miga-base 0.5.10.0 → 0.6.0.0

data/lib/miga/version.rb

@@ -10,15 +10,15 @@ 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, 10, 0]
+  VERSION = [0.6, 0, 0]
 
   ##
   # Nickname for the current major.minor version.
-  VERSION_NAME = 'collotype'
+  VERSION_NAME = 'lithograph'
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 2, 25)
+  VERSION_DATE = Date.new(2020, 3, 7)
 
   ##
   # Reference of MiGA.

data/scripts/cds.bash

@@ -28,7 +28,7 @@ case "$TYPE" in
     P_LEN=0
     BEST_CT=0
     echo "# Codon table selection:" > "${DATASET}.ct.t"
-    for ct in 4 11 ; do
+    for ct in 11 4 ; do
       prodigal -a "${DATASET}.faa.$ct" -d "${DATASET}.fna.$ct" \
         -o "${DATASET}.gff3.$ct" -f gff -q -p single -g "$ct" \
         -i "../05.assembly/${DATASET}.LargeContigs.fna"
@@ -36,7 +36,7 @@ case "$TYPE" in
         | perl -pe 's/[^A-Z]//ig' | wc -c | awk '{print $1}')
       echo "# codon table $ct total length: $C_LEN aa" \
         >> "${DATASET}.ct.t"
-      if [[ $C_LEN > $P_LEN ]] ; then
+      if [[ $C_LEN > $(($P_LEN * 11 / 10)) ]] ; then
         for x in faa fna gff3 ; do
           mv "${DATASET}.$x.$ct" "${DATASET}.$x"
         done

data/scripts/miga.bash

@@ -10,11 +10,6 @@ SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
 function exists { [[ -e "$1" ]] ; }
 function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
 
-for i in $(miga plugins -P "$PROJECT") ; do
-  # shellcheck source=/dev/null
-  . "$i/scripts-plugin.bash"
-done
-
 if [[ "$SCRIPT" != "d" && "$SCRIPT" != "p" ]] ; then
   echo '############'
   echo -n "Date: " ; miga date

data/scripts/stats.bash

@@ -14,7 +14,7 @@ miga date > "$DATASET.start"
 # Calculate statistics
 for i in raw_reads trimmed_fasta assembly cds essential_genes ssu distances taxonomy ; do
   echo "# $i"
-  miga result_stats --compute-and-save -P "$PROJECT" -D "$DATASET" -r $i
+  miga stats --compute-and-save -P "$PROJECT" -D "$DATASET" -r $i
 done
 
 # Finalize

data/test/hook_test.rb

@@ -0,0 +1,110 @@
+require 'test_helper'
+require 'miga/project'
+
+class HookTest < Test::Unit::TestCase
+  
+  def setup
+    $tmp = Dir.mktmpdir
+    ENV['MIGA_HOME'] = $tmp
+    FileUtils.touch("#{ENV['MIGA_HOME']}/.miga_rc")
+    FileUtils.touch("#{ENV['MIGA_HOME']}/.miga_daemon.json")
+    $p1 = MiGA::Project.new(File.expand_path('project1', $tmp))
+    $d1 = $p1.add_dataset('dataset1')
+  end
+
+  def teardown
+    FileUtils.rm_rf $tmp
+    ENV['MIGA_HOME'] = nil
+  end
+
+  def test_add_hook
+    assert_nil($d1.hooks[:on_save])
+    $d1.add_hook(:on_save, :run_lambda, Proc.new { $counter += 1 })
+    assert_equal(1, $d1.hooks[:on_save].size)
+    $counter = 1
+    $d1.save
+    assert_equal(2, $counter)
+  end
+
+  def test_missing_action
+    $d1.add_hook(:on_save, :this_is_not_an_action)
+    assert_raise do
+      $d1.save
+    end
+  end
+
+  class MyHanger
+    include MiGA::Common::Hooks
+  end
+
+  def test_empty_hooks
+    a = MyHanger.new
+    assert_equal({}, a.hooks)
+  end
+
+  def test_dataset_result_hooks
+    $res = :test
+    $counter = 1
+    $d1.add_hook(:on_result_ready,
+      :run_lambda, Proc.new { |r| $res = r })
+    $d1.add_hook(:on_result_ready_trimmed_reads,
+      :run_lambda, Proc.new { $counter += 1 })
+    FileUtils.touch(File.expand_path(
+      "data/02.trimmed_reads/#{$d1.name}.1.clipped.fastq", $p1.path))
+    FileUtils.touch(File.expand_path(
+      "data/02.trimmed_reads/#{$d1.name}.done", $p1.path))
+    assert_equal(:test, $res)
+    $d1.add_result(:trimmed_reads)
+    assert_equal(:trimmed_reads, $res)
+    assert_equal(2, $counter)
+  end
+
+  def test_dataset_clear_run_counts
+    $d1.metadata[:_try_something] = 1
+    $d1.metadata[:_not_a_counter] = 1
+    $d1.save
+    assert_equal(1, $d1.metadata[:_try_something])
+    $d1.add_hook(:on_remove, :clear_run_counts)
+    $d1.remove!
+    assert_nil($d1.metadata[:_try_something])
+    assert_equal(1, $d1.metadata[:_not_a_counter])
+  end
+
+  def test_dataset_run_cmd
+    f = File.expand_path('hook_ds_cmd', $tmp)
+    $d1.metadata[:on_remove] = [[:run_cmd, "echo {{dataset}} > '#{f}'"]]
+    assert(! File.exist?(f))
+    $d1.remove!
+    assert(File.exist? f)
+    assert_equal($d1.name, File.read(f).chomp)
+  end
+
+  def test_project_run_cmd
+    f = File.expand_path('hook_pr_cmd', $tmp)
+    $p1.add_hook(:on_save, :run_cmd, "echo {{project}} > '#{f}'")
+    assert(! File.exist?(f))
+    $p1.save
+    assert(File.exist? f)
+    assert_equal($p1.path, File.read(f).chomp)
+  end
+
+  def test_project_result_hooks
+    $res = :test
+    $counter = 1
+    $p1.add_hook(:on_result_ready,
+      :run_lambda, Proc.new { |r| $res = r })
+    $p1.add_hook(:on_result_ready_project_stats,
+      :run_lambda, Proc.new { $counter += 1 })
+    %w[taxonomy.json metadata.db done].each do |ext|
+      FileUtils.touch(File.expand_path(
+        "data/90.stats/miga-project.#{ext}", $p1.path))
+    end
+    assert_equal(:project_stats, $p1.next_task(nil, false))
+    assert_equal(:test, $res)
+    assert_equal(1, $counter)
+    assert_equal(:haai_distances, $p1.next_task)
+    assert_equal(:project_stats, $res)
+    assert_equal(2, $counter)
+  end
+
+end

data/utils/subclades.R

@@ -133,7 +133,7 @@ subclade_clustering <- function(out_base, thr, ani.d, dist_rdata) {
 
   # Classify genomes
   say("Classify => k :", top.n, "| n :", length(labels(ani.d)))
-  ani.cl <- pam(ani.d, top.n, pamonce=1)
+  ani.cl <- pam(ani.d, top.n)
   ani.types <- ani.cl$clustering
   ani.medoids <- ani.cl$medoids
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.5.10.0
+  version: 0.6.0.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-02-25 00:00:00.000000000 Z
+date: 2020-03-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -121,7 +121,6 @@ files:
 - lib/miga/cli/action/ncbi_get.rb
 - lib/miga/cli/action/new.rb
 - lib/miga/cli/action/next_step.rb
-- lib/miga/cli/action/plugins.rb
 - lib/miga/cli/action/preproc_wf.rb
 - lib/miga/cli/action/quality_wf.rb
 - lib/miga/cli/action/rm.rb
@@ -139,18 +138,20 @@ files:
 - lib/miga/common.rb
 - lib/miga/common/base.rb
 - lib/miga/common/format.rb
+- lib/miga/common/hooks.rb
 - lib/miga/common/path.rb
 - lib/miga/daemon.rb
 - lib/miga/daemon/base.rb
 - lib/miga/dataset.rb
 - lib/miga/dataset/base.rb
+- lib/miga/dataset/hooks.rb
 - lib/miga/dataset/result.rb
 - lib/miga/json.rb
 - lib/miga/metadata.rb
 - lib/miga/project.rb
 - lib/miga/project/base.rb
 - lib/miga/project/dataset.rb
-- lib/miga/project/plugins.rb
+- lib/miga/project/hooks.rb
 - lib/miga/project/result.rb
 - lib/miga/remote_dataset.rb
 - lib/miga/remote_dataset/base.rb
@@ -158,6 +159,8 @@ files:
 - lib/miga/result.rb
 - lib/miga/result/base.rb
 - lib/miga/result/dates.rb
+- lib/miga/result/source.rb
+- lib/miga/result/stats.rb
 - lib/miga/tax_dist.rb
 - lib/miga/tax_index.rb
 - lib/miga/taxonomy.rb
@@ -189,6 +192,7 @@ files:
 - test/common_test.rb
 - test/daemon_test.rb
 - test/dataset_test.rb
+- test/hook_test.rb
 - test/json_test.rb
 - test/metadata_test.rb
 - test/project_test.rb

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

@@ -1,28 +0,0 @@
-# @package MiGA
-# @license Artistic-2.0
-
-require 'miga/cli/action'
-
-class MiGA::Cli::Action::Plugins < MiGA::Cli::Action
-
-  def parse_cli
-    cli.parse do |opt|
-      cli.opt_object(opt, [:project])
-      opt.on(
-        '--install PATH',
-        'Install the specified plugin in the project'
-        ){ |v| cli[:install] = v }
-      opt.on(
-        '--uninstall PATH',
-        'Uninstall the specified plugin from the project'
-        ){ |v| cli[:uninstall] = v }
-    end
-  end
-
-  def perform
-    p = cli.load_project
-    p.install_plugin(cli[:install]) unless cli[:install].nil?
-    p.uninstall_plugin(cli[:uninstall]) unless cli[:uninstall].nil?
-    p.plugins.each { |i| cli.puts i }
-  end
-end

data/lib/miga/project/plugins.rb

@@ -1,41 +0,0 @@
-# @package MiGA
-# @license Artistic-2.0
-
-##
-# Helper module including specific functions handle plugins.
-module MiGA::Project::Plugins
-
-  ##
-  # Installs the plugin in the specified path.
-  def install_plugin(path)
-    abs_path = File.absolute_path(path)
-    raise "Plugin already installed in project: #{abs_path}." unless
-      metadata[:plugins].nil? or not metadata[:plugins].include?(abs_path)
-    raise "Malformed MiGA plugin: #{abs_path}." unless
-      File.exist?(File.expand_path("miga-plugin.json", abs_path))
-    self.metadata[:plugins] ||= []
-    self.metadata[:plugins] << abs_path
-    save
-  end
-
-  ##
-  # Uninstall the plugin in the specified path.
-  def uninstall_plugin(path)
-    abs_path = File.absolute_path(path)
-    raise "Plugin not currently installed: #{abs_path}." if
-      metadata[:plugins].nil? or not metadata[:plugins].include?(abs_path)
-    self.metadata[:plugins].delete(abs_path)
-    save
-  end
-
-  ##
-  # List plugins installed in the project.
-  def plugins ; metadata[:plugins] ||= [] ; end
-
-  ##
-  # Loads the plugins installed in the project.
-  def load_plugins
-    plugins.each { |pl| require File.expand_path("lib-plugin.rb", pl) }
-  end
-
-end