earnaud
commented
3 years ago I would add how was uploaded the data object matching urn:uuid:5374d070-e834-4690-987f-d0d0789360b5 :
I based myself on the recommended {dataone} method and wrote the uploadDP() function:
function(
# connection arguments
endpoint, # data.frame of 1 row and 4 columns: name, mn, cn, description
token, # metacat token matching the selected cn and mn
# content
eml, # eml file to upload
data, # data file(s) to upload
scripts = NULL, # script file(s) to upload
# options
use.doi = FALSE # WIP
) {
options(dataone_test_token = token)
options(dataone_token = token)
# Set variables ----
# devmsg: function combining message() and sprintf()
devmsg(tag = "upload", "* Sending data package to %s", endpoint$name)
d1c <- dataone::D1Client(
endpoint |>
dplyr::select(cn) |>
as.character(),
endpoint |>
dplyr::select(mn) |>
as.character()
)
# unused
if (use.doi) {
doi <- dataone::generateIdentifier(d1c@mn, "DOI")
} # TODO check this feature
# Write DP ----
# set data package
dp <- methods::new("DataPackage")
# * metadata ----
# Add metadata to the data package
devmsg(tag = "upload", "* Set metadata")
metadata_id <- generateIdentifier(d1c@mn, scheme = "uuid")
doc <- EML::read_eml(eml)
eml.format <- doc$schemaLocation |>
gsub(
pattern = "(eml-[0-9]+\\.[0-9]+\\.[0-9]+).+$",
replacement = "\\1"
)
metadataObj <- methods::new(
"DataObject",
id = metadata_id,
format = eml.format,
filename = eml
)
dp <- datapack::addMember(dp, metadataObj)
# * data ----
# Add data to the data package
devmsg(tag = "upload", "* Set data")
data.formats <- mime::guess_type(data)
for(d in seq(data)) {
dataObj <- methods::new(
"DataObject",
format = data.formats[d],
filename = data[d]
)
dp <- datapack::addMember(dp, do = dataObj, mo = metadataObj)
}
# * scripts ----
# Add scripts to the data package
if (length(scripts) != 0) {
devmsg(tag = "upload", "* Set scripts")
scripts.formats <- mime::guess_type(scripts)
for(d in seq(scripts)) {
scriptObj <- methods::new(
"DataObject",
format = scripts.formats[d],
filename = scripts[d]
)
dp <- datapack::addMember(dp, do = scriptObj, mo =metadataObj)
}
}
# Access rules ----
# TODO allow customized access rules
# Upload ----
devmsg(tag = "upload", "* Upload")
packageId <- try(
dataone::uploadDataPackage(d1c, dp, public = TRUE, quiet = FALSE)
)
if (class(packageId) == "try-error")
browser()
else
devmsg(tag = "upload", "* Success (resource map ID: %s)", packageId)
# empty dataone token cache since function shall be used in a multiuser shiny app
options(dataone_test_token = NULL)
options(dataone_token = NULL)
# return(package_id)
return(metadata_id) # was the same as packageId
}I am targetting the metadata_id since it is the one displayed here :
I thought this was a complete data package ID.
In https://github.com/DataONEorg/rdataone/issues/203, @earnaud reported this situation:
At the time of writing this issue, the Solr doc for
urn:uuid:5374d070-e834-4690-987f-d0d0789360b5doesn't have aresourceMapfield.We should probably:
getDataPackagesends the client's auth token