adds database append functions

.lintr

@@ -0,0 +1,2 @@
+linters: with_defaults(line_length_linter(120))
+exclusions: list()

DESCRIPTION

@@ -1,29 +1,30 @@
-Package: nsqipr
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
-Authors@R: 
-    person(given = "Dylan",
-           family = "Russell",
-           role = c("aut", "cre"),
-           email = "dyl.russell@gmail.com",
-           comment = c(ORCID = "0000-0002-9543-9897"))
-Description: What the package does (one paragraph).
-License: CC0
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0
-Suggests: 
-    knitr,
-    rmarkdown,
-    testthat,
-    spelling
-VignetteBuilder: knitr
-URL: https://github.com/doctortickle/nsqipr
-BugReports: https://github.com/doctortickle/nsqipr/issues
-Language: en-US
-Imports: 
-    stringr,
-    DBI,
-    odbc,
-    readr
+Package: nsqipr
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person(given = "Dylan",
+           family = "Russell",
+           role = c("aut", "cre"),
+           email = "dyl.russell@gmail.com",
+           comment = c(ORCID = "0000-0002-9543-9897"))
+Description: What the package does (one paragraph).
+License: CC0
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.0
+Suggests: 
+    knitr,
+    rmarkdown,
+    testthat,
+    spelling
+VignetteBuilder: knitr
+URL: https://github.com/doctortickle/nsqipr
+BugReports: https://github.com/doctortickle/nsqipr/issues
+Language: en-US
+Imports: 
+    stringr,
+    DBI,
+    odbc,
+    readr,
+    magrittr

R/dbcon.R

@@ -1,52 +1,56 @@
-#conn <- DBI::dbconnnect(odbc::odbc(),
+#conn <- DBI::dbConnect(odbc::odbc(),
 #                      Driver   = nsqip_db_driver,
-#                      Server   = nsqip_db_ip, # Public IP of the PostgreSQL database
+#                      Server   = nsqip_db_ip,
 #                      Database = nsqip_db,
 #                      UID      = nsqip_db_user,
 #                      PWD      = nsqip_db_pw,
-#                      Port     = nsqip_db_port) # odbc() allows interface with RStudio connnections pane.
+#                      Port     = nsqip_db_port
+#)
 
-connDb <- function(driver, ip, db, port, user, pw) {
-  DBI::dbconnnect(odbc::odbc(),
-                 Driver = driver,
-                 Server = ip,
-                 Databse = db,
-                 Port = port,
-                 UID = user,
-                 PWD = pw
-                 )
-}
-
-addToNsqip <- function(file) {
-  df <- readr::read_delim(file,
-                    delim = "\t",
-                    na = c("","NA","-99","NULL")
-                    )
-  DBI::dbCreateTable(conn,
-                     name = 'puf',
-                     fields = df)
-  DBI::dbAppendTable(conn,
-                     name = 'puf',
-                     value = df)
-}
+#conn <- function(driver, ip, db, port, user, pw) {
+#  DBI::dbConnect(odbc::odbc(),
+#                 Driver = driver,
+#                 Server = ip,
+#                 Databse = db,
+#                 Port = port,
+#                 UID = user,
+#                 PWD = pw
+#                 )
+#}
 
-importData <- function(driver, ip, db, port, user, pw, dir) {
-  conn <- connDb(driver, ip, db, port, user, pw)
-  files <- list.files(path = dir, pattern = "*.txt", full.names = TRUE, recursive = FALSE)
-  lapply(files, writeData, conn)
+import_data_dir <- function(conn, dir) {
+  if (file_test("-d", dir)) {
+    files <- list.files(path = dir, pattern = "*.txt",
+                        full.names = TRUE, recursive = FALSE)
+    lapply(files, write_data, conn)
+  } else if (file_test("-f", dir)) {
+    write_data(conn, dir)
+  } else {
+    stop(paste(dir,'is an invalid file or directory path.', sep = " "))
+  }
 }
 
-writeData <- function(file, conn) {
-  createDF(file)
+write_data <- function(conn, file) {
+  df <- create_df(file)
+  tablename <- parse_filename(file)
+  if (!DBI::dbExistsTable(conn, tablename)) {
+    DBI::dbCreateTable(conn, tablename, df)
+  }
+  DBI::dbAppendTable(conn, tablename, df)
 }
 
-parseFilename <- function(file) {
-  pattern <- stringr::regex("acs_nsqip_puf|puf_tar_[a-z]{1,4}", ignore_case = TRUE)
+parse_filename <- function(file) {
+  pattern <- stringr::regex("acs_nsqip_puf|puf_tar_[a-z]{1,4}",
+                            ignore_case = TRUE)
   stopifnot(stringr::str_detect(file, pattern))
   tablename <- stringr::str_extract(file, pattern)
   stringr::str_to_lower(tablename)
 }
 
-assertTableExists <- function(conn, tablename) {
-  stopifnot(DBI::dbExistsTable(conn, tablename))
+create_df <- function(file) {
+  nas <- c("", "NA", "-99","NULL")
+  df <- readr::read_tsv(file, na = nas, guess_max = 30000,
+                          trim_ws = TRUE) %>%
+    dplyr::rename_all(tolower) %>%
+    dplyr::mutate(dplyr::across(where(is.character), stringr::str_to_sentence))
 }

R/utils-pipe.R

@@ -0,0 +1,11 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+NULL

nsqipr.Rproj

@@ -1,22 +1,22 @@
-Version: 1.0
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-LineEndingConversion: Posix
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

tests/spelling.R

@@ -1,3 +1,3 @@
-if(requireNamespace('spelling', quietly = TRUE))
+if (requireNamespace("spelling", quietly = TRUE))
   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
                              skip_on_cran = TRUE)

tests/testthat/test-dbcon.R

@@ -1,14 +1,13 @@
 testthat::test_that("parseFilename correctly picks out the table name", {
   testthat::expect_equal(parseFilename("puf_tar_cea_2015.txt"), "puf_tar_cea")
-  testthat::expect_equal(parseFilename('PUF_TAR_CEA_2015.txt'), "puf_tar_cea")
-  testthat::expect_equal(parseFilename('puf_tar_gyne_2015.txt'), "puf_tar_gyne")
-  testthat::expect_equal(parseFilename('PUF_TAR_GYNE_2015.txt'), "puf_tar_gyne")
-  testthat::expect_equal(parseFilename('puf_tar_hep_update_2015.txt'), "puf_tar_hep")
-  testthat::expect_equal(parseFilename('PUF_TAR_HEP_UPDATE_2015.TXT'), "puf_tar_hep")
+  testthat::expect_equal(parseFilename("PUF_TAR_CEA_2015.txt"), "puf_tar_cea")
+  testthat::expect_equal(parseFilename("puf_tar_gyne_2015.txt"), "puf_tar_gyne")
+  testthat::expect_equal(parseFilename("PUF_TAR_GYNE_2015.txt"), "puf_tar_gyne")
+  testthat::expect_equal(parseFilename("puf_tar_hep_update_2015.txt"), "puf_tar_hep")
+  testthat::expect_equal(parseFilename("PUF_TAR_HEP_UPDATE_2015.TXT"), "puf_tar_hep")
   testthat::expect_equal(parseFilename("acs_nsqip_puf_05_06_vr1.txt"), "acs_nsqip_puf")
   testthat::expect_equal(parseFilename("ACS_NSQIP_PUF_05_06_vr1.txt"), "acs_nsqip_puf")
   testthat::expect_equal(parseFilename("acs_nsqip_puf18.txt"), "acs_nsqip_puf")
   testthat::expect_equal(parseFilename("ACS_NSQIP_PUF18.txt"), "acs_nsqip_puf")
   testthat::expect_equal(parseFilename("ACS_NSQIP_PUF_05_06_vr1.txt"), "acs_nsqip_puf")
 })
-