miga-base 1.3.12.0 → 1.3.12.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 45ab052e74f73fe87a2383443285dae3fb218c659618c1d2d7278ff8bb0de6f4
-  data.tar.gz: 553c70d1a5c15093686260a0dec176a0f8ecd196f0884218484ff9964e416661
+  metadata.gz: cf660d951441269a671b7fb57d3e91a572fdb62d5ffbaeda9ff412042798759b
+  data.tar.gz: 1721194dcce4a70e4cad66ca4cea5db88f521323022b62c2c93740458a1b0bea
 SHA512:
-  metadata.gz: 27a87882655d6875f482042d388273ce46135329919f9738913022af6fd97f411e9db6238b4bd7fbcc50d7d605da51f447d85b68ff77758cf324ce9e59c7e592
-  data.tar.gz: 116737b9a5ca99d97a8ad8f704a5df9146177c2d9603c8c4b19e631baa52e60183888369dcec96f671238f6ad934ce8c6324bc368aaff8bc8645f3b1d3dee247
+  metadata.gz: ff0b9c3a8db37fa9b0d75a0b884154b416669e068eab9f22f406facf9822345a38baccc224138a15fb5e9e1dff786e55e2ebc0d870573b892f056bf7e18e275a
+  data.tar.gz: af7dcea647e3ead8fdbde6f917264efd93335cc9c7878bd7a4b43b8dbb27434882dff76728fa984c5724802a581421ddd333f6cfe46ab1d6c75fb4bb953bc378

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

@@ -69,9 +69,10 @@ module MiGA::Cli::Action::Download::Base
       '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 @@ module MiGA::Cli::Action::Download::Base
   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
 
 

data/lib/miga/common/net.rb

@@ -123,10 +123,11 @@ module MiGA::Common::Net
 
   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

data/lib/miga/remote_dataset.rb

@@ -67,6 +67,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
     # Get the MiGA::Taxonomy object for the lineage of the taxon with TaxID
     # +id+ using the local NCBI Taxonomy dump.
     def taxonomy_from_ncbi_dump(id)
+      id = id.to_i unless id.is_a? Integer
       MiGA::Taxonomy.new(ns: 'ncbi').tap do |tax|
         while @ncbi_taxonomy_names[id]
           tax << { @ncbi_taxonomy_names[id][1] => @ncbi_taxonomy_names[id][0] }

data/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, 2].freeze
 
   ##
   # Nickname for the current major.minor version.

data/test/net_test.rb

@@ -37,15 +37,13 @@ class FormatTest < Test::Unit::TestCase
     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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.12.0
+  version: 1.3.12.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R