rbbt-util 5.21.28 → 5.21.29

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1d60e1fb5bc0d15492a72771a4f32aab98c20d0c
-  data.tar.gz: a733159fcdff84ca2ec384b4b0e3b5853225ac3c
+  metadata.gz: 8751b62ac731fd443fffb25c525ca7cbfb40267e
+  data.tar.gz: b4ee9c2d532fbdd0fb9b460ae31889203d285565
 SHA512:
-  metadata.gz: 42973d86f709b72c9c527e6e41161917de93393eba19e2067591ad521e841158d4dda453cd56138298a382c9bd89a4548ec0a3017dabeb177ced502192049f3e
-  data.tar.gz: c5b4a7bbcf9ec659d178d8a66a17a4019308cf92b363be1d269f456790e58fd23d2f0b3fe9156a961a90e2993b3ee26f053338ca9bd0add19851155ff4ad2dbe
+  metadata.gz: a16c7143fb568582b630111fad7286c870b7a5595694c77a98da2b8c2a9d8848b5f8826e230d43b58f73a8649018c3f33ff181f48c1342fb965870efc016592e
+  data.tar.gz: 7d6b94d23c4d99829d23cb94d2bc89e89021a3fce32d7755ba8df1d4c1c3c20c15af0fc055775c4af4c6989c4b77b3e6aa699fa7c256d233490aeed43eb10e56

data/share/rbbt_commands/system/clean

@@ -99,7 +99,7 @@ TSV.traverse jobs, :_bar => "Checking job status" do |file,i|
     status = status.to_s
   end
 
-  next unless status =~ /\bnopid/ or status =~ /\berror$/ or status =~ /\bmissing$/ or status =~ /\baborted$/ or status =~ /\bdead$/ or status =~ /\bsync$/ or status == "" or (force and status == 'noinfo')
+  next unless (force and status =~ /done/) status =~ /\bnopid/ or status =~ /\berror$/ or status =~ /\bmissing$/ or status =~ /\baborted$/ or status =~ /\bdead$/ or status =~ /\bsync$/ or status == "" or (force and status == 'noinfo')
   puts "  Removing #{ file } - #{status}" 
   Step.clean(file) 
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.28
+  version: 5.21.29
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -487,82 +487,82 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_workflow.rb
+- test/test_helper.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/util/test_concurrency.rb
 - test/rbbt/util/test_log.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_R.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_pipes.rb
+- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/test_excel2tsv.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_misc.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_association.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_doc.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/test_persist.rb
 - test/rbbt/test_fix_width_table.rb
-- test/test_helper.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb