tests/testthat/test-get_dataset.R

In regutools: regutools: an R package for data extraction from RegulonDB

context("get_dataset")
test_that("Function get dataset works as expected", {
    ## Connect to the RegulonDB database if necessary
    if (!exists("regulondb_conn")) {
          regulondb_conn <- connect_database()
      }

    ## Build a regulondb object
    regdb <-
        regulondb(
            database_conn = regulondb_conn,
            organism = "prueba",
            genome_version = "prueba",
            database_version = "prueba"
        )
    query <- get_dataset(
        regdb,
        dataset = "GENE",
        attributes = c("posleft", "posright", "name", "strand"),
        filters = list(name = c("araC", "crp", "lacI"))
    )
    expect_s4_class(query, "regulondb_result")
    expect_error(
        get_dataset(
            regdb,
            dataset = "GENE",
            attributes = c("posleft", "posright", "name", "strand"),
            filters = list(name = c("araC", "crp", "lacI")),
            output_format = "ss"
        )
    )
    expect_s4_class(
        suppressWarnings(
            get_dataset(
                regdb,
                dataset = "GENE",
                attributes = c("posleft", "posright", "name", "strand"),
                and = FALSE,
                output_format = "GRanges"
            )
        ),
        "GRanges"
    )
    expect_s4_class(
        get_dataset(
            regdb,
            dataset = "OPERON",
            filters = list(name = c("araC")),
            output_format = "GRanges"
        ),
        "GRanges"
    )


    expect_s4_class(
        suppressWarnings(
            get_dataset(regdb,
                dataset = "OPERON",
                output_format = "GRanges"
            )
        ),
        "GRanges"
    )


    expect_s4_class(
        get_dataset(
            regdb,
            dataset = "GENE",
            filters = list(name = c("araC", "crp", "lacI")),
            attributes = c("posleft", "posright", "name", "strand", "dna_sequence"),
            output_format = "DNAStringSet"
        ),
        "DNAStringSet"
    )

    expect_s4_class(
        get_dataset(
            regdb,
            dataset = "GENE",
            filters = list(name = c("araC", "crp", "lacI")),
            attributes = c("posleft", "posright", "name", "strand", "dna_sequence"),
            output_format = "DNAStringSet"
        ),
        "DNAStringSet"
    )
    expect_warning(
        get_dataset(
            regdb,
            dataset = "PROMOTER",
            attributes = c(
                "name",
                "strand",
                "promoter_sequence"
            ),
            output_format = "BStringSet"
        ),
        "Dropped 92 entries where sequence data were NAs"
    )


    expect_error(
        suppressWarnings(
            get_dataset(
                regdb,
                dataset = "PROMOTER",
                filters = list(name = c("araC", "crp", "lacI")),
                attributes = c("name", "strand"),
                output_format = "DNAStringSet"
            )
        ),
        "Not enough information to convert to a Biostrings object.\nPlease add the following column to the regulondb_result object: \n\tpromoter_sequence\n"
    )

    expect_error(
        get_dataset(
            regdb,
            dataset = "GENE",
            filters = list(name = c("araC", "crp", "lacI")),
            attributes = c(
                "posleft",
                "posright",
                "name",
                "strand"
            ),
            output_format = "BStringSet"
        )
    )


    expect_error(get_dataset(
        regdb,
        dataset = "OPERON",
        attributes = c("name"),
        output_format = "GRanges"
    ))

    expect_warning(get_dataset(
        regdb,
        dataset = "GENE",
        attributes = c("posleft", "posright", "name", "strand"),
        filters = list(name = c("thisisnotagene"))
    ))
    # Errors
    expect_error(
        get_dataset(
            regdb,
            dataset = "GENE",
            attributes = query,
            filters = list(name = c("thisisnotagene"))
        ),
        "Parameter 'attributes' must be a vector"
    )
    expect_error(
        get_dataset(
            regdb,
            attributes = c("posleft", "posright", "name", "strand"),
            filters = list(name = c("thisisnotagene"))
        ),
        "Non dataset provided"
    )
    expect_error(
        get_dataset(
            regdb,
            dataset = "GENe",
            attributes = c("posleft", "posright", "name", "strand"),
            filters = list(name = c("thisisnotagene"))
        ),
        "Invalid dataset. See valid datasets in list_datasets()"
    )
    expect_error(get_dataset(
        regdb,
        dataset = "GENE",
        attributes = c("posleft", "posright", "name", "stran"),
        filters = list(name = c("thisisnotagene"))
    ))
    expect_error(
        get_dataset(
            regdb,
            dataset = "GENE",
            attributes = c("posleft", "posright", "name", "strand"),
            filters = list(name = c("araC")),
            partialmatch = "names"
        ),
        "Partialmatch \"names\" do not exist"
    )

    expect_error(
        get_dataset(
            regdb,
            dataset = "GENE",
            attributes = c("posleft", "posright", "name", "strand"),
            filters = list(name = c("araC")),
            partialmatch = "posleft"
        ),
        "Partialmatch \"posleft\" not defined in 'filters'"
    )
})