miga-base 1.2.15.1 → 1.2.15.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0ad52d75f0a01d681043530335e20e89ecfb46822a8166dd7c0993b9822882f9
-  data.tar.gz: 28bf47b3e257718cb3071ebf48d2f0fd63a8797116f8108faa789643940aac3f
+  metadata.gz: 02ee43a4f918d4adb45bc28c20386965eeea6a6a7447a7bb56efbd7017c4ee54
+  data.tar.gz: c7d16aff20c61fd64833a3aa2f9ca66aaa6f3caedc19a03ae08cd1b9bd08b720
 SHA512:
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-  data.tar.gz: 41755ac99346b7dbbdf1a971158f98c99ca970d4134b912b17989d4776ae528902fed6df68d7f477fecfcc02657fae0350f311e3195c2211bc4e0945744366c8
+  metadata.gz: 94ca45cab979c73e767cd05dfaceca410b6cedef44a5d9b0d16e4439651d872013fadc23a54d3ed6355bf6ed045f673e8e80424979e17af7dae0a32cd22e89d7
+  data.tar.gz: 0d83195dcbe7afb4fbfce02d492ed63c93776f1756037aa6412ab94b6378ae54d983a0583c3cf1c27e5c9a9b2dca108d386a60aaabce80a7af083d53a9cf0648

data/lib/miga/remote_dataset.rb

@@ -12,14 +12,32 @@ class MiGA::RemoteDataset < MiGA::MiGA
   # Class-level
 
   class << self
-    def ncbi_asm_acc2id(acc)
+    ##
+    # Translate an NCBI Assembly Accession (+acc+) to corresponding internal
+    # NCBI ID, with up to +retrials+ retrials if the returned JSON document
+    # does not conform to the expected format
+    def ncbi_asm_acc2id(acc, retrials = 3)
       return acc if acc =~ /^\d+$/
 
       search_doc = MiGA::Json.parse(
         download(:ncbi_search, :assembly, acc, :json),
         symbolize: false, contents: true
       )
-      (search_doc['esearchresult']['idlist'] || []).first
+      out = (search_doc['esearchresult']['idlist'] || []).first
+      if out.nil?
+        raise MiGA::RemoteDataMissingError.new(
+          "NCBI Assembly Accession not found: #{acc}"
+        )
+      end
+      return out
+    rescue MiGA::RemoteDataMissingError => e
+      if retrials <= 0
+        raise e
+      else
+        MiGA::MiGA.DEBUG("#{self}.ncbi_asm_acc2id - RETRY #{retrials}")
+        retrials -= 1
+        retry
+      end
     end
   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, 15, 1].freeze
+  VERSION = [1.2, 15, 2].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, 1, 24)
+  VERSION_DATE = Date.new(2023, 1, 25)
 
   ##
   # References of MiGA

data/test/remote_dataset_test.rb

@@ -63,7 +63,9 @@ class RemoteDatasetTest < Test::Unit::TestCase
 
   def test_asm_acc2id
     declare_remote_access
-    assert_nil(MiGA::RemoteDataset.ncbi_asm_acc2id('NotAnAccession'))
+    assert_raise(MiGA::RemoteDataMissingError) do
+      MiGA::RemoteDataset.ncbi_asm_acc2id('NotAnAccession', 1)
+    end
     id = MiGA::RemoteDataset.ncbi_asm_acc2id('GCA_004684205.1')
     assert_equal('2514661', id)
     assert_equal(id, MiGA::RemoteDataset.ncbi_asm_acc2id(id))

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.15.1
+  version: 1.2.15.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-01-24 00:00:00.000000000 Z
+date: 2023-01-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons