miga-base 0.7.3.0 → 0.7.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: bdc51401c6680d63872e7aab594eab50dbc500e6662d244a6fa04f6b6ea2587d
+  metadata.gz: 7e3f943800139b48778d227b3f0680bd71cac91774037f9f9e115842ccb3e6f4
+  data.tar.gz: 351042f7e77d3b2a3189a27fc37ead6c4fdb02ad519ba72a760d8e75a50dddf3
 SHA512:
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+  data.tar.gz: 75a5c9f95150c0177f1cf29a2bac58547bb51e60f75fe1d3c42acc3a3945aee161d51e1af479187459312b39c9164a6955d28232cbeb923cb8dbe5b748b590d8

data/lib/miga/common/with_daemon.rb

@@ -46,7 +46,7 @@ module MiGA::Common::WithDaemon
   # Is the daemon active?
   def active?
     return false unless File.exist? alive_file
-    last_alive > Time.now - 60
+    (last_alive || Time.new(0)) > Time.now - 60
   end
 
   ##

data/lib/miga/common/with_daemon_class.rb

@@ -26,9 +26,10 @@ module MiGA::Common::WithDaemonClass
   def last_alive(path)
     f = alive_file(path)
     f = terminated_file(path) unless File.exist? f
-    return nil unless File.exist? f
     c = File.read(f)
     return nil if c.nil? || c.empty?
     Time.parse(c)
+  rescue Errno::ENOENT
+    return nil
   end
 end

data/lib/miga/tax_dist.rb

@@ -43,7 +43,6 @@ module MiGA::TaxDist
             keys.each do |i|
               v = row.shift
               next if v == 'NA' # <- missing data
-              next if i == 1 # <- namespace, not a taxonomic rank
               rank = i.zero? ? :root : MiGA::Taxonomy.KNOWN_RANKS[i]
               vals[rank] = v.to_f
             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 = [0.7, 3, 0]
+  VERSION = [0.7, 3, 1]
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 4, 22)
+  VERSION_DATE = Date.new(2020, 4, 23)
 
   ##
   # Reference of MiGA.

data/utils/distance/database.rb

@@ -5,6 +5,7 @@ module MiGA::DistanceRunner::Database
   ##
   # Check for corrupt files and create empty databases
   def initialize_dbs!(for_ref)
+    $stderr.puts "Initializing databases (for_ref = #{for_ref})"
     @dbs = {}
     @tmp_dbs = {}
     @db_counts = {}

data/utils/distance/pipeline.rb

@@ -4,7 +4,7 @@ module MiGA::DistanceRunner::Pipeline
 
   # Recursively classify the dataset, returning an Array with two entries:
   # classification and cluster number
-  def classify(clades, classif, metric, result_fh, val_cls=nil)
+  def classify(clades, classif, metric, result_fh, val_cls = nil)
     dir = File.expand_path(classif, clades)
     med = File.expand_path('miga-project.medoids', dir)
     return [classif,val_cls] unless File.size? med
@@ -32,6 +32,7 @@ module MiGA::DistanceRunner::Pipeline
 
   # Builds a tree with all visited medoids from any classification level
   def build_medoids_tree(metric)
+    $stderr.puts "Building medoids tree (metric = #{metric})"
     db = query_db(metric)
     return unless File.size? db
     out_base = File.expand_path(dataset.name, home)
@@ -61,6 +62,7 @@ module MiGA::DistanceRunner::Pipeline
 
   # Tests taxonomy
   def tax_test
+    $stderr.puts "Testing taxonomy | opts = #{opts}"
     # Get taxonomy of closest relative
     from_ref_project = (project != ref_project)
     res_dir = from_ref_project ?
@@ -95,6 +97,7 @@ module MiGA::DistanceRunner::Pipeline
 
   # Transfer the taxonomy to the current dataset
   def transfer_taxonomy(tax)
+    $stderr.puts "Transferring taxonomy"
     return if tax.nil?
     pval = (project.metadata[:tax_pvalue] || 0.05).to_f
     tax_a = tax.

data/utils/distance/runner.rb

@@ -53,10 +53,12 @@ class MiGA::DistanceRunner
     @opts[:ani_p] ||= 'blast+'
     @opts[:distances_checkpoint] ||= 10
     @opts[:distances_checkpoint] = @opts[:distances_checkpoint].to_i
+    $stderr.puts "Options: #{opts}"
   end
 
   # Launch the appropriate analysis
   def go!
+    $stderr.puts "Launching analysis"
     return if dataset.is_multi?
     Dir.mktmpdir do |tmp_dir|
       @tmp = tmp_dir
@@ -67,6 +69,7 @@ class MiGA::DistanceRunner
 
   # Launch analysis for reference datasets
   def go_ref!
+    $stderr.puts "Launching analysis for reference dataset"
     # Initialize databases
     initialize_dbs! true
 
@@ -84,6 +87,7 @@ class MiGA::DistanceRunner
   ##
   # Launch analysis for query datasets
   def go_query!
+    $stderr.puts "Launching analysis for query dataset"
     # Check if project is ready
     tsk = ref_project.is_clade? ? [:subclades, :ani] : [:clade_finding, :aai]
     res = ref_project.result(tsk[0])
@@ -129,6 +133,7 @@ class MiGA::DistanceRunner
 
   # Launch analysis for taxonomy jobs
   def go_taxonomy!
+    $stderr.puts "Launching taxonomy analysis"
     return unless project.metadata[:ref_project]
     go_query! # <- yeah, it's actually the same, just different ref_project
   end

data/utils/distance/temporal.rb

@@ -6,7 +6,11 @@ module MiGA::DistanceRunner::Temporal
 
   # Copy input files to the (local) temporal folder
   def create_temporals
-    rf = {essential_genes: :ess_genes, cds: :proteins, assembly: :largecontigs}
+    rf = {
+      essential_genes: :ess_genes,
+      cds: :proteins,
+      assembly: :largecontigs
+    }
     rf.each do |res, file|
       r = dataset.result(res)
       f = r.nil? ? nil : r.file_path(file)
@@ -37,6 +41,7 @@ module MiGA::DistanceRunner::Temporal
 
   # Copies temporal databases back to the MiGA Project
   def checkpoint!(metric)
+    $stderr.puts "Checkpoint (metric = #{metric})"
     SQLite3::Database.new(tmp_dbs[metric]) do |conn|
       conn.execute("select count(*) from #{metric==:haai ? :aai : metric}")
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.3.0
+  version: 0.7.3.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-22 00:00:00.000000000 Z
+date: 2020-04-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons