rbbt-util 5.26.91 → 5.26.92

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/rbbt/workflow/util/archive.rb

@@ -86,7 +86,8 @@ class Step
         end if dep.info[:dependencies]
       end
 
-      rec_dependencies.each do |dep|
+      rec_dependencies.each do |path|
+        dep = Workflow.load_step path
         job_files << dep.path
         job_files << dep.files_dir if Dir.glob(dep.files_dir + '/*').any?
         job_files << dep.info_file if File.exists?(dep.info_file)

data/share/rbbt_commands/system/status

@@ -3,7 +3,7 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 require 'rbbt/workflow'
-require 'rbbt/workflow/provenance'
+require 'rbbt/workflow/util/provenance'
 require 'rbbt/monitor'
 
 $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.91
+  version: 5.26.92
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-28 00:00:00.000000000 Z
+date: 2019-11-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -535,93 +535,93 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.6
+rubygems_version: 3.0.4
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_entity.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/remote/test_client.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.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/test_helper.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/test_association.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_traverse.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_tmpfile.rb
+- test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_lock.rb
+- test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/test_semaphore.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/simpleopt/test_get.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_open.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_log.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleopt.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/test_simpleDSL.rb
+- test/rbbt/util/test_python.rb
+- test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_change_id.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_excel.rb
 - test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/test_association.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/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_excel.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/test_hpc.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/remote/test_client.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_entity.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.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/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_lmdb.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/test_knowledge_base.rb
+- test/rbbt/resource/test_path.rb