wrappers for bioentity endpoints and tests

R/getBioEntityInfoFromIndra.R

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+
+#' Call API to get UniProt IDs from UniProt mnemonic IDs
+#' @param uniprotMnemonicIds list of UniProt mnemonic ids
+#' @return list of UniProt IDs
+#' @importFrom jsonlite toJSON
+#' @importFrom httr POST add_headers content
+#' @keywords internal
+#' @noRd
+.callGetUniprotIdsFromUniprotMnemonicIdsApi <- function(uniprotMnemonicIds) {
+    apiUrl <- "http://localhost:5000/api/get_uniprot_ids_from_uniprot_mnemonic_ids"
+
+    requestBody <- list(uniprot_mnemonic_ids = uniprotMnemonicIds)
+    requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
+
+    res <- POST(
+        apiUrl,
+        body = requestBody,
+        add_headers("Content-Type" = "application/json"),
+        encode = "raw"
+    )
+    res <- content(res)
+    return(res)
+}
+
+#' Call API to get HGNC IDs from UniProt IDs
+#' @param uniprotIds list of UniProt IDs
+#' @return list of HGNC IDs
+#' @importFrom jsonlite toJSON
+#' @importFrom httr POST add_headers content
+#' @keywords internal
+#' @noRd
+.callGetHgncIdsFromUniprotIdsApi <- function(uniprotIds) {
+    apiUrl <- "http://localhost:5000/api/get_hgnc_ids_from_uniprot_ids"
+
+    requestBody <- list(uniprot_ids = uniprotIds)
+    requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
+
+    res <- POST(
+        apiUrl,
+        body = requestBody,
+        add_headers("Content-Type" = "application/json"),
+        encode = "raw"
+    )
+    res <- content(res)
+    return(res)
+}
+
+#' Call API to get HGNC names from HGNC IDs
+#' @param hgncIds list of HGNC IDs
+#' @return list of HGNC names
+#' @importFrom jsonlite toJSON
+#' @importFrom httr POST add_headers content
+#' @keywords internal
+#' @noRd
+.callGetHgncNamesFromHgncIdsApi <- function(hgncIds) {
+    apiUrl <- "http://localhost:5000/api/get_hgnc_names_from_hgnc_ids"
+
+    requestBody <- list(hgnc_ids = hgncIds)
+    requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
+
+    res <- POST(
+        apiUrl,
+        body = requestBody,
+        add_headers("Content-Type" = "application/json"),
+        encode = "raw"
+    )
+    res <- content(res)
+    return(res)
+}
+
+#' Call API to check if genes are kinases
+#' @param genes list of gene names
+#' @return list indicating if genes are kinases
+#' @importFrom jsonlite toJSON
+#' @importFrom httr POST add_headers content
+#' @keywords internal
+#' @noRd
+.callIsKinaseApi <- function(genes) {
+    apiUrl <- "http://localhost:5000/api/is_kinase"
+
+    requestBody <- list(genes = genes)
+    requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
+
+    res <- POST(
+        apiUrl,
+        body = requestBody,
+        add_headers("Content-Type" = "application/json"),
+        encode = "raw"
+    )
+    res <- content(res)
+    return(res)
+}
+
+#' Call API to check if genes are phosphatases
+#' @param genes list of gene names
+#' @return list indicating if genes are phosphatases
+#' @importFrom jsonlite toJSON
+#' @importFrom httr POST add_headers content
+#' @keywords internal
+#' @noRd
+.callIsPhosphataseApi <- function(genes) {
+    apiUrl <- "http://localhost:5000/api/is_phosphatase"
+
+    requestBody <- list(genes = genes)
+    requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
+
+    res <- POST(
+        apiUrl,
+        body = requestBody,
+        add_headers("Content-Type" = "application/json"),
+        encode = "raw"
+    )
+    res <- content(res)
+    return(res)
+}
+
+#' Call API to check if genes are transcription factors
+#' @param genes list of gene names
+#' @return list indicating if genes are transcription factors
+#' @importFrom jsonlite toJSON
+#' @importFrom httr POST add_headers content
+#' @keywords internal
+#' @noRd
+.callIsTranscriptionFactorApi <- function(genes) {
+    apiUrl <- "http://localhost:5000/api/is_transcription_factor"
+
+    requestBody <- list(genes = genes)
+    requestBody <- jsonlite::toJSON(requestBody, auto_unbox = TRUE)
+
+    res <- POST(
+        apiUrl,
+        body = requestBody,
+        add_headers("Content-Type" = "application/json"),
+        encode = "raw"
+    )
+    res <- content(res)
+    return(res)
+}

tests/testthat/test-getBioEntityInfoFromIndra.R

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+# Test .callGetUniprotIdsFromUniprotMnemonicIdsApi
+test_that(".callGetUniprotIdsFromUniprotMnemonicIdsApi works correctly", {
+    uniprotMnemonicIds <- list("CLH1_HUMAN")
+    result <- .callGetUniprotIdsFromUniprotMnemonicIdsApi(uniprotMnemonicIds)
+    expect_type(result, "list")
+    expect_true(length(result) == 1)
+    expected_value <- list(CLH1_HUMAN = "Q00610")
+    expect_equal(result, expected_value)
+})
+
+# Test .callGetHgncIdsFromUniprotIdsApi
+test_that(".callGetHgncIdsFromUniprotIdsApi works correctly", {
+    uniprotIds <- list("Q00610")
+    result <- .callGetHgncIdsFromUniprotIdsApi(uniprotIds)
+    expect_type(result, "list")
+    expect_true(length(result) == 1)
+    expected_value <- list("Q00610" = "2092")
+    expect_equal(result, expected_value)
+})
+
+# Test .callGetHgncNamesFromHgncIdsApi
+test_that(".callGetHgncNamesFromHgncIdsApi works correctly", {
+    hgncIds <- list("2092")
+    result <- .callGetHgncNamesFromHgncIdsApi(hgncIds)
+    expect_type(result, "list")
+    expect_true(length(result) == 1)
+    expected_value <- list("2092" = "CLTC")
+    expect_equal(result, expected_value)
+})
+
+# Test .callIsKinaseApi
+test_that(".callIsKinaseApi works correctly", {
+    kinaseGenes <- list("CHEK1")
+    result <- .callIsKinaseApi(kinaseGenes)
+    expect_type(result, "list")
+    expect_true(length(result) == 1)
+    expected_value <- list("CHEK1" = TRUE)
+    expect_equal(result, expected_value)
+})
+
+# Test .callIsPhosphataseApi
+test_that(".callIsPhosphataseApi works correctly", {
+    phosphataseGenes <- list("MTM1")
+    result <- .callIsPhosphataseApi(phosphataseGenes)
+    expect_type(result, "list")
+    expect_true(length(result) == 1)
+    expected_value <- list("MTM1" = TRUE)
+    expect_equal(result, expected_value)
+})
+
+# Test .callIsTranscriptionFactorApi
+test_that(".callIsTranscriptionFactorApi works correctly", {
+    transcriptionFactorGenes <- list("STAT1")
+    result <- .callIsTranscriptionFactorApi(transcriptionFactorGenes)
+    expect_type(result, "list")
+    expect_true(length(result) == 1)
+    expected_value <- list("STAT1" = TRUE)
+    expect_equal(result, expected_value)
+})