miga-base 1.3.21.5 → 1.3.22.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/miga/cli/action/wf.rb +8 -1
- data/lib/miga/daemon.rb +11 -5
- data/lib/miga/project/base.rb +1 -1
- data/lib/miga/version.rb +2 -2
- data/utils/distance/commands.rb +9 -4
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 18af6df383be9cb5a5ecba8ed914ec5c1878a70c8e8cb3825a590049b44a06b5
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data.tar.gz: a79ed870803ce5e4c7eb8e3380c79e43157de8090790d7d0ca9ace51fc6b12c7
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: bce0394b7a0f750df581b767992d5eb54f842b40aa06bbfa5dbd8b7d0d6e8f8ae813930432756369e6da07a9b0a95d1c6067147d5e6ae2fae7df697f46a0b41d
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data.tar.gz: 8f5c085855514811ae1b781d4e58ce3af1b82034d0d92e10b3a558fd2130d7312fba7eb548852e67083eff310435bbb44bde074c342971acca140f9be80c88af
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data/lib/miga/cli/action/wf.rb
CHANGED
@@ -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',
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@@ -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',
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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
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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')
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@@ -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
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k
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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
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data/lib/miga/project/base.rb
CHANGED
@@ -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,
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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,
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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.
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##
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# Date of the current gem relese.
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VERSION_DATE = Date.new(2025,
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VERSION_DATE = Date.new(2025, 2, 17)
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##
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# References of MiGA
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data/utils/distance/commands.rb
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@@ -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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-
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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?
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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.
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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-
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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
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