Merge pull request #24 from jasenfinch/devel

v1.1.0

Author: Jasen Finch

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# 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]
+  pull_request:
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,36 +14,42 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     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:
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v1
-        with:
-          extra-packages: pkgdown
-          needs: website
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |
           sudo apt install mono-xbuild
           
-      - name: Setup R dependencies
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
         run: |
           rawrr::installRawFileReaderDLLs()
           rawrr::buildRawrrExe()
           msconverteR::get_pwiz_container()
+          pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -1,4 +1,4 @@
-# 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:
@@ -15,28 +15,44 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v1
-        with:
-          extra-packages: covr
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |
           sudo apt install mono-xbuild
-          
-      - name: Setup R dependencies
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
         run: |
           rawrr::installRawFileReaderDLLs()
           rawrr::buildRawrrExe()
           msconverteR::get_pwiz_container()
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -6,3 +6,5 @@ grover.txt
 doc
 Meta
 docs
+/doc/
+/Meta/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: grover
 Title: Web API Framework for Mass Spectrometry Data Transfer
-Version: 1.0.9
+Version: 1.1.0
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",
@@ -43,4 +43,4 @@ Suggests:
 Remotes: wilsontom/msconverteR,
         bioc::rawrr
 VignetteBuilder: knitr
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3

NAMESPACE

@@ -82,12 +82,15 @@ importFrom(plumber,serializer_content_type)
 importFrom(progress,progress_bar)
 importFrom(purrr,map)
 importFrom(purrr,map_chr)
+importFrom(purrr,map_lgl)
 importFrom(purrr,walk)
 importFrom(rawrr,readFileHeader)
 importFrom(rawrr,readIndex)
 importFrom(readr,read_file)
 importFrom(rjson,fromJSON)
 importFrom(rjson,toJSON)
+importFrom(stats,na.omit)
+importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_c)
 importFrom(stringr,str_detect)

NEWS.md

@@ -1,3 +1,13 @@
+# grover 1.1.0
+
+* Added the `exclude` argument to [`convertDirectory`](https://jasenfinch.github.io/grover/reference/convert.html) and [`runInfo`](https://jasenfinch.github.io/grover/reference/info.html) to exclude raw files matching the specified patterns.
+
+* [`runInfo`](https://jasenfinch.github.io/grover/reference/info.html) now collates the sample information client-side and so the `time_out` argument has been removed.
+
+* The [`grover::groverAPI`](https://jasenfinch.github.io/grover/reference/groverAPI.html) `log_dir` and `temp_dir` argument directories are now created recursively if they do not already exist.
+
+* Improved the naming of the [`grover::groverAPI`](https://jasenfinch.github.io/grover/reference/groverAPI.html) log files to include the current system date.
+
 # 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.

R/allGenerics.R

@@ -101,7 +101,8 @@ setGeneric('convertDirectory',function(grover_client,
                                        args = '', 
                                        outDir = '.',
                                        zip = TRUE,
-                                       overwrite = FALSE){
+                                       overwrite = FALSE,
+                                       exclude = character()){
   standardGeneric('convertDirectory')
 })
 
@@ -143,7 +144,7 @@ setGeneric('sampleInfo',function(grover_client,instrument,directory,file){
 
 #' @rdname info
 
-setGeneric('runInfo',function(grover_client,instrument,directory,time_out = 100){
+setGeneric('runInfo',function(grover_client,instrument,directory,exclude = character()){
   standardGeneric('runInfo')
 })
 

R/api.R

@@ -28,11 +28,11 @@ groverAPI <- function(grover_host,
   temp_dir <- path.expand(temp_dir)
 
   if (!dir.exists(log_dir)){
-    dir.create(log_dir)
+    dir.create(log_dir,recursive = TRUE)
   }
 
   if (!dir.exists(temp_dir)){
-    dir.create(temp_dir)
+    dir.create(temp_dir,recursive = TRUE)
   }
 
   if (isFALSE(background)) {
@@ -70,7 +70,6 @@ groverAPI <- function(grover_host,
     env$hostListDirectories <- hostListDirectories
     env$hostListInstruments <- hostListInstruments
     env$hostSampleInfo <- hostSampleInfo
-    env$hostRunInfo <- hostRunInfo
     env$hostTidy <- hostTidy
     env$hostFileInfo <- hostFileInfo
     env$hostDirectoryFileInfo <- hostDirectoryFileInfo
@@ -132,7 +131,10 @@ API <- function(host,
 
     message(stringr::str_c('API logs can be found at ',log_dir))
 
-    logger::log_appender(logger::appender_tee(tempfile("plumber_", log_dir, ".log")))
+    logger::log_appender(logger::appender_tee(paste0(log_dir,
+                                                    '/grover_',
+                                                    Sys.Date(),
+                                                    '.log')))
 
     api <- plumber::pr()
 
@@ -155,7 +157,6 @@ API <- function(host,
     api <- plumber::pr_get(api,'/listDirectories',hostListDirectories)
     api <- plumber::pr_get(api,'/listInstruments',hostListInstruments)
     api <- plumber::pr_get(api,'/sampleInfo',hostSampleInfo)
-    api <- plumber::pr_get(api,'/runInfo',hostRunInfo)
     api <- plumber::pr_put(api,'/tidy',hostTidy)
 
     api <- plumber::pr_get(api,'/fileInfo',hostFileInfo)

R/client-conversion.R

@@ -9,6 +9,7 @@
 #' @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 
+#' @param exclude A character vector of regular expression patterns for which raw files with matching patterns will not be converted.
 #' @return A vector of file paths to converted data files.
 #' @importFrom tools file_path_sans_ext
 #' @importFrom stringr str_split
@@ -18,6 +19,8 @@
 #' @importFrom progress progress_bar
 #' @importFrom crayon yellow bold
 #' @importFrom R.utils gzip
+#' @importFrom purrr map_lgl
+#' @importFrom stats setNames na.omit
 #' @export
 
 setMethod('convertFile',signature = 'GroverClient',
@@ -126,7 +129,8 @@ setMethod('convertDirectory',signature = 'GroverClient',
                    args = '', 
                    outDir = '.',
                    zip = TRUE,
-                   overwrite = FALSE){
+                   overwrite = FALSE,
+                   exclude = character()){
 
             outDir <- str_c(outDir,directory,sep = '/')
 
@@ -141,9 +145,18 @@ setMethod('convertDirectory',signature = 'GroverClient',
 
             raw_files <- listRawFiles(grover_client,instrument,directory)
 
+            raw_files <- raw_files[exclude %>% 
+                                     map(
+                                       ~!grepl(.x,raw_files)) %>% 
+                                     setNames(seq_along(.)) %>% 
+                                     as_tibble() %>% 
+                                     split(1:nrow(.)) %>% 
+                                     map_lgl(all)] %>% 
+              na.omit()
+            
             if (isFALSE(overwrite)){
               files <- raw_files[!(file_path_sans_ext(raw_files) %in% 
-                                 file_path_sans_ext(local_files,compression = zip))] 
+                                     file_path_sans_ext(local_files,compression = zip))] 
             } else {
               files <- raw_files
             }

R/client-info.R

@@ -6,7 +6,7 @@
 #' @param instrument instrument name
 #' @param directory directory name
 #' @param file file name
-#' @param time_out maximum request time in seconds. This may need to be increased for larger directories.
+#' @param exclude A character vector of regular expression patterns for which the information matching files will not be retrieved.
 #' @importFrom rjson fromJSON
 #' @export
 
@@ -63,32 +63,49 @@ setMethod('sampleInfo',signature = 'GroverClient',
 #' @export
 
 setMethod('runInfo',signature = 'GroverClient',
-          function(grover_client, instrument, directory,time_out = 100) {
+          function(grover_client, instrument, directory,exclude = character()) {
             files <- listRawFiles(grover_client, instrument, directory)
 
+            files <- files[exclude %>% 
+                             map(
+                               ~!grepl(.x,files)) %>% 
+                             setNames(seq_along(.)) %>% 
+                             as_tibble() %>% 
+                             split(1:nrow(.)) %>% 
+                             map_lgl(all)] %>% 
+              na.omit()
+            
             message('\nGenrating run info table for ',
                     bold(blue(directory)),
                     ' containing ',
                     bold(yellow(length(files))),
                     ' .raw files\n')
 
-            cmd <-  str_c(hostURL(grover_client),
-                          "/runInfo?", 
-                          "auth=",auth(grover_client), 
-                          "&instrument=",instrument,
-                          "&directory=",directory)
+            pb <- progress_bar$new(
+              format = "[:bar] :percent eta: :eta",
+              total = length(files), clear = FALSE)
+            pb$tick(0)
 
-            run_info <- GET(cmd,timeout(time_out))
+            run_info <- files %>% 
+              purrr::map_dfr(~{
+                suppressMessages({
+                  sample_info <- sampleInfo(
+                    grover_client = grover_client,
+                    instrument = instrument,
+                    directory = directory,
+                    file = .x)
+                })
+                
+                pb$tick()
+                
+                return(sample_info)
+              })
 
-            if (run_info$status_code == 200) {
-              run_info <- run_info %>%
-                content() %>%
-                unlist() %>%
-                fromJSON() %>%
-                as_tibble()
-            } else {
-             stop(str_c('Failed to retrieve with status code ', 
-                        run_info$status_code),call. = FALSE) 
+            failed <- files[!(files %in% run_info$`RAW file`)]
+            
+            if (length(failed) > 0) {
+              warning(str_c('Unable to retrieve information for files: ',
+                            str_c(failed,collapse = ', ')),call. = FALSE)
             }
 
             return(run_info)