metis_jar_path.Rd
  38. 14
      man/simba_driver_version.Rd
  39. 12
      man/use_credentials.Rd
  40. 0
      metis-jars.Rproj
  41. 8
      tests/test-all.R
  42. 6
      tests/testthat/test-metis-lite.R
  43. 11
      tests/testthat/test-metis.jars.R

3
.Rbuildignore

@ -8,5 +8,6 @@
^NOTES\.*html$ ^NOTES\.*html$
^\.codecov\.yml$ ^\.codecov\.yml$
^README_files$ ^README_files$
^doc$ ^docs$
^CONDUCT\.md$ ^CONDUCT\.md$
^\.bash_profile

26
DESCRIPTION

@ -1,29 +1,27 @@
Package: metis.lite Package: metis.jars
Type: Package Type: Package
Title: Access and Query Amazon Athena via DBI/JDBC Title: Amazon Athena JDBC Driver Wrapper Supporting the 'metis' Package
Version: 0.3.0 Version: 2.0.6
Date: 2019-02-14 Date: 2019-02-17
Authors@R: c( Authors@R: c(
person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"), person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-5670-2640")) comment = c(ORCID = "0000-0001-5670-2640"))
) )
Maintainer: Bob Rudis <bob@rud.is> Maintainer: Bob Rudis <bob@rud.is>
Encoding: UTF-8 Encoding: UTF-8
Description: Methods are provides to connect to 'Amazon' 'Athena', lookup schemas/tables, Description: Contents of the Amazon Athena JDBC Driver
perform queries and retrieve query results. A lightweight 'RJDBC' implementation <https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html>
is included along with additional helpers for 'dplyr'/'dplyr' suppprt. provided to support functions in the 'metis' package. Version number
reflects the version number of the included 'JAR' file.
SystemRequirements: JDK 1.8+ SystemRequirements: JDK 1.8+
License: MIT + file LICENSE License: Apache License (>= 2.0)
Copyright: file inst/COPYRIGHTS
Suggests: Suggests:
testthat, testthat,
covr covr
Depends: Depends:
R (>= 3.2.0), R (>= 3.2.0)
RJDBC
Imports: Imports:
rJava, rJava,
DBI, utils
bit64,
dbplyr,
aws.signature
RoxygenNote: 6.1.1 RoxygenNote: 6.1.1

2
LICENSE

@ -1,2 +0,0 @@
YEAR: 2019
COPYRIGHT HOLDER: Bob Rudis

215
LICENSE.md

@ -1,21 +1,194 @@
# MIT License Apache License
==============
Copyright (c) 2019 Bob Rudis
_Version 2.0, January 2004_
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### APPENDIX: How to apply the Apache License to your work
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Copyright 2019 Bob Rudis
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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See the License for the specific language governing permissions and
limitations under the License.

31
NAMESPACE

@ -1,27 +1,8 @@
# Generated by roxygen2: do not edit by hand # Generated by roxygen2: do not edit by hand
export(Athena) export(athena_supported_types)
export(athena_connect) export(metis_jar_path)
export(db_data_type.AthenaConnection) export(simba_driver_version)
export(read_credentials) import(rJava)
export(sql_translate_env.AthenaConnection) importFrom(utils,compareVersion)
export(use_credentials) importFrom(utils,packageVersion)
exportClasses(AthenaConnection)
exportClasses(AthenaDriver)
exportClasses(AthenaResult)
exportMethods(dbConnect)
exportMethods(dbExistsTable)
exportMethods(dbGetInfo)
exportMethods(dbGetQuery)
exportMethods(dbListFields)
exportMethods(dbListTables)
exportMethods(dbReadTable)
exportMethods(dbSendQuery)
exportMethods(fetch)
import(DBI)
import(RJDBC)
import(bit64)
import(dbplyr)
importFrom(aws.signature,read_credentials)
importFrom(aws.signature,use_credentials)
importFrom(rJava,.jcall)

19
NEWS.md

@ -1,19 +1,4 @@
0.3.0 2.0.6
========= =========
- Added `sql_translate_env.AthenaConnection()` - Refactor
- Handles Athena JDBC column types!
0.2.0
=========
- Updated authentication provider to be `com.amazonaws.athena.jdbc.shaded.com.amazonaws.auth.DefaultAWSCredentialsProviderChain` (via @dabdine)
- Now supports additional DBI/RJDBC methods including: `dbExistsTable()`,
`dbListFields()`, `dbListTables()`, `dbReadTable()`
- More documentation
- Added code of conduct
0.1.0
=========
- Using the `cloudyr` `aws.signature` package vs DIY

16
R/a-utils.R

@ -1,16 +0,0 @@
set_names <- function (object = nm, nm) {
names(object) <- nm
object
}
as_logical <- function(x) {
as.logical(as.integer(x))
}
as_date <- function(x) {
as.Date(x, origin = "1970-01-01")
}
as_posixct <- function(x) {
as.POSIXct(x, origin = "1970-01-01 00:00:00")
}

223
R/jdbc.r

@ -1,223 +0,0 @@
structure(
0:6,
.Names = c(
"OFF", "FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE"
)
)-> .ll_trans
#' AthenaJDBC
#'
#' @export
setClass(
"AthenaDriver",
representation(
"JDBCDriver",
identifier.quote = "character",
jdrv = "jobjRef"
)
)
#' AthenaJDBC
#'
#' @export
Athena <- function(identifier.quote = '`') {
JDBC(
driverClass = "com.simba.athena.jdbc.Driver",
system.file("java", "AthenaJDBC42_2.0.6.jar", package = "metis.lite"),
identifier.quote = identifier.quote
) -> drv
return(as(drv, "AthenaDriver"))
}
#' AthenaJDBC
#'
#' Connect to Athena
#'
#' @section Driver Configuration Options:
#'
#' - `BinaryColumnLength`: <int> The maximum data length for `BINARY` columns. Default `32767L`
#' - `ComplexTypeColumnLength`: <int> The maximum data length for `ARRAY`, `MAP`, and `STRUCT` columns. Default `65535L`
#' - `StringColumnLength`: <int> The maximum data length for `STRING` columns. Default `255L`
#'
#' @param provider JDBC auth provider (ideally leave default)
#' @param region AWS region the Athena tables are in
#' @param s3_staging_dir A write-able bucket on S3 that you have permissions for
#' @param schema_name LOL if only this actually worked with Amazon's hacked Presto driver
#' @param max_error_retries,connection_timeout,socket_timeout
#' technical connection info that you should only muck with if you know what you're doing.
#' @param log_path,log_level The Athena JDBC driver can (shockingly) provide a decent bit
#' of data in logs. Set this to a temporary directory or something log4j can use. For
#' `log_level` use the names ("INFO", "DEBUG", "WARN", "ERROR", "ALL", "OFF", "FATAL", "TRACE") or
#' their corresponding integer values 0-6.
#' @param ... passed on to the driver. See Details.
#' @references [Connect with JDBC](https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html);
#' [Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide](https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf)
#' @export
setMethod(
"dbConnect",
"AthenaDriver",
def = function(
drv,
provider = "com.simba.athena.amazonaws.auth.DefaultAWSCredentialsProviderChain",
region = "us-east-1",
s3_staging_dir = Sys.getenv("AWS_S3_STAGING_DIR"),
schema_name = "default",
fetch_size = 1000L,
max_error_retries = 10,
connection_timeout = 10000,
socket_timeout = 10000,
log_path = "",
log_level = 0,
...) {
conn_string = sprintf(
'jdbc:awsathena://athena.%s.amazonaws.com:443/%s', region, schema_name
)
if (!(log_level %in% 0:6)) log_level <- .ll_trans[log_level]
callNextMethod(
drv,
conn_string,
S3OutputLocation = s3_staging_dir,
Schema = schema_name,
MaxErrorRetry = max_error_retries,
ConnectTimeout = connection_timeout,
SocketTimeout = socket_timeout,
LogPath = log_path,
LogLevel = log_level,
AwsCredentialsProviderClass = provider,
...
) -> jc
jc <- as(jc, "AthenaConnection")
jc@fetch_size <- as.integer(fetch_size)
return(jc)
}
)
#' AthenaJDBC
#'
#' @export
setClass("AthenaConnection", representation("JDBCConnection", jc="jobjRef", identifier.quote="character", fetch_size="integer"))
# setClass("AthenaConnection", contains = "JDBCConnection")
#' AthenaJDBC
#'
#' @export
setClass("AthenaResult", contains = "JDBCResult")
#' AthenaJDBC
#'
#' @param conn Athena connection
#' @param statement SQL statement
#' @param ... unused
#' @export
setMethod(
"dbSendQuery",
signature(conn="AthenaConnection", statement="character"),
definition = function(conn, statement, ...) {
return(as(callNextMethod(), "AthenaResult"))
}
)
#' AthenaJDBC
#'
#' @param conn Athena connection
#' @param pattern table name pattern
#' @param schema Athena schema name
#' @param ... unused
#' @export
setMethod(
"dbListTables",
signature(conn="AthenaConnection"),
definition = function(conn, pattern='*', schema, ...) {
if (missing(pattern)) {
dbGetQuery(
conn, sprintf("SHOW TABLES IN %s", schema)
) -> x
} else {
dbGetQuery(
conn, sprintf("SHOW TABLES IN %s %s", schema, dbQuoteString(conn, pattern))
) -> x
}
x$tab_name
}
)
#' AthenaJDBC
#'
#' @param conn Athena connection
#' @param name table name
#' @param schema Athena schema name
#' @param ... unused
#' @export
setMethod(
"dbExistsTable",
signature(conn="AthenaConnection", name="character"),
definition = function(conn, name, schema, ...) {
length(dbListTables(conn, schema=schema, pattern=name)) > 0
}
)
#' AthenaJDBC
#'
#' @param conn Athena connection
#' @param name table name
#' @param schema Athena schema name
#' @param ... unused
#' @export
setMethod(
"dbListFields",
signature(conn="AthenaConnection", name="character"),
definition = function(conn, name, schema, ...) {
query <- sprintf("SELECT * FROM %s.%s LIMIT 1", schema, name)
res <- dbGetQuery(conn, query)
colnames(res)
}
)
#' AthenaJDBC
#'
#' @param conn Athena connection
#' @param name table name
#' @param schema Athena schema name
#' @param ... unused
#' @export
setMethod(
"dbReadTable",
signature(conn="AthenaConnection", name="character"),
definition = function(conn, name, schema, ...) {
query <- sprintf("SELECT * FROM %s.%s LIMIT 1", schema, dbQuoteString(conn, name))
dbGetQuery(conn, query)
}
)

32
R/metis-jars-package.R

@ -0,0 +1,32 @@
#' Amazon Athena JDBC Driver Wrapper Supporting the 'metis' Package
#'
#' Contents of the Amazon Athena JDBC Driver
#' <https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html>
#' provided to support functions in the 'metis' package. Version number
#' reflects the version number of the included 'JAR' file.
#'
#' @name metis.jars
#'
#' @section IMPORTANT:
#'
#' Until a release of 'rJava' newer than '0.9.10' is on CRAN signals sent
#' from interrupting Athena JDBC calls crash the R interpreter. You therefore
#' 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`:
#'
#' options(
#' "java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs")
#' )
#'
#'
#' @md
#' @encoding UTF-8
#' @keywords internal
#' @docType package
#' @author Bob Rudis (bob@@rud.is)
#' @import rJava
#' @importFrom utils packageVersion compareVersion
#' @references [Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide](https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf)
NULL

48
R/metis-lite-package.R

@ -1,48 +0,0 @@
#' Access and Query Amazon Athena via DBI/JDBC
#'
#' Methods are provides to connect to 'Amazon' 'Athena', lookup schemas/tables,
#' perform queries and retrieve query results. A lightweight 'RJDBC' implementation
#' is included along with an interface to the 'AWS' command-line utility.
#'
#' @name metis.lite
#'
#' @section 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")
#' )
#' }
#'
#' @md
#' @encoding UTF-8
#' @keywords internal
#' @docType package
#' @author Bob Rudis (bob@@rud.is)
#' @import RJDBC DBI bit64 dbplyr
#' @references [Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide](https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf)
NULL
#' Use Credentials from .aws/credentials File
#'
#' @md
#' @importFrom aws.signature use_credentials read_credentials
#' @references [aws.signature::use_credentials()] / [aws.signature::read_credentials()]
#' @name use_credentials
#' @rdname use_credentials
#' @inheritParams aws.signature::use_credentials
#' @export
NULL
#' @name read_credentials
#' @rdname use_credentials
#' @export
NULL

68
R/metis.r

@ -1,68 +0,0 @@
#' Simplified Athena JDBC connection helper
#'
#' Handles the up-front JDBC config
#'
#' @md
#' @param default_schema default schema (you'll still need to fully qualify non-default schema table names)
#' @param region AWS region (Ref: <http://docs.aws.amazon.com/general/latest/gr/rande.html#athena>)
#' @param s3_staging_dir the Amazon S3 location to which your query output is written. The JDBC driver then asks Athena to read the results and provide rows of data back to the user.
#' @param max_error_retries the maximum number of retries that the JDBC client attempts to make a request to Athena.
#' @param connection_timeout the maximum amount of time, in milliseconds, to make a successful connection to Athena before an attempt is terminated.
#' @param socket_timeout the maximum amount of time, in milliseconds, to wait for a socket in order to send data to Athena.
# @param retry_base_delay minimum delay amount, in milliseconds, between retrying attempts to connect Athena.
# @param retry_max_backoff_time maximum delay amount, in milliseconds, between retrying attempts to connect Athena.
#' @param log_path local path of the Athena JDBC driver logs. If no log path is provided, then no log files are created.
#' @param log_level log level of the Athena JDBC driver logs. Use names
#' "OFF", "FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE".
#' @param ... passed on to the driver
#' @export
#' @references [Connect with JDBC](https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html);
#' [Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide](https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf)
#' @examples \dontrun{
#' use_credentials("personal")
#'
#' athena_connect(
#' default_schema = "sampledb",
#' s3_staging_dir = "s3://accessible-bucket",
#' log_path = "/tmp/athena.log",
#' log_level = "DEBUG"
#' ) -> ath
#'
#' dbListTables(ath)
#'
#' dbGetQuery(ath, "SELECT * FROM sampledb.elb_logs LIMIT 1")
#'
#' }
athena_connect <- function(
default_schema = "default",
region = c("us-east-1", "us-east-2", "us-west-2"),
s3_staging_dir = Sys.getenv("AWS_S3_STAGING_DIR"),
max_error_retries = 10,
connection_timeout = 10000,
socket_timeout = 10000,
log_path = "",
log_level = c("OFF", "FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE"),
...
) {
athena_jdbc <- Athena()
region <- match.arg(region, c("us-east-1", "us-east-2", "us-west-2"))
log_level <- match.arg(log_level, c("OFF", "FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE"))
dbConnect(
athena_jdbc,
schema_name = default_schema,
region = region,
s3_staging_dir = s3_staging_dir,
max_error_retries = max_error_retries,
connection_timeout = connection_timeout,
socket_timeout = socket_timeout,
log_path = log_path,
log_level = log_level,
...
) -> con
con
}

15
R/metis_jar_path.R

@ -0,0 +1,15 @@
#' Retrieve the fully-qualified path to the included Athena JAR file
#'
#' @export
#' @examples
#' metis_jar_path()
metis_jar_path <- function() {
list.files(
path = system.file("java", package = "metis.jars"),
pattern = "Ath.*jar$",
full.names = TRUE
)[1]
}

124
R/sql_translate_env.R

@ -1,124 +0,0 @@
#' @rdname Athena
#' @keywords internal
#' @export
db_data_type.AthenaConnection <- function(con, fields, ...) {
print("\n\n\ndb_data_type\n\n\n")
data_type <- function(x) {
switch(
class(x)[1],
integer64 = "BIGINT",
logical = "BOOLEAN",
integer = "INTEGER",
numeric = "DOUBLE",
factor = "CHARACTER",
character = "CHARACTER",
Date = "DATE",
POSIXct = "TIMESTAMP",
stop("Can't map type ", paste(class(x), collapse = "/"),
" to a supported database type.")
)
}
vapply(fields, data_type, character(1))
}
#' @rdname Athena
#' @keywords internal
#' @export
sql_translate_env.AthenaConnection <- function(con) {
x <- con
dbplyr::sql_variant(
scalar = dbplyr::sql_translator(
.parent = dbplyr::base_scalar,
`!=` = dbplyr::sql_infix("<>"),
as.integer64 = function(x) dbplyr::build_sql("CAST(", x, "AS BIGINT)"),
as.numeric = function(x) dbplyr::build_sql("CAST(", x, " AS DOUBLE)"),
as.character = function(x) dbplyr::build_sql("CAST(", x, " AS CHARACTER)"),
as.date = function(x) dbplyr::build_sql("CAST(", x, " AS DATE)"),
as.Date = function(x) dbplyr::build_sql("CAST(", x, " AS DATE)"),
as.POSIXct = function(x) dbplyr::build_sql("CAST(", x, " AS TIMESTAMP)"),
as.posixct = function(x) dbplyr::build_sql("CAST(", x, " AS TIMESTAMP)"),
as.logical = function(x) dbplyr::build_sql("CAST(", x, " AS BOOLEAN)"),
date_part = function(x, y) dbplyr::build_sql("DATE_PART(", x, ",", y ,")"),
grepl = function(x, y) dbplyr::build_sql("CONTAINS(", y, ", ", x, ")"),
gsub = function(x, y, z) dbplyr::build_sql("REGEXP_REPLACE(", z, ", ", x, ",", y ,")"),
trimws = function(x) dbplyr::build_sql("TRIM(both ' ' FROM ", x, ")"),
cbrt = dbplyr::sql_prefix("CBRT", 1),
degrees = dbplyr::sql_prefix("DEGREES", 1),
e = dbplyr::sql_prefix("E", 0),
row_number = dbplyr::sql_prefix("row_number", 0),
lshift = dbplyr::sql_prefix("LSHIFT", 2),
mod = dbplyr::sql_prefix("MOD", 2),
age = dbplyr::sql_prefix("AGE", 1),
negative = dbplyr::sql_prefix("NEGATIVE", 1),
pi = dbplyr::sql_prefix("PI", 0),
pow = dbplyr::sql_prefix("POW", 2),
radians = dbplyr::sql_prefix("RADIANS", 1),
rand = dbplyr::sql_prefix("RAND", 0),
rshift = dbplyr::sql_prefix("RSHIFT", 2),
trunc = dbplyr::sql_prefix("TRUNC", 2),
contains = dbplyr::sql_prefix("CONTAINS", 2),
convert_to = dbplyr::sql_prefix("CONVERT_TO", 2),
convert_from = dbplyr::sql_prefix("CONVERT_FROM", 2),
string_binary = dbplyr::sql_prefix("STRING_BINARY", 1),
binary_string = dbplyr::sql_prefix("BINARY_STRING", 1),
to_char = dbplyr::sql_prefix("TO_CHAR", 2),
to_date = dbplyr::sql_prefix("TO_DATE", 2),
to_number = dbplyr::sql_prefix("TO_NUMBER", 2),
char_to_timestamp = dbplyr::sql_prefix("TO_TIMESTAMP", 2),
double_to_timestamp = dbplyr::sql_prefix("TO_TIMESTAMP", 1),
char_length = dbplyr::sql_prefix("CHAR_LENGTH", 1),
flatten = dbplyr::sql_prefix("FLATTEN", 1),
kvgen = dbplyr::sql_prefix("KVGEN", 1),
repeated_count = dbplyr::sql_prefix("REPEATED_COUNT", 1),
repeated_contains = dbplyr::sql_prefix("REPEATED_CONTAINS", 2),
ilike = dbplyr::sql_prefix("ILIKE", 2),
init_cap = dbplyr::sql_prefix("INIT_CAP", 1),
length = dbplyr::sql_prefix("LENGTH", 1),
lower = dbplyr::sql_prefix("LOWER", 1),
tolower = dbplyr::sql_prefix("LOWER", 1),
ltrim = dbplyr::sql_prefix("LTRIM", 2),
nullif = dbplyr::sql_prefix("NULLIF", 2),
position = function(x, y) dbplyr::build_sql("POSITION(", x, " IN ", y, ")"),
regexp_replace = dbplyr::sql_prefix("REGEXP_REPLACE", 3),
rtrim = dbplyr::sql_prefix("RTRIM", 2),
rpad = dbplyr::sql_prefix("RPAD", 2),
rpad_with = dbplyr::sql_prefix("RPAD", 3),
lpad = dbplyr::sql_prefix("LPAD", 2),
lpad_with = dbplyr::sql_prefix("LPAD", 3),
strpos = dbplyr::sql_prefix("STRPOS", 2),
substr = dbplyr::sql_prefix("SUBSTR", 3),
trim = function(x, y, z) dbplyr::build_sql("TRIM(", x, " ", y, " FROM ", z, ")"),
upper = dbplyr::sql_prefix("UPPER", 1),
toupper = dbplyr::sql_prefix("UPPER", 1)
),
aggregate = dbplyr::sql_translator(
.parent = dbplyr::base_agg,
n = function() dbplyr::sql("COUNT(*)"),
cor = dbplyr::sql_prefix("CORR"),
cov = dbplyr::sql_prefix("COVAR_SAMP"),
sd = dbplyr::sql_prefix("STDDEV_SAMP"),
var = dbplyr::sql_prefix("VAR_SAMP"),
n_distinct = function(x) {
dbplyr::build_sql(dbplyr::sql("COUNT(DISTINCT "), x, dbplyr::sql(")"))
}
),
window = dbplyr::sql_translator(
.parent = dbplyr::base_win,
n = function() { dbplyr::win_over(dbplyr::sql("count(*)"),
partition = dbplyr::win_current_group()) },
cor = dbplyr::win_recycled("corr"),
cov = dbplyr::win_recycled("covar_samp"),
sd = dbplyr::win_recycled("stddev_samp"),
var = dbplyr::win_recycled("var_samp"),
all = dbplyr::win_recycled("bool_and"),
any = dbplyr::win_recycled("bool_or")
)
)
}

15
R/types.R

@ -0,0 +1,15 @@
#' Retrieve the current supported type names in Athena
#'
#' @export
#' @examples
#' athena_supported_types()
athena_supported_types <- function() {
gsub(
"^AJ_|_TYPE_NAME$", "",
grep(
"^AJ_",
names(rJava::J("com.simba.athena.athena.AthenaTypes")),
value=TRUE
)
)
}

8
R/version.R

@ -0,0 +1,8 @@
#' Retrieve the version of the Simba Athena JDBC driver included with the package
#'
#' @export
#' @examples
#' simba_driver_version()
simba_driver_version <- function() {
rJava::J("com.simba.athena.athena.core.AJDriver")$AJ_DRIVER_VERSION
}

121
R/z-dbGetQuery.R

@ -1,121 +0,0 @@
list(
"-7" = as.logical, # BIT
"-6" = as.integer, # TINYINT
"-5" = bit64::as.integer64, # BIGINT
"-4" = as.character, # LONGVARBINARY
"-3" = as.character, # VARBINARY
"-2" = as.character, # BINARY
"-1" = as.character, # LONGVARCHAR
"0" = as.character, # NULL
"1" = as.character, # CHAR
"2" = as.double, # NUMERIC
"3" = as.double, # DECIMAL
"4" = as.integer, # INTEGER
"5" = as.integer, # SMALLINT
"6" = as.double, # FLOAT
"7" = as.double, # REAL
"8" = as.double, # DOUBLE
"12" = as.character, # VARCHAR
"16" = as_logical, # BOOLEAN
"91" = as_date, # DATE
"92" = as.character, # TIME
"93" = as_posixct, # TIMESTAMP
"2003" = as.character, # ARRAY
"1111" = as.character # OTHER
) -> .jdbc_converters
#' @export
#' @keywords internal
setMethod("dbGetInfo", "AthenaDriver", def=function(dbObj, ...)
list(
name = "AthenaJDBC",
driver_version = list.files(system.file("java", package="metis.lite"), "jar$")[1],
package_version = utils::packageVersion("metis.lite")
)
)
#' @export
#' @keywords internal
setMethod("dbGetInfo", "AthenaConnection", def=function(dbObj, ...)
list(
name = "AthenaJDBC",
driver_version = list.files(system.file("java", package="metis.lite"), "jar$")[1],
package_version = utils::packageVersion("metis.lite")
)
)
#' Fetch records from a previously executed query
#'
#' Fetch the next `n` elements (rows) from the result set and return them
#' as a data.frame.
#'
#' @param res An object inheriting from [DBIResult-class], created by
#' [dbSendQuery()].
#' @param 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.
#' @param ... Other arguments passed on to methods.
#' @export
setMethod(
"fetch",
signature(res="AthenaResult", n="numeric"),
def = function(res, n, block = 1000L, ...) {
nms <- c()
athena_type_convert <- list()
cols <- .jcall(res@md, "I", "getColumnCount")
for (i in 1:cols) {
ct <- as.character(.jcall(res@md, "I", "getColumnType", i))
athena_type_convert[[i]] <- .jdbc_converters[[ct]]
nms <- c(nms, .jcall(res@md, "S", "getColumnLabel", i))
# message(ct, "|", tail(nms, 1))
}
athena_type_convert <- set_names(athena_type_convert, nms)
out <- callNextMethod(res = res, n = n, block = block, ...)
# print(str(out))
for (nm in names(athena_type_convert)) {
f <- athena_type_convert[[nm]]
if (length(f) == 0) f <- as.character # catchall in case AMZN is tricksy
out[[nm]] <- f(out[[nm]])
}
out
}
)
#' AthenaJDBC
#'
#' @param conn Athena connection
#' @param statement SQL statement
#' @param ... unused
#' @importFrom rJava .jcall
#' @export
setMethod(
"dbGetQuery",
signature(conn="AthenaConnection", statement="character"),
definition = function(conn, statement, ...) {
r <- dbSendQuery(conn, statement, ...)
on.exit(.jcall(r@stat, "V", "close"))
res <- fetch(r, -1, block = conn@fetch_size)
class(res) <- c("tbl_df", "tbl", "data.frame")
res
}
)

27
R/zzz.R

@ -1,11 +1,24 @@
.onAttach <- function(libname, pkgname) {
if (interactive()) {
jv <- utils::packageVersion("rJava")
if (utils::compareVersion(toString(jv), "0.9.10") < 1) {
o <- getOption("java.parameters", "")
if (!any(grepl("\\-Xrs", o))) {
packageStartupMessage(
"Did not find '-Xrs' in java.parameters option. Until rJava is updated, ",
"please set this up in your/an Rprofile or at the start of scripts. ",
"See the 'IMPORTANT' section under ?`metis.jars-package`."
)
}
}
}
}
.onLoad <- function(libname, pkgname) { .onLoad <- function(libname, pkgname) {
rJava::.jpackage(pkgname, jars = "*", lib.loc = libname) rJava::.jpackage(pkgname, jars = "*", lib.loc = libname)
rJava::.jaddClassPath(dir(file.path(getwd(), "inst/java"), full.names = TRUE)) rJava::.jaddClassPath(dir(file.path(getwd(), "inst/java"), full.names = TRUE))
o <- getOption("java.parameters", "")
if (!any(grepl("-Xrs", o))) {
packageStartupMessage(
"Did not find '-Xrs' in java.parameters option. Until rJava is updated, ",
"please set this up in your/an Rprofile or at the start of scripts."
)
}
} }

135
README.Rmd

@ -4,64 +4,47 @@ editor_options:
chunk_output_type: console chunk_output_type: console
--- ---
# metis # metis.jars
Access and Query Amazon Athena via DBI/JDBC Amazon Athena JDBC Driver Wrapper Supporting the 'metis' Package
## Description ## Description
In Greek mythology, Metis was Athena's "helper" so methods are provided to help you accessing and querying Amazon Athena via DBI/JDBC and/or `dplyr`. Contents of the Amazon Athena JDBC Driver
#' Methods are provides to connect to 'Amazon' 'Athena', lookup schemas/tables, <https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html>
provided to support functions in the 'metis' package. Version number
reflects the version number of the included 'JAR' file.
## IMPORTANT ## 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`: Until a release of 'rJava' newer than '0.9.10' is on CRAN signals sent
from interrupting Athena JDBC calls crash the R interpreter. You therefore
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`:
```r ```r
if (!grepl("-Xrs", getOption("java.parameters", ""))) { options(
options( "java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs")
"java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs") )
)
}
``` ```
## What's Inside The Tin? ## What's Inside The Tin?
The following functions are implemented: The following functions are implemented:
Easy-interface connection helper: - `athena_supported_types`: Retrieve the current supported type names in Athena
- `metis_jar_path()` : Retrieve the fully-qualified path to the included Athena JAR file
- `athena_connect` Simplified Athena JDBC connection helper - `simba_driver_version`: Retrieve the version of the Simba Athena JDBC driver included with the package
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`
- `dbExistsTable-method`
- `dbGetQuery-method`
- `dbListFields-method`
- `dbListTables-method`
- `dbReadTable-method`
- `dbSendQuery-method`
Pulled in from other `cloudyr` pkgs:
- `read_credentials`: Use Credentials from .aws/credentials File
- `use_credentials`: Use Credentials from .aws/credentials File
## Installation ## Installation
```{r eval=FALSE} ```{r eval=FALSE}
devtools::install_git("https://git.sr.ht/~hrbrmstr/metis-lite") devtools::install_git("https://git.sr.ht/~hrbrmstr/metis-jars")
# OR # OR
devtools::install_gitlab("hrbrmstr/metis-lite") devtools::install_gitlab("hrbrmstr/metis-jars")
# OR # OR
devtools::install_github("hrbrmstr/metis-lite") devtools::install_github("hrbrmstr/metis-jars")
``` ```
```{r message=FALSE, warning=FALSE, include=FALSE} ```{r message=FALSE, warning=FALSE, include=FALSE}
@ -71,84 +54,18 @@ options(width=120)
## Usage ## Usage
```{r message=FALSE, warning=FALSE} ```{r message=FALSE, warning=FALSE}
library(metis.lite) library(metis.jars)
# current verison # current verison
packageVersion("metis.lite") packageVersion("metis.jars")
```
```{r message=FALSE, warning=FALSE}
library(rJava)
library(RJDBC)
library(metis.lite)
library(magrittr)
library(dbplyr)
library(dplyr)
dbConnect(
drv = metis.lite::Athena(),
schema_name = "sampledb",
provider = "com.simba.athena.amazonaws.auth.PropertiesFileCredentialsProvider",
AwsCredentialsProviderArguments = path.expand("~/.aws/athenaCredentials.props"),
s3_staging_dir = "s3://aws-athena-query-results-569593279821-us-east-1",
) -> con
dbListTables(con, schema="sampledb")
dbExistsTable(con, "elb_logs", schema="sampledb")
dbListFields(con, "elb_logs", "sampledb")
dbGetQuery(con, "SELECT * FROM sampledb.elb_logs LIMIT 10") %>%
glimpse()
``` ```
### Check types
```{r} ```{r}
dbGetQuery(con, " simba_driver_version()
SELECT
CAST('chr' AS CHAR(4)) achar,
CAST('varchr' AS VARCHAR) avarchr,
CAST(SUBSTR(timestamp, 1, 10) AS DATE) AS tsday,
CAST(100.1 AS DOUBLE) AS justadbl,
CAST(127 AS TINYINT) AS asmallint,
CAST(100 AS INTEGER) AS justanint,
CAST(100000000000000000 AS BIGINT) AS abigint,
CAST(('GET' = 'GET') AS BOOLEAN) AS is_get,
ARRAY[1, 2, 3] AS arr1,
ARRAY['1', '2, 3', '4'] AS arr2,
MAP(ARRAY['foo', 'bar'], ARRAY[1, 2]) AS mp,
CAST(ROW(1, 2.0) AS ROW(x BIGINT, y DOUBLE)) AS rw,
CAST('{\"a\":1}' AS JSON) js
FROM elb_logs
LIMIT 1
") %>%
glimpse()
```
#### dplyr athena_supported_types()
```{r} metis_jar_path()
tbl(con, sql("
SELECT
CAST('chr' AS CHAR(4)) achar,
CAST('varchr' AS VARCHAR) avarchr,
CAST(SUBSTR(timestamp, 1, 10) AS DATE) AS tsday,
CAST(100.1 AS DOUBLE) AS justadbl,
CAST(127 AS TINYINT) AS asmallint,
CAST(100 AS INTEGER) AS justanint,
CAST(100000000000000000 AS BIGINT) AS abigint,
CAST(('GET' = 'GET') AS BOOLEAN) AS is_get,
ARRAY[1, 2, 3] AS arr,
ARRAY['1', '2, 3', '4'] AS arr,
MAP(ARRAY['foo', 'bar'], ARRAY[1, 2]) AS mp,
CAST(ROW(1, 2.0) AS ROW(x BIGINT, y DOUBLE)) AS rw,
CAST('{\"a\":1}' AS JSON) js
FROM elb_logs
LIMIT 1
")) %>%
glimpse()
``` ```
## Code of Conduct ## Code of Conduct

212
README.md

@ -1,223 +1,81 @@
# metis # metis.jars
Access and Query Amazon Athena via DBI/JDBC Amazon Athena JDBC Driver Wrapper Supporting the ‘metis’ Package
## Description ## Description
In Greek mythology, Metis was Athena’s “helper” so methods are provided Contents of the Amazon Athena JDBC Driver
to help you accessing and querying Amazon Athena via DBI/JDBC and/or <https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html>
`dplyr`. \#’ Methods are provides to connect to ‘Amazon’ ‘Athena’, provided to support functions in the ‘metis’ package. Version number
lookup schemas/tables, reflects the version number of the included ‘JAR’ file.
## IMPORTANT ## IMPORTANT
Since R 3.5 (I don’t remember this happening in R 3.4.x) signals sent Until a release of ‘rJava’ newer than ‘0.9.10’ is on CRAN signals sent
from interrupting Athena JDBC calls crash the R interpreter. You need to from interrupting Athena JDBC calls crash the R interpreter. You
set the `-Xrs` option to avoid signals being passed on to the JVM owner. therefore need to set the `-Xrs` option to avoid signals being passed on
That has to be done *before* `rJava` is loaded so you either need to to the JVM owner. That has to be done *before* `rJava` is loaded so you
remember to put it at the top of all scripts *or* stick this in your either need to remember to put it at the top of all scripts *or* stick
local `~/.Rprofile` and/or sitewide `Rprofile`: this in your local `~/.Rprofile` and/or sitewide `Rprofile`:
``` r ``` r
if (!grepl("-Xrs", getOption("java.parameters", ""))) { options(
options( "java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs")
"java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs") )
)
}
``` ```
## What’s Inside The Tin? ## What’s Inside The Tin?
The following functions are implemented: The following functions are implemented:
Easy-interface connection helper: - `athena_supported_types`: Retrieve the current supported type names
in Athena
- `athena_connect` Simplified Athena JDBC connection helper - `metis_jar_path()` : Retrieve the fully-qualified path to the
included Athena JAR file
Custom JDBC Classes: - `simba_driver_version`: Retrieve the version of the Simba Athena
JDBC driver included with the package
- `Athena`: AthenaJDBC (make a new Athena con obj)
- `AthenaConnection-class`: AthenaJDBC
- `AthenaDriver-class`: AthenaJDBC
- `AthenaResult-class`: AthenaJDBC
Custom JDBC Class Methods:
- `dbConnect-method`
- `dbExistsTable-method`
- `dbGetQuery-method`
- `dbListFields-method`
- `dbListTables-method`
- `dbReadTable-method`
- `dbSendQuery-method`
Pulled in from other `cloudyr` pkgs:
- `read_credentials`: Use Credentials from .aws/credentials File
- `use_credentials`: Use Credentials from .aws/credentials File
## Installation ## Installation
``` r ``` r
devtools::install_git("https://git.sr.ht/~hrbrmstr/metis-lite") devtools::install_git("https://git.sr.ht/~hrbrmstr/metis-jars")
# OR # OR
devtools::install_gitlab("hrbrmstr/metis-lite") devtools::install_gitlab("hrbrmstr/metis-jars")
# OR # OR
devtools::install_github("hrbrmstr/metis-lite") devtools::install_github("hrbrmstr/metis-jars")
``` ```
## Usage ## Usage
``` r ``` r
library(metis.lite) library(metis.jars)
# current verison # current verison
packageVersion("metis.lite") packageVersion("metis.jars")
```
## [1] '0.3.0'
``` r
library(rJava)
library(RJDBC)
library(metis.lite)
library(magrittr)
library(dbplyr)
library(dplyr)
dbConnect(
drv = metis.lite::Athena(),
schema_name = "sampledb",
provider = "com.simba.athena.amazonaws.auth.PropertiesFileCredentialsProvider",
AwsCredentialsProviderArguments = path.expand("~/.aws/athenaCredentials.props"),
s3_staging_dir = "s3://aws-athena-query-results-569593279821-us-east-1",
) -> con
dbListTables(con, schema="sampledb")
```
## [1] "elb_logs"
``` r
dbExistsTable(con, "elb_logs", schema="sampledb")
```
## [1] TRUE
``` r
dbListFields(con, "elb_logs", "sampledb")
``` ```
## [1] "timestamp" "elbname" "requestip" "requestport" ## [1] '2.0.6'
## [5] "backendip" "backendport" "requestprocessingtime" "backendprocessingtime"
## [9] "clientresponsetime" "elbresponsecode" "backendresponsecode" "receivedbytes"
## [13] "sentbytes" "requestverb" "url" "protocol"
``` r ``` r
dbGetQuery(con, "SELECT * FROM sampledb.elb_logs LIMIT 10") %>% simba_driver_version()
glimpse()
``` ```
## Observations: 10 ## [1] "02.00.06.1008"
## Variables: 16
## $ timestamp <chr> "2014-09-29T18:18:51.826955Z", "2014-09-29T18:18:51.920462Z", "2014-09-29T18:18:52.2725…
## $ elbname <chr> "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo", "lb-demo",…
## $ requestip <chr> "255.48.150.122", "249.213.227.93", "245.108.120.229", "241.112.203.216", "241.43.107.2…
## $ requestport <int> 62096, 62096, 62096, 62096, 56454, 33254, 18918, 64352, 1651, 56454
## $ backendip <chr> "244.238.214.120", "248.99.214.228", "243.3.190.175", "246.235.181.255", "241.112.203.2…
## $ backendport <int> 8888, 8888, 8888, 8888, 8888, 8888, 8888, 8888, 8888, 8888
## $ requestprocessingtime <dbl> 9.0e-05, 9.7e-05, 8.7e-05, 9.4e-05, 7.6e-05, 8.3e-05, 6.3e-05, 5.4e-05, 8.2e-05, 8.7e-05
## $ backendprocessingtime <dbl> 0.007410, 0.256533, 0.442659, 0.016772, 0.035036, 0.029892, 0.034148, 0.014858, 0.01518…
## $ clientresponsetime <dbl> 0.000055, 0.000075, 0.000131, 0.000078, 0.000057, 0.000043, 0.000033, 0.000043, 0.00007…
## $ elbresponsecode <chr> "302", "302", "200", "200", "200", "200", "200", "200", "200", "200"
## $ backendresponsecode <chr> "200", "200", "200", "200", "200", "200", "200", "200", "200", "200"
## $ receivedbytes <S3: integer64> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
## $ sentbytes <S3: integer64> 0, 0, 58402, 152213, 20766, 32370, 3408, 3884, 84245, 3831
## $ requestverb <chr> "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET", "GET"
## $ url <chr> "http://www.abcxyz.com:80/", "http://www.abcxyz.com:80/accounts/login/?next=/", "http:/…
## $ protocol <chr> "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HTTP/1.1", "HT…
### Check types
``` r ``` r
dbGetQuery(con, " athena_supported_types()
SELECT
CAST('chr' AS CHAR(4)) achar,
CAST('varchr' AS VARCHAR) avarchr,
CAST(SUBSTR(timestamp, 1, 10) AS DATE) AS tsday,
CAST(100.1 AS DOUBLE) AS justadbl,
CAST(127 AS TINYINT) AS asmallint,
CAST(100 AS INTEGER) AS justanint,
CAST(100000000000000000 AS BIGINT) AS abigint,
CAST(('GET' = 'GET') AS BOOLEAN) AS is_get,
ARRAY[1, 2, 3] AS arr1,
ARRAY['1', '2, 3', '4'] AS arr2,
MAP(ARRAY['foo', 'bar'], ARRAY[1, 2]) AS mp,
CAST(ROW(1, 2.0) AS ROW(x BIGINT, y DOUBLE)) AS rw,
CAST('{\"a\":1}' AS JSON) js
FROM elb_logs
LIMIT 1
") %>%
glimpse()
``` ```
## Observations: 1 ## [1] "BOOLEAN" "TINYINT" "SMALLINT" "INT" "INTEGER" "BIGINT" "REAL" "FLOAT" "DOUBLE"
## Variables: 13 ## [10] "DECIMAL" "DATE" "TIMESTAMP" "BINARY" "VARBINARY" "CHAR" "VARCHAR" "STRING" "ARRAY"
## $ achar <chr> "chr " ## [19] "MAP" "ROW" "STRUCT"
## $ avarchr <chr> "varchr"
## $ tsday <date> 2014-09-26
## $ justadbl <dbl> 100.1
## $ asmallint <int> 127
## $ justanint <int> 100
## $ abigint <S3: integer64> 100000000000000000
## $ is_get <lgl> TRUE
## $ arr1 <chr> "1, 2, 3"
## $ arr2 <chr> "1, 2, 3, 4"
## $ mp <chr> "{bar=2, foo=1}"
## $ rw <chr> "{x=1, y=2.0}"
## $ js <chr> "\"{\\\"a\\\":1}\""
#### dplyr
``` r ``` r
tbl(con, sql(" metis_jar_path()
SELECT
CAST('chr' AS CHAR(4)) achar,
CAST('varchr' AS VARCHAR) avarchr,
CAST(SUBSTR(timestamp, 1, 10) AS DATE) AS tsday,
CAST(100.1 AS DOUBLE) AS justadbl,
CAST(127 AS TINYINT) AS asmallint,
CAST(100 AS INTEGER) AS justanint,
CAST(100000000000000000 AS BIGINT) AS abigint,
CAST(('GET' = 'GET') AS BOOLEAN) AS is_get,
ARRAY[1, 2, 3] AS arr,
ARRAY['1', '2, 3', '4'] AS arr,
MAP(ARRAY['foo', 'bar'], ARRAY[1, 2]) AS mp,
CAST(ROW(1, 2.0) AS ROW(x BIGINT, y DOUBLE)) AS rw,
CAST('{\"a\":1}' AS JSON) js
FROM elb_logs
LIMIT 1
")) %>%
glimpse()
``` ```
## Observations: ?? ## [1] "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/metis.jars/java/AthenaJDBC42_2.0.6.jar"
## Variables: 13
## Database: AthenaConnection
## $ achar <chr> "chr "
## $ avarchr <chr> "varchr"
## $ tsday <date> 2014-09-27
## $ justadbl <dbl> 100.1
## $ asmallint <int> 127
## $ justanint <int> 100
## $ abigint <S3: integer64> 100000000000000000
## $ is_get <lgl> TRUE
## $ arr <chr> "1, 2, 3"
## $ arr <chr> "1, 2, 3, 4"
## $ mp <chr> "{bar=2, foo=1}"
## $ rw <chr> "{x=1, y=2.0}"
## $ js <chr> "\"{\\\"a\\\":1}\""
## Code of Conduct ## Code of Conduct

69
inst/COPYRIGHTS

@ -0,0 +1,69 @@
The metis.jars package is released under the Apache 2.0 License
The include AthenaJDBC42_2.0.6.jar JAR has the following license:
-----------------
License for AWS SDK for Java
Apache License
Version 2.0, January 2004
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document.
"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License.
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"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution."
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END OF TERMS AND CONDITIONS
Note: Other license terms may apply to certain, identified software files contained within or distributed with the accompanying software if such terms are included in the directory containing the accompanying software. Such other license terms will then apply in lieu of the terms of the software license above.
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18
man/Athena.Rd

@ -1,18 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r, R/sql_translate_env.R
\name{Athena}
\alias{Athena}
\alias{db_data_type.AthenaConnection}
\alias{sql_translate_env.AthenaConnection}
\title{AthenaJDBC}
\usage{
Athena(identifier.quote = "`")
db_data_type.AthenaConnection(con, fields, ...)
sql_translate_env.AthenaConnection(con)
}
\description{
AthenaJDBC
}
\keyword{internal}

9
man/AthenaConnection-class.Rd

@ -1,9 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{class}
\name{AthenaConnection-class}
\alias{AthenaConnection-class}
\title{AthenaJDBC}
\description{
AthenaJDBC
}

9
man/AthenaDriver-class.Rd

@ -1,9 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{class}
\name{AthenaDriver-class}
\alias{AthenaDriver-class}
\title{AthenaJDBC}
\description{
AthenaJDBC
}

9
man/AthenaResult-class.Rd

@ -1,9 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{class}
\name{AthenaResult-class}
\alias{AthenaResult-class}
\title{AthenaJDBC}
\description{
AthenaJDBC
}

57
man/athena_connect.Rd

@ -1,57 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/metis.r
\name{athena_connect}
\alias{athena_connect}
\title{Simplified Athena JDBC connection helper}
\usage{
athena_connect(default_schema = "default", region = c("us-east-1",
"us-east-2", "us-west-2"),
s3_staging_dir = Sys.getenv("AWS_S3_STAGING_DIR"),
max_error_retries = 10, connection_timeout = 10000,
socket_timeout = 10000, log_path = "", log_level = c("OFF",
"FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE"), ...)
}
\arguments{
\item{default_schema}{default schema (you'll still need to fully qualify non-default schema table names)}
\item{region}{AWS region (Ref: \url{http://docs.aws.amazon.com/general/latest/gr/rande.html#athena})}
\item{s3_staging_dir}{the Amazon S3 location to which your query output is written. The JDBC driver then asks Athena to read the results and provide rows of data back to the user.}
\item{max_error_retries}{the maximum number of retries that the JDBC client attempts to make a request to Athena.}
\item{connection_timeout}{the maximum amount of time, in milliseconds, to make a successful connection to Athena before an attempt is terminated.}
\item{socket_timeout}{the maximum amount of time, in milliseconds, to wait for a socket in order to send data to Athena.}
\item{log_path}{local path of the Athena JDBC driver logs. If no log path is provided, then no log files are created.}
\item{log_level}{log level of the Athena JDBC driver logs. Use names
"OFF", "FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE".}
\item{...}{passed on to the driver}
}
\description{
Handles the up-front JDBC config
}
\examples{
\dontrun{
use_credentials("personal")
athena_connect(
default_schema = "sampledb",
s3_staging_dir = "s3://accessible-bucket",
log_path = "/tmp/athena.log",
log_level = "DEBUG"
) -> ath
dbListTables(ath)
dbGetQuery(ath, "SELECT * FROM sampledb.elb_logs LIMIT 1")
}
}
\references{
\href{https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html}{Connect with JDBC};
\href{https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf}{Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide}
}

14
man/athena_supported_types.Rd

@ -0,0 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/types.R
\name{athena_supported_types}
\alias{athena_supported_types}
\title{Retrieve the current supported type names in Athena}
\usage{
athena_supported_types()
}
\description{
Retrieve the current supported type names in Athena
}
\examples{
athena_supported_types()
}

48
man/dbConnect-AthenaDriver-method.Rd

@ -1,48 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{methods}
\name{dbConnect,AthenaDriver-method}
\alias{dbConnect,AthenaDriver-method}
\title{AthenaJDBC}
\usage{
\S4method{dbConnect}{AthenaDriver}(drv,
provider = "com.simba.athena.amazonaws.auth.DefaultAWSCredentialsProviderChain",
region = "us-east-1",
s3_staging_dir = Sys.getenv("AWS_S3_STAGING_DIR"),
schema_name = "default", fetch_size = 1000L,
max_error_retries = 10, connection_timeout = 10000,
socket_timeout = 10000, log_path = "", log_level = 0, ...)
}
\arguments{
\item{provider}{JDBC auth provider (ideally leave default)}
\item{region}{AWS region the Athena tables are in}
\item{s3_staging_dir}{A write-able bucket on S3 that you have permissions for}
\item{schema_name}{LOL if only this actually worked with Amazon's hacked Presto driver}
\item{max_error_retries, connection_timeout, socket_timeout}{technical connection info that you should only muck with if you know what you're doing.}
\item{log_path, log_level}{The Athena JDBC driver can (shockingly) provide a decent bit
of data in logs. Set this to a temporary directory or something log4j can use. For
`log_level` use the names ("INFO", "DEBUG", "WARN", "ERROR", "ALL", "OFF", "FATAL", "TRACE") or
their corresponding integer values 0-6.}
\item{...}{passed on to the driver. See Details.}
}
\description{
Connect to Athena
}
\section{Driver Configuration Options}{
- `BinaryColumnLength`: <int> The maximum data length for `BINARY` columns. Default `32767L`
- `ComplexTypeColumnLength`: <int> The maximum data length for `ARRAY`, `MAP`, and `STRUCT` columns. Default `65535L`
- `StringColumnLength`: <int> The maximum data length for `STRING` columns. Default `255L`
}
\references{
[Connect with JDBC](https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html);
[Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide](https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf)
}

22
man/dbExistsTable-AthenaConnection-character-method.Rd

@ -1,22 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{methods}
\name{dbExistsTable,AthenaConnection,character-method}
\alias{dbExistsTable,AthenaConnection,character-method}
\title{AthenaJDBC}
\usage{
\S4method{dbExistsTable}{AthenaConnection,character}(conn, name, schema,
...)
}
\arguments{
\item{conn}{Athena connection}
\item{name}{table name}
\item{schema}{Athena schema name}
\item{...}{unused}
}
\description{
AthenaJDBC
}

19
man/dbGetQuery-AthenaConnection-character-method.Rd

@ -1,19 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/z-dbGetQuery.R
\docType{methods}
\name{dbGetQuery,AthenaConnection,character-method}
\alias{dbGetQuery,AthenaConnection,character-method}
\title{AthenaJDBC}
\usage{
\S4method{dbGetQuery}{AthenaConnection,character}(conn, statement, ...)
}
\arguments{
\item{conn}{Athena connection}
\item{statement}{SQL statement}
\item{...}{unused}
}
\description{
AthenaJDBC
}

22
man/dbListFields-AthenaConnection-character-method.Rd

@ -1,22 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{methods}
\name{dbListFields,AthenaConnection,character-method}
\alias{dbListFields,AthenaConnection,character-method}
\title{AthenaJDBC}
\usage{
\S4method{dbListFields}{AthenaConnection,character}(conn, name, schema,
...)
}
\arguments{
\item{conn}{Athena connection}
\item{name}{table name}
\item{schema}{Athena schema name}
\item{...}{unused}
}
\description{
AthenaJDBC
}

22
man/dbListTables-AthenaConnection-method.Rd

@ -1,22 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{methods}
\name{dbListTables,AthenaConnection-method}
\alias{dbListTables,AthenaConnection-method}
\title{AthenaJDBC}
\usage{
\S4method{dbListTables}{AthenaConnection}(conn, pattern = "*", schema,
...)
}
\arguments{
\item{conn}{Athena connection}
\item{pattern}{table name pattern}
\item{schema}{Athena schema name}
\item{...}{unused}
}
\description{
AthenaJDBC
}

21
man/dbReadTable-AthenaConnection-character-method.Rd

@ -1,21 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{methods}
\name{dbReadTable,AthenaConnection,character-method}
\alias{dbReadTable,AthenaConnection,character-method}
\title{AthenaJDBC}
\usage{
\S4method{dbReadTable}{AthenaConnection,character}(conn, name, schema, ...)
}
\arguments{
\item{conn}{Athena connection}
\item{name}{table name}
\item{schema}{Athena schema name}
\item{...}{unused}
}
\description{
AthenaJDBC
}

19
man/dbSendQuery-AthenaConnection-character-method.Rd

@ -1,19 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
\docType{methods}
\name{dbSendQuery,AthenaConnection,character-method}
\alias{dbSendQuery,AthenaConnection,character-method}
\title{AthenaJDBC}
\usage{
\S4method{dbSendQuery}{AthenaConnection,character}(conn, statement, ...)
}
\arguments{
\item{conn}{Athena connection}
\item{statement}{SQL statement}
\item{...}{unused}
}
\description{
AthenaJDBC
}

24
man/fetch-AthenaResult-numeric-method.Rd

@ -1,24 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/z-dbGetQuery.R
\docType{methods}
\name{fetch,AthenaResult,numeric-method}
\alias{fetch,AthenaResult,numeric-method}
\title{Fetch records from a previously executed query}
\usage{
\S4method{fetch}{AthenaResult,numeric}(res, n, block = 1000L, ...)
}
\arguments{
\item{res}{An object inheriting from [DBIResult-class], created by
[dbSendQuery()].}
\item{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.}
\item{...}{Other arguments passed on to methods.}
}
\description{
Fetch the next `n` elements (rows) from the result set and return them
as a data.frame.
}

35
man/metis.jars.Rd

@ -0,0 +1,35 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/metis-jars-package.R
\docType{package}
\encoding{UTF-8}
\name{metis.jars}
\alias{metis.jars}
\alias{metis.jars-package}
\title{Amazon Athena JDBC Driver Wrapper Supporting the 'metis' Package}
\description{
Contents of the Amazon Athena JDBC Driver
\url{https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.html}
provided to support functions in the 'metis' package. Version number
reflects the version number of the included 'JAR' file.
}
\section{IMPORTANT}{
Until a release of 'rJava' newer than '0.9.10' is on CRAN signals sent
from interrupting Athena JDBC calls crash the R interpreter. You therefore
need to set the \code{-Xrs} option to avoid signals being passed on to the JVM
owner. That has to be done \emph{before} \code{rJava} is loaded so you either need
to remember to put it at the top of all scripts \emph{or} stick this
in your local \code{~/.Rprofile} and/or sitewide \code{Rprofile}:\preformatted{options(
"java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs")
)
}
}
\references{
\href{https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf}{Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide}
}
\author{
Bob Rudis (bob@rud.is)
}
\keyword{internal}

35
man/metis.lite.Rd

@ -1,35 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/metis-lite-package.R
\docType{package}
\encoding{UTF-8}
\name{metis.lite}
\alias{metis.lite}
\alias{metis.lite-package}
\title{Access and Query Amazon Athena via DBI/JDBC}
\description{
Methods are provides to connect to 'Amazon' 'Athena', lookup schemas/tables,
perform queries and retrieve query results. A lightweight 'RJDBC' implementation
is included along with an interface to the 'AWS' command-line utility.
}
\section{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 \code{-Xrs} option to avoid
signals being passed on to the JVM owner. That has to be done \emph{before} \code{rJava} is
loaded so you either need to remember to put it at the top of all scripts \emph{or} stick this
in your local #' \code{~/.Rprofile} and/or sitewide \code{Rprofile}:\preformatted{if (!grepl("-Xrs", getOption("java.parameters", ""))) {
options(
"java.parameters" = c(getOption("java.parameters", default = NULL), "-Xrs")
)
}
}
}
\references{
\href{https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC_2.0.6/docs/Simba+Athena+JDBC+Driver+Install+and+Configuration+Guide.pdf}{Simba Athena JDBC Driver with SQL Connector Installation and Configuration Guide}
}
\author{
Bob Rudis (bob@rud.is)
}
\keyword{internal}

14
man/metis_jar_path.Rd

@ -0,0 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/metis_jar_path.R
\name{metis_jar_path}
\alias{metis_jar_path}
\title{Retrieve the fully-qualified path to the included Athena JAR file}
\usage{
metis_jar_path()
}
\description{
Retrieve the fully-qualified path to the included Athena JAR file
}
\examples{
metis_jar_path()
}

14
man/simba_driver_version.Rd

@ -0,0 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/version.R
\name{simba_driver_version}
\alias{simba_driver_version}
\title{Retrieve the version of the Simba Athena JDBC driver included with the package}
\usage{
simba_driver_version()
}
\description{
Retrieve the version of the Simba Athena JDBC driver included with the package
}
\examples{
simba_driver_version()
}

12
man/use_credentials.Rd

@ -1,12 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/metis-lite-package.R
\name{use_credentials}
\alias{use_credentials}
\alias{read_credentials}
\title{Use Credentials from .aws/credentials File}
\description{
Use Credentials from .aws/credentials File
}
\references{
\code{\link[aws.signature:use_credentials]{aws.signature::use_credentials()}} / \code{\link[aws.signature:read_credentials]{aws.signature::read_credentials()}}
}

0
metis-lite.Rproj → metis-jars.Rproj

8
tests/test-all.R

@ -1,2 +1,8 @@
options(
"java.parameters" = unique(
c(getOption("java.parameters", default = NULL), "-Xrs")
)
)
library(testthat) library(testthat)
test_check("metis-lite") test_check("metis.jars")

6
tests/testthat/test-metis-lite.R

@ -1,6 +0,0 @@
context("basic functionality")
test_that("we can do something", {
#expect_that(some_function(), is_a("data.frame"))
})

11
tests/testthat/test-metis.jars.R

@ -0,0 +1,11 @@
options(
"java.parameters" = unique(
c(getOption("java.parameters", default = NULL), "-Xrs")
)
)
context("JAR loads; classes available")
expect_is(simba_driver_version(), "character")
expect_is(athena_supported_types(), "character")
expect_is(metis_jar_path(), "character")
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