rbbt-util 5.21.4 → 5.21.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 98f603bb50ea1c28bf43f270dc31d9ff89f4a7c5
+  metadata.gz: 641642d8cd4871a267b75c1d4c9e41eb0ff5c81b
+  data.tar.gz: 28b2ec23f29f39f04c618277058d7a691c17bc4c
 SHA512:
-  metadata.gz: 6f978e2e64d4b4562b196ddfd9cf18c44a99ce4b816822b93643e9df9360296cdcb1583892124e1563fc6fff7652b46ae199ec580c7fde2b56cdaa2cafdb94c4
-  data.tar.gz: f9aa689208b9997cbc10c42d16d39b9df17938fd70a01adcf2ac0acb515220db662c27995ee68838bf49f1329a3cec8ab2d4db919e3151d3307d0474da048ce6
+  metadata.gz: 28bb8d81971d76843af4e9f38b20a31bb66c5bead0b6ecd7967711207ac67d69e723bf14d51e2dbfc454804e073d614f89bbaae5026008facdd93d4352b9cc42
+  data.tar.gz: 88998bb05a0aa162e8cf6fb10a22fec38f4c78a8afaa83a2277d91060315346d55e46ce298e98c24862786e7e85020372940d7a9310f8a92822f670ee788cbbf

data/lib/rbbt/resource/path.rb

@@ -96,6 +96,7 @@ module Path
     rsearch_paths = (resource and resource.respond_to?(:search_paths)) ? resource.search_paths : nil 
     key_elems = [where, caller_lib, rsearch_paths, paths]
     key = Misc.digest(key_elems.inspect)
+    self.sub!('~/', Etc.getpwuid.dir + '/')
     @path[key] ||= begin
                      paths = [paths, rsearch_paths, self.search_paths, SEARCH_PATHS].reverse.compact.inject({}){|acc,h| acc.merge! h; acc }
                      where = paths[:default] if where == :default

data/lib/rbbt/util/cmd.rb

@@ -132,8 +132,6 @@ module CMD
         serr.close
       end
 
-      #SmartIO.tie sout, pid, cmd, post, in_content, sin, serr
-      #
       ConcurrentStream.setup sout, :pids => pids, :autojoin => no_wait, :no_fail => no_fail 
 
       sout
@@ -147,6 +145,7 @@ module CMD
       end
 
       ConcurrentStream.setup sout, :pids => pids, :autojoin => no_wait, :no_fail => no_fail
+
       out = StringIO.new sout.read
       sout.close unless sout.closed?
 

data/share/rbbt_commands/rsync

@@ -0,0 +1,47 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+RSync a directory, commonly ~/.rbbt/ 
+
+$ rbbt rsync [options] <source_location> <target_location> -- [rsync_options]
+
+You can specify extra rsync options after --
+
+-h--help Print this help
+-e--exclude* Additional excludes separated by ','
+-es--excludes* Replace exlude list with these; separated by ','
+-t--test Do a verbose dry run
+-p--print Print command
+EOF
+if options[:help]
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.doc
+  end
+  exit 0
+end
+
+excludes = %w(.save .crap .source tmp filecache  open-remote workflows apps software jobs sinatra PCAWG)
+excludes += options[:exclude].split(/,\s*/)
+excludes_str = excludes.collect{|s| "--exclude '#{s}'" } * " "
+
+test_str = options[:test] ? '-nv' : ''
+
+source, target, _sep, *other = ARGV
+
+cmd = "rsync -a #{test_str} #{excludes_str} #{source} #{target} #{other * " "}"
+
+if options[:print]
+  puts cmd 
+  exit 0
+else
+  io = CMD.cmd(cmd, :log => true, :pipe => true)
+  Misc.consume_stream(io, false, STDOUT)
+end

data/share/rbbt_commands/workflow/install

@@ -39,7 +39,7 @@ workflow_dir = Rbbt.etc.workflow_dir.exists? ? Path.setup(Rbbt.etc.workflow_dir.
 
 FileUtils.mkdir_p workflow_dir unless File.exist? workflow_dir
 
-all_workflows = workflow_dir.glob("*/.git").collect{|d| File.basename(File.dirname(d))}
+all_workflows = workflow_dir.find.glob("*/.git").collect{|d| File.basename(File.dirname(d))}
 workflows = workflow == 'all' ? all_workflows : workflow.split(",")
 
 Misc.in_dir(workflow_dir) do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.4
+  version: 5.21.5
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -337,6 +337,7 @@ files:
 - share/rbbt_commands/resource/find
 - share/rbbt_commands/resource/get
 - share/rbbt_commands/resource/produce
+- share/rbbt_commands/rsync
 - share/rbbt_commands/stat/abs
 - share/rbbt_commands/stat/density
 - share/rbbt_commands/stat/log
@@ -483,82 +484,82 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
+- test/rbbt/test_workflow.rb
 - test/rbbt/resource/test_path.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/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/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_open.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_pipes.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_omics.rb
-- test/rbbt/util/misc/test_multipart_payload.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/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_doc.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/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/tsv/test_parallel.rb
-- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_matrix.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/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/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
 - test/rbbt/test_fix_width_table.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
+- test/test_helper.rb