Remove usages of log_message in interactive functions

NCEAS · Sep 12, 2017 · 574c6c2 · 574c6c2
1 parent 8c242e8
commit 574c6c2
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Showing 6 changed files with 104 additions and 104 deletions.
diff --git 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
     })
 
@@ -167,22 +167,22 @@ 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
     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
     })
 
@@ -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
     })
 
@@ -246,41 +246,41 @@ 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
       })
 
       if (inherits(update_response, "error")) {
         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
@@ -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)) {
@@ -321,35 +321,35 @@ 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
     if (!file.exists(metadata_path)) {
       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
@@ -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
@@ -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
       })