miga-base 0.5.2.1 → 0.5.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 609dfcbd7207f1a2a63dc76f9674357182734d19eaea1e26bb857286b2932e05
+  metadata.gz: d51a2778df35e38e9396c342db79907aa8b63019e33d62f08a745664c01fc14b
+  data.tar.gz: 2e553ce8b5fc59aee8aa74f5262d34175c19bbf52c41efa6817353e8e20dbff5
 SHA512:
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-  data.tar.gz: 3bebfccfff429d53b131e8f8716e9af51c61abd686267d496d1e0f71524edc85d91623e1b86d7202257edafaaf8d0089957fd87224524a7ef65e73f604d96173
+  metadata.gz: 0c2ebed3117669c8dce789d731dd478a9eaf8dd8ca9a14e89cf1692908264bca6541073407f7d922a3f72e1edd47d5128275a391b5acc798687edb6302d0b66d
+  data.tar.gz: 64f0d0fc5af1bca2a3d2fb3ad3a79fdb31a91c95ef346e2cd2b89cc4342a0189ee7a814adae6b7cf5b80b5ce4a80e99cd1196c71afe1138f769fd0f0d91cf3d7

data/lib/miga/cli/action/quality_wf.rb

@@ -25,7 +25,6 @@ class MiGA::Cli::Action::QualityWf < MiGA::Cli::Action
       %w[project_stats haai_distances aai_distances ani_distances clade_finding]
         .map { |i| ["run_#{i}", false] }
     ]
-    p_metadata[:ess_coll] = cli[:ess_coll]
     d_metadata = { run_distances: false }
     d_metadata[:run_mytaxa_scan] = false unless cli[:mytaxa]
     p = create_project(:assembly, p_metadata, d_metadata)

data/lib/miga/cli/action/wf.rb

@@ -115,16 +115,18 @@ module MiGA::Cli::Action::Wf
     call_cli([
       'new',
       '-P', cli[:outdir],
-      '-t', cli[:project_type],
-      '-m', p_metadata.map{ |k,v| "#{k}=#{v}" }.join(',')
-    ])
+      '-t', cli[:project_type]
+    ]) unless MiGA::Project.exist? cli[:outdir]
+    # Define project metadata
+    p = cli.load_project(:outdir, '-o')
+    [:haai_p, :aai_p, :ani_p, :ess_coll].each { |i| p_metadata[i] = cli[i] }
+    transfer_metadata(p, p_metadata)
     # Download datasets
     call_cli([
       'ncbi_get',
       '-P', cli[:outdir],
       '-T', cli[:ncbi_taxon],
-      (cli[:ncbi_draft] ? '--all' : '--complete'),
-      '-m', d_metadata.map{ |k,v| "#{k}=#{v}" }.join(',')
+      (cli[:ncbi_draft] ? '--all' : '--complete')
     ]) unless cli[:ncbi_taxon].nil?
     # Add datasets
     call_cli([
@@ -132,15 +134,11 @@ module MiGA::Cli::Action::Wf
       '-P', cli[:outdir],
       '-t', cli[:dataset_type],
       '-i', stage,
-      '-R', cli[:regexp],
-      '-m', d_metadata.map{ |k,v| "#{k}=#{v}" }.join(',')
+      '-R', cli[:regexp]
     ] + cli.files) unless cli.files.empty?
-    p = MiGA::Project.load(cli[:outdir])
-    raise "Impossible to create project: #{cli[:outdir]}" if p.nil?
-    [:haai_p, :aai_p, :ani_p].each do |i|
-      p.metadata[i] = cli[i] unless cli[i].nil?
-    end
-    p.save
+    # Define datasets metadata
+    p.load
+    p.each_dataset { |d| transfer_metadata(d, d_metadata) }
     p
   end
 
@@ -159,7 +157,7 @@ module MiGA::Cli::Action::Wf
 
   def cleanup
     return unless cli[:clean]
-    cli.say "Cleaning up intermediate files"
+    cli.say 'Cleaning up intermediate files'
     %w[data daemon metadata miga.project.json].each do |f|
       FileUtils.rm_rf(File.expand_path(f, cli[:outdir]))
     end
@@ -180,4 +178,14 @@ module MiGA::Cli::Action::Wf
     Dir.chdir(cwd)
   end
 
+  def transfer_metadata(obj, md)
+    # Clear old metadata
+    obj.metadata.each do |k,v|
+      obj.metadata[k] = nil if k.to_s =~ /^run_/ || k == :ref_project
+    end
+    # Transfer and save
+    md.each { |k, v| obj.metadata[k] = v }
+    obj.save
+  end
+
 end

data/lib/miga/cli/base.rb

@@ -84,7 +84,7 @@ module MiGA::Cli::Base
 
   @@EXECS = @@TASK_DESC.keys
 
-  @@FILE_REGEXP = %r{^(?:.*/)?(.+?)(?:\..*(?:[12]|Reads|Contigs))?(?:\.f[nastq]+)?$}i
+  @@FILE_REGEXP = %r{^(?:.*/)?(.+?)(\.[A-Z]*([12]|Reads|Contigs))?(\.f[nastq]+)?$}i
 
 end
 

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 = [0.5, 2, 1]
+  VERSION = [0.5, 3, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 1, 8)
+  VERSION_DATE = Date.new(2020, 1, 11)
 
   ##
   # Reference of MiGA.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.5.2.1
+  version: 0.5.3.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-01-08 00:00:00.000000000 Z
+date: 2020-01-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons