miga-base 0.7.15.2 → 0.7.16.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 9d2ea26b71d226f0cbddebb214912a82b432886efb72e8bb6523b4b2f5aa588c
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data/lib/miga/cli/action/doctor.rb

@@ -37,6 +37,7 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
   @@OPERATIONS = {
     status: ['status', 'Update metadata status of all datasets'],
     db: ['databases', 'Check integrity of database files'],
+    bidir: ['bidirectional', 'Check distances are bidirectional'],
     dist: ['distances', 'Check distance summary tables'],
     files: ['files', 'Check for outdated files'],
     cds: ['cds', 'Check for gzipped genes and proteins'],
@@ -85,6 +86,24 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     cli.say
   end
 
+  ##
+  # Perform bidirectional operation with MiGA::Cli +cli+
+  def check_bidir(cli)
+    cli.say 'Checking that reference distances are bidirectional'
+    ref_ds = cli.load_project.each_dataset.select(&:ref?)
+    ref_names = ref_ds.map(&:name)
+    n, k = ref_ds.size, 0
+    ref_ds.each do |d|
+      cli.advance('Datasets:', k += 1, n, false)
+      saved = saved_targets(d)
+      next if saved.nil?
+
+      to_save = ref_names - saved
+      to_save.each { |k| save_bidirectional(cli.load_project.dataset(k), d) }
+    end
+    cli.say
+  end
+
   ##
   # Perform distances operation with MiGA::Cli +cli+
   def check_dist(cli)

data/lib/miga/cli/action/doctor/base.rb

@@ -99,4 +99,46 @@ module MiGA::Cli::Action::Doctor::Base
     cli.say '- Removing tables, recompute'
     res.remove!
   end
+
+  ##
+  # Returns all targets identified by AAI
+  def saved_targets(dataset)
+    # Return nil if distance or database are not retrievable
+    dist = dataset.result(:distances) or return
+    path = dist.file_path(:aai_db) or return
+
+    o = []
+    SQLite3::Database.new(path) do |conn|
+      o = conn.execute('select seq2 from aai').map(&:first)
+    end
+    o
+  end
+
+  ##
+  # Saves all the distance estimates in +a+ -> +b+ into the +b+ databases
+  # (as +b+ -> +a+), where both +a+ and +b+ are MiGA::Dataset objects
+  def save_bidirectional(a, b)
+    each_database_file(a) do |db_file, metric, result|
+      data = nil
+      SQLite3::Database.new(db_file) do |conn|
+        data =
+          conn.execute(
+            "select seq1, seq2, #{metric}, sd, n, omega " +
+            "from #{metric} where seq2 = ? limit 1", b.name
+          ).first
+      end
+      next if data.nil? || data.empty?
+
+      db_file_b = File.join(File.dirname(db_file), "#{b.name}.db")
+      next unless File.exist?(db_file_b)
+
+      data[0], data[1] = data[1], data[0]
+      SQLite3::Database.new(db_file_b) do |conn|
+        conn.execute(
+          "insert into #{metric} (seq1, seq2, #{metric}, sd, n, omega) " +
+          "values(?, ?, ?, ?, ?, ?)", data
+        )
+      end
+    end
+  end
 end

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ 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 = [0.7, 15, 2]
+  VERSION = [0.7, 16, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 8, 12)
+  VERSION_DATE = Date.new(2020, 10, 13)
 
   ##
   # Reference of MiGA.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.15.2
+  version: 0.7.16.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-08-12 00:00:00.000000000 Z
+date: 2020-10-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons