From 574c6c208a7a6b389397ca8d192a6434969472a7 Mon Sep 17 00:00:00 2001
From: Bryce Mecum <petridish@gmail.com>
Date: Mon, 11 Sep 2017 16:26:35 -0800
Subject: [PATCH] Remove usages of log_message in interactive functions

---
 R/access.R    |  42 +++++++++----------
 R/editing.R   |  38 ++++++++---------
 R/helpers.R   |   8 ++--
 R/inserting.R |   2 +-
 R/packaging.R | 114 +++++++++++++++++++++++++-------------------------
 R/sysmeta.R   |   4 +-
 6 files changed, 104 insertions(+), 104 deletions(-)

diff --git a/R/access.R b/R/access.R
index b427ae1..c1829a7 100644
--- a/R/access.R
+++ b/R/access.R
@@ -33,11 +33,11 @@ set_rights_holder <- function(mn, pids, subject) {
 
     # Change rightsHolder (if needed)
     if (sysmeta@rightsHolder == subject) {
-      log_message(paste0("rightsHolder field is already set to ", subject, ". System Metadata not updated."))
+      message(paste0("rightsHolder field is already set to ", subject, ". System Metadata not updated."))
       result[i] <- TRUE
     } else {
       # Update System Metadata
-      log_message(paste0("Updating rightsHolder for PID ", pid, " from ", sysmeta@rightsHolder, " to ", subject, "."))
+      message(paste0("Updating rightsHolder for PID ", pid, " from ", sysmeta@rightsHolder, " to ", subject, "."))
 
       sysmeta@rightsHolder <- subject
 
@@ -47,7 +47,7 @@ set_rights_holder <- function(mn, pids, subject) {
                                       sysmeta = sysmeta)
       },
       error = function(e) {
-        log_message(e)
+        message(e)
         e
       })
 
@@ -103,10 +103,10 @@ set_access <- function(mn, pids, subjects, permissions=c("read", "write", "chang
 
     if (changed) {
       result[pid] <- TRUE
-      log_message(paste0("Updating System Metadata for ", pid, "."))
+      message(paste0("Updating System Metadata for ", pid, "."))
       dataone::updateSystemMetadata(mn, pid, sysmeta)
     } else {
-      log_message(paste0("No changes needed for ", pid, ". Not updating."))
+      message(paste0("No changes needed for ", pid, ". Not updating."))
       result[pid] <- FALSE
     }
   }
@@ -154,8 +154,8 @@ remove_public_read <- function(mn, pids) {
       dataone::getSystemMetadata(mn, pid)
     },
     error = function(e) {
-      log_message(paste0("Failed to get system metadata for PID '", pid, "' on MN '", mn@endpoint, "'.\n"))
-      log_message(e)
+      message(paste0("Failed to get system metadata for PID '", pid, "' on MN '", mn@endpoint, "'.\n"))
+      message(e)
       e
     })
 
@@ -167,13 +167,13 @@ remove_public_read <- function(mn, pids) {
     changed <- FALSE
 
     if (!datapack::hasAccessRule(sysmeta, "public", "read")) {
-      log_message(paste0("Skipping setting public read because ", pid, " is not public."))
+      message(paste0("Skipping setting public read because ", pid, " is not public."))
       next
     }
 
     changed <- TRUE
 
-    log_message(paste0("Removing public read access on ", pid, "."))
+    message(paste0("Removing public read access on ", pid, "."))
     sysmeta@accessPolicy <- sysmeta@accessPolicy[!(grepl("public", sysmeta@accessPolicy$subject) & grepl("read", sysmeta@accessPolicy$permission)),]
 
     # Update the sysmeta
@@ -181,8 +181,8 @@ remove_public_read <- function(mn, pids) {
       dataone::updateSystemMetadata(mn, pid, sysmeta)
     },
     error = function(e) {
-      log_message(paste0("Failed to update System Metadata for PID '", pid, "'.\n"))
-      log_message(e)
+      message(paste0("Failed to update System Metadata for PID '", pid, "'.\n"))
+      message(e)
       e
     })
 
@@ -230,8 +230,8 @@ set_rights_and_access <- function(mn, pids, subject, permissions=c("read", "writ
       dataone::getSystemMetadata(mn, pid)
     },
     error = function(e) {
-      log_message(paste0("Failed to get system metadata for PID '", pid, "' on MN '", mn@endpoint, "'.\n"))
-      log_message(e)
+      message(paste0("Failed to get system metadata for PID '", pid, "' on MN '", mn@endpoint, "'.\n"))
+      message(e)
       e
     })
 
@@ -246,33 +246,33 @@ set_rights_and_access <- function(mn, pids, subject, permissions=c("read", "writ
     if (subject != sysmeta@rightsHolder) {
       changed <- TRUE
 
-      log_message(paste0("Setting rights holder to ", subject, "."))
+      message(paste0("Setting rights holder to ", subject, "."))
       sysmeta@rightsHolder <- subject
     } else {
-      log_message(paste0("Skipping setting rightsHolder as rightsHolder is already ", sysmeta@rightsHolder, ".\n"))
+      message(paste0("Skipping setting rightsHolder as rightsHolder is already ", sysmeta@rightsHolder, ".\n"))
     }
 
     for (permission in permissions) {
       if (datapack::hasAccessRule(sysmeta, subject, permission)) {
-        log_message(paste0("Skipping the addition of permission '", permission, "' for subject '", subject, "'\n"))
+        message(paste0("Skipping the addition of permission '", permission, "' for subject '", subject, "'\n"))
         next
       }
 
       changed <- TRUE
 
-      log_message(paste0("Adding permission '", permission, "' for subject '", subject, "'\n"))
+      message(paste0("Adding permission '", permission, "' for subject '", subject, "'\n"))
       sysmeta <- datapack::addAccessRule(sysmeta, subject, permission)
     }
 
     if (changed == TRUE) {
-      log_message(paste0("Updating System Metadata for ", pid, "."))
+      message(paste0("Updating System Metadata for ", pid, "."))
 
       update_response <- tryCatch({
         dataone::updateSystemMetadata(mn, pid, sysmeta)
       },
       error = function(e) {
-        log_message(paste0("Failed to update System Metadata for PID '", pid, "'.\n"))
-        log_message(e)
+        message(paste0("Failed to update System Metadata for PID '", pid, "'.\n"))
+        message(e)
         e
       })
 
@@ -280,7 +280,7 @@ set_rights_and_access <- function(mn, pids, subject, permissions=c("read", "writ
         stop("Failed update.")
       }
     } else {
-      log_message(paste0("No changes needed for ", pid, "."))
+      message(paste0("No changes needed for ", pid, "."))
     }
 
     # Save the result for this PID
diff --git a/R/editing.R b/R/editing.R
index 89efded..d9fdbb4 100644
--- a/R/editing.R
+++ b/R/editing.R
@@ -56,7 +56,7 @@ publish_object <- function(mn,
 
   # Get the clone_pid sysmeta to use for the rightsHolder and accessPolicy, and replicationPolicy
   if (!is.null(clone_pid)) {
-    log_message(paste0("Cloning System Metadata for new object from ", clone_pid, "."))
+    message(paste0("Cloning System Metadata for new object from ", clone_pid, "."))
     clone_sysmeta <- dataone::getSystemMetadata(mn, clone_pid)
   }
 
@@ -80,7 +80,7 @@ publish_object <- function(mn,
   sysmeta <- clear_replication_policy(sysmeta)
 
   if (!is.null(sid)) {
-    log_message(paste0("Setting SID to '", sid, "'."))
+    message(paste0("Setting SID to '", sid, "'."))
     sysmeta@seriesId <- sid
   }
 
@@ -143,7 +143,7 @@ update_object <- function(mn, pid, path, format_id=NULL, new_pid=NULL, sid=NULL)
          paste0("The format_id of '", format_id, "' is not a valid format ID. See https://cn.dataone.org/cn/v2/formats for the current list. This package stores a copy and may be out of date with that list so please email the author if needed."))
   }
 
-  log_message(paste0("Updating object ", pid, " with the file at ", path, "."))
+  message(paste0("Updating object ", pid, " with the file at ", path, "."))
 
   # Generate a PID if needed
   if (is.null(new_pid)) {
@@ -321,7 +321,7 @@ publish_update <- function(mn,
   # Get some things from the node
   if (is.null(metadata_path)) {
     # Get the metadata doc
-    log_message("Getting metadata from the MN.")
+    message("Getting metadata from the MN.")
     eml <- EML::read_eml(rawToChar(dataone::getObject(mn, metadata_pid)), asText = TRUE)
   } else {
     # Alternatively, read an edited metadata file from disk if provided
@@ -329,27 +329,27 @@ publish_update <- function(mn,
       stop(paste0("Metadata doesn't exist: ", metadata_path))
     }
 
-    log_message(paste0("Getting metadata from the path: ", metadata_path, "."))
+    message(paste0("Getting metadata from the path: ", metadata_path, "."))
     eml <- EML::read_eml(metadata_path)
   }
 
   # get the metadata sysmeta from the node
   metadata_sysmeta <- dataone::getSystemMetadata(mn, metadata_pid)
 
-  log_message("Downloaded EML and sysmeta...")
+  message("Downloaded EML and sysmeta...")
 
   # Generate PIDs for our updated objects
   if (is.null(identifier)) {
     if (use_doi) {
-      log_message("Minting a new DOI")
+      message("Minting a new DOI")
       metadata_updated_pid <- dataone::generateIdentifier(mn, scheme = "DOI")
-      log_message(paste0("Minted a new DOI of ", metadata_updated_pid, "."))
+      message(paste0("Minted a new DOI of ", metadata_updated_pid, "."))
     } else {
       metadata_updated_pid <- new_uuid()
-      log_message(paste0("Using generated UUID PID of ", metadata_updated_pid, "."))
+      message(paste0("Using generated UUID PID of ", metadata_updated_pid, "."))
     }
   } else {
-    log_message(paste0("Using manually-specified identifier of ", identifier, "."))
+    message(paste0("Using manually-specified identifier of ", identifier, "."))
     metadata_updated_pid <- identifier
   }
 
@@ -428,7 +428,7 @@ publish_update <- function(mn,
                     metadata_pid,
                     metadata_sysmeta@rightsHolder)
 
-  log_message(paste0("Updated metadata document ", metadata_pid, " with ", metadata_updated_pid, "."))
+  message(paste0("Updated metadata document ", metadata_pid, " with ", metadata_updated_pid, "."))
 
   # Update the resource map
   #########################
@@ -443,7 +443,7 @@ publish_update <- function(mn,
 
   set_rights_holder(mn, response[["resource_map"]], metadata_sysmeta@rightsHolder)
 
-  log_message("Updated resource map")
+  message("Updated resource map")
 
   # Update the parent resource map to add the new package
   #######################################################
@@ -452,12 +452,12 @@ publish_update <- function(mn,
       stop("Missing required parameters to update parent package.")
     }
 
-    log_message("Updating parent resource map...")
+    message("Updating parent resource map...")
 
     # Check to see if the just-updated package is in the list of
     # parent_child_pids, notify the user, and add it to the list
     if (!(resmap_updated_pid %in% parent_child_pids)) {
-      log_message("Adding the new resource map to the list of child PIDs in the parent package.")
+      message("Adding the new resource map to the list of child PIDs in the parent package.")
       parent_child_pids <- c(parent_child_pids, resmap_updated_pid)
     }
 
@@ -514,7 +514,7 @@ create_resource_map <- function(mn,
             nchar(metadata_pid) > 0)
 
   if (check_first) {
-    log_message("Checking all the object passed in as arguments exist before going on...")
+    message("Checking all the object passed in as arguments exist before going on...")
 
     stopifnot(object_exists(mn, metadata_pid))
     if (!is.null(data_pids))
@@ -598,7 +598,7 @@ update_resource_map <- function(mn,
             nchar(metadata_pid) > 0)
 
   if (check_first) {
-    log_message("Checking all the object passed in as arguments exist before going on...")
+    message("Checking all the object passed in as arguments exist before going on...")
 
     stopifnot(object_exists(mn, resource_map_pid))
     stopifnot(object_exists(mn, metadata_pid))
@@ -646,7 +646,7 @@ update_resource_map <- function(mn,
 
   rm(sysmeta)
 
-  log_message(paste0("Getting updated copy of System Metadata for ", resource_map_pid))
+  message(paste0("Getting updated copy of System Metadata for ", resource_map_pid))
   sysmeta <- dataone::getSystemMetadata(mn, resource_map_pid)
   stopifnot(class(sysmeta) == "SystemMetadata")
 
@@ -671,7 +671,7 @@ update_resource_map <- function(mn,
   }
 
   # Update it
-  log_message(paste0("Updating resource map..."))
+  message(paste0("Updating resource map..."))
   resmap_update_response <- dataone::updateObject(mn,
                                                   pid = resource_map_pid,
                                                   newpid = identifier,
@@ -686,7 +686,7 @@ update_resource_map <- function(mn,
     file.remove(new_rm_path)
   }
 
-  log_message(paste0("Successfully updated ", resource_map_pid, " with ", identifier, "."))
+  message(paste0("Successfully updated ", resource_map_pid, " with ", identifier, "."))
 
   return(resmap_update_response)
 }
diff --git a/R/helpers.R b/R/helpers.R
index 32148c0..c853398 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -36,7 +36,7 @@ create_dummy_metadata <- function(mn, data_pids=NULL) {
   sysmeta <- add_admin_group_access(sysmeta)
   sysmeta <- datapack::addAccessRule(sysmeta, "public", "read")
 
-  log_message(paste0("Creating metadata ", pid))
+  message(paste0("Creating metadata ", pid))
   pid <- dataone::createObject(mn, pid, metadata_file, sysmeta)
 
   # Remove the temporary EML File
@@ -77,7 +77,7 @@ create_dummy_object <- function(mn) {
   sysmeta <- add_admin_group_access(sysmeta)
   sysmeta <- datapack::addAccessRule(sysmeta, "public", "read")
 
-  log_message(paste0("Creating object ", pid))
+  message(paste0("Creating object ", pid))
   create_response <- dataone::createObject(mn, pid, tmp, sysmeta)
 
   file.remove(tmp)
@@ -134,7 +134,7 @@ create_dummy_package <- function(mn, size = 2) {
   sysmeta <- add_admin_group_access(sysmeta)
   sysmeta <- datapack::addAccessRule(sysmeta, "public", "read")
 
-  log_message(paste0("Creating resource map ", pid))
+  message(paste0("Creating resource map ", pid))
   resource_map_pid <- dataone::createObject(mn, pid, resmap_path, sysmeta)
 
   list(metadata = meta_pid,
@@ -178,7 +178,7 @@ create_dummy_parent_package <- function(mn, children) {
   sysmeta <- add_admin_group_access(sysmeta)
   sysmeta <- datapack::addAccessRule(sysmeta, "public", "read")
 
-  log_message(paste0("Creating parent package map ", pid))
+  message(paste0("Creating parent package map ", pid))
   create_response <- createObject(mn, pid, resmap_path, sysmeta)
 
   list(parent = create_response,
diff --git a/R/inserting.R b/R/inserting.R
index 702355e..34202a8 100644
--- a/R/inserting.R
+++ b/R/inserting.R
@@ -47,7 +47,7 @@ create_from_folder <- function(mn, path, data_pids=NULL) {
         publish_object(mn, data_path, data_format_ids[data_path])
       },
       error = function(e) {
-        log_message(e)
+        message(e)
         e
       })
 
diff --git a/R/packaging.R b/R/packaging.R
index 090c2dc..0b4cd18 100644
--- a/R/packaging.R
+++ b/R/packaging.R
@@ -27,7 +27,7 @@ insert_file <- function(inventory, file, env=NULL) {
   validate_environment(env)
 
   if (is_token_expired(env$mn)) {
-    log_message("Token is expired. Returning un-modified inventory.")
+    message("Token is expired. Returning un-modified inventory.")
     return(inventory)
   }
 
@@ -42,7 +42,7 @@ insert_file <- function(inventory, file, env=NULL) {
     identifier_scheme <- env$data_identifier_scheme
   }
 
-  log_message(paste0("Using identifier scheme ", identifier_scheme, "."))
+  message(paste0("Using identifier scheme ", identifier_scheme, "."))
 
   # Determine the PID to use
   inventory_file[1,"pid"] <- get_or_create_pid(inventory_file[1,],
@@ -50,7 +50,7 @@ insert_file <- function(inventory, file, env=NULL) {
                                                scheme = identifier_scheme)
 
   if (is.na(inventory_file[1,"pid"])) {
-    log_message(paste0("PID was NA for file ", file, ".\n"))
+    message(paste0("PID was NA for file ", file, ".\n"))
     return(inventory_file)
   }
 
@@ -61,7 +61,7 @@ insert_file <- function(inventory, file, env=NULL) {
                             env$rights_holder)
 
   if (is.null(sysmeta)) {
-    log_message(paste0("System Metadata creation failed for file ", file, ".\n"))
+    message(paste0("System Metadata creation failed for file ", file, ".\n"))
     return(inventory_file)
   }
 
@@ -73,7 +73,7 @@ insert_file <- function(inventory, file, env=NULL) {
   }
 
   if (inventory_file[1,"created"] == FALSE) {
-    log_message(paste0("Object creation failed for file ", file, ".\n"))
+    message(paste0("Object creation failed for file ", file, ".\n"))
     return(inventory_file)
   }
 
@@ -106,7 +106,7 @@ insert_package <- function(inventory, package, env=NULL) {
   validate_environment(env)
 
   if (is_token_expired(env$mn)) {
-    log_message("Token is expired. Returning un-modified inventory.")
+    message("Token is expired. Returning un-modified inventory.")
     return(inventory)
   }
 
@@ -148,7 +148,7 @@ insert_package <- function(inventory, package, env=NULL) {
                                                          scheme = env$metadata_identifier_scheme)
 
     if (is.na(files[files_idx_metadata,"pid"])) {
-      log_message(paste0("Metadata PID was NA for package ", package, ".\n"))
+      message(paste0("Metadata PID was NA for package ", package, ".\n"))
       return(files)
     }
 
@@ -159,7 +159,7 @@ insert_package <- function(inventory, package, env=NULL) {
                                        env$rights_holder)
 
     if (is.null(metadata_sysmeta)) {
-      log_message(paste0("System Metadata creation failed for metadata object in package ", package, ".\n"))
+      message(paste0("System Metadata creation failed for metadata object in package ", package, ".\n"))
       return(files)
     }
 
@@ -177,11 +177,11 @@ insert_package <- function(inventory, package, env=NULL) {
     }
 
     if (files[files_idx_metadata,"created"] == FALSE) {
-      log_message(paste0("Object creation failed for metadata object in package ", package, ".\n"))
+      message(paste0("Object creation failed for metadata object in package ", package, ".\n"))
       return(files)
     }
   } else {
-    log_message("Skipped creating metadata because it was already created.")
+    message("Skipped creating metadata because it was already created.")
   }
 
   # Insert data files if needed
@@ -190,11 +190,11 @@ insert_package <- function(inventory, package, env=NULL) {
     for (data_idx in files_idx_data) {
       # Skip if already created
       if (files[data_idx,"created"] == TRUE) {
-        log_message(paste0("File ", files[data_idx,"filename"], " in package ", package, " already created. Moving on to the next data object.\n"))
+        message(paste0("File ", files[data_idx,"filename"], " in package ", package, " already created. Moving on to the next data object.\n"))
         next
       }
 
-      log_message(paste0("Processing data index ", data_idx, " in package ", package, "\n"))
+      message(paste0("Processing data index ", data_idx, " in package ", package, "\n"))
 
       # Determine the PID to use for the data
       files[data_idx,"pid"] <- get_or_create_pid(files[data_idx,],
@@ -202,7 +202,7 @@ insert_package <- function(inventory, package, env=NULL) {
                                                  scheme = env$data_identifier_scheme)
 
       if (is.na(files[data_idx,"pid"])) {
-        log_message(paste0("Data PID was NA for file ", files[data_idx,'filename'], " in package ", package, ". Stopping early.\n"))
+        message(paste0("Data PID was NA for file ", files[data_idx,'filename'], " in package ", package, ". Stopping early.\n"))
         return(files)
       }
 
@@ -213,7 +213,7 @@ insert_package <- function(inventory, package, env=NULL) {
                                      env$rights_holder)
 
       if (is.null(metadata_sysmeta)) {
-        log_message(paste0("System Metadata creation failed for metadata object in package ", package, ".\n"))
+        message(paste0("System Metadata creation failed for metadata object in package ", package, ".\n"))
         return(files)
       }
 
@@ -226,35 +226,35 @@ insert_package <- function(inventory, package, env=NULL) {
       }
 
       if (files[data_idx,"created"] == FALSE) {
-        log_message(paste0("Object creation failed for metadata object in package ", package, ".\n"))
+        message(paste0("Object creation failed for metadata object in package ", package, ".\n"))
         return(files)
       }
     }
   } else {
-    log_message("Skipped creating data files because they were all created.")
+    message("Skipped creating data files because they were all created.")
   }
 
   # At this point, all of the metadata and data should be created, let's check
   if (!all(is.character(files[,"pid"])) && !all(files[,"created"] == TRUE)) {
-    log_message(paste0("Not all files in package ", package, " have PIDs and are created. Skipping Resource Map creation.\n"))
+    message(paste0("Not all files in package ", package, " have PIDs and are created. Skipping Resource Map creation.\n"))
     return(files)
   }
 
   # Generate and create() the Resource Map
-  log_message(paste0("Generating resource map for package ", package, ".\n"))
+  message(paste0("Generating resource map for package ", package, ".\n"))
   resource_map_pid <- generate_resource_map_pid(files[files_idx_metadata,"pid"])
   resource_map_filepath <- generate_resource_map(files[files_idx_metadata,"pid"],
                                                  files[files_idx_data,"pid"],
                                                  child_pids)
 
-  log_message(paste0("Resource map PID is ", resource_map_pid, " for package with metadata file ", files[files_idx_metadata,"file"], ".\n"))
+  message(paste0("Resource map PID is ", resource_map_pid, " for package with metadata file ", files[files_idx_metadata,"file"], ".\n"))
 
   resource_map_format_id <- "http://www.openarchives.org/ore/terms"
   resource_map_checksum <- digest::digest(resource_map_filepath, algo = "sha256")
   resource_map_size_bytes <- file.info(resource_map_filepath)$size
   resource_map_file_name <- paste0(stringr::str_replace_all(resource_map_pid, ":", "_"), ".xml")
 
-  log_message(paste0("Generating system metadata for resource map for package ", package, ".\n"))
+  message(paste0("Generating system metadata for resource map for package ", package, ".\n"))
   resource_map_sysmeta <- new("SystemMetadata",
                               identifier = resource_map_pid,
                               formatId = resource_map_format_id,
@@ -271,7 +271,7 @@ insert_package <- function(inventory, package, env=NULL) {
 
   resource_map_sysmeta <- add_access_rules(resource_map_sysmeta)
 
-  log_message(paste0("Creating resource map for package ", package, ".\n"))
+  message(paste0("Creating resource map for package ", package, ".\n"))
   create_resource_map_response <- NULL
   create_resource_map_response <- tryCatch({
     dataone::createObject(env$mn,
@@ -280,8 +280,8 @@ insert_package <- function(inventory, package, env=NULL) {
                           sysmeta = resource_map_sysmeta)
   },
   error = function(e) {
-    log_message(paste0("Error encountered while calling create() on the Resource Map for package ", package, ".\n"))
-    log_message(e$message)
+    message(paste0("Error encountered while calling create() on the Resource Map for package ", package, ".\n"))
+    message(e$message)
     e
   }
   )
@@ -295,7 +295,7 @@ insert_package <- function(inventory, package, env=NULL) {
     files$resmap_created <- TRUE
   }
 
-  log_message(print(files))
+  message(print(files))
 
   return(files)
 }
@@ -522,11 +522,11 @@ get_or_create_pid <- function(file, mn, scheme="UUID") {
 
   # Check if the existing PID is a valid one
   if (!is.na(pid) && is.character(pid) && nchar(pid) > 0) {
-    log_message(paste0("Using existing PID of ", pid, "\n"))
+    message(paste0("Using existing PID of ", pid, "\n"))
     return(pid)
   }
 
-  log_message(paste0("Minting new PID with scheme ", scheme, "\n"))
+  message(paste0("Minting new PID with scheme ", scheme, "\n"))
 
   if (scheme == "UUID") {
     pid <- paste0("urn:uuid:", uuid::UUIDgenerate())
@@ -538,8 +538,8 @@ get_or_create_pid <- function(file, mn, scheme="UUID") {
         dataone::generateIdentifier(mn, scheme)
       },
       error = function(e) {
-        log_message(paste0("Error generating identifier for file ", file[1,"file"], ".\n"))
-        log_message(e$message)
+        message(paste0("Error generating identifier for file ", file[1,"file"], ".\n"))
+        message(e$message)
         e
       }
     )
@@ -613,8 +613,8 @@ create_sysmeta <- function(file, base_path, submitter, rights_holder) {
 
     },
     error = function(e) {
-      log_message(paste0("Error generated during the call to create_sysmeta() for the metadata file ", file[1,"file"], "\n"))
-      log_message(e$message)
+      message(paste0("Error generated during the call to create_sysmeta() for the metadata file ", file[1,"file"], "\n"))
+      message(e$message)
       e
     }
   )
@@ -673,8 +673,8 @@ create_object <- function(file, sysmeta, base_path, mn) {
                             sysmeta = sysmeta)
     },
     error = function(e) {
-      log_message(paste0("Error generated during the call to MNStorage.create() for the metadata file ", file[1,"file"], "\n"))
-      log_message(e$message)
+      message(paste0("Error generated during the call to MNStorage.create() for the metadata file ", file[1,"file"], "\n"))
+      message(e$message)
       e
     })
 
@@ -689,14 +689,14 @@ create_object <- function(file, sysmeta, base_path, mn) {
   # Print out the insert rate
   time_diff_sec <- round(as.numeric(Sys.time() - before_time, "secs"), 2)
   mb_per_s <- round(file_size_mb / time_diff_sec, 2)
-  log_message(paste0("Inserted ", file_size_mb, " MB in ", time_diff_sec, " s (", mb_per_s, " MB/s)\n"))
+  message(paste0("Inserted ", file_size_mb, " MB in ", time_diff_sec, " s (", mb_per_s, " MB/s)\n"))
 
   if (is.character(response) && nchar(response) > 0) {
     result <- TRUE
-    log_message(paste0("Successfully created object with PID ", response, " for file ", file[1,"file"], ".\n"))
+    message(paste0("Successfully created object with PID ", response, " for file ", file[1,"file"], ".\n"))
   } else {
     result <- FALSE
-    log_message(paste0("Failed to created object with PID ", response, " for file ", file[1,"file"], ".\n"))
+    message(paste0("Failed to created object with PID ", response, " for file ", file[1,"file"], ".\n"))
   }
 
   result
@@ -830,7 +830,7 @@ update_package <- function(inventory,
 
   # Check the token
   if (is_token_expired(env$mn)) {
-    log_message("Token is expired. Returning un-modified inventory.")
+    message("Token is expired. Returning un-modified inventory.")
     return(package_files)
   }
 
@@ -839,28 +839,28 @@ update_package <- function(inventory,
   data_file_idx <- which(package_files$is_metadata == FALSE)
   stopifnot(length(metadata_file_idx) == 1)
 
-  log_message(paste0("Updating package ", package, "\n"))
+  message(paste0("Updating package ", package, "\n"))
 
   # Find the converted EML documente
   if (!file.exists(env$alternate_path)) {
-    log_message(paste0("Alternate path location of ", env$alternate_path, " does not exist. Returning.\n"))
+    message(paste0("Alternate path location of ", env$alternate_path, " does not exist. Returning.\n"))
     return(package_files)
   }
 
   eml_file_path <- path_join(c(env$alternate_path, package_files[metadata_file_idx,"file"]))
 
   if (!file.exists(eml_file_path)) {
-    log_message(paste0("EML file not found at path ", eml_file_path, ".\n"))
+    message(paste0("EML file not found at path ", eml_file_path, ".\n"))
     return(package_files)
   }
 
-  log_message(paste0("Converted document is at ", eml_file_path, "\n"))
+  message(paste0("Converted document is at ", eml_file_path, "\n"))
 
   # Get a new PID and replace the packageId
   new_pid <- package_files[metadata_file_idx,"pid"]
   old_pid <- package_files[metadata_file_idx,"pid_old"]
 
-  log_message(paste0("Updating object with old PID ", old_pid, " with new PID ", new_pid, ".\n"))
+  message(paste0("Updating object with old PID ", old_pid, " with new PID ", new_pid, ".\n"))
 
   stopifnot(!is.na(new_pid),
             is.character(new_pid),
@@ -878,12 +878,12 @@ update_package <- function(inventory,
   # Call MNStorage.update on the metadata object
   # Does this PID even exist? Stop now if it doesn't.
   if (!object_exists(env$mn_base_url, old_pid)) {
-    log_message(paste0("Object with PID ", old_pid, " not found. Returning package.\n"))
+    message(paste0("Object with PID ", old_pid, " not found. Returning package.\n"))
     return(package_files)
   }
 
   # Update the object if it doesn't exist on the MN
-  log_message(paste0("Checking if metadata object with pid ", new_pid, " already exists.\n"))
+  message(paste0("Checking if metadata object with pid ", new_pid, " already exists.\n"))
 
   if (!object_exists(env$mn_base_url, new_pid)) {
     sysmeta <- new("SystemMetadata",
@@ -910,8 +910,8 @@ update_package <- function(inventory,
                             sysmeta = sysmeta)
     },
     error = function(e) {
-      log_message(paste0("Error produced during call to updateObject for metadata ", package_files[metadata_file_idx,"file"], " in package ", package, "\n"))
-      log_message(e)
+      message(paste0("Error produced during call to updateObject for metadata ", package_files[metadata_file_idx,"file"], " in package ", package, "\n"))
+      message(e)
       e
     })
 
@@ -923,10 +923,10 @@ update_package <- function(inventory,
     # Set the updated flag to TRUE
     package_files$updated <- TRUE
 
-    log_message(paste0("Inserted updated metadata object for package ", package, "\n"))
+    message(paste0("Inserted updated metadata object for package ", package, "\n"))
   }
   else {
-    log_message(paste0("Metadata object already exists. Moving on to the resource map.\n"))
+    message(paste0("Metadata object already exists. Moving on to the resource map.\n"))
   }
 
 
@@ -973,12 +973,12 @@ update_package <- function(inventory,
   # Check if the new resource map already exists
 
   if (object_exists(env$mn_base_url, resource_map_pid)) {
-    log_message(paste0("The new resource map with PID ", resource_map_pid, " already exists. Finishing up.\n"))
+    message(paste0("The new resource map with PID ", resource_map_pid, " already exists. Finishing up.\n"))
   } else {
     # Now check if the OLD resource map exists
 
     if (!object_exists(env$mn_base_url, old_resmap_pid)) {
-      log_message(paste0("Old resource map with PID ", resource_map_pid, " doesn't exist. Using createObject instead of updateObject.\n"))
+      message(paste0("Old resource map with PID ", resource_map_pid, " doesn't exist. Using createObject instead of updateObject.\n"))
 
       create_response <- tryCatch({
         dataone::createObject(x = env$mn,
@@ -987,17 +987,17 @@ update_package <- function(inventory,
                               sysmeta = resource_map_sysmeta)
       },
       error = function(e) {
-        log_message(paste0("Error produced during call to createObject for resource map ", resource_map_pid, " in package ", package, "\n"))
-        log_message(e)
+        message(paste0("Error produced during call to createObject for resource map ", resource_map_pid, " in package ", package, "\n"))
+        message(e)
         e
       })
 
       if (inherits(create_response, "error")) {
-        log_message("There was an error calling createObject. Returning package files as is.\n")
+        message("There was an error calling createObject. Returning package files as is.\n")
         return(package_files)
       }
 
-      log_message(create_response)
+      message(create_response)
     } else {
       # Update the old resource map
       update_response <- tryCatch({
@@ -1008,17 +1008,17 @@ update_package <- function(inventory,
                               sysmeta = resource_map_sysmeta)
       },
       error = function(e) {
-        log_message(paste0("Error produced during call to updateObject for resource map ", package_files[metadata_file_idx,"file"], " in package ", package, "\n"))
-        log_message(e)
+        message(paste0("Error produced during call to updateObject for resource map ", package_files[metadata_file_idx,"file"], " in package ", package, "\n"))
+        message(e)
         e
       })
 
       if (inherits(update_response, "error")) {
-        log_message("There was an error calling updateObject Returning package files as is.\n")
+        message("There was an error calling updateObject Returning package files as is.\n")
         return(package_files)
       }
 
-      log_message(update_response)
+      message(update_response)
     }
   }
 
diff --git a/R/sysmeta.R b/R/sysmeta.R
index 09d64b6..235c1b5 100644
--- a/R/sysmeta.R
+++ b/R/sysmeta.R
@@ -67,7 +67,7 @@ remove_public_access <- function(sysmeta) {
 #' @examples
 add_admin_group_access <- function(sysmeta) {
   if (!inherits(sysmeta, "SystemMetadata")) {
-    log_message(paste0("An object of class ", class(sysmeta), " was passed in. Returning unmodified object.\n"))
+    message(paste0("An object of class ", class(sysmeta), " was passed in. Returning unmodified object.\n"))
     return(sysmeta)
   }
 
@@ -97,7 +97,7 @@ replace_subject <- function(sysmeta,
                             from="cn=arctic-data-admins,dc=dataone,dc=org",
                             to="CN=arctic-data-admins,DC=dataone,DC=org") {
   if (!inherits(sysmeta, "SystemMetadata")) {
-    log_message(paste0("An object of class ", class(sysmeta), " was passed in. Returning unmodified object.\n"))
+    message(paste0("An object of class ", class(sysmeta), " was passed in. Returning unmodified object.\n"))
     return(sysmeta)
   }