miga-base 0.3.1.2 → 0.3.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 787c36c0ff7eb3a77d1b6fd4dd73015b4b49850e
-  data.tar.gz: 2a4ec0d82f8be2bb8e486d3d5410d909b01f3522
+  metadata.gz: 6d05cad62382523776174b6300e3a3cc8cbf87b6
+  data.tar.gz: 71db2e7e0d361c770f978ab265d862e52cd30727
 SHA512:
-  metadata.gz: 71bf56e6cbfdeb36d3f19c9a4ea4aaac8160537ca3b7a95c6bff44d83e07298f8df3889fd3719eaaf9beae4adf9024b1f53e7a9ff743aadeb802c29664838fed
-  data.tar.gz: d351e7f4374a7859b3661a554c967f11406dcc696763da6e3b623025412ed9dcfe8bfe46f6125d22ef5ab341df1e978d93b0e54e222462faa55b7746dca931ef
+  metadata.gz: 761cf711acb535bacc7e789e16545904b2147f498caf9edcb190f7d2a3a6417bf567d86175bb255ff3d1c353bf7b9eaffdc50f9fb998458f2db81d91286a5217
+  data.tar.gz: 91bdc8ddbb06407ea78b120a96823dd46efb5521f85423a5840b0f2e72771f9d67c6ccf8291fd6e7033ebd711a0d1c32c5c48ad2f4e98179ec4d36d108b91347

data/actions/doctor.rb

@@ -0,0 +1,78 @@
+#!/usr/bin/env ruby
+
+# @package MiGA
+# @license Artistic-2.0
+
+o = {q:true, v:false}
+OptionParser.new do |opt|
+  opt_banner(opt)
+  opt_object(opt, o, [:project])
+  opt.on("-v", "--verbose",
+    "Print additional information on advance."){ |v| o[:v]=v }
+  opt_common(opt, o)
+end.parse!
+
+##=> Main <=
+opt_require(o, project:"-P")
+
+$stderr.puts "Loading project" unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+[:ani, :aai].each do |dist|
+  r = p.result("#{dist}_distances")
+  next if r.nil?
+  $stderr.puts "o Checking #{dist} table for consistent datasets" unless o[:q]
+  ok = true
+  fix = {}
+  Zlib::GzipReader.open(r.file_path(:matrix)) do |fh|
+    fh.each_line do |ln|
+      next if $.==1
+      r = ln.split("\t")
+      if p.dataset(r[1]).nil? or p.dataset(r[2]).nil?
+        fix[r[2]] = true unless p.dataset(r[2]).nil?
+        fix[r[1]] = true unless p.dataset(r[1]).nil?
+        ok = false
+      end
+    end
+  end
+  
+  $stderr.puts "  - Fixing #{fix.size} datasets" unless fix.empty? or o[:q]
+  fix.keys.each do |d_n|
+    $stderr.puts "    > Fixing #{d_n}." if o[:v]
+    p.dataset(d_n).cleanup_distances!
+  end
+  
+  unless ok
+    $stderr.puts "  - Removing tables, recompute" unless o[:q]
+    r.remove!
+  end
+end
+
+$stderr.puts "o Looking for outdated files in results" unless o[:q]
+p.each_dataset do |d|
+  d.each_result do |r_k, r|
+    ok = true
+    r.each_file do |_f_sym, _f_rel, f_abs|
+      unless File.exist? f_abs
+        ok = false
+        break
+      end
+    end
+    unless ok
+      $stderr.puts "  - Registering again #{d.name}:#{r_k}" if o[:v]
+      d.add_result(r_k, true, force:true)
+    end
+  end
+end
+
+#$stderr.puts "o Looking for unarchived essential genes." unless o[:q]
+#p.each_dataset do |d|
+#  TODO: Check unarchived protein files
+#end
+
+#$stderr.puts "o Checking for taxonomy/distances consistency" unless o[:q]
+# TODO: Find 95%ANI clusters with entries from different species
+
+$stderr.puts "Done" unless o[:q]
+

data/bin/miga

@@ -15,9 +15,10 @@ $task_desc = {
   new: "Creates an empty MiGA project.",
   about: "Displays information about a MiGA project.",
   plugins: "Lists or (un)installs plugins in a MiGA project.",
+  doctor: "Performs consistency checks on a MiGA project.",
   # Datasets
   add: "Creates an empty dataset in a pre-existing MiGA project.",
-  get: "Creates an empty dataset in a pre-existing MiGA project.",
+  get: "Downloads a dataset from public databases into a MiGA project.",
   rm: "Removes a dataset from an MiGA project.",
   find: "Finds unregistered datasets based on result files.",
   ln: "Link datasets (including results) from one project to another.",

data/lib/miga/remote_dataset.rb

@@ -71,7 +71,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
   end
 
   ##
-  # Download data usint a REST method from the +universe+ in the database +db+
+  # Download data using a REST method from the +universe+ in the database +db+
   # with IDs +ids+ and in +format+. Returns the doc as String.
   def self.download_rest(universe, db, ids, format)
     u = @@UNIVERSE[universe]
@@ -85,10 +85,12 @@ class MiGA::RemoteDataset < MiGA::MiGA
   end
   
   ##
-  # Download data usint a REST method from the +universe+ in the database +db+
+  # Download data using a GET request from the +universe+ in the database +db+
   # with IDs +ids+ and in +format+. Returns the doc as String.
   def self.download_net(universe, db, ids, format)
-    url = sprintf(@@UNIVERSE[universe][:url], db, ids.join(","), format, map_to)
+    u = @@UNIVERSE[universe]
+    map_to = u[:dbs][db].nil? ? nil : u[:dbs][db][:map_to]
+    url = sprintf(u[:url], db, ids.join(","), format, map_to)
     doc = ""
     @timeout_try = 0
     begin

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, 1, 2]
+  VERSION = [0.3, 1, 3]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2017, 11, 22)
+  VERSION_DATE = Date.today
   
   ##
   # Reference of MiGA.

data/test/remote_dataset_test.rb

@@ -38,4 +38,26 @@ class RemoteDatasetTest < Test::Unit::TestCase
     assert_equal("Lentivirus", tx[:g])
   end
 
+  def test_net_ftp
+    cjac = "ftp://ftp.ebi.ac.uk/pub/databases/ena/tsa/public/ga/GAPJ01.fasta.gz"
+    n = "Cjac_L14"
+    rd = MiGA::RemoteDataset.new(cjac, :assembly_gz, :web)
+    assert_equal([cjac], rd.ids)
+    omit_if(!$remote_tests, "Remote access is error-prone.")
+    p = $p1
+    assert_nil(p.dataset(n))
+    rd.save_to(p, n)
+    p.add_dataset(n)
+    assert_equal(MiGA::Dataset, p.dataset(n).class)
+    assert_equal(MiGA::Result, p.dataset(n).result(:assembly).class)
+  end
+
+  # This test is too expensive (too much time to run it!)
+  #def test_net_timeout
+  #  omit_if(!$remote_tests, "Remote access is error-prone.")
+  #  bad = "ftp://example.com/miga"
+  #  rd = MiGA::RemoteDataset.new(bad, :assembly, :web)
+  #  assert_raise(Net::ReadTimeout) { rd.save_to($p1, "bad") }
+  #end
+
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.1.2
+  version: 0.3.1.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-11-22 00:00:00.000000000 Z
+date: 2017-11-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -123,6 +123,7 @@ files:
 - actions/add_result.rb
 - actions/daemon.rb
 - actions/date.rb
+- actions/doctor.rb
 - actions/files.rb
 - actions/find.rb
 - actions/get.rb