Fix some issues

NAMESPACE

@@ -116,7 +116,6 @@ importFrom(httr,modify_url)
 importFrom(httr,timeout)
 importFrom(janitor,clean_names)
 importFrom(janitor,make_clean_names)
-importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(plotly,ggplotly)
@@ -193,5 +192,3 @@ importFrom(utils,data)
 importFrom(utils,download.file)
 importFrom(utils,head)
 importFrom(utils,untar)
-importFrom(xml2,read_html)
-importFrom(xml2,read_xml)

R/assign_peptide_type.R

@@ -94,13 +94,13 @@ assign_peptide_type <- function(data,
     )) %>%
     # Reassign semi-tryptic peptides at position 2 to fully-tryptic if no start == 1
     dplyr::mutate(pep_type = dplyr::if_else(
-      pep_type == "semi-tryptic" & {{ start }} == 2 & !.data$has_start_1 & .data$C_term_tryp,
+      .data$pep_type == "semi-tryptic" & {{ start }} == 2 & !.data$has_start_1 & .data$C_term_tryp,
       "fully-tryptic",
       .data$pep_type
     )) %>%
     # Reassign non-tryptic peptides at position 2 to semi-tryptic if no start == 1
     dplyr::mutate(pep_type = dplyr::if_else(
-      pep_type == "non-tryptic" & {{ start }} == 2 & !.data$has_start_1 & !.data$C_term_tryp,
+      .data$pep_type == "non-tryptic" & {{ start }} == 2 & !.data$has_start_1 & !.data$C_term_tryp,
       "fully-tryptic",
       .data$pep_type
     )) %>%
@@ -111,7 +111,7 @@ assign_peptide_type <- function(data,
   result <- data %>%
     dplyr::left_join(
       peptide_data %>%
-        dplyr::select({{ aa_before }}, {{ last_aa }}, {{ aa_after }}, {{ protein_id }}, {{ start }}, .data$pep_type),
+        dplyr::select({{ aa_before }}, {{ last_aa }}, {{ aa_after }}, {{ protein_id }}, {{ start }}, "pep_type"),
       by = c(
         rlang::as_name(rlang::enquo(aa_before)),
         rlang::as_name(rlang::enquo(last_aa)),

R/qc_cvs.R

@@ -122,7 +122,7 @@ The function does not handle log2 transformed data.",
         dplyr::mutate({{ condition }} := forcats::fct_expand({{ condition }}, "combined")) %>%
         dplyr::mutate({{ condition }} := replace({{ condition }}, .data$type == "cv_combined", "combined")) %>%
         dplyr::mutate({{ condition }} := forcats::fct_relevel({{ condition }}, "combined")) %>%
-        dplyr::select(-.data$type) %>%
+        dplyr::select(-"type") %>%
         dplyr::group_by({{ condition }}) %>%
         dplyr::mutate(median = stats::median(.data$values)) %>%
         dplyr::distinct()

R/try_query.R

@@ -22,8 +22,6 @@
 #' @importFrom curl has_internet
 #' @importFrom httr GET timeout http_error message_for_status http_status content accept
 #' @importFrom readr read_tsv read_csv
-#' @importFrom jsonlite fromJSON
-#' @importFrom xml2 read_html read_xml
 #'
 #' @return A data frame that contains the table from the url.
 try_query <-
@@ -90,11 +88,13 @@ try_query <-
     # Change variable to not show progress if readr is used
     options(readr.show_progress = FALSE)
 
-    # Check if the content is gzip compressed
-    if (!is.null(query_result$headers[["content-encoding"]]) && query_result$headers[["content-encoding"]] == "gzip") {
-      # Retrieve the content as raw bytes using httr::content
-      raw_content <- httr::content(query_result, type = "raw")
+    # Retrieve the content as raw bytes using httr::content
+    raw_content <- httr::content(query_result, type = "raw")
+    # Check for gzip magic number (1f 8b) before decompression
+    compressed <- length(raw_content) >= 2 && raw_content[1] == as.raw(0x1f) && raw_content[2] == as.raw(0x8b)
 
+    # Check if the content is gzip compressed
+    if (!is.null(query_result$headers[["content-encoding"]]) && query_result$headers[["content-encoding"]] == "gzip" && compressed) {
       # Decompress the raw content using base R's `memDecompress`
       decompressed_content <- memDecompress(raw_content, type = "gzip")
 

tests/testthat/test-auxiliary_functions.R

@@ -38,7 +38,7 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
             last_aa = last_aa,
             aa_after = aa_after,
             protein_id = protein_id,
-            start_pos = start
+            start = start
           ))
       })
       expect_is(assigned_types, "data.frame")
@@ -61,9 +61,9 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
 
     test_that("find_peptide and assign_peptide_type work", {
       expect_is(assigned_types, "data.frame")
-      expect_equal(nrow(assigned_types), 3)
+      expect_equal(nrow(assigned_types), 6)
       expect_equal(ncol(assigned_types), 9)
-      expect_equal(assigned_types$pep_type, c("fully-tryptic", "fully-tryptic", "non-tryptic"))
+      expect_equal(assigned_types$pep_type, c("fully-tryptic", "semi-tryptic", "non-tryptic", "non-tryptic", "fully-tryptic", "fully-tryptic"))
     })
 
     test_that("deprecated sequence_coverage works", {
@@ -75,9 +75,9 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
         ))
       })
       expect_is(coverage, "data.frame")
-      expect_equal(nrow(coverage), 3)
+      expect_equal(nrow(coverage), 6)
       expect_equal(ncol(coverage), 10)
-      expect_equal(unique(round(coverage$coverage, digits = 1)), 7.7)
+      expect_equal(unique(round(coverage$coverage, digits = 1)), c(7.7, 3.2))
     })
 
     coverage <- calculate_sequence_coverage(
@@ -88,14 +88,14 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
 
     test_that("calculate_sequence_coverage works", {
       expect_is(coverage, "data.frame")
-      expect_equal(nrow(coverage), 3)
+      expect_equal(nrow(coverage), 6)
       expect_equal(ncol(coverage), 10)
-      expect_equal(unique(round(coverage$coverage, digits = 1)), 7.7)
+      expect_equal(unique(round(coverage$coverage, digits = 1)), c(7.7, 3.2))
     })
 
     plot_data <- coverage %>%
       dplyr::mutate(
-        fold_change = c(3, -0.4, 2.1),
+        fold_change = c(3, -0.4, 2.1, 0.1, -0.1, 0.2),
         protein_length = nchar(protein_sequence)
       )
 
@@ -121,7 +121,7 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
         end_position = end,
         protein_length = protein_length,
         coverage = coverage,
-        protein_id = protein_id,
+        facet = protein_id,
         colouring = pep_type
       )
       expect_is(p, "ggplot")