rbbt-util 5.32.2 → 5.32.9

data/test/rbbt/persist/tsv/test_tokyocabinet.rb

@@ -51,7 +51,7 @@ class TestPersistTSVTC < Test::Unit::TestCase
     end
   end
 
-  def test_annotation_persist_with_repeitions
+  def test_annotation_persist_with_repetitions
     TmpFile.with_file do |tmp|
       entity1 = "Entity 1"
       entity2 = "Entity 2"

data/test/rbbt/util/test_migrate.rb

@@ -0,0 +1,36 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt-util'
+require 'rbbt/util/migrate'
+
+class TestMigrate < Test::Unit::TestCase
+  def _test_source_locate
+    assert_equal 'var/jobs/', Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user)).last
+    assert Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1].include?(File.join(ENV["HOME"], '.rbbt/var/jobs/'))
+  end
+
+  def test_migrate
+    Open.rm_rf Rbbt.tmp.test.migration_test.find(:user)
+    test_file = Rbbt.tmp.test.migration_test.migration_test_file.find(:user)
+    Open.write(test_file, "TEST")
+    TmpFile.with_file do |tmpdir|
+      Misc.in_dir tmpdir do
+        Log.with_severity 0 do
+          Rbbt.migrate('tmp/test/migration_test/migration_test_file', :current)
+        end
+      end
+      assert_equal "TEST", Open.read(File.join(tmpdir, 'tmp/test/migration_test/migration_test_file'))
+    end
+  end
+
+  def __test_migrate_turbo
+    Log.with_severity 0 do
+    TmpFile.with_file do |tmpdir|
+      Misc.in_dir tmpdir do
+        Rbbt.migrate('etc/config', :current, :source => 'mn1')
+      end
+      assert_equal "TEST", Open.read(File.join(tmpdir, 'etc/config'))
+    end
+    end
+  end
+end
+

data/test/rbbt/workflow/util/test_archive.rb

@@ -0,0 +1,31 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt-util'
+require 'rbbt/workflow'
+require 'rbbt/workflow/util/archive'
+
+module ArchiveTestWF
+  extend Workflow
+  task :test_archive => :string do
+    Open.write(file(:file1), "Test file")
+    "TEST"
+  end
+end
+
+class TestClass < Test::Unit::TestCase
+  def test_migrate
+    job = ArchiveTestWF.job(:test_archive)
+    job.run
+
+    Log.with_severity 0 do
+      TmpFile.with_file do |tmpdir|
+        Misc.in_dir tmpdir do
+          Step.migrate(job.path, :current, :delete => false, :print => false)
+        end
+        assert_equal "TEST", Open.read(File.join(tmpdir, 'var/jobs/ArchiveTestWF/test_archive/Default'))
+      end
+    end
+
+
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.2
+  version: 5.32.9
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-04-26 00:00:00.000000000 Z
+date: 2021-05-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -165,7 +165,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 description: Utilities for handling tsv files, caches, etc
-email: miguel.vazquez@cnio.es
+email: miguel.vazquez.g@bsc.es
 executables:
 - rbbt_query.rb
 - rbbt_exec.rb
@@ -282,6 +282,7 @@ files:
 - lib/rbbt/util/log/progress.rb
 - lib/rbbt/util/log/progress/report.rb
 - lib/rbbt/util/log/progress/util.rb
+- lib/rbbt/util/migrate.rb
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/misc/annotated_module.rb
 - lib/rbbt/util/misc/bgzf.rb
@@ -377,6 +378,11 @@ files:
 - share/rbbt_commands/hpc/tail
 - share/rbbt_commands/hpc/task
 - share/rbbt_commands/log
+- share/rbbt_commands/lsf/clean
+- share/rbbt_commands/lsf/list
+- share/rbbt_commands/lsf/orchestrate
+- share/rbbt_commands/lsf/tail
+- share/rbbt_commands/lsf/task
 - share/rbbt_commands/migrate
 - share/rbbt_commands/migrate_job
 - share/rbbt_commands/purge_job
@@ -386,6 +392,11 @@ files:
 - share/rbbt_commands/resource/produce
 - share/rbbt_commands/resource/read
 - share/rbbt_commands/rsync
+- share/rbbt_commands/slurm/clean
+- share/rbbt_commands/slurm/list
+- share/rbbt_commands/slurm/orchestrate
+- share/rbbt_commands/slurm/tail
+- share/rbbt_commands/slurm/task
 - share/rbbt_commands/stat/abs
 - share/rbbt_commands/stat/boxplot
 - share/rbbt_commands/stat/compare_lists
@@ -522,6 +533,7 @@ files:
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_log.rb
+- test/rbbt/util/test_migrate.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
 - test/rbbt/util/test_procpath.rb
@@ -536,13 +548,14 @@ files:
 - test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/util/test_archive.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
 - test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -557,101 +570,104 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.7.6
+signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
+- test/test_helper.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_association.rb
+- test/rbbt/hpc/test_slurm.rb
+- test/rbbt/hpc/test_batch.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/test_packed_index.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_fix_width_table.rb
 - test/rbbt/workflow/test_remote_workflow.rb
-- test/rbbt/workflow/util/test_orchestrator.rb
 - test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_schedule.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/test_schedule.rb
+- test/rbbt/workflow/util/test_archive.rb
+- test/rbbt/workflow/util/test_orchestrator.rb
 - test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_colorize.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/util/test_migrate.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_procpath.rb
-- test/rbbt/util/misc/test_development.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/R/test_eval.rb
 - test/rbbt/util/R/test_model.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_colorize.rb
 - test/rbbt/util/test_config.rb
 - test/rbbt/util/test_log.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
 - test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
 - test/rbbt/util/test_python.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_chain_methods.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
+- test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/misc/test_lock.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_development.rb
+- test/rbbt/util/misc/test_format.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/test_hpc.rb
+- test/rbbt/test_persist.rb
 - test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_stream.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/test_association.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_hpc.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/test_helper.rb
+- test/rbbt/tsv/parallel/test_through.rb