diff --git a/R/packaging.R b/R/packaging.R
index 7002d33..9dec754 100644
--- a/R/packaging.R
+++ b/R/packaging.R
@@ -448,6 +448,10 @@ generate_resource_map <- function(metadata_pid,
message("Adding ", nrow(other_statements), " custom statement(s) to the Resource Map.")
+ # Add an NA dataTypeURI to all the statements so the subsequent rbind works
+ # This is fine because they're all URIs and they don't need a datType
+ relationships$dataTypeURI <- NA
+
relationships <- rbind(relationships,
other_statements)
}
@@ -1037,65 +1041,21 @@ update_package <- function(inventory,
parse_resource_map <- function(path) {
stopifnot(file.exists(path))
- world <- new("World")
- storage <- new("Storage",
- world,
- "hashes",
- name = "",
- options = "hash-type='memory'")
- model <- new("Model", world, storage, options = "")
- parser <- new("Parser", world)
-
- redland::parseFileIntoModel(parser, world, path, model)
-
- query <- new("Query",
- world,
- "select ?s ?p ?o where { ?s ?p ?o }",
- base_uri = NULL,
- query_language = "sparql",
- query_uri = NULL)
-
- queryResult <- redland::executeQuery(query, model)
-
- statements <- data.frame()
-
- while(!is.null(result <- redland::getNextResult(queryResult))) {
- statements <- rbind(statements,
- data.frame(subject = result$s,
- predicate = result$p,
- object = result$o,
- stringsAsFactors = FALSE))
- }
-
- # Remove < and > around URIs. We do this because redland needs them to be
- # without those characters or it complains about being unable to convert into
- # a qname
- statements$subject <- stringr::str_replace_all(statements$subject, "^[<]", "")
- statements$predicate <- stringr::str_replace_all(statements$predicate, "^[<]", "")
- statements$object <- stringr::str_replace_all(statements$object, "^[<]", "")
- statements$subject <- stringr::str_replace_all(statements$subject, "[>]$", "")
- statements$predicate <- stringr::str_replace_all(statements$predicate, "[>]$", "")
- statements$object <- stringr::str_replace_all(statements$object, "[>]$", "")
-
- statements
+ rm <- new("ResourceMap")
+ datapack::parseRDF(rm, path)
+ datapack:::getTriples(rm)
}
#' Filter statements related to packaging
#'
+#' This is intended to be called after `datapack::getTriples` has been called
+#' on a ResourceMap.
+#'
#' This function was written specifically for the case of updating a resource
#' map while preserving any extra statements that have been added such as PROV
#' statements. Statements are filtered according to these rules:
#'
-#' 1. If the subject or object is the ore:ResourceMap resource
-#' 2. If the subject or object is the ore:Aggregation resource
-#' 3. If the predicate is cito:documents or cito:isDocumentedBy
-#' 4. Once filters 1-3 have been executed, any remaining triples are considered
-#' for removal if they look like dangling dc:identifier statements
-#'
-#' The consequence of filter 4 is that dc:identifier statements are left in if
-#' they are still in use by another statement
-#'
#' @param statements (data.frame) A set of Statements to be filtered
#'
#' @return (data.frame) The filtered Statements
@@ -1106,36 +1066,11 @@ filter_packaging_statements <- function(statements) {
stopifnot(is.data.frame(statements))
if (nrow(statements) == 0) return(statements)
- # Collect URIs we're going to use to filter by
- resource_map_uri <- statements[grepl("http://www.w3.org/1999/02/22-rdf-syntax-ns#type", statements$predicate) & grepl("http://www.openarchives.org/ore/terms/ResourceMap", statements$object),"subject"]
- aggregation_uri <- statements[grepl("http://www.w3.org/1999/02/22-rdf-syntax-ns#type", statements$predicate) & grepl("http://www.openarchives.org/ore/terms/Aggregation", statements$object),"subject"]
-
- # Filter statements by subject
- statements <- statements[!(statements$subject %in% c(resource_map_uri, aggregation_uri)),]
-
- # Filter statements by object
- statements <- statements[!(statements$object %in% c(resource_map_uri, aggregation_uri)),]
-
# Filter cito:documents / cito:isDocumentedBy statements
statements <- statements[!(statements$predicate == "http://purl.org/spar/cito/documents"),]
statements <- statements[!(statements$predicate == "http://purl.org/spar/cito/isDocumentedBy"),]
-
- # If this is a simple package without extra statements, then we should just be
- # left with some dc:identifier statements left over. Here we try to detect
- # that case by collecting the unique subjects taking part in dc:identifier
- # statements and filtering statements about subjects with only one statement
- # about them
-
- dc_identifiers <- unique(statements[statements$predicate == "http://purl.org/dc/terms/identifier", "subject"])
-
- for (identifier in dc_identifiers) {
- if (nrow(statements[statements$subject == identifier | statements$object == identifier,]) == 1) {
- statements <- statements[!(statements$subject == identifier | statements$object == identifier),]
- }
- }
-
- # Remove <NA> introduced by the second filter statement
- statements <- statements[complete.cases(statements),]
+ statements <- statements[!(statements$predicate == "http://purl.org/dc/terms/identifier"),]
+ statements <- statements[!((statements$predicate == "http://xmlns.com/foaf/0.1/name" & statements$object == "DataONE R Client")),]
statements
}
diff --git a/tests/testthat/test_editing.R b/tests/testthat/test_editing.R
index a088262..0d607c3 100644
--- a/tests/testthat/test_editing.R
+++ b/tests/testthat/test_editing.R
@@ -15,7 +15,8 @@ test_that("we can publish an update", {
update <- publish_update(mn,
package$metadata,
package$resource_map,
- package$data)
+ package$data,
+ check_first = FALSE)
expect_named(update, c("metadata", "resource_map", "data"))
expect_true(all(object_exists(mn, unlist(update))))
@@ -36,7 +37,8 @@ test_that("an identifier can be manually specified when publishing an update", {
package$metadata,
package$resource_map,
package$data,
- identifier = new_identifier)
+ identifier = new_identifier,
+ check_first = FALSE)
expect_equal(update$metadata, new_identifier)
})
@@ -53,7 +55,7 @@ test_that("we can create a resource map", {
response <- create_resource_map(mn, metadata_pid, data_pid)
expect_true(object_exists(mn, response))
- expect_equal(response, get_package(mn, metadata_pid)$resource_map)
+ expect_equal(response, get_package(mn, response)$resource_map)
})
@@ -121,7 +123,7 @@ test_that("SIDs are maintained when publishing an update to an object with a SID
sid = new_sid)
resmap_pid <- create_resource_map(mn, metadata_pid = pid)
- response <- publish_update(mn, pid, resmap_pid)
+ response <- publish_update(mn, pid, resmap_pid, check_first = FALSE)
sysmeta <- getSystemMetadata(mn, response$metadata)
expect_equal(sysmeta@seriesId, new_sid)
@@ -143,7 +145,10 @@ test_that("we can publish an update to an object", {
csv <- data.frame(x = 1:50)
write.csv(csv, tmp)
- upd <- update_object(mn, old, tmp)
+ suppressWarnings({
+ upd <- update_object(mn, old, tmp)
+ })
+
file.remove(tmp)
sm <- dataone::getSystemMetadata(mn, upd)
@@ -181,27 +186,26 @@ test_that("extra statements are maintained between updates", {
# Add some PROV triples to the Resource Map
rm <- tempfile()
writeLines(rawToChar(dataone::getObject(mn, pkg$resource_map)), rm)
- # statements <- data.frame(subject = paste0("https://cn.dataone.org/cn/v2/resolve/", URLencode(pkg$data[1], reserved = TRUE)),
- # predicate = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
- # object = "http://www.w3.org/ns/prov#Entity")
- #
- # statements <- rbind(statements,
- # data.frame(subject = paste0("https://cn.dataone.org/cn/v2/resolve/", URLencode(pkg$data[2], reserved = TRUE)),
- # predicate = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
- # object = "http://www.w3.org/ns/prov#Entity"))
statements <- data.frame(subject = paste0("https://cn.dataone.org/cn/v2/resolve/", URLencode(pkg$data[1], reserved = TRUE)),
predicate = "http://www.w3.org/ns/prov#wasDerivedFrom",
- object = paste0("https://cn.dataone.org/cn/v2/resolve/", URLencode(pkg$data[2], reserved = TRUE)))
-
- new_rm <- update_resource_map(mn, pkg$resource_map, pkg$metadata, pkg$data, other_statements = statements, public = TRUE)
+ object = paste0("https://cn.dataone.org/cn/v2/resolve/", URLencode(pkg$data[2], reserved = TRUE)),
+ subjectType = "uri",
+ objectType = "uri",
+ dataTypeURI = NA)
+
+ new_rm <- update_resource_map(mn,
+ pkg$resource_map,
+ pkg$metadata,
+ pkg$data,
+ other_statements = statements,
+ public = TRUE)
rm <- tempfile()
writeLines(rawToChar(dataone::getObject(mn, new_rm)), rm)
statements <- parse_resource_map(rm)
expect_true("http://www.w3.org/ns/prov#wasDerivedFrom" %in% statements$predicate)
-
new_new_rm <- update_resource_map(mn, new_rm, pkg$metadata, pkg$data, public = TRUE)
rm <- tempfile()
writeLines(rawToChar(dataone::getObject(mn, new_new_rm)), rm)
@@ -220,7 +224,7 @@ test_that("rightsholder is properly set back after publishing an update", {
set_result <- set_rights_holder(mn, unlist(pkg), "CN=arctic-data-admins,DC=dataone,DC=org")
expect_true(all(set_result))
- new_pkg <- publish_update(mn, pkg$metadata, pkg$resource_map, pkg$data)
+ new_pkg <- publish_update(mn, pkg$metadata, pkg$resource_map, pkg$data, check_first = FALSE)
rhs <- lapply(unlist(pkg), function(pid) {
dataone::getSystemMetadata(mn, pid)@rightsHolder
})