Add EML object as an alternative option for metadata_path

.travis.yml

@@ -5,11 +5,13 @@ r:
   - oldrel
   - release
   - devel
+r_packages: ncdf4
 sudo: false
 cache: packages
 addons:
   apt:
+    update: true
     packages:
       - librdf0-dev
       - libnetcdf-dev
-      - r-cran-ncdf4
+      - netcdf-bin

DESCRIPTION

@@ -15,27 +15,27 @@ Depends:
     R (>= 3.2.3)
 Imports:
     digest,
-    dplyr,
     dataone,
     datapack,
     EML,
     httr,
     methods,
-    ncdf4,
     stringr,
     stringi,
     tools,
     uuid,
-    yaml,
     xml2,
     XML
 License: MIT + file LICENSE
 LazyData: true
 Suggests:
+    dplyr,
     testthat,
     humaniformat,
     knitr,
+    ncdf4,
     rmarkdown,
+    yaml,
     xslt
 RoxygenNote: 6.0.1
 VignetteBuilder: knitr

R/attributes.R

@@ -12,6 +12,12 @@
 get_ncdf4_attributes <- function(nc) {
   stopifnot(is(nc, "ncdf4") || file.exists(nc))
 
+  if (!requireNamespace("ncdf4")) {
+    stop(call. = FALSE, 
+         "The package 'ncdf4' must be installed to run this function. ",
+         "Please install it and try again.")
+  }
+
   # Read the file in if `nc` is a character vector
   if (is.character(nc)) {
     nc <- ncdf4::nc_open(nc)

R/editing.R

@@ -233,7 +233,7 @@ update_object <- function(mn, pid, path, format_id=NULL, new_pid=NULL, sid=NULL)
 #' @param parent_data_pids (character)  Optional. Identifier for the data objects of the parent package. Not optional if the parent package contains data objects.
 #' @param parent_child_pids (character) Optional. Resource map identifier(s) of child packages in the parent package.  \code{resource_map_pid} should not be included. Not optional if the parent package contains other child packages.
 #' @param child_pids (character) Optional. Child packages resource map PIDs.
-#' @param metadata_path (character) Optional. Path to a metadata file to update with. If this is not set, the existing metadata document will be used.
+#' @param metadata_path (character or eml) Optional. An eml class object or a path to a metadata file to update with. If this is not set, the existing metadata document will be used.
 #' @param public (logical) Optional. Make the update public. If FALSE, will set the metadata and resource map to private (but not the data objects).
 #' This applies to the new metadata PID and its resource map and data object.
 #' access policies are not affected.
@@ -367,6 +367,15 @@ publish_update <- function(mn,
     # Get the metadata doc
     message("Getting metadata from the MN.")
     eml <- EML::read_eml(rawToChar(dataone::getObject(mn, metadata_pid)), asText = TRUE)
+
+  } else if(class(metadata_path) == "eml") {
+      # If an eml object is provided, use it directly after validating
+      if(!eml_validate(metadata_path)){
+        stop("The EML object is not valid.")
+      }
+
+      eml <- metadata_path
+
   } else {
     # Alternatively, read an edited metadata file from disk if provided
     if (!file.exists(metadata_path)) {

R/environment.R

@@ -38,6 +38,12 @@ env_get <- function() {
 #'
 #'
 env_load <- function(name=NULL, path=NULL, skip_mn=FALSE) {
+  if (!requireNamespace("yaml")) {
+    stop(call. = FALSE, 
+         "The package 'yaml' must be installed to run this function. ",
+         "Please install it and try again.")
+  }
+
   # Determine the environment to load
   if (is.null(name)) {
     name <- env_get()

R/util.R

@@ -109,6 +109,12 @@ get_netcdf_format_id <- function(path) {
             nchar(path) > 0,
             file.exists(path))
 
+  if (!requireNamespace("ncdf4")) {
+    stop(call. = FALSE, 
+         "The package 'ncdf4' must be installed to run this function. ",
+         "Please install it and try again.")
+  }
+
   # Try to open the file, capturing errors
   cdf_file <- try({
     ncdf4::nc_open(path)