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boB Rudis 1 vuosi sitten
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13 muutettua tiedostoa jossa 140 lisäystä ja 169 poistoa
  1. +1
    -0
      .Rbuildignore
  2. +4
    -6
      DESCRIPTION
  3. +2
    -0
      LICENSE
  4. +21
    -0
      LICENSE.md
  5. +3
    -7
      NAMESPACE
  6. +12
    -0
      R/a-utils.R
  7. +7
    -113
      R/jdbc.r
  8. +5
    -19
      R/metis-lite-package.R
  9. +71
    -0
      R/z-dbGetQuery.R
  10. +2
    -2
      man/Athena.Rd
  11. +2
    -2
      man/dbConnect-AthenaDriver-method.Rd
  12. +1
    -1
      man/dbGetQuery-AthenaConnection-character-method.Rd
  13. +9
    -19
      man/metis.lite.Rd

+ 1
- 0
.Rbuildignore Näytä tiedosto

@@ -1,3 +1,4 @@
^LICENSE\.md$
^.*\.Rproj$
^\.Rproj\.user$
^\.travis\.yml$


+ 4
- 6
DESCRIPTION Näytä tiedosto

@@ -13,7 +13,7 @@ Description: Methods are provides to connect to 'Amazon' 'Athena', lookup schema
perform queries and retrieve query results. A lightweight 'RJDBC' implementation
is included along with an interface to the 'AWS' command-line utility.
SystemRequirements: JDK 1.8+
License: AGPL
License: MIT + file LICENSE
Suggests:
testthat,
covr
@@ -23,9 +23,7 @@ Depends:
Imports:
rJava,
DBI,
dplyr,
readr,
aws.signature,
uuid,
jsonlite
bit64,
dbplyr,
aws.signature
RoxygenNote: 6.1.1

+ 2
- 0
LICENSE Näytä tiedosto

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

+ 21
- 0
LICENSE.md Näytä tiedosto

@@ -0,0 +1,21 @@
# MIT License

Copyright (c) 2019 Bob Rudis

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

+ 3
- 7
NAMESPACE Näytä tiedosto

@@ -1,10 +1,10 @@
# Generated by roxygen2: do not edit by hand

S3method(db_data_type,AthenaConnection)
S3method(sql_translate_env,AthenaConnection)
export(Athena)
export(athena_connect)
export(db_data_type.AthenaConnection)
export(read_credentials)
export(sql_translate_env.AthenaConnection)
export(use_credentials)
exportClasses(AthenaConnection)
exportClasses(AthenaDriver)
@@ -18,11 +18,7 @@ exportMethods(dbReadTable)
exportMethods(dbSendQuery)
import(DBI)
import(RJDBC)
import(dplyr)
import(bit64)
importFrom(aws.signature,read_credentials)
importFrom(aws.signature,use_credentials)
importFrom(jsonlite,fromJSON)
importFrom(rJava,.jcall)
importFrom(readr,type_convert)
importFrom(sys,exec_internal)
importFrom(uuid,UUIDgenerate)

+ 12
- 0
R/a-utils.R Näytä tiedosto

@@ -0,0 +1,12 @@
set_names <- function (object = nm, nm) {
names(object) <- nm
object
}

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")
}

+ 7
- 113
R/jdbc.r Näytä tiedosto

@@ -1,31 +1,9 @@
.jt <- list(
BIT = -7,
TINYINT = -6,
BIGINT = -5,
LONGVARBINARY = -4,
VARBINARY = -3,
BINARY = -2,
LONGVARCHAR = -1,
.NULL = 0,
CHAR = 1,
NUMERIC = 2,
DECIMAL = 3,
INTEGER = 4,
SMALLINT = 5,
FLOAT = 6,
REAL = 7,
DOUBLE = 8,
VARCHAR = 12,
DATE = 91,
TIME = 92,
TIMESTAMP = 93,
OTHER = 1111
)

stats::setNames(
structure(
0:6,
c("OFF", "FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE")
) -> .ll_trans
.Names = c(
"OFF", "FATAL", "ERROR", "WARNING", "INFO", "DEBUG", "TRACE"
)
)-> .ll_trans

#' AthenaJDBC
#'
@@ -85,10 +63,8 @@ setMethod(
max_error_retries = 10,
connection_timeout = 10000,
socket_timeout = 10000,
# retry_base_delay = 100,
# retry_max_backoff_time = 1000,
log_path,
log_level,
log_path = "",
log_level = 0,
...) {

conn_string = sprintf(
@@ -105,8 +81,6 @@ setMethod(
MaxErrorRetry = max_error_retries,
ConnectTimeout = connection_timeout,
SocketTimeout = socket_timeout,
# retry_base_delay = retry_base_delay,
# retry_max_backoff_time = retry_max_backoff_time,
LogPath = log_path,
LogLevel = log_level,
AwsCredentialsProviderClass = provider,
@@ -149,86 +123,6 @@ setMethod(
#' 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, type_convert=FALSE, ...) {

r <- dbSendQuery(conn, statement, ...)

on.exit(.jcall(r@stat, "V", "close"))

structure(
list(
cols = list(),
default = structure(list(), class = c("collector_guess", "collector"))
),
class = "col_spec"
) -> l

cols <- .jcall(r@md, "I", "getColumnCount")
nms <- c()

cts <- rep(0L, cols)
for (i in 1:cols) {
ct <- .jcall(r@md, "I", "getColumnType", i)
if (ct == .jt$CHAR) {
l$cols[[i]] <- col_character()
} else if (ct == .jt$NUMERIC) {
l$cols[[i]] <- col_double()
} else if (ct == .jt$DECIMAL) {
l$cols[[i]] <- col_double()
} else if (ct == .jt$INTEGER) {
l$cols[[i]] <- col_integer()
} else if (ct == .jt$SMALLINT) {
l$cols[[i]] <- col_integer()
} else if (ct == .jt$TINYINT) {
l$cols[[i]] <- col_integer()
} else if (ct == .jt$BIGINT) {
l$cols[[i]] <- col_double()
} else if (ct == .jt$FLOAT) {
l$cols[[i]] <- col_double()
} else if (ct == .jt$REAL) {
l$cols[[i]] <- col_double()
} else if (ct == .jt$DOUBLE) {
l$cols[[i]] <- col_double()
} else if (ct == .jt$VARCHAR) {
l$cols[[i]] <- col_character()
} else if (ct == .jt$DATE) {
l$cols[[i]] <- col_date()
} else if (ct == .jt$TIME) {
l$cols[[i]] <- col_time()
} else if (ct == .jt$TIMESTAMP) {
l$cols[[i]] <- col_datetime()
} else if (ct == .jt$BIT) {
l$cols[[i]] <- col_logical()
} else {
l$cols[[i]] <- col_character()
}
nms[i] <- .jcall(r@md, "S", "getColumnLabel", i)
}

l$cols <- stats::setNames(l$cols, nms)

res <- fetch(r, -1, block=1000)
res <- readr::type_convert(res, col_types = l)

class(res) <- c("tbl_df", "tbl", "data.frame")

res

}

)
#' AthenaJDBC
#'
#' @param conn Athena connection
#' @param pattern table name pattern
#' @param schema Athena schema name
#' @param ... unused


+ 5
- 19
R/metis-lite-package.R Näytä tiedosto

@@ -10,16 +10,7 @@
#'
#' 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`:
#'
#'
#' @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
#' 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`:
#'
@@ -30,24 +21,19 @@
#' )
#' }
#'
#' @md
#' @encoding UTF-8
#' @keywords internal
#' @docType package
#' @author Bob Rudis (bob@@rud.is)
#' @import RJDBC
#' @keywords internal
#' @import DBI
#' @import dplyr
#' @importFrom jsonlite fromJSON
#' @importFrom readr type_convert
#' @importFrom uuid UUIDgenerate
#' @importFrom sys exec_internal
#' @importFrom aws.signature use_credentials read_credentials
#' @import RJDBC DBI bit64 dbplyr
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


+ 71
- 0
R/z-dbGetQuery.R Näytä tiedosto

@@ -0,0 +1,71 @@
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
"1111" = as.character # OTHER
) -> .jdbc_converters

#' 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, type_convert=FALSE, ...) {

r <- dbSendQuery(conn, statement, ...)

on.exit(.jcall(r@stat, "V", "close"))

#message("dbGetQuery()")

nms <- c()
athena_type_convert <- list()

cols <- .jcall(r@md, "I", "getColumnCount")

for (i in 1:cols) {
ct <- as.character(.jcall(r@md, "I", "getColumnType", i))
athena_type_convert[[i]] <- .jdbc_converters[[ct]]
nms <- c(nms, .jcall(r@md, "S", "getColumnLabel", i))
}

athena_type_convert <- set_names(athena_type_convert, nms)

res <- fetch(r, -1, block = 1000)

for (nm in names(athena_type_convert)) {
res[[nm]] <- athena_type_convert[[nm]](res[[nm]])
}

class(res) <- c("tbl_df", "tbl", "data.frame")

res

}

)

+ 2
- 2
man/Athena.Rd Näytä tiedosto

@@ -8,9 +8,9 @@
\usage{
Athena(identifier.quote = "`")

\method{db_data_type}{AthenaConnection}(con, fields, ...)
db_data_type.AthenaConnection(con, fields, ...)

\method{sql_translate_env}{AthenaConnection}(con)
sql_translate_env.AthenaConnection(con)
}
\description{
AthenaJDBC


+ 2
- 2
man/dbConnect-AthenaDriver-method.Rd Näytä tiedosto

@@ -10,8 +10,8 @@
region = "us-east-1",
s3_staging_dir = Sys.getenv("AWS_S3_STAGING_DIR"),
schema_name = "default", max_error_retries = 10,
connection_timeout = 10000, socket_timeout = 10000, log_path,
log_level, ...)
connection_timeout = 10000, socket_timeout = 10000, log_path = "",
log_level = 0, ...)
}
\arguments{
\item{provider}{JDBC auth provider (ideally leave default)}


+ 1
- 1
man/dbGetQuery-AthenaConnection-character-method.Rd Näytä tiedosto

@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jdbc.r
% Please edit documentation in R/z-dbGetQuery.R
\docType{methods}
\name{dbGetQuery,AthenaConnection,character-method}
\alias{dbGetQuery,AthenaConnection,character-method}


+ 9
- 19
man/metis.lite.Rd Näytä tiedosto

@@ -15,25 +15,15 @@ is included along with an interface to the 'AWS' command-line utility.


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`:



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")
)
}
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")
)
}
}
}

\author{


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