rbbt-util 5.32.2 → 5.32.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 612e1472bae3839b68f143d639025a9bb19294525ecc0e95df99702883af31d3
-  data.tar.gz: bea8c5ec09525363447c5bdc140f899f8a22ccb311d225da061b01d6f68bcf10
+  metadata.gz: 5623a5f5b4b78dc051b02bfaa9f7503f999bc58b7cc3569d8a58f9caead7b212
+  data.tar.gz: 195a44841df5ef636806413bf4bcfe1b36304d0b9e4178d3e787b1ee2e5d5a71
 SHA512:
-  metadata.gz: 0aef55d55b97f40011aeaa3f09450dd623ad6d682b4b3ef5dc3f2df603efeeede2e50b3be2f4f586e502adb6a4a0fd898113d3c5c892212170edb4cde7b7f6a7
-  data.tar.gz: 81261ef8e8da6ada5c1d8e672fdbd31ff6dc67a7a08edb4b6a3dcee10cfc6ed3f7abacf0c3628d604839e2743de043793c5169a147bd9b528c2afd614dca62b9
+  metadata.gz: 9d9a436961cd66fd58bdd1b3908879b16f3e9f7a09d1d05a5d4e1980ad3c0a960a102895ca257bbd18298352c59f0448d21520c749bb652dc63c0042ef56d694
+  data.tar.gz: 9c9ec75fd411deb4849ed02834294da897a38ca2230a2af78e1bcb8722fe8ab1c1dd4eebe41e073270da02d60288363eb548f3bfdbf8cabd31256d5616ce9d09

data/lib/rbbt/resource.rb

@@ -6,6 +6,7 @@ require 'set'
 
  
 module Resource
+  class ResourceNotFound < RbbtException; end
 
   class << self
     attr_accessor :lock_dir
@@ -154,16 +155,14 @@ module Resource
       rake_dir, content = rake_for(path)
       rake_dir = Path.setup(rake_dir.dup, self.pkgdir, self)
     else
-      begin
-        if path !~ /\.(gz|bgz)$/
-          begin
-            produce(path.annotate(path + '.gz'), force)
-          rescue
-            produce(path.annotate(path + '.bgz'), force)
-          end
+      if path !~ /\.(gz|bgz)$/
+        begin
+          produce(path.annotate(path + '.gz'), force)
+        rescue ResourceNotFound
+          produce(path.annotate(path + '.bgz'), force)
         end
-      rescue
-        raise "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
+      else
+        raise ResourceNotFound, "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
       end
     end
 
@@ -174,7 +173,7 @@ module Resource
     end
 
     if type and not File.exist?(final_path) or force
-      Log.medium "Producing: #{ final_path }"
+      Log.medium "Producing: (#{self.to_s}) #{ final_path }"
       lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
 
       Misc.lock lock_filename do

data/lib/rbbt/workflow/usage.rb

@@ -122,7 +122,7 @@ module Workflow
       last = _prov_tasks(workflow.dep_tree(task_name))
 
       if child
-        description << "->" << task_name.to_s
+        description << "-> " << task_name.to_s
       elsif first
         description << "" << task_name.to_s
       else
@@ -198,7 +198,7 @@ module Workflow
         puts Misc.format_definition_list_item(name.to_s, description, Log.terminal_width, 20, :yellow)
 
         prov_string = prov_string(dep_tree(name))
-        puts Log.color :blue, " ->" + prov_string if prov_string && ! prov_string.empty?
+        puts Misc.format_paragraph Log.color(:blue, "-> " + prov_string) if prov_string && ! prov_string.empty?
       end
 
     else

data/lib/rbbt/workflow/util/trace.rb

@@ -10,6 +10,9 @@ module Workflow
       started = job.info[:started]
       ddone = job.info[:done]
 
+      started = Time.parse started if String === started
+      ddone = Time.parse ddone if String === ddone
+
       code = [job.workflow, job.task_name].compact.collect{|s| s.to_s} * " · "
       code = job.name + " - " + code
 
@@ -140,7 +143,13 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
       info = tasks_info[task] ||= IndiferentHash.setup({})
       dep_info = IndiferentHash.setup(dep.info)
 
-      time = dep_info[:done] - dep_info[:started]
+      ddone = dep_info[:done]
+      started = dep_info[:started]
+
+      started = Time.parse started if String === started
+      ddone = Time.parse ddone if String === ddone
+
+      time = ddone - started
       info[:time] ||= []
       info[:time] << time
 
@@ -196,7 +205,7 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
 
     end
 
-    jobs = jobs.uniq.sort_by{|job| t = job.info[:started]; t || Open.mtime(job.path) || Time.now }
+    jobs = jobs.uniq.sort_by{|job| t = job.info[:started] || Open.mtime(job.path) || Time.now; Time === t ? t : Time.parse(t) }
 
     data = trace_job_times(jobs, options[:fix_gap])
 

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"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.2
+  version: 5.32.4
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-04-26 00:00:00.000000000 Z
+date: 2021-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -542,7 +542,7 @@ homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -557,101 +557,102 @@ 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_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_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