add lintr

seroanalytics · Aug 14, 2024 · 495b4d8 · 495b4d8
1 parent 83ad743
commit 495b4d8
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Showing 5 changed files with 35 additions and 20 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -6,4 +6,5 @@
 ^docker$
 ^\.github$
 ^\.idea$
-^\uploads$
+^\uploads$
+^.lintr
diff --git a/.lintr b/.lintr
@@ -0,0 +1,2 @@
+linters: linters_with_defaults(object_usage_linter = NULL, indentation_linter = NULL, commented_code_linter = NULL)
+encoding: "UTF-8"
diff --git a/R/api.R b/R/api.R
@@ -3,27 +3,32 @@ target_get_root <- function() {
 }
 
 target_get_version <- function() {
-  jsonlite::toJSON(as.character(utils::packageVersion("serovizr")), auto_unbox = TRUE)
+  jsonlite::toJSON(as.character(utils::packageVersion("serovizr")),
+                   auto_unbox = TRUE)
 }
 
 target_post_dataset <- function(req, res) {
   parsed <- Rook::Multipart$parse(req)
   file_body <- utils::read.csv(parsed$file$tempfile)
   filename <- parsed$file$filename
-  filename <- stringr::str_remove_all(filename, paste0(".", tools::file_ext(filename)))
+  filename <- stringr::str_remove_all(filename,
+                                      paste0(".", tools::file_ext(filename)))
   path <- file.path("uploads", filename)
   if (file.exists(path)) {
     res$status <- 400L
-    error <- list(error = "BAD_REQUEST", detail = paste("A dataset called", filename,
-                                                        "already exists. Please choose a unique name for this dataset."))
+    msg <- paste(filename, "already exists.",
+                 "Please choose a unique name for this dataset.")
+    error <- list(error = "BAD_REQUEST",
+                  detail = msg)
     return(list(status = "failure", errors = list(error), data = NULL))
   }
   required_cols <- c("value", "biomarker")
   missing_cols <- required_cols[!(required_cols %in% colnames(file_body))]
   if (length(missing_cols) > 0) {
     res$status <- 400L
     error <- list(error = "BAD_REQUEST",
-                  detail = paste("Missing required columns:", paste(missing_cols, collapse = ", ")))
+                  detail = paste("Missing required columns:",
+                                 paste(missing_cols, collapse = ", ")))
     return(list(status = "failure", errors = list(error), data = NULL))
   }
 
@@ -51,7 +56,8 @@ target_get_datasets <- function() {
 }
 
 target_get_trace <- function(name, biomarker, facet = NULL, trace = NULL) {
-  logger::log_info(paste("Requesting data from", name, "with biomarker", biomarker))
+  logger::log_info(paste("Requesting data from", name,
+                         "with biomarker", biomarker))
   logger::log_info(paste("Filtering by facet variables", facet))
   dat <- read_dataset(name)
   cols <- colnames(dat)
@@ -63,7 +69,7 @@ target_get_trace <- function(name, biomarker, facet = NULL, trace = NULL) {
   #                             code = "BAD_REQUEST", status_code = 400L)
   # }
   # dat <- dat[dat[facet_var] == facet_level & dat["biomarker"] == biomarker,]
-  dat <- dat[dat["biomarker"] == biomarker,]
+  dat <- dat[dat["biomarker"] == biomarker, ]
   dat$value <- log(dat$value)
   if (length(trace) > 0) {
     logger::log_info(paste("Disaggregating by trace variables", trace))

diff --git a/R/router.R b/R/router.R
@@ -7,7 +7,8 @@ build_routes <- function() {
 
   pr$handle(get_root())
   pr$handle(get_version())
-  pr$handle("POST", "/dataset/", function(req, res) target_post_dataset(req, res),
+  pr$handle("POST", "/dataset/",
+            function(req, res) target_post_dataset(req, res),
             serializer = plumber::serializer_unboxed_json())
   pr$handle(get_dataset())
   pr$handle(get_datasets())
@@ -16,17 +17,19 @@ build_routes <- function() {
 
 
 get_root <- function() {
-  porcelain::porcelain_endpoint$new("GET",
-                                    "/",
-                                    target_get_root,
-                                    returning = porcelain::porcelain_returning_json())
+  porcelain::porcelain_endpoint$new(
+    "GET",
+    "/",
+    target_get_root,
+    returning = porcelain::porcelain_returning_json())
 }
 
 get_version <- function() {
-  porcelain::porcelain_endpoint$new("GET",
-                                    "/version",
-                                    target_get_version,
-                                    returning = porcelain::porcelain_returning_json("Version"))
+  porcelain::porcelain_endpoint$new(
+    "GET",
+    "/version",
+    target_get_version,
+    returning = porcelain::porcelain_returning_json("Version"))
 }
 
 get_dataset <- function() {
@@ -38,14 +41,16 @@ get_dataset <- function() {
 
 get_datasets <- function() {
   porcelain::porcelain_endpoint$new(
-    "GET", "/datasets/",
+    "GET",
+    "/datasets/",
     target_get_datasets,
     returning = porcelain::porcelain_returning_json("Datasets"))
 }
 
 get_trace <- function() {
   porcelain::porcelain_endpoint$new(
-    "GET", "/dataset/<name>/<biomarker>/",
+    "GET",
+    "/dataset/<name>/<biomarker>/",
     target_get_trace,
     porcelain::porcelain_input_query(facet = "string", trace = "string"),
     returning = porcelain::porcelain_returning_json())

diff --git a/README.md b/README.md
@@ -2,7 +2,8 @@
 
 <!-- badges: start -->
 [![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
-[![R-CMD-check.yaml](https://github.com/seroanalytics/serovizr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/seroanalytics/serovizr/actions/workflows/R-CMD-check.yaml)[![Codecov test coverage](https://codecov.io/gh/seroanalytics/serovizr/branch/master/graph/badge.svg)](https://codecov.io/gh/seroanalytics/serovizr?branch=master)
+[![R-CMD-check.yaml](https://github.com/seroanalytics/serovizr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/seroanalytics/serovizr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/seroanalytics/serovizr/branch/master/graph/badge.svg)](https://codecov.io/gh/seroanalytics/serovizr?branch=master)
 <!-- badges: end -->
 
 R API for the SeroViz app. Based on the [porcelain](https://github.com/reside-ic/porcelain) framework.