miga-base 1.2.2.3 → 1.2.4.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3b3fd16e90667560b5cba41046eb92613187279fd7194d1825cc3dee9690273d
-  data.tar.gz: 84043b09c234b825ba0b89ca057b4301a97d5234a87282583516abffbc377e05
+  metadata.gz: 6fbc57d93921f48449936b8af3a44de4cb2cfddd14becca1f1fcf434dd8eb9ef
+  data.tar.gz: b4486a1cc7fee96070321b1d59c444f2a784daa50f536998e890d059767dc56a
 SHA512:
-  metadata.gz: 2e0d76139cfd93f77a91ee266bd596d74e8881da94fb750d97b03bb6c491424e75af208177687525d284ae3fe96e77f1e373f0bdce0583445a4070f3ed09cac0
-  data.tar.gz: 5bd98ea9eb89bcb4af4b74128c2d84ac1f32047322bb2177f7d47543efcc4122a4f8c23f463e8ae8291c8e6dff753182a39fd11fbdf42679975e5b2dba0ca571
+  metadata.gz: 7520ddd688f9767cf0baed5c53f5ba2b948d56f0bb847a2826e17fae823f2b3e34141c645196544c3269165aba0bbb83959c62d2187ad3d8151c1b180fb885b7
+  data.tar.gz: 643f3ddc30c470977089dc8fa812a69dd8d549e00bd1cd5afde928eb5ec4f457d2ababf6d5d1533c5835f2bd3f9df4228e12ef712b31767ae501084180d0291c

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

@@ -128,7 +128,9 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
     end
 
     sub_cli.say 'Locating remote dataset'
-    RemoteDataset.new(sub_cli[:ids], sub_cli[:db], sub_cli[:universe])
+    RemoteDataset.new(
+      sub_cli[:ids].chomp, sub_cli[:db].chomp, sub_cli[:universe].chomp
+    )
   end
 
   def update_metadata(sub_cli, p, rd)

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

@@ -5,7 +5,7 @@ require 'miga/cli/action'
 
 class MiGA::Cli::Action::Run < MiGA::Cli::Action
   def parse_cli
-    cli.defaults = { try_load: false, thr: 1, env: false }
+    cli.defaults = { try_load: false, thr: 1, env: false, check_first: false }
     cli.parse do |opt|
       cli.opt_object(opt, [:project, :dataset_opt, :result_opt])
       opt.on(
@@ -25,6 +25,10 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
         '-e', '--environment',
         'Load PROJECT, DATASET, and CORES from the environment'
       ) { |v| cli[:env] = v }
+      opt.on(
+        '--check-first',
+        'Check if the result exists, and run only if it does not'
+      ) { |v| cli[:check_first] = v }
     end
   end
 
@@ -51,6 +55,15 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
     # Load project
     p = cli.load_project
 
+    # Check if result already exists
+    if cli[:check_first]
+      obj = cli[:dataset] ? p.dataset(cli[:dataset]) : p
+      if obj.result(cli[:result])
+        cli.say('Result already exists')
+        return
+      end
+    end
+
     # Prepare command
     miga = MiGA.root_path
     opts = {}

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

@@ -69,15 +69,20 @@ module MiGA::Cli::Action::Wf
       'By default: ~/.miga_daemon.json'
     ) { |v| cli[:daemon_json] = v }
     opt.on(
-      '-j', '--jobs INT',
+      '-j', '--jobs INT', Integer,
       'Number of parallel jobs to execute',
       'By default controlled by the daemon configuration (maxjobs)'
-    ) { |v| cli[:jobs] = v.to_i }
+    ) { |v| cli[:jobs] = v }
     opt.on(
-      '-t', '--threads INT',
+      '-t', '--threads INT', Integer,
       'Number of CPUs to use per job',
       'By default controlled by the daemon configuration (ppn)'
-    ) { |v| cli[:threads] = v.to_i }
+    ) { |v| cli[:threads] = v }
+    opt.on(
+      '--threads-project INT', Integer,
+      'Number of CPUs to use per project-wide job',
+      'By default controlled by the daemon configuration (ppn_project or ppn)'
+    ) { |v| cli[:threads_project] = v }
   end
 
   def opts_for_wf_distances(opt)
@@ -184,9 +189,10 @@ module MiGA::Cli::Action::Wf
 
   def run_daemon
     cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
-    cmd += ['--json', cli[:daemon_json]] unless cli[:daemon_json].nil?
-    cmd += ['--max-jobs', cli[:jobs]] unless cli[:jobs].nil?
-    cmd += ['--ppn', cli[:threads]] unless cli[:threads].nil?
+    cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
+    cmd += ['--max-jobs', cli[:jobs]] if cli[:jobs]
+    cmd += ['--ppn', cli[:threads]] if cli[:threads]
+    cmd += ['--ppn-project', cli[:threads_project]] if cli[:threads_project]
     cmd += ['--debug', MiGA::MiGA.debug_trace? ? '2' : '1'] if MiGA::MiGA.debug?
     cwd = Dir.pwd
     call_cli(cmd)

data/lib/miga/common/with_daemon_class.rb

@@ -29,7 +29,7 @@ module MiGA::Common::WithDaemonClass
     return nil if c.nil? || c.empty?
 
     Time.parse(c)
-  rescue Errno::ENOENT
+  rescue Errno::ENOENT, ArgumentError
     return nil
   end
 end

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.2, 2, 3].freeze
+  VERSION = [1.2, 4, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2022, 2, 9)
+  VERSION_DATE = Date.new(2022, 4, 27)
 
   ##
   # References of MiGA

data/utils/distance/commands.rb

@@ -216,11 +216,12 @@ module MiGA::DistanceRunner::Commands
       next unless target_ess
 
       # hAAI
-      h = aairb_cmd(
-            tmp_file('ess_genes.fa'), target_ess,
-            dataset.name, target.name, tmp_dbs[:haai],
-            aai_save_rbm: false, aai_p: opts[:haai_p], checkpoint: :haai
-          )&.chomp&.to_f
+      aairb_cmd(
+        tmp_file('ess_genes.fa'), target_ess,
+        dataset.name, target.name, tmp_dbs[:haai],
+        aai_save_rbm: false, aai_p: opts[:haai_p], checkpoint: :haai
+      )
+      h = value_from_db(dataset.name, target.name, tmp_dbs[:haai], :haai)
       next if h.nil? || h.zero? || h > 90.0
 
       # Estimated AAI

data/utils/index_metadata.rb

@@ -19,6 +19,7 @@ end
 p.each_dataset do |d|
   next unless d.ref? && d.active?
 
+  db.execute('BEGIN TRANSACTION')
   searchable(db, d, :name, d.name)
   d.metadata.each do |k, v|
     next if [:created, :updated].include? k
@@ -26,4 +27,5 @@ p.each_dataset do |d|
     v = v.sorted_ranks.map { |r| r[1] }.join(' ') if k == :tax
     searchable(db, d, k, v)
   end
+  db.execute('COMMIT')
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.2.3
+  version: 1.2.4.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-02-09 00:00:00.000000000 Z
+date: 2022-04-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons