rbbt-util 5.25.25 → 5.25.26

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 8ce259a222668ea4311a54a765811db4af367938
+  metadata.gz: 332e52f2862068fad1da1a881a2d481423e709ca
+  data.tar.gz: c27385464c185c1d726251a7b67668b48b3d94f0
 SHA512:
-  metadata.gz: f622b574101a0b536bd616c72af176eb402e67d351ba6e8362796bf97873a1a38f0bcd6ba9ac4ceb5ed009675b08b6a346aac35ac33873aa8dbe4c7fefd2679f
-  data.tar.gz: 226434c03c89bc69e3c39ece4d6ff2930a42721d032053946294ad941e34227180fceebb72c2757701832c415aba10876423ac60f6e20e52e252611b83dfddf2
+  metadata.gz: 4eef47ef223160fc7b9b4211d632df7ce43782cb1808f9c6d393bc6f60e278efb4f09f789cb0add14ffbbe8dd03ecc21d4ef2f17bce1efbe7248e3d33cc890db
+  data.tar.gz: 816afdb536c064923a881d9cb15590615be70cc54320929aa06d06d5133e2f7611c25d42d6296cb49cf0d60da34d2403ae7efb57e155da3b320cf999d14266bd

data/lib/rbbt/util/cmd.rb

@@ -54,50 +54,6 @@ module CMD
 
     in_content = StringIO.new in_content if String === in_content
 
-    #sout, serr, sin = Misc.pipe, Misc.pipe, Misc.pipe
-
-    #pid = fork {
-    #  begin
-    #    Misc.purge_pipes(sin.last,sout.last,serr.last)
-
-    #    sin.last.close
-    #    sout.first.close
-    #    serr.first.close
-
-    #    if IO === in_content
-    #      in_content.close if in_content.respond_to?(:close) and not in_content.closed?
-    #    end
-
-    #    STDERR.reopen serr.last
-    #    serr.last.close
-
-    #    STDIN.reopen sin.first
-    #    sin.first.close
-
-    #    STDOUT.reopen sout.last
-    #    sout.last.close
-
-    #    STDOUT.sync = STDERR.sync = true
-
-    #    exec(ENV, cmd)
-
-    #    exit(-1)
-    #  rescue Exception
-    #    Log.debug{ "ProcessFailed: #{$!.message}" } if log
-    #    Log.debug{ "Backtrace: \n" + $!.backtrace * "\n" } if log
-    #    raise ProcessFailed, $!.message
-    #  end
-    #}
-
-    #sin.first.close
-    #sout.last.close
-    #serr.last.close
-
-
-    #sin = sin.last
-    #sout = sout.first
-    #serr = serr.first
-
     sin, sout, serr, wait_thr = begin
                                   Open3.popen3(ENV, cmd)
                                 rescue
@@ -139,8 +95,8 @@ module CMD
     if pipe
       err_thread = Thread.new do
         while line = serr.gets
-          Log.log "STDERR [#{pid}]: " +  line, stderr if Integer === stderr and log
-        end
+          Log.log "STDERR [#{pid}]: " +  line, stderr 
+        end if Integer === stderr and log
         serr.close
       end
 
@@ -181,13 +137,17 @@ module CMD
 
     io = cmd(*all_args)
     pid = io.pids.first
-    while line = io.gets
-      if pid
-        Log.debug "STDOUT [#{pid}]: " + line
-      else
-        Log.debug "STDOUT: " + line
+
+    while c = io.getc
+      STDERR << c
+      if c == "\n"
+        if pid
+          Log.logn "STDOUT [#{pid}]: ", 0
+        else
+          Log.logn "STDOUT: ", 0
+        end
       end
-    end
+    end 
     io.join
 
     nil

data/lib/rbbt/util/log.rb

@@ -160,7 +160,7 @@ module Log
   end
 
   LAST = "log"
-  def self.log(message = nil, severity = MEDIUM, &block)
+  def self.logn(message = nil, severity = MEDIUM, &block)
     return if severity < self.severity 
     message ||= block.call if block_given?
     return if message.nil?
@@ -174,13 +174,21 @@ module Log
     str = prefix << " " << message.to_s
 
     LOG_MUTEX.synchronize do
-      STDERR.puts str
+      STDERR.write str
       Log::LAST.replace "log"
-      logfile.puts str unless logfile.nil?
+      logfile.write str unless logfile.nil?
       nil
     end
   end
 
+  def self.log(message = nil, severity = MEDIUM, &block)
+    return if severity < self.severity 
+    message ||= block.call if block_given?
+    return if message.nil?
+    message = message + "\n" unless message[-1] == "\n"
+    self.logn message, severity, &block
+  end
+
   def self.log_obj_inspect(obj, level, file = $stdout)
     stack = caller
 

data/lib/rbbt/util/open.rb

@@ -750,7 +750,7 @@ module Open
       begin
         if File.symlink?(file) || File.stat(file).nlink > 1
           if File.exists?(file + '.info')
-            file = file + '.info'
+            return Step::INFO_SERIALIAZER.load(Open.open(file + '.info'))[:done]
           else
             file = Pathname.new(file).realpath.to_s 
           end
@@ -762,6 +762,19 @@ module Open
     end
   end
 
+  def self.update_mtime(path, target)
+    if File.symlink?(target) || File.stat(target).nlink > 1
+      if File.exists?(target + '.info')
+        target = target + '.info'
+      else
+        target = Pathname.new(target).realpath.to_s 
+      end
+    end
+
+    CMD.cmd("touch -r '#{path}' '#{target}'")
+    CMD.cmd("touch -r '#{path}.info' '#{target}'") if File.exists?(path + '.info')
+  end
+
   def self.atime(file)
     if (dir_sub_path = find_repo_dir(file))
       get_atime_from_repo(*dir_sub_path)

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

@@ -154,7 +154,7 @@ class Step
       dep_done = dep.done?
 
       begin
-        if this_mtime && dep_done && Open.exists?(dep.path) && (Open.mtime(dep.path) > this_mtime)
+        if this_mtime && dep_done && Open.exists?(dep.path) && (Open.mtime(dep.path) > this_mtime + 1)
           outdated_time << dep
         end
       rescue
@@ -209,7 +209,9 @@ class Step
         no_load = :stream if no_load
 
         Open.write(pid_file, Process.pid.to_s) unless Open.exists?(path) or Open.exists?(pid_file)
-        result = Persist.persist "Job", @task.result_type, :file => path, :check => persist_checks, :no_load => no_load do 
+        result_type = @task.result_type
+        result_type = info[:result_type] if result_type.nil?
+        result = Persist.persist "Job", result_type, :file => path, :check => persist_checks, :no_load => no_load do 
           if Step === Step.log_relay_step and not self == Step.log_relay_step
             relay_log(Step.log_relay_step) unless self.respond_to? :relay_step and self.relay_step
           end

data/lib/rbbt/workflow/usage.rb

@@ -130,4 +130,27 @@ module Workflow
         end
       end
   end
+
+  def SOPT_str(task)
+    sopt_options = []
+    self.rec_inputs(task.name).each do |name|
+      short = name.to_s.chars.first
+      boolean = self.rec_input_types(task.name)[name].to_sym == :boolean
+
+      sopt_options << "-#{short}--#{name}#{boolean ? "" : "*"}"
+    end
+
+    sopt_options * ":"
+  end
+
+  def get_SOPT(task)
+    sopt_option_string = self.SOPT_str(task)
+    SOPT.get sopt_option_string
+  end
+
+  def self.get_SOPT(workflow, task)
+    workflow = Workflow.require_workflow workflow if String === workflow
+    task = workflow.tasks[task.to_sym] if String === task || Symbol === task
+    workflow.get_SOPT(task)
+  end
 end

data/share/rbbt_commands/workflow/prov

@@ -76,7 +76,8 @@ def report_msg(status, name, path, info = nil)
                rescue
                    nil
                end
-  str = if not Open.remote?(path) and (Open.exists?(path) and $main_mtime and path_mtime and ($main_mtime - path_mtime) < 0)
+  str = if not Open.remote?(path) and (Open.exists?(path) and $main_mtime and path_mtime and ($main_mtime - path_mtime) < -2)
+          iii [path, path_mtime, $main_mtime, $main_mtime - path_mtime]
     status_msg(status.to_s) << " " << [workflow, task, path].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
   else
     status_msg(status.to_s) << " " << [workflow, task, path].compact * " " 
@@ -111,11 +112,11 @@ def touch(step)
   return unless File.exists?(step.path)
   step.dependencies.each do |dep|
     next unless Open.exists?(dep.path)
-    touch(dep)
-    if Open.mtime(step.path) < Open.mtime(dep.path) 
+    if Open.mtime(dep.path) > Open.mtime(step.path) + 1
       Log.debug("Updating #{step.path} to #{dep.path}")
-      CMD.cmd("touch -r '#{dep.path}' '#{step.path}'")
+      Open.update_mtime(dep.path, step.path)
     end
+    touch(dep)
   end if step.dependencies
 end
 

data/share/rbbt_commands/workflow/task

@@ -48,18 +48,6 @@ def usage(workflow = nil, task = nil, exception=nil)
   true
 end
 
-def SOPT_options(workflow, task)
-  sopt_options = []
-  workflow.rec_inputs(task.name).each do |name|
-    short = name.to_s.chars.first
-    boolean = workflow.rec_input_types(task.name)[name].to_sym == :boolean
-    
-    sopt_options << "-#{short}--#{name}#{boolean ? "" : "*"}"
-  end
-
-  sopt_options * ":"
-end
-
 def get_value_stream(value)
   if value == "-"
     io = Misc.open_pipe do |sin|
@@ -289,8 +277,7 @@ usage workflow, task and exit 0 if help
 name = options.delete(:jobname) 
 
 # get job args
-sopt_option_string = SOPT_options(workflow, task)
-job_options = SOPT.get sopt_option_string
+job_options = workflow.get_SOPT(task)
 
 if options[:load_inputs]
   task_info = workflow.task_info(task_name)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.25
+  version: 5.25.26
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-24 00:00:00.000000000 Z
+date: 2019-02-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake