miga-base 1.3.13.0 → 1.3.13.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8659bae6ee7d40a76a464840a56b4aff77f9a848d777349e98d8c316717b0021
-  data.tar.gz: dab1cbd8ee24503b4dfbe0e8b034da195120251c258c798bbba92668a52d3cfa
+  metadata.gz: 7452e6019471294f9f1b21ef675ff65a4b582eb51df3f0d59c4ee8a084f79540
+  data.tar.gz: 1fb9ba522229fa36265c9f5b261c57c44f98e0d31275acd7903c0e4e79f9791a
 SHA512:
-  metadata.gz: '09a916e1db7bb4912111e83c2d832a779a245c8eb326aee3cfcead8611d484f737a1cbcae1a1279a2673a2f31a8252c859b533b7ae9b6c74c8881b41e63e7c40'
-  data.tar.gz: 43e7065632d2642abb0c6bb5fac8ae96e0696c0f48b128376fa5d1ac929c1c7b787df61af78bee5a4824049da7b2baf976f9bb3d3f083184ca02deefc166114e
+  metadata.gz: 6519c3bdcf8ce9bfb252a023f9a0dc19ab6534e44f21e8db3199148ae7c2d9588848e18739111b6d444287cf0c6e383ace2b75f77de5bef5da55ea7b7979450e
+  data.tar.gz: cb8b25241a73c301c8ceef0c2e08286348047df7a47576a46687444c89d7716f057c87cb5bfa9ed9016a44bcc63aeb5ed96cac1bb46442fe3b574a9923254b69

data/lib/miga/remote_dataset/download.rb

@@ -186,15 +186,21 @@ class MiGA::RemoteDataset
     # Looks for the entry +id+ in +dbfrom+, and returns the linked
     # identifier in +db+ (or nil).
     def ncbi_map(id, dbfrom, db)
+      attempts = 0
       doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
       return if doc.empty?
 
-      tree = MiGA::Json.parse(doc, contents: true)
-      [:linksets, 0, :linksetdbs, 0, :links, 0].each do |i|
-        tree = tree[i]
-        break if tree.nil?
+      begin
+        tree = MiGA::Json.parse(doc, contents: true)
+      rescue => e
+        sleep 5 # <- Usually caused by busy servers: BLOB ID IS NOT IMPLEMENTED
+        DEBUG "RETRYING after: #{e}"
+        doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
+        return if doc.empty?
+        tree = MiGA::Json.parse(doc, contents: true)
       end
-      tree
+
+      tree&.dig(:linksets, 0, :linksetdbs, 0, :links, 0)
     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, 0].freeze
+  VERSION = [1.3, 13, 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(2024, 3, 10)
+  VERSION_DATE = Date.new(2024, 3, 15)
 
   ##
   # References of MiGA

data/utils/distance/commands.rb

@@ -27,7 +27,7 @@ module MiGA::DistanceRunner::Commands
     # Launch comparisons
     pending_targets(targets, :aai).each do |target|
       # Full AAI
-      target_cds = target.result(:cds).file_path(:proteins) or next
+      target_cds = target.result(:cds)&.file_path(:proteins) or next
       aairb_cmd(
         tmp_file('proteins.fa'), target_cds,
         dataset.name, target.name, tmp_dbs[:aai], checkpoint: :aai

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.13.0
+  version: 1.3.13.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-03-10 00:00:00.000000000 Z
+date: 2024-03-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons