Merge pull request #23 from jasenfinch/devel

v1.0.9

.github/workflows/R-CMD-check.yaml

@@ -1,8 +1,8 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master,devel]
+    branches: [main, master, devel]
   pull_request:
     branches: [main, master]
 
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +29,33 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v1
-        with:
-          extra-packages: rcmdcheck
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |
           sudo apt install mono-xbuild
+      
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Setup R dependencies
+      - name: Set up R dependencies
         run: |
           rawrr::installRawFileReaderDLLs()
           rawrr::buildRawrrExe()
           msconverteR::get_pwiz_container()
         shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: grover
 Title: Web API Framework for Mass Spectrometry Data Transfer
-Version: 1.0.8
+Version: 1.0.9
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",
@@ -12,6 +12,7 @@ URL: https://jasenfinch.github.io/grover/
 BugReports: https://github.com/jasenfinch/grover/issues
 License: GPL-3
 Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
 Imports: callr,
         cli,
         crayon,
@@ -42,4 +43,4 @@ Suggests:
 Remotes: wilsontom/msconverteR,
         bioc::rawrr
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.2

NAMESPACE

@@ -81,6 +81,7 @@ importFrom(plumber,pr_run)
 importFrom(plumber,serializer_content_type)
 importFrom(progress,progress_bar)
 importFrom(purrr,map)
+importFrom(purrr,map_chr)
 importFrom(purrr,walk)
 importFrom(rawrr,readFileHeader)
 importFrom(rawrr,readIndex)

NEWS.md

@@ -1,3 +1,17 @@
+# grover 1.0.9
+
+* The [`grover::groverAPI`](https://jasenfinch.github.io/grover/reference/groverAPI.html) `log_dir` and `temp_dir` argument directories are now created if they do not already exist.
+
+* The [`grover::groverAPI`](https://jasenfinch.github.io/grover/reference/groverAPI.html) `temp_dir` argument default is now `tempdir()`. 
+
+* [`grover::extant`](https://jasenfinch.github.io/grover/reference/extant.html) now returns `TRUE` if the specified API is accessible and `FALSE` if not.
+
+* The argument `overwrite` has now been added to [`grover::convertFile`](https://jasenfinch.github.io/grover/reference/convert.html) and [`grover::convertDirectory`](https://jasenfinch.github.io/grover/reference/convert.html) to enable the overwriting of local mzML files with the same file name as the raw files to be converted.
+
+* Removed the `build_vignettes` argument from the installation instructions in the package README as the package documetation is available online from https://jasenfinch.github.io/grover.
+
+* Removed the Introduction vignette as the majority of this information was duplicated in the package README.
+
 # grover 1.0.8
 
 * Added Bioconductor package [`rawrr](https://bioconductor.org/packages/release/bioc/html/rawrr.html) as a `bioc` remote to ensure the package can be installed correctly using [`pak`](https://pak.r-lib.org/) and [`renv`](https://rstudio.github.io/renv/articles/renv.html).
@@ -50,4 +64,4 @@
 
 * Fixed conversion argument helpers to work correctly with `msconverteR`.
 
-* Converted files now returned correctly by the API.
+* Converted files now returned correctly by the API.

R/allGenerics.R

@@ -88,7 +88,8 @@ setGeneric('convertFile',function(grover_client,
                                   file, 
                                   args = '',
                                   outDir = '.',
-                                  zip = TRUE){
+                                  zip = TRUE,
+                                  overwrite = FALSE){
   standardGeneric('convertFile')
 })
 
@@ -99,7 +100,8 @@ setGeneric('convertDirectory',function(grover_client,
                                        directory, 
                                        args = '', 
                                        outDir = '.',
-                                       zip = TRUE){
+                                       zip = TRUE,
+                                       overwrite = FALSE){
   standardGeneric('convertDirectory')
 })
 

R/api.R

@@ -22,10 +22,18 @@
 groverAPI <- function(grover_host,
                       background = FALSE,
                       log_dir = '~/.grover/logs',
-                      temp_dir = '~/.grover/temp'){
+                      temp_dir = tempdir()){
 
-  log_dir <- normalizePath(log_dir)
-  temp_dir <- normalizePath(temp_dir)
+  log_dir <- path.expand(log_dir)
+  temp_dir <- path.expand(temp_dir)
+
+  if (!dir.exists(log_dir)){
+    dir.create(log_dir)
+  }
+
+  if (!dir.exists(temp_dir)){
+    dir.create(temp_dir)
+  }
 
   if (isFALSE(background)) {
     API(host(grover_host),

R/client-check.R

@@ -1,7 +1,9 @@
+
 #' Check the existance of a grover API
 #' @rdname extant
 #' @description Check grover API is still extistant.
 #' @param grover_client S4 object of class GroverGlient
+#' @return `TRUE` if the API host is accessible and `FALSE` if not.
 #' @importFrom httr GET content
 #' @export
 
@@ -16,12 +18,14 @@ setMethod('extant',signature = 'GroverClient',
                 GET() %>%
                 content() %>%
                 unlist()},silent = TRUE)
-
-             if (answer != "I'm still here!") {
-              answer <- 'grover is MIA!'
-             }
 
-            return(answer)
+            status <- ifelse(
+              answer == "I'm still here!",
+              TRUE,
+              FALSE
+            )
+
+            return(status)
           }
 )
 

R/client-conversion.R

@@ -8,6 +8,7 @@
 #' @param args arguments to pass to msconverteR::convert_files
 #' @param outDir output directory path for converted files
 #' @param zip zip converted file 
+#' @param overwrite overwrite local mzML files that already exist at the `outDir` path that have the same file name as the raw files to be converted 
 #' @return A vector of file paths to converted data files.
 #' @importFrom tools file_path_sans_ext
 #' @importFrom stringr str_split
@@ -26,7 +27,8 @@ setMethod('convertFile',signature = 'GroverClient',
                    file, 
                    args = NULL, 
                    outDir = '.',
-                   zip = TRUE){
+                   zip = TRUE,
+                   overwrite = FALSE){
 
             converted_file <- file %>%
               file_path_sans_ext() %>%
@@ -78,7 +80,8 @@ setMethod('convertFile',signature = 'GroverClient',
                 zipped_file_path <- str_c(outDir,'/',fileName,'.mzML.gz')
 
                 gzip(converted_file_path,
-                     zipped_file_path)
+                     zipped_file_path,
+                     overwrite = overwrite)
 
                 converted_file_path <- zipped_file_path
               }
@@ -113,6 +116,7 @@ setMethod('convertFile',signature = 'GroverClient',
           })
 
 #' @rdname convert
+#' @importFrom purrr map_chr
 #' @export
 
 setMethod('convertDirectory',signature = 'GroverClient',
@@ -121,25 +125,41 @@ setMethod('convertDirectory',signature = 'GroverClient',
                    directory, 
                    args = '', 
                    outDir = '.',
-                   zip = TRUE){
+                   zip = TRUE,
+                   overwrite = FALSE){
+
+            outDir <- str_c(outDir,directory,sep = '/')
 
-            files <- listRawFiles(grover_client,instrument,directory)
+            if (!dir.exists(outDir)) {
+              dir_create(outDir) 
+            }
+
+            local_files <- list.files(
+              outDir,
+              pattern = '.mzML'
+            )
+
+            raw_files <- listRawFiles(grover_client,instrument,directory)
+
+            if (isFALSE(overwrite)){
+              files <- raw_files[!(file_path_sans_ext(raw_files) %in% 
+                                 file_path_sans_ext(local_files,compression = zip))] 
+            } else {
+              files <- raw_files
+            }
 
             message('\nConverting ',
-                    bold(blue(directory)),
-                    ' containing ',
                     bold(yellow(length(files))),
-                    ' .raw files\n')
-
-            outDir <- str_c(outDir,directory,sep = '/')
-            dir_create(outDir)
+                    ' .raw files from directory ',
+                    bold(blue(directory)),
+                    '\n')
 
             pb <- progress_bar$new(
               format = "[:bar] :percent eta: :eta",
               total = length(files), clear = FALSE)
             pb$tick(0)
 
-            results <- map(seq_len(length(files)),~{
+            results <- map_chr(seq_len(length(files)),~{
               file <- files[.]
               suppressMessages({
                 res <- convertFile(grover_client,
@@ -148,7 +168,8 @@ setMethod('convertDirectory',signature = 'GroverClient',
                                    file,
                                    args,
                                    outDir,
-                                   zip)
+                                   zip,
+                                   overwrite)
               })
               pb$tick()
               return(res)

README.md

@@ -3,7 +3,7 @@
 
 <!-- badges: start -->
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![R-CMD-check](https://github.com/jasenfinch/grover/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/grover/actions)
+[![R-CMD-check](https://github.com/jasenfinch/grover/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jasenfinch/grover/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/jasenfinch/grover/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/grover?branch=master)
 [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/grover/blob/master/DESCRIPTION)
 [![GitHub release](https://img.shields.io/github/release/jasenfinch/grover.svg)](https://GitHub.com/jasenfinch/grover/releases/)
@@ -26,15 +26,13 @@ The package functionality is platform independent with file conversion and sampl
 The `grover` package can be installed from GitHub using the following:
 
 ```
-remotes::install_github('jasenfinch/grover',build_vignettes = TRUE)
+remotes::install_github('jasenfinch/grover')
 ```
 
 ### Learn more
 
 The package documentation can be browsed online at <https://jasenfinch.github.io/grover/>. 
 
-If this is your first time using `grover` see the [Introduction to grover](https://jasenfinch.github.io/grover/articles/introduction.html) vignette for information on how to get started.
-
 If you believe you've found a bug in `grover`, please file a bug (and, if
 possible, a [reproducible example](https://reprex.tidyverse.org)) at
 <https://github.com/jasenfinch/grover/issues>.