miga-base 0.3.10.0 → 0.3.11.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 27d4c5ad304eb34c537ac2e625501b21682421567c555eb7152453d00b65a49e
-  data.tar.gz: bacf38077a05bec6c25dcbdd630b7a4f18f140ed4588877ac78254f3d9fc381d
+  metadata.gz: 0ff35e9287b082caf6870106450201c9153fcc4a9dc9788f5774460eb7751b38
+  data.tar.gz: e697b18e2df16c2c1fd4d8ee98ec837c78686e293f724b411a09a7f28bac10f1
 SHA512:
-  metadata.gz: 9b4d8fe08eaa514a76d3c6b62d0788aa44eb2f95e4cb56eb256671033a6f2ee29482c8ffc5186c614d4f587a4af1a6d85dd1b87a980fd2edc11ebb94330b4e07
-  data.tar.gz: a02db245387ff5185541ad98fb7556d018320eb69763cafbb37a96e1fb2fe8918b9701f13de6513a97ecd5902104414b47d380a62abf7528bb0dab5d35dc61cd
+  metadata.gz: 99face7b9b75edcf2e3f1e9210448a32a08b53ee2853e4548774405b276e6c3e82e475bbe9a876d91ee0c41d0df924756fd965828a1bc121cfcf0d4bc62f82cd
+  data.tar.gz: 42477e3181d69fc1959f78f6e8711d84890cd401467715378f0e4df8e0520944efacbc475cb40f612d4b64449f3b9f5dc3e44b2a6de15852f7442f3a3e10bd75

data/actions/doctor.rb

@@ -5,35 +5,37 @@
 
 require "sqlite3"
 
-o = {q:true, ld:false,
-  db: true, dist: true, files: true,
-  ess: true, mts: true, start: true, tax: true}
+tasks = {
+  db: ['databases', 'Check database files integrity'],
+  dist: ['distances', 'Check distance summary tables.'],
+  files: ['files', 'Check for outdated files.'],
+  ess: ['essential-genes', 'Check for unarchived essential genes'],
+  mts: ['mytaxa-scan', 'Check for unarchived MyTaxa scan'],
+  start: ['start', 'Check for lingering .start files'],
+  tax: ['taxonomy', 'Check for taxonomy consistency (not implemented)']
+}
+o = {q: true, ld: false}
+tasks.keys.each{ |i| o[i] = true }
+tasks_n = Hash[tasks.map{ |k,v| [v[0], k] }]
+
 OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project])
-  opt.on("-l", "--list-datasets",
-    "List all fixed datasets on advance."){ |v| o[:ld]=v }
-  opt.on("--ignore-databases",
-    "Do not check database files integrity."){ |v| o[:db]=!v }
-  opt.on("--ignore-distances",
-    "Do not check distance tables."){ |v| o[:dist]=!v }
-  opt.on("--ignore-files",
-    "Do not check for outdated files."){ |v| o[:files]=!v }
-  opt.on("--ignore-essential-genes",
-    "Do not check unarchived essential genes."){ |v| o[:ess]=!v }
-  opt.on("--ignore-mytaxa-scan",
-    "Do not check unarchived MyTaxa scan."){ |v| o[:mts]=!v }
-  opt.on("--ignore-start",
-    "Do not check lingering legacy .start files."){ |v| o[:start]=!v }
-  opt.on("--ignore-taxonomy",
-    "Do not check taxonomy consistency."){ |v| o[:tax]=!v }
-  opt_common(opt, o)
+  opt.on('-l', '--list-datasets',
+    'List all fixed datasets on advance.'){ |v| o[:ld]=v }
+  opt.on('--ignore TASK1,TASK2', Array,
+    'Do not perform the task(s) listed. Available tasks are:',
+    * tasks.values.map{ |v| "#{v[0]}: #{v[1]}" }
+    ){ |v| v.map{ |i| o[tasks_n[i]] = false } }
+  opt.on('--only TASK',
+    'Perform only the specified task (see --ignore).'
+    ){ |v| tasks.keys.each{ |i| o[i] = false }; o[v] = true }
 end.parse!
 
 ##=> Main <=
-opt_require(o, project:"-P")
+opt_require(o, project: '-P')
 
-$stderr.puts "Loading project" unless o[:q]
+$stderr.puts 'Loading project' unless o[:q]
 p = MiGA::Project.load(o[:project])
 raise "Impossible to load project: #{o[:project]}" if p.nil?
 
@@ -48,7 +50,7 @@ def check_sqlite3_database(db_file, metric)
 end
 
 if o[:db]
-  $stderr.puts "o Checking databases integrity" unless o[:q]
+  $stderr.puts 'o Checking databases integrity' unless o[:q]
   p.each_dataset do |d|
     [:distances, :taxonomy].each do |r_key|
       r = d.result(r_key) or next
@@ -97,20 +99,20 @@ end
   
   unless notok.empty?
     unless o[:q]
-      $stderr.puts "  - Unregistered datasets detected: "
+      $stderr.puts '  - Unregistered datasets detected: '
       if notok.size < 3
-        $stderr.puts "    - #{notok.keys.join(", ")}"
+        $stderr.puts "    - #{notok.keys.join(', ')}"
       else
-        $stderr.puts "    - #{notok.keys.first} and other #{notok.size-1}"
+        $stderr.puts "    - #{notok.size}, including #{notok.keys.first}"
       end
-      $stderr.puts "  - Removing tables, recompute"
+      $stderr.puts '  - Removing tables, recompute'
     end
     res.remove!
   end
 end if o[:dist]
 
 if o[:files]
-  $stderr.puts "o Looking for outdated files in results" unless o[:q]
+  $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
@@ -122,14 +124,14 @@ if o[:files]
       end
       unless ok
         $stderr.puts "    > Registering again #{d.name}:#{r_k}" if o[:ld]
-        d.add_result(r_k, true, force:true)
+        d.add_result(r_k, true, force: true)
       end
     end
   end
 end
 
 if o[:ess]
-  $stderr.puts "o Looking for unarchived essential genes." unless o[:q]
+  $stderr.puts 'o Looking for unarchived essential genes.' unless o[:q]
   p.each_dataset do |d|
     res = d.result(:essential_genes)
     next if res.nil?
@@ -148,7 +150,7 @@ if o[:ess]
 end
 
 if o[:mts]
-  $stderr.puts "o Looking for unarchived MyTaxa Scan runs." unless o[:q]
+  $stderr.puts 'o Looking for unarchived MyTaxa Scan runs.' unless o[:q]
   p.each_dataset do |d|
     res = d.result(:mytaxa_scan)
     next if res.nil?
@@ -178,7 +180,7 @@ if o[:mts]
 end
 
 if o[:start]
-  $stderr.puts "o Looking for legacy .start files lingering." unless o[:q]
+  $stderr.puts 'o Looking for legacy .start files lingering.' unless o[:q]
   p.each_dataset do |d|
     d.each_result do |r_k, r|
       if File.exist? r.path(:start)
@@ -194,5 +196,5 @@ if o[:tax]
   # TODO: Find 95%ANI clusters with entries from different species
 end
 
-$stderr.puts "Done" unless o[:q]
+$stderr.puts 'Done' unless o[:q]
 

data/lib/miga/daemon.rb

@@ -192,9 +192,16 @@ class MiGA::Daemon < MiGA::MiGA
   def flush!
     # Check for finished jobs
     @jobs_running.select! do |job|
-      r = (job[:ds].nil? ? project : job[:ds]).add_result(job[:job], false)
-      say "Completed pid:#{job[:pid]} for #{job[:task_name]}." unless r.nil?
-      r.nil?
+      ongoing = case job[:job].to_s
+      when 'd'
+        not job[:ds].next_preprocessing(false).nil?
+      when 'p'
+        not project.next_task(nil, false).nil?
+      else
+        (job[:ds].nil? ? project : job[:ds]).add_result(job[:job], false).nil?
+      end
+      say "Completed pid:#{job[:pid]} for #{job[:task_name]}." unless ongoing
+      ongoing
     end
     # Avoid single datasets hogging resources
     @jobs_to_run.rotate! rand(jobs_to_run.size)

data/lib/miga/project/result.rb

@@ -58,8 +58,10 @@ module MiGA::Project::Result
 
   ##
   # Get the next task from +tasks+, saving intermediate results if +save+.
+  # If +tasks+ is +nil+ (default), it uses the entire list of tasks.
   # Returns a Symbol.
-  def next_task(tasks = @@DISTANCE_TASKS+@@INCLADE_TASKS, save = true)
+  def next_task(tasks = nil, save = true)
+    tasks ||= @@DISTANCE_TASKS+@@INCLADE_TASKS
     tasks.find do |t|
       if metadata["run_#{t}"] == false or
             (!is_clade? and @@INCLADE_TASKS.include?(t) and

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, 10, 0]
+  VERSION = [0.3, 11, 0]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2019, 04, 9)
+  VERSION_DATE = Date.new(2019, 04, 17)
   
   ##
   # Reference of MiGA.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.10.0
+  version: 0.3.11.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-09 00:00:00.000000000 Z
+date: 2019-04-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons