1. immunogenViewer
  2. Commit e1d8bcba2f4efbee7207da4da2e78570f5ee82eb
Browse code

Implement first function and unit testing

Katharina Waury authored on 23/11/2023 15:52:05
Showing 5 changed files
DESCRIPTION
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@@ -9,3 +9,9 @@ Description: More about what it does (maybe more than one line)
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 License: Apache License (>= 2)
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 Encoding: UTF-8
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 LazyData: true
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+Suggests:
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+    testthat (>= 3.0.0)
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+Config/testthat/edition: 3
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+Imports:
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+    httr,
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+    jsonlite
R/getProteinFeatures.R
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+getProteinFeatures <- function(uniprot) {
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+  print("Hello, world!")
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+  return(NULL)
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+}
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+
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+
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+accessUniprot <- function(uniprot) {
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+
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+  if (is.character(uniprot) == FALSE) {
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+    warning("Please provide a valid UniProt ID.")
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+    return(NULL)
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+  }
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+
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+  # create protein-specific UniProt URL
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+  url <- paste0("https://www.uniprot.org/uniprot/", uniprot, ".json")
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+
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+  # make the GET request
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+  response <- httr::GET(url = url)
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+
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+  print(response$status_code == 200)
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+
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+  # check if request was successful
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+  if (response$status_code == 200) {
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+
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+    # parse JSON response
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+    result <- jsonlite::fromJSON(httr::content(response, "text", encoding="UTF-8"))
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+    return(result)
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+
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+  } else {
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+
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+    warning("Error fetching data from UniProt.")
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+    return(NULL)
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+  }
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+}
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+
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+
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+# accessPredictProtein <- function(uniprot) {
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+#
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+#   # create protein-specific UniProt URL
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+#   url <- paste0("https://api.predictprotein.org/v1/results/", uniprot)
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+#
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+#   # Make the GET request
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+#   response <- http::GET(url = url)
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+#
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+#   # Check if the request was successful
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+#   if (http_status(response)$category == "Success") {
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+#
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+#     # Parse JSON response
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+#     result <- fromJSON(content(response, "text"))
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+#     return(result)
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+#
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+#   } else {
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+#
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+#     warning("Error fetching data from UniProt.")
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+#     return(NULL)
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+#   }
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+# }
R/hello.R
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-# Hello, world!
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-#
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-# This is an example function named 'hello'
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-# which prints 'Hello, world!'.
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-#
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-# You can learn more about package authoring with RStudio at:
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-#
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-#   http://r-pkgs.had.co.nz/
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-#
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-# Some useful keyboard shortcuts for package authoring:
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-#
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-#   Install Package:           'Ctrl + Shift + B'
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-#   Check Package:             'Ctrl + Shift + E'
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-#   Test Package:              'Ctrl + Shift + T'
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-
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-hello <- function() {
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-  print("Hello, world!")
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-}
tests/testthat.R
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+# This file is part of the standard setup for testthat.
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+# It is recommended that you do not modify it.
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+#
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+# Where should you do additional test configuration?
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+# Learn more about the roles of various files in:
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+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
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+# * https://testthat.r-lib.org/articles/special-files.html
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+
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+library(testthat)
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+library(immunogenViewer)
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+
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+test_check("immunogenViewer")
tests/testthat/test-getProteinFeatures.R
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+test_that("Only strings are accepted for UniProt IDs", {
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+  expect_null(accessUniprot(NULL))
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+  expect_null(accessUniprot(4))
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+  expect_null(accessUniprot(3.14))
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+})
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+
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+test_that("Warning is raised if UniProt ID is incorrect", {
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+  expect_null(accessUniprot("Hello"))
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+  expect_null(accessUniprot("A00000"))
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+})