rbbt-util 5.20.9 → 5.20.10

data/lib/rbbt/workflow/accessor.rb

@@ -324,7 +324,7 @@ class Step
   end
 
   def done?
-    path and File.exists? path
+    path and File.exist? path
   end
 
   def streaming?
@@ -426,8 +426,8 @@ class Step
     provenance = {}
     dependencies.each do |dep|
       next unless dep.path.exists?
-      if File.exists? dep.info_file
-        provenance[dep.path] = dep.provenance if File.exists? dep.path
+      if File.exist? dep.info_file
+        provenance[dep.path] = dep.provenance if File.exist? dep.path
       else
         provenance[dep.path] = nil
       end
@@ -438,7 +438,7 @@ class Step
   def provenance_paths
     provenance = {}
     dependencies.each do |dep|
-      provenance[dep.path] = dep.provenance_paths if File.exists? dep.path
+      provenance[dep.path] = dep.provenance_paths if File.exist? dep.path
     end
     provenance
   end

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

@@ -4,7 +4,7 @@ class Step
   STREAM_CACHE = {}
   STREAM_CACHE_MUTEX = Mutex.new
   def self.purge_stream_cache
-    Log.medium "Purging dup. stream cache"
+    Log.debug "Purging dup. stream cache"
     STREAM_CACHE_MUTEX.synchronize do
       #STREAM_CACHE.collect{|k,s| 
       #  Thread.new do

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

@@ -116,7 +116,7 @@ class Step
           begin
             run_dependencies
           rescue Exception
-            FileUtils.rm pid_file if File.exists?(pid_file)
+            FileUtils.rm pid_file if File.exist?(pid_file)
             stop_dependencies
             raise $!
           end
@@ -174,7 +174,7 @@ class Step
               ensure
                 join
                 Step.purge_stream_cache
-                FileUtils.rm pid_file if File.exists?(pid_file)
+                FileUtils.rm pid_file if File.exist?(pid_file)
               end
             end
             stream.abort_callback = Proc.new do
@@ -183,7 +183,7 @@ class Step
               rescue
                 Log.exception $!
                 stop_dependencies
-                FileUtils.rm pid_file if File.exists?(pid_file)
+                FileUtils.rm pid_file if File.exist?(pid_file)
               end
             end
           else
@@ -192,7 +192,7 @@ class Step
             set_info :time_elapsed, (time_elapsed = done_time - start_time)
             log :done, "Completed step #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i}+#{(total_time_elapsed - time_elapsed).to_i} sec."
             Step.purge_stream_cache
-            FileUtils.rm pid_file if File.exists?(pid_file)
+            FileUtils.rm pid_file if File.exist?(pid_file)
           end
 
           result
@@ -243,7 +243,7 @@ class Step
       Misc.pre_fork
       begin
         RbbtSemaphore.wait_semaphore(semaphore) if semaphore
-        FileUtils.mkdir_p File.dirname(path) unless File.exists? File.dirname(path)
+        FileUtils.mkdir_p File.dirname(path) unless File.exist? File.dirname(path)
         begin
           @forked = true
           res = run true
@@ -377,7 +377,7 @@ class Step
   end
 
   def soft_grace
-    until done? or File.exists?(info_file)
+    until done? or File.exist?(info_file)
       sleep 1 
     end
     self

data/share/rbbt_commands/app/install

@@ -11,10 +11,10 @@ raise "No app specified" if app.nil?
 
 app_dir = Rbbt.etc.app_dir.exists? ? Rbbt.etc.app_dir.read.strip : Rbbt.apps.find(:user)
 
-FileUtils.mkdir_p app_dir unless File.exists? app_dir
+FileUtils.mkdir_p app_dir unless File.exist? app_dir
 
 Misc.in_dir(app_dir) do
-  if File.exists? app
+  if File.exist? app
     Misc.in_dir(app) do
       `git pull`
     end

data/share/rbbt_commands/app/start

@@ -62,7 +62,7 @@ Misc.in_dir(app_dir) do
     ENV["RBBT_WORKFLOW_TASK_STREAM"] = 'true'
   end
 
-  config_ru_file = File.exists?('./config.ru') ? './config.ru' : Rbbt.share['config.ru'].find
+  config_ru_file = File.exist?('./config.ru') ? './config.ru' : Rbbt.share['config.ru'].find
 
   if options[:options]
     options[:options].split(";").each do |pair|

data/share/rbbt_commands/log

@@ -24,7 +24,11 @@ ERROR
 EOF
 rbbt_usage and exit 0 if options[:help] 
 if ARGV.empty?
-  puts Rbbt.etc.log_severity.read
+  if Rbbt.etc.log_severity.exists?                                                                                                                                                         
+    puts Rbbt.etc.log_severity.read                                                                                                                                                      
+  else                                                                                                                                                                                     
+    puts Rbbt.etc.log_severity.find + ' does not exist'                                                                                                                                  
+  end                                                                                                                                                                                      
 else
   Open.write(Rbbt.etc.log_severity, ARGV[0].upcase)
 end

data/share/rbbt_commands/resource/exists

@@ -47,7 +47,7 @@ resource = Kernel.const_get(resource)
 if options[:create]
   exists = resource[path].exists?
 else
-  exists = File.exists? resource[path].find
+  exists = File.exist? resource[path].find
 end
 
 if exists

data/share/rbbt_commands/study/task

@@ -59,7 +59,7 @@ def fix_options(workflow, task, job_options)
               case
               when value == '-'
                 STDIN.read
-              when (String === value and File.exists?(value) and not File.directory?(value))
+              when (String === value and File.exist?(value) and not File.directory?(value))
                 Open.read(value)
               else
                 value
@@ -71,7 +71,7 @@ def fix_options(workflow, task, job_options)
                 str = case
                 when value == '-'
                   STDIN.read
-                when (String === value and File.exists?(value))
+                when (String === value and File.exist?(value))
                   Open.read(value)
                 else
                   value
@@ -214,7 +214,7 @@ else
 end
 
 if Step === res
-  puts Open.read(res.path) if File.exists? res.path
+  puts Open.read(res.path) if File.exist? res.path
 else
   if res.respond_to? :gets
     while line = res.gets

data/share/rbbt_commands/system/clean

@@ -87,9 +87,9 @@ jobs.each do |file,i|
   pid = info[:pid]
 
   status = info[:status].to_s
-  status = :missing if status == "done" and not File.exists? file
+  status = :missing if status == "done" and not File.exist? file
   status = :dead if status != "done" and pid and not Misc.pid_exists?(pid)
-  status = :sync if status != "done" and File.exists? file
+  status = :sync if status != "done" and File.exist? file
 
   status = status.to_s
   next unless status =~ /\berror$/ or status =~ /\bmissing$/ or status =~ /\baborted$/ or status =~ /\bdead$/ or status =~ /\bsync$/ or status == "" or (force and status == 'noinfo')

data/share/rbbt_commands/system/deleted_files

@@ -25,7 +25,7 @@ Dir.glob('/proc/*/fd/*').each do |file|
   rescue
     next
   end
-  next if File.exists? dest
+  next if File.exist? dest
   pids[pid] ||= []
   pids[pid] << dest
 end

data/share/rbbt_commands/system/status

@@ -116,7 +116,7 @@ jobs = Rbbt.job_info workflow, task
 workflows = {}
 
 jobs.each do |file,info|
-  next unless all or not info[:done] or not File.exists? file
+  next unless all or not info[:done] or not File.exist? file
   workflow = info[:workflow]
   task = info[:task]
   workflows[workflow] ||= {}
@@ -139,10 +139,10 @@ workflows.sort.each do |workflow,tasks|
 
       pid = info[:pid]
       status = info[:status]
-      status = :missing if status == :done and not File.exists? file
+      status = :missing if status == :done and not File.exist? file
       status = status.to_s
       if status != "done" and pid and not Misc.pid_exists?(pid)
-        if File.exists? file
+        if File.exist? file
           status << Log.color(:red, " (out of sync)") 
         else
           status << Log.color(:red, " (dead)") 

data/share/rbbt_commands/tsv/info

@@ -56,7 +56,7 @@ else
     end
   end
 
-  if String === file and not Open.remote? file and File.exists? file
+  if String === file and not Open.remote? file and File.exist? file
     rows = `wc -l '#{ file }' 2>/dev/null|cut -f 1 -d' '`
   else
     rows = "Could not get rows of #{Misc.fingerprint file}"

data/share/rbbt_commands/tsv/subset

@@ -30,7 +30,7 @@ raise ParameterException, "Please specify the tsv file as argument" if file.nil?
 subset = options[:subset]
 raise ParameterException, "Please specify a subset of keys" if subset.nil?
 
-if File.exists?(subset)
+if File.exist?(subset)
   subset = Open.read(subset).split("\n")
 else
   subset = subset.split(',')

data/share/rbbt_commands/workflow/example

@@ -36,7 +36,7 @@ def run_task(workflow, task, name)
       end
     end
     sleep 0.5
-    path = Open.read(res).strip.split("\n").last if File.exists? res
+    path = Open.read(res).strip.split("\n").last if File.exist? res
   end
   path = "NO RESULT" if path.nil? or path.empty?
 

data/share/rbbt_commands/workflow/install

@@ -37,7 +37,7 @@ raise "No workflow specified" if workflow.nil?
 
 workflow_dir = Rbbt.etc.workflow_dir.exists? ? Path.setup(Rbbt.etc.workflow_dir.read.strip) : Rbbt.workflows.find(:user)
 
-FileUtils.mkdir_p workflow_dir unless File.exists? 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))}
 workflows = workflow == 'all' ? all_workflows : workflow.split(",")
@@ -45,12 +45,12 @@ workflows = workflow == 'all' ? all_workflows : workflow.split(",")
 Misc.in_dir(workflow_dir) do
   workflows.each do |workflow|
     case
-    when File.exists?(Misc.snake_case(workflow))
+    when File.exist?(Misc.snake_case(workflow))
       Log.info "Updating: " + workflow
       Misc.in_dir(Misc.snake_case(workflow)) do
         `git pull`
       end
-    when File.exists?(workflow)
+    when File.exist?(workflow)
       Misc.in_dir(workflow) do
         Log.info "Updating: " + workflow
         `git pull`

data/share/rbbt_commands/workflow/monitor

@@ -40,9 +40,9 @@ def list_jobs(options)
   info_files.each do |file|
     clean_file = file.sub('.info','')
     begin
-      next if File.exists? clean_file and $quick
+      next if File.exist? clean_file and $quick
       info = Step::INFO_SERIALIAZER.load(Open.read(file, :mode => 'rb'))
-      next if (File.exists?(clean_file) or info[:status] == :done) and (info[:children_pids].nil? or info[:children_done] or info[:children_pids].select{|pid| Misc.pid_exists? pid}.empty?)
+      next if (File.exist?(clean_file) or info[:status] == :done) and (info[:children_pids].nil? or info[:children_done] or info[:children_pids].select{|pid| Misc.pid_exists? pid}.empty?)
     rescue Exception
       puts "Error parsing info file: #{ file }"
       info = nil
@@ -75,16 +75,16 @@ end
 
 def remove_job(file)
   clean_file = file.sub('.info','')
-  FileUtils.rm file if File.exists? file
-  FileUtils.rm clean_file if File.exists? clean_file
-  FileUtils.rm_rf clean_file + '.files' if File.exists? clean_file + '.files'
+  FileUtils.rm file if File.exist? file
+  FileUtils.rm clean_file if File.exist? clean_file
+  FileUtils.rm_rf clean_file + '.files' if File.exist? clean_file + '.files'
 end
 
 def clean_jobs(options)
   info_files.each do |file|
     clean_file = file.sub('.info','')
     info = nil
-    next if File.exists? clean_file
+    next if File.exist? clean_file
     begin
       info = Step::INFO_SERIALIAZER.load(Open.read(file, :mode => 'rb'))
     rescue Exception

data/share/rbbt_commands/workflow/prov

@@ -64,7 +64,7 @@ def report(step, offset = 0)
   status = info[:status] || :missing
   status = :remote if Open.remote?(path)
   name = info[:name] || File.basename(path)
-  status = :unsync if status == :done and not File.exists? path
+  status = :unsync if status == :done and not File.exist? path
   str = " " * offset
   str << report_msg(status, name, path)
   info[:dependencies].each do |task,name,path|
@@ -80,6 +80,6 @@ def report(step, offset = 0)
 end
 
 step = get_step file
-$main_mtime = File.exists?(step.path) ? File.mtime(step.path) : nil
+$main_mtime = File.exist?(step.path) ? File.mtime(step.path) : nil
 
 puts report(step).strip

data/share/rbbt_commands/workflow/server

@@ -46,7 +46,7 @@ options[:Bind] ||= "0.0.0.0"
 workflow = ARGV.shift
 workflows = options[:workflows] || "" 
 
-workflow = File.expand_path(workflow) if File.exists?(workflow)
+workflow = File.expand_path(workflow) if File.exist?(workflow)
 
 ENV["RServe-session"] = options[:RServe_session] || workflow
 
@@ -68,7 +68,7 @@ TmpFile.with_file do |app_dir|
       ENV["RBBT_WORKFLOW_TASK_STREAM"] = 'true'
     end
 
-    config_ru_file = File.exists?('./workflow_config.ru') ? './config.ru' : Rbbt.share['workflow_config.ru'].find
+    config_ru_file = File.exist?('./workflow_config.ru') ? './config.ru' : Rbbt.share['workflow_config.ru'].find
 
 
     if options[:options]

data/share/rbbt_commands/workflow/task

@@ -95,7 +95,7 @@ def fix_options(workflow, task, job_options)
                 case
                 when value == '-'
                   STDIN.read
-                when (String === value and File.exists?(value) and not File.directory?(value))
+                when (String === value and File.exist?(value) and not File.directory?(value))
                   Open.read(value)
                 else
                   value
@@ -113,7 +113,7 @@ def fix_options(workflow, task, job_options)
                         when value == '-'
                           array_separator ||= "\n"
                           STDIN.read
-                        when (String === value and File.exists?(value))
+                        when (String === value and File.exist?(value))
                           array_separator ||= "\n"
                           Open.read(value)
                         else
@@ -487,7 +487,7 @@ when Step
     end
   else
     res.join
-    out.puts Open.read(res.path) if File.exists? res.path
+    out.puts Open.read(res.path) if File.exist? res.path
   end
 else
   out.puts res.to_s

data/test/rbbt/test_resource.rb

@@ -69,8 +69,8 @@ class TestTSV < Test::Unit::TestCase
   end
 
   def test_libdir
-    assert File.exists? TestResource[].share.Rlib["util.R"].find :lib
-    assert File.exists? TestResource[].share.Rlib["util.R"].find 
+    assert File.exist? TestResource[].share.Rlib["util.R"].find :lib
+    assert File.exist? TestResource[].share.Rlib["util.R"].find 
   end
 
   def __test_server

data/test/rbbt/workflow/test_step.rb

@@ -12,7 +12,7 @@ class TestStep < Test::Unit::TestCase
     TmpFile.with_file do |tmp|
       step = Step.new tmp, task
       assert_equal "TEST", step.run
-      assert File.exists? tmp
+      assert File.exist? tmp
       step = Step.new tmp, task2
       assert_equal "TEST", step.run
     end
@@ -102,7 +102,7 @@ class TestStep < Test::Unit::TestCase
 
   def __test_fork
     TmpFile.with_file do |lock|
-      task  = Task.setup do while not File.exists?(lock) do sleep 1; end; "TEST" end
+      task  = Task.setup do while not File.exist?(lock) do sleep 1; end; "TEST" end
       TmpFile.with_file do |tmp|
         step = Step.new tmp, task
         job = step.fork
@@ -118,7 +118,7 @@ class TestStep < Test::Unit::TestCase
 
   def __test_abort
     TmpFile.with_file do |lock|
-      task  = Task.setup do while not File.exists?(lock) do sleep 1; end; "TEST" end
+      task  = Task.setup do while not File.exist?(lock) do sleep 1; end; "TEST" end
       TmpFile.with_file do |tmp|
         step = Step.new tmp, task
         job = step.fork
@@ -148,9 +148,6 @@ class TestStep < Test::Unit::TestCase
       end
     end
   end
-
-  def test_messages
-    TmpFile.with_file do |lock|
       task  = Task.setup do 
         message "WRITE"
         Open.write(file("test"),"TEST")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.20.9
+  version: 5.20.10
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-08 00:00:00.000000000 Z
+date: 2016-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -280,7 +280,6 @@ files:
 - lib/rbbt/util/misc/omics.rb
 - lib/rbbt/util/misc/options.rb
 - lib/rbbt/util/misc/pipes.rb
-- lib/rbbt/util/misc/progress.rb
 - lib/rbbt/util/misc/system.rb
 - lib/rbbt/util/named_array.rb
 - lib/rbbt/util/open.rb