rbbt-util 5.25.30 → 5.25.31

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 525a2fcc360f03ebb4278678105b3e333979bd05
+  metadata.gz: f68692725942b4b7093433ae6cd3ce2b021e6fcc
+  data.tar.gz: 76ec7e3c0cc49cbe6f056d5203624a31eb53192f
 SHA512:
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-  data.tar.gz: 0ea18d479d5e4ef308fdc9143577eda23c82c578f7b5d1599b1f318acc9e8b86bcb9ad6e0af75de3ddfd1f7e670caac152d1ca7a79ed5bcb483d1254436f8ad2
+  metadata.gz: 26b78cd83316c25d6326664aef707fc777e659c4655de66ddc205830833a8bba73007acbf538aee9c5c465e1e888f73e90e259bec8bc9a1f2b83b2bcdfb74953
+  data.tar.gz: c93486946a1b6714ecea32026c1d1b5a9d7fa25c4e491024d8b4a34da3542f154320bb47dc7ea62df0a3368264525bac8870455af046d83544a2e1bd9b642eb9

data/bin/rbbt

@@ -59,7 +59,7 @@ $ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value
 -ck--config_keys*       #{Log.color :yellow, "Override some config keys"}
 EOF
 
-if options[:jobname_as_inputs]
+if options[:jobname_show_inputs]
   ENV["RBBT_INPUT_JOBNAME"] = "true"
 end
 

data/lib/rbbt/annotations.rb

@@ -162,6 +162,9 @@ module Annotated
       object.respond_to?(:clean_annotations) ?
         object.clean_annotations(true) : 
         object.inject([]){|acc,e| acc << Annotated.purge(e); acc}
+    when TSV
+      object.unnamed = true
+      object
     when Hash
       new = {}
       object.each do |key, value|

data/lib/rbbt/tsv/parser.rb

@@ -545,6 +545,7 @@ module TSV
 
       # first line
       line = self.rescue_first_line
+      line = stream.gets
 
       if @tsv_grep
 

data/lib/rbbt/util/misc/inspect.rb

@@ -176,7 +176,7 @@ module Misc
       next if k == :monitor or k == "monitor" or k == :in_situ_persistence or k == "in_situ_persistence"
       _v = hash[k]
       _k = k
-      v = Annotated.purge(_v)
+      v = TSV === _v ? _v : Annotated.purge(_v)
       k = Annotated.purge(k)
 
       case
@@ -184,6 +184,9 @@ module Misc
         str << k.to_s << "=>true" 
       when FalseClass === v
         str << k.to_s << "=>false" 
+      when TSV === v
+        iii :TSV
+        str << k.to_s << "=>" << obj2md5(v)
       when Hash === v
         str << k.to_s << "=>" << hash2md5(v)
       when Symbol === v

data/lib/rbbt/util/simpleopt/get.rb

@@ -27,7 +27,7 @@ module SOPT
         values[input] = value
       else
         if value.nil? and %w(F false FALSE no).include?(args[i])
-          Log.warn "Boolean values must are best specified as #{current}=[true|false], not #{ current } [true|false]. Token '#{args[i]}' following '#{current}' automatically assigned as value" 
+          Log.warn "Boolean values are best specified as #{current}=[true|false], not #{ current } [true|false]. Token '#{args[i]}' following '#{current}' automatically assigned as value" 
           value = args.delete_at(i)
         end
         values[input] = %w(F false FALSE no).include?(value)? false : true

data/lib/rbbt/workflow.rb

@@ -386,7 +386,8 @@ module Workflow
 
     task_info = task_info(taskname)
     task_inputs = task_info[:inputs]
-    Persist.memory("STEP", :taskname => taskname, :jobname => jobname, :inputs => inputs.values_at(*task_inputs), :repo => step_cache) do
+    persist_inputs = inputs.values_at(*task_inputs)
+    Persist.memory("STEP", :taskname => taskname, :jobname => jobname, :inputs => persist_inputs, :repo => step_cache) do
       __job(taskname, jobname, inputs)
     end
   end

data/lib/rbbt/workflow/step/run.rb

@@ -83,6 +83,7 @@ class Step
       next unless input.respond_to? :rewind
       begin
         input.rewind
+        input.first_line = nil if TSV::Parser === input
         Log.debug "Rewinded #{Misc.fingerprint input}"
       rescue
       end

data/share/Rlib/util.R

@@ -188,12 +188,12 @@ rbbt.tsv2matrix <- function(data){
   return(new);
 }
 
-rbbt.tsv.write <- function(filename, data, key.field = NULL, extra_headers = NULL){
+rbbt.tsv.write <- function(filename, data, key.field = NULL, extra_headers = NULL, eol="\n", ...){
 
   if (is.null(key.field)){ key.field = attributes(data)$key.field;}
   if (is.null(key.field)){ key.field = "ID";}
 
-  f = file(filename, 'w');
+  f = file(filename, 'wb');
 
   if (!is.null(extra_headers)){
       extra_headers = paste("#: ", extra_headers, "\n", sep="");
@@ -205,9 +205,9 @@ rbbt.tsv.write <- function(filename, data, key.field = NULL, extra_headers = NUL
   header = paste(header, "\n", sep="");
   cat(header, file=f);
   
-  close(f);
+  write.table(data, file=f, quote=FALSE, append=TRUE, col.names=FALSE, row.names=TRUE, sep="\t", eol="\n", ...);
 
-  write.table(data, file=filename, quote=FALSE, append=TRUE, col.names=FALSE, row.names=TRUE, sep="\t");
+  close(f);
 
   return(NULL);
 }

data/share/rbbt_commands/workflow/info

@@ -148,7 +148,7 @@ end
 if recursive
   inputs = step.info[:inputs]
   inputs = {}
-  deps = step.info[:dependencies].collect{|v| get_step v.last }
+  deps = (step.info[:dependencies] || []).collect{|v| get_step v.last }
 
   while deps.any? do
     dep = deps.shift

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.30
+  version: 5.25.31
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-01 00:00:00.000000000 Z
+date: 2019-03-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -511,90 +511,90 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.2.3
+rubygems_version: 2.6.13
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_knowledge_base.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/association/test_database.rb
-- test/rbbt/test_association.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/test_entity.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_step.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_bgzf.rb
-- test/rbbt/util/misc/test_lock.rb
 - test/rbbt/util/misc/test_pipes.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_semaphore.rb
-- test/rbbt/util/test_config.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/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_plot.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/test_cmd.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_chain_methods.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_open.rb
 - test/rbbt/util/test_simpleopt.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_fix_width_table.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_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_stream.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_index.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_filter.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_parallel.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/test_packed_index.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/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_persist.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/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.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_enrichment.rb
 - test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
 - test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_entity.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/test_tsv.rb
 - test/test_helper.rb