miga-base 1.3.9.4 → 1.3.9.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 436166fe9bbc76b69f014879610440e9646261f1a06dbc134418b79fa3da9b08
-  data.tar.gz: fb835c9bfa4829a3ac1c5ae8bdc1c5998cd8b9c4a55d3988538b9c24b2f4329f
+  metadata.gz: d4b28c04587658e8efa8fcbd012d003b24d1526c1563d82d33a4ae68f561926c
+  data.tar.gz: d835e3bf5474c897c000d7b2f096dda0946a0ee759fa9d43b017b5f4ffdf324f
 SHA512:
-  metadata.gz: 77e76a0dea664321aad58b4eee310d91cd9fa34c6ae0339451c83d2d169cbf9c160ed6c469401d0155280a28612ae8cde47a0c00be739371986f64621e44ef68
-  data.tar.gz: cdece24eb38d804b729c3c7f9018f7f3e835db258a59abe1ce560baf8bce29223a957f8498b96d6a647994361903d2d8179f2c6e6890451923dd44c5ae6cbcd8
+  metadata.gz: 6121ff05020da43565f597167e0a36a948bc5d4d8507ab38128e2bfdfd72000d0bddff02e20ad3bf3ef62fd0d5dd48cc7db68c2a77c662ba24baa7185fd3763d
+  data.tar.gz: f19fb727f8adb2620fa92c742421466cd1668991d5ce6bf80571f5a633b7f0b0767d83159871151681d0cd7469e296b6698c2efea32d65e63f570e55d5df5881

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

@@ -79,7 +79,7 @@ module MiGA::Cli::Action::Download::Ncbi
 
     if cli[:ncbi_list_json]
       cli.say "Saving remote list: #{cli[:ncbi_list_json]}"
-      MiGA::Json.generate_plain(list, cli[:ncbi_list_json])
+      MiGA::Json.generate_fast(list, cli[:ncbi_list_json])
     end
 
     list

data/lib/miga/json.rb

@@ -75,6 +75,13 @@ class MiGA::Json < MiGA::MiGA
       generate_generic(:generate, obj, path)
     end
 
+    ##
+    # Generates and returns plain JSON to represent +obj+ without checking for
+    # circular references. If +path+ is passed, it saves the JSON in that file.
+    def generate_fast(obj, path = nil)
+      generate_generic(:fast_generate, obj, path)
+    end
+
     private
 
     def generate_generic(method, obj, path)

data/lib/miga/project/dataset.rb

@@ -26,7 +26,7 @@ module MiGA::Project::Dataset
   ##
   # Returns MiGA::Dataset
   def dataset(name)
-    name = name.miga_name
+    name = name.to_s.miga_name
     return nil unless MiGA::Dataset.exist?(self, name)
 
     @datasets ||= {}

data/lib/miga/remote_dataset/download.rb

@@ -65,7 +65,7 @@ class MiGA::RemoteDataset
         :ncbi_datasets_download, :genome, opts[:ids],
         :zip, nil, opts[:extra], opts[:obj]
       )
-      zip_tmp = Tempfile.new('asm.zip')
+      zip_tmp = Tempfile.new(['asm', '.zip'], encoding: zipped.encoding.to_s)
       zip_tmp.print(zipped)
       zip_tmp.close
 
@@ -76,7 +76,7 @@ class MiGA::RemoteDataset
           if entry.file? && entry.name =~ /_genomic\.fna$/
             DEBUG "Extracting: #{entry.name}"
             entry.get_input_stream do |ifh|
-              cont = MiGA::MiGA.normalize_encoding(ifh.read) + "\n"
+              cont = MiGA::MiGA.normalize_encoding(ifh.read).chomp + "\n"
               ofh&.print(cont)
               o += cont
             end

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, 9, 4].freeze
+  VERSION = [1.3, 9, 6].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 1, 23)
+  VERSION_DATE = Date.new(2024, 1, 24)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.9.4
+  version: 1.3.9.6
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-01-23 00:00:00.000000000 Z
+date: 2024-01-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons