rbbt-util 5.28.9 → 5.28.10
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- checksums.yaml +4 -4
- data/lib/rbbt/entity.rb +1 -1
- data/lib/rbbt/fix_width_table.rb +5 -4
- data/lib/rbbt/persist.rb +1 -1
- data/lib/rbbt/persist/tsv/adapter.rb +0 -1
- data/lib/rbbt/persist/tsv/fix_width_table.rb +5 -3
- data/lib/rbbt/tsv/dumper.rb +6 -2
- data/lib/rbbt/util/cmd.rb +1 -0
- data/lib/rbbt/util/misc/bgzf.rb +1 -1
- data/lib/rbbt/util/named_array.rb +1 -1
- data/lib/rbbt/util/open.rb +17 -16
- data/lib/rbbt/workflow/definition.rb +2 -1
- data/lib/rbbt/workflow/integration/ansible.rb +53 -0
- data/lib/rbbt/workflow/integration/ansible/workflow.rb +60 -0
- data/lib/rbbt/workflow/step.rb +5 -0
- data/lib/rbbt/workflow/step/accessor.rb +1 -1
- data/lib/rbbt/workflow/util/archive.rb +2 -0
- data/lib/rbbt/workflow/util/orchestrator.rb +22 -9
- data/share/rbbt_commands/ansible +55 -0
- data/share/rbbt_commands/purge_job +0 -1
- data/share/rbbt_commands/workflow/forget_deps +9 -0
- data/test/rbbt/association/test_index.rb +6 -6
- data/test/rbbt/knowledge_base/test_query.rb +3 -3
- data/test/rbbt/knowledge_base/test_registry.rb +1 -1
- data/test/rbbt/persist/tsv/test_cdb.rb +0 -7
- data/test/rbbt/persist/tsv/test_kyotocabinet.rb +2 -8
- data/test/rbbt/persist/tsv/test_leveldb.rb +0 -6
- data/test/rbbt/persist/tsv/test_lmdb.rb +0 -6
- data/test/rbbt/persist/tsv/test_tokyocabinet.rb +15 -14
- data/test/rbbt/test_entity.rb +0 -1
- data/test/rbbt/test_knowledge_base.rb +3 -4
- data/test/rbbt/test_persist.rb +10 -6
- data/test/rbbt/test_workflow.rb +17 -16
- data/test/rbbt/tsv/test_accessor.rb +11 -0
- data/test/rbbt/tsv/test_attach.rb +0 -2
- data/test/rbbt/tsv/test_index.rb +6 -7
- data/test/rbbt/tsv/test_manipulate.rb +2 -3
- data/test/rbbt/util/R/test_model.rb +2 -1
- data/test/rbbt/util/R/test_plot.rb +0 -2
- data/test/rbbt/util/concurrency/test_processes.rb +1 -1
- data/test/rbbt/util/misc/test_bgzf.rb +11 -7
- data/test/rbbt/util/misc/test_lock.rb +0 -1
- data/test/rbbt/util/misc/test_multipart_payload.rb +1 -1
- data/test/rbbt/util/misc/test_pipes.rb +0 -5
- data/test/rbbt/util/test_R.rb +1 -0
- data/test/rbbt/util/test_log.rb +4 -6
- data/test/rbbt/util/test_misc.rb +0 -2
- data/test/rbbt/util/test_open.rb +0 -1
- data/test/rbbt/util/test_python.rb +17 -1
- data/test/rbbt/workflow/test_remote_workflow.rb +1 -1
- data/test/rbbt/workflow/test_step.rb +8 -3
- data/test/rbbt/workflow/util/test_orchestrator.rb +50 -0
- metadata +5 -4
- data/test/rbbt/workflow/remote/test_client.rb +0 -56
@@ -0,0 +1,55 @@
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#!/usr/bin/env ruby
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require 'rbbt-util'
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require 'rbbt/util/simpleopt'
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$0 = "rbbt #{$previous_commands*" "} #{ File.basename(__FILE__) }" if $previous_commands
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options = SOPT.setup <<EOF
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Run ansible
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$ #{$0} [options] <rules.yml|->
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Use - to read from STDIN
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-h--help Print this help
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-dr--dry_run Only print the playbook
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-H--hosts* hosts to run it on
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EOF
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if options[:help]
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if defined? rbbt_usage
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rbbt_usage
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else
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puts SOPT.doc
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end
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exit 0
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end
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require 'rbbt/workflow/integration/ansible'
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playbook, task = ARGV
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playbook_file = Rbbt.share.ansible["test.yaml"].find if playbook.nil?
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dry_run = options.delete :dry_run
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if ! Misc.filename?(playbook_file)
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playbook_file = Rbbt.share.ansible.glob(playbook + ".*").first
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end
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if ! Misc.filename?(playbook_file)
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recipe = Rbbt.share.recipes.glob(playbook + ".*").first
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playbook_file = Ansible.playbook recipe, task, options
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end
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if dry_run
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if Hash === playbook_file
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ppp playbook_file.to_yaml
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else
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ppp Log.color :magenta, playbook_file
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ppp Open.read(playbook_file)
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end
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else
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Ansible.play playbook_file
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end
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@@ -13,6 +13,8 @@ Make a job forget all its dependencies and archive their meta-data
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$ #{$0} [options] <job_path>
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-h--help Print this help
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-p--purge Purge dependencies
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-r--recursive_purge Purge dependencies recursively
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EOF
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if options[:help]
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@@ -31,4 +33,11 @@ step = Workflow.load_step path
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step.archive_deps
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step.copy_files_dir
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dependencies = step.dependencies
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step.set_info :dependencies, []
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if options[:purge]
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dependencies.each do |dependency|
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Step.purge(dependency.path, options[:recursive_purge])
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end
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end
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@@ -73,21 +73,21 @@ TP53 NFKB1|GLI1 activation|activation true|true
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def test_index_flat
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require 'rbbt/sources/tfacts'
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file =
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file = TFactS.regulators
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tsv = Association.index(file, :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true)
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assert tsv.match("TP53").length > 10
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end
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def test_index_flat_to_matrix
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require 'rbbt/sources/tfacts'
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file =
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file = TFactS.regulators
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tsv = Association.index(file, :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true)
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assert(tsv.to_matrix(false))
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end
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def test_filter_no_block
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require 'rbbt/sources/tfacts'
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file =
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file = TFactS.regulators
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tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
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tsv.unnamed = false
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matches = tsv.filter :directed?
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@@ -96,7 +96,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
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def test_filter_no_block_value
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require 'rbbt/sources/tfacts'
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file =
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file = TFactS.regulators
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tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
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tsv.unnamed = false
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matches = tsv.filter :Effect, "inhibition"
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@@ -105,7 +105,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
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def test_filter_block_value_field
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require 'rbbt/sources/tfacts'
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file =
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file = TFactS.regulators
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tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
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tsv.unnamed = false
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matches = tsv.filter :Effect do |value|
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@@ -116,7 +116,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
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def test_filter_block_no_value_field
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require 'rbbt/sources/tfacts'
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file =
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file = TFactS.regulators
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tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:undirected => false, :source => "SG=~Associated Gene Name", :target => "TG=~Associated Gene Name"), :persist => true)
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tsv.unnamed = false
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matches = tsv.filter do |key,values|
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@@ -22,7 +22,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
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:namespace => "Hsa"
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}
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EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
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EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
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KNOWLEDGE_BASE = KnowledgeBase.new Rbbt.tmp.test.kb_foo2, "Hsa"
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KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
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assert_equal 6, KNOWLEDGE_BASE.subset(:effects, :all).length
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assert_equal 4, KNOWLEDGE_BASE.subset(:effects, :all).target_entity.uniq.length
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assert_equal %w(Effect), KNOWLEDGE_BASE.subset(:effects, :all).info.first.keys
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assert_equal %w(Effect), KNOWLEDGE_BASE.subset(:effects, :all).info.first.keys
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end
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end
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def
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def _test_subset_all_persist_format
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assert KNOWLEDGE_BASE.subset(:effects, :all).target_entity.reject{|e| e =~ /^ENS/}.empty?
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end
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@@ -45,7 +45,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
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def test_index_flat
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require 'rbbt/sources/tfacts'
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file =
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file = TFactS.regulators
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KNOWLEDGE_BASE.register :tfacts, file, :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true
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assert KNOWLEDGE_BASE.subset(:tfacts, :source => ["TP53"], :target => :all).length > 10
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end
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@@ -4,19 +4,12 @@ require 'rbbt/annotations'
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require 'rbbt/util/tmpfile'
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require 'test/unit'
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module TestAnnotation
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extend Annotation
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self.annotation :test_annotation
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end
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class TestPersistTSVCDB < Test::Unit::TestCase
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if Persist.respond_to? :open_cbd
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def test_organism
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require 'rbbt/sources/organism'
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TmpFile.with_file nil do |tmp_file|
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file = CMD.cmd("head -n 1000000", :in => Organism.identifiers("Hsa").open, :pipe => true)
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tsv = Organism.identifiers("Hsa").tsv(:key_field => "Associated Gene Name", :fields => ["Ensembl Gene ID"], :type => :single, :persist => true, :persist_engine => "CDB", :persist_dir => tmp_file)
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assert_equal "ENSG00000141510", tsv["TP53"]
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end
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@@ -5,15 +5,9 @@ require 'rbbt/annotations'
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require 'rbbt/util/tmpfile'
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require 'test/unit'
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module TestAnnotation
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extend Annotation
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self.annotation :test_annotation
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end
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class TestPersistTSVKC < Test::Unit::TestCase
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if Persist.respond_to? :open_kyotocabinet
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def
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def test_organism_kch
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require 'rbbt/sources/organism'
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TmpFile.with_file do |tmp_file|
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tsv = Organism.identifiers("Hsa").tsv :key_field => "Associated Gene Name", :fields => ["Ensembl Gene ID"], :type => :single, :persist => true, :persist_engine => "kch", :persist_dir => tmp_file
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end
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def
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def test_organism_kct
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require 'rbbt/sources/organism'
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TmpFile.with_file do |tmp_file|
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tsv = Organism.identifiers("Hsa").tsv :key_field => "Associated Gene Name", :fields => ["Ensembl Gene ID"], :type => :single, :persist => true, :persist_engine => "kct", :persist_dir => tmp_file
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@@ -4,12 +4,6 @@ require 'rbbt/annotations'
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require 'rbbt/util/tmpfile'
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require 'test/unit'
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module TestAnnotation
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extend Annotation
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self.annotation :test_annotation
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end
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class TestPersistTSVLevelDB < Test::Unit::TestCase
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if Persist.respond_to? :open_leveldb
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@@ -4,7 +4,8 @@ require 'rbbt/annotations'
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require 'rbbt/util/tmpfile'
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require 'test/unit'
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module TestAnnotationModule
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extend Annotation
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self.annotation :test_annotation
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@@ -25,8 +26,8 @@ class TestPersistTSVTC < Test::Unit::TestCase
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entity1 = "Entity 1"
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entity2 = "Entity 2"
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TestAnnotationModule.setup(entity1, :test_annotation => "1")
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TestAnnotationModule.setup(entity2, :test_annotation => "2")
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annotations = [entity1, entity2]
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@@ -56,9 +57,9 @@ class TestPersistTSVTC < Test::Unit::TestCase
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entity2 = "Entity 2"
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entity2bis = "Entity 2"
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TestAnnotationModule.setup(entity1, :test_annotation => "1")
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TestAnnotationModule.setup(entity2, :test_annotation => "2")
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TestAnnotationModule.setup(entity2bis, :test_annotation => "2")
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annotations = [entity1, entity2, entity2bis]
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@@ -105,8 +106,8 @@ class TestPersistTSVTC < Test::Unit::TestCase
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entity1 = "Entity 1"
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entity2 = "Entity 2"
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TestAnnotationModule.setup(entity1, :test_annotation => "1")
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TestAnnotationModule.setup(entity2, :test_annotation => "2")
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annotations = [entity1, entity2]
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@@ -138,7 +139,7 @@ class TestPersistTSVTC < Test::Unit::TestCase
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entity2 = "Entity 2"
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annotations = [entity1, entity2]
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TestAnnotationModule.setup(annotations, :test_annotation => "1")
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annotations.extend AnnotatedArray
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persisted_annotations = Persist.persist("Test", :annotations, :annotation_repo => repo) do
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@@ -171,11 +172,11 @@ class TestPersistTSVTC < Test::Unit::TestCase
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entity2 = "Entity 2"
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annotations = [entity1, entity2]
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TestAnnotationModule.setup(annotations, :test_annotation => "1")
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annotations.extend AnnotatedArray
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annotations_ary = [annotations]
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TestAnnotationModule.setup(annotations_ary, :test_annotation => "1")
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annotations_ary.extend AnnotatedArray
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persisted_annotations = Persist.persist("Test", :annotations, :annotation_repo => repo) do
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@@ -210,9 +211,9 @@ class TestPersistTSVTC < Test::Unit::TestCase
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entity2 = "Entity 2"
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entity2bis = "Entity 2"
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-
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TestAnnotationModule.setup(entity1, :test_annotation => "1")
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TestAnnotationModule.setup(entity2, :test_annotation => "2")
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TestAnnotationModule.setup(entity2bis, :test_annotation => "2")
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annotations = [entity1, entity2, entity2bis]
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data/test/rbbt/test_entity.rb
CHANGED
@@ -62,7 +62,7 @@ class TestKnowledgeBase < Test::Unit::TestCase
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kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
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kb.format = {"Gene" => "Ensembl Gene ID"}
|
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65
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-
kb.register :tfacts,
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kb.register :tfacts, TFactS.regulators, :source =>"=~Associated Gene Name"
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66
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kb.get_index(:tfacts).reverse
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|
end
|
@@ -74,7 +74,7 @@ class TestKnowledgeBase < Test::Unit::TestCase
|
|
74
74
|
kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
|
75
75
|
kb.format = {"Gene" => "Ensembl Gene ID"}
|
76
76
|
|
77
|
-
kb.register :tfacts,
|
77
|
+
kb.register :tfacts, TFactS.regulators, :source =>"=~Associated Gene Name"
|
78
78
|
|
79
79
|
assert_equal "Ensembl Gene ID", kb.get_database(:tfacts).key_field
|
80
80
|
|
@@ -113,10 +113,9 @@ class TestKnowledgeBase < Test::Unit::TestCase
|
|
113
113
|
|
114
114
|
def test_knowledge_base_reuse
|
115
115
|
organism = Organism.default_code("Hsa")
|
116
|
-
Log.severity = 0
|
117
116
|
TmpFile.with_file do |tmpdir|
|
118
117
|
Path.setup(tmpdir)
|
119
|
-
Association.index(
|
118
|
+
Association.index(TFactS.regulators, :persist_file => tmpdir.tfacts, :format => {"Gene" => "Ensembl Gene ID"}, :namespace => Organism.default_code("Hsa"))
|
120
119
|
|
121
120
|
kb = KnowledgeBase.load(tmpdir)
|
122
121
|
assert kb.identify_source('tfacts', "TP53") =~ /ENSG/
|
data/test/rbbt/test_persist.rb
CHANGED
@@ -4,12 +4,6 @@ require 'rbbt/annotations'
|
|
4
4
|
require 'rbbt/util/tmpfile'
|
5
5
|
require 'test/unit'
|
6
6
|
|
7
|
-
module TestAnnotation
|
8
|
-
extend Annotation
|
9
|
-
|
10
|
-
self.annotation :test_annotation
|
11
|
-
end
|
12
|
-
|
13
7
|
class TestPersist < Test::Unit::TestCase
|
14
8
|
|
15
9
|
def test_array_persist
|
@@ -78,4 +72,14 @@ class TestPersist < Test::Unit::TestCase
|
|
78
72
|
stream.join
|
79
73
|
end
|
80
74
|
end
|
75
|
+
|
76
|
+
def test_newer
|
77
|
+
TmpFile.with_file("Test1") do |tmp1|
|
78
|
+
sleep 1
|
79
|
+
TmpFile.with_file("Test1") do |tmp2|
|
80
|
+
assert Persist.newer?(tmp1, tmp2)
|
81
|
+
assert ! Persist.newer?(tmp2, tmp1)
|
82
|
+
end
|
83
|
+
end
|
84
|
+
end
|
81
85
|
end
|
data/test/rbbt/test_workflow.rb
CHANGED
@@ -204,7 +204,6 @@ class TestWorkflow < Test::Unit::TestCase
|
|
204
204
|
|
205
205
|
def test_update_on_input_dependency_update
|
206
206
|
Open.repository_dirs << File.join(ENV["HOME"],".rbbt/tmp/test/workflow")
|
207
|
-
Log.severity = 0
|
208
207
|
Misc.with_env "RBBT_UPDATE", "true" do
|
209
208
|
send_input_dep_to_reverse_job = TestWF.job(:send_input_dep_to_reverse, nil, :name => "Miguel")
|
210
209
|
send_input_dep_to_reverse_job.clean
|
@@ -376,21 +375,23 @@ class TestWorkflow < Test::Unit::TestCase
|
|
376
375
|
def test_delete_dep
|
377
376
|
job = TestWF.job(:t3).recursive_clean
|
378
377
|
job.run
|
379
|
-
|
380
|
-
|
381
|
-
|
382
|
-
|
383
|
-
|
384
|
-
|
385
|
-
|
386
|
-
|
387
|
-
|
388
|
-
|
389
|
-
|
390
|
-
|
391
|
-
|
392
|
-
|
393
|
-
|
378
|
+
Misc.with_env "RBBT_UPDATE", 'true' do
|
379
|
+
assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
|
380
|
+
job = TestWF.job(:t3)
|
381
|
+
job.step(:t1).clean
|
382
|
+
assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
|
383
|
+
job = TestWF.job(:t3).recursive_clean
|
384
|
+
job.run
|
385
|
+
assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
|
386
|
+
job = TestWF.job(:t3)
|
387
|
+
sleep 1
|
388
|
+
Open.touch job.step(:t1).path
|
389
|
+
Misc.with_env "RBBT_UPDATE", "false" do
|
390
|
+
assert job.updated?
|
391
|
+
end
|
392
|
+
Misc.with_env "RBBT_UPDATE", "true" do
|
393
|
+
assert ! job.updated?
|
394
|
+
end
|
394
395
|
end
|
395
396
|
end
|
396
397
|
|
@@ -222,6 +222,17 @@ row2 aa|aa|AA|AA b1|b2|B1|B2 Id1|Id1|Id2|Id2
|
|
222
222
|
end
|
223
223
|
end
|
224
224
|
|
225
|
+
def test_to_s_no_fields
|
226
|
+
file1 =<<-EOF
|
227
|
+
row6 dd dd ee
|
228
|
+
row1 a b c
|
229
|
+
row2 A B C
|
230
|
+
row3 1 2 3
|
231
|
+
EOF
|
232
|
+
tsv1 = TSV.open StringIO.new(file1), :sep => " "
|
233
|
+
assert tsv1.to_s(:sort, true).include?('dd')
|
234
|
+
end
|
235
|
+
|
225
236
|
def test_to_s_unmerge_expand
|
226
237
|
content =<<-EOF
|
227
238
|
#Id ValueA ValueB OtherID
|