miga-base 1.2.17.2 → 1.2.17.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 50f8bda6b07f6b7da95f3342e96b290c401a8810c35e2406309d28559111de2d
-  data.tar.gz: 99dd4709f330f90fc71b213c42ce60bade2ac32127fb123ae450cb0a54885176
+  metadata.gz: 57016515d9789927d6eda96e04be04dd9d47e6f330ea8f2f489971d7f0ad3845
+  data.tar.gz: 3e42b22e637fc5ad47405eaac88fcc7ba00d94abfe86035c8a8a613b54e06bbe
 SHA512:
-  metadata.gz: 18666049e37b300ceaf367cd1fa1847556a1a84a6878095b9e931c6665f1559a427e00a844ec764de470ab25b92ebd1c48753b782a89c779a4974f2eb63b5385
-  data.tar.gz: c2b4d46070dc7fa7bef02dc7a4147472a32d1863dd86871a2c29c9fde4a1ea906f3d29659bbadab24ebcd57095d3db826120bff8bb831994d6dc6f372d6b569e
+  metadata.gz: c2b8cf60bfc487960e66d4a35a61fcb691d166baf31656e115c28dd3854276e062f6c9325d2d4ff924a563327a01c05f4ecfd570004deb54db05b065b955281a
+  data.tar.gz: 6124879ca61700d6cf58aaa27c2db405874b1fdcaeed829b835662eeb92f6a59383f1fb2ed5bb073d5b97d1bef2ed15f0580821a267cd6f5f0c65ef2dbb2f1bc

data/lib/miga/remote_dataset/download.rb

@@ -61,7 +61,7 @@ class MiGA::RemoteDataset
     # Supported +opts+ (Hash) are the same as #download_rest and #ncbi_asm_rest.
     def ncbi_gb_rest(opts)
       # Simply use defaults, but ensure that the URL can be properly formed
-      o = download_rest(opts.merge(universe: :ncbi, db: :nuccore, format: :gb))
+      o = download_rest(opts.merge(universe: :ncbi, db: :nuccore))
       return o unless o.strip.empty?
 
       MiGA::MiGA.DEBUG 'Empty sequence, attempting download from NCBI assembly'

data/lib/miga/remote_dataset.rb

@@ -134,7 +134,10 @@ class MiGA::RemoteDataset < MiGA::MiGA
       # Get taxonomy
       @metadata[:tax] = get_gtdb_taxonomy
     when :seqcode
-      # Do nothing, taxonomy already defined
+      # Taxonomy already defined
+      # Copy IDs over to allow additional metadata linked
+      @metadata[:ncbi_asm] = @metadata[:seqcode_asm]
+      @metadata[:ncbi_nuccore] = @metadata[:seqcode_nuccore]
     end
 
     if metadata[:get_ncbi_taxonomy]
@@ -276,6 +279,10 @@ class MiGA::RemoteDataset < MiGA::MiGA
   def get_type_status_ncbi_asm(metadata)
     return metadata if ncbi_asm_json_doc.nil?
 
+    metadata[:suspect] = (ncbi_asm_json_doc['exclfromrefseq'] || [])
+    metadata[:suspect] = nil if metadata[:suspect].empty?
+    return metadata if metadata[:is_type] # If predefined, as in SeqCode
+
     from_type = ncbi_asm_json_doc['from_type']
     from_type = ncbi_asm_json_doc['fromtype'] if from_type.nil?
     case from_type
@@ -292,8 +299,6 @@ class MiGA::RemoteDataset < MiGA::MiGA
       metadata[:is_type] = true
       metadata[:type_rel] = from_type
     end
-    metadata[:suspect] = (ncbi_asm_json_doc['exclfromrefseq'] || [])
-    metadata[:suspect] = nil if metadata[:suspect].empty?
     MiGA.DEBUG "Got type: #{from_type}"
     metadata
   end
@@ -306,7 +311,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
     File.open("#{base}.start", 'w') { |ofh| ofh.puts Time.now.to_s }
     if udb[:format] == :fasta_gz
       download "#{l_ctg}.gz"
-      system "gzip -d '#{l_ctg}.gz'"
+      system "gzip -fd '#{l_ctg}.gz'"
     else
       download l_ctg
     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 = [1.2, 17, 2].freeze
+  VERSION = [1.2, 17, 3].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, 21)
+  VERSION_DATE = Date.new(2023, 2, 22)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.17.2
+  version: 1.2.17.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-02-21 00:00:00.000000000 Z
+date: 2023-02-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons