miga-base 1.3.20.11 → 1.3.21.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: d71e38b02f3e54695a4e2c40b07b910ebaf8719511f20fb5c19198aa9b4dbae2
+  metadata.gz: 922c48fb762203b174d2bd7448590c1d30a5ce1d14ef877e55f625b57acfb274
+  data.tar.gz: edee96be95f283d4bf017e6221ebb73951eb77a9a9041eb957a54ebbf6e517f1
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+  metadata.gz: 972dd057f0344ca7131fb166333959ecc7352a3aa7672e0a73e07b730a2a5d8003bcc3b1f23644c2a2bdec5ae01f1aa512bf37fcc9448d6612fc5f9205af7fae
+  data.tar.gz: e3ff7e91bdc10d0e989d1409d54af3eba821f33c5104e7f1c4ee1ac60b3e30e4b0c2d03170822e94a10063c5a7e648d7b989fb3a8a26e73646dab65a6cabd68b

data/lib/miga/dataset.rb

@@ -196,4 +196,19 @@ class MiGA::Dataset < MiGA::MiGA
       [name, how_many]
     )
   end
+
+  ##
+  # Retrieves the option with name +key+ from the dataset's metadata
+  # extending support to relative paths in +:db_project+
+  def option_by_metadata(key)
+    case key.to_sym
+    when :db_project
+      y = metadata[key] or return
+      ref_location = project.option(:db_proj_dir) || File.dirname(project.path)
+      y = File.expand_path(y, ref_location)
+      return y
+    end
+
+    super
+  end
 end

data/lib/miga/project.rb

@@ -143,8 +143,8 @@ class MiGA::Project < MiGA::MiGA
   def option_by_metadata(key)
     case key.to_sym
     when :ref_project, :db_proj_dir
-      y = metadata[key]
-      y = File.expand_path(y, path) if y && y =~ /^[^\/]/
+      y = metadata[key] or return
+      y = File.expand_path(y, path)
       return y
     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, 20, 11].freeze
+  VERSION = [1.3, 21, 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, 9, 13)
+  VERSION_DATE = Date.new(2024, 9, 28)
 
   ##
   # References of MiGA

data/scripts/distances.bash

@@ -22,6 +22,7 @@ fi
 ruby -I "$MIGA/lib" "$MIGA/utils/distances.rb" "$PROJECT" "$DATASET"
 
 # Finalize
+refproject=no
 fastaai=no
 aai=no
 ani=no
@@ -29,6 +30,10 @@ blast=no
 blat=no
 diamond=no
 fastani=no
+REF_PROJECT=$(miga option -P "$PROJECT" -D "$DATASET" -k db_project)
+
+[[ -d "$REF_PROJECT" ]] && refproject=yes
+
 if [[ ! -s "${DATASET}.empty" ]] ; then
   case $(miga option -P "$PROJECT" -k haai_p) in
     fastaai)
@@ -76,6 +81,14 @@ cat <<VERSIONS \
   | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
 => MiGA
 $(miga --version)
+$(
+  if [[ "$refproject" == "yes" ]] ; then
+    echo "=> Reference Project"
+    miga about -P "$REF_PROJECT" -m name
+    echo "=> Reference Project Release"
+    miga about -P "$REF_PROJECT" -m release
+  fi
+)
 $(
   if [[ "$fastaai" == "yes" ]] ; then
     echo "=> FastAAI"

data/scripts/taxonomy.bash

@@ -25,6 +25,7 @@ blat=no
 diamond=no
 fastani=no
 REF_PROJECT=$(miga option -P "$PROJECT" -k ref_project)
+
 if [[ -d "$REF_PROJECT" ]] ; then
   refproject=yes
 

data/utils/distance/runner.rb

@@ -19,9 +19,7 @@ class MiGA::DistanceRunner
       @ref_project = MiGA::Project.load(ref_path)
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
     elsif !opts[:run_taxonomy] && dataset.option(:db_project)
-      ref_location = project.option(:db_proj_dir) || File.dirname(project.path)
-      ref_path = File.expand_path(dataset.option(:db_project), ref_location)
-      @ref_project = MiGA::Project.load(ref_path)
+      @ref_project = MiGA::Project.load(dataset.option(:db_project))
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
     else
       @ref_project = project

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.20.11
+  version: 1.3.21.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-09-13 00:00:00.000000000 Z
+date: 2024-09-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons