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create pid_to_eml_entity function deprecate old functions #91

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Merged
jagoldstein merged 3 commits into from
Jun 21, 2018
Merged

create pid_to_eml_entity function deprecate old functions #91

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3555412
created pid_to_eml_entity function
areevesman May 17, 2018
879edbc
cleaned up whitespace
areevesman May 18, 2018
d9b00b2
updated example
maier-m May 25, 2018
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5 changes: 1 addition & 4 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -40,21 +40,18 @@ export(mdq_run)
export(new_uuid)
export(object_exists)
export(parse_resource_map)
export(pid_to_eml_datatable)
export(pid_to_eml_other_entity)
export(pid_to_eml_entity)
export(pid_to_eml_physical)
export(publish_object)
export(publish_update)
export(remove_public_read)
export(set_abstract)
export(set_access)
export(set_file_name)
export(set_other_entities)
export(set_public_read)
export(set_rights_and_access)
export(set_rights_holder)
export(show_indexing_status)
export(sysmeta_to_eml_other_entity)
export(sysmeta_to_eml_physical)
export(update_object)
export(update_resource_map)
Expand Down
236 changes: 85 additions & 151 deletions R/eml.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,102 +3,107 @@
#' Helpers for creating EML.


#' Create EML otherEntity objects for a set of PIDs
#'
#' Note this is a wrapper around sysmeta_to_other_entity which handles the task of
#' creating the EML otherEntity.
#' Create EML entity from a DataONE pid
#'
#' @param mn (MNode) Member Node where the PID is associated with an object.
#' @param pids (character) The PID of the object to create the sub-tree for.
#' @param pid (character) The PID of the object to create the sub-tree for.
#' @param entityType (character) What kind of objects to create from the input. Either "dataTable",
#' "spatialRaster", "spatialVector", "storedProcedure", "view", "otherEntity".
#' @param ... (optional) Additional arguments to be passed to \code{new(entityType, ...)}. See example
#'
#' @return (list of otherEntity) The otherEntity object(s)
#' @return (list) The entity object
#' @export
#'
#' @examples
#' \dontrun{
#' # Generate EML otherEntity objects for all the data in a package
#' pkg <- get_package(mn, pid)
#' pid_to_other_entity(mn, pkg$data)
#' #Generate EML otherEntity
#' pid_to_eml_entity(mn,
#' pid,
#' entityType = "otherEntity",
#' entityName = "Entity Name",
#' entityDescription = "Description about entity")
#'
#' }
pid_to_eml_other_entity <- function(mn, pids) {
pid_to_eml_entity <- function(mn,
pid,
entityType = "otherEntity",
...) {

stopifnot(is(mn, "MNode"))
stopifnot(is.character(pids),
all(nchar(pids)) > 0)
stopifnot(is.character(pid),
nchar(pid) > 0)

sysmeta <- lapply(pids, function(pid) { getSystemMetadata(mn, pid) })
sysmeta_to_eml_other_entity(sysmeta)
stopifnot(entityType %in% c("dataTable",
"spatialRaster",
"spatialVector",
"storedProcedure",
"view",
"otherEntity"))

systmeta <- getSystemMetadata(mn, pid)
physical <- sysmeta_to_eml_physical(systmeta)

# Create entity
entity <- new(entityType,
physical = pid_to_eml_physical(mn, pid),
...)

# Set entity slots
if (length(slot(entity, "id")) == 0) {
entity@id <- new("xml_attribute", systmeta@identifier)
}

if (length(slot(entity, "scope")) == 0) {
entity@scope <- new("xml_attribute", "document")
}

if (length(slot(entity, "entityName")) == 0) {

if (!is.na(systmeta@fileName)) {
entity@entityName <- new("entityName", systmeta@fileName)
}
}

if (entityType == "otherEntity" && length(slot(entity, "entityType")) == 0) {
entity@entityType <- "Other"
}

return(entity)
}


#' Create an EML code\code{dataTable} object for a given PID.
#' This function is deprecated. See \link{pid_to_eml_entity}.
#'
#' This function generates an \code{attributeList} and \code{physical} and constructs a \code{dataTable}.
#' @param mn (MNode) Member Node where the PID is associated with an object.
#' @param pids (character) The PID of the object to create the sub-tree for.
#'
pid_to_eml_other_entity <- function(mn, pids) {
.Deprecated(new = "pid_to_eml_entity",
package = "arcticdtautils",
old = "pid_to_eml_other_entity")
}


#' This function is deprecated. See \link{pid_to_eml_entity}.
#'
#' @param mn (MNode) Member Node where the PID is associated with an object.
#' @param pid (character) The PID of the object to create the \code{dataTable} for.
#' @param attributes (data.frame) Optional data frame of attributes. Follows the convention in \link[EML]{set_attributes}.
#' @param factors (data.frame) Optional data frame of enumerated attribute values (factors). Follows the convention in \link[EML]{set_attributes}.
#' @param name (character) Optional field to specify \code{entityName}, otherwise will be extracted from system metadata.
#' @param description (character) Optional field to specify \code{entityDescription}, otherwise will match name.
#' @param validateAttributes (logical) If set to FALSE or if attributes are not passed into the function, attribute validation test will not run.
#'
#' @return (dataTable) The \code{dataTable} object
#' @export
#' @param validateAttributes (logical) If set to FALSE or if attributes are not passed into the function, attribute validatio
#'
#' @examples
#' \dontrun{
#' # Generate a dataTable for a given pid
#' attributes <- create_dummy_attributes_dataframe(10)
#' name <- "1234.csv"
#' description <- "A description of this entity."
#' dataTable <- pid_to_eml_datatable(mn, pid, attributes, name=name, description=description)
#' }
pid_to_eml_datatable <- function(mn,
pid,
attributes = NULL,
factors = NULL,
name = NULL,
description = NULL,
validateAttributes = TRUE) {
stopifnot(is(mn, "MNode"))
stopifnot(is.character(pid),
nchar(pid) > 0)

dataTable <- new("dataTable", physical = pid_to_eml_physical(mn, pid))

if(!is.null(attributes)) {
stopifnot(is.data.frame(attributes))

if (is.null(factors)) {
attributes <- set_attributes(attributes)
} else {
stopifnot(is.data.frame(factors))
attributes <- set_attributes(attributes, factors)
}

if (validateAttributes == TRUE) {
stopifnot(eml_validate_attributes(attributes))
}

dataTable@attributeList <- attributes
}

if (is.null(name)) {
name <- getSystemMetadata(mn, pid)@fileName

if (is.na(name)) {
stop(call. = FALSE,
"'Name' must either be specified in the function call or must exist in the system metadata.")
}
}

dataTable@entityName <- name

if (!is.null(description)) {
dataTable@entityDescription <- description
}

dataTable
.Deprecated(new = "pid_to_eml_entity",
package = "arcticdtautils",
old = "pid_to_eml_other_entity")
}


Expand Down Expand Up @@ -128,45 +133,14 @@ pid_to_eml_physical <- function(mn, pids) {
sysmeta_to_eml_physical(sysmeta)
}

#' Create an EML otherEntity for the given object from the System Metadata
#' This function is deprecated. See \link{pid_to_eml_entity}.
#'
#' @param sysmeta (SystemMetadata) One or more System Metadata objects
#'
#' @return (list of otherEntity) The otherEntity object(s)
#' @export
#'
#' @examples
#' \dontrun{
#' # Generate EML otherEntity objects for all the data in a package
#' pkg <- get_package(mn, pid)
#' sm <- lapply(pkg$data, function(pid) { getSystemMetadata(mn, pid) })
#' sysmeta_to_other_entity(sm)
#'}
sysmeta_to_eml_other_entity <- function(sysmeta) {
work <- function(x) {
other_entity <- new("otherEntity")
other_entity@id <- new("xml_attribute", x@identifier)
other_entity@scope <- new("xml_attribute", "document")

if (is.na(x@fileName)) {
other_entity@entityName <- new("entityName", "NA")
}
else {
other_entity@entityName <- new("entityName", x@fileName)
}

other_entity@entityType <- "Other"

phys <- sysmeta_to_eml_physical(x)
other_entity@physical <- new("ListOfphysical", phys)

other_entity
}


if (!is(sysmeta, "list")) sysmeta <- list(sysmeta)

lapply(sysmeta, work)
.Deprecated(new = "pid_to_eml_entity",
package = "arcticdtautils",
old = "sysmeta_to_other_entity")
}


Expand Down Expand Up @@ -236,56 +210,16 @@ sysmeta_to_eml_physical <- function(sysmeta) {
lapply(sysmeta, work)
}

#' Creates and sets EML otherEntity elements to an existing EML document,
#' replacing any existing otherEntities
#'
#' This function is slow because it needs get the System Metadata for each
#' element of `pids` in order to get the fileName, checksum, etc.
#' This function is deprecated. See \link{pid_to_eml_entity}.
#'
#' @param mn (MNode) The Member Node the objects exist on.
#' @param path (character) The location on disk of the EML file.
#' @param pids (character) One or more PIDs for the objects.
#'
#' @return (character) The path to the updated EML file.
#' @export
#'
#' @examples
#' \dontrun{
#' mn <- MNode(...) # Set up a connection to an MN
#' eml_path <- "/path/to/your/eml.xml"
#' set_other_entities(mn, eml_path, "a_data_pid")
#' }
set_other_entities <- function(mn, path, pids) {
stopifnot(is(mn, "MNode"))
stopifnot(file.exists(path))
stopifnot(all(is.character(pids)),
all(nchar(pids) > 0))

if (length(pids) == 0) {
message("Skipped adding EML otherEntity elements because no pids were specified.")
return(path)
}

# Get the metadata document from the MN and load it as an EML document
doc <- EML::read_eml(path)
stopifnot(is(doc, "eml"))

message("Setting EML otherEntity elements. This can take a while if there are lots of PIDs...")

# Generate otherEntity elements
other_entities <- pid_to_eml_other_entity(mn, pids)

# Concatenate the existing and new otherEntity elements and put back in the
# EML
if (length(other_entities) > 0) {
doc@dataset@otherEntity <- new("ListOfotherEntity", other_entities)
}

# Write the modified document back to disk and stop
EML::write_eml(doc, path)
stopifnot(EML::eml_validate(path) == TRUE)

path
.Deprecated(new = "pid_to_eml_entity",
package = "arcticdtautils",
old = "set_other_entities")
}

#' Get the Metacat docid for the given identifier
Expand Down Expand Up @@ -603,10 +537,10 @@ eml_individual_name <- function(given_names=NULL, sur_name) {
stopifnot(all(sapply(given_names, is.character)))
stopifnot(all(lengths(given_names) > 0))

givens <- lapply(given_names, function(given_name) {
x <- new("givenName")
x@.Data <- given_name
x
givens <- lapply(given_names, function(given_name) {
x <- new("givenName")
x@.Data <- given_name
x
})

indiv_name@givenName <- new("ListOfgivenName", givens)
Expand Down Expand Up @@ -660,7 +594,7 @@ eml_project <- function(title,
# Title
titles <- lapply(title, function(x) { as(x, "title") })
project@title <- as(titles, "ListOftitle")

# Personnel
if(!all(sapply(personnelList, function(x) { is(x, "personnel") }))) {
stop(call. = FALSE,
Expand Down
18 changes: 3 additions & 15 deletions man/pid_to_eml_datatable.Rd
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