miga-base 1.3.14.7 → 1.3.15.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b637dd7bbd8ebd512621bf3781286c3f8f94f0ce916ade1d9913a08e93d31019
-  data.tar.gz: bca1c28c21031b4ceafba9192b2345124bed56278855829f255d2b0f9df0e933
+  metadata.gz: 0b28d0e279592c817bf22a7ada5e292cfae35fff6d64b170499a9b8a9e662e89
+  data.tar.gz: 5653a537b9468d7d4ec9a7a02712be6c3a4481d020909b757cc443ddab50f097
 SHA512:
-  metadata.gz: '028b1b2c993a2b21528fb1d29a3b29d7a9f6333f6a8408e47773d84813341217d733cbdb4686a95264189df186ad884182b44ee2c2da86d3ccf696c02241971d'
-  data.tar.gz: 3e78e598542be5bfba5845e0ff8e4744d6413c5d0714be6bfef5e1202e02c9910fe569f1692b325dbaaef5697355cc9ee1eff90d0503730993ddf5bcf468a8e7
+  metadata.gz: 9f28050603a5e0a015b284cb09e88621a2650ef0eb6580b9ca6edf362dfd2ae19a50848e476ad9a7f66d4aa8c3a28ed51cdfef1f0566de72d3ba3b6f16596ce6
+  data.tar.gz: 9e0aa59955542a9ac42f009965cc6e66e9fb7d55269298e554652b20afaca312454d1fbff09a08cd2660e9f2cbf33e10f120117ed5f5ddf853d871a4817f2de0

data/lib/miga/cli/action/download/seqcode.rb

@@ -32,8 +32,8 @@ module MiGA::Cli::Action::Download::Seqcode
         :seqcode, :'type-genomes', nil, :json, nil, page: current_page
       )
       doc = MiGA::Json.parse(json, contents: true)
-      current_page = doc[:current_page] + 1
-      total_pages  = doc[:total_pages]
+      current_page = doc.dig(:response, :current_page) + 1
+      total_pages  = doc.dig(:response, :total_pages)
 
       doc[:values].each do |name|
         next unless name[:type_material]

data/lib/miga/dataset/result/add.rb

@@ -261,10 +261,12 @@ module MiGA::Dataset::Result::Add
   def add_result_distances_nonref(base)
     return nil unless
       result_files_exist?(base, %w[.aai-medoids.tsv .aai.db]) ||
-      result_files_exist?(base, %w[.ani-medoids.tsv .ani.db])
+      result_files_exist?(base, %w[.ani-medoids.tsv .ani.db]) ||
+      result_files_exist?(base, %w[.empty])
 
     add_files_to_ds_result(
       MiGA::Result.new("#{base}.json"), name,
+      empty: '.empty',
       aai_medoids: '.aai-medoids.tsv',
       haai_db: '.haai.db',
       aai_db: '.aai.db',

data/lib/miga/remote_dataset/base.rb

@@ -22,7 +22,7 @@ module MiGA::RemoteDataset::Base
   @@_EUTILS        = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
   @@_EBI_API       = 'https://www.ebi.ac.uk/Tools/'
   @@_GTDB_API      = 'https://gtdb-api.ecogenomic.org/'
-  @@_SEQCODE_API   = 'https://disc-genomics.uibk.ac.at/seqcode/'
+  @@_SEQCODE_API   = 'https://api.seqco.de/v1/'
   @@_EUTILS_BUILD  = lambda { |service, q|
     q[:api_key] = ENV['NCBI_API_KEY'] if ENV['NCBI_API_KEY']
     uri_safe_join(@@_EUTILS, "#{service}.fcgi")

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, 14, 7].freeze
+  VERSION = [1.3, 15, 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(2024, 4, 24)
+  VERSION_DATE = Date.new(2024, 5, 6)
 
   ##
   # References of MiGA

data/scripts/distances.bash

@@ -29,44 +29,46 @@ blast=no
 blat=no
 diamond=no
 fastani=no
-case $(miga option -P "$PROJECT" -k haai_p) in
-  fastaai)
-    fastaai=yes
-    ;;
-  diamond)
-    diamond=yes
-    aai=yes
-    ;;
-  blast)
-    blast=yes
-    aai=yes
-    ;;
-esac
+if [[ ! -s "${DATASET}.empty" ]] ; then
+  case $(miga option -P "$PROJECT" -k haai_p) in
+    fastaai)
+      fastaai=yes
+      ;;
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
 
-case $(miga option -P "$PROJECT" -k aai_p) in
-  diamond)
-    diamond=yes
-    aai=yes
-    ;;
-  blast)
-    blast=yes
-    aai=yes
-    ;;
-esac
+  case $(miga option -P "$PROJECT" -k aai_p) in
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
 
-case $(miga option -P "$PROJECT" -k ani_p) in
-  blast)
-    blast=yes
-    ani=yes
-    ;;
-  blat)
-    blat=yes
-    ani=yes
-    ;;
-  fastani)
-    fastani=yes
-    ;;
-esac
+  case $(miga option -P "$PROJECT" -k ani_p) in
+    blast)
+      blast=yes
+      ani=yes
+      ;;
+    blat)
+      blat=yes
+      ani=yes
+      ;;
+    fastani)
+      fastani=yes
+      ;;
+  esac
+fi
 
 
 miga date > "${DATASET}.done"

data/utils/distance/runner.rb

@@ -35,7 +35,7 @@ class MiGA::DistanceRunner
 
   # Launch the appropriate analysis
   def go!
-    $stderr.puts "Launching analysis"
+    $stderr.puts 'Launching analysis'
     return if dataset.multi?
 
     Dir.mktmpdir do |tmp_dir|
@@ -68,6 +68,14 @@ class MiGA::DistanceRunner
   # Launch analysis for query datasets
   def go_query!
     $stderr.puts 'Launching analysis for query dataset'
+
+    # Check if the project is empty
+    if ref_project.dataset_ref_active.empty?
+      out_base = File.expand_path(dataset.name, home)
+      File.open("#{out_base}.empty", 'w') { |fh| fh.puts 'Empty ref_project' }
+      return
+    end
+
     # Check if project is ready
     tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
     res = ref_project.result(tsk[0])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.14.7
+  version: 1.3.15.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-04-24 00:00:00.000000000 Z
+date: 2024-05-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons