adding messages to functions for backwards compatibility and converti…

…ng secchi_estimated column to logical

R/open.R

@@ -45,7 +45,11 @@ open_database <- function() {
 #' @export
 
 open_fish <- function(con, quiet = FALSE) {
-  if (is.null(con)) {
+  if (any(lapply(show_cache(), tools::file_ext) == "parquet")) {
+    stop("Parquet files detected in cache. This version of deltafish uses SQLite as the backend. Please run clear_cache(), then create_fish_db() to update your local copy.")
+  }
+
+  if (missing(con)) {
     stop("argument 'con' must be provided. This should be the object created by open_database()")
   }
 
@@ -67,7 +71,11 @@ open_fish <- function(con, quiet = FALSE) {
 #' @export
 
 open_survey <- function(con) {
-  if (is.null(con)) {
+  if (any(lapply(show_cache(), tools::file_ext) == "parquet")) {
+    stop("Parquet files detected in cache. This version of deltafish uses SQLite as the backend. Please run clear_cache(), then create_fish_db() to update your local copy.")
+  }
+
+  if (missing(con)) {
     stop("argument 'con' must be provided. This should be the object created by open_database()")
   }
 
@@ -85,7 +93,11 @@ open_survey <- function(con) {
 #' @export
 
 open_length_conv <- function(con) {
-  if (is.null(con)) {
+  if (any(lapply(show_cache(), tools::file_ext) == "parquet")) {
+    stop("Parquet files detected in cache. This version of deltafish uses SQLite as the backend. Please run clear_cache(), then create_fish_db() to update your local copy.")
+  }
+
+  if (missing(con)) {
     stop("argument 'con' must be provided. This should be the object created by open_database()")
   }
 
@@ -98,9 +110,11 @@ open_length_conv <- function(con) {
 #' Collect data into R and convert dates/datetimes into the correct data types with the correct time zone.
 #' It is recommended to use this function instead of \code{collect} because the database RSQLite does not
 #' support date and time data types, so they are stored as character vectors.
-#' Although some date and time operations are still posssible, when you \code{collect} the dataset, the
+#' Although some date and time operations are still possible, when you \code{collect} the dataset, the
 #' Date and Datetime columns will be character vectors. This function will convert those columns
 #' (if they exist in your collected dataset) into the correct date and datetime format.
+#' RSQLite also does not have a logical data type and logical values are stored as integers.
+#' Thus, the Secchi_estimated column is converted to logical by this function as well.
 #'
 #' @param data A DBI table that can be treated like a data.frame. See `open_fish()` and `open_survey()`
 #' @importFrom magrittr %>%
@@ -122,6 +136,13 @@ collect_data <- function(data) {
       } else {
         .
       }
+    } %>%
+    {
+      if ("Secchi_estimated" %in% names(.)) {
+        dplyr::mutate(., Secchi_estimated = as.logical(.data$Secchi_estimated))
+      } else {
+        .
+      }
     }
 }
 
@@ -132,8 +153,8 @@ collect_data <- function(data) {
 #' @param con A DBI connection object from open_database()
 #'
 #' @export
-close_database <- function(con) {
-  if (is.null(con)) {
+close_database <- function(con = NULL) {
+  if (missing(con)) {
     stop("argument 'con' must be provided. This should be the object created by open_database()")
   }
   DBI::dbDisconnect(con)

tests/testthat/test-07_collect_data.R

@@ -6,24 +6,26 @@ raw <- open_survey(con) %>%
   summarise(
     N = n(),
     N_NA_Date = sum(as.integer(is.na(Date)), na.rm = T),
-    N_NA_Datetime = sum(as.integer(is.na(Datetime)), na.rm = T)
+    N_NA_Datetime = sum(as.integer(is.na(Datetime)), na.rm = T),
+    N_SE_1 = sum(Secchi_estimated, na.rm = T)
   ) %>%
   collect()
 
-raw_no_dates <- open_survey(con) %>%
-  select(-Date, -Datetime) %>%
+raw_no_dates_SE <- open_survey(con) %>%
+  select(-Date, -Datetime, -Secchi_estimated) %>%
   collect()
 
 col <- open_survey(con) %>%
   collect_data() %>%
   summarise(
     N = n(),
     N_NA_Date = sum(as.integer(is.na(Date))),
-    N_NA_Datetime = sum(as.integer(is.na(Datetime)))
+    N_NA_Datetime = sum(as.integer(is.na(Datetime))),
+    N_SE_T = sum(Secchi_estimated, na.rm = T)
   )
 
-col_no_dates <- open_survey(con) %>%
-  select(-Date, -Datetime) %>%
+col_no_dates_SE <- open_survey(con) %>%
+  select(-Date, -Datetime, -Secchi_estimated) %>%
   collect_data()
 
 post_filt_date <- open_survey(con) %>%
@@ -56,7 +58,7 @@ test_that("collect_data does not change number of rows of survey dataset", {
 })
 
 test_that("collect_data does not change the dataset when the date and datetime columns are missing", {
-  expect_equal(raw_no_dates, col_no_dates)
+  expect_equal(raw_no_dates_SE, col_no_dates_SE)
 })
 
 test_that("collect_data does not change number of rows with NA dates", {
@@ -67,6 +69,10 @@ test_that("collect_data does not change number of rows with NA datetimes", {
   expect_equal(raw$N_NA_Datetime, col$N_NA_Datetime)
 })
 
+test_that("collect_data does not change number of TRUE values for Secchi_estimated", {
+  expect_equal(raw$N_SE_1, col$N_SE_T)
+})
+
 test_that("Filtering by date works correctly", {
   expect_equal(pre_filt_date, post_filt_date)
   expect_equal(pre_filt_date2, post_filt_date)