diff --git a/base/db/R/check.missing.files.R b/base/db/R/check.missing.files.R index 29ce044f68..f3a496cf5d 100644 --- a/base/db/R/check.missing.files.R +++ b/base/db/R/check.missing.files.R @@ -1,7 +1,6 @@ #' Function to check if result has empty or missing files #' #' @param result A list of dataframes with file paths -#' @param outname Name of the output file #' @param existing.input Existing input records #' @param existing.dbfile Existing dbfile records #' @return A list of dataframes with file paths, a list of strings with the output file name, a list of existing input records, and a list of existing dbfile records diff --git a/base/db/R/convert_input.R b/base/db/R/convert_input.R index a074a68938..042c9da08d 100644 --- a/base/db/R/convert_input.R +++ b/base/db/R/convert_input.R @@ -380,7 +380,7 @@ convert_input <- if (!is.null(ensemble) && ensemble) { return.all <-TRUE - } else{ + } else { return.all <- FALSE } existing.dbfile <- dbfile.input.check(siteid = site.id, @@ -518,6 +518,10 @@ convert_input <- # Get machine information machine.info <- get.machine.info(host, input.args = input.args, input.id = input.id) + if (any(sapply(machine.info, is.null))) { + PEcAn.logger::logger.error("failed lookup of inputs or dbfiles") + return(NULL) + } machine <- machine.info$machine input <- machine.info$input dbfile <- machine.info$dbfile diff --git a/base/db/R/get.machine.info.R b/base/db/R/get.machine.info.R index 31f489dadd..14123a586e 100644 --- a/base/db/R/get.machine.info.R +++ b/base/db/R/get.machine.info.R @@ -18,7 +18,7 @@ get_machine_info <- function(host, input.args, input.id = NULL, con = NULL) { return(NULL) } - if (missing(input.id) || is.na(input.id) || is.null(input.id)) { + if (is.na(input.id) || is.null(input.id)) { input <- dbfile <- NULL } else { input <- db.query(paste("SELECT * from inputs where id =", input.id), con) @@ -71,7 +71,7 @@ get_machine_info <- function(host, input.args, input.id = NULL, con = NULL) { #' @param con database connection #' @return list of machine host and machine information #' @author Abhinav Pandey -get.machine.host <- function(host, con = NULL) { +get_machine_host <- function(host, con) { #Grab machine info of host machine machine.host <- ifelse(host$name == "localhost", PEcAn.remote::fqdn(), host$name) machine <- db.query(paste0( diff --git a/base/db/tests/testthat/test.check.missing.files.R b/base/db/tests/testthat/test.check.missing.files.R index bc61bb1ad4..75a531283d 100644 --- a/base/db/tests/testthat/test.check.missing.files.R +++ b/base/db/tests/testthat/test.check.missing.files.R @@ -1,7 +1,7 @@ test_that("`check_missing_files()` able to return correct missing files", { # Mock `purrr::map_dfr` - mocked_res <- mockery::mock(data.frame(file = c("A", "B"), file_size = c(100, 200), missing = c(FALSE, FALSE), empty = c(FALSE, FALSE))) - mockery::stub(check_missing_files, "purrr::map_dfr", mocked_res) + mocked_size <- mockery::mock(100,200) + mockery::stub(check_missing_files, "file.size", mocked_res) res <- check_missing_files( result = list(data.frame(file = c("A", "B"))), @@ -9,8 +9,6 @@ test_that("`check_missing_files()` able to return correct missing files", { existing.dbfile = data.frame() ) - # Print the structure of `res` for debugging - str(res) expect_equal(length(res), 2) expect_true(is.list(res[[1]]))