Add file upload logic to adjust ZIP folders extraction by removing nesting in singleton uploads

BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/file_collection/file_collection.rb

@@ -72,13 +72,44 @@ def extract_collection_from_archive_file(archive_file_name)
 
     self.remove_unwanted_files
 
+    # we flatten directory if archive file names coincide with only entry
+    if extra_nesting? # archive name/dir is same as its only 1st level entry, and is dir e.g. subx archive has only subx folder
+      basename = File.basename(directory)
+      self.addlog_context(self, "The only directory #{basename} inside similarly named archive, reducing nesting by one level.")
+      subdir = File.join(directory, basename)
+
+      # simple system("mv #{escaped_subdir}/* #{escaped_directory}") would fail on 3ple nested folder subx/subx/subx
+      #
+      tmpdir  = File.join(directory, ".tmp_#{basename}_#{Time.now.strftime('%Y%m%d%H%M%S%N')}_#{rand(1_000_000_000)}")
+      # todo consider a safer tmp dir solution - require 'mkmpdir'; Dir.mktmpdir(".tmp_#{basename}_", directory)
+      FileUtils.mv(subdir, tmpdir)
+      # Move tmpdir's children up into directory
+      Dir.children(tmpdir).each do |f|
+        FileUtils.mv(File.join(tmpdir, f), directory)
+      end
+
+      self.remove_unwanted_files
+    end
+    @dir_list = nil
     self.sync_to_provider
     self.set_size!
     self.save
 
     true
   end
 
+  # Detect a file collection with only dir, which has the same name as the collection.
+  # CBRAIN currently creates a FileCollection with the name of the ZIP file and puts
+  # in it the results of extracting the archive. What often happens then is that the
+  # resulting unintended level, e.g. for "sub-01.zip" we
+  # get "sub-01/sub-01/...".
+  def extra_nesting?
+    directory = self.cache_full_path
+    basename  = File.basename(directory)
+    entries   = Dir.entries(directory) - %w( . .. )
+    return entries.size == 1 && File.directory?(File.join(directory, basename))
+  end
+
   # Calculates and sets the size attribute (active recount forced)
   def set_size!
     allfiles       = self.list_files(:all, :regular) || []
@@ -135,7 +166,6 @@ def merge_collections(userfiles)
 
   # Mathieu Desrosiers
   # Returns an array of the relative paths to first level subdirectories contained in this collection.
-  # this function only for usage in spmbatch, feel free to contact me if you would like to remove it.
   def list_first_level_dirs
     return @dir_list if @dir_list
     Dir.chdir(self.cache_full_path.parent) do
@@ -409,5 +439,3 @@ def list_fake_files
   end
 
 end
-
-

BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/file_collection/views/_file_collection.html.erb

@@ -33,4 +33,3 @@
            :locals => { :base_directory => base_dir } %>
 
 <div id="sub_viewer_filecollection_cbrain"></div>
-

BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/file_collection/views/_file_collection_top_table.html.erb

@@ -33,6 +33,11 @@
 <p class="medium_paragraphs">
 The table below shows what is <em>inside</em> <strong><%= @userfile.name %>/</strong>
 </p>
+<% if @userfile.extra_nesting? %>
+  <p class="medium_paragraphs">
+    This file collection only contains a folder with the same name as the collection, this is probably <strong> not </strong> what you want.
+  </p>
+<% end %>
 <table class="plain_file_list" class="resource_list">
   <tr class="list-odd">
     <th>
@@ -48,4 +53,3 @@ The table below shows what is <em>inside</em> <strong><%= @userfile.name %>/</st
             :locals  => { :base_directory => base_dir }
   %>
 </table>
-

BrainPortal/spec/models/file_collection_spec.rb

@@ -86,6 +86,7 @@
       allow(file_collection).to receive(:sync_to_provider)
       allow(file_collection).to receive(:set_size!)
       allow(file_collection).to receive(:save)
+      allow(file_collection).to receive(:extra_nesting?)
     end
 
     it "should execute 'gunzip' if archive is a *.tar.gz" do
@@ -224,4 +225,3 @@
   end
 
 end
-