tests/testthat/test_queries.R

In rols: An R interface to the Ontology Lookup Service

## context("queries and iface.R code")

## children/getTermChildren - not implemented
## getChildrenFromRoot - not implemented
## getTermsByExactName - not implemented
## getTermsByAnnotationData - not implemented

## test_that("olsVersion/getVersion", {
##               v <- olsVersion()
##               expect_is(v, "character")
##               expect_identical(length(v), 5L)
##           })

## test_that("term/getTermById", {
##               expect_identical(term("GO:0005794", "GO"),
##                                "Golgi apparatus")
##               expect_null(term("GO:0000000", "GO"))
##               expect_warning(term("GO:0000000", "GO"))
##               expect_identical(term("210797", "NEWT"),
##                                "Golfingia vulgaris (Marine worm)")
##           })

## test_that("termMetadata/getTermMetadata", {
##               mtd <- termMetadata("GO:0005802", "GO")
##               expect_null(rols:::print.termMetadata(mtd))
##               expect_identical(mtd["exact_synonym_2"], c(exact_synonym_2 = "TGN"))
##               expect_identical(length(mtd), 9L)
##           })

## test_that("termXrefs/getTermXrefs", {
##               ans <- termXrefs("TGN transport vesicle", "GO")
##               ans2 <- termXrefs("TGN", "GO")
##               expect_equal(grep("GOC", ans), 1L)
##               expect_equal(grep("GOC", ans2), 3L)
##           })

## test_that("onologyNames/getOntologyNames", {
##               onms <- ontologyNames()
##               expect_is(onms, "character")
##               expect_true(length(onms) >= 93)
##           })

## test_that("ontologyLoadDate/getOntologyLoadDate", {
##               onms <- ontologyNames()
##               xx <- sapply(onms, ontologyLoadDate)
##               expect_is(xx, "character")
##               expect_identical(length(onms), length(xx))
##           })

## test_that("allIds/getAllTermsFromOntology", {
##               allms <- allIds("MS", simplify=FALSE)
##               expect_is(allms, "Map")
##               expect_true(length(allms) >= 5266)
##               allms2 <- allIds("MS", simplify=TRUE)
##               expect_is(allms2, "character")
##               expect_identical(length(allms), length(allms2))
##           })

## test_that("rootId/getRootTerms",{
##               goroot <- rootId("GO")
##               goans <-
##                   structure(c("biological_process",
##                               "cellular_component",
##                               "molecular_function"),
##                             .Names = c("GO:0008150",
##                                 "GO:0005575", "GO:0003674"))
##               expect_identical(goroot, goans)              
##           })

## test_that("olsQuery/getTermsByName", {
##               tgn <- olsQuery("tgn","GO")
##               tgnres <- structure(c("TGN", "clathrin coat of TGN vesicle",
##                                     "TGN to endosome transport",
##                                     "TGN transport vesicle",
##                                     "TGN transport vesicle membrane"),
##                                   .Names = c("GO:0005802", "GO:0030130",
##                                       "GO:0006895", "GO:0030140", "GO:0012510")) 
##               expect_identical(tgn, tgnres)

##               esi2 <- olsQuery("ESI", "MS")
##               esi1 <- olsQuery("ESI", "MS", exact = TRUE)
##               expect_identical(length(esi1), 1L)
##               expect_identical(length(esi2), 2L)
##               expect_true(esi1 %in% esi2)

##               expect_warning(olsQuery("tgn", exact=TRUE))
##               expect_message(x <- olsQuery("foobar", "GO", exact=TRUE),
##                              "Empty query results after 3 attempts.")
##               expect_equal(length(x), 0L)              
##           })

## test_that("olsQuery/getPrefixedTermsByName", {
##               tgngo <- olsQuery("tgn","GO")
##               tgn <- olsQuery("tgn") 
##               expect_true(all(paste("GO", tgngo, sep = ":") %in% tgn))              
## })

## test_that("parents/getTermParents", {
##               x <- parents("GO:0005802", "GO")
##               ans <- structure(c("Golgi apparatus part", "Golgi apparatus",
##                                  "Golgi subcompartment", "organelle subcompartment"),
##                                .Names = c("GO:0044431", "GO:0005794",
##                                    "GO:0098791", "GO:0031984"))
##               expect_equal(x, ans)
##           })


## test_that("childrenRelations/getTermRelations", {
##               x <- childrenRelations("GO:0005802", "GO")
##               ans <- structure("part_of", .Names = "GO:0032588")
##               expect_equal(x, ans)
##               x <- childrenRelations("GO:0005802", "MS")
##               ans <- structure(list(), .Names = character(0))
##               expect_equal(x, ans)
## })


## test_that("isIdObsolete/isObsolete", {
##               expect_true(isIdObsolete("GO:0005563", "GO"))
##               expect_true(!isIdObsolete("GO:0030533", "GO"))
##           })