Merge pull request #104 from OuhscBbmc/dev

Dev
OuhscBbmc · Dec 10, 2019 · 4a789ff · 4a789ff
2 parents 015124a + 315844b
commit 4a789ff
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Showing 53 changed files with 258 additions and 127 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,7 @@ Package: OuhscMunge
 Title: Data Manipulation Operations
 Description: Data manipulation operations frequently used in OUHSC BBMC
     projects.
-Version: 0.1.9.9010
-Date: 2019-02-27
+Version: 0.1.9.9011
 Authors@R: person("Will", "Beasley", email="wibeasley@hotmail.com", role=c("aut", "cre"),
     comment = c(ORCID = "0000-0002-5613-5006"))
 URL: https://github.com/OuhscBbmc/OuhscMunge, http://ouhsc.edu/bbmc/
@@ -28,10 +27,10 @@ Imports:
     testit,
     tibble,
 Suggests:
-    odbc (>= 1.1.6),
+    odbc (>= 1.2.0),
     RODBC,
     RODBCext,
     testthat
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
diff --git a/R/execute-sql-file.R b/R/execute-sql-file.R
@@ -11,6 +11,8 @@
 #' (which typically returns a scalar).  Otherwise, `DBI::dbGetQuery()` is used,
 #' (which will return a `tibble::tibble`).  Required `logical`.
 #' @param minimum_row_count If `execute` is false, the returned dataset should have at least this many rows, or an error will be thrown.  Default of 0.  Required integer.
+#' @param timezone The server time zone.  Passed to [DBI::dbConnect()].
+#' @param timezone_out The time zone returned to R. Passed to [DBI::dbConnect()].  See https://www.tidyverse.org/blog/2019/12/odbc-1-2-0/.
 #'
 #' @return A vector of converted names.
 #'
@@ -22,17 +24,32 @@
 #' execute_sql_file("inst/condense-date.sql", "cdw_cache_staging")
 #' }
 
-execute_sql_file <- function( path_sql, dsn, execute=TRUE, minimum_row_count=0L ) {
+execute_sql_file <- function(
+  path_sql,
+  dsn,
+  execute                       = TRUE,
+  minimum_row_count             = 0L,
+  timezone                      = "UTC",
+  timezone_out                  = "UTC"
+) {
   checkmate::expect_file_exists(path_sql)
   checkmate::assert_character(path_sql, min.chars=2, min.len=1, max.len=1, any.missing=F)
   checkmate::assert_character(dsn     , min.chars=2, min.len=1, max.len=1, any.missing=F)
   checkmate::assert_logical(  execute              , len=1, any.missing=F)
+  checkmate::assert_character(timezone                                      , len=1L, any.missing=F)
+  checkmate::assert_character(timezone_out                                  , len=1L, any.missing=F)
 
   sql   <- readr::read_file(path_sql)
   checkmate::assert_character(sql     , min.chars=2, min.len=1, max.len=1, any.missing=F)
 
   tryCatch({
-    channel <- odbc::dbConnect(odbc::odbc(), dsn)
+    channel <- odbc::dbConnect(
+      odbc::odbc(),
+      dsn,
+      timezone      = timezone,
+      timezone_out  = timezone_out
+    )
+
     if( execute ) {
       returned_value <- DBI::dbExecute(channel, sql)
     } else {

diff --git a/R/snake-case.R b/R/snake-case.R
@@ -12,7 +12,8 @@
 #' @return A vector of converted names.
 #'
 #' @note This series of regexes has an advantages over the current
-#' implementations of [lettercase::str_snake_case()] and [`snakecase::to_snake_case()`].
+#' implementations of [`lettercase::str_snake_case()`](https://github.com/decisionpatterns/lettercase)
+#' and [`snakecase::to_snake_case()`].
 #' The former converts "PatientDOB" to "patientdob" and the latter converts
 #' "patient.dob" to "patient_._dob".  I'll keep an eye on these packages
 #' (*i.e.*, [lettercase #1](https://github.com/decisionpatterns/lettercase/issues/1) for 'camelCase'

diff --git a/R/upload-sqls-odbc.R b/R/upload-sqls-odbc.R
@@ -12,6 +12,8 @@
 #' @param create_table If the table structure has not yet been defined in the database, it will be created if `create_table` is `TRUE`.
 #' @param convert_logical_to_integer Convert all `logical` columns to `integer`.  This helps the database store the values as bits.
 #' @param transaction Should the clear and upload steps be wrapped in a rollback transaction?
+#' @param timezone The server time zone.  Passed to [DBI::dbConnect()].
+#' @param timezone_out The time zone returned to R. Passed to [DBI::dbConnect()].  See https://www.tidyverse.org/blog/2019/12/odbc-1-2-0/.
 #' @param verbose Write a message about the status of a successful upload.
 #'
 #' @details
@@ -33,7 +35,9 @@
 #'   clear_table                = TRUE,
 #'   transaction                = TRUE,
 #'   verbose                    = TRUE,
-#'   convert_logical_to_integer = TRUE
+#'   convert_logical_to_integer = TRUE,
+#'   timezone                   = "America/Chicago",
+#'   timezone_out               = "America/Chicago"
 #' )
 #' }
 
@@ -46,7 +50,10 @@ upload_sqls_odbc <- function(
   clear_table                   = FALSE,
   create_table                  = FALSE,
   convert_logical_to_integer    = FALSE,
+  timezone                      = "UTC",
+  timezone_out                  = "UTC",
   transaction                   = FALSE,
+
   verbose                       = TRUE
 ) {
 
@@ -59,6 +66,8 @@ upload_sqls_odbc <- function(
   checkmate::assert_logical(  create_table                                  , len=1L, any.missing=F)
   checkmate::assert_logical(  convert_logical_to_integer                    , len=1L, any.missing=F)
   checkmate::assert_logical(  transaction                                   , len=1L, any.missing=F)
+  checkmate::assert_character(timezone                                      , len=1L, any.missing=F)
+  checkmate::assert_character(timezone_out                                  , len=1L, any.missing=F)
   checkmate::assert_logical(  verbose                                       , len=1L, any.missing=F)
 
   start_time <- base::Sys.time()
@@ -95,8 +104,10 @@ upload_sqls_odbc <- function(
 
 
   channel <- DBI::dbConnect(
-    drv   = odbc::odbc(),
-    dsn   = dsn_name
+    drv           = odbc::odbc(),
+    dsn           = dsn_name,
+    timezone      = timezone,
+    timezone_out  = timezone_out
   )
 
   if( create_table) {

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/code-of-conduct.html b/docs/code-of-conduct.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/license.html b/docs/license.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.3.1
+pandoc: 2.7.2
 pkgdown: 1.4.1
 pkgdown_sha: ~
 articles: []

diff --git a/docs/reference/OuhscMunge.html b/docs/reference/OuhscMunge.html
diff --git a/docs/reference/assert.html b/docs/reference/assert.html
diff --git a/docs/reference/clump_date.html b/docs/reference/clump_date.html
diff --git a/docs/reference/cut_with_nas.html b/docs/reference/cut_with_nas.html
diff --git a/docs/reference/date_range.html b/docs/reference/date_range.html
diff --git a/docs/reference/deterge.html b/docs/reference/deterge.html
diff --git a/docs/reference/execute_sql_file.html b/docs/reference/execute_sql_file.html
diff --git a/docs/reference/first_nonmissing.html b/docs/reference/first_nonmissing.html