Do not require numeric uids but require that they are coercible

stitam · Dec 22, 2024 · 2e8b5f0 · 2e8b5f0
1 parent 8519771
commit 2e8b5f0
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Showing 4 changed files with 6 additions and 10 deletions.
diff --git a/R/ncbi_get_meta.R b/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)

diff --git a/R/ncbi_get_summary.R b/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)

diff --git a/R/ncbi_link_uid.R b/R/ncbi_link_uid.R
@@ -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(

diff --git a/R/ncbi_recover_id.R b/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.")
   }