rbbt-util 5.19.17 → 5.19.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7250e5af7af076517a13c322c1fe43506d9ece3d
-  data.tar.gz: c9ec9ec07c60be34a6f95c9bde5fd2deae7b3bbd
+  metadata.gz: 64ccfc0af909dbc006460786c31cd03ecb5a09d4
+  data.tar.gz: 221e3508c946239991fbb3fa8e4f9a4649cc954a
 SHA512:
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-  data.tar.gz: 8e98021bdafe0d005fea0047826a5068709dc009e84c941feaae4d9d1d48c4feac291c2915faf70c213ed71560ee74296fe02420c9656b325a38f6becbe0a357
+  metadata.gz: 585970e6c3d50f7edd9b9188e5e45a7938b821bd0d6ed69b03b08b8fd6ee893cdff167d7804005ea96c7e5f5f3dea68445e4755d6be8724b3a8d5e03e31e94e3
+  data.tar.gz: 3f3d63792bdd57aee6b3e7b863c7af2ed65e77706edcc55b1fda8b185dc0207bfd2e193b197d67f91bbf5afc7c8fbf0bc384654f4aeb2c510f5fde11d49e0ce5

data/lib/rbbt/monitor.rb

@@ -2,8 +2,10 @@ require 'rbbt'
 
 module Rbbt
 
-  LOCK_DIRS = Rbbt.share.find_all  + Rbbt.var.cache.persistence.find_all +  Rbbt.var.jobs.find_all +
-    Rbbt.tmp.tsv_open_locks.find_all + Rbbt.tmp.persist_locks.find_all + Rbbt.tmp.sensiblewrite_lock_dir.find_all +
+  #LOCK_DIRS = Rbbt.share.find_all  + Rbbt.var.cache.persistence.find_all +  Rbbt.var.jobs.find_all +
+  #  Rbbt.tmp.tsv_open_locks.find_all + Rbbt.tmp.persist_locks.find_all + Rbbt.tmp.sensiblewrite_lock_dir.find_all +
+  #  Rbbt.tmp.produce_locks.find_all + Rbbt.tmp.step_info_locks.find_all
+  LOCK_DIRS = Rbbt.tmp.tsv_open_locks.find_all + Rbbt.tmp.persist_locks.find_all + Rbbt.tmp.sensiblewrite_lock_dir.find_all +
     Rbbt.tmp.produce_locks.find_all + Rbbt.tmp.step_info_locks.find_all
 
   SENSIBLE_WRITE_DIRS = Misc.sensiblewrite_dir.find_all
@@ -48,7 +50,7 @@ module Rbbt
   def self.locks(dirs = LOCK_DIRS)
     dirs.collect do |dir|
       next unless Open.exists? dir
-      `find "#{ dir }" -name "*.lock"`.split "\n"
+      `find "#{ dir }" -name "*.lock" 2>/dev/null`.split "\n"
     end.compact.flatten
   end
 
@@ -67,7 +69,7 @@ module Rbbt
           lock_info[f][:ppid] = info[:ppid]
         end
       rescue Exception
-        Log.exception $!
+        #Log.exception $!
       end
     end
     lock_info
@@ -78,7 +80,7 @@ module Rbbt
   def self.sensiblewrites(dirs = SENSIBLE_WRITE_DIRS)
     dirs.collect do |dir|
       next unless Open.exists? dir
-      `find "#{ dir }" -not -name "*.lock" -not -type d`.split "\n"
+      `find "#{ dir }" -not -name "*.lock" -not -type d 2>/dev/null`.split "\n"
     end.compact.flatten
   end
 
@@ -100,7 +102,7 @@ module Rbbt
   def self.persists(dirs = PERSIST_DIRS)
     dirs.collect do |dir|
       next unless Open.exists? dir
-      `find "#{ dir }" -name "*.persist"`.split "\n"
+      `find "#{ dir }" -name "*.persist" 2>/dev/null`.split "\n"
     end.compact.flatten
   end
 
@@ -140,7 +142,7 @@ module Rbbt
           task = File.basename(taskdir)
           next if tasks and not tasks.include? task
 
-          files = `find "#{ taskdir }/" -not -type d -not -path "*/*.files/*"`.split("\n").sort
+          files = `find "#{ taskdir }/" -not -type d -not -path "*/*.files/*" 2>/dev/null`.split("\n").sort
           _files = Set.new files
           TSV.traverse files, :type => :array, :into => jobs do |file|
             if m = file.match(/(.*).info$/)

data/lib/rbbt/tsv/stream.rb

@@ -78,7 +78,7 @@ module TSV
       else
         fields = fields.compact.flatten
       end
-      options = options.merge(input_options.first)
+      options = options.merge(input_options.first || {})
       options[:type] = :list if options[:type] == :single
       options[:type] = :double if fix_flat
 

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

@@ -37,7 +37,7 @@ module Misc
       ":" << obj.to_s
     when String
       if obj.length > 100
-        "'" << obj.slice(0,30) << "<...#{obj.length}...>" << obj.slice(-10,30) << " " << "'"
+        "'" << obj.slice(0,30) << "<...#{obj.length}...>" << obj.slice(-10,30)<< "'"
       else 
         "'" << obj << "'"
       end

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

@@ -256,7 +256,9 @@ module Misc
           end
 
           begin
-            Open.mv tmp_path, path, lock_options
+            Misc.insist do
+              Open.mv tmp_path, path, lock_options
+            end
           rescue Exception
             raise $! unless File.exists? path
           end
@@ -273,7 +275,7 @@ module Misc
           content.abort if content.respond_to? :abort
           Open.rm path if File.exists? path
         rescue Exception
-          Log.medium "Exception in sensiblewrite: #{$!.message} -- #{ Log.color :blue, path }"
+          Log.medium "Exception in sensiblewrite: [#{Process.pid}] #{$!.message} -- #{ Log.color :blue, path }"
           Log.exception $!
           content.abort if content.respond_to? :abort
           Open.rm path if File.exists? path

data/lib/rbbt/workflow/accessor.rb

@@ -84,7 +84,7 @@ class Step
     begin
       Misc.insist do
         begin
-          return @info_cache if @info_cache and File.ctime(info_file) < @info_cache_time
+          return @info_cache if @info_cache and @info_cache_time and File.ctime(info_file) < @info_cache_time
         rescue Exception
           raise $!
         end
@@ -94,8 +94,13 @@ class Step
             Misc.insist(2, 1, info_file) do
               Misc.insist(3, 0.2, info_file) do
                 raise TryAgain, "Info locked" if check_lock and info_lock.locked?
-                Open.open(info_file) do |file|
-                  INFO_SERIALIAZER.load(file) #|| {}
+                info_lock.lock if check_lock and false
+                begin
+                  Open.open(info_file) do |file|
+                    INFO_SERIALIAZER.load(file) #|| {}
+                  end
+                ensure
+                  info_lock.unlock if check_lock and false
                 end
               end
             end

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

@@ -164,7 +164,7 @@ class Step
             end
           else
             Log.info "#{Log.color :cyan, "dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} starting -- #{Log.color :blue, dependency.path}"
-            dependency.run(true) 
+            dependency.run(true).grace
           end
         else
           Log.info "#{Log.color :cyan, "dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} done -- #{Log.color :blue, dependency.path}"
@@ -215,7 +215,6 @@ class Step
             raise $!
           end
 
-
           set_info :inputs, Misc.remove_long_items(Misc.zip2hash(task.inputs, @inputs)) unless task.inputs.nil?
 
           set_info :started, (start_time = Time.now)

data/share/rbbt_commands/system/clean

@@ -13,7 +13,7 @@ Clean orphaned files
 
 $ rbbt system clean <workflow> <task>
 
--a--all Print all jobs, not only uncompleted
+-a--all Apply to all jobs, not only uncompleted
 -f--force Remove regardless of been active
 -h--help Print this help
 EOF

data/share/rbbt_commands/tsv/sort

@@ -29,7 +29,7 @@ if field =~ /^\d+$/
 else
   parser = TSV.parse_header(file, options)
   field_pos = parser.all_fields.index(field) + 1
-  saved_line = parser.line
+  saved_line = parser.first_line
 end
 
 rest = ARGV.inject("-t\"\t\" -g -k#{field_pos}"){|acc,e| acc << " '#{e}'" }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.17
+  version: 5.19.18
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-02-22 00:00:00.000000000 Z
+date: 2016-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake