tests/testthat/test_functions-EnsDb.R

In YTLogos/ensembldb: Utilities to create and use Ensembl-based annotation databases

test_that(".addFilter .dropFilter and .activeFilter work", {
    gf <- GenenameFilter("BCL2")
    ## .addFilter and .activeFilter
    edb_2 <- ensembldb:::.addFilter(edb, filter = gf)
    expect_equal(AnnotationFilterList(gf),
                 ensembldb:::getProperty(edb_2, "FILTER"))
    expect_equal(AnnotationFilterList(gf),
                 ensembldb:::.activeFilter(edb_2))
    edb_2 <- ensembldb:::.addFilter(edb_2, filter = gf)
    expect_equal(AnnotationFilterList(AnnotationFilterList(gf),
                                      AnnotationFilterList(gf)),
                 ensembldb:::getProperty(edb_2, "FILTER"))
    edb_2 <- ensembldb:::.addFilter(edb, filter = ~ tx_id == 3 &
                                             tx_biotype == "protein_coding")
    flts <- ensembldb:::.activeFilter(edb_2)
    expect_equal(flts, ensembldb:::getProperty(edb_2, "FILTER"))
    expect_equal(flts, AnnotationFilter(~ tx_id == 3 &
                                            tx_biotype == "protein_coding"))
    
    ## Errors
    expect_error(ensembldb:::.addFilter(edb, "blabla"))
    expect_error(ensembldb:::filter(edb, "blabla"))
    expect_error(ensembldb:::.addFilter(edb))
    
    ## .dropFilter
    edb_2 <- ensembldb:::.dropFilter(edb_2)
    expect_equal(ensembldb:::.activeFilter(edb_2), NA)

    ## Same but with the methods.
    gf <- GenenameFilter("BCL2")
    ## .addFilter and .activeFilter
    edb_2 <- addFilter(edb, filter = gf)
    expect_equal(AnnotationFilterList(gf),
                 ensembldb:::getProperty(edb_2, "FILTER"))
    edb_2 <- filter(edb, filter = gf)
    expect_equal(AnnotationFilterList(gf),
                 ensembldb:::getProperty(edb_2, "FILTER"))
    expect_equal(AnnotationFilterList(gf),
                 activeFilter(edb_2))
    edb_2 <- addFilter(edb_2, filter = gf)
    expect_equal(AnnotationFilterList(AnnotationFilterList(gf),
                                      AnnotationFilterList(gf)),
                 ensembldb:::getProperty(edb_2, "FILTER"))
    edb_2 <- addFilter(edb, filter = ~ tx_id == 3 &
                                tx_biotype == "protein_coding")
    flts <- activeFilter(edb_2)
    expect_equal(flts, ensembldb:::getProperty(edb_2, "FILTER"))
    expect_equal(flts, AnnotationFilter(~ tx_id == 3 &
                                            tx_biotype == "protein_coding"))
    
    ## Errors
    expect_error(addFilter(edb, "blabla"))
    expect_error(addFilter(edb))
    
    ## .dropFilter
    edb_2 <- dropFilter(edb_2)
    expect_equal(activeFilter(edb_2), NA)
})