miga-base 0.3.8.1 → 0.3.9.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 854b0793698f158b73ba2aab35638610db3e7044acf91a760fcd6ab272b81172
+  metadata.gz: 33ad423a2b44c3375e96d247399c77e3e576739a27a46f02315d454bb9905fcf
+  data.tar.gz: 6696a87a2328dc0db4d2fdc193ea01eed18ada3b53cb772ef40525dfcb596cdc
 SHA512:
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+  metadata.gz: 230c1c4cf1af60d42a2d27c1fbe018e90f01f8ebc4a559e354bc32d1b9dbdec1ffcc4d832dcb7894fb96f0c255bfb84e3635d16d683c4e1585c1c354d8591020
+  data.tar.gz: db5bb0f064dab5dcfe45ebad1027d7d1fd16d2c992f5907e3cb1a124ed45785acf828ca67d9c84e7be6017622faeff1b6e7a32c9e9a72dd26e336953ef93813d

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.3, 8, 1]
+  VERSION = [0.3, 9, 0]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2019, 02, 28)
+  VERSION_DATE = Date.new(2019, 03, 07)
   
   ##
   # Reference of MiGA.

data/utils/distance/runner.rb

@@ -19,20 +19,26 @@ class MiGA::DistanceRunner
   def initialize(project_path, dataset_name, opts_hash={})
     @opts = opts_hash
     @project = MiGA::Project.load(project_path) or
-          raise "No project at #{project_path}"
+      raise "No project at #{project_path}"
     @dataset = project.dataset(dataset_name)
     @home = File.expand_path('data/09.distances', project.path)
     # Default opts
     @opts[:aai_save_rbm] ||= ENV.fetch('MIGA_AAI_SAVE_RBM') do
       project.is_clade? ? 'save-rbm' : 'no-save-rbm'
     end
-    @opts[:thr] ||= ENV.fetch("CORES"){ 2 }.to_i
-    if opts[:run_taxonomy] && project.metadata[:ref_project]
+    @opts[:thr] ||= ENV.fetch('CORES'){ 2 }.to_i
+    if opts[:run_taxonomy] and project.metadata[:ref_project]
+      ref_path = project.metadata[:ref_project]
       @home = File.expand_path('05.taxonomy', @home)
-      @ref_project = MiGA::Project.load(project.metadata[:ref_project])
-      if @ref_project.nil?
-        raise "Cannot load reference project: #{project.metadata[:ref_project]}"
+      @ref_project = MiGA::Project.load(ref_path)
+      raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
+    elsif !opts[:run_taxonomy] and dataset.metadata[:db_project]
+      ref_path = dataset.metadata[:db_project]
+      if project.metadata[:db_proj_dir]
+        ref_path = File.expand_path(project.metadata[:db_proj_dir], ref_path)
       end
+      @ref_project = MiGA::Project.load(ref_path)
+      raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
     else
       @ref_project = project
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.8.1
+  version: 0.3.9.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-02-28 00:00:00.000000000 Z
+date: 2019-03-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons