rbbt-util 5.32.4 → 5.32.10
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc/slurm.rb +4 -0
- data/lib/rbbt/persist/tsv/adapter.rb +1 -5
- data/lib/rbbt/resource.rb +58 -40
- data/lib/rbbt/util/cmd.rb +14 -4
- data/lib/rbbt/util/migrate.rb +118 -0
- data/lib/rbbt/workflow.rb +11 -0
- data/lib/rbbt/workflow/util/archive.rb +31 -102
- data/share/rbbt_commands/hpc/orchestrate +3 -1
- data/share/rbbt_commands/hpc/task +3 -1
- data/share/rbbt_commands/lsf/clean +212 -0
- data/share/rbbt_commands/lsf/list +311 -0
- data/share/rbbt_commands/lsf/orchestrate +58 -0
- data/share/rbbt_commands/lsf/tail +55 -0
- data/share/rbbt_commands/lsf/task +57 -0
- data/share/rbbt_commands/migrate +3 -76
- data/share/rbbt_commands/slurm/clean +212 -0
- data/share/rbbt_commands/slurm/list +311 -0
- data/share/rbbt_commands/slurm/orchestrate +58 -0
- data/share/rbbt_commands/slurm/tail +55 -0
- data/share/rbbt_commands/slurm/task +57 -0
- data/test/rbbt/util/test_migrate.rb +36 -0
- data/test/rbbt/workflow/util/test_archive.rb +31 -0
- metadata +18 -3
@@ -0,0 +1,36 @@
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1
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+
require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
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2
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require 'rbbt-util'
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3
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+
require 'rbbt/util/migrate'
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4
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+
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5
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+
class TestMigrate < Test::Unit::TestCase
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6
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+
def _test_source_locate
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7
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assert_equal 'var/jobs/', Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user)).last
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8
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+
assert Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1].include?(File.join(ENV["HOME"], '.rbbt/var/jobs/'))
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9
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end
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10
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+
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11
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def test_migrate
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12
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Open.rm_rf Rbbt.tmp.test.migration_test.find(:user)
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13
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test_file = Rbbt.tmp.test.migration_test.migration_test_file.find(:user)
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14
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Open.write(test_file, "TEST")
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15
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+
TmpFile.with_file do |tmpdir|
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16
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Misc.in_dir tmpdir do
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17
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Log.with_severity 0 do
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18
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Rbbt.migrate('tmp/test/migration_test/migration_test_file', :current)
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19
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end
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20
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end
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21
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assert_equal "TEST", Open.read(File.join(tmpdir, 'tmp/test/migration_test/migration_test_file'))
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22
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end
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23
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end
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24
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+
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25
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def __test_migrate_turbo
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26
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Log.with_severity 0 do
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27
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TmpFile.with_file do |tmpdir|
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28
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Misc.in_dir tmpdir do
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29
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Rbbt.migrate('etc/config', :current, :source => 'mn1')
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30
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end
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31
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assert_equal "TEST", Open.read(File.join(tmpdir, 'etc/config'))
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32
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end
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33
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end
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34
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end
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35
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end
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36
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@@ -0,0 +1,31 @@
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require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
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2
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require 'rbbt-util'
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3
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require 'rbbt/workflow'
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4
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require 'rbbt/workflow/util/archive'
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5
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+
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6
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module ArchiveTestWF
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7
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extend Workflow
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8
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task :test_archive => :string do
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9
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Open.write(file(:file1), "Test file")
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10
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"TEST"
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11
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end
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12
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end
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13
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14
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class TestClass < Test::Unit::TestCase
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15
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def test_migrate
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16
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job = ArchiveTestWF.job(:test_archive)
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17
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job.run
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18
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19
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Log.with_severity 0 do
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20
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TmpFile.with_file do |tmpdir|
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21
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Misc.in_dir tmpdir do
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22
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Step.migrate(job.path, :current, :delete => false, :print => false)
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23
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end
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24
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assert_equal "TEST", Open.read(File.join(tmpdir, 'var/jobs/ArchiveTestWF/test_archive/Default'))
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25
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end
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26
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end
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27
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|
28
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+
|
29
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end
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30
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end
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31
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-util
|
3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 5.32.
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4
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+
version: 5.32.10
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Miguel Vazquez
|
8
8
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autorequire:
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9
9
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bindir: bin
|
10
10
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cert_chain: []
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11
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-
date: 2021-04
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11
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+
date: 2021-05-04 00:00:00.000000000 Z
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12
12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: rake
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@@ -165,7 +165,7 @@ dependencies:
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165
165
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- !ruby/object:Gem::Version
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166
166
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version: '0'
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167
167
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description: Utilities for handling tsv files, caches, etc
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168
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-
email: miguel.vazquez@
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168
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+
email: miguel.vazquez.g@bsc.es
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169
169
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executables:
|
170
170
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- rbbt_query.rb
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171
171
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- rbbt_exec.rb
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@@ -282,6 +282,7 @@ files:
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282
282
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- lib/rbbt/util/log/progress.rb
|
283
283
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- lib/rbbt/util/log/progress/report.rb
|
284
284
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- lib/rbbt/util/log/progress/util.rb
|
285
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+
- lib/rbbt/util/migrate.rb
|
285
286
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- lib/rbbt/util/misc.rb
|
286
287
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- lib/rbbt/util/misc/annotated_module.rb
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287
288
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- lib/rbbt/util/misc/bgzf.rb
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@@ -377,6 +378,11 @@ files:
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377
378
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- share/rbbt_commands/hpc/tail
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378
379
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- share/rbbt_commands/hpc/task
|
379
380
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- share/rbbt_commands/log
|
381
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+
- share/rbbt_commands/lsf/clean
|
382
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+
- share/rbbt_commands/lsf/list
|
383
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+
- share/rbbt_commands/lsf/orchestrate
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384
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+
- share/rbbt_commands/lsf/tail
|
385
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+
- share/rbbt_commands/lsf/task
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380
386
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- share/rbbt_commands/migrate
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381
387
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- share/rbbt_commands/migrate_job
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382
388
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- share/rbbt_commands/purge_job
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@@ -386,6 +392,11 @@ files:
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386
392
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- share/rbbt_commands/resource/produce
|
387
393
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- share/rbbt_commands/resource/read
|
388
394
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- share/rbbt_commands/rsync
|
395
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+
- share/rbbt_commands/slurm/clean
|
396
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+
- share/rbbt_commands/slurm/list
|
397
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+
- share/rbbt_commands/slurm/orchestrate
|
398
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+
- share/rbbt_commands/slurm/tail
|
399
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+
- share/rbbt_commands/slurm/task
|
389
400
|
- share/rbbt_commands/stat/abs
|
390
401
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- share/rbbt_commands/stat/boxplot
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391
402
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- share/rbbt_commands/stat/compare_lists
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@@ -522,6 +533,7 @@ files:
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|
522
533
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- test/rbbt/util/test_excel2tsv.rb
|
523
534
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- test/rbbt/util/test_filecache.rb
|
524
535
|
- test/rbbt/util/test_log.rb
|
536
|
+
- test/rbbt/util/test_migrate.rb
|
525
537
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- test/rbbt/util/test_misc.rb
|
526
538
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- test/rbbt/util/test_open.rb
|
527
539
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- test/rbbt/util/test_procpath.rb
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@@ -536,6 +548,7 @@ files:
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|
536
548
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- test/rbbt/workflow/test_schedule.rb
|
537
549
|
- test/rbbt/workflow/test_step.rb
|
538
550
|
- test/rbbt/workflow/test_task.rb
|
551
|
+
- test/rbbt/workflow/util/test_archive.rb
|
539
552
|
- test/rbbt/workflow/util/test_orchestrator.rb
|
540
553
|
- test/test_helper.rb
|
541
554
|
homepage: http://github.com/mikisvaz/rbbt-util
|
@@ -583,12 +596,14 @@ test_files:
|
|
583
596
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- test/rbbt/workflow/test_doc.rb
|
584
597
|
- test/rbbt/workflow/step/test_dependencies.rb
|
585
598
|
- test/rbbt/workflow/test_schedule.rb
|
599
|
+
- test/rbbt/workflow/util/test_archive.rb
|
586
600
|
- test/rbbt/workflow/util/test_orchestrator.rb
|
587
601
|
- test/rbbt/workflow/test_task.rb
|
588
602
|
- test/rbbt/workflow/test_step.rb
|
589
603
|
- test/rbbt/test_tsv.rb
|
590
604
|
- test/rbbt/test_annotations.rb
|
591
605
|
- test/rbbt/test_knowledge_base.rb
|
606
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+
- test/rbbt/util/test_migrate.rb
|
592
607
|
- test/rbbt/util/test_simpleDSL.rb
|
593
608
|
- test/rbbt/util/concurrency/processes/test_socket.rb
|
594
609
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- test/rbbt/util/concurrency/test_processes.rb
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