From 961742d2916b1cc3afa2bd328d4ee0be817bffc5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= <rene.wiegandt@mpi-bn.mpg.de>
Date: Fri, 13 Jul 2018 07:34:25 -0400
Subject: [PATCH] Fixed more style mistakes, added try/catch warning handling

---
 R/parser.R                     | 15 +++++++--------
 tests/testthat/test_mqparser.R | 34 +++++++++++++++++-----------------
 2 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/R/parser.R b/R/parser.R
index 57b8141..475ecb1 100644
--- a/R/parser.R
+++ b/R/parser.R
@@ -87,7 +87,7 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # @return String level of given column
   get_sample_level <- function(col_head, isSample, full_list) {
     # Get the level of all 'sample' columns.
-    # Default: level <- "sample"
+    # Default: level is "sample"
     if (grepl("Ratio", col_head, perl = TRUE)) {
       if (grepl("type", col_head, perl = TRUE)) return("feature")
       return("contrast")
@@ -191,14 +191,13 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   proteinGroups <- data.table::fread(proteinGroups_in, header = TRUE, quote = "")
   summary_file <- data.table::fread(summary_in, header = TRUE)
 
-  if (config == "") {
+  meta_config <- tryCatch({
+    rjson::fromJSON(file = config)
+  }, error = function(cond) {
     stop("Could not read config file")
-  }
-
-  meta_config <- tryCatch({rjson::fromJSON(file = config)},
-                          error = function(cond) {
-                            stop("Could not read config file")
-                          })
+  }, warning = function(w) {
+    stop("Could not read config file")
+  })
 
   # getting experiment names
   if ("Experiment" %in% colnames(summary_file)) {
diff --git a/tests/testthat/test_mqparser.R b/tests/testthat/test_mqparser.R
index e36f613..616056c 100644
--- a/tests/testthat/test_mqparser.R
+++ b/tests/testthat/test_mqparser.R
@@ -1,29 +1,29 @@
 context("MaxQuant parser")
 
-testthat::test_that("all needed input parameteres are given", {
-  expect_error(wilson::parse_MaxQuant(),"The proteinGroups file was not given")
-  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "/path/path/"),"The summary file was not given")
-  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "/path/path/",summary_in = "/path/path/"),
+test_that("all needed input parameteres are given", {
+  expect_error(wilson::parse_MaxQuant(), "The proteinGroups file was not given")
+  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "./path/path/"), "The summary file was not given")
+  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "./path/path/", summary_in = "./path/path/"),
                                       "The output file was not given")
-  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "/path/path/",summary_in = "/path/path/",
-                                      outfile = "/path/path/"),"The output_reduced file was not given")
+  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "./path/path/", summary_in = "./path/path/",
+                                      outfile = "./path/path/"), "The output_reduced file was not given")
 })
 
-testthat::test_that("mq_parser",{
+test_that("mq_parser", {
 
-  expect_error(wilson::parse_MaxQuant(proteinGroups_in = system.file("/tests/testthat", "proteinGroups_test.txt", package = "wilson"),
-                                      summary_in = system.file("/tests/testthat", "summary_test_2.txt", package = "wilson"),
+  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt",
+                                      summary_in = "summary_test_2.txt",
                                       outfile = "./out", outfile_reduced = "./outres" ),
                "wrong format on summary file: column \'Experiment\' misssing")
-  expect_true(wilson::parse_MaxQuant(proteinGroups_in = system.file("/tests/testthat", "proteinGroups_test.txt", package = "wilson"),
-                                      summary_in = system.file("/tests/testthat", "summary_test.txt", package = "wilson"),
-                                      outfile = "./out", outfile_reduced = "./outres", config = system.file("/tests/testthat", "success_config.json", package = "wilson")))
-  expect_error(wilson::parse_MaxQuant(proteinGroups_in = system.file("/tests/testthat", "proteinGroups_test.txt", package = "wilson"),
-                                      summary_in = system.file("/tests/testthat", "summary_test.txt", package = "wilson"),
+  expect_true(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt",
+                                      summary_in = "summary_test.txt",
+                                      outfile = "./out", outfile_reduced = "./outres", config = "success_config.json"))
+  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt",
+                                      summary_in = "summary_test.txt",
                                       outfile = "./out", outfile_reduced = "./outres", config = "" ),
                "Could not read config file")
-  expect_error(wilson::parse_MaxQuant(proteinGroups_in = system.file("/tests/testthat", "proteinGroups_test.txt", package = "wilson"),
-                                      summary_in = system.file("/tests/testthat", "summary_test.txt", package = "wilson"),
-                                      outfile = "./out", outfile_reduced = "./outres", config = system.file("/tests/testthat", "fail_config.json", package = "wilson") ),
+  expect_error(wilson::parse_MaxQuant(proteinGroups_in = "proteinGroups_test.txt",
+                                      summary_in = "summary_test.txt",
+                                      outfile = "./out", outfile_reduced = "./outres", config = "fail_config.json" ),
                "reduced_list is missing in config file")
 })