tests/testthat/test.D1Client.R
In DataONEorg/rdataone: R Interface to the DataONE REST API
test_that("dataone library loads", {
expect_true(require(dataone))
})
test_that("D1Client constructors", {
skip_on_cran()
library(dataone)
#cli <- new("D1Client")
expect_false(is.null(d1cProd))
expect_match(class(d1cProd), "D1Client")
expect_match(d1cProd@cn@baseURL, "https://cn.dataone.org/cn")
#cli <- new("D1Client", env="PROD", mNodeid="urn:node:KNB")
expect_false(is.null(d1cKNB))
expect_match(class(d1cKNB), "D1Client")
expect_match(d1cKNB@cn@baseURL, "https://cn.dataone.org/cn")
expect_match(d1cKNB@mn@baseURL, "https://knb.ecoinformatics.org/knb/d1/mn")
# Skip the remainder of the tests because these test environments are
# often down due to upgrades, reconfiguring, testing new features.
skip_on_cran()
cli <- new("D1Client", cn=cnStaging, mn=getMNode(cnStaging, "urn:node:mnTestKNB"))
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn-stage.test.dataone.org/cn")
expect_match(cli@mn@baseURL, "https://dev.nceas.ucsb.edu/knb/d1/mn")
cli <- D1Client()
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn.dataone.org/cn")
cli <- D1Client("STAGING")
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn-stage.test.dataone.org/cn")
# Skip the hightly unstable environments when testing on cran
skip_on_cran()
cli <- D1Client("SANDBOX")
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn-sandbox.test.dataone.org/cn")
#cli <- D1Client("DEV")
#expect_false(is.null(cli))
#expect_match(class(cli), "D1Client")
#expect_match(cli@cn@baseURL, "https://cn-dev.test.dataone.org/cn")
})
test_that("D1Client methods", {
skip_on_cran()
# Test listMemberNodes
#cli <- D1Client("PROD")
nodes <- listMemberNodes(d1cProd)
expect_gt(length(nodes), 0)
expect_identical(class(nodes), "list")
# The remainder of this test uses development machines.
skip_on_cran()
# Test getEndPoint()
cli <- D1Client("STAGING")
cnUrl <- getEndpoint(cli)
expect_match(cnUrl, "https://cn-stage.test.dataone.org/cn")
# Test getMNodeId()
cli <- D1Client("STAGING", "urn:node:mnTestKNB")
expect_match(getMNodeId(cli), "urn:node:mnTestKNB")
# Test setMNodeId
cli <- new("D1Client", env="STAGING")
cli <- setMNodeId(cli, "urn:node:mnTestKNB")
expect_match(cli@mn@identifier, "urn:node:mnTestKNB")
})
test_that("D1Client getDataObject", {
skip_on_cran()
library(dataone)
library(digest)
#cli <- D1Client("PROD", "urn:node:KNB")
expect_false(is.null(d1cKNB))
expect_match(class(d1cKNB), "D1Client")
expect_match(d1cKNB@cn@baseURL, "https://cn.dataone.org/cn")
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cKNB@mn))
if(authValid) {
# Skip if Mac OS and X.509 Certificate
if(dataone:::getAuthMethod(am, d1cKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
}
# Try retrieving a known object from the PROD environment
pid <- "solson.5.1"
obj <- getDataObject(d1cKNB, pid, checksumAlgorithm="SHA-256")
cname <- class(obj)[1]
expect_match(cname, "DataObject")
expect_match(class(obj@sysmeta), "SystemMetadata")
expect_match(getIdentifier(obj), pid)
expect_match(getFormatId(obj), "text/csv")
data <- getData(obj)
sha256 <- digest(data, algo="sha256", serialize=FALSE, file=FALSE)
expect_match(sha256, obj@sysmeta@checksum)
})
test_that("D1Client uploadDataObject with raw data works", {
skip_on_cran()
library(dataone)
library(datapack)
# Create a DataObject with a raw R object and upload to DataONE
data <- charToRaw("1,2,3\n4,5,6\n")
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
expect_false(is.null(d1cTest))
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
# Create DataObject for the science data
do <- new("DataObject", format="text/csv", dataobj=data, mnNodeId=getMNodeId(d1cTest))
expect_match(do@sysmeta@identifier, "urn:uuid")
newId <- uploadDataObject(d1cTest, do, replicate=FALSE, preferredNodes=NA, public=TRUE)
expect_true(!is.null(newId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataObject with filename works", {
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
expect_false(is.null(d1cTest))
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
# Create DataObject for the science data
do <- new("DataObject", format="text/csv", mnNodeId=getMNodeId(d1cTest), filename=csvfile)
expect_match(do@sysmeta@identifier, "urn:uuid")
newId <- uploadDataObject(d1cTest, do, replicate=FALSE, preferredNodes=NA , public=TRUE)
expect_true(!is.null(newId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataPackage works", {
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
#d1c <- D1Client("SANDBOX2", "urn:node:mnDemo2")
#d1c <- D1Client("DEV2", "urn:node:mnDevUCSB2")
expect_false(is.null(d1cTest))
#preferredNodes <- c("urn:node:mnDemo9")
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create DataObject for the science data
sciObj <- new("DataObject", format="text/csv", mnNodeId=getMNodeId(d1cTest), filename=csvfile)
# It's possible to set access rules for DataObject now, or for all DataObjects when they are uploaded to DataONE via uploadDataPackage
expect_match(sciObj@sysmeta@identifier, "urn:uuid")
sciObj <- setPublicAccess(sciObj)
accessRules <- data.frame(subject=c("uid=smith,ou=Account,dc=example,dc=com", "uid=slaughter,o=unaffiliated,dc=example,dc=org"), permission=c("write", "changePermission"))
sciObj <- addAccessRule(sciObj, accessRules)
dp <- addMember(dp, sciObj)
expect_true(is.element(sciObj@sysmeta@identifier, getIdentifiers(dp)))
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
expect_match(metadataObj@sysmeta@identifier, "urn:uuid")
dp <- addMember(dp, metadataObj)
expect_true(is.element(metadataObj@sysmeta@identifier, getIdentifiers(dp)))
# Associate the metadata object with the science object it describes
dp <- insertRelationship(dp, subjectID=getIdentifier(metadataObj), objectIDs=getIdentifier(sciObj))
# Upload the data package to DataONE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, preferredNodes=preferredNodes, public=TRUE, accessRules=accessRules)
expect_true(!is.null(resourceMapId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataPackage works for a minimal DataPackage", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
expect_false(is.null(d1cTest))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
expect_match(metadataObj@sysmeta@identifier, "urn:uuid")
dp <- addMember(dp, metadataObj)
expect_true(is.element(metadataObj@sysmeta@identifier, getIdentifiers(dp)))
# Upload the data package to DataONE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, preferredNodes=preferredNodes, public=TRUE)
expect_true(!is.null(resourceMapId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client updateDataPackage works", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
library(xml2)
library(digest)
# Create a csv file for the science object
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
#d1c <- D1Client("STAGING2", "urn:node:mnTestKNB")
#d1c <- D1Client("DEV2", "urn:node:mnDevUCSB1")
expect_false(is.null(d1cTestKNB))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTestKNB@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTestKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile)
metadataId <- getIdentifier(metadataObj)
# Associate the metadata object with each data object using the 'insertRelationships' method.
# Since a relationship type (the predicate argument) is not specified, the default relationship
# of 'cito:documents' is used, to indicate the the metadata object documents each data object.
# See "http://purl.org/spar/cito", for further information about the "Citation Type Ontology".
dp <- addMember(dp, metadataObj)
sourceData <- system.file("extdata/sample.csv", package="dataone")
sourceObj <- new("DataObject", format="text/csv", filename=sourceData)
dp <- addMember(dp, sourceObj, metadataObj)
resolveURL <- sprintf("%s/%s/object", d1cTestKNB@mn@baseURL, d1cTestKNB@mn@APIversion)
# Update the distribution URL in the metadata with the identifier that has been assigned to
# this DataObject. This provides a direct link between the detailed information for this package
# member and DataONE, which will assist DataONE in accessing and displaying this detailed information.
xpathToURL <- "//dataTable/physical/distribution[../objectName/text()=\"OwlNightj.csv\"]/online/url"
newURL <- sprintf("%s/%s", resolveURL, getIdentifier(sourceObj))
dp <- updateMetadata(dp, metadataId, xpath=xpathToURL, newURL)
metadataId <- selectMember(dp, name="sysmeta@formatId", value="eml://ecoinformatics.org/eml-2.1.1")
metadataObj <- getMember(dp, metadataId)
progFile <- system.file("extdata/filterSpecies.R", package="dataone")
progObj <- new("DataObject", format="application/R", filename=progFile, mediaType="text/x-rsrc")
dp <- addMember(dp, progObj, metadataObj)
xpathToURL <- "//otherEntity/physical/distribution[../objectName/text()=\"filterObs.R\"]/online/url"
newURL <- sprintf("%s/%s", resolveURL, getIdentifier(progObj))
dp <- updateMetadata(dp, metadataId, xpath=xpathToURL, newURL)
metadataId <- selectMember(dp, name="sysmeta@formatId", value="eml://ecoinformatics.org/eml-2.1.1")
metadataObj <- getMember(dp, metadataId)
outputData <- system.file("extdata/filteredSpecies.csv", package="dataone")
outputObj <- new("DataObject", format="text/csv", filename=outputData)
dp <- addMember(dp, outputObj, metadataObj)
xpathToURL <- "//dataTable/physical/distribution[../objectName/text()=\"Strix-occidentalis-obs.csv\"]/online/url"
newURL <- sprintf("%s/%s", resolveURL, getIdentifier(outputObj))
dp <- updateMetadata(dp, metadataId, xpath=xpathToURL, newURL)
# Upload the data package to DataONE
newPkg <- uploadDataPackage(d1cTestKNB, dp, public=TRUE, quiet=TRUE, as="DataPackage")
pkgId <- newPkg@resmapId
expect_true(!is.na(pkgId))
# Sleep for 90 secondsl to let indexing finish for the package. Because we are imposing a wait on this
# package, this test is not suitable for use in CRAN.
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client updateDataPackage with new package using previously uploaded objects works", {
# Test the typical workflow of creating a DataONE package by first uploading all data objects for the package,
# then creating a package from the already uploaded objects.
skip_on_cran()
library(dataone)
library(datapack)
library(xml2)
library(digest)
expect_false(is.null(d1cTestKNB))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTestKNB@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTestKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
# First upload objects to DataONE that will be collected into a package
sourceData <- system.file("extdata/OwlNightj.csv", package="dataone")
sourceObj <- new("DataObject", format="text/csv", filename=sourceData)
sourceObj <- addAccessRule(sourceObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
sourceId <- uploadDataObject(d1cTestKNB, sourceObj, public=T, quiet=T)
expect_true(!is.na(sourceId))
progFile <- system.file("extdata/filterObs.R", package="dataone")
progObj <- new("DataObject", format="application/R", filename=progFile, mediaType="text/x-rsrc")
progObj <- addAccessRule(progObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
progId <- uploadDataObject(d1cTestKNB, progObj, public=T, quiet=T)
expect_true(!is.na(progId))
outputData <- system.file("extdata/Strix-occidentalis-obs.csv", package="dataone")
outputObj <- new("DataObject", format="text/csv", filename=outputData)
outputObj <- addAccessRule(outputObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
outputId <- uploadDataObject(d1cTestKNB, outputObj, public=T, quiet=T)
expect_true(!is.na(outputId))
# Create a new package, and download each member (lazyLoaded) that was just uploaded, then add them
# to the package and upload. This workflow does not require that package members are downloaded with
# lazyLoad, this is done here just for efficiency. If a package member is downloaded without lazyLoad,
# it will not be-reuploaded when the package is uploaded, unless it has been updated (i.e. updated contents,
# or sysmeta).
pkg <- new("DataPackage")
# Create metadata object that describes the package
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile)
metadataObj <- addAccessRule(metadataObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
pkg <- addMember(pkg, metadataObj)
metadataId <- getIdentifier(metadataObj)
newSourceObj <- getDataObject(d1cTestKNB, sourceId, lazyLoad=T, quiet=T)
pkg <- addMember(pkg, newSourceObj, metadataObj)
newProgObj <- getDataObject(d1cTestKNB, progId, lazyLoad=T, quiet=T)
pkg <- addMember(pkg, newProgObj, metadataObj)
newOutputObj <- getDataObject(d1cTestKNB, outputId, lazyLoad=T, quiet=T)
pkg <- addMember(pkg, newOutputObj, metadataObj)
resourceMapId <- uploadDataPackage(d1cTestKNB, pkg, public=TRUE, quiet=T)
expect_false(is.na(resourceMapId))
# Now test that we can download the newly created package and add an existing object
# Now add a new package member that was omitted from the original package
auxFile <- system.file("extdata/WeatherInf.txt", package="dataone")
auxObj <- new("DataObject", format="text/plain", file=auxFile)
auxObj <- addAccessRule(auxObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
auxId <- uploadDataObject(d1cTestKNB, auxObj, public=T, quiet=T)
expect_true(!is.na(auxId))
# Have to sleep just a bit, as indexing can take awhile to complete
# Keep trying for ten seconds for the package to be indexed
done <- FALSE
trys <- 0
while(!done) {
if(trys > 10) break
Sys.sleep(1)
queryParams <- sprintf('q=id:"%s"', resourceMapId)
result <- query(d1cTestKNB@mn, queryParams, as="list")
# Now download the package that was just created, and ensure that the checksums are all the
# requested type.
if(length(result) == 0) {
trys <- trys + 1
next
} else {
done <- TRUE
}
newAuxObj <- getDataObject(d1cTestKNB, auxId, lazyLoad=T, quiet=T)
editPkg <- getDataPackage(d1cTestKNB, identifier=resourceMapId, lazyLoad=TRUE, quiet=TRUE)
}
expect_true(done)
editPkg <- addMember(editPkg, newAuxObj, metadataObj)
newResmapId <- uploadDataPackage(d1cTestKNB, editPkg, public=TRUE, quiet=T)
expect_false(is.na(newResmapId))
expect_false(resourceMapId == newResmapId)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client getDataPackage with checksumAlgorithm specified works", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
library(xml2)
library(digest)
# Create a csv file for the science object
expect_false(is.null(d1cTestKNB))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTestKNB@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTestKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
sha256 <- "SHA-256"
md5 <- "MD5"
checksumAlgorithm <- sha256
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile, checksum=checksumAlgorithm)
metadataId <- getIdentifier(metadataObj)
dp <- addMember(dp, metadataObj)
sourceData <- system.file("extdata/sample.csv", package="dataone")
sourceObj <- new("DataObject", format="text/csv", filename=sourceData, checksum=checksumAlgorithm)
dp <- addMember(dp, sourceObj, metadataObj)
progFile <- system.file("extdata/filterSpecies.R", package="dataone")
progObj <- new("DataObject", format="application/R", filename=progFile, mediaType="text/x-rsrc", checksum=checksumAlgorithm)
dp <- addMember(dp, progObj, metadataObj)
outputData <- system.file("extdata/filteredSpecies.csv", package="dataone")
outputObj <- new("DataObject", format="text/csv", filename=outputData, checksum=checksumAlgorithm)
dp <- addMember(dp, outputObj, metadataObj)
# Upload the data package to DataONE
pkgId <- uploadDataPackage(d1cTestKNB, dp, public=TRUE, quiet=TRUE)
expect_true(!is.na(pkgId))
# Have to sleep just a bit, as indexing can take awhile to complete
# Keep trying for ten seconds for the package to be indexed
done <- FALSE
trys <- 0
while(!done) {
if(trys > 10) break
Sys.sleep(1)
queryParams <- sprintf('q=id:"%s"', pkgId)
result <- query(d1cTestKNB@mn, queryParams, as="list")
# Now download the package that was just created, and ensure that the checksums are all the
# requested type.
if(length(result) == 0) {
trys <- trys + 1
next
} else {
done <- TRUE
}
pkg <- getDataPackage(d1cTestKNB, identifier=pkgId, lazyLoad=TRUE, limit="0MB", quiet=TRUE, checksumAlgorithm=sha256)
algorithms <- getValue(pkg, name="sysmeta@checksumAlgorithm")
expect_true(all(algorithms == sha256))
# Download the package again, requesting a different checksum type, and ensure that the checksums are all the
# new type.
pkg <- getDataPackage(d1cTestKNB, identifier=pkgId, lazyLoad=TRUE, limit="0MB", quiet=TRUE, checksumAlgorithm=md5)
algorithms <- getValue(pkg, name="sysmeta@checksumAlgorithm")
expect_true(all(algorithms==md5))
}
expect_true(done)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client listMemberNodes() works", {
skip_on_cran()
library(dataone)
#d1c <- D1Client("PROD")
nodelist <- listMemberNodes(d1cProd)
expect_true(length(nodelist) > 0)
expect_match(class(nodelist[[1]]), "Node")
expect_match(nodelist[[1]]@identifier, "urn:node:")
expect_match(nodelist[[1]]@type, "cn|mn")
expect_match(nodelist[[1]]@state, "up")
expect_match(nodelist[[length(nodelist)]]@identifier, "urn:node:")
expect_match(nodelist[[length(nodelist)]]@baseURL, "http")
expect_match(nodelist[[length(nodelist)]]@subject, "urn:node:")
expect_match(nodelist[[length(nodelist)]]@type, "cn|mn")
})
test_that("D1Client updateDataPackage works for a metadata only DataPackage", {
skip_on_cran()
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
# This is a long running test, so it should be run manually, which means
# running "test_file("tests/testthat/packageUpdate.R"), as this file is not
# run by default by testthat due to the name not including 'test*'
library(dataone)
library(datapack)
library(xml2)
library(digest)
# Create a csv file for the science object
expect_false(is.null(d1cTest))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile)
metadataId <- getIdentifier(metadataObj)
# Associate the metadata object with each data object using the 'insertRelationships' method.
# Since a relationship type (the predicate argument) is not specified, the default relationship
# of 'cito:documents' is used, to indicate the the metadata object documents each data object.
# See "http://purl.org/spar/cito", for further information about the "Citation Type Ontology".
dp <- addMember(dp, metadataObj)
pkgId <- uploadDataPackage(d1cTest, dp, public=TRUE, quiet=TRUE)
expect_true(!is.na(pkgId))
done <- FALSE
trys <- 0
while(!done) {
if(trys > 10) break
Sys.sleep(1)
queryParams <- sprintf('q=id:"%s"', pkgId)
result <- query(d1cTest@mn, queryParams, as="list")
# Now download the package that was just created, and ensure that the checksums are all the
# requested type.
if(length(result) == 0) {
trys <- trys + 1
next
} else {
done <- TRUE
}
# Test the download by specifying the metadata id of the package. The 'getDataPackage()' function
# should be able determine the package id based on the metadata id.
testPkg <- getDataPackage(d1cTest, metadataId, quiet=T)
expect_equal(pkgId, testPkg@resmapId)
}
expect_true(done)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client downloadObject", {
skip_on_cran()
library(dataone)
#cli <- D1Client("PROD", "urn:node:KNB")
expect_false(is.null(d1cKNB))
expect_match(class(d1cKNB), "D1Client")
expect_match(d1cKNB@cn@baseURL, "https://cn.dataone.org/cn")
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cKNB@mn))
if(authValid) {
# Skip if Mac OS and X.509 Certificate
if(dataone:::getAuthMethod(am, d1cKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
}
# Try downloading a known object from the PROD environment
pid <- "solson.5.1"
path <- tempdir()
file <- downloadObject(d1cKNB, pid, path)
expect_match(class(file), "path")
expect_true(file.exists(file))
unlink(file)
})
test_that("D1Client uploadDataPackage public argument works", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
expect_false(is.null(d1cTest))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
expect_match(metadataObj@sysmeta@identifier, "urn:uuid")
# give metadata object an access policy without public read
metadataObj <- addAccessRule(metadataObj, "CN=arctic-data-admins,DC=dataone,DC=org", "read")
metadataObj <- addAccessRule(metadataObj, "CN=arctic-data-admins,DC=dataone,DC=org", "write")
metadataObj <- addAccessRule(metadataObj, "CN=arctic-data-admins,DC=dataone,DC=org", "changePermission")
dp <- addMember(dp, metadataObj)
expect_true(is.element(metadataObj@sysmeta@identifier, getIdentifiers(dp)))
# Upload the data package to DataONE with public set to TRUE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, preferredNodes=preferredNodes, public=TRUE)
expect_true(!is.null(resourceMapId))
# check that all members of the package have public read
sys_rm <- getSystemMetadata(d1cTest@mn, resourceMapId)
sys_mo <- getSystemMetadata(d1cTest@mn, metadataObj@sysmeta@identifier)
expect_true("public" %in% sys_rm@accessPolicy$subject)
expect_true("public" %in% sys_mo@accessPolicy$subject)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataPackage doesn't change the rightsHolder", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
# set rightsHolder on metadata to a test ORCID
metadataObj@sysmeta@rightsHolder <- "http://orcid.org/0000-0000-0000-0000"
dp <- addMember(dp, metadataObj)
# set rightsHolder on resource map to a test ORCID
dp@sysmeta@rightsHolder <- "http://orcid.org/0000-0000-0000-0000"
# Upload the data package to DataONE with public set to TRUE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, public=TRUE)
# check that all members of the package have public read
sys_rm <- getSystemMetadata(d1cTest@mn, resourceMapId)
sys_mo <- getSystemMetadata(d1cTest@mn, metadataObj@sysmeta@identifier)
expect_equal("http://orcid.org/0000-0000-0000-0000", sys_rm@rightsHolder)
expect_equal("http://orcid.org/0000-0000-0000-0000", sys_rm@rightsHolder)
} else {
skip("This test requires valid authentication.")
}
})
DataONEorg/rdataone documentation built on June 16, 2022, 7:01 p.m.
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test_that("dataone library loads", {
expect_true(require(dataone))
})
test_that("D1Client constructors", {
skip_on_cran()
library(dataone)
#cli <- new("D1Client")
expect_false(is.null(d1cProd))
expect_match(class(d1cProd), "D1Client")
expect_match(d1cProd@cn@baseURL, "https://cn.dataone.org/cn")
#cli <- new("D1Client", env="PROD", mNodeid="urn:node:KNB")
expect_false(is.null(d1cKNB))
expect_match(class(d1cKNB), "D1Client")
expect_match(d1cKNB@cn@baseURL, "https://cn.dataone.org/cn")
expect_match(d1cKNB@mn@baseURL, "https://knb.ecoinformatics.org/knb/d1/mn")
# Skip the remainder of the tests because these test environments are
# often down due to upgrades, reconfiguring, testing new features.
skip_on_cran()
cli <- new("D1Client", cn=cnStaging, mn=getMNode(cnStaging, "urn:node:mnTestKNB"))
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn-stage.test.dataone.org/cn")
expect_match(cli@mn@baseURL, "https://dev.nceas.ucsb.edu/knb/d1/mn")
cli <- D1Client()
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn.dataone.org/cn")
cli <- D1Client("STAGING")
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn-stage.test.dataone.org/cn")
# Skip the hightly unstable environments when testing on cran
skip_on_cran()
cli <- D1Client("SANDBOX")
expect_false(is.null(cli))
expect_match(class(cli), "D1Client")
expect_match(cli@cn@baseURL, "https://cn-sandbox.test.dataone.org/cn")
#cli <- D1Client("DEV")
#expect_false(is.null(cli))
#expect_match(class(cli), "D1Client")
#expect_match(cli@cn@baseURL, "https://cn-dev.test.dataone.org/cn")
})
test_that("D1Client methods", {
skip_on_cran()
# Test listMemberNodes
#cli <- D1Client("PROD")
nodes <- listMemberNodes(d1cProd)
expect_gt(length(nodes), 0)
expect_identical(class(nodes), "list")
# The remainder of this test uses development machines.
skip_on_cran()
# Test getEndPoint()
cli <- D1Client("STAGING")
cnUrl <- getEndpoint(cli)
expect_match(cnUrl, "https://cn-stage.test.dataone.org/cn")
# Test getMNodeId()
cli <- D1Client("STAGING", "urn:node:mnTestKNB")
expect_match(getMNodeId(cli), "urn:node:mnTestKNB")
# Test setMNodeId
cli <- new("D1Client", env="STAGING")
cli <- setMNodeId(cli, "urn:node:mnTestKNB")
expect_match(cli@mn@identifier, "urn:node:mnTestKNB")
})
test_that("D1Client getDataObject", {
skip_on_cran()
library(dataone)
library(digest)
#cli <- D1Client("PROD", "urn:node:KNB")
expect_false(is.null(d1cKNB))
expect_match(class(d1cKNB), "D1Client")
expect_match(d1cKNB@cn@baseURL, "https://cn.dataone.org/cn")
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cKNB@mn))
if(authValid) {
# Skip if Mac OS and X.509 Certificate
if(dataone:::getAuthMethod(am, d1cKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
}
# Try retrieving a known object from the PROD environment
pid <- "solson.5.1"
obj <- getDataObject(d1cKNB, pid, checksumAlgorithm="SHA-256")
cname <- class(obj)[1]
expect_match(cname, "DataObject")
expect_match(class(obj@sysmeta), "SystemMetadata")
expect_match(getIdentifier(obj), pid)
expect_match(getFormatId(obj), "text/csv")
data <- getData(obj)
sha256 <- digest(data, algo="sha256", serialize=FALSE, file=FALSE)
expect_match(sha256, obj@sysmeta@checksum)
})
test_that("D1Client uploadDataObject with raw data works", {
skip_on_cran()
library(dataone)
library(datapack)
# Create a DataObject with a raw R object and upload to DataONE
data <- charToRaw("1,2,3\n4,5,6\n")
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
expect_false(is.null(d1cTest))
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
# Create DataObject for the science data
do <- new("DataObject", format="text/csv", dataobj=data, mnNodeId=getMNodeId(d1cTest))
expect_match(do@sysmeta@identifier, "urn:uuid")
newId <- uploadDataObject(d1cTest, do, replicate=FALSE, preferredNodes=NA, public=TRUE)
expect_true(!is.null(newId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataObject with filename works", {
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
expect_false(is.null(d1cTest))
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
# Create DataObject for the science data
do <- new("DataObject", format="text/csv", mnNodeId=getMNodeId(d1cTest), filename=csvfile)
expect_match(do@sysmeta@identifier, "urn:uuid")
newId <- uploadDataObject(d1cTest, do, replicate=FALSE, preferredNodes=NA , public=TRUE)
expect_true(!is.null(newId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataPackage works", {
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
#d1c <- D1Client("SANDBOX2", "urn:node:mnDemo2")
#d1c <- D1Client("DEV2", "urn:node:mnDevUCSB2")
expect_false(is.null(d1cTest))
#preferredNodes <- c("urn:node:mnDemo9")
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create DataObject for the science data
sciObj <- new("DataObject", format="text/csv", mnNodeId=getMNodeId(d1cTest), filename=csvfile)
# It's possible to set access rules for DataObject now, or for all DataObjects when they are uploaded to DataONE via uploadDataPackage
expect_match(sciObj@sysmeta@identifier, "urn:uuid")
sciObj <- setPublicAccess(sciObj)
accessRules <- data.frame(subject=c("uid=smith,ou=Account,dc=example,dc=com", "uid=slaughter,o=unaffiliated,dc=example,dc=org"), permission=c("write", "changePermission"))
sciObj <- addAccessRule(sciObj, accessRules)
dp <- addMember(dp, sciObj)
expect_true(is.element(sciObj@sysmeta@identifier, getIdentifiers(dp)))
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
expect_match(metadataObj@sysmeta@identifier, "urn:uuid")
dp <- addMember(dp, metadataObj)
expect_true(is.element(metadataObj@sysmeta@identifier, getIdentifiers(dp)))
# Associate the metadata object with the science object it describes
dp <- insertRelationship(dp, subjectID=getIdentifier(metadataObj), objectIDs=getIdentifier(sciObj))
# Upload the data package to DataONE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, preferredNodes=preferredNodes, public=TRUE, accessRules=accessRules)
expect_true(!is.null(resourceMapId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataPackage works for a minimal DataPackage", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
expect_false(is.null(d1cTest))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
expect_match(metadataObj@sysmeta@identifier, "urn:uuid")
dp <- addMember(dp, metadataObj)
expect_true(is.element(metadataObj@sysmeta@identifier, getIdentifiers(dp)))
# Upload the data package to DataONE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, preferredNodes=preferredNodes, public=TRUE)
expect_true(!is.null(resourceMapId))
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client updateDataPackage works", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
library(xml2)
library(digest)
# Create a csv file for the science object
#d1c <- D1Client("STAGING", "urn:node:mnStageUCSB2")
#d1c <- D1Client("STAGING2", "urn:node:mnTestKNB")
#d1c <- D1Client("DEV2", "urn:node:mnDevUCSB1")
expect_false(is.null(d1cTestKNB))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTestKNB@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTestKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile)
metadataId <- getIdentifier(metadataObj)
# Associate the metadata object with each data object using the 'insertRelationships' method.
# Since a relationship type (the predicate argument) is not specified, the default relationship
# of 'cito:documents' is used, to indicate the the metadata object documents each data object.
# See "http://purl.org/spar/cito", for further information about the "Citation Type Ontology".
dp <- addMember(dp, metadataObj)
sourceData <- system.file("extdata/sample.csv", package="dataone")
sourceObj <- new("DataObject", format="text/csv", filename=sourceData)
dp <- addMember(dp, sourceObj, metadataObj)
resolveURL <- sprintf("%s/%s/object", d1cTestKNB@mn@baseURL, d1cTestKNB@mn@APIversion)
# Update the distribution URL in the metadata with the identifier that has been assigned to
# this DataObject. This provides a direct link between the detailed information for this package
# member and DataONE, which will assist DataONE in accessing and displaying this detailed information.
xpathToURL <- "//dataTable/physical/distribution[../objectName/text()=\"OwlNightj.csv\"]/online/url"
newURL <- sprintf("%s/%s", resolveURL, getIdentifier(sourceObj))
dp <- updateMetadata(dp, metadataId, xpath=xpathToURL, newURL)
metadataId <- selectMember(dp, name="sysmeta@formatId", value="eml://ecoinformatics.org/eml-2.1.1")
metadataObj <- getMember(dp, metadataId)
progFile <- system.file("extdata/filterSpecies.R", package="dataone")
progObj <- new("DataObject", format="application/R", filename=progFile, mediaType="text/x-rsrc")
dp <- addMember(dp, progObj, metadataObj)
xpathToURL <- "//otherEntity/physical/distribution[../objectName/text()=\"filterObs.R\"]/online/url"
newURL <- sprintf("%s/%s", resolveURL, getIdentifier(progObj))
dp <- updateMetadata(dp, metadataId, xpath=xpathToURL, newURL)
metadataId <- selectMember(dp, name="sysmeta@formatId", value="eml://ecoinformatics.org/eml-2.1.1")
metadataObj <- getMember(dp, metadataId)
outputData <- system.file("extdata/filteredSpecies.csv", package="dataone")
outputObj <- new("DataObject", format="text/csv", filename=outputData)
dp <- addMember(dp, outputObj, metadataObj)
xpathToURL <- "//dataTable/physical/distribution[../objectName/text()=\"Strix-occidentalis-obs.csv\"]/online/url"
newURL <- sprintf("%s/%s", resolveURL, getIdentifier(outputObj))
dp <- updateMetadata(dp, metadataId, xpath=xpathToURL, newURL)
# Upload the data package to DataONE
newPkg <- uploadDataPackage(d1cTestKNB, dp, public=TRUE, quiet=TRUE, as="DataPackage")
pkgId <- newPkg@resmapId
expect_true(!is.na(pkgId))
# Sleep for 90 secondsl to let indexing finish for the package. Because we are imposing a wait on this
# package, this test is not suitable for use in CRAN.
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client updateDataPackage with new package using previously uploaded objects works", {
# Test the typical workflow of creating a DataONE package by first uploading all data objects for the package,
# then creating a package from the already uploaded objects.
skip_on_cran()
library(dataone)
library(datapack)
library(xml2)
library(digest)
expect_false(is.null(d1cTestKNB))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTestKNB@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTestKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
# First upload objects to DataONE that will be collected into a package
sourceData <- system.file("extdata/OwlNightj.csv", package="dataone")
sourceObj <- new("DataObject", format="text/csv", filename=sourceData)
sourceObj <- addAccessRule(sourceObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
sourceId <- uploadDataObject(d1cTestKNB, sourceObj, public=T, quiet=T)
expect_true(!is.na(sourceId))
progFile <- system.file("extdata/filterObs.R", package="dataone")
progObj <- new("DataObject", format="application/R", filename=progFile, mediaType="text/x-rsrc")
progObj <- addAccessRule(progObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
progId <- uploadDataObject(d1cTestKNB, progObj, public=T, quiet=T)
expect_true(!is.na(progId))
outputData <- system.file("extdata/Strix-occidentalis-obs.csv", package="dataone")
outputObj <- new("DataObject", format="text/csv", filename=outputData)
outputObj <- addAccessRule(outputObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
outputId <- uploadDataObject(d1cTestKNB, outputObj, public=T, quiet=T)
expect_true(!is.na(outputId))
# Create a new package, and download each member (lazyLoaded) that was just uploaded, then add them
# to the package and upload. This workflow does not require that package members are downloaded with
# lazyLoad, this is done here just for efficiency. If a package member is downloaded without lazyLoad,
# it will not be-reuploaded when the package is uploaded, unless it has been updated (i.e. updated contents,
# or sysmeta).
pkg <- new("DataPackage")
# Create metadata object that describes the package
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile)
metadataObj <- addAccessRule(metadataObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
pkg <- addMember(pkg, metadataObj)
metadataId <- getIdentifier(metadataObj)
newSourceObj <- getDataObject(d1cTestKNB, sourceId, lazyLoad=T, quiet=T)
pkg <- addMember(pkg, newSourceObj, metadataObj)
newProgObj <- getDataObject(d1cTestKNB, progId, lazyLoad=T, quiet=T)
pkg <- addMember(pkg, newProgObj, metadataObj)
newOutputObj <- getDataObject(d1cTestKNB, outputId, lazyLoad=T, quiet=T)
pkg <- addMember(pkg, newOutputObj, metadataObj)
resourceMapId <- uploadDataPackage(d1cTestKNB, pkg, public=TRUE, quiet=T)
expect_false(is.na(resourceMapId))
# Now test that we can download the newly created package and add an existing object
# Now add a new package member that was omitted from the original package
auxFile <- system.file("extdata/WeatherInf.txt", package="dataone")
auxObj <- new("DataObject", format="text/plain", file=auxFile)
auxObj <- addAccessRule(auxObj, "http://orcid.org/0000-0002-2192-403X", "changePermission")
auxId <- uploadDataObject(d1cTestKNB, auxObj, public=T, quiet=T)
expect_true(!is.na(auxId))
# Have to sleep just a bit, as indexing can take awhile to complete
# Keep trying for ten seconds for the package to be indexed
done <- FALSE
trys <- 0
while(!done) {
if(trys > 10) break
Sys.sleep(1)
queryParams <- sprintf('q=id:"%s"', resourceMapId)
result <- query(d1cTestKNB@mn, queryParams, as="list")
# Now download the package that was just created, and ensure that the checksums are all the
# requested type.
if(length(result) == 0) {
trys <- trys + 1
next
} else {
done <- TRUE
}
newAuxObj <- getDataObject(d1cTestKNB, auxId, lazyLoad=T, quiet=T)
editPkg <- getDataPackage(d1cTestKNB, identifier=resourceMapId, lazyLoad=TRUE, quiet=TRUE)
}
expect_true(done)
editPkg <- addMember(editPkg, newAuxObj, metadataObj)
newResmapId <- uploadDataPackage(d1cTestKNB, editPkg, public=TRUE, quiet=T)
expect_false(is.na(newResmapId))
expect_false(resourceMapId == newResmapId)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client getDataPackage with checksumAlgorithm specified works", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
library(xml2)
library(digest)
# Create a csv file for the science object
expect_false(is.null(d1cTestKNB))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTestKNB@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTestKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
sha256 <- "SHA-256"
md5 <- "MD5"
checksumAlgorithm <- sha256
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile, checksum=checksumAlgorithm)
metadataId <- getIdentifier(metadataObj)
dp <- addMember(dp, metadataObj)
sourceData <- system.file("extdata/sample.csv", package="dataone")
sourceObj <- new("DataObject", format="text/csv", filename=sourceData, checksum=checksumAlgorithm)
dp <- addMember(dp, sourceObj, metadataObj)
progFile <- system.file("extdata/filterSpecies.R", package="dataone")
progObj <- new("DataObject", format="application/R", filename=progFile, mediaType="text/x-rsrc", checksum=checksumAlgorithm)
dp <- addMember(dp, progObj, metadataObj)
outputData <- system.file("extdata/filteredSpecies.csv", package="dataone")
outputObj <- new("DataObject", format="text/csv", filename=outputData, checksum=checksumAlgorithm)
dp <- addMember(dp, outputObj, metadataObj)
# Upload the data package to DataONE
pkgId <- uploadDataPackage(d1cTestKNB, dp, public=TRUE, quiet=TRUE)
expect_true(!is.na(pkgId))
# Have to sleep just a bit, as indexing can take awhile to complete
# Keep trying for ten seconds for the package to be indexed
done <- FALSE
trys <- 0
while(!done) {
if(trys > 10) break
Sys.sleep(1)
queryParams <- sprintf('q=id:"%s"', pkgId)
result <- query(d1cTestKNB@mn, queryParams, as="list")
# Now download the package that was just created, and ensure that the checksums are all the
# requested type.
if(length(result) == 0) {
trys <- trys + 1
next
} else {
done <- TRUE
}
pkg <- getDataPackage(d1cTestKNB, identifier=pkgId, lazyLoad=TRUE, limit="0MB", quiet=TRUE, checksumAlgorithm=sha256)
algorithms <- getValue(pkg, name="sysmeta@checksumAlgorithm")
expect_true(all(algorithms == sha256))
# Download the package again, requesting a different checksum type, and ensure that the checksums are all the
# new type.
pkg <- getDataPackage(d1cTestKNB, identifier=pkgId, lazyLoad=TRUE, limit="0MB", quiet=TRUE, checksumAlgorithm=md5)
algorithms <- getValue(pkg, name="sysmeta@checksumAlgorithm")
expect_true(all(algorithms==md5))
}
expect_true(done)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client listMemberNodes() works", {
skip_on_cran()
library(dataone)
#d1c <- D1Client("PROD")
nodelist <- listMemberNodes(d1cProd)
expect_true(length(nodelist) > 0)
expect_match(class(nodelist[[1]]), "Node")
expect_match(nodelist[[1]]@identifier, "urn:node:")
expect_match(nodelist[[1]]@type, "cn|mn")
expect_match(nodelist[[1]]@state, "up")
expect_match(nodelist[[length(nodelist)]]@identifier, "urn:node:")
expect_match(nodelist[[length(nodelist)]]@baseURL, "http")
expect_match(nodelist[[length(nodelist)]]@subject, "urn:node:")
expect_match(nodelist[[length(nodelist)]]@type, "cn|mn")
})
test_that("D1Client updateDataPackage works for a metadata only DataPackage", {
skip_on_cran()
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
# This is a long running test, so it should be run manually, which means
# running "test_file("tests/testthat/packageUpdate.R"), as this file is not
# run by default by testthat due to the name not including 'test*'
library(dataone)
library(datapack)
library(xml2)
library(digest)
# Create a csv file for the science object
expect_false(is.null(d1cTest))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/strix-pacific-northwest.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", filename=emlFile)
metadataId <- getIdentifier(metadataObj)
# Associate the metadata object with each data object using the 'insertRelationships' method.
# Since a relationship type (the predicate argument) is not specified, the default relationship
# of 'cito:documents' is used, to indicate the the metadata object documents each data object.
# See "http://purl.org/spar/cito", for further information about the "Citation Type Ontology".
dp <- addMember(dp, metadataObj)
pkgId <- uploadDataPackage(d1cTest, dp, public=TRUE, quiet=TRUE)
expect_true(!is.na(pkgId))
done <- FALSE
trys <- 0
while(!done) {
if(trys > 10) break
Sys.sleep(1)
queryParams <- sprintf('q=id:"%s"', pkgId)
result <- query(d1cTest@mn, queryParams, as="list")
# Now download the package that was just created, and ensure that the checksums are all the
# requested type.
if(length(result) == 0) {
trys <- trys + 1
next
} else {
done <- TRUE
}
# Test the download by specifying the metadata id of the package. The 'getDataPackage()' function
# should be able determine the package id based on the metadata id.
testPkg <- getDataPackage(d1cTest, metadataId, quiet=T)
expect_equal(pkgId, testPkg@resmapId)
}
expect_true(done)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client downloadObject", {
skip_on_cran()
library(dataone)
#cli <- D1Client("PROD", "urn:node:KNB")
expect_false(is.null(d1cKNB))
expect_match(class(d1cKNB), "D1Client")
expect_match(d1cKNB@cn@baseURL, "https://cn.dataone.org/cn")
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cKNB@mn))
if(authValid) {
# Skip if Mac OS and X.509 Certificate
if(dataone:::getAuthMethod(am, d1cKNB@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
}
# Try downloading a known object from the PROD environment
pid <- "solson.5.1"
path <- tempdir()
file <- downloadObject(d1cKNB, pid, path)
expect_match(class(file), "path")
expect_true(file.exists(file))
unlink(file)
})
test_that("D1Client uploadDataPackage public argument works", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
testdf <- data.frame(x=1:10,y=11:20)
csvfile <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".csv")
write.csv(testdf, csvfile, row.names=FALSE)
expect_false(is.null(d1cTest))
preferredNodes <- NA
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
expect_match(metadataObj@sysmeta@identifier, "urn:uuid")
# give metadata object an access policy without public read
metadataObj <- addAccessRule(metadataObj, "CN=arctic-data-admins,DC=dataone,DC=org", "read")
metadataObj <- addAccessRule(metadataObj, "CN=arctic-data-admins,DC=dataone,DC=org", "write")
metadataObj <- addAccessRule(metadataObj, "CN=arctic-data-admins,DC=dataone,DC=org", "changePermission")
dp <- addMember(dp, metadataObj)
expect_true(is.element(metadataObj@sysmeta@identifier, getIdentifiers(dp)))
# Upload the data package to DataONE with public set to TRUE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, preferredNodes=preferredNodes, public=TRUE)
expect_true(!is.null(resourceMapId))
# check that all members of the package have public read
sys_rm <- getSystemMetadata(d1cTest@mn, resourceMapId)
sys_mo <- getSystemMetadata(d1cTest@mn, metadataObj@sysmeta@identifier)
expect_true("public" %in% sys_rm@accessPolicy$subject)
expect_true("public" %in% sys_mo@accessPolicy$subject)
} else {
skip("This test requires valid authentication.")
}
})
test_that("D1Client uploadDataPackage doesn't change the rightsHolder", {
# Test that a DataPackage with only one member (metadata in this case) and not
# user defined relationships is created and uploaded correctly.
skip_on_cran()
library(dataone)
library(datapack)
# Create a csv file for the science object
# Set 'subject' to authentication subject, if available, so we will have permission to change this object
am <- AuthenticationManager()
suppressMessages(authValid <- dataone:::isAuthValid(am, d1cTest@mn))
if (authValid) {
if(dataone:::getAuthMethod(am, d1cTest@mn) == "cert" && grepl("apple-darwin", sessionInfo()$platform)) skip("Skip authentication w/cert on Mac OS X")
dp <- new("DataPackage")
# Create metadata object that describes science data
emlFile <- system.file("extdata/sample-eml.xml", package="dataone")
metadataObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", mnNodeId=getMNodeId(d1cTest), filename=emlFile)
# set rightsHolder on metadata to a test ORCID
metadataObj@sysmeta@rightsHolder <- "http://orcid.org/0000-0000-0000-0000"
dp <- addMember(dp, metadataObj)
# set rightsHolder on resource map to a test ORCID
dp@sysmeta@rightsHolder <- "http://orcid.org/0000-0000-0000-0000"
# Upload the data package to DataONE with public set to TRUE
resourceMapId <- uploadDataPackage(d1cTest, dp, replicate=TRUE, numberReplicas=1, public=TRUE)
# check that all members of the package have public read
sys_rm <- getSystemMetadata(d1cTest@mn, resourceMapId)
sys_mo <- getSystemMetadata(d1cTest@mn, metadataObj@sysmeta@identifier)
expect_equal("http://orcid.org/0000-0000-0000-0000", sys_rm@rightsHolder)
expect_equal("http://orcid.org/0000-0000-0000-0000", sys_rm@rightsHolder)
} else {
skip("This test requires valid authentication.")
}
})
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