miga-base 1.3.21.5 → 1.3.22.0

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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@@ -124,6 +124,13 @@ module MiGA::Cli::Action::Wf
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  cli[:aai_p] = 'diamond'
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  cli[:ani_p] = 'fastani'
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  end
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+ opt.on(
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+ '--only-ani', 'Alias to: --haai-p no --aai-p no',
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+ 'Use only for collections with expected AAI around or above 85%'
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+ ) do
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+ cli[:haai_p] = 'no'
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+ cli[:aai_p] = 'no'
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+ end
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  opt.on(
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  '--haai-p STRING',
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  'hAAI search engine. One of: blast+, fastaai, blat, diamond, fastaai, no',
@@ -131,7 +138,7 @@ module MiGA::Cli::Action::Wf
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  ) { |v| cli[:haai_p] = v }
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  opt.on(
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  '--aai-p STRING',
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- 'AAI search engine. One of: blast+, blat, diamond (default)'
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+ 'AAI search engine. One of: blast+, blat, diamond (default), no'
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  ) { |v| cli[:aai_p] = v }
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  opt.on(
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  '--ani-p STRING',
data/lib/miga/daemon.rb CHANGED
@@ -183,7 +183,7 @@ class MiGA::Daemon < MiGA::MiGA
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  end
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  ##
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- # Traverse datasets, and returns boolean indicating if at any reference
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+ # Traverse datasets, and returns boolean indicating if any reference
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  # datasets are incomplete
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  def check_datasets
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  l_say(2, 'Checking datasets')
@@ -196,11 +196,17 @@ class MiGA::Daemon < MiGA::MiGA
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  queue_job(:d, ds)
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  end
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  unless show_log?
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+ @_check_datasets_reported_done ||= false
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  n = project.dataset_names.count
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- k = jobs_to_run.size + jobs_running.size
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- k -= 1 unless get_job(:maintenance).nil?
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- advance('Datasets:', n - k, n, false)
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- miga_say if k == 0
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+ k = (jobs_to_run + jobs_running).select { |i| !i[:ds].nil? }.size
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+ if k > 0
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+ advance('Datasets:', n - k, n, false)
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+ @_check_datasets_reported_done = false
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+ elsif !@_check_datasets_reported_done
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+ advance('Datasets:', n, n, false)
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+ miga_say
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+ @_check_datasets_reported_done = true
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+ end
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  end
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  o
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  end
@@ -142,7 +142,7 @@ module MiGA::Project::Base
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  },
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  aai_p: {
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  desc: 'Value of aai.rb -p on AAI', default: 'diamond', type: String,
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- in: %w[blast+ blast blat diamond]
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+ in: %w[blast+ blast blat diamond no]
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  },
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  ani_p: {
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  desc: 'Value of ani.rb -p on ANI', default: 'fastani', type: String,
data/lib/miga/version.rb CHANGED
@@ -12,7 +12,7 @@ module MiGA
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  # - String indicating release status:
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  # - rc* release candidate, not released as gem
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  # - [0-9]+ stable release, released as gem
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- VERSION = [1.3, 21, 5].freeze
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+ VERSION = [1.3, 22, 0].freeze
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  ##
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  # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
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  ##
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  # Date of the current gem relese.
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- VERSION_DATE = Date.new(2025, 1, 16)
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+ VERSION_DATE = Date.new(2025, 2, 17)
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  ##
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  # References of MiGA
@@ -60,10 +60,15 @@ module MiGA::DistanceRunner::Commands
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  # Note that ANI values may be returned for lower (or failing) AAIs if the
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  # value is already stored in the database
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  def ani_after_aai(targets, aai_limit = 85.0)
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- # Run AAI and select targets with AAI ≥ aai_limit
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- aai = aai(targets)
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- sbj = aai.each_with_index.map { |i, k| targets[k] if i&.> aai_limit }
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- sbj.compact!
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+ sbj =
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+ if opts[:aai_p] == 'no'
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+ # If we skip AAI, run ANI for all targets
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+ targets
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+ else
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+ # Otherwise, run AAI and select targets with AAI ≥ aai_limit
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+ aai = aai(targets)
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+ aai.each_with_index.map { |i, k| targets[k] if i&.> aai_limit }.compact
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+ end
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  # Run ANI
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  ani(sbj) unless sbj.empty?
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: miga-base
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  version: !ruby/object:Gem::Version
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- version: 1.3.21.5
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+ version: 1.3.22.0
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  platform: ruby
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  authors:
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  - Luis M. Rodriguez-R
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2025-01-16 00:00:00.000000000 Z
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+ date: 2025-02-17 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: daemons