From cea670e412536becf1ade4edf8d7ec9df19c0cc8 Mon Sep 17 00:00:00 2001
From: boB Rudis <bob@rud.is>
Date: Sat, 16 Feb 2019 06:52:27 -0500
Subject: [PATCH] update

---
 .Rbuildignore                                      |   1 +
 DESCRIPTION                                        |  10 +-
 LICENSE                                            |   2 +
 LICENSE.md                                         |  21 ++++
 NAMESPACE                                          |  10 +-
 R/a-utils.R                                        |  12 +++
 R/jdbc.r                                           | 120 ++-------------------
 R/metis-lite-package.R                             |  24 +----
 R/z-dbGetQuery.R                                   |  71 ++++++++++++
 man/Athena.Rd                                      |   4 +-
 man/dbConnect-AthenaDriver-method.Rd               |   4 +-
 ...dbGetQuery-AthenaConnection-character-method.Rd |   2 +-
 man/metis.lite.Rd                                  |  28 ++---
 13 files changed, 140 insertions(+), 169 deletions(-)
 create mode 100644 LICENSE
 create mode 100644 LICENSE.md
 create mode 100644 R/a-utils.R
 create mode 100644 R/z-dbGetQuery.R

diff --git a/.Rbuildignore b/.Rbuildignore
index edf18c6..f31e09b 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,4 @@
+^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
diff --git a/DESCRIPTION b/DESCRIPTION
index 977e571..849a9c7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -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
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..b6a10f1
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2019
+COPYRIGHT HOLDER: Bob Rudis
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..c36552c
--- /dev/null
+++ b/LICENSE.md
@@ -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.
diff --git a/NAMESPACE b/NAMESPACE
index c14e274..e85874e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -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)
diff --git a/R/a-utils.R b/R/a-utils.R
new file mode 100644
index 0000000..17268fa
--- /dev/null
+++ b/R/a-utils.R
@@ -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")
+}
diff --git a/R/jdbc.r b/R/jdbc.r
index d99a140..3859cbc 100644
--- a/R/jdbc.r
+++ b/R/jdbc.r
@@ -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
diff --git a/R/metis-lite-package.R b/R/metis-lite-package.R
index 3d72b10..11f6182 100644
--- a/R/metis-lite-package.R
+++ b/R/metis-lite-package.R
@@ -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
diff --git a/R/z-dbGetQuery.R b/R/z-dbGetQuery.R
new file mode 100644
index 0000000..5440275
--- /dev/null
+++ b/R/z-dbGetQuery.R
@@ -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
+
+  }
+
+)
\ No newline at end of file
diff --git a/man/Athena.Rd b/man/Athena.Rd
index 0f5dfa5..f919af0 100644
--- a/man/Athena.Rd
+++ b/man/Athena.Rd
@@ -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
diff --git a/man/dbConnect-AthenaDriver-method.Rd b/man/dbConnect-AthenaDriver-method.Rd
index 0db47cd..98d65e2 100644
--- a/man/dbConnect-AthenaDriver-method.Rd
+++ b/man/dbConnect-AthenaDriver-method.Rd
@@ -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)}
diff --git a/man/dbGetQuery-AthenaConnection-character-method.Rd b/man/dbGetQuery-AthenaConnection-character-method.Rd
index aa9b744..6261007 100644
--- a/man/dbGetQuery-AthenaConnection-character-method.Rd
+++ b/man/dbGetQuery-AthenaConnection-character-method.Rd
@@ -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}
diff --git a/man/metis.lite.Rd b/man/metis.lite.Rd
index fb17bc6..511f31c 100644
--- a/man/metis.lite.Rd
+++ b/man/metis.lite.Rd
@@ -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{