miga-base 1.4.3.0 → 1.4.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 3f6c844d8a17d4c74bbe7d3a4df8cbae41d10d0263f42c34a0cd555de9164a70
+  metadata.gz: a71abecf373fd0b61a6148010a4c4f2ae08bb1088fbc5c185c95a2e35e761d74
+  data.tar.gz: 021b16610dbf57f81e31e04745bbf04189fe82a836245883c4f68fe80ef99cf6
 SHA512:
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+  data.tar.gz: 17d801e447570c9390295828f3317649080c4d9d2d1c6f9e1a39f8c3903b5bd8aa2a6f2dbc9e702210d75dc4e72a99b14bce6bd1b56c856bf1b46d0ebe53e220

data/lib/miga/remote_dataset/base.rb

@@ -64,8 +64,9 @@ module MiGA::RemoteDataset::Base
     },
     gtdb: {
       dbs: {
-        # This is a dummy entry plugged directly to +ncbi_asm_get+
-        assembly: { stage: :assembly, format: :fasta, getter: :ncbi_asm },
+        assembly: {
+          stage: :assembly, format: :fasta, getter: :ncbi_or_embl_asm
+        },
         # The 'taxon' namespace actually returns a list of genomes (+format+)
         taxon: {
           stage: :metadata, format: :genomes, map_to: [:assembly],
@@ -84,8 +85,9 @@ module MiGA::RemoteDataset::Base
     },
     seqcode: {
       dbs: {
-        # These are dummy entries plugged directly to +ncbi_*_get+
-        assembly: { stage: :assembly, format: :fasta, getter: :ncbi_asm },
+        assembly: {
+          stage: :assembly, format: :fasta, getter: :ncbi_or_embl_asm
+        },
         nuccore:  { stage: :assembly, format: :fasta, getter: :ncbi_gb },
         # This is the list of type genomes
         :'type-genomes' => { stage: :metadata, format: :json }

data/lib/miga/remote_dataset/download.rb

@@ -49,6 +49,28 @@ class MiGA::RemoteDataset
       doc
     end
 
+    ##
+    # Attempts to download from NCBI Assembly and, if that fails, moves to EMBL
+    # instead. This is the default for SeqCode because some assemblies don't
+    # synchronize fast enough, and in the case of MAGs some never do. This is
+    # also the default for GTDB since it could be affected in the future too,
+    # although at present GTDB only sources data from NCBI. Supported +opts+ are
+    # the same as for +ncbi_asm_get+
+    def ncbi_or_embl_asm_get(opts)
+      begin
+        ncbi_asm_get(opts)
+      rescue
+        # The actual error thrown by `ncbi_asm_get` is rather uniformative and
+        # could change in the future. Right now, the URL resolves correctly, but
+        # the file is corrupted, so the actual error is `Zip::Error`. Hopefully
+        # NCBI will implement an actual 404 Error that can be caught here more
+        # narrowly, but for now it's safer to catch broadly here.
+
+        opts_embl = opts.dup.merge(universe: :ebi, db: :embl)
+        download_get(opts_embl)
+      end
+    end
+
     ##
     # Download data from NCBI Assembly database using the REST method.
     # Supported +opts+ (Hash) include:

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 = [1.4, 3, 0].freeze
+  VERSION = [1.4, 3, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2026, 7, 22)
+  VERSION_DATE = Date.new(2026, 8, 7)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.4.3.0
+  version: 1.4.3.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-07-22 00:00:00.000000000 Z
+date: 2026-08-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons