Update tests for testthat 3e compatibility (#125)

inst/tests/test.ResourceMap.R

@@ -1,4 +1,3 @@
-context("ResourceMap")
 test_that("datapack library loads", {
   expect_true(library(datapack, logical.return=TRUE))
 })
@@ -48,20 +47,20 @@ test_that("ResourceMap creation from DataPackage triples", {
 
   relations <- getRelationships(dp)
   # Test if the data frame with retrieved relationships was constructed correctly
-  expect_that(nrow(relations), equals(7))
+  expect_equal(nrow(relations), 7)
   expect_match(relations[relations$subject == mdId, 'predicate'], "documents")
 
   # Now initialize a ResourceMap with the relationships.
   resMapId <- sprintf("resourceMap:%s", UUIDgenerate())  
   resMap <- new("ResourceMap", id=resMapId)
-  expect_that(class(resMap)[[1]], equals("ResourceMap"))
+  expect_equal(class(resMap)[[1]], "ResourceMap")
   resMap <- createFromTriples(resMap, relations, getIdentifiers(dp))
 
   # Serialize the ResourceMap to a file.
   filePath <- sprintf("%s/%s.rdf", tempdir(), resMapId)
   status <- serializeRDF(resMap, filePath)
   found <- grep("wasDerivedFrom", readLines(filePath))
-  expect_that(length(found), is_more_than(0))
+  expect_gt(length(found), 0)
 
   freeResourceMap(resMap)
   rm(resMap)

inst/tests/test.SystemMetadata.R

@@ -1,29 +1,28 @@
-context("SystemMetadata")
 test_that("datapack library loads", {
 	expect_true(library(datapack, logical.return = TRUE))
 })
 test_that("SystemMetadata constructors", {
     library(datapack)
     sysmeta <- new("SystemMetadata")
-    expect_that(sysmeta@serialVersion, equals(1))
+    expect_equal(sysmeta@serialVersion, 1)
     expect_true(is.na(sysmeta@identifier))
     sysmeta <- new("SystemMetadata", identifier="TestId", formatId="text/csv")
-    expect_that(sysmeta@identifier, equals("TestId"))
-    expect_that(sysmeta@formatId, equals("text/csv"))
+    expect_equal(sysmeta@identifier, "TestId")
+    expect_equal(sysmeta@formatId, "text/csv")
 })
 test_that("XML SystemMetadata parsing works", {
   library(datapack)
   library(XML)
   testid <- "doi:10.xxyy/AA/tesdoc123456789"
   sysmeta <- new("SystemMetadata")
-  expect_that(sysmeta@serialVersion, equals(1))
+  expect_equal(sysmeta@serialVersion, 1)
   doc <- xmlParseDoc("../testfiles/sysmeta.xml", asText=FALSE)
   expect_match(xmlValue(xmlRoot(doc)[["identifier"]]), testid)
   xml <- xmlRoot(doc)
   #getEncoding(doc)
   sysmeta <- parseSystemMetadata(sysmeta, xmlRoot(xml))
   expect_match(sysmeta@identifier, testid)
-  expect_that(nrow(sysmeta@accessPolicy), equals(5))
+  expect_equal(nrow(sysmeta@accessPolicy), 5)
   expect_match(as.character(sysmeta@accessPolicy$permission[[1]]), "read")
   expect_true(sysmeta@archived)
   csattrs <- xmlAttrs(xml[["checksum"]])
@@ -39,13 +38,13 @@ test_that("XML SystemMetadata parsing works", {
   # Parse v2.0 system metadata
   testid <- "0007f892-0d8f-4451-94e9-94d02ba5dd0d_0"
   sysmeta <- new("SystemMetadata")
-  expect_that(sysmeta@serialVersion, equals(1))
+  expect_equal(sysmeta@serialVersion, 1)
   doc <- xmlParseDoc("../testfiles/sysmeta-v2.xml", asText=FALSE)
   expect_match(xmlValue(xmlRoot(doc)[["identifier"]]), testid)
   xml <- xmlRoot(doc)
   sysmeta <- parseSystemMetadata(sysmeta, xmlRoot(xml))
   expect_match(sysmeta@identifier, testid)
-  expect_that(nrow(sysmeta@accessPolicy), equals(1))
+  expect_equal(nrow(sysmeta@accessPolicy), 1)
   expect_match(as.character(sysmeta@accessPolicy$permission[[1]]), "read")
   expect_false(sysmeta@archived)
   csattrs <- xmlAttrs(xml[["checksum"]])
@@ -57,7 +56,7 @@ test_that("XML SystemMetadata parsing works", {
   # Parse v2.0 system metadata, checking parsing of replication policy
   testid <- "0007f892-0d8f-4451-94e9-94d02ba5dd0d_0"
   sysmeta <- new("SystemMetadata")
-  expect_that(sysmeta@serialVersion, equals(1))
+  expect_equal(sysmeta@serialVersion, 1)
   doc <- xmlParseDoc("../testfiles/sysmeta-v2-repfalse.xml", asText=FALSE)
   expect_match(xmlValue(xmlRoot(doc)[["identifier"]]), testid)
   xml <- xmlRoot(doc)
@@ -67,7 +66,7 @@ test_that("XML SystemMetadata parsing works", {
   # Parse v2.0 system metadata, checking parsing when missing numReplicas
   testid <- "arctic-data.9794.1"
   sysmeta <- new("SystemMetadata")
-  expect_that(sysmeta@serialVersion, equals(1))
+  expect_equal(sysmeta@serialVersion, 1)
   doc <- xmlParseDoc("../testfiles/sysmeta-v2-repfalse-zero-reps.xml", asText=FALSE)
   expect_match(xmlValue(xmlRoot(doc)[["identifier"]]), testid)
   xml <- xmlRoot(doc)
@@ -80,7 +79,7 @@ test_that("XML SystemMetadata serialization works", {
     library(XML)
     testid <- "doi:10.xxyy/AA/tesdoc123456789"
     sysmeta <- new("SystemMetadata")
-    expect_that(sysmeta@serialVersion, equals(1))
+    expect_equal(sysmeta@serialVersion, 1)
     xml <- xmlParseDoc("../testfiles/sysmeta.xml", asText=FALSE)
     expect_match(xmlValue(xmlRoot(xml)[["identifier"]]), testid)
     sysmeta <- parseSystemMetadata(sysmeta, xmlRoot(xml))
@@ -124,7 +123,7 @@ test_that("SystemMetadata XML constructor works", {
     xml <- xmlRoot(doc)
     sysmeta <- SystemMetadata(xmlRoot(xml))
     expect_match(sysmeta@identifier, testid)
-    expect_that(nrow(sysmeta@accessPolicy), equals(5))
+    expect_equal(nrow(sysmeta@accessPolicy), 5)
     expect_match(as.character(sysmeta@accessPolicy$permission[[1]]), "read")
     expect_true(sysmeta@archived)
     csattrs <- xmlAttrs(xml[["checksum"]])
@@ -142,22 +141,22 @@ test_that("SystemMetadata validation works", {
     expect_true(isValid)
     sysmeta <- new("SystemMetadata", identifier="foo", checksum="jdhdjhfd", rightsHolder="ff")
     errors <- validate(sysmeta)
-    expect_that(length(errors), equals(2))
+    expect_equal(length(errors), 2)
 })
 
 test_that("SystemMetadata accessPolicy can be constructed and changed", {
     apolicy=data.frame(list("public", "read"))
     colnames(apolicy) <- c("subject", "permission")
     sysmeta <- new("SystemMetadata", identifier="foo", formatId="text/csv", size=59, checksum="jdhdjhfd", rightsHolder="ff", accessPolicy=apolicy)
-    expect_that(sysmeta@serialVersion, equals(1))
-    expect_that(nrow(sysmeta@accessPolicy), equals(1))
+    expect_equal(sysmeta@serialVersion, 1)
+    expect_equal(nrow(sysmeta@accessPolicy), 1)
     expect_match(as.character(sysmeta@accessPolicy$permission[[1]]), "read")
 
     sysmeta <- addAccessRule(sysmeta, "foo", "write")
-    expect_that(nrow(sysmeta@accessPolicy), equals(2))
+    expect_equal(nrow(sysmeta@accessPolicy), 2)
     # Try to add same rule again and make sure it didn't get duplicated
     sysmeta <- addAccessRule(sysmeta, "foo", "write")
-    expect_that(nrow(sysmeta@accessPolicy), equals(2))
+    expect_equal(nrow(sysmeta@accessPolicy), 2)
     expect_match(as.character(sysmeta@accessPolicy$permission[[2]]), "write")
     expect_true(hasAccessRule(sysmeta, "foo", "write"))
     apolicy=data.frame(subject=c("bar", "baz"), permission= c("changePermission", "write"))
@@ -167,7 +166,7 @@ test_that("SystemMetadata accessPolicy can be constructed and changed", {
     expect_true(hasAccessRule(sysmeta, "bar", "changePermission"))
     expect_true(hasAccessRule(sysmeta, "baz", "write"))
     expect_true(!hasAccessRule(sysmeta, "baz", "changePermission"))
-    expect_that(nrow(sysmeta@accessPolicy), equals(4))
+    expect_equal(nrow(sysmeta@accessPolicy), 4)
     expect_match(as.character(sysmeta@accessPolicy$permission[[4]]), "write")
     expect_match(as.character(sysmeta@accessPolicy$subject[[4]]), "baz")    
 })

inst/tests/test_DataObject.R

@@ -1,5 +1,3 @@
-context("DataObject")
-
 test_that("datapack library loads", {
     expect_true(library(datapack, logical.return = TRUE))
 })
@@ -15,27 +13,27 @@ test_that("DataObject constructors work", {
 
     # Test the constructor that builds a DataObject object
     do <- new("DataObject", identifier, data, filename="test.cvs", format=format, user=user, mnNodeId=node)
-    expect_that(class(do)[[1]], equals("DataObject"))
-    expect_that(do@sysmeta@serialVersion, equals(1))
-    expect_that(do@sysmeta@identifier, equals(identifier))
-    expect_that(do@sysmeta@submitter, equals(user))
-    expect_that(do@sysmeta@size, equals(length(data)))
-    expect_that(length(do@data), equals(length(data)))
-    expect_that(getIdentifier(do), equals(identifier))
-    expect_that(getFormatId(do), equals(format))
+    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)
     sha1 <- digest(data, algo="sha1", serialize=FALSE, file=FALSE)
     sm <- new("SystemMetadata", identifier=identifier, formatId=format, size=length(data), submitter=user, rightsHolder=user, checksum=sha1, originMemberNode=node, authoritativeMemberNode=node)
-    expect_that(sm@identifier, equals(identifier))
+    expect_equal(sm@identifier, identifier)
 
     # Now test the constructor that passes in SystemMetadata and data
     do <- new("DataObject", sm, data, filename="test.csv")
-    expect_that(do@sysmeta@serialVersion, equals(1))
-    expect_that(do@sysmeta@identifier, equals(identifier))
-    expect_that(do@sysmeta@submitter, equals(user))
-    expect_that(do@sysmeta@size, equals(length(data)))
-    expect_that(length(do@data), equals(length(data)))
-    expect_that(getIdentifier(do), equals(identifier))
-    expect_that(getFormatId(do), equals(format))
+    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)
 
     # Now test the constructor that passes in SystemMetadata and a filename (not data)
     tf <- tempfile()
@@ -44,13 +42,13 @@ test_that("DataObject constructors work", {
     close(con)
     sha1_file <- digest(tf, algo="sha1", serialize=FALSE, file=TRUE)
     do <- new("DataObject", sm, filename=tf)
-    expect_that(do@sysmeta@serialVersion, equals(1))
-    expect_that(do@sysmeta@identifier, equals(identifier))
-    expect_that(do@sysmeta@submitter, equals(user))
-    expect_that(do@sysmeta@size, equals(length(data)))
-    expect_that(file.info(tf)$size, equals(length(data)))
-    expect_that(getIdentifier(do), equals(identifier))
-    expect_that(getFormatId(do), equals(format))
+    expect_equal(do@sysmeta@serialVersion, 1)
+    expect_equal(do@sysmeta@identifier, identifier)
+    expect_equal(do@sysmeta@submitter, user)
+    expect_equal(do@sysmeta@size, length(data))
+    expect_equal(file.info(tf)$size, length(data))
+    expect_equal(getIdentifier(do), identifier)
+    expect_equal(getFormatId(do), format)
     data2 <- getData(do)
     sha1_get_data <- digest(data2, algo="sha1", serialize=FALSE, file=FALSE)
     expect_match(sha1_get_data, sha1)
@@ -59,11 +57,11 @@ test_that("DataObject constructors work", {
     # 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_that(do@targetPath, equals(targetPath))
+    expect_equal(do@targetPath, targetPath)
 
     targetPath="data/rasters/test.csv"
     do <- new("DataObject", sm, data, filename="test.csv", targetPath=targetPath)
-    expect_that(do@targetPath, equals(targetPath))
+    expect_equal(do@targetPath, targetPath)
 })
 test_that("DataObject accessPolicy methods", {
     library(datapack)
@@ -75,7 +73,7 @@ test_that("DataObject accessPolicy methods", {
     node <- "urn:node:KNB"
 
     do <- new("DataObject", identifier, data, format, user, node, filename="test.csv")
-    expect_that(class(do)[[1]], equals("DataObject"))
+    expect_equal(class(do)[[1]], "DataObject")
 
     # Public access should not be present at first
     canRead <- canRead(do, "uid=anybody,DC=somedomain,DC=org")