Merge pull request #25 from jasenfinch/devel

v1.1.1
jasenfinch · Jan 18, 2023 · dcf5f12 · dcf5f12
2 parents 55f66fe + 846145b
commit dcf5f12
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -18,8 +18,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
-          - {os: windows-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'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: grover
 Title: Web API Framework for Mass Spectrometry Data Transfer
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,12 @@
+# grover 1.1.1
+
+* Ensure that [`grover::convertDirectory`](https://jasenfinch.github.io/grover/reference/convert.html) returns the file paths of the converted .mzML files for all the of the raw files in the specified directory.
+
 # 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.
+* Added the `exclude` argument to [`grover::convertDirectory`](https://jasenfinch.github.io/grover/reference/convert.html) and [`grover::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.
+* [`grover::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.
 

diff --git a/R/client-conversion.R b/R/client-conversion.R
@@ -188,6 +188,14 @@ setMethod('convertDirectory',signature = 'GroverClient',
               return(res)
             })
 
+            converted_files <- list.files(outDir,
+                                          full.names = TRUE,
+                                          pattern = '.mzML') %>% 
+              {
+                .[file_path_sans_ext(basename(.),compression = zip) %in% 
+                    file_path_sans_ext(raw_files)]
+              }
+
             message()
 
             failed <- files[is.na(results)]
@@ -197,7 +205,7 @@ setMethod('convertDirectory',signature = 'GroverClient',
                             str_c(failed,collapse = ', ')),call. = FALSE)
             }
 
-            return(results)
+            return(converted_files)
           })
 
 #' @rdname convert