Add open_marker_symbol_in_mgi()

- Renamed `open_marker_in_mgi()` to `open_marker_id_in_mgi()`
- Add `open_marker_symbol_in_mgi()`

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mgi.report.reader
 Title: Read Mouse Genome Informatics Reports
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: c(
     person("Ramiro", "Magno", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5226-3441")),

NAMESPACE

@@ -3,7 +3,8 @@
 export(chromosomes)
 export(feature_types)
 export(marker_types)
-export(open_marker_in_mgi)
+export(open_marker_id_in_mgi)
+export(open_marker_symbol_in_mgi)
 export(read_report)
 export(report_example)
 export(report_file)

NEWS.md

@@ -7,7 +7,10 @@
 keyed column for improved look-up performance.
 * Mappings from symbols to symbols/identifiers is backed up by memoised functions
 making interactive experience a bit nicer.
-* Added bundled tiny examples of MRK_List1.rpt, accessible with `report_example()`.
+* Added bundled tiny examples of MRK_List1.rpt, accessible with
+`report_example()`, for examples and unit tests.
+* Renamed `open_marker_in_mgi()` to `open_marker_id_in_mgi()`, and added
+`open_marker_symbol_in_mgi()`.
 
 # mgi.report.reader 0.1.2
 

R/browser.R

@@ -35,9 +35,9 @@ mgi_reports_index_md <- function() {
   paste0("[MGI Reports Index](",mgi_reports_index_url(),")")
 }
 
-#' Browse MGI markers online
+#' Browse MGI markers identifiers online
 #'
-#' [open_marker_in_mgi()] launches the web browser and opens a tab for each MGI
+#' [open_marker_id_in_mgi()] launches the web browser and opens a tab for each MGI
 #' accession identifier on the Mouse Genome Informatics web interface:
 #' \url{https://www.informatics.jax.org}.
 #'
@@ -48,14 +48,14 @@ mgi_reports_index_md <- function() {
 #'
 #' @examples
 #' # Read about Acta1 (actin alpha 1, skeletal muscle) online.
-#' open_marker_in_mgi("MGI:87902")
+#' open_marker_id_in_mgi("MGI:87902")
 #'
-#' # `open_marker_in_mgi()` is vectorized, so you can open multiple pages.
+#' # `open_marker_id_in_mgi()` is vectorized, so you can open multiple pages.
 #' # NB: think twice if you really need to open many tabs at once.
-#' open_marker_in_mgi(c("MGI:87902", "MGI:87909"))
+#' open_marker_id_in_mgi(c("MGI:87902", "MGI:87909"))
 #'
 #' @export
-open_marker_in_mgi <- function(marker_id) {
+open_marker_id_in_mgi <- function(marker_id) {
   if (!(all(is_mgi_identifier(marker_id))))
     stop("`marker_id` must be a character vector of valid MGI identifiers.")
 
@@ -75,3 +75,42 @@ open_marker_in_mgi <- function(marker_id) {
     return(invisible(TRUE))
   }
 }
+
+#' Browse MGI markers symbols online
+#'
+#' [open_marker_symbol_in_mgi()] launches the web browser and opens a tab for each MGI
+#' symbol on the Mouse Genome Informatics web interface:
+#' \url{https://www.informatics.jax.org}.
+#'
+#' @inheritParams common-args
+#'
+#' @returns Returns `TRUE` if successful, or `FALSE` otherwise. But note that
+#'   this function is run for its side effect of launching the browser.
+#'
+#' @examples
+#' # Read about Acta1 (actin alpha 1, skeletal muscle) online.
+#' open_marker_symbol_in_mgi("Acta1")
+#'
+#' # `open_marker_symbol_in_mgi()` is vectorized, so you can open multiple pages.
+#' # NB: think twice if you really need to open many tabs at once.
+#' open_marker_symbol_in_mgi(c("Acta1", "Hes1"))
+#'
+#' @export
+open_marker_symbol_in_mgi <- function(marker_symbol) {
+
+  if (interactive()) {
+    msg <- paste("You are about to open",
+                 length(marker_symbol),
+                 "pages in your browser.")
+    if (length(marker_symbol) > 10L)
+      if (!sure(before_question = msg))
+        return(invisible(FALSE))
+
+    urls <- paste0(mgi_base_url(), "/quicksearch/summary?queryType=exactPhrase&query=", marker_symbol)
+    lapply(urls, utils::browseURL)
+
+    return(invisible(TRUE))
+  } else {
+    return(invisible(TRUE))
+  }
+}

R/docs.R

@@ -4,6 +4,7 @@
 #' `r desc_package_name()`.
 #'
 #' @param marker_id A character vector. MGI accession identifiers.
+#' @param marker_symbol A character vector. MGI marker symbols.
 #'
 #' @param report_key A character vector. A key used to uniquely refer to an MGI
 #'   report.

_pkgdown.yml

@@ -77,6 +77,7 @@ reference:
   - marker_types
   - feature_types
 
-- subtitle: Helpers
+- subtitle: Browse MGI Webserver
   contents:
-  - open_marker_in_mgi
+  - open_marker_id_in_mgi
+  - open_marker_symbol_in_mgi