tests/testthat/test_DataObject.R

In datapack: A Flexible Container to Transport and Manipulate Data and Associated Resources

test_that("datapack library loads", {
    expect_true(library(datapack, logical.return = TRUE))
})

test_that("DataObject constructors work", {
    library(datapack)
    library(digest)
    identifier <- "id1"
    user <- "matt"
    data <- charToRaw("1,2,3\n4,5,6\n")
    format <- "text/csv"
    node <- "urn:node:KNB"
    
    # Test the constructor that builds a DataObject object
    do <- new("DataObject", identifier, data, filename="test.cvs", format=format, user=user, mnNodeId=node)
    expect_equal(class(do)[[1]], "DataObject")
    expect_equal(do@sysmeta@serialVersion, 1)
    expect_equal(do@sysmeta@identifier, identifier)
    expect_equal(do@sysmeta@submitter, user)
    expect_equal(do@sysmeta@size, length(data))
    expect_equal(length(do@data), length(data))
    expect_equal(getIdentifier(do), identifier)
    expect_equal(getFormatId(do), format)
    sha <- digest(data, algo="sha256", serialize=FALSE, file=FALSE)
    sm <- new("SystemMetadata", identifier=identifier, formatId=format, size=length(data), submitter=user, rightsHolder=user, checksum=sha, originMemberNode=node, authoritativeMemberNode=node)
    expect_equal(sm@identifier, identifier)
    
    # Now test the constructor that passes in SystemMetadata and data
    do <- new("DataObject", sm, data, filename="test.csv")
    expect_equal(do@sysmeta@serialVersion, 1)
    expect_equal(do@sysmeta@identifier, identifier)
    expect_equal(do@sysmeta@submitter, user)
    expect_equal(do@sysmeta@checksumAlgorithm, "SHA-256")
    expect_equal(do@sysmeta@checksum, sha)
    expect_equal(do@sysmeta@size, length(data))
    expect_equal(do@sysmeta@size, length(data))
    expect_equal(length(do@data), length(data))
    expect_equal(getIdentifier(do), identifier)
    expect_equal(getFormatId(do), format)
    
    # Now test the constructor that passes in SystemMetadata and a filename (not data)
    tf <- tempfile()
    con <- file(tf, "wb")
    writeBin(data, con)
    close(con)
    sha_file <- digest(tf, algo="sha256", serialize=FALSE, file=TRUE)
    do <- new("DataObject", sm, filename=tf, checksumAlgorith="SHA-256")
    expect_equal(do@sysmeta@serialVersion, 1)
    expect_equal(do@sysmeta@identifier, identifier)
    expect_equal(do@sysmeta@submitter, user)
    expect_equal(do@sysmeta@checksumAlgorithm, "SHA-256")
    expect_equal(do@sysmeta@checksum, sha)
    expect_equal(do@sysmeta@size, length(data))
    expect_equal(file.info(tf)$size, length(data))
    expect_equal(getIdentifier(do), identifier)
    expect_equal(getFormatId(do), format)
    data2 <- getData(do)
    sha_get_data <- digest(data2, algo="sha256", serialize=FALSE, file=FALSE)
    expect_match(sha_get_data, sha)
    expect_match(sha_file, do@sysmeta@checksum)
    expect_match(sha_get_data, do@sysmeta@checksum)
    
    # Verify that the DataObject initialization prepares the sysmeta correctly, if it is not
    # included in the parameter list.
    
    sha_file <- digest(tf, algo="sha1", serialize=FALSE, file=TRUE)
    do <- new("DataObject", identifier, filename=tf, checksumAlgorith="SHA1")
    expect_equal(do@sysmeta@checksum, sha_file)
    expect_equal(do@sysmeta@checksumAlgorithm, "SHA1")
    
    sha_file <- digest(tf, algo="md5", serialize=FALSE, file=TRUE)
    do <- new("DataObject", identifier, filename=tf, checksumAlgorith="MD5")
    expect_equal(do@sysmeta@checksum, sha_file)
    expect_equal(do@sysmeta@checksumAlgorithm, "MD5")
    
    unlink(tf)
    
    # Test that the constructor works for a data path, with a few different forms
    targetPath="./data/rasters/test.csv"
    do <- new("DataObject", sm, data, filename="test.csv", targetPath=targetPath)
    expect_equal(do@targetPath, targetPath)
    
    targetPath="data/rasters/test.csv"
    do <- new("DataObject", sm, data, filename="test.csv", targetPath=targetPath)
    expect_equal(do@targetPath, targetPath)

})
test_that("DataObject accessPolicy methods", {
    library(datapack)
    library(digest)
    identifier <- "id1"
    user <- "matt"
    data <- charToRaw("1,2,3\n4,5,6")
    format <- "text/csv"
    node <- "urn:node:KNB"
    
    do <- new("DataObject", identifier, data, format, user, node, filename="test.csv")
    expect_equal(class(do)[[1]], "DataObject")
    
    # Public access should not be present at first
    canRead <- canRead(do, "uid=anybody,DC=somedomain,DC=org")
    expect_false(canRead)
    
    # Test that setting public access works
    do <- setPublicAccess(do)
    isPublic <- hasAccessRule(do@sysmeta, "public", "read")
    expect_true(isPublic)
    
    # Test that custom access rules can be added to sysmeta of a DataObject
    accessRules <- data.frame(subject=c("uid=smith,ou=Account,dc=example,dc=com", 
                                        "uid=wiggens,o=unaffiliated,dc=example,dc=org"), 
                              permission=c("write", "changePermission"), stringsAsFactors=FALSE)
    do <- addAccessRule(do, accessRules)
    expect_true(hasAccessRule(do@sysmeta, "uid=smith,ou=Account,dc=example,dc=com", "write"))
    expect_true(hasAccessRule(do@sysmeta, "uid=wiggens,o=unaffiliated,dc=example,dc=org", "changePermission"))
    expect_false(hasAccessRule(do@sysmeta, "uid=smith,ou=Account,dc=example,dc=com", "changePermission"))
    
    # Public access should now be possible
    canRead <- canRead(do, "uid=anybody,DC=somedomain,DC=org")
    expect_true(canRead)
    
    # Test that an access policy can be cleared, i.e. all access rules removed.
    do <- clearAccessPolicy(do)
    expect_true(nrow(do@sysmeta@accessPolicy) == 0)
    expect_false(hasAccessRule(do@sysmeta, "uid=smith,ou=Account,dc=example,dc=com", "write"))
    expect_false(hasAccessRule(do@sysmeta, "uid=wiggens,o=unaffiliated,dc=example,dc=org", "changePermission"))
    expect_false(hasAccessRule(do@sysmeta, "uid=smith,ou=Account,dc=example,dc=com", "changePermission"))
    
    # Chech using parameter "y" as a character string containing the subject of the access rule:
    do <- new("DataObject", identifier, data, format, user, node, filename="test.csv")
    do <- addAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "write")
    do <- addAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "changePermission")
    expect_true(hasAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "write"))
    expect_true(hasAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "changePermission"))
    do <- removeAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "changePermission")
    expect_false(hasAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "changePermission"))
    do <- removeAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "write")
    expect_false(hasAccessRule(do, "uid=smith,ou=Account,dc=example,dc=com", "write"))
        
    # Check parameter "y" as a data.frame containing one or more access rules:
    # Add write, changePermission for uid=jones,...
    do <- addAccessRule(do, "uid=jones,ou=Account,dc=example,dc=com", "write")
    do <- addAccessRule(do, "uid=jones,ou=Account,dc=example,dc=com", "changePermission")
    expect_true(hasAccessRule(do, "uid=jones,ou=Account,dc=example,dc=com", "write"))
    expect_true(hasAccessRule(do, "uid=jones,ou=Account,dc=example,dc=com", "changePermission"))
        
    # Now take privs for uid=jones,... away
    accessRules <- data.frame(subject=c("uid=jones,ou=Account,dc=example,dc=com", 
                                        "uid=jones,ou=Account,dc=example,dc=com"), 
                                        permission=c("write", "changePermission"))
    do <- removeAccessRule(do, accessRules)
    expect_false(hasAccessRule(do, "uid=jones,ou=Account,dc=example,dc=com", "write"))
    expect_false(hasAccessRule(do, "uid=jones,ou=Account,dc=example,dc=com", "changePermission"))
})

test_that("DataObject updateXML method", {
    library(datapack)
    library(XML)
    
    # Use a realistic value to update the XML of the metadata object
    resolveURL <- "https://cn.dataone.org/cn/v2/resolve"
    
    # Create the metadata object with a sample EML file
    sampleMeta <- system.file("./extdata/sample-eml.xml", package="datapack")
    metaObj <- new("DataObject", format="eml://ecoinformatics.org/eml-2.1.1", file=sampleMeta)
    
    # Create a sample data object
    sampleData <- system.file("./extdata/sample-data.csv", package="datapack") 
    dataObj <- new("DataObject", format="text/csv", file=sampleData)
    
    # In the metadata object, insert the newly assigned data 
    xp <- sprintf("//dataTable/physical/distribution[../objectName/text()=\"%s\"]/online/url", "sample-data.csv") 
    newURL <- sprintf("%s/%s", resolveURL, getIdentifier(dataObj))
    metaObj <- updateXML(metaObj, xpath=xp, replacement=newURL)
    
    # Now retrieve the new value from the metadata using an independent method (not using datapack) and see
    # if the metadata was actually updated.
    metadataDoc <- xmlInternalTreeParse(rawToChar(getData(metaObj)))
    nodeSet = xpathApply(metadataDoc,xp)
    URL <- xmlValue(nodeSet[[1]])
    
    expect_match(newURL, URL)
})

test_that("pathToPOSIX is correctly sanitizing file paths", {
    library(datapack)

    # This is a valid POSIX path; don't filter :
    drivePath <- "c:/test/myFile.csv"
    drivePathExpected <- "c:/test/myFile.csv"
    
    # The '..' characters should be removed
    traversalPath <- "data/../moreData/../../rasters/myFile.csv"
    traversalPathExpected <- "data/_/moreData/_/_/rasters/myFile.csv"
    
    # The The particular characters aren't allowed in POSIX
    specialCharacterPath <- "geo-data/?home/%APPDATA/myFile.csv"
    specialCharacterPathExpexted <- "geo-data/_home/%APPDATA/myFile.csv"
    
    windowsPath <- "c:\\Windows\\System32"
    windowsPathExpected <- "c:/Windows/System32"
    expect_equal(pathToPOSIX(drivePath) , drivePathExpected)
    expect_equal(pathToPOSIX(traversalPath),traversalPathExpected)
    expect_equal(pathToPOSIX(specialCharacterPath), specialCharacterPathExpexted)
    expect_equal(pathToPOSIX(windowsPath), windowsPathExpected)
})