Merge pull request #20 from jasenfinch/devel

v1.0.6
jasenfinch · May 9, 2021 · fd87eb7 · fd87eb7
2 parents a03a65b + ef4bc1c
commit fd87eb7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: grover
 Title: Web API Framework for Mass Spectrometry Data Transfer
-Version: 1.0.5
+Version: 1.0.6
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",
@@ -26,8 +26,9 @@ Imports: callr,
         progress,
         purrr,
         rawrr,
-        rjson,
         readr,
+        rjson,
+        R.utils,
         stringr,
         tibble,
         tictoc,

diff --git a/NAMESPACE b/NAMESPACE
@@ -37,6 +37,7 @@ exportMethods(sampleInfo)
 exportMethods(show)
 exportMethods(transferDirectory)
 exportMethods(transferFile)
+importFrom(R.utils,gzip)
 importFrom(callr,r_bg)
 importFrom(crayon,blue)
 importFrom(crayon,bold)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# grover 1.0.6
+
+* [`grover::converFile`](https://jasenfinch.github.io/grover/reference/convert.html) creates the output directory if it doesn't already exist.
+
+* converted files now correctly zipped by [`grover::converFile`](https://jasenfinch.github.io/grover/reference/convert.html) to ensure they are readable by the [`mzR`](https://www.bioconductor.org/packages/release/bioc/html/mzR.html) package.
+
 # grover 1.0.5
 
 * File conversion methods [`grover::converFile`](https://jasenfinch.github.io/grover/reference/convert.html) and [`grover::convertDirectory`](https://jasenfinch.github.io/grover/reference/convert.html) now return the file path of the converted file.

diff --git a/R/client-conversion.R b/R/client-conversion.R
@@ -16,6 +16,7 @@
 #' @importFrom fs dir_create file_delete
 #' @importFrom progress progress_bar
 #' @importFrom crayon yellow bold
+#' @importFrom R.utils gzip
 #' @export
 
 setMethod('convertFile',signature = 'GroverClient',
@@ -44,7 +45,7 @@ setMethod('convertFile',signature = 'GroverClient',
                          '&args=')
 
             if (is.null(args)) {
-             args <- ''
+              args <- ''
             }
 
             cmd <- str_c(cmd,args)
@@ -59,18 +60,19 @@ setMethod('convertFile',signature = 'GroverClient',
               convertedFile <- convertedFile %>%
                 content(as = 'text',encoding = 'UTF-8')
 
+              if (!dir.exists(outDir)){
+                dir_create(outDir)
+              }
+
               converted_file_path <- str_c(outDir,'/',fileName,'.mzML')
 
               writeLines(convertedFile,converted_file_path)
 
               if (isTRUE(zip)){
                 zipped_file_path <- str_c(outDir,'/',fileName,'.mzML.gz')
 
-                zip(zipped_file_path,
-                    converted_file_path,
-                    flags = '-q')
-
-                fs::file_delete(converted_file_path)
+                gzip(converted_file_path,
+                     zipped_file_path)
 
                 converted_file_path <- zipped_file_path
               }

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/client-usage.html b/docs/articles/client-usage.html
diff --git a/docs/articles/client-usage_files/header-attrs-2.8/header-attrs.js b/docs/articles/client-usage_files/header-attrs-2.8/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/hosting.html b/docs/articles/hosting.html
diff --git a/docs/articles/hosting_files/header-attrs-2.8/header-attrs.js b/docs/articles/hosting_files/header-attrs-2.8/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html
diff --git a/docs/articles/introduction_files/header-attrs-2.8/header-attrs.js b/docs/articles/introduction_files/header-attrs-2.8/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   client-usage: client-usage.html
   hosting: hosting.html
   introduction: introduction.html
-last_built: 2021-04-26T23:30Z
+last_built: 2021-05-09T11:32Z
 
diff --git a/docs/reference/GroverClient-accessors.html b/docs/reference/GroverClient-accessors.html
diff --git a/docs/reference/GroverClient-class.html b/docs/reference/GroverClient-class.html
diff --git a/docs/reference/GroverHost-accessors.html b/docs/reference/GroverHost-accessors.html
diff --git a/docs/reference/GroverHost-class.html b/docs/reference/GroverHost-class.html
diff --git a/docs/reference/conversionArgs.html b/docs/reference/conversionArgs.html
diff --git a/docs/reference/convert.html b/docs/reference/convert.html