miga-base 1.2.0.1 → 1.2.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 27068ded9d2ff63c3575a5aafd3fa68374f4bcf8aef924354e0c9cbde7dc1f6d
-  data.tar.gz: ef438e828180d304a9e3449d49551ace933a5e5a46128970b3c8bc385c836d58
+  metadata.gz: afb7c816474f73c547c7f54982293fe72c24d7829184801ab51fc848adf3d9e3
+  data.tar.gz: 06d51ebc47e96c28072c8415321014535ea7576d9e6f1c381e3ca62dc880df15
 SHA512:
-  metadata.gz: 894cbeca2aa4f5e29c6bd6e1c23c9c358b9f3b497960998116169fa62d7122da78417e357789dc9b9b7bfdfad824f835b3daa035d1320cb948e5cdc4b1d74bb3
-  data.tar.gz: 8bea4585b36855195f3a2d76005a6ff664133c1df639a677402907c88fd8f6b0a25fb34cc4bd0e9e38bc7666dbe3a382644137dcf5cddd4005c93256d2c75c05
+  metadata.gz: a4f5279fdba54ad1f8bcbce86cb84a7643b473b7742686e8e9992f8c4af7c982d5776a5a06775b10df67b61de90c4a32f915b51a17a9b11a223474574e7f8159
+  data.tar.gz: bcd547a1dc5337fbf036ba8e2df6de6db4c4fb34979afeb30ce6c1a692e76166b5412457fb3cc778e03cb601a192af0c8d33709b2e5d7233508dfdbd1c5156ed

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

@@ -1,5 +1,4 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
 
 require 'miga/cli/action'
 
@@ -42,33 +41,53 @@ class MiGA::Cli::Action::Ls < MiGA::Cli::Action
         '-s', '--silent',
         'No output and exit with non-zero status if the dataset list is empty'
       ) { |v| cli[:silent] = v }
+      opt.on(
+        '--exec CMD',
+        'Command to execute per dataset, with the following token variables:',
+        '~ {{dataset}}: Name of the dataset',
+        '~ {{project}}: Path to the project'
+      ) { |v| cli[:exec] = v }
     end
   end
 
   def perform
     ds = cli.load_and_filter_datasets(cli[:silent])
+    p  = cli.load_project
     exit(ds.empty? ? 1 : 0) if cli[:silent]
-    if !cli[:datum].nil?
+
+    head = nil
+    fun  = nil
+    if cli[:datum]
       cli[:tabular] = true
-      format_table(ds, [nil, nil]) { |d| [d.name, d.metadata[cli[:datum]]] }
-    elsif !cli[:fields].nil?
-      format_table(ds, [:name] + cli[:fields]) do |d|
-        [d.name] + cli[:fields].map { |f| d.metadata[f] }
-      end
+      head = [nil, nil]
+      fun  = proc { |d| [d.name, d.metadata[cli[:datum]]] }
+    elsif cli[:fields]
+      head = [:name] + cli[:fields]
+      fun  = proc { |d| [d.name] + cli[:fields].map { |f| d.metadata[f] } }
     elsif cli[:info]
-      format_table(ds, Dataset.INFO_FIELDS) { |d| d.info }
+      head = Dataset.INFO_FIELDS
+      fun  = proc(&:info)
     elsif cli[:processing]
-      comp = %w[- done queued]
-      format_table(ds, [:name] + MiGA::Dataset.PREPROCESSING_TASKS) do |d|
-        [d.name] + d.profile_advance.map { |i| comp[i] }
+      head = [:name] + MiGA::Dataset.PREPROCESSING_TASKS
+      fun  = proc do |d|
+        [d.name] + d.profile_advance.map { |i| %w[- done queued][i] }
       end
     elsif cli[:taskstatus]
-      format_table(ds, [:name] + MiGA::Dataset.PREPROCESSING_TASKS) do |d|
-        [d.name] + d.results_status.values
-      end
+      head = [:name] + MiGA::Dataset.PREPROCESSING_TASKS
+      fun  = proc { |d| [d.name] + d.results_status.values }
     else
       cli[:tabular] = true
-      format_table(ds, [nil]) { |d| [d.name] }
+      head = [nil]
+      fun  = proc { |d| [d.name] }
+    end
+
+    format_table(ds, head) do |d|
+      if cli[:exec]
+        MiGA::MiGA.run_cmd(
+          cli[:exec].miga_variables(dataset: d.name, project: p.path)
+        )
+      end
+      fun[d]
     end
   end
 

data/lib/miga/cli/base.rb

@@ -1,5 +1,4 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
 
 module MiGA::Cli::Base
   @@TASK_DESC = {
@@ -20,10 +19,10 @@ module MiGA::Cli::Base
     add: 'Create a dataset in a MiGA project',
     get: 'Download a dataset from public databases into a MiGA project',
     ncbi_get: 'Download all genomes in a taxon from NCBI into a MiGA project',
-    rm: 'Remove a dataset from an MiGA project',
+    rm: 'Remove a dataset from a MiGA project',
     find: 'Find unregistered datasets based on result files',
     ln: 'Link datasets (including results) from one project to another',
-    ls: 'List all registered datasets in an MiGA project',
+    ls: 'List all registered datasets in a MiGA project',
     archive: 'Generate a tar-ball with all files from select datasets',
     # Results
     add_result: 'Register a result',

data/lib/miga/common/format.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require 'tempfile'
 
 ##
@@ -37,13 +39,13 @@ module MiGA::Common::Format
         tmp_path = tmp_fh.path
         fh = File.open(file, 'r')
       end
-      buffer = ''
+      buffer = ''.dup
       fh.each_line do |ln|
         ln.chomp!
         if ln =~ /^>\s*(\S+)(.*)/
           id, df = $1, $2
           tmp_fh.print buffer.wrap_width(80)
-          buffer = ''
+          buffer = ''.dup
           tmp_fh.puts ">#{id.gsub(/[^A-Za-z0-9_\|\.]/, '_')}#{df}"
         else
           buffer << ln.gsub(/[^A-Za-z\.\-]/, '')
@@ -165,7 +167,7 @@ class String
   ##
   # Replace {{variables}} using the +vars+ hash
   def miga_variables(vars)
-    o = "#{self}"
+    o = self.dup
     vars.each { |k, v| o.gsub!("{{#{k}}}", v.to_s) }
     o
   end

data/lib/miga/common.rb

@@ -1,5 +1,4 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
 
 require 'zlib'
 require 'stringio'

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 = [1.2, 0, 1].freeze
+  VERSION = [1.2, 1, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2021, 12, 11)
+  VERSION_DATE = Date.new(2021, 12, 12)
 
   ##
   # References of MiGA

data/test/format_test.rb

@@ -58,6 +58,9 @@ class FormatTest < Test::Unit::TestCase
     assert_equal(50.0, o[:gc])
     assert_equal(5, o[:n50])
     assert_equal(4.0, o[:med])
+    o = MiGA::MiGA.seqs_length(f, :fasta, skew: true)
+    assert_equal(-50.0, o[:at_skew])
+    assert_equal(-25.0, o[:gc_skew])
   end
 
   def test_seqs_length_fastq
@@ -77,4 +80,22 @@ class FormatTest < Test::Unit::TestCase
     assert_equal('123  45', tab[2])
     assert_equal('678  90', tab[3])
   end
+
+  def test_miga_name
+    assert_not('a-bad-name'.miga_name?)
+    assert('a_good_one'.miga_name?)
+
+    assert('After_it_s_fixed_', 'After it\'s fixed!'.miga_name)
+
+    assert('A sp.', 'A_sp_'.unmiga_name)
+    assert('B str. C', 'B_sp_C'.unmiga_name)
+    assert('The X content', 'The_x_content'.unmiga_name)
+  end
+
+  def test_miga_variables
+    assert_equal(
+      '1 a box!',
+      '{{n}} {{my}} {{secret}}!'.miga_variables(my: 'a', secret: :box, n: 1)
+    )
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.0.1
+  version: 1.2.1.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-12-11 00:00:00.000000000 Z
+date: 2021-12-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons