Do not expect numeric UIDs but expect that they are coercible to numeric

R/ena2ncbi.R

@@ -2,7 +2,7 @@
 #'
 #' Take a vector of ENA accessions and convert them to NCBI accessions.
 #' @param accessions character; a vector or ENA accessions.
-#' @param type character; type of accessions. Supported types: `sample`, 
+#' @param type character; type of ENA accessions. Supported types: `sample`, 
 #' `study`.
 #' @return A tibble with two columns, `ena` and `ncbi`.
 #' @examples

R/ncbi2ena.R

@@ -2,8 +2,8 @@
 #'
 #' Take a vector of NCBI accessions and convert them to ENA accessions.
 #' @param accessions character; a vector or ENA accessions.
-#' @param type character; type of accessions. Supported types: `biosample`, 
-#' `bioproject`.
+#' @param type character; type of NCBI accessions. Supported types:
+#' `biosample`, `bioproject`.
 #' @return A tibble with two columns, `ncbi` and `ena`.
 #' @examples
 #' ncbi2ena("SAMEA111452506", type = "biosample")

R/ncbi_get_meta.R

@@ -150,9 +150,7 @@ ncbi_get_meta <- function(
     if ("ncbi_uid" %in% class(query)) {
       query <- query$uid
     }
-    if (!is.numeric(query)) {
-      stop("Query must be an ncbi_uid object or a numeric vector or UIDs.")
-    }
+    query <- as_numeric(query)
     idlist <- get_idlist(query, batch_size, verbose)
     res <- sapply(idlist, function(x) {
       foo_from_ids(x, db = db)

R/ncbi_get_summary.R

@@ -81,9 +81,7 @@ ncbi_get_summary <- function(
       }
       return(res)
     }
-    if (!is.numeric(query)) {
-      stop("Query must be an ncbi_uid object or a numeric vector or UIDs.")
-    }
+    query <- as_numeric(query)
     idlist <- get_idlist(query, batch_size = batch_size, verbose = verbose)
     res <- lapply(idlist, function(x) {
       foo_from_ids(x, db = db, verbose = verbose)

R/ncbi_link_uid.R

@@ -92,7 +92,7 @@ ncbi_link_uid <- function(
   foo_from_ids <- function(x, from, to) {
     if (length(x) == 1 && is.na(x)) {
       if (verbose) message("No valid UIDs.")
-      return(tibble::tibble(query = x, uid = NA_real_))
+      return(tibble::tibble(query = x, uid = NA_integer_))
     }
     id_hit <- suppressWarnings(wrap(
         "entrez_link",
@@ -131,9 +131,7 @@ ncbi_link_uid <- function(
   } else {
     query_vector <- query
   }
-  if (!is.numeric(query_vector)) {
-    stop("Query must be an ncbi_uid object or a numeric vector or UIDs.")
-  }
+  query_vector <- as_numeric(query_vector)
   idlist <- get_idlist(query_vector, batch_size, verbose)
   res <- lapply(idlist, function(x) {
     foo_from_ids(

R/ncbi_recover_id.R

@@ -44,8 +44,8 @@ ncbi_recover_id <- function(
       msg <- "Specify a 'db' argument or query an object of class 'ncbi_uid'."
       stop(msg)
     }
+    query <- as_numeric(query)
   }
-  db <- match.arg(db, ncbi_dbs())
   summaries <- ncbi_get_summary(
     query,
     db = db,
@@ -64,6 +64,8 @@ ncbi_recover_id <- function(
     id <- unname(sapply(summaries, function(x) x$accessionversion))
   } else if (db == "protein") {
     id <- unname(sapply(summaries, function(x) x$accessionversion))
+  } else if (db == "pubmed") {
+    id <- unname(sapply(summaries, function(x) x$uid))
   } else {
     stop("Not supported.")
   }

R/utils.R

@@ -204,4 +204,16 @@ get_mc_cores <- function(mc_cores, verbose = getOption("verbose")) {
     mc_cores <- n_cores
   }
   return(mc_cores)
+}
+
+#' Convert a vector to numeric
+#' 
+#' @param x vector; Vector to convert.
+#' @noRd
+as_numeric <- function(x) {
+  numeric_x <- suppressWarnings(as.numeric(x))
+  if (any(is.na(numeric_x) & !is.na(x))) {
+    stop("Query must be either an ncbi_uid object or a vector of UIDs.")
+  }
+  return(numeric_x)
 }

tests/testthat/test-ena2ncbi.R

@@ -34,3 +34,10 @@ test_that("ena2ncbi() removes invalid queries and returns the rest", {
   )
   expect_equal(dim(E), c(2,2))
 })
+
+test_that("ena2ncbi() works with studies", {
+  G <- ena2ncbi("ERP161024", type = "study")
+  expect_equal(dim(G), c(1,2))
+  expect_equal(names(G), c("ena", "ncbi"))
+  expect_equal(G$ncbi, "PRJEB76496")
+})

tests/testthat/test-ncbi_recover_id.R

@@ -27,3 +27,11 @@ test_that("ncbi_recover_id() works with nuccore", {
   id <- ncbi_recover_id(uid)
   expect_equal(id,"OP617744.1")
 })
+
+test_that("ncbi_recover_id() works with pubmed", {
+  uid <- ncbi_get_uid(examples$pubmed, db = "pubmed")
+  id1 <- ncbi_recover_id(uid)
+  id2 <- ncbi_recover_id(uid$uid, db = "pubmed")
+  expect_equal(id1, c("39332413", "36759752"))
+  expect_equal(id1, c("39332413", "36759752"))
+})