miga-base 1.2.15.4 → 1.2.16.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8ee87db325ab9759e42953f999099553c0921eca9fc6739db3b132f624b93177
-  data.tar.gz: e423b05412fba8256e0b3d9a6b8411c70b1f45d6addfe01129e842319d24baf9
+  metadata.gz: '0215026559d070f36a5eacddecaa2a2c4c4717f6506add25b76f1988dfb86483'
+  data.tar.gz: 944b5ba3f76e75a988932963db73ab23795f0a266233f555e5617f875aad1d53
 SHA512:
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-  data.tar.gz: 7692908ef9e69de7526955956a9c6c4d74d3939d69509ac1bfb1a4981248fab6fc2b54091ea56a380f80c913ceddb6179b09f4f1fef37a10cfe1b50bd7e8e74b
+  metadata.gz: 70b1fb8640127febebf776f80faf75d59b25ab145152ad5d49d78b9a408e5e653cf874bb9e5c5c0749ae4bb790b46ffe9eff504ac646df5c558b72f4ba155be0
+  data.tar.gz: ca8d6a4f389b721b4240f70b0da6d02ea8f70c52d0e09b5622d168745a1f082a6fc0b5c5a4d92e2b85844d42bb17e682a52cbd788a0664496c2814c958ce6b7a

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

@@ -52,10 +52,22 @@ module MiGA::Cli::Action::Download::Ncbi
   end
 
   def remote_list
-    cli.say 'Downloading genome list'
+    doc =
+      if cli[:ncbi_table_file]
+        cli.say 'Reading genome list from file'
+        File.open(cli[:ncbi_table_file], 'r')
+      else
+        cli.say 'Downloading genome list'
+        url = remote_list_url
+        MiGA::RemoteDataset.download_url(url)
+      end
+    ds = parse_csv_as_datasets(doc)
+    doc.close if cli[:ncbi_table_file]
+    ds
+  end
+  
+  def parse_csv_as_datasets(doc)
     ds = {}
-    url = remote_list_url
-    doc = MiGA::RemoteDataset.download_url(url)
     CSV.parse(doc, headers: true).each do |r|
       asm = r['assembly']
       next if asm.nil? || asm.empty? || asm == '-'

data/lib/miga/cli/action/ncbi_get.rb

@@ -29,6 +29,12 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
         '--api-key STRING',
         '::HIDE::' # For backwards compatibility
       ) { |v| ENV['NCBI_API_KEY'] = v }
+      opt.on(
+        '--ncbi-table-file STRING',
+        '::HIDE::' # Only meant for debugging
+        # It can take the table returned by NCBI and parse it from a file
+        # instead of downloading it directly
+      ) { |v| cli[:ncbi_table_file] = v }
       opt.on(
         '--ncbi-api-key STRING',
         'NCBI API key'

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 = [1.2, 15, 4].freeze
+  VERSION = [1.2, 16, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 2, 7)
+  VERSION_DATE = Date.new(2023, 2, 8)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.15.4
+  version: 1.2.16.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-02-07 00:00:00.000000000 Z
+date: 2023-02-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons