Allow for empty --ncbi-taxonomy-dump

lib/miga/cli/action/download/base.rb

@@ -69,9 +69,10 @@ def cli_save_actions(opt)
       'Path to an output file with the list of all datasets listed remotely'
     ) { |v| cli[:remote_list] = v }
     opt.on(
-      '--ncbi-taxonomy-dump STRING',
-      'Path to an NCBI Taxonomy dump directory to query instead of API calls'
-    ) { |v| cli[:ncbi_taxonomy_dump] = v }
+      '--ncbi-taxonomy-dump [path]',
+      'Path to an NCBI Taxonomy dump directory to query instead of API calls',
+      'If the path is not passed, the dump is automatically downloaded'
+    ) { |v| cli[:ncbi_taxonomy_dump] = v || true }
   end
 
   def generic_perform
@@ -97,8 +98,21 @@ def load_tasks
   def load_ncbi_taxonomy_dump
     return unless cli[:ncbi_taxonomy_dump]
 
-    cli.say "Reading NCBI Taxonomy dump: #{cli[:ncbi_taxonomy_dump]}"
-    MiGA::RemoteDataset.use_ncbi_taxonomy_dump(cli[:ncbi_taxonomy_dump], cli)
+    if cli[:ncbi_taxonomy_dump] == true
+      cli.say 'Downloading and reading NCBI Taxonomy dump'
+      Dir.mktmpdir do |dir|
+        file = 'taxdump.tar.gz'
+        path = File.join(dir, file)
+        url  = 'https://ftp.ncbi.nih.gov/pub/taxonomy/%s' % file
+
+        File.open(path, 'wb') { |fh| fh.print MiGA::MiGA.net_method(:get, url) }
+        MiGA::MiGA.run_cmd('cd "%s" && tar -zxf "%s"' % [dir, file])
+        MiGA::RemoteDataset.use_ncbi_taxonomy_dump(dir, cli)
+      end
+    else
+      cli.say "Reading NCBI Taxonomy dump: #{cli[:ncbi_taxonomy_dump]}"
+      MiGA::RemoteDataset.use_ncbi_taxonomy_dump(cli[:ncbi_taxonomy_dump], cli)
+    end
   end
 
 

lib/miga/common/net.rb

@@ -123,10 +123,11 @@ def http_request(method, url, *opts)
 
   def net_method(method, uri, *opts)
     attempts ||= 0
+    uri = URI.parse(uri) if uri.is_a? String
     DEBUG "#{method.to_s.upcase}: #{uri} #{opts}"
     case method.to_sym
     when :ftp
-      download_file_ftp(uri)
+      download_file_ftp(uri, *opts)
     else
       http_request(method, uri, *opts)
     end

lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 12, 0].freeze
+  VERSION = [1.3, 12, 1].freeze
 
   ##
   # Nickname for the current major.minor version.

test/net_test.rb

@@ -37,15 +37,13 @@ def test_download_file_ftp
     f = tmpfile('t/test.txt')
     d = File.dirname(f)
     assert(!Dir.exist?(d))
-    # TODO
-    # Bring back when I can connect to the Gatech's FTP
-    ### m = MiGA::MiGA
-    ### m.download_file_ftp(:miga_online_ftp, 'api_test.txt', f)
-    ### assert(Dir.exist?(d))
-    ### assert_equal('miga', File.read(f).chomp)
-    ### File.unlink(f)
-    ### m.download_file_ftp(:miga_db, '../api_test.txt', f)
-    ### assert_equal('miga', File.read(f).chomp)
+    m = MiGA::MiGA
+    m.download_file_ftp(:miga_online_ftp, 'api_test.txt', f)
+    assert(Dir.exist?(d))
+    assert_equal('miga', File.read(f).chomp)
+    File.unlink(f)
+    m.download_file_ftp(:miga_db, '../api_test.txt', f)
+    assert_equal('miga', File.read(f).chomp)
   end
 
   def test_encoding