miga-base 1.3.13.8 → 1.3.13.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e3bafd65eb344dccfd8a2b1601a2fc28282c17f8826565c6d0393161ad407b6b
-  data.tar.gz: cf47cca552f8651fe821af0431f579ef8958fb81371974fe5233391077a6405d
+  metadata.gz: 805637216225db5718e2a8a085046a64beae0ec816da3ecc01fda274194b83aa
+  data.tar.gz: 7c063bcd35554dd6ac7784ddeb37cf3a8e5b1f3ac3349f3ba4af9c5a7425806b
 SHA512:
-  metadata.gz: 9d8bebf5ac6267645fcaf2129d61dc516552a63790ef329310631c8db6e55f14d5ebcbe486eccef8898cd0a3036e6a448810ffe41a44810f351e2217a1f31817
-  data.tar.gz: 252d4fa1a39137358ce381bcdecebc9f1b5a40321c99b3ed059755555dbee3fd931fd77209d14d3b59ed236e51c53fa97d4668f9ad153ec7bdc2f02d205a1161
+  metadata.gz: 74fe73270087e6ceb32fea09e2a2b13e1f8687c96fe39b42f68c0fdbea5d172b15ab946843ba184667071c34f3080a3e12613b7ecf078d90656514f96654044b
+  data.tar.gz: 6d4e2ff50403236cdc90349aa67263590781c7ff4694cafb2bf35b81b57480026f3f59543145181e20f71b4cbee85d5682adf11d9813e86ea25ef1c40291c345

data/lib/miga/json.rb

@@ -3,7 +3,7 @@
 require 'json'
 begin
   require 'oj'
-  OJ.mimic_JSON()
+  Oj.mimic_JSON()
 rescue LoadError
   # Do nothing if not available
 end

data/lib/miga/remote_dataset/base.rb

@@ -134,6 +134,15 @@ module MiGA::RemoteDataset::Base
       end,
       method: :get
     },
+    ncbi_fetch: {
+      dbs: { nuccore: { stage: :metadata, format: :gb } },
+      uri: lambda do |opts|
+        @@_EUTILS_BUILD[:efetch,
+          db: opts[:db], id: opts[:ids], rettype: opts[:format], retmode: :text
+        ]
+      end,
+      method: :get
+    },
     ncbi_search: {
       dbs: {
         assembly: { stage: :metadata, format: :json },

data/lib/miga/remote_dataset/download.rb

@@ -107,9 +107,12 @@ class MiGA::RemoteDataset
 
       MiGA::MiGA.DEBUG 'Empty sequence, attempting download as WGS records'
       a, b = opts[:obj].metadata[:ncbi_wgs].split('-', 2)
-      pref = longest_common_prefix([a, b])
-      rang = a[pref.size .. -1].to_i .. b[pref.size .. -1].to_i
-      ids  = rang.map { |k| "%s%0#{a.size - pref.size}i" % [pref, k] }
+      ids  = [a]
+      unless b.nil?
+        pref = longest_common_prefix([a, b])
+        rang = a[pref.size .. -1].to_i .. b[pref.size .. -1].to_i
+        ids  = rang.map { |k| "%s%0#{a.size - pref.size}i" % [pref, k] }
+      end
       download_rest(opts.merge(universe: :ncbi, db: :nuccore, ids: ids))
     end
 

data/lib/miga/remote_dataset.rb

@@ -300,6 +300,16 @@ class MiGA::RemoteDataset < MiGA::MiGA
       metadata[:web_assembly_gz] ||=
         '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
     end
+
+    # If all conditions are right, try getting the WGS range
+    if @_ncbi_asm_json_doc['wgs'] && !@_ncbi_asm_json_doc['wgs'].empty? &&
+         metadata[:ncbi_nuccore] && !metadata[:ncbi_wgs]
+      doc = self.class.download(:ncbi_fetch, :nuccore, metadata[:ncbi_nuccore], :gb).split(/\n/)
+      ln  = doc.grep(/^WGS\s+\S+-\S+/).first
+      wgs = ln&.gsub(/^WGS\s+(\S+-\S+).*/, '\1')
+      metadata[:ncbi_wgs] = wgs if wgs
+    end
+
     @_ncbi_asm_json_doc
   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, 13, 8].freeze
+  VERSION = [1.3, 13, 10].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, 3, 23)
+  VERSION_DATE = Date.new(2024, 4, 1)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.13.8
+  version: 1.3.13.10
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-03-23 00:00:00.000000000 Z
+date: 2024-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons